diff --git a/.gitignore b/.gitignore index dada89ac5e..fa5114aa12 100644 --- a/.gitignore +++ b/.gitignore @@ -1,67 +1,73 @@ CMakeLists.txt.user* .clang_complete ########## Git related # Patches and similar *.patch *.diff *.rej *.orig ########## IDE specific ## Office ~$* ## vim Session.vim *.swp *.swo ## Emacs \#*\# /.emacs.desktop /.emacs.desktop.lock .elc auto-save-list tramp .\#* ## Eclipse .cproject .project .settings/ # Org-mode .org-id-locations *_archive ########## OS specific ## Windows files to ignore # Windows image file caches Thumbs.db ehthumbs.db # Folder config file Desktop.ini # Recycle Bin used on file shares $RECYCLE.BIN/ ## OSX specific .DS_Store .AppleDouble .LSOverride Icon # Thumbnails ._* # Files that might appear on external disk .Spotlight-V100 .Trashes ## Linux *~ + +*.cmake + +*.cmake + +*.xml diff --git a/Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/QmitkBasicImageProcessing.dox b/Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/QmitkBasicImageProcessing.dox index 58326c13d8..dc07ee60cd 100644 --- a/Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/QmitkBasicImageProcessing.dox +++ b/Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/QmitkBasicImageProcessing.dox @@ -1,132 +1,132 @@ /** \page org_mitk_views_basicimageprocessing The Basic Image Processing Plugin -\image html ImageProcessing_48.png "Icon of the Plugin" +\image html QmitkBasicImageProcessingIcon.png "Icon of the Plugin" \section QmitkBasicImageProcessingUserManualSummary Summary This view provides an easy interface to fundamental image preprocessing and enhancement filters. It offers filter operations on 3D and 4D images in the areas of noise suppression, morphological operations, edge detection and image arithmetics, as well as image inversion and downsampling. Please see \ref QmitkBasicImageProcessingUserManualDetails for more detailed information on usage and supported filters. If you encounter problems using the view, please have a look at the \ref QmitkBasicImageProcessingUserManualTrouble page. \section QmitkBasicImageProcessingUserManualDetails Details Manual sections: - \ref QmitkBasicImageProcessingUserManualOverview - \ref QmitkBasicImageProcessingUserManualFilters - \ref QmitkBasicImageProcessingUserManualUsage - \ref QmitkBasicImageProcessingUserManualTrouble \section QmitkBasicImageProcessingUserManualOverview Overview This view provides an easy interface to fundamental image preprocessing and image enhancement filters. It offers a variety of filter operations in the areas of noise suppression, morphological operations, edge detection and image arithmetics. At the moment, the view can be used with all 3D and 4D image types loadable by MITK. 2D image support will be added in the future. All filters are encapsulated from the Insight Segmentation and Registration Toolkit (ITK, www.itk.org). -\image html BIP_Overview.png "MITK with the Basic Image Processing view" +\image html QmitkBasicImageProcessingOverview.png "MITK with the Basic Image Processing view" This document will tell you how to use this view, but it is assumed that you already know how to use MITK in general. \section QmitkBasicImageProcessingUserManualFilters Filters This section will not describe the fundamental functioning of the single filters in detail, though. If you want to know more about a single filter, please have a look at http://www.itk.org/Doxygen316/html/classes.html or in any good digital image processing book. For total denoising filter, please see Tony F. Chan et al., "The digital TV filter and nonlinear denoising". Available filters are:

\a Single image operations

\a Dual image operations

\section QmitkBasicImageProcessingUserManualUsage Usage All you have to do to use a filter is to: A busy cursor appeares; when it vanishes, the operation is completed. Your filtered image is displayed and selected for further processing. (If the checkbox "Hide original image" is not selected, you will maybe not see the filter result imideately, because your filtered image is possibly hidden by the original.) For two image operations, please make sure that the correct second image is selected in the drop down menu, and the image order is correct. For sure, image order only plays a role for image subtraction and division. These are conducted (Image1 - Image2) or (Image1 / Image2), respectively. Please Note: When you select a 4D image, you can select the time step for the filter to work on via the time slider at the top of the GUI. The 3D image at this time step is extracted and processed. The result will also be a 3D image. This means, a true 4D filtering is not yet supported. \section QmitkBasicImageProcessingUserManualTrouble Troubleshooting I get an error when using a filter on a 2D image.
2D images are not yet supported... I use a filter on a 4D image, and the output is 3D.
When you select a 4D image, you can select the time step for the filter to work on via the time slider at the top of the GUI. The 3D image at this time step is extracted and processed. The result will also be a 3D image. This means, a true 4D filtering is not supported by now. A filter crashes during execution.
Maybe your image is too large. Some filter operations, like derivatives, take a lot of memory. Try downsampling your image first. All other problems.
Please report to the MITK mailing list. See http://www.mitk.org/wiki/Mailinglist on how to do this. */ diff --git a/Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/ImageProcessing_48.png b/Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/QmitkBasicImageProcessingIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/ImageProcessing_48.png rename to Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/QmitkBasicImageProcessingIcon.png diff --git a/Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/BIP_Overview.png b/Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/QmitkBasicImageProcessingOverview.png similarity index 100% rename from Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/BIP_Overview.png rename to Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/QmitkBasicImageProcessingOverview.png diff --git a/Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/QmitkCmdLineModulesViewManual.dox similarity index 100% rename from Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/Manual.dox rename to Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/QmitkCmdLineModulesViewManual.dox diff --git a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/DataManager_48.png b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDataManagerIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/DataManager_48.png rename to Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDataManagerIcon.png diff --git a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/Image_properties.png b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDataManagerImageProperties.png similarity index 100% rename from Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/Image_properties.png rename to Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDataManagerImageProperties.png diff --git a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/Overview.png b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDataManagerOverview.png similarity index 100% rename from Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/Overview.png rename to Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDataManagerOverview.png diff --git a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/Preferences.png b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDataManagerPreferences.png similarity index 100% rename from Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/Preferences.png rename to Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDataManagerPreferences.png diff --git a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/Parent-Child.png b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDataManagerPreferencesGenealogy.png similarity index 100% rename from Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/Parent-Child.png rename to Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDataManagerPreferencesGenealogy.png diff --git a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/PropertyList.png b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDataManagerPropertyList.png similarity index 100% rename from Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/PropertyList.png rename to Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDataManagerPropertyList.png diff --git a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/Surface_Properties.png b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDataManagerSurfaceProperties.png similarity index 100% rename from Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/Surface_Properties.png rename to Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDataManagerSurfaceProperties.png diff --git a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox index 8d95aeb632..9418d9c083 100644 --- a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox +++ b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox @@ -1,108 +1,108 @@ /** \page org_mitk_views_datamanager The DataManager -\image html DataManager_48.png "Icon of the Module" +\image html QmitkDataManagerIcon.png "Icon of the Module" \section QmitkDataManagerIntroduction Introduction The Datamanager is the central componenent to manage medical data like images, surfaces, etc.. After loading one or more data into the Datamanager the data are shown in the four-view window, the so called Standard View. The user can now start working on the data by just clicking into the standard view or by using the MITK-modules such as "Segmentation" or "Basic Image Processing". Available sections: - \ref QmitkDataManagerIntroduction - \ref QmitkDataManagerLoading - \ref QmitkDataManagerSaving - \ref QmitkDataManagerProperties - \ref QmitkDataManagerPropertiesList - \ref QmitkDataManagerPropertiesVisibility - \ref QmitkDataManagerPropertiesRepresentation - \ref QmitkDataManagerPropertiesPreferences - \ref QmitkDataManagerPropertyList -\image html Overview.png "How MITK looks when starting" +\image html QmitkDataManagerOverview.png "How MITK looks when starting" \section QmitkDataManagerLoading Loading Data There are three ways of loading data into the Datamanager as so called Data-Elements. The user can just drag and drop data into the Datamanager or directly into one of the four parts of the Standard View. He can as well use the Open-Button in the right upper corner. Or he can use the standard "File->Open"-Dialog on the top. A lot of file-formats can be loaded into MITK, for example The user can also load a series of 2D images (e.g. image001.png, image002.png ...) to a MITK 3D volume. To do this, just drag and drop one of those 2D data files into the Datamanager by holding the ALT key. After loading one or more data into the Datamanager they appear as Data-Elements in a sorted list inside the Datamanager. Data-Elements can also be sorted hierarchically as a parent-child-relation. For example after using the Segmentation-Module on Data-Element1 the result is created as Data-Element2, which is a child of Data-Element1 (see Screenshot1). The order can be changed by drag and drop. -\image html Parent-Child.png "Screenshot1" +\image html QmitkDataManagerPreferencesGenealogy.png "Screenshot1" The listed Data-Elements are shown in the standard view. Here the user can scale or rotate the medical objects or he can change the cutting planes of the object by just using the mouse inside this view. \section QmitkDataManagerSaving Saving Data There are two ways of saving data from the Datamanger. The user can either save the whole project with all Data-Elements by clicking on "File"->"Save Project" or he can save single Data-Elements by right-clicking->"Save", directly on a Data-Element. When saving the whole project, the sorting of Data-Elements is saved as well. By contrast the sorting is lost, when saving a single Data-Element. \section QmitkDataManagerProperties Working with the Datamanager \subsection QmitkDataManagerPropertiesList List of Data-Elements The Data-Elements are listed in the Datamanager. As described above the elements can be sorted hierarchically as a parent-child-relation. For example after using the Segmentation-Module on Data-Element1 the result is created as Data-Element2, which is a child of Data-Element1 (see Screenshot1). By drag and drop the sorting of Data-Elements and their hierarchical relation can be changed. \subsection QmitkDataManagerPropertiesVisibility Visibility of Data-Elements By default all loaded Data-Elements are visible in the standard view. The visibility can be changed by right-clicking on the Data-Element and then choosing "Toogle visibility". The box in front of the Data-Element in the Datamanager shows the visibility. A green-filled box means a visible Data-Element, an empty box means an invisible Data-Element (see Screenshot1). \subsection QmitkDataManagerPropertiesRepresentation Representation of Data-Elements There are different types of representations how to show the Data-Element inside the standard view. By right-clicking on the Data-Element all options are listed (see Screenshot2 and Screenshot 3). -\image html Image_properties.png "Screenshot2: Properties for images" -\image html Surface_Properties.png "Screenshot3: Properties for surfaces" +\image html QmitkDataManagerImageProperties.png "Screenshot 2: Properties for images" +\image html QmitkDataManagerSurfaceProperties.png "Screenshot 3: Properties for surfaces" \subsection QmitkDataManagerPropertiesPreferences Preferences For the datamanager there are already some default hotkeys like the del-key for deleting a Data-Element. The whole list is seen in Screenshot4. From here the Hotkeys can also be changed. The preference page is found in "Window"->"Preferences". -\image html Preferences.png "Screenshot4" +\image html QmitkDataManagerPreferences.png "Screenshot4" \section QmitkDataManagerPropertyList Property List The Property List displays all the properties the currently selected Data-Element has. Which properties these are depends on the Data-Element. Examples are opacity, shader, visibility. These properties can be changed by clicking on the appropriate field in the "value" column. -\image html PropertyList.png "Screenshot5: Property List" +\image html QmitkDataManagerPropertyList.png "Screenshot5: Property List" */ diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox similarity index 92% rename from Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/Manual.dox rename to Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox index 10ce7a89b0..44c254af4d 100644 --- a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox @@ -1,121 +1,121 @@ /** \page org_mitk_gui_qt_dicom The Dicom Plugin -\image html dcm-icon.png "Icon of Dicom" +\image html QmitkDicomIcon.png "Icon of Dicom" \note To this article requires a basic knowlage of DICOM. Available sections: - \ref org_mitk_gui_qt_dicomOverview - \ref org_mitk_gui_qt_dicomDataHandling - \ref org_mitk_gui_qt_dicomQueryRetrieve \section org_mitk_gui_qt_dicomOverview Overview The DICOM editor is an experimental editor which allows for loading of DICOM images as well as server communication. It features a highly experimental query/retrieve (you need to configure your PACS correspondingly) as well as a DICOM browser. The DICOM browser allows you to navigate the DICOM folder/cd depending on its metadata (patient/study/series) and import selected series for viewing in your MITK based application. It also allows you to store your dicom data in an internal database so you can easily access often used dicom images. It is based on the commonTK (CTK) DICOM funcionality. \section org_mitk_gui_qt_dicomDataHandling Data handling -\image html DicomPluginControls.png "The dicom Plugin controls" +\image html QmitkDicomPluginControls.png "The dicom Plugin controls" In the image above you see the start page of the dicom plugin. On top of the start page you see four buttons. The Local Storage, the Import CD, the Import Folder and the Query Retrieve button. If you press one of these buttons, the dicom plugin will switch to your local dicom image storage or will start importing dicom images from CD or a folder on your hard drive or it will open the query retrieve screen. \subsection org_mitk_gui_qt_dicomStorage Data storage -\image html DicomPluginExtended.png "The DICOM data storage" +\image html QmitkDicomPluginExtended.png "The DICOM data storage" If you open the dicom plugin the dicom data storage will be displayed. You are able to see all your stored dicom image data. You can browse your data by clicking on the left arrow beside the name of your data. There are three levels available. The first level is the patient level where you can see the patient data. On the second level you can see the dicom studies for the patient. on the third level you can see all available series refering to it's study. You can delete the data by selecting it and pressing the delete button. Be careful if you have selected a patient or a study all refering data be deleted. So if you delete a patient the patient and all studies and series refered to the patient will be deleted. If you delete a study all series of the study will be deleted. If you want to view the dicom data you have to select a series and click on the View button. The data will appear in the DataManager and will be dispayed. -\image html DicomDisplayDataManager.png "Viewed image" +\image html QmitkDicomDisplayDataManager.png "Viewed image" \subsection org_mitk_gui_qt_dicomImport Data import -\image html ImportDialogCopy.png "The import dialog checked" +\image html QmitkDicomImportDialogCopy.png "The import dialog checked" There are two diffrent ways to import DICOM data. The First one is to directly imort it into your DICOM data storage. To achieve this you should toggle the checkbox 'Copy on import'. The second approach is, to have a look at the data first before importing it. To do that you simply don't check 'Copy on import'. This will leed you to the leed you to the 'External Dicom Data' screen which provides you a preview of the data containing in youre choosen folder. You can import the data here by selecting it and pressing the 'Download' button. It is also possible to view DICOM series directly in Mitk by selecting it here and pressing the 'View' button. \section org_mitk_gui_qt_dicomQueryRetrieve Query/Retrieve \warning This plugin is experimental and not all of the described features behave as expected. \note The query retrieve plugin only works if the PACS you are calling knows your machine settings. There are also issues when you are running a firewall. The query retrieve workflow allows you to get DICOM data from a server. -\image html DicomQueryRetrieve.png "The query retrieve screen" +\image html QmitkDicomQueryRetrieve.png "The query retrieve screen" \subsection org_mitk_gui_qt_dicomQuery Query -\image html DicomNodes.png "The DICOM network configuration" +\image html QmitkDicomNodes.png "The DICOM network configuration" By performing a DICOM query you will ask a server for it's DICOM data. This requires to setup the DICOM network configuration of your system and the server. By clicking on 'Add Server' a new plain server field will appear. Now you can give it a name of your choice. Fill the servers "DICOM name" the AETitle. Type in it's url, it's port and the specific DICOM protocoll you want to use for image transfer. \note I recommend not to use CGET because most of the PACS systems (Image Servers) don't support that protocoll. You can configure the DICOM network configuration of your machine by editing the 'Calling AETiltle', the 'Storage AETitle' and The 'Storage Port' text fields. But normaly you don't have to change your configuration. -\image html DicomFilterWidget.png "The DICOM search options" +\image html QmitkDicomFilterWidget.png "The DICOM search options" After you have finished your network configuration and before you start the query you should use the 'Search Options' to specify your query. Otherwise all data on the server will be queried and you will have to wait for a long time. You can specify your query by searching for a specific patient name or a study or a serie or a specific DICOM object by it's id. You are allowed to include or exclude DICOM modalities from your query and you can specify a specific time in which the DICOM images you are searching fo might been captured. When you finished that you can click the query button and the queried DICOM data will appear. \subsection org_mitk_gui_qt_dicomRetrieve Retrieve -\image html DicomRetrieve.png "The queried DICOM data." +\image html QmitkDicomRetrieve.png "The queried DICOM data." After the query you are able to select the queried data and click the 'Retrieve' button. This will store the queried DICOM data into your DICOM storage. Click on the 'Local Storage' button and work with your new data. */ diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomDisplayDataManager.png b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomDisplayDataManager.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomDisplayDataManager.png rename to Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomDisplayDataManager.png diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/ExternalView.png b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomExternalView.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/ExternalView.png rename to Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomExternalView.png diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomFilterWidget.png b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomFilterWidget.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomFilterWidget.png rename to Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomFilterWidget.png diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/dcm-icon.png b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/dcm-icon.png rename to Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomIcon.png diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/ImportDialogCopy.png b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomImportDialogCopy.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/ImportDialogCopy.png rename to Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomImportDialogCopy.png diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomNodes.png b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomNodes.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomNodes.png rename to Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomNodes.png diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomPluginControls.png b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomPluginControls.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomPluginControls.png rename to Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomPluginControls.png diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomPluginExtended.png b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomPluginExtended.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomPluginExtended.png rename to Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomPluginExtended.png diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomPlugin.png b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomPluginExtended2.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomPlugin.png rename to Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomPluginExtended2.png diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/Queried.png b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomQueried.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/Queried.png rename to Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomQueried.png diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomQueryRetrieve.png b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomQueryRetrieve.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomQueryRetrieve.png rename to Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomQueryRetrieve.png diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomRetrieve.png b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomRetrieve.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/DicomRetrieve.png rename to Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomRetrieve.png diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/StartDicomPlugin.png b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomStartPlugin.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/StartDicomPlugin.png rename to Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicomStartPlugin.png diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox index 16a5f3da53..5e161cc832 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox @@ -1,89 +1,89 @@ /** \page org_mitk_diffusionimagingapp_perspectives_connectomics The Connectomics Perspective -\image html connectomics_perspective.png "Icon of the Perspective" +\image html QmitkDiffusionimagingConnectomicsPerspective.png "Icon of the Perspective" The connectomics perspective is a collection of views which provide functionality for the work with brain connectivity networks. Currently there exist the following views: \subpage org_mitk_views_connectomicsdata provides network generation either from data or synthetically. \subpage org_mitk_views_connectomicsnetworkoperations provides functionalies to operate and process on networks and other data. \subpage org_mitk_views_connectomicsstatistics provides statistical measures for networks. \section org_mitk_diffusionimagingapp_perspectives_connectomicsTrouble Troubleshooting No known problems. All other problems.
Please report to the MITK mailing list. See http://www.mitk.org/wiki/Mailinglist on how to do this. */ /** \page org_mitk_views_connectomicsdata The Connectomics Network Data View \image html QmitkConnectomicsDataViewIcon_48.png "Icon of the View" This view can be used to create a network from a parcellation and a fiber image as well as to create synthetic networks. \image html dataview.png "The user interface" To create a network select first a parcellation of the brain (e.g. as provided by freesurfer ) by CTRL+Leftclick and secondly a fiber image ( as created using a tractography view). Then click on the "Create Network" button. Additionally you have the option to create artificial networks, for testing purposes. Currently choices are: */ /** \page org_mitk_views_connectomicsnetworkoperations The Connectomics Network Operations View \image html QmitkConnectomicsNetworkOperationsViewIcon_48.png "Icon of the View" This view can be used modify networks and related data. \image html operationsview.png "The user interface" Select a parcellation and press "Convert to RGBA" to create a RGBA image. By doing this conversion it is much easier to discern the different parcels. Furthermore MITK supports 3D visualization of an RGBA image. Select a network and press "Create Connectivity Matrix Image" to create a 2D image of the connectivity matrix. By default the weight of a connection is used as grey value. Using the "Rescale" option will rescale the weights so highest one is 255. Using the "Binary" option will result in a binary connectivity matrix. */ /** \page org_mitk_views_connectomicsstatistics The Connectomics Statistics View \image html QmitkConnectomicsStatisticsViewIcon_48.png "Icon of the View" This view can be used to show statistical analysis of a network. \image html statisticsview.png "The user interface" To calculate network statistics select a network in the datamanager. At this time the following statistics are calculated for the entire network: Furthermore some statistics are calculated on a per node basis and displayed as histograms: */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/QmitkDiffusionimagingConnectomicsManual.dox similarity index 92% copy from Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox copy to Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/QmitkDiffusionimagingConnectomicsManual.dox index 16a5f3da53..f295d4e4a6 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/QmitkDiffusionimagingConnectomicsManual.dox @@ -1,89 +1,89 @@ /** \page org_mitk_diffusionimagingapp_perspectives_connectomics The Connectomics Perspective -\image html connectomics_perspective.png "Icon of the Perspective" +\image html QmitkDiffusionimagingConnectomicsPerspective.png "Icon of the Perspective" The connectomics perspective is a collection of views which provide functionality for the work with brain connectivity networks. Currently there exist the following views: \subpage org_mitk_views_connectomicsdata provides network generation either from data or synthetically. \subpage org_mitk_views_connectomicsnetworkoperations provides functionalies to operate and process on networks and other data. \subpage org_mitk_views_connectomicsstatistics provides statistical measures for networks. \section org_mitk_diffusionimagingapp_perspectives_connectomicsTrouble Troubleshooting No known problems. All other problems.
Please report to the MITK mailing list. See http://www.mitk.org/wiki/Mailinglist on how to do this. */ /** \page org_mitk_views_connectomicsdata The Connectomics Network Data View \image html QmitkConnectomicsDataViewIcon_48.png "Icon of the View" This view can be used to create a network from a parcellation and a fiber image as well as to create synthetic networks. -\image html dataview.png "The user interface" +\image html QmitkDiffusionimagingDataView.png "The user interface" To create a network select first a parcellation of the brain (e.g. as provided by freesurfer ) by CTRL+Leftclick and secondly a fiber image ( as created using a tractography view). Then click on the "Create Network" button. Additionally you have the option to create artificial networks, for testing purposes. Currently choices are: */ /** \page org_mitk_views_connectomicsnetworkoperations The Connectomics Network Operations View \image html QmitkConnectomicsNetworkOperationsViewIcon_48.png "Icon of the View" This view can be used modify networks and related data. -\image html operationsview.png "The user interface" +\image html QmitkDiffusionimagingOperationsView.png "The user interface" Select a parcellation and press "Convert to RGBA" to create a RGBA image. By doing this conversion it is much easier to discern the different parcels. Furthermore MITK supports 3D visualization of an RGBA image. Select a network and press "Create Connectivity Matrix Image" to create a 2D image of the connectivity matrix. By default the weight of a connection is used as grey value. Using the "Rescale" option will rescale the weights so highest one is 255. Using the "Binary" option will result in a binary connectivity matrix. */ /** \page org_mitk_views_connectomicsstatistics The Connectomics Statistics View \image html QmitkConnectomicsStatisticsViewIcon_48.png "Icon of the View" This view can be used to show statistical analysis of a network. -\image html statisticsview.png "The user interface" +\image html QmitkDiffusionimagingStatisticsView.png "The user interface" To calculate network statistics select a network in the datamanager. At this time the following statistics are calculated for the entire network: Furthermore some statistics are calculated on a per node basis and displayed as histograms: */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/connectomics_perspective.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/QmitkDiffusionimagingConnectomicsPerspective.png similarity index 100% rename from Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/connectomics_perspective.png rename to Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/QmitkDiffusionimagingConnectomicsPerspective.png diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/dataview.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/QmitkDiffusionimagingDataView.png similarity index 100% rename from Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/dataview.png rename to Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/QmitkDiffusionimagingDataView.png diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/operationsview.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/QmitkDiffusionimagingOperationsView.png similarity index 100% rename from Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/operationsview.png rename to Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/QmitkDiffusionimagingOperationsView.png diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/statisticsview.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/QmitkDiffusionimagingStatisticsView.png similarity index 100% rename from Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/statisticsview.png rename to Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/QmitkDiffusionimagingStatisticsView.png diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingUserManual.dox index 97a399a1ca..aadb6ce47a 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingUserManual.dox @@ -1,140 +1,140 @@ /** \page org_mitk_gui_qt_diffusionimaging MITK Diffusion Imaging (MITK-DI) This module provides means to diffusion weighted image reconstruction, visualization and quantification. Diffusion tensors as well as different q-ball reconstruction schemes are supported. Q-ball imaging aims at recovering more detailed information about the orientations of fibers from diffusion MRI measurements and, in particular, to resolve the orientations of crossing fibers. Available sections: - \ref QmitkDiffusionImagingUserManualIssues - \ref QmitkDiffusionImagingUserManualPreprocessing - \ref QmitkDiffusionImagingUserManualTensorReconstruction - \ref QmitkDiffusionImagingUserManualQBallReconstruction - \ref QmitkDiffusionImagingUserManualDicomImport - \ref QmitkDiffusionImagingUserManualFslImport - \ref QmitkDiffusionImagingUserManualQuantification - \ref QmitkDiffusionImagingUserManualVisualizationSettings - \ref QmitkDiffusionImagingUserManualReferences - \ref QmitkDiffusionImagingUserManualTechnicalDetail - \ref QmitkDiffusionImagingUserManualSubManuals \section QmitkDiffusionImagingUserManualIssues Known Issues \li Dicom Import: The dicom import has so far only been implemented for Siemens dicom images. MITK-DI is capable of reading the nrrd format, which is documented elsewhere [1, 2]. These files can be created by combining the raw image data with a corresponding textual header file. The file extension should be changed from *.nrrd to *.dwi or from *.nhdr to *.hdwi respectively in order to let MITK-DI recognize the diffusion related header information provided in the files. \section QmitkDiffusionImagingUserManualPreprocessing Preprocessing The preprocessing view gives an overview over the important features of a diffusion weighted image like the number of gradient directions, b-value and the measurement frame. Additionally it allows the extraction of the B0 image, reduction of gradient directions and the generation of a binary brain mask. The image volume can be modified by applying a new mesurement frame, which is useful if the measurement frame is not set correctly in the image header, or by averaging redundant gradient directions. -\image html prepro1.png Preprocessing +\image html QmitkDiffusionimagingPreprocessing1.png Preprocessing \section QmitkDiffusionImagingUserManualTensorReconstruction Tensor Reconstruction The tensor reconstruction view allows ITK based tensor reconstruction [3]. The advanced settings for ITK reconstruction let you configure a manual threshold on the non-diffusion weighted image. All voxels below this threshold will not be reconstructed and left blank. It is also possible to check for negative eigenvalues. The according voxels are also left blank. -\image html tensor1.png ITK tensor reconstruction +\image html QmitkDiffusionimagingTensor1.png ITK tensor reconstruction A few seconds (depending on the image size) after the reconstruction button is hit, a colored image should appear in the main window. -\image html tensor4.png Tensor image after reconstruction +\image html QmitkDiffusionimagingTensor4.png Tensor image after reconstruction To assess the quality of the tensor fit it has been proposed to calculate the model residual [9]. This calculates the residual between the measured signal and the signal predicted by the model. Large residuals indicate an inadequacy of the model or the presence of artefacts in the signal intensity (noise, head motion, etc.). To use this option: Select a DWI dataset, estimate a tensor, select both the DWI node and the tensor node in the datamanager and press Residual Image Calculation. MITK-Diffusion can show the residual for every voxel averaged over all volumes or (in the plot widget) summarized per volume or for every slice in every volume. Clicking in the widget where the residual is shown per slice will automatically let the cross-hair jump to that position in the DWI dataset. If Percentage of outliers is checked, the per volume plot will show the percentage of outliers per volume. Otherwise it will show the mean together with the first and third quantile of residuals. See [9] for more information. -\image html residuals.png The residual widget +\image html QmitkDiffusionimagingResiduals.png The residual widget The view also allows the generation of artificial diffusion weighted or Q-Ball images from the selected tensor image. The ODFs of the Q-Ball image are directly initialized from the tensor values and afterwards normalized. The diffusion weighted image is estimated using the l2-norm image of the tensor image as B0. The gradient images are afterwards generated using the standard tensor equation. \section QmitkDiffusionImagingUserManualQBallReconstruction Q-Ball Reconstruction The q-ball reonstruction view implements a variety of reconstruction methods. The different reconstruction methods are described in the following: \li Numerical: The original, numerical q-ball reconstruction presented by Tuch et al. [5] \li Standard (SH): Descoteaux's reconstruction based on spherical harmonic basis functions [6] \li Solid Angle (SH): Aganj's reconstruction with solid angle consideration [7] \li ADC-profile only: The ADC-profile reconstructed with spherical harmonic basis functions \li Raw signal only: The raw signal reconstructed with spherical harmonic basis functions -\image html qballs1.png The q-ball resonstruction view +\image html QmitkDiffusionimagingQBalls1.png The q-ball resonstruction view B0 threshold works the same as in tensor reconstruction. The maximum l-level configures the size of the spherical harmonics basis. Larger l-values (e.g. l=8) allow higher levels of detail, lower levels are more stable against noise (e.g. l=4). Lambda is a regularisation parameter. Set it to 0 for no regularisation. lambda = 0.006 has proven to be a stable choice under various settings. -\image html qballs2.png Advanced q-ball reconstruction settings +\image html QmitkDiffusionimagingQBalls2.png Advanced q-ball reconstruction settings This is how a q-ball image should initially look after reconstruction. Standard q-balls feature a relatively low GFA and thus appear rather dark. Adjust the level-window to solve this. -\image html qballs3.png q-ball image after reconstruction +\image html QmitkDiffusionimagingQBalls3.png q-ball image after reconstruction \section QmitkDiffusionImagingUserManualDicomImport Dicom Import The dicom import does not cover all hardware manufacturers but only Siemens dicom images. MITK-DI is also capable of reading the nrrd format, which is documented elsewhere [1, 2]. These files can be created by combining the raw image data with a corresponding textual header file. The file extension should be changed from *.nrrd to *.dwi or from *.nhdr to *.hdwi respectively in order to let MITK-DI recognize the diffusion related header information provided in the files. In case your dicom images are readable by MITK-DI, select one or more input dicom folders and click import. Each input folder must only contain DICOM-images that can be combined into one vector-valued 3D output volume. Different patients must be loaded from different input-folders. The folders must not contain other acquisitions (e.g. T1,T2,localizer). In case many imports are performed at once, it is recommended to set the the optional output folder argument. This prevents the images from being kept in memory. -\image html dicom1.png Dicom import +\image html QmitkDiffusionimagingDicom1.png Dicom import The option "Average duplicate gradients" accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "blur radius" > 0 is configured. \section QmitkDiffusionImagingUserManualFslImport FSL Import FSL diffusion data can be imported with MITK Diffusion. FSL diffusion datasets consist of 3 files: a nifty file (filename.nii.gz or filename.nii), a bvecs file (filename.bvecs), which is a text file containing the gradient vectors, and a bvals file (filename.bvecs), containing the b-values. Due to the system that selects suitable file readers, MITK will not recognize these files as diffusion datasets. In order to make MITK recognize it as diffusion, the extension must be changed from .nii.gz to .fslgz (so the new name is filename.fslgz) or from filename.nii to filename.fsl. The bvecs and bvals files have to be renamed as well(to filename.fsl.bvecs/filenames.fsl.bvecs or to filename.fslgz.bvecs/filename.fslgz.bvals). MITK can also save diffusion weighted images in FSL format. To do this the extension of the new file should be changed to .fsl or .fslgz upon saving the file. -\image html fslsave.png Save a dwi dataset as fsl +\image html QmitkDiffusionimagingFSLSave.png Save a dwi dataset as fsl \section QmitkDiffusionImagingUserManualQuantification Quantification The quantification view allows the derivation of different scalar anisotropy measures for the reconstructed tensors (Fractional Anisotropy, Relative Anisotropy, Axial Diffusivity, Radial Diffusivity) or q-balls (Generalized Fractional Anisotropy). -\image html quantification.png Anisotropy quantification +\image html QmitkDiffusionimagingQuantification.png Anisotropy quantification \section QmitkDiffusionImagingUserManualVisualizationSettings ODF Visualization Setting In this small view, the visualization of ODFs and diffusion images can be configured. Depending on the selected image in the data storage, different options are shown here. For tensor or q-ball images, the visibility of glyphs in the different render windows (T)ransversal, (S)agittal, and (C)oronal can be configured here. The maximal number of glyphs to display can also be configured here for. This is usefull to keep the system response time during rendering feasible. The other options configure normalization and scaling of the glyphs. In diffusion images, a slider lets you choose the desired image channel from the vector of images (each gradient direction one image) for rendering. Furthermore reinit can be performed and texture interpolation toggled. This is how a visualization with activated glyphs should look like: -\image html visualization3.png Q-ball image with ODF glyph visibility toggled ON +\image html QmitkDiffusionimagingVisualization3.png Q-ball image with ODF glyph visibility toggled ON \section QmitkDiffusionImagingUserManualReferences References 1. http://teem.sourceforge.net/nrrd/format.html 2. http://www.cmake.org/Wiki/Getting_Started_with_the_NRRD_Format 3. C.F.Westin, S.E.Maier, H.Mamata, A.Nabavi, F.A.Jolesz, R.Kikinis, "Processing and visualization for Diffusion tensor MRI", Medical image Analysis, 2002, pp 93-108 5. Tuch, D.S., 2004. Q-ball imaging. Magn Reson Med 52, 1358-1372. 6. Descoteaux, M., Angelino, E., Fitzgibbons, S., Deriche, R., 2007. Regularized, fast, and robust analytical Q-ball imaging. Magn Reson Med 58, 497-510. 7. Aganj, I., Lenglet, C., Sapiro, G., 2009. ODF reconstruction in q-ball imaging with solid angle consideration. Proceedings of the Sixth IEEE International Symposium on Biomedical Imaging Boston, MA. 8. Goh, A., Lenglet, C., Thompson, P.M., Vidal, R., 2009. Estimating Orientation Distribution Functions with Probability Density Constraints and Spatial Regularity. Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv LNCS 5761, 877 ff. 9. J.-D. Tournier, S. Mori, A. Leemans., 2011. Diffusion Tensor Imaging and Beyond. Magn Reson Med 65, 1532-1556. \section QmitkDiffusionImagingUserManualTechnicalDetail Technical Information for Developers The diffusion imaging module uses additional properties beside the ones in use in other modules, for further information see \ref DiffusionImagingPropertiesPage . \section QmitkDiffusionImagingUserManualSubManuals Manuals of componentes The MITK Diffusion tools consist of further components, which have their own documentation, see: \li \subpage org_mitk_views_fiberprocessing \li \subpage org_mitk_views_gibbstracking \li \subpage org_mitk_views_odfdetails \li \subpage org_mitk_views_partialvolumeanalysisview \li \subpage org_mitk_views_screenshotmaker \li \subpage org_mitk_views_stochasticfibertracking \li \subpage org_mitk_views_ivim \li \subpage org_mitk_diffusionimagingapp_perspectives_connectomics \li \subpage org_mitk_views_tractbasedspatialstatistics \li \subpage org_mitk_views_odfmaximaextraction \li \subpage org_mitk_views_streamlinetracking \li \subpage org_mitk_views_fiberfoxview */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/dicom1.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionimagingDicom1.png similarity index 100% rename from Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/dicom1.png rename to Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionimagingDicom1.png diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/dicom2.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionimagingDicom2.png similarity index 100% rename from Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/dicom2.png rename to Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionimagingDicom2.png diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/fslimport.png 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view provides everything needed to process fiber bundles. -\image html fiberprocessing.png The Fiber Processing View +\image html QmitkDiffusionimagingFiberprocessing.png The Fiber Processing View Fiber extraction: Place ROIs in the 2D render widgets (cricles or polygons) and extract fibers from the bundle that pass through these ROIs by selecting the according ROI and fiber bundle in the datamanger and starting the extraction. The ROIs can be combined via logical operations. All fibers that pass through the thus generated composite ROI are extracted. The extraction can also be performed using 3D ROIs represented as closed surface meshes. In this extraction method, the logical operations are not implemented at the moment. The selected fiber bundle can be smoothed by interpolating the fiber points using Kochanek splines with the specified number of points per cm. If a float image with pixel values between 0 and 1 is selcted, the fiber bundle can be colored according to the pixel values. Generation of additional data from fiber bundles: \li Tract density image: generate a 2D heatmap from a fiber bundle \li Binary envelope: generate a binary image from a fiber bundle \li Fiber bundle image: generate a 2D rgba image representation of the fiber bundle \li Fiber endings image: generate a 2D binary image showing the locations of fiber endpoints \li Fiber endings pointset: generate a poinset containing the locations of fiber endpoints */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox index 22ba4ed943..dd2fd2a959 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox @@ -1,106 +1,106 @@ /** \page org_mitk_views_fiberfoxview Fiberfox This view provides the user interface for Fiberfox [1], an interactive simulation tool for defining artificial white matter fibers and generating corresponding diffusion weighted images. Arbitrary fiber configurations like bent, crossing, kissing, twisting, and fanning bundles can be intuitively defined by positioning only a few 3D waypoints to trigger the automated generation of synthetic fibers. From these fibers a diffusion weighted signal is simulated using a flexible combination of various diffusion models. It can be modified using specified acquisition settings such as gradient direction, b-value, signal-to-noise ratio, image size, and resolution. Available sections: - \ref QmitkFiberfoxViewUserManualFiberDefinition - \ref QmitkFiberfoxViewUserManualSignalGeneration - \ref QmitkFiberfoxViewUserManualKnownIssues - \ref QmitkFiberfoxViewUserManualReferences -\image html Fiberfox.png Fig. 1: Screenshot of the Fiberfox framework. The four render windows display an axial (top left), sagittal (top right) and coronal (bottom left) 2D cut as well as a 3D view of a synthetic fiber helix and the fiducials used to define its shape. In the 2D views the helix is superimposing the baseline volume of the corresponding diffusion weighted image. The sagittal render window shows a close-up view on one of the circular fiducials. +\image html QmitkDiffusionimagingFiberfox.png Fig. 1: Screenshot of the Fiberfox framework. The four render windows display an axial (top left), sagittal (top right) and coronal (bottom left) 2D cut as well as a 3D view of a synthetic fiber helix and the fiducials used to define its shape. In the 2D views the helix is superimposing the baseline volume of the corresponding diffusion weighted image. The sagittal render window shows a close-up view on one of the circular fiducials. \section QmitkFiberfoxViewUserManualFiberDefinition Fiber Definition Fiber strands are defined simply by placing markers in a 3D image volume. The fibers are then interpolated between these fiducials. Example: \li Chose an image volume to place the markers used to define the fiber pathway. If you don't have such an image available switch to the "Signal Generation" tab, define the size and spacing of the desired image and click "Generate Image". If no fiber bundle is selected, this will generate a dummy image that can be used to place the fiducials. \li Start placing fiducials at the desired positions to define the fiber pathway. To do that, click on the button with the circle pictogram, then click at the desired position and plane in the image volume and drag your mouse while keeping the button pressed to generate a circular shape. Adjust the shape using the control points (Fig. 2). The position of control point D introduces a twist of the fibers between two successive fiducials. The actual fiber generation is triggered automatically as soon as you place the second control point. \li In some cases the fibers are entangled in a way that can't be resolved by introducing an additional fiber twist. Fiberfox tries to avoid these situations, which arise from different normal orientations of succeeding fiducials, automatically. In rare cases this is not successful. Use the double-arrow button to flip the fiber positions of the selected fiducial in one dimension. Either the problem is resolved now or you can resolve it manually by adjusting the twist-control point. -\image html Fiberfox-Fiducial.png Fig. 2: Control points defining the actual shape of the fiducial. A specifies the fiducials position in space, B and C the two ellipse radii and D the twisting angle between two successive fiducials. +\image html QmitkDiffusionimagingFiberfoxFiducial.png Fig. 2: Control points defining the actual shape of the fiducial. A specifies the fiducials position in space, B and C the two ellipse radii and D the twisting angle between two successive fiducials. Fiber Options: \li Real Time Fibers: If checked, each parameter adjustment (fiducial position, number of fibers, ...) will be directly applied to the selected fiber bundle. If unchecked, the fibers will only be generated if the corresponding button "Generate Fibers" is clicked. \li Advanced Options: Show/hide advanced options \li #Fibers: Specifies the number of fibers that will be generated for the selected bundle. \li Fiber Sampling: Adjusts the number of points per cm that make up the fiber. A higher sampling rate is needed if high curvatures are modeled. \li Tension, Continuity, Bias: Parameters controlling the shape of the splines interpolation the fiducials. See Wikipedia for details. Fiducial Options: \li Use Constant Fiducial Radius: If checked, all fiducials are treated as circles with the same radius. The first fiducial of the bundle defines the radius of all other fiducials. \li Align with grid: Click to shift all fiducial center points to the next voxel center. Operations: \li Rotation: Define the rotation of the selected fiber bundle around each axis (in degree). \li Translation: Define the translation of the selected fiber bundle along each axis (in mm). \li Scaling: Define a scaling factor for the selected fiber bundle in each dimension. \li Transform Selection: Apply specified rotation, translation and scaling to the selected Bundle/Fiducial \li Copy Bundles: Add copies of the selected fiber bundles to the datamanager. \li Join Bundles: Add new bundle to the datamanager that contains all fibers from the selected bundles. \li Include Fiducials: If checked, the specified transformation is also applied to the fiducials belonging to the selected fiber bundle and the fiducials are also copied. -\image html FiberfoxExamples.png Fig. 3: Examples of artificial crossing (a,b), fanning (c,d), highly curved (e,f), kissing (g,h) and twisting (i,j) fibers as well as of the corresponding tensor images generated with Fiberfox. +\image html QmitkDiffusionimagingFiberfoxExamples.png Fig. 3: Examples of artificial crossing (a,b), fanning (c,d), highly curved (e,f), kissing (g,h) and twisting (i,j) fibers as well as of the corresponding tensor images generated with Fiberfox. \section QmitkFiberfoxViewUserManualSignalGeneration Signal Generation To generate an artificial signal from the input fibers we follow the concepts recently presented by Panagiotaki et al. in a review and taxonomy of different compartment models [2]: a flexible model combining multiple compartments is used to simulate the anisotropic diffusion inside (intra-axonal compartment) and between axons (inter-axonal compartment), isotropic diffusion outside of the axons (extra-axonal compartment 1) and the restricted diffusion in other cell types (extra-axonal compartment 2) weighted according to their respective volume fraction. A diffusion weighted image is generated from the fibers by selecting the according fiber bundle in the datamanager and clicking "Generate Image". If some other diffusion weighted image is selected together with the fiber bundle, Fiberfox directly uses the parameters of the selected image (size, spacing, gradient directions, b-values) for the signal generation process. Additionally a binary image can be selected that defines the tissue area. Voxels outside of this mask will contain no signal, only noise. Basic Image Settings: \li Image Dimensions: Specifies actual image size (number of voxels in each dimension). \li Image Spacing: Specifies voxel size in mm. Beware that changing the voxel size also changes the signal strength, e.g. increasing the resolution from 2x2x2 mm to 1x1x1 mm decreases the signal obtained for each voxel by a factor 8. \li Gradient Directions: Number of gradients directions distributed equally over the half sphere. 10% baseline images are automatically added. \li b-Value: Diffusion weighting in s/mm². If an existing diffusion weighted image is used to set the basic parameters, the b-value is defined by the gradient direction magnitudes of this image, which also enables the use of multiple b-values. Advanced Image Settings (activate checkbox "Advanced Options"): \li Repetitions: Specifies the number of averages used for the acquisition to reduce noise. \li Signal Scale: Additional scaling factor for the signal in each voxel. The default value of 125 results in a maximum signal amplitude of 1000 for 2x2x2 mm voxels. Beware that changing this value without changing the noise variance results in a changed SNR. Adjustment of this value might be needed if the overall signal values are much too high or much too low (depends on a variety of factors like voxel size and relaxation times). \li Echo Time TE: Time between the 90° excitation pulse and the first spin echo. Increasing this time results in a stronger T2-relaxation effect (Wikipedia). \li Line Readout Time: Time to read one line in k-space. Increasing this time results in a stronger T2* effect which causes an attenuation of the higher frequencies in phase direction (here along y-axis) which again results in a blurring effect of sharp edges perpendicular to the phase direction. \li Tinhom Relaxation: Time constant specifying the signal decay due to magnetic field inhomogeneities (also called T2'). Together with the tissue specific relaxation time constant T2 this defines the T2* decay constant: T2*=(T2 T2')/(T2+T2') \li Fiber Radius (in µm): Used to calculate the volume fractions of the used compartments (fiber, water, etc.). If set to 0 (default) the fiber radius is set automatically so that the voxel containing the most fibers is filled completely. A realistic axon radius ranges from about 5 to 20 microns. Using the automatic estimation the resulting value might very well be much larger or smaller than this range. \li Interpolation Shrink: The signal generated at each position along the fibers is distributed on the surrounding voxels using an interpolation scheme shaped like an arctangent function. Large values result in a steeper interpolation scheme approximating a nearest neighbor interpolation. Very small values result in an almost linear interpolation. \li Enforce Pure Fiber Voxels: If checked, the actual volume fractions of the single compartments are ignored. A voxel will either be filled by the intra axonal compartment completely or will contain no fiber at all. \li Output k-Space Image: Some of the effects simulated in our framework are modeled in the k-space representation of the actual image. Checking this box will output this frequency representation (amplitude spectrum). Compartment Settings: The group-boxes "Intra-axonal Compartment", "Inter-axonal Compartment" and "Extra-axonal Compartments" allow the specification which model to use and the corresponding model parameters. Currently the following models are implemented: \li Stick: The “stick” model describes diffusion in an idealized cylinder with zero radius. Parameter: Diffusivity d \li Zeppelin: Cylindrically symmetric diffusion tensor. Parameters: Parallel diffusivity d|| and perpendicular diffusivity d⊥ \li Tensor: Full diffusion tensor. Parameters: Parallel diffusivity d|| and perpendicular diffusivity constants d⊥1 and d⊥2 \li Ball: Isotropic compartment. Parameter: Diffusivity d \li Astrosticks: Consists of multiple stick models pointing in different directions. The single stick orientations can either be distributed equally over the sphere or are sampled randomly. The model represents signal coming from a type of glial cell called astrocytes, or populations of axons with arbitrary orientation. Parameters: randomization of the stick orientations and diffusivity of the sticks d. \li Dot: Isotropically restricted compartment. No parameter. For a detailed description of the single models, please refer to Panagiotaki et al. "Compartment models of the diffusion MR signal in brain white matter: A taxonomy and comparison."[2]. Additionally to the model parameters, each compartment has its own T2 signal relaxation constant (in ms). Noise and Artifacts: \li Variance: Adds Rician noise with the specified variance to the signal. \li Gibbs Ringing: Ringing artifacts occurring on edges in the image due to the frequency low-pass filtering caused by the limited size of the k-space. The higher the oversampling factor, the larger the distance from the corresponding edge in which the ringing is still visible. \section QmitkFiberfoxViewUserManualKnownIssues Known Issues \li If fiducials are created in one of the marginal slices of the underlying image, a position change of the fiducial can be observed upon selection/deselection. If the fiducial is created in any other slice this bug does not occur. \li If a scaling factor is applied to the selcted fiber bundle, the corresponding fiducials are not scaled accordingly. \li In some cases the automatic update of the selected fiber bundle is not triggered even if "Real Time Fibers" is checked, e.g. if a fiducial is deleted. If this happens on can always force an update by pressing the "Generate Fibers" button. If any other issues or feature requests arises during the use of Fiberfox, please don't hesitate to send us an e-mail or directly report the issue in our bugtracker: http://bugs.mitk.org/ \section QmitkFiberfoxViewUserManualReferences References [1] Peter F. Neher, Bram Stieltjes, Frederik B. Laun, Hans-Peter Meinzer, and Klaus H. Fritzsche: Fiberfox: A novel tool to generate software phantoms of complex fiber geometries. In proceedings: ISMRM 2013 [2] Panagiotaki, E., Schneider, T., Siow, B., Hall, M.G., Lythgoe, M.F., Alexander, D.C.: Compartment models of the diffusion mr signal in brain white matter: A taxonomy and comparison. Neuroimage 59 (2012) 2241–2254 */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox index 8424ea110f..4b562c4d21 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox @@ -1,44 +1,44 @@ /** \page org_mitk_views_gibbstracking Gibbs Tracking View This view provides the user interface for the Gibbs Tracking algorithm, a global fiber tracking algorithm, originally proposed by Reisert et.al. [1]. Available sections: - \ref QmitkGibbsTrackingUserManualInputData - \ref QmitkGibbsTrackingUserManualParameters - \ref QmitkGibbsTrackingUserManualTrackingSurveillance - \ref QmitkGibbsTrackingUserManualReferences -\image html gibbstrackingview.png The Gibbs Tracking View +\image html QmitkDiffusionimagingGibbsTrackingView.png The Gibbs Tracking View \section QmitkGibbsTrackingUserManualInputData Input Data Mandatory Input: \li One Q-Ball image selected in the datamanager Optional Input: \li Mask Image: Float image used as probability mask for the generation of fiber segments. Usually used as binary brain mask to reduce the searchspace of the algorithm and to avoid fibers resulting from noise outside of the brain. \section QmitkGibbsTrackingUserManualParameters Q-Ball Reconstruction \li Number of iterations: More iterations causes the algorithm to be more stable but also to take longer to finish the tracking. Rcommended: 10⁷-10⁹ iterations. \li Particle length/width/weight controlling the contribution of each particle to the model M \li Start and end temperature controlling how fast the process reaches a stable state. (usually no change needed) \li Weighting between the internal (affinity of the model to long and straigt fibers) and external energy (affinity of the model towards the data). (usually no change needed). \li Minimum fiber length constraint (in mm). Shorter fibers are discarded after the tracking. The automatic selection of parameters for the particle length/width and weight are determined directly from the input image using information about the image spacing and GFA. -\image html gibbstrackingviewadvanced.png Advanced Tracking Parameters +\image html QmitkDiffusionimagingGibbsTrackingViewAdvanced.png Advanced Tracking Parameters \section QmitkGibbsTrackingUserManualTrackingSurveillance Surveilance of the tracking process Once started, the tracking can be monitored via the textual output that informs about the tracking progress and several stats of the current state of the algorithm. If enabled, the intermediate tracking results are displayed in the renderwindows each second. This live visualization should usually be disabled for performance reasons. It can be turned on and off during the tracking process via the according checkbox. The button next to this checkbox allows the visualization of only the next iteration step. \section QmitkGibbsTrackingUserManualReferences References [1] Reisert, M., Mader, I., Anastasopoulos, C., Weigel, M., Schnell, S., Kiselev, V.: Global fiber reconstruction becomes practical. Neuroimage 54 (2011) 955-962 */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox index f54439baa9..69adba038f 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox @@ -1,8 +1,8 @@ /** \page org_mitk_views_odfdetails ODF Details View This view provides detailed information about the orentation distribution function at the current crosshair position (if a Tensor/Q-Ball image is selected). A visualization of the ODF as well as statistical information are displayed. -\image html odfdetails.png The Gibbs Tracking View +\image html QmitkDiffusionimagingODFDetails.png The Gibbs Tracking View */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfMaximaExtractionViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfMaximaExtractionViewUserManual.dox index 41cb736484..59bf4f19df 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfMaximaExtractionViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfMaximaExtractionViewUserManual.dox @@ -1,51 +1,51 @@ /** \page org_mitk_views_odfmaximaextraction Peak Extraction View This view provides the user interface to extract the peaks of tensors and the spherical harmonic representation of Q-Balls. Available sections: - \ref OdfMaxUserManualInputData - \ref OdfMaxUserManualOutputData - \ref OdfMaxUserManualMethods - \ref OdfMaxUserManualParameters - \ref OdfMaxUserManualReferences -\image html peakextractionview.png Peak Extraction View +\image html QmitkDiffusionimagingPeakExtractionView.png Peak Extraction View \section OdfMaxUserManualInputData Input Data Mandatory Input: \li DTI image or image containing the spherical harmonic coefficients. The SH coefficient images can be obtain from the Q-Ball reconstruction view by enabling the checkbox in the advanced options. Optional Input: \li Binary mask to define the extraction area. \section OdfMaxUserManualOutputData Output Data \li Vector field: 3D representation of the resulting peaks. Only for visualization purposes (the peaks are scaled additionally to the specified normalization to improve the visualization)! \li #Directions per Voxel: Image containing the number of extracted peaks per voxel as image value. \li Direction Images: One image for each of the extracted peaks per voxel. Each voxel contains one direction vector as image value. Use this output for evaluation purposes of the extracted peaks. \section OdfMaxUserManualMethods Peak Extraction Methods \li If a tensor image is used as input, the output is simply the largest eigenvector of each voxel. \li The finite differences extraction uses a higly sampled version of the image ODFs, extracts all local maxima and clusters the resulting directions that point in a similar direction. \li For details about the analytical method (experimental) please refer to [1]. -\image html peaks.png Peaks extracted from the ODFs of a crossing Phantom using the finite differences method. +\image html QmitkDiffusionimagingPeaks.png Peaks extracted from the ODFs of a crossing Phantom using the finite differences method. \section OdfMaxUserManualParameters Input Parameters \li Vector normalization method (no normalization, maximum normalization of the vecors of one voxel and independent normalization of each vecor). \li SH Order: Specify the order of the spherical harmonic coefficients. \li Maximum number of peaks to extract. If more peaks are found only the largest are kept. \li Threshold to discard small peaks. Value relative to the largest peak of the respective voxel. \li Absolute threshold on the peak size. To evaluate this threshold the peaks are additionally weighted by their GFA (low GFA voxels are more likely to be discarded). This threshold is only used for the finite differences extraction method. \section OdfMaxUserManualReferences References [1] Aganj et al. Proceedings of the Thirteenth International Conference on Medical Image Computing and Computer Assisted Intervention 2010 */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox index 7308a7018d..f0d6829499 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox @@ -1,23 +1,23 @@ /** \page org_mitk_views_partialvolumeanalysisview Partial Volume Analysis The "Partial Volume Analysis" view can be found in the "Quantification" perspective. It allows for robust quantification of diffusion or other scalar measures in the presents of two classes (e.g. fiber vs. non-fiber) and partial volume between them. The algorithm estimates a probabilistic segmentation of the three classes and returns a weighted average of the measure of interest within the each class. -\image html pvanalysisview.png The Partial Volume Analysis View +\image html QmitkDiffusionimagingPVAnalysisView.png The Partial Volume Analysis View \section QmitkPVAAnalysisUserManualExport Export All measures are automatically written to the clipboard once the estimation is updated. The histogram export is provided by the button underneath the histogram. The values can be pasted to excel or any text editor. \section QmitkPVAAnalysisUserManualAdvancedSettings Advanced Settings Are not recommended for use yet. \section QmitkPVAAnalysisUserManualSuggestedReadings Suggested Readings Diffusion tensor imaging in primary brain tumors: reproducible quantitative analysis of corpus callosum infiltration and contralateral involvement using a probabilistic mixture model. Stieltjes B, Schlüter M, Didinger B, Weber MA, Hahn HK, Parzer P, Rexilius J, Konrad-Verse O, Peitgen HO, Essig M. Neuroimage. 2006 Jun;31(2):531-42. Epub 2006 Feb 14. PMID: 16478665 */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox index 0ed40d2add..e9f313b9a5 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox @@ -1,31 +1,31 @@ /** \page org_mitk_views_stochasticfibertracking Stochastic Tracking View This view provides the user interface for the Stochastic Fibertracking algorithm, proposed by Ngo [1]. Available sections: - \ref QmitkStochasticTrackingUserManualInputData - \ref QmitkStochasticTrackingUserManualParameters - \ref QmitkStochasticTrackingUserManualReferences -\image html stochastictrackingview.png Stochastic Tracking View +\image html QmitkDiffusionimagingStochasticTrackingQmitkDiffusionimagingSWPhantomRois.png Stochastic Tracking View \section QmitkStochasticTrackingUserManualInputData Input Data Mandatory Input: \li One DWI Image image selected in the datamanager \li One or more ROIs selected in the datamanager For a successful execution of the stochastic tractography filter, a DWI input and a binary image defining the desired ROI are required. The ROI serves as the origin from where on the fibers are beeing tracked. To generate the seed ROI the segmentation view in the quantification perspective can be used or a binary image can be loaded. \section QmitkStochasticTrackingUserManualParameters Input Parameters \li Parameters such as max. tract length, number of seeds per voxel and likelihood cache size in MB can be controlled individually. \li After successfully setting necessary Input and Parameter, pressing the command button executes the algorithm. \section QmitkStochasticTrackingUserManualReferences References [1] Tri M. Ngo, Polina Golland, and Tri M. Ngo. A stochastic tractography system and applications, 2007 */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox index e6fd7bdd84..821fca46a8 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox @@ -1,40 +1,40 @@ /** \page org_mitk_views_streamlinetracking Streamline Tracking View This view provides the user interface for basic streamline fiber tractography on diffusion tensor images. FACT and TEND tracking methods are available. Available sections: - \ref StrTrackUserManualInputData - \ref StrTrackUserManualParameters - \ref StrTrackUserManualReferences -\image html streamlinetrackingview.png Streamline Tracking View +\image html QmitkDiffusionimagingStreamlineTrackingQmitkDiffusionimagingSWPhantomRois.png Streamline Tracking View \section StrTrackUserManualInputData Input Data Mandatory Input: \li One DTI Image image selected in the datamanager Optional Input: \li Binary mask used to define the seed voxels. If no seed mask is specified, the whole image volume is seeded. \li Binary mask used to constrain the generated streamlines. Streamlines can not leave the mask area. \section StrTrackUserManualParameters Input Parameters \li FA Threshold: If the streamline reaches a position with an FA value lower than the speciefied threshold, it is not tracked any further. \li Min. Curvature Radius: If the streamline has a higher curvature than specified, it is not tracked any further. It is defined as the radius of the circle specified by three successive streamline positions. \li f and g values to balance between FACT [1] and TEND [2,3] tracking. For further information please refer to [2,3] \li Step Size: The algorithm proceeds along the streamline with a fixed stepsize. Default is 0.1*minSpacing. \li Min. Tract Length: Shorter fibers are discarded. \li Seeds per voxel: If set to 1, the seed is defined as the voxel center. If > 1 the seeds are distributet randomly inside the voxel. By default the image values are not interpolated. Enable according checkbox to use trilinear interpolation of the tensors as well as the FA values. Keep in mind that in the noninterpolated case, the TEND term is only applied once per voxel. In the interpolated case the TEND term is applied at each integration step which results in much higher curvatures and has to be compensated by an according choice of f and g. \section StrTrackUserManualReferences References [1] Mori et al. Annals Neurology 1999\n [2] Weinstein et al. Proceedings of IEEE Visualization 1999\n [3] Lazar et al. Human Brain Mapping 2003\n */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkTbssViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkTbssViewUserManual.dox index 462747ae25..01d1b2a747 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkTbssViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkTbssViewUserManual.dox @@ -1,66 +1,66 @@ /** \page org_mitk_views_tractbasedspatialstatistics The TBSS View -\image html tbss.png "Icon of the View" +\image html QmitkDiffusionimagingTBSS.png "Icon of the View" \section QmitkTractbasedSpatialStatistics Summary This view can be used to locally explore data resulting from preprocessing with the TBSS view of FSL This document will tell you how to use this view, but it is assumed that you already know how to use MITK in general and how to work with the TBSS view of FSL. If you encounter problems using the view, please have a look at the \ref QmitkTractbasedSpatialStatisticsUserManualTrouble page. Sections: - \ref QmitkTractbasedSpatialStatisticsUserManualOverview - \ref QmitkTractbasedSpatialStatisticsUserManualFSLImport - \ref QmitkTractbasedSpatialStatisticsUserManualRois - \ref QmitkTractbasedSpatialStatisticsUserManualProfiles - \ref QmitkTractbasedSpatialStatisticsUserManualFiberPlotting - \ref QmitkTractbasedSpatialStatisticsUserManualTroubleshooting - \ref QmitkTractbasedSpatialStatisticsUserManualReferences \section QmitkTractbasedSpatialStatisticsUserManualOverview Overview This view is currently under development and as such the interface as well as the capabilities are likely to change significantly between different versions. This documentation describes the features of this current version. \section QmitkTractbasedSpatialStatisticsUserManualFSLImport FSL Import The FSL import allows to import data that has been preprocessed by FSL. FSL creates output images that typically have names like all_FA_skeletonized.nii.gz that are 4-dimensional images that contain registered images of all subjects. By loading this 4D image into the datamanager and listing the groups with the correct number of subjects, in the order of occurrence in the 4D image, in the TBSS-View using the Add button and clicking the import subject data a TBSS file is created that contains all the information needed for tract analysis. The diffusion measure of the image can be set as well. -\image html fslimport.png "FSL Import" +\image html QmitkDiffusionimagingFSLImport.png "FSL Import" \section QmitkTractbasedSpatialStatisticsUserManualRois Regions of Interest (ROIs) To create a ROI the mean FA skeleton (typically called mean_FA_skeleton.nii.gz) that is created by FSL should be loaded in to the datamanager and selected. By using the Pointlistwidget points should be set on the skeleton (make sure to select points with relatively high FA values). Points are set by first selecting the button with the '+' and than shift-leftclick in the image. When the correct image is selected in the datamanager the Create ROI button is enabled. Clicking this will create a region of interest that passes through the previously selected points. The roi appears in the datamanager. Before doing so, the name of the roi and the information on the structure on which the ROI lies can be set. This will be saved as extra information in the roi-image. Before the ROI is calculated, a pop-up window will ask the user to provide a threshold value. This should be the same threshold that was previously used in FSL to create a binary mask of the FA skeleton. When this is not done correctly, the region of interest will possible contain zero-valued voxels. -\image html tbssRoi.png "Regions of Interest (ROIs)" +\image html QmitkDiffusionimagingTBSSRoi.png "Regions of Interest (ROIs)" \section QmitkTractbasedSpatialStatisticsUserManualProfiles y selecting a tbss image with group information and a region of interest image (as was created in a previous stap). A profile plot is drawn in the plot canvas. By clicking in the graph the crosshairs jump to the corresponding location in the image. -\image html profiles.png "Profile plots" +\image html QmitkDiffusionimagingProfiles.png "Profile plots" \section QmitkTractbasedSpatialStatisticsUserManualFiberPlotting It is also possible to use fiber bundles to plot values in images. However, unlike TBSS this only works on 3D volumes (one subject only). To plot the values of a 3D volume using fiber tracking results, we need, fiber data and two planar circles as Regions of Interest that define the region that must be plotted. For every fiber that passes through both ROIs the values at the corresponding positions in the volume are plotted. Every fiber is resampled to the number of segments specified in the GUI. The average value can also be plotted. The subset of the fibers between the ROIs can be cut out by pressing the Cut button. -\image html trackingplot.png "Plot of fiber tracts" +\image html QmitkDiffusionimagingTrackingPlot.png "Plot of fiber tracts" \section QmitkTractbasedSpatialStatisticsUserManualTroubleshooting Troubleshooting Please report to the MITK mailing list. See http://www.mitk.org/wiki/Mailinglist on how to do this. \section QmitkTractbasedSpatialStatisticsUserManualReferences References 1. S.M. Smith, M. Jenkinson, H. Johansen-Berg, D. Rueckert, T.E. Nichols, C.E. Mackay, K.E. Watkins, O. Ciccarelli, M.Z. Cader, P.M. Matthews, and T.E.J. Behrens. Tract-based spatial statistics: Voxelwise analysis of multi-subject diffusion data. NeuroImage, 31:1487-1505, 2006. 2. S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-219, 2004. */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkUserIVIMViewManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkUserIVIMViewManual.dox index b46d32f9dd..e293f219f8 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkUserIVIMViewManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkUserIVIMViewManual.dox @@ -1,41 +1,41 @@ /** \page org_mitk_views_ivim Intra-voxel incoherent motion estimation (IVIM) The required input for the "Intra-voxel incoherent motion estimation" (IVIM) is a diffusion weighted image (.dwi or .hdwi) that was acquired with several different b-values. -\image html ivimview.png The IVIM View +\image html QmitkDiffusionimagingIVIMView.png The IVIM View Once an input image is selected in the datamanager, the IVIM view allows for interactive exploration of the dataset (click around in the image and watch the estimated parameters in the figure of the view) as well as generation of f-, D-, and D*-maps (activate the checkmarks and press "Generate Output Images"). The "neglect b<" threshold allows you to ignore b-values smaller then a threshold for the initial fit of f and D. D* is then estimated using all measurements. The exact values of the current fit are always given in the legend underneath the figure. \section QmitkDiffusionImagingUserManualInputData Region of interest analysis Create region of interest: To create a new segmentatin, open the "quantification" perspective, select the tab "Segmentation", and create a segmentation of the structure of interest. Alternatively, of course, you may also load a binary image from file or generate your segmentation in any other possible way. IVIM in region of interset: Go back to the "IVIM" perspective and select both, the diffusion image and the segmentation (holding the CTRL key). A red message should appear "Averaging N voxels". \section QmitkDiffusionImagingUserManualInputData Export All model parameters and corresponding curves can be exported to clipboard using the buttons underneath the figure. \section QmitkDiffusionImagingUserManualInputData Advanced Settings Advanced users, that know what they are doing, can change the method for the model-fit under "Advanced Settings" on the very bottom of the view. 3-param fit, linear fit of f/D, and fix D* are among the options. \section QmitkDiffusionImagingUserManualInputData Suggested Readings Toward an optimal distribution of b values for intravoxel incoherent motion imaging. Lemke A, Stieltjes B, Schad LR, Laun FB. Magn Reson Imaging. 2011 Jul;29(6):766-76. Epub 2011 May 5. PMID: 21549538 Differentiation of pancreas carcinoma from healthy pancreatic tissue using multiple b-values: comparison of apparent diffusion coefficient and intravoxel incoherent motion derived parameters. Lemke A, Laun FB, Klauss M, Re TJ, Simon D, Delorme S, Schad LR, Stieltjes B. Invest Radiol. 2009 Dec;44(12):769-75. PMID: 19838121 */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/MitkDiffusionImagingAppQtHelpCollectionProject.qhcp b/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/MitkDiffusionImagingAppQtHelpCollectionProject.qhcp index a9a39d92fe..788796713d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/MitkDiffusionImagingAppQtHelpCollectionProject.qhcp +++ b/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/MitkDiffusionImagingAppQtHelpCollectionProject.qhcp @@ -1,22 +1,22 @@ MITK Diffusion Help - assistant-logo.png + assistant-logo.png qthelp://org.mitk.gui.qt.diffusionimagingapp/bundle/index.html - assistant-icon.png + QmitkDiffusionimagingAppAssistantIcon.png false false true MitkDIApp About MITK Diffusion Help - - about-logo.png - + + QmitkDiffusionimagingAppAboutLogo.png + - + - + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/about-logo.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/QmitkDiffusionimagingAppAboutLogo.png similarity index 100% rename from Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/about-logo.png rename to Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/QmitkDiffusionimagingAppAboutLogo.png diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/assistant-icon.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/QmitkDiffusionimagingAppAssistantIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/assistant-icon.png rename to Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/QmitkDiffusionimagingAppAssistantIcon.png diff --git a/Plugins/org.mitk.gui.qt.dtiatlasapp/documentation/MitkDTIAtlasAppQtHelpCollectionProject.qhcp b/Plugins/org.mitk.gui.qt.dtiatlasapp/documentation/MitkDTIAtlasAppQtHelpCollectionProject.qhcp index fa48318c3b..f3cd113067 100644 --- a/Plugins/org.mitk.gui.qt.dtiatlasapp/documentation/MitkDTIAtlasAppQtHelpCollectionProject.qhcp +++ b/Plugins/org.mitk.gui.qt.dtiatlasapp/documentation/MitkDTIAtlasAppQtHelpCollectionProject.qhcp @@ -1,22 +1,22 @@ MITK 3M3 Help - assistant-logo.png + assistant-logo.png qthelp://org.mitk.gui.qt.dtiatlasapp/bundle/index.html - assistant-icon.png + QmitkDTIAtlasAppAssistantIcon.png false false true Mitk3M3 About MITK 3M3 Help - - about-logo.png - + + QmitkDTIAtlasAppAboutLogo.png + - + - + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.dtiatlasapp/documentation/about-logo.png b/Plugins/org.mitk.gui.qt.dtiatlasapp/documentation/QmitkDTIAtlasAppAboutLogo.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dtiatlasapp/documentation/about-logo.png rename to Plugins/org.mitk.gui.qt.dtiatlasapp/documentation/QmitkDTIAtlasAppAboutLogo.png diff --git a/Plugins/org.mitk.gui.qt.dtiatlasapp/documentation/assistant-icon.png b/Plugins/org.mitk.gui.qt.dtiatlasapp/documentation/QmitkDTIAtlasAppAssistantIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.dtiatlasapp/documentation/assistant-icon.png rename to Plugins/org.mitk.gui.qt.dtiatlasapp/documentation/QmitkDTIAtlasAppAssistantIcon.png diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkColourImageProcessing.dox b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkColourImageProcessing.dox index dea970f477..a8795c4b51 100644 --- a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkColourImageProcessing.dox +++ b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkColourImageProcessing.dox @@ -1,34 +1,34 @@ /** \page org_mitk_views_colourimageprocessing The Colour Image Processing Module -\image html ColorImageProcessing.png "Icon of the Module" +\image html QmitkExamplesColorImageProcessing.png "Icon of the Module" \section QmitkColourImageProcessingUserManualSummary Summary This module allows the user to create coloured images from medical images. Generally, these coloured images would be used in presentations, research papers, or as a teaching aide. \section QmitkColourImageProcessingUserManualOverview Overview The purpose of this module is to create coloured images, which can then be later used in presentations, research papers, or anything else the user desires. Furthermore, different body sections can be assigned a different colour. These images are not particularly useful for further image processing, but provide nice, clear, diagrams. Please note that ultrasound images cannot be coloured. \section QmitkColourImageProcessingUserManualFilters Creating Coloured Images Open an image in mitk, then click on the colour wheel button. Make sure the image you loaded is selected.

\ Image -> RGBAimage

Clicking on this button creates an RGBA image from your medical image, which should appear in your data manager.

\ Image + mask -> RGBAimage

Before clicking on this button, a mask is needed. A mask is generally created using the segmentation tool. Make sure both the mask and image are selected, then click on the image + mask -> RGBA image button. This creates an RGBA image that is coloured only in section defined by the mask.

\ Image + mask + color-> RGBAimage

This functions the same way as the Image + mask -> RGBAimage. The difference is that the user can select the colour of the section represented by the mask. This is done by clicking on the colour next to the Image + mask + color-> RGBAimage button If multiple RGBA images are created with different colours, they can be combined into one image. Ensure that the desired coloured images are selected, then click on the combine RGBA images button. */ diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/MITKExamples.dox b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamples.dox similarity index 100% rename from Plugins/org.mitk.gui.qt.examples/documentation/UserManual/MITKExamples.dox rename to Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamples.dox diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/ColorImageProcessing.png b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesColorImageProcessing.png similarity index 100% rename from Plugins/org.mitk.gui.qt.examples/documentation/UserManual/ColorImageProcessing.png rename to Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesColorImageProcessing.png diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/IsoSurfaceGUI.png b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesIsoSurfaceGUI.png similarity index 100% rename from Plugins/org.mitk.gui.qt.examples/documentation/UserManual/IsoSurfaceGUI.png rename to Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesIsoSurfaceGUI.png diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/IsoSurfaceIcon.png b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesIsoSurfaceIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.examples/documentation/UserManual/IsoSurfaceIcon.png rename to Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesIsoSurfaceIcon.png diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/regiongrowing.png b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesRegionGrowing.png similarity index 100% rename from Plugins/org.mitk.gui.qt.examples/documentation/UserManual/regiongrowing.png rename to Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesRegionGrowing.png diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/regiongrowing.xpm b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesRegionGrowing.xpm similarity index 100% rename from Plugins/org.mitk.gui.qt.examples/documentation/UserManual/regiongrowing.xpm rename to Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesRegionGrowing.xpm diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/SimpleExample.png b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesSimpleExample.png similarity index 100% rename from Plugins/org.mitk.gui.qt.examples/documentation/UserManual/SimpleExample.png rename to Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesSimpleExample.png diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/SimpleMeasurementGUI.png b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesSimpleMeasurementGUI.png similarity index 100% rename from Plugins/org.mitk.gui.qt.examples/documentation/UserManual/SimpleMeasurementGUI.png rename to Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesSimpleMeasurementGUI.png diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/SimpleMeasurementIcon.png b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesSimpleMeasurementIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.examples/documentation/UserManual/SimpleMeasurementIcon.png rename to Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesSimpleMeasurementIcon.png diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/viewInitializationIcon.png b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesViewInitializationIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.examples/documentation/UserManual/viewInitializationIcon.png rename to Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesViewInitializationIcon.png diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/viewInitializationIcon.xpm b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesViewInitializationIcon.xpm similarity index 100% rename from Plugins/org.mitk.gui.qt.examples/documentation/UserManual/viewInitializationIcon.xpm rename to Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkExamplesViewInitializationIcon.xpm diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkIsoSurfaceUserManual.dox b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkIsoSurfaceUserManual.dox index 1e8bb8c1f5..839eb435f0 100644 --- a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkIsoSurfaceUserManual.dox +++ b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkIsoSurfaceUserManual.dox @@ -1,37 +1,37 @@ /** \page org_mitk_views_isosurface The Iso Surface Module -\image html IsoSurfaceIcon.png "Icon of the Module" +\image html QmitkExamplesIsoSurfaceIcon.png "Icon of the Module" Available sections: - \ref QmitkIsoSurfaceUserManualOverview - \ref QmitkIsoSurfaceUserManualFeatures - \ref QmitkIsoSurfaceUserManualUsage - \ref QmitkIsoSurfaceUserManualTroubleshooting \section QmitkIsoSurfaceUserManualOverview Overview IsoSurface is a program module for creating surfaces (e.g. polygon structures) out of images. The user defines a threshold that seperates object and background inside the image. Pixels that belong to the object need grey values below the threshold. Pixles with grey values above the threshold will be ignored. The result is a polygon object that can be saved as an *.stl-object. \section QmitkIsoSurfaceUserManualFeatures Features - Creates a surface by thresholding an image \section QmitkIsoSurfaceUserManualUsage Usage How to create a surface: - Load an image into the program, for example by drag & drop - Look for a meaningful threshold. All pixel grey values of the image that are lower than the threshold will be used to create the surface. All grey values that are higher than the surface will be ignored. You can find the best threshold by using the Volumetry-Functionality or by reading the grey value while clicking on a pixel (see picture 2). - Insert the threshold into the GUI - Press the Button "Create Surface" -\image html IsoSurfaceGUI.png "Graphical User Interface of Iso Surface" +\image html QmitkExamplesIsoSurfaceGUI.png "Graphical User Interface of Iso Surface" \section QmitkIsoSurfaceUserManualTroubleshooting Troubleshooting */ diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkRegionGrowingUserManual.dox b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkRegionGrowingUserManual.dox index 2b1f8a2467..34fc50069c 100644 --- a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkRegionGrowingUserManual.dox +++ b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkRegionGrowingUserManual.dox @@ -1,29 +1,29 @@ /** \page org_mitk_views_regiongrowing The Region Growing View -\image html regiongrowing.png "Icon of the View" +\image html QmitkExamplesRegionGrowing.png "Icon of the View" Available documentation sections: - \ref QmitkRegionGrowingUserManualOverview - \ref QmitkRegionGrowingUserManualUsage \section QmitkRegionGrowingUserManualOverview Overview The Region growing view provides a programming example, showing developers how to create new views for MITK with a graphical user interface (GUI) that also uses some ITK image filters. For the programmers: this functionality is the result of tutorial step 9 \section QmitkRegionGrowingUserManualUsage Usage */ diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkSimpleExampleUserManual.dox b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkSimpleExampleUserManual.dox index 12df11bc6d..aad01f8ae9 100644 --- a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkSimpleExampleUserManual.dox +++ b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkSimpleExampleUserManual.dox @@ -1,21 +1,21 @@ /** \page org_mitk_views_simpleexample The Simple Example module -\image html SimpleExample.png "Icon of the Module" +\image html QmitkExamplesSimpleExample.png "Icon of the Module" \section QmitkSimpleExampleViewUserManualSummary Summary This module is namely a simple example for simple image interaction. It offers: */ diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkSimpleMeasurementUserManual.dox b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkSimpleMeasurementUserManual.dox index f3aadf2c81..e56a5ff4d9 100644 --- a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkSimpleMeasurementUserManual.dox +++ b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/QmitkSimpleMeasurementUserManual.dox @@ -1,44 +1,44 @@ /** \page org_mitk_views_simplemeasurement The Simple Measurement Module -\image html SimpleMeasurementIcon.png "Icon of the Module" +\image html QmitkExamplesSimpleMeasurementIcon.png "Icon of the Module" Available sections: - \ref QmitkSimpleMeasurementUserManualOverview - \ref QmitkSimpleMeasurementUserManualFeatures - \ref QmitkSimpleMeasurementUserManualUsage \section QmitkSimpleMeasurementUserManualOverview Overview SimpleMeasurement is a program module that allows to measure distances, angles and paths on a dataset. \section QmitkSimpleMeasurementUserManualFeatures Features \section QmitkSimpleMeasurementUserManualUsage Usage To use the SimpleMeasurement Module, a data set must first be loaded. This can be done by drag & drop. Choose the simplemeasurement method you need by pressing the according button. What the different modes mean and how to use them: -\image html SimpleMeasurementGUI.png Graphical User Interface of SimpleMeasurement +\image html QmitkExamplesSimpleMeasurementGUI.png Graphical User Interface of SimpleMeasurement */ diff --git a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/org_mitk_gui_qt_viewinitialization.dox b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/org_mitk_gui_qt_viewinitialization.dox index f192b11dd4..3749b65895 100644 --- a/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/org_mitk_gui_qt_viewinitialization.dox +++ b/Plugins/org.mitk.gui.qt.examples/documentation/UserManual/org_mitk_gui_qt_viewinitialization.dox @@ -1,8 +1,8 @@ /** \page org_mitk_views_viewinitialitzation The View Initialization Module -\image html viewInitializationIcon.png "Icon of the Module" +\image html QmitkExamplesViewInitializationIcon.png "Icon of the Module" This view serves as a sandbox for understanding and experimenting with the geometry initialization parameters. For example, to view the axial slices from above instead of from below. It is not intended for end users, but for developers. */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.examples/files.cmake b/Plugins/org.mitk.gui.qt.examples/files.cmake deleted file mode 100644 index 18a5f2d363..0000000000 --- a/Plugins/org.mitk.gui.qt.examples/files.cmake +++ /dev/null @@ -1,60 +0,0 @@ -set(SRC_CPP_FILES - -) - -set(INTERNAL_CPP_FILES - mitkPluginActivator.cpp - colourimageprocessing/QmitkColourImageProcessingView.cpp - colourimageprocessing/mitkColourImageProcessor.cpp - isosurface/QmitkIsoSurface.cpp - simpleexample/QmitkSimpleExampleView.cpp - simplemeasurement/QmitkSimpleMeasurement.cpp - viewinitialization/QmitkViewInitializationView.cpp - volumetry/QmitkVolumetryView.cpp -) - -set(UI_FILES - src/internal/colourimageprocessing/QmitkColourImageProcessingViewControls.ui - src/internal/isosurface/QmitkIsoSurfaceControls.ui - src/internal/simpleexample/QmitkSimpleExampleViewControls.ui - src/internal/simplemeasurement/QmitkSimpleMeasurementControls.ui - src/internal/viewinitialization/QmitkViewInitializationViewControls.ui - src/internal/volumetry/QmitkVolumetryViewControls.ui -) - -set(MOC_H_FILES - src/internal/mitkPluginActivator.h - src/internal/colourimageprocessing/QmitkColourImageProcessingView.h - src/internal/isosurface/QmitkIsoSurface.h - src/internal/simpleexample/QmitkSimpleExampleView.h - src/internal/simplemeasurement/QmitkSimpleMeasurement.h - src/internal/viewinitialization/QmitkViewInitializationView.h - src/internal/volumetry/QmitkVolumetryView.h -) - -set(CACHED_RESOURCE_FILES - plugin.xml - resources/ColorImageProcessing.png - resources/isoSurface.xpm - resources/SimpleExample.png - resources/SimpleMeasurement.png - resources/viewInitializationIcon.xpm - resources/volumetryIcon.xpm -) - -set(QRC_FILES - resources/QmitkColourImageProcessingView.qrc - resources/isosurface.qrc - resources/QmitkVolumetryView.qrc -) - -set(CPP_FILES ) - -foreach(file ${SRC_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/${file}) -endforeach(file ${SRC_CPP_FILES}) - -foreach(file ${INTERNAL_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/internal/${file}) -endforeach(file ${INTERNAL_CPP_FILES}) - diff --git a/Plugins/org.mitk.gui.qt.examples/plugin.xml b/Plugins/org.mitk.gui.qt.examples/plugin.xml deleted file mode 100644 index 2518a132ec..0000000000 --- a/Plugins/org.mitk.gui.qt.examples/plugin.xml +++ /dev/null @@ -1,57 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Plugins/org.mitk.gui.qt.examples/resources/QmitkColourImageProcessingView.qrc b/Plugins/org.mitk.gui.qt.examples/resources/QmitkColourImageProcessingView.qrc index df29929cd9..484a6a3a47 100644 --- a/Plugins/org.mitk.gui.qt.examples/resources/QmitkColourImageProcessingView.qrc +++ b/Plugins/org.mitk.gui.qt.examples/resources/QmitkColourImageProcessingView.qrc @@ -1,5 +1,5 @@ - ColorImageProcessing.png + QmitkExamplesColorImageProcessing.png diff --git a/Plugins/org.mitk.gui.qt.examplesopencv/documentation/UserManual/videoplayer.gif b/Plugins/org.mitk.gui.qt.examplesopencv/documentation/UserManual/QmitkVideoPlayer.gif similarity index 100% rename from Plugins/org.mitk.gui.qt.examplesopencv/documentation/UserManual/videoplayer.gif rename to Plugins/org.mitk.gui.qt.examplesopencv/documentation/UserManual/QmitkVideoPlayer.gif diff --git a/Plugins/org.mitk.gui.qt.examplesopencv/documentation/UserManual/VideoPlayerUserManual.dox b/Plugins/org.mitk.gui.qt.examplesopencv/documentation/UserManual/QmitkVideoPlayerUserManual.dox similarity index 90% rename from Plugins/org.mitk.gui.qt.examplesopencv/documentation/UserManual/VideoPlayerUserManual.dox rename to Plugins/org.mitk.gui.qt.examplesopencv/documentation/UserManual/QmitkVideoPlayerUserManual.dox index dc7e5657b3..2dc72c452d 100644 --- a/Plugins/org.mitk.gui.qt.examplesopencv/documentation/UserManual/VideoPlayerUserManual.dox +++ b/Plugins/org.mitk.gui.qt.examplesopencv/documentation/UserManual/QmitkVideoPlayerUserManual.dox @@ -1,16 +1,16 @@ /** \page org_videoplayer The Video Player Module -\image html videoplayer.gif "Icon of the Module" +\image html QmitkVideoPlayer.gif "Icon of the Module" Available sections: - \ref QmitkVideoPlayerUserManualOverview \section QmitkVideoPlayerUserManualOverview Overview VideoPlayer is a program module that allows to play video files or grab frames directly from a connected camera with an intuitive user interface. Its main purpose is to demonstrate the usage of the OpenCV toolkit in MITK. */ diff --git a/Plugins/org.mitk.gui.qt.examplesopencv/files.cmake b/Plugins/org.mitk.gui.qt.examplesopencv/files.cmake deleted file mode 100644 index 6d4570edac..0000000000 --- a/Plugins/org.mitk.gui.qt.examplesopencv/files.cmake +++ /dev/null @@ -1,29 +0,0 @@ -set(SRC_CPP_FILES - -) - -set(INTERNAL_CPP_FILES - videoplayer/QmitkVideoPlayer.cpp - mitkPluginActivator.cpp -) - -set(MOC_H_FILES - src/internal/mitkPluginActivator.h - src/internal/videoplayer/QmitkVideoPlayer.h -) - -set(CACHED_RESOURCE_FILES - resources/videoplayer.gif - plugin.xml -) - -set(QRC_FILES -) - -foreach(file ${SRC_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/${file}) -endforeach(file ${SRC_CPP_FILES}) - -foreach(file ${INTERNAL_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/internal/${file}) -endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.examplesopencv/plugin.xml b/Plugins/org.mitk.gui.qt.examplesopencv/plugin.xml deleted file mode 100644 index 40948d03a5..0000000000 --- a/Plugins/org.mitk.gui.qt.examplesopencv/plugin.xml +++ /dev/null @@ -1,17 +0,0 @@ - - - - - - - - - - diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox index 20f6d10a85..a6a556d45d 100644 --- a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox +++ b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox @@ -1,118 +1,118 @@ /** \page MITKUserManualPage The MITK User Manual Welcome to the basic MITK user manual. This document tries to give a concise overview of the basic functions of MITK and be an comprehensible guide on using them. Available sections: - \ref MITKUserManualPageOverview - \ref MITKUserManualPageUserInterface - \ref MITKUserManualPagePerspectives \section MITKUserManualPageOverview About MITK MITK is an open-source framework that was originally developed as a common framework for Ph.D. students in the Division of Medical and Biological Informatics (MBI) at the German Cancer Research Center. MITK aims at supporting the development of leading-edge medical imaging software with a high degree of interaction. MITK re-uses virtually anything from VTK and ITK. Thus, it is not at all a competitor to VTK or ITK, but an extension, which tries to ease the combination of both and to add features not supported by VTK or ITK. Research institutes, medical professionals and companies alike can use MITK as a basic framework for their research and even commercial (thorough code research needed) software due to the BSD-like software license. Research institutes will profit from the high level of integration of ITK and VTK enhanced with data management, advanced visualization and interaction functionality in a single framework that is supported by a wide variety of researchers and developers. You will not have to reinvent the wheel over and over and can concentrate on your work. Medical Professionals will profit from MITK and the MITK applications by using its basic functionalities for research projects. But nonetheless they will be better off, unless they are programmers themselves, to cooperate with a research institute developing with MITK to get the functionalitiy they need. MITK and the MITK applications are not certified medical products and may be used in a research setting only. They must not be used in patient care. \section MITKUserManualPageUserInterface The User Interface The layout of the MITK applications is designed to give a clear distinction between the different work areas. The following figure gives an overview of the main sections of the user interface. -\image html GUI_Commented.png "The Common MITK Application Graphical User Interface" +\image html QmitkExtGUICommented.png "The Common MITK Application Graphical User Interface" The datamanager and the \ref MITKUserManualPagePerspectives have their own help sections. This document explains the use of: - The \ref MITKUserManualPageMultiWidget - The \ref MITKUserManualPageMenu - The \ref MITKUserManualPageLevelWindow - The \ref MITKUserManualPageMemoryUsage - The \ref MITKUserManualPageViews \section MITKUserManualPageMultiWidget Four Window View \subsection MITKUserManualPageMultiWidgetOverview Overview The four window view is the heart of the MITK image viewing. The standard layout is three 2D windows and one 3D window, with the axial window in the top left quarter, the sagittal window in the top right quarter, the coronal window in the lower left quarter and the 3D window in the lower right quarter. The different planes form a crosshair that can be seen in the 3D window. Once you select a point within the picture, informations about it are displayed at the bottom of the screen. \subsection MITKUserManualPageMultiWidgetNavigation Navigation Left click in any of the 2D windows centers the crosshair on that point. Pressing the right mouse button and moving the mouse zooms in and out. By scrolling with the mouse wheel you can navigate through the slices of the active window and pressing the mouse wheel while moving the mouse pans the image section. In the 3D window you can rotate the object by pressing the left mouse button and moving the mouse, zoom either with the right mouse button as in 2D or with the mouse wheel, and pan the object by moving the mouse while the mouse wheel is pressed. Placing the cursor within the 3D window and holding the "F" key allows free flight into the 3D view. \subsection MITKUserManualPageMultiWidgetCustomizingViews Customizing By moving the cursor to the upper right corner of any window you can activate the window menu. It consists of three buttons. -\image html Crosshair_Modes.png "Crosshair" +\image html QmitkExtCrosshairModes.png "Crosshair" The crosshair button allows you toggle the crosshair, reset the view and change the behaviour of the planes. Activating either of the rotation modes allows you to rotate the planes visible in a 2D window by moving the mouse cursor close to them and click and dragging once it changes to indicate that rotation can be done. The swivel mode is recommended only for advanced users as the planes can be moved freely by clicking and dragging anywhere within a 2D window. The middle button expands the corresponding window to fullscreen within the four window view. -\image html Views_Choices.png "Layout Choices" +\image html QmitkExtViewsChoices.png "Layout Choices" The right button allows you to choose between many different layouts of the four window view to use the one most suited to your task. \section MITKUserManualPageMenu Menu \subsection MITKUserManualPageFile File This dialog allows you to save, load and clear entire projects, this includes any nodes in the data manager. \subsection MITKUserManualPageEdit Edit This dialog supports undo and redo operations as well as the image navigator, which gives you sliders to navigate through the data quickly. \subsection MITKUserManualPageWindow Window This dialog allows you to open a new window, change between perspectives and reset your current one to default settings. If you want to use an operation of a certain perspective within another perspective the "Show View" menu allows to select a specific function that is opened and can be moved within the working areas according to your wishes. Be aware that not every function works with every perspective in a meaningful way. The Preferences dialog allows you to adjust and save your custom settings. -\image html Window_Dropdown.png "Preferences" +\image html QmitkExtWindowDropdown.png "Preferences" \subsection MITKUserManualPageHelp Help This dialog contains this help, the welcome screen and information about MITK. \section MITKUserManualPageLevelWindow Levelwindow Once an image is loaded the levelwindow appears to the right hand side of the four window view. With this tool you can adjust the range of grey values displayed and the gradient between them. Moving the lower boundary up results in any pixels having a value lower than that boundary to be displayed as black. Lowering the upper boundary causes all pixels having a value higher than it to be displayed as white. The pixels with a value between the lower and upper boundary are displayed in different shades of grey. This way a smaller levelwindow results in higher contrasts while cutting of the information outside its range whereas a larger levelwindow displays more information at the cost of contrast and detail. You can pick the levelwindow with the mouse to move it up and down, while moving the mouse cursor to the left or right to change its size. Picking one of the boundaries with a left click allows you to change the size symmetrically. Holding CTRL and clicking a boundary adjusts only that value. \section MITKUserManualPageMemoryUsage System Load Indicator The System Load Indicator in the lower right hand corner of the screen gives information about the memory currently required by the MITK application. Keep in mind that image processing is a highly memory intensive task and monitor the indicator to avoid your system freezing while constantly swapping to the hard drive. \section MITKUserManualPageViews Views Each solution for a specific problem that is self contained is realized as a single view. Thus you can create a workflow for your problem by combining the capabilities of different views to suit your needs. One elegant way to do this is by combining views in \ref MITKUserManualPagePerspectives. By pressing and holding the left mouse button on a views tab you can move it around to suit your needs, even out of the application window. \section MITKUserManualPagePerspectives Perspectives The different tasks that arise in medical imaging need very different approaches. To acknowledge this circumstance MITK supplies a framework that can be build uppon by very different solutions to those tasks. These solutions are called perspectives, each of them works independently of others although they might be used in sequence to achieve the solution of more difficult problems. It is possible to switch between the perspectives using the "Window"->"Open Perspective" dialog. See \ref MITKUserManualPageMenu for more information about switching perspectives. */ diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/QmitkExtUserManual.dox similarity index 97% copy from Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox copy to Plugins/org.mitk.gui.qt.ext/documentation/UserManual/QmitkExtUserManual.dox index 20f6d10a85..a6a556d45d 100644 --- a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox +++ b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/QmitkExtUserManual.dox @@ -1,118 +1,118 @@ /** \page MITKUserManualPage The MITK User Manual Welcome to the basic MITK user manual. This document tries to give a concise overview of the basic functions of MITK and be an comprehensible guide on using them. Available sections: - \ref MITKUserManualPageOverview - \ref MITKUserManualPageUserInterface - \ref MITKUserManualPagePerspectives \section MITKUserManualPageOverview About MITK MITK is an open-source framework that was originally developed as a common framework for Ph.D. students in the Division of Medical and Biological Informatics (MBI) at the German Cancer Research Center. MITK aims at supporting the development of leading-edge medical imaging software with a high degree of interaction. MITK re-uses virtually anything from VTK and ITK. Thus, it is not at all a competitor to VTK or ITK, but an extension, which tries to ease the combination of both and to add features not supported by VTK or ITK. Research institutes, medical professionals and companies alike can use MITK as a basic framework for their research and even commercial (thorough code research needed) software due to the BSD-like software license. Research institutes will profit from the high level of integration of ITK and VTK enhanced with data management, advanced visualization and interaction functionality in a single framework that is supported by a wide variety of researchers and developers. You will not have to reinvent the wheel over and over and can concentrate on your work. Medical Professionals will profit from MITK and the MITK applications by using its basic functionalities for research projects. But nonetheless they will be better off, unless they are programmers themselves, to cooperate with a research institute developing with MITK to get the functionalitiy they need. MITK and the MITK applications are not certified medical products and may be used in a research setting only. They must not be used in patient care. \section MITKUserManualPageUserInterface The User Interface The layout of the MITK applications is designed to give a clear distinction between the different work areas. The following figure gives an overview of the main sections of the user interface. -\image html GUI_Commented.png "The Common MITK Application Graphical User Interface" +\image html QmitkExtGUICommented.png "The Common MITK Application Graphical User Interface" The datamanager and the \ref MITKUserManualPagePerspectives have their own help sections. This document explains the use of: - The \ref MITKUserManualPageMultiWidget - The \ref MITKUserManualPageMenu - The \ref MITKUserManualPageLevelWindow - The \ref MITKUserManualPageMemoryUsage - The \ref MITKUserManualPageViews \section MITKUserManualPageMultiWidget Four Window View \subsection MITKUserManualPageMultiWidgetOverview Overview The four window view is the heart of the MITK image viewing. The standard layout is three 2D windows and one 3D window, with the axial window in the top left quarter, the sagittal window in the top right quarter, the coronal window in the lower left quarter and the 3D window in the lower right quarter. The different planes form a crosshair that can be seen in the 3D window. Once you select a point within the picture, informations about it are displayed at the bottom of the screen. \subsection MITKUserManualPageMultiWidgetNavigation Navigation Left click in any of the 2D windows centers the crosshair on that point. Pressing the right mouse button and moving the mouse zooms in and out. By scrolling with the mouse wheel you can navigate through the slices of the active window and pressing the mouse wheel while moving the mouse pans the image section. In the 3D window you can rotate the object by pressing the left mouse button and moving the mouse, zoom either with the right mouse button as in 2D or with the mouse wheel, and pan the object by moving the mouse while the mouse wheel is pressed. Placing the cursor within the 3D window and holding the "F" key allows free flight into the 3D view. \subsection MITKUserManualPageMultiWidgetCustomizingViews Customizing By moving the cursor to the upper right corner of any window you can activate the window menu. It consists of three buttons. -\image html Crosshair_Modes.png "Crosshair" +\image html QmitkExtCrosshairModes.png "Crosshair" The crosshair button allows you toggle the crosshair, reset the view and change the behaviour of the planes. Activating either of the rotation modes allows you to rotate the planes visible in a 2D window by moving the mouse cursor close to them and click and dragging once it changes to indicate that rotation can be done. The swivel mode is recommended only for advanced users as the planes can be moved freely by clicking and dragging anywhere within a 2D window. The middle button expands the corresponding window to fullscreen within the four window view. -\image html Views_Choices.png "Layout Choices" +\image html QmitkExtViewsChoices.png "Layout Choices" The right button allows you to choose between many different layouts of the four window view to use the one most suited to your task. \section MITKUserManualPageMenu Menu \subsection MITKUserManualPageFile File This dialog allows you to save, load and clear entire projects, this includes any nodes in the data manager. \subsection MITKUserManualPageEdit Edit This dialog supports undo and redo operations as well as the image navigator, which gives you sliders to navigate through the data quickly. \subsection MITKUserManualPageWindow Window This dialog allows you to open a new window, change between perspectives and reset your current one to default settings. If you want to use an operation of a certain perspective within another perspective the "Show View" menu allows to select a specific function that is opened and can be moved within the working areas according to your wishes. Be aware that not every function works with every perspective in a meaningful way. The Preferences dialog allows you to adjust and save your custom settings. -\image html Window_Dropdown.png "Preferences" +\image html QmitkExtWindowDropdown.png "Preferences" \subsection MITKUserManualPageHelp Help This dialog contains this help, the welcome screen and information about MITK. \section MITKUserManualPageLevelWindow Levelwindow Once an image is loaded the levelwindow appears to the right hand side of the four window view. With this tool you can adjust the range of grey values displayed and the gradient between them. Moving the lower boundary up results in any pixels having a value lower than that boundary to be displayed as black. Lowering the upper boundary causes all pixels having a value higher than it to be displayed as white. The pixels with a value between the lower and upper boundary are displayed in different shades of grey. This way a smaller levelwindow results in higher contrasts while cutting of the information outside its range whereas a larger levelwindow displays more information at the cost of contrast and detail. You can pick the levelwindow with the mouse to move it up and down, while moving the mouse cursor to the left or right to change its size. Picking one of the boundaries with a left click allows you to change the size symmetrically. Holding CTRL and clicking a boundary adjusts only that value. \section MITKUserManualPageMemoryUsage System Load Indicator The System Load Indicator in the lower right hand corner of the screen gives information about the memory currently required by the MITK application. Keep in mind that image processing is a highly memory intensive task and monitor the indicator to avoid your system freezing while constantly swapping to the hard drive. \section MITKUserManualPageViews Views Each solution for a specific problem that is self contained is realized as a single view. Thus you can create a workflow for your problem by combining the capabilities of different views to suit your needs. One elegant way to do this is by combining views in \ref MITKUserManualPagePerspectives. By pressing and holding the left mouse button on a views tab you can move it around to suit your needs, even out of the application window. \section MITKUserManualPagePerspectives Perspectives The different tasks that arise in medical imaging need very different approaches. To acknowledge this circumstance MITK supplies a framework that can be build uppon by very different solutions to those tasks. These solutions are called perspectives, each of them works independently of others although they might be used in sequence to achieve the solution of more difficult problems. It is possible to switch between the perspectives using the "Window"->"Open Perspective" dialog. See \ref MITKUserManualPageMenu for more information about switching perspectives. */ diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Crosshair_Modes.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/QmitkExtCrosshairModes.png similarity index 100% rename from Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Crosshair_Modes.png rename to Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/QmitkExtCrosshairModes.png diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/GUI.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/QmitkExtGUI.png similarity index 100% rename from Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/GUI.png rename to Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/QmitkExtGUI.png diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/GUI_Commented.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/QmitkExtGUICommented.png similarity index 100% rename from Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/GUI_Commented.png rename to Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/QmitkExtGUICommented.png diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Top_Right_Corner_Menu.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/QmitkExtTopRightCornerMenu.png similarity index 100% rename from Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Top_Right_Corner_Menu.png rename to Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/QmitkExtTopRightCornerMenu.png diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Views_Choices.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/QmitkExtViewsChoices.png similarity index 100% rename from Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Views_Choices.png rename to Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/QmitkExtViewsChoices.png diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Window_Dropdown.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/QmitkExtWindowDropdown.png similarity index 100% rename from Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Window_Dropdown.png rename to Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/QmitkExtWindowDropdown.png diff --git a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/icon.png b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTExamplesIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/icon.png rename to Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTExamplesIcon.png diff --git a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTExamplesManual.dox similarity index 100% rename from Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/Manual.dox rename to Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTExamplesManual.dox diff --git a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTtrackingLab.dox b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTrackingLab.dox similarity index 85% rename from Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTtrackingLab.dox rename to Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTrackingLab.dox index ce837e1b15..3d090b0923 100644 --- a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTtrackingLab.dox +++ b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTrackingLab.dox @@ -1,19 +1,19 @@ /** \page org_igttrackinglab The IGT-TrackingLab -\image html icon.png "Icon of the Module" +\image html QmitkIGTExamplesIcon.png "Icon of the Module" Available sections: - \ref QmitkIGTTrackingLabUsersManualOverview \section QmitkIGTTrackingLabUsersManualOverview Describe the features of your awesome plugin here */ diff --git a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTutorial.dox b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTutorial.dox index 8a75747d0e..860f9ad8af 100644 --- a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTutorial.dox +++ b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTutorial.dox @@ -1,14 +1,14 @@ /** \page org_imageguidedtherapytutorial The MITK-IGT Tutorial Module -\image html ImageGuidedTherapy.png "Icon of the Module" +\image html QmitkImageGuidedTherapyIcon.png "Icon of the Module" \section QmitkIGTTutorialUserManualSummary Summary This module is not meant as a end-user module. It contains tutorial program code that explains how to use the MITK-IGT component. It contains only two buttons. The "Start image guided therapy" button will create a virtual tracking device and a virtual tool. It will move the tool around on random paths in a tracking volume of 200x200x200 mm. The tool is visualized with a cone. If you do not see a cone moving around, you will need to initialize the rendering views correctly. Use the DataManager view to perform a global reinit. */ diff --git a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/ImageGuidedTherapy.png b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkImageGuidedTherapyIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/ImageGuidedTherapy.png rename to Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkImageGuidedTherapyIcon.png diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/configurationWidget.png b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingConfigurationWidget.png similarity index 100% rename from Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/configurationWidget.png rename to Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingConfigurationWidget.png diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/iconNavigationToolManager.png b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingIconNavigationToolManager.png similarity index 100% rename from Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/iconNavigationToolManager.png rename to Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingIconNavigationToolManager.png diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/iconTrackingToolbox.png b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingIconTrackingToolbox.png similarity index 100% rename from Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/iconTrackingToolbox.png rename to Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingIconTrackingToolbox.png diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingManual.dox similarity index 100% rename from Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/Manual.dox rename to Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingManual.dox diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/NavigationToolManagemantStartScreen.png b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingNavigationToolManagemantStartScreen.png similarity index 100% rename from Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/NavigationToolManagemantStartScreen.png rename to Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingNavigationToolManagemantStartScreen.png diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/NavigationToolManagementAddTool.png b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingNavigationToolManagementAddTool.png similarity index 100% rename from Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/NavigationToolManagementAddTool.png rename to Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingNavigationToolManagementAddTool.png diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/screenshot_complete.jpg.png b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingScreenshotComplete.png similarity index 100% rename from Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/screenshot_complete.jpg.png rename to Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingScreenshotComplete.png diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/screenshot_mitk.png b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingScreenshotMitk.png similarity index 100% rename from Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/screenshot_mitk.png rename to Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingScreenshotMitk.png diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/screenshotNavigationDataPlayer.png b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingScreenshotNavigationDataPlayer.png similarity index 100% rename from Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/screenshotNavigationDataPlayer.png rename to Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingScreenshotNavigationDataPlayer.png diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/trackingToolsWidget.png b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingToolsWidget.png similarity index 100% rename from Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/trackingToolsWidget.png rename to Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingToolsWidget.png diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/iconNavigationDataPlayer.png b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingiconNavigationDataPlayer.png similarity index 100% rename from Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/iconNavigationDataPlayer.png rename to Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTrackingiconNavigationDataPlayer.png diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolManager.dox b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolManager.dox index 0068963460..3c4d1715ba 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolManager.dox +++ b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolManager.dox @@ -1,47 +1,47 @@ /** \page org_mitk_views_igtnavigationtoolmanager The MITK-IGT Navigation Tool Manager -\image html iconNavigationToolManager.png "Icon of the Module" +\image html QmitkIGTTrackingIconNavigationToolManager.png "Icon of the Module" \section QmitkMITKIGTNavigationToolManager Introduction This view allows for creating and editing NavigationToolStorages. These storages contains naviagtion tools of a tracking device, can be saved permanently and used later for any other IGT application. Available sections: - \ref QmitkMITKIGTNavigationToolManager - \ref QmitkMITKIGTNavigationToolManagerToolOverview - \ref QmitkMITKIGTNavigationToolManagerManagingNavigationToolStorage - \ref QmitkMITKIGTNavigationToolManagerAddingEditingNavigationTools \section QmitkMITKIGTNavigationToolManagerToolOverview Navigation Tools Overview A navigation tool of MITK-IGT represents a tracking tool (e.g. an emt sensor or an optically tracked tool) and it's corresponding data, like it's name and it's surface. A navigation tool is a generalized container for any trackable object in combination with it's additional information. Every navigation tool has different properties which are: Note that not all properties are needed for all types of tools. A tool definition file, for example, is only needed by optical tracking tools (e.g. a .rom file for Polaris or a toolfile for the MicronTracker). A tool associated with the aurora system is alwalys identified by it's serial number. You can also detect Aurora tools automatically with the TrackingToolbox view and edit the automatically detected tool storage later with this view. \section QmitkMITKIGTNavigationToolManagerManagingNavigationToolStorage Managing Navigation Tool Storage In order to create a new storage container, or edit an existing one, you can use the buttons "add", "edit" and "delete" to manage the contained navigation tools. If you click "edit" or "delete" the operation is applied on the currently selected tool, as shown in the screenshot below. If you want to create a new storage container, just start adding tools when you start the program and save the storage container. To edit an existing tool storage container click "load" and add/edit/delete tools. -\image html NavigationToolManagemantStartScreen.png "Screenshot of the main view of NavigationToolManagent" +\image html QmitkIGTTrackingNavigationToolManagemantStartScreen.png "Screenshot of the main view of NavigationToolManagent" \section QmitkMITKIGTNavigationToolManagerAddingEditingNavigationTools Adding / Editing Navigation Tools If you add or edit a navigation tool, an input mask, as shown in the screenshot below, appears. The tool identifier is filled automatically, if you change it, remember that it is unique in the current storage. Also, choose a valid surface for every tool, this is nessesary for correct tool visualization. The other information depends on the tracking system type. So choose a tool file for the Polaris or the MicronTracker system and type in a serial number for the Aurora system. Two identical tools with the same serial number are also possible, they are assigned by the order in which they are attached to the device. As long as they also have the same surface, this should not be a problem. The tool type is additional information which is not needed by the tracking device but might be needed by further IGT applications. -\image html NavigationToolManagementAddTool.png "Screenshot of add/edit navigation tool screen" +\image html QmitkIGTTrackingNavigationToolManagementAddTool.png "Screenshot of add/edit navigation tool screen" */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTTrackingToolbox.dox b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTTrackingToolbox.dox index 0d1c66231c..a396ef0986 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTTrackingToolbox.dox +++ b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTTrackingToolbox.dox @@ -1,64 +1,64 @@ /** \page org_mitk_views_igttrackingtoolbox The MITK-IGT Tracking Toolbox -\image html iconTrackingToolbox.png "Icon of the module" +\image html QmitkIGTTrackingIconTrackingToolbox.png "Icon of the module" Available sections: - \ref QmitkMITKIGTTrackingToolboxIntroduction - \ref QmitkMITKIGTTrackingToolboxWorkflow - \ref QmitkMITKIGTTrackingToolboxConnecting - \ref QmitkMITKIGTTrackingToolboxLoadingTools - \ref QmitkMITKIGTTrackingToolboxAutoDetection - \ref QmitkMITKIGTTrackingToolboxStartTracking - \ref QmitkMITKIGTTrackingToolboxLogging - \ref QmitkMITKIGTTrackingOptions \section QmitkMITKIGTTrackingToolboxIntroduction Introduction The MITK-IGT Tracking Toolbox is a view which allows you to connect to a tracking device, track and visualize navigation tools and write the tracked data into a log file. Currently the devices Polaris, Aurora (both Northern Digital Inc. (NDI); Waterloo, Ontario, Canada) and MicronTracker (Claron Technology, Inc.; Toronto, Ontario, Canada) are supported. The MicroBird family (Ascension Technology Corporation, Inc.; Burlington, USA) will hopefully follow soon since it is already supported by the tracking layer of IGT. The logging feature of the Tracking Toolbox supports logging in XML or CSV format. -\image html screenshot_mitk.png "MITK Screenshot with the TrackingToolbox activated" +\image html QmitkIGTTrackingScreenshotMitk.png "MITK Screenshot with the TrackingToolbox activated" \section QmitkMITKIGTTrackingToolboxWorkflow General workflow Introduction A general Workflow with the Tracking Toolbox may be: \section QmitkMITKIGTTrackingToolboxConnecting Tracking Device Configuration The tracking device can be specified in the tracking device configuration section located in the upper area of the tracking tab. As shown in the screenshot below, you choose your tracking device in the drop down menu. If you use a tracking system connected to a serial port, like Aurora or Polaris, you then need to specifiy the serial port. In case of the MicronTracker you only need to ensure that all drivers are installed correctly and integrated into MITK. If you want to check the connection, press "test connection". The results are displayed in the small black box on the right. -\image html configurationWidget.png "Tracking Device Configuration" +\image html QmitkIGTTrackingConfigurationWidget.png "Tracking Device Configuration" \section QmitkMITKIGTTrackingToolboxLoadingTools Loading tools To load tools which can be tracked you need a predefined tracking tool storage. If you use the Aurora system you also have the possibility to automatically detect the connected tools. In this case a tracking tool storage is created by the software (see section below). Otherwise you can use the MITK view NavigationToolManager to define a navigation tool storage. There you can create navigation tools with the corresponding toolfiles, visualization surfaces and so on. Please see NavigationToolManager manual for more details. Navigation tool storages can be loaded by pressing the button "Load Tools". Please ensure that the tracking device type of the tools matches the chosen tracking device, otherwise you will get an error message if you try to start tracking. All loaded tools will then be displayed in grey as shown in the screenshot below. If you start tracking they will become green if the tools were found and red if they were not found inside the tracking volume. -\image html trackingToolsWidget.png "Tracking Tools" +\image html QmitkIGTTrackingToolsWidget.png "Tracking Tools" \section QmitkMITKIGTTrackingToolboxAutoDetection Auto detection of tools (only Aurora) If the Aurora tracking system is used, a button "Auto Detection" appears. If you press this button the software connects to the system and automatically detects all connected tools. You will then be asked whether you want to save the detected tools as a tool storage to the hard drive. You might want to do this if you want to use or modify this tool storage later. In the automatically detected tool storage the tools are named AutoDetectedTools1, AutoDetectedTools2, and so on. Small spheres are used as tool surfaces. After autodetection the detected tools are loaded automatically even if you did not save them. \section QmitkMITKIGTTrackingToolboxStartTracking Start/stop tracking Tracking can simply be started by pressing "Start Tracking". Note that options may not be changed during tracking. Once tracking has started the tracking volume (only if the option is on) and the tools are visualized in the 3D view of MITK. \section QmitkMITKIGTTrackingToolboxLogging Logging features If your device is tracking, you are able to log the tracking data by using the logging tab. You first must define a file name. You can then choose whether you want comma seperated (csv) or xml format. Press "Start Logging" to start logging. You can also limit the number of logged frames, which will cause the logging to stop automatically after the given number. \section QmitkMITKIGTTrackingOptions Options In the options tab you can enable or disable the visualization of the tracking volume and of the tool quaternions. If enabled, the tool quaternions are shown in the tool information. You can also define the update rate of the tracking data. The update rate should not be set higher than the update rate of the tracking system. */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkNavigationDataPlayer.dox b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkNavigationDataPlayer.dox index c6dec7930e..e61a603553 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkNavigationDataPlayer.dox +++ b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkNavigationDataPlayer.dox @@ -1,18 +1,18 @@ /** \page org_mitk_views_navigationdataplayer NavigationData Player -\image html iconNavigationDataPlayer.png "Icon of NavigationData Player" +\image html QmitkIGTTrackingiconNavigationDataPlayer.png "Icon of NavigationData Player" Available sections: - \ref NavigationDataPlayerOverview \section NavigationDataPlayerOverview The navigation data player plays recorded or artificial navigation data of one ore more tracking tools and visualizes their trajectory. For that purpose select an input file (*.xml only) and select which tracking tool's trajectory should be visualized. If you additionally activate the checkbox "Splines" the trajectory curve will be smoothed via spline interpolation. Press the button "start" for starting the player and the visualization. If "Sequential Mode" is checked, the navigation data are played sequentially without regarding the recorded time steps. You can use the resolution field to define which part of the samples you want to use. E.g. 1 = every sample; 2 = every second sample; 3 = every third sample, ... -\image html screenshotNavigationDataPlayer.png "Screenshot of the NavigationData Player" +\image html QmitkIGTTrackingScreenshotNavigationDataPlayer.png "Screenshot of the NavigationData Player" */ diff --git a/Plugins/org.mitk.gui.qt.igttracking/files.cmake b/Plugins/org.mitk.gui.qt.igttracking/files.cmake deleted file mode 100644 index 0d6a7d71e5..0000000000 --- a/Plugins/org.mitk.gui.qt.igttracking/files.cmake +++ /dev/null @@ -1,50 +0,0 @@ -set(SRC_CPP_FILES - -) - -set(INTERNAL_CPP_FILES - mitkPluginActivator.cpp - QmitkMITKIGTNavigationToolManagerView.cpp - QmitkMITKIGTTrackingToolboxView.cpp - QmitkNavigationDataPlayerView.cpp -) - -set(UI_FILES - src/internal/QmitkMITKIGTNavigationToolManagerViewControls.ui - src/internal/QmitkMITKIGTTrackingToolboxViewControls.ui - src/internal/QmitkNavigationDataPlayerViewControls.ui -) - -set(MOC_H_FILES - src/internal/mitkPluginActivator.h - src/internal/QmitkMITKIGTNavigationToolManagerView.h - src/internal/QmitkMITKIGTTrackingToolboxView.h - src/internal/QmitkNavigationDataPlayerView.h -) - -# list of resource files which can be used by the plug-in -# system without loading the plug-ins shared library, -# for example the icon used in the menu and tabs for the -# plug-in views in the workbench -set(CACHED_RESOURCE_FILES - resources/iconNavigationDataPlayer.png - resources/iconNavigationToolManager.xpm - resources/iconTrackingToolBox.xpm - plugin.xml -) - -# list of Qt .qrc files which contain additional resources -# specific to this plugin -set(QRC_FILES - -) - -set(CPP_FILES ) - -foreach(file ${SRC_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/${file}) -endforeach(file ${SRC_CPP_FILES}) - -foreach(file ${INTERNAL_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/internal/${file}) -endforeach(file ${INTERNAL_CPP_FILES}) \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.igttracking/plugin.xml b/Plugins/org.mitk.gui.qt.igttracking/plugin.xml deleted file mode 100644 index 3c2f94738e..0000000000 --- a/Plugins/org.mitk.gui.qt.igttracking/plugin.xml +++ /dev/null @@ -1,19 +0,0 @@ - - - - - - - - - - \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/icon.png b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropperIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/icon.png rename to Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropperIcon.png diff --git a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/icon.xpm b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropperIcon.xpm similarity index 100% rename from Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/icon.xpm rename to Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropperIcon.xpm diff --git a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropperUserManual.dox b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropperUserManual.dox index 26abe156ce..8bd0021bc1 100644 --- a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropperUserManual.dox +++ b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropperUserManual.dox @@ -1,41 +1,41 @@ /** \page org_mitk_views_imagecropper The Image Cropper Plugin -\image html icon.png "Icon of the Plugin" +\image html QmitkImageCropperIcon.png "Icon of the Plugin" Available sections: - \ref QmitkImageCropperUserManualOverview - \ref QmitkImageCropperUserManualFeatures - \ref QmitkImageCropperUserManualUsage - \ref QmitkImageCropperUserManualTroubleshooting \section QmitkImageCropperUserManualOverview Overview ImageCropper is a functionality which allows the user to manually crop an image by means of a bounding box. The functionality does not create a new image, it only hides parts of the original image. \section QmitkImageCropperUserManualFeatures Features - Crop a selected image using a bounding box. - Set the border voxels to a specific user defined value after cropping. \section QmitkImageCropperUserManualUsage Usage First select from the drop down menu the image to crop. The three 2D widgets show yellow rectangles representing the bounding box in each plane (axial, sagital, coronal), the lower right 3D widget shows the entire volume of the bounding box.\n - To change the size of bounding box press control + right click and move the cursor up/down or left/right in one of the three 2D views.\n - To change the orientation of the bounding box press control + middle click and move the cursor up/down or left/right in one of the three 2D views.\n - To move the bounding box press control + left click and move the cursor to the wanted position in one of the three 2D views.\n To show the result press the [crop] button.\n To crop the image again press the [New bounding box!] button.\n\n All actions can be undone by using the global undo function (Ctrl+Z).\n To set the border voxels to a specific value after cropping the image, activate the corresponding checkbox and choose a gray value. \section QmitkImageCropperUserManualTroubleshooting Troubleshooting */ diff --git a/Plugins/org.mitk.gui.qt.imagecropper/files.cmake b/Plugins/org.mitk.gui.qt.imagecropper/files.cmake deleted file mode 100644 index 7c65fcb8a2..0000000000 --- a/Plugins/org.mitk.gui.qt.imagecropper/files.cmake +++ /dev/null @@ -1,37 +0,0 @@ -set(SRC_CPP_FILES - -) - -set(INTERNAL_CPP_FILES - mitkImageCropperPluginActivator.cpp - QmitkImageCropper.cpp - mitkImageCropperEventInterface.cpp -) - -set(UI_FILES - src/internal/QmitkImageCropperControls.ui -) - -set(MOC_H_FILES - src/internal/mitkImageCropperPluginActivator.h - src/internal/QmitkImageCropper.h -) - -set(CACHED_RESOURCE_FILES - resources/icon.xpm - plugin.xml -) - -set(QRC_FILES - resources/imagecropper.qrc -) - -set(CPP_FILES) - -foreach(file ${SRC_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/${file}) -endforeach(file ${SRC_CPP_FILES}) - -foreach(file ${INTERNAL_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/internal/${file}) -endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.imagecropper/plugin.xml b/Plugins/org.mitk.gui.qt.imagecropper/plugin.xml deleted file mode 100644 index 38c0158df5..0000000000 --- a/Plugins/org.mitk.gui.qt.imagecropper/plugin.xml +++ /dev/null @@ -1,18 +0,0 @@ - - - - - - - - - - - diff --git a/Plugins/org.mitk.gui.qt.imagecropper/resources/imagecropper.qrc b/Plugins/org.mitk.gui.qt.imagecropper/resources/imagecropper.qrc index 23ba0b9ba0..a8c8084f2d 100644 --- a/Plugins/org.mitk.gui.qt.imagecropper/resources/imagecropper.qrc +++ b/Plugins/org.mitk.gui.qt.imagecropper/resources/imagecropper.qrc @@ -1,9 +1,9 @@ - icon.xpm + QmitkImageCropperIcon.xpm btn_ctrl.xpm mouse_left.xpm mouse_middle.xpm mouse_right.xpm diff --git a/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/ImageNavigator.png b/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmitkImageNavigatorOverview.png similarity index 100% rename from Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/ImageNavigator.png rename to Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmitkImageNavigatorOverview.png diff --git a/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/Slider.png b/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmitkImageNavigatorSlider.png similarity index 100% rename from Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/Slider.png rename to Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmitkImageNavigatorSlider.png diff --git a/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmtikImageNavigator.dox b/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmtikImageNavigator.dox index 86ed33d160..2edb5b17cf 100644 --- a/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmtikImageNavigator.dox +++ b/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmtikImageNavigator.dox @@ -1,15 +1,15 @@ /** \page org_mitk_views_imagenavigator The Image Navigator -\image html Slider.png "Icon of the Module" +\image html QmitkImageNavigatorSlider.png "Icon of the Module" -\image html ImageNavigator.png "Image Navigator" +\image html QmitkImageNavigatorOverview.png "Image Navigator" Fast movement through the available data can be achieved by using the Image Navigator. By moving the sliders around you can scroll quickly through the slides and timesteps. By entering numbers in the relevant fields you can jump directly to your point of interest. The "Show detail" checkbox enables you to see the world coordinates in millimetres and the index/voxel coordinates. These may be edited to jump to a specific location. */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.imagenavigator/files.cmake b/Plugins/org.mitk.gui.qt.imagenavigator/files.cmake deleted file mode 100644 index 71882b2e41..0000000000 --- a/Plugins/org.mitk.gui.qt.imagenavigator/files.cmake +++ /dev/null @@ -1,36 +0,0 @@ -set(SRC_CPP_FILES - -) - -set(INTERNAL_CPP_FILES - QmitkImageNavigatorView.cpp - mitkImageNavigatorPluginActivator.cpp -) - -set(UI_FILES - src/internal/QmitkImageNavigatorViewControls.ui -) - -set(MOC_H_FILES - src/internal/mitkImageNavigatorPluginActivator.h - src/internal/QmitkImageNavigatorView.h -) - -set(CACHED_RESOURCE_FILES - resources/Slider.png - plugin.xml -) - -set(QRC_FILES - resources/QmitkImageNavigatorView.qrc -) - - -foreach(file ${SRC_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/${file}) -endforeach(file ${SRC_CPP_FILES}) - -foreach(file ${INTERNAL_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/internal/${file}) -endforeach(file ${INTERNAL_CPP_FILES}) - diff --git a/Plugins/org.mitk.gui.qt.imagenavigator/plugin.xml b/Plugins/org.mitk.gui.qt.imagenavigator/plugin.xml deleted file mode 100644 index 0abe6b9d63..0000000000 --- a/Plugins/org.mitk.gui.qt.imagenavigator/plugin.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - - - - - - diff --git a/Plugins/org.mitk.gui.qt.imagenavigator/resources/QmitkImageNavigatorView.qrc b/Plugins/org.mitk.gui.qt.imagenavigator/resources/QmitkImageNavigatorView.qrc index e84b3a8cff..b27921b302 100644 --- a/Plugins/org.mitk.gui.qt.imagenavigator/resources/QmitkImageNavigatorView.qrc +++ b/Plugins/org.mitk.gui.qt.imagenavigator/resources/QmitkImageNavigatorView.qrc @@ -1,5 +1,5 @@ - Slider.png + QmitkImageNavigatorSlider.png diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics.dox b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics.dox index 545034b0b3..663b8c0945 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics.dox +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics.dox @@ -1,54 +1,54 @@ /** \page org_mitk_views_imagestatistics The Image Statistics View -\image html ImageStatistic_48.png "Icon of the View" +\image html QmitkMeasurementToolboxImageStatistic.png "Icon of the View" \section QmitkImageStatisticsUserManualSummary Summary This view provides an easy interface to quickly compute some features of a whole image or a region of interest. This document will tell you how to use this view, but it is assumed that you already know how to use MITK in general. Please see \ref QmitkImageStatisticsUserManualDetails for more detailed information on usage and supported filters. If you encounter problems using the view, please have a look at the \ref QmitkImageStatisticsUserManualTrouble page. \section QmitkImageStatisticsUserManualDetails Details Manual sections: - \ref QmitkImageStatisticsUserManualOverview - \ref QmitkImageStatisticsUserManualUsage - \ref QmitkImageStatisticsUserManualTrouble \section QmitkImageStatisticsUserManualOverview Overview This view provides an easy interface to quickly compute some features of a whole image or a region of interest. -\image html Screenshot1.png "The interface" +\image html QmitkMeasurementToolboxScreenshot.jpg "The interface" \section QmitkImageStatisticsUserManualUsage Usage After selection of an image or a binary mask of an image in the datamanager, the Image Statistics view shows some statistical information. If a mask is selected, the name of the mask and the name of the image, to which the mask is applied, are shown at the top. Check "Ignore zero-valued voxels" to hide voxels with grayvalue zero. Below it is the statistics window which displays the calculated statistical features (such as mean, standard deviation...). Beneath the statistics window is the histogram window, which shows the histogram of the current selection. At top of the histogram window are two radiobuttons. Toggle one of them to either show the histogram as a barchart or as a lineplot. Use mousewheel to zoom in and out the histogram. With the left mouse button the histogram is pannable in zoomed state. If the histogram is displayed as a barchart a tooltip is available by hovering over one of the bins. A tooltip is also available, if an intesity profile is created for a path element as mask. At the bottom of each view is one button. They copy their respective data in csv format to the clipboard. \section QmitkImageStatisticsUserManualTrouble Troubleshooting No known problems. All other problems.
Please report to the MITK mailing list. See http://www.mitk.org/wiki/Mailinglist on how to do this. */ diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox index c990dbef5a..78a2af3f68 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox @@ -1,134 +1,134 @@ /** \page org_mitk_views_measurement The Measurement View -\image html Measurement_48.png "Icon of the View" +\image html QmitkMeasurementToolboxMeasurement.png "Icon of the View" \section QmitkMeasurementUserManualOverview Overview The Measurement view enables the user to interact with 2D images or single slices of 3D image stacks and planar figure data types. It allows to measure distances, angels, pathes and several geometric figures on a dataset. Available Sections: - \ref QmitkMeasurementUserManualOverview - \ref QmitkMeasurementUserManualFeatures - \ref SubOne - \ref SubTwo - \ref SubThree - \ref SubFour - \ref SubFive - \ref SubSix - \ref SubSeven - \ref QmitkMeasurementUserManualUsage - \ref One - \ref Two - \ref Three - \ref Four The workflow to use this view is: -\image html Workflow.png +\image html QmitkMeasurementToolboxWorkflow.png The workflow is repeatedly useable with the same or different measurement figures, which are correlated to the choosen image and can be saved together with it for future use. On pressing the Measurement icon (see picture below the page title) in the view button line the basic appearance of the view is as follws. -\image html Basic_Screen_edited.JPG +\image html QmitkMeasurementToolboxBasicScreenEdited.jpg The standard working plane is "Axial" but the other standard viewplanes ("Saggital" and "Coronal") are also valid for measurements. To swap between the view planes refer to the application user manual. \section QmitkMeasurementUserManualFeatures Features The view as it is depicted below offers the following features in the order of apperance on the image from top to bottom: -\image html Measurement_View.JPG +\image html QmitkMeasurementToolboxMeasurementView.png The first information is the selected image's name (here: DICOM-MRI-Image) followed by the measurement figures button line with the seven measurement figures. From left to right the buttons are connected with the following functions: \subsection SubOne Draw Line Draws a line between two set points and returns the distance between these points. \subsection SubTwo Draw Path Draws a path between several set points (two and more) and calculates the circumference, that is all line's length summed up. Add the final point by double left click. \subsection SubThree Draw Angle Draws two lines from three set points connected in the second set point and returns the inner angle at the second point. \subsection SubFour Draw Four Point Angle Draws two lines that may but must not intersect from four set points. The returned angle is the one depicted in the icon. \subsection SubFive Draw Circle Draws a circle by setting two points, whereas the first set point is the center and the second the radius of the circle. The measured values are the radius and the included area. \subsection SubSix Draw Rectangle Draws a rectangle by setting two points at the opposing edges of the rectangle starting with the upper left edge. The measured values are the circumference and the included area. \subsection SubSeven Draw Polygon Draws a polygon by setting three or more points. The measured values are the circumference and the included area. Add the final point by double left click. Below the buttonline the statistics window is situated, it displays the results of the actual measurements from the selected measurement figures. The content of the statistics window can be copied to the clipboard with the correspondig button for further use in a table calculation programm (e.g. Open Office Calc etc.). -\image html Image_processed.JPG +\image html QmitkMeasurementToolboxImageProcessed.jpg The last row contains again a button line to swap from the measurement perspective (activated in the image) to other supported MITK perspectives. \section QmitkMeasurementUserManualUsage Usage This Section is subdivided into four subsections:
  1. Add an image
  2. Work with measurement figures
  3. Save the image with measurement information
  4. Remove measurement figures or image
Let's start with subsection 1 \subsection One Add an image There are two possible ways to add an image to the programm. One is to grap the image with left mouse click from your prefered file browser and simply drag&drop it to the View Plane field. The other way is to use the -\image html OpenButton.png +\image html QmitkMeasurementToolboxOpenButton.png button in the upper left corner of the application. A dialog window appears showing the file tree of the computer. Navigate to the wanted file and select it with the left mouse click. Afterwards just use the dialog's open button. The wanted image appears in the View Plane and in the Data Manager the images name appears as a new tree node. Now the image is loaded it can be adjusted in the usual way ( zoom in/out: right mouse button + moving the mouse up and down, moving the image: press mouse wheel and move the mouse to the wished direction, scroll through the slices( only on 3D images): scroll mouse wheel up and down). -\image html Image_Loaded_Screen.JPG +\image html QmitkMeasurementToolboxImageLoadedScreen.jpg After the image is loaded the image's name appears in the Data Manager. By left-clicking on the image name the buttonline becomes activated. \subsection Two Work with measurement figures The measurement view comes with seven measurement figures(see picture below), that can be applied to the images. -\image html MeasurementFigureButtonline.jpg +\image html QmitkMeasurementToolboxQmitkMeasurementToolboxMeasurementFigureButtonline.png The results of the measurement with each of these figures is shown in the statistics window and in the lower right corner of the view plane. -\image html Image_processed_Screen.JPG +\image html QmitkMeasurementToolboxImageProcessedScreen.jpg When applying more then one measurement figure to the image the actual measurement figure is depicted in red and the displayed values belong to this measurement figure. All measurement figures become part of the Data Manager as a node of the image tree. \subsection Three Save the image with measurement information After applying the wanted measurement figures the entire scene consisting of the image and the measurement figures can be saved for future use. Therefore just click the right mouse button when over the image item in the Data Manager and choose the item "Save" in the opening item list. Following to that a save dialog appears where the path to the save folder can be set. Afterwards just accept your choice with the save button. \subsection Four Remove measurement figures or image If the single measurement figures or the image is not needed any longer, it can be removed solely or as an entire group. The image can't be removed without simultaneously removing all the dependent measurement figures that belong to the image tree in the Data Manager. To remove just select the wanted items in the data manager list by left-click on it or if several items wanted to be removed left click on all wanted by simultaneously holding the ctrl-button pressed. For more detailed usage of the save/remove functionality refer to the Data Manager User Manual. +\image html QmitkMeasurementToolboxMeasurementGUI.png Graphical User Interface of Measurement --> */ diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/BasicScreen.png b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxBasicScreen.png similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/BasicScreen.png rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxBasicScreen.png diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Basic_Screen_edited.jpg b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxBasicScreenEdited.jpg similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Basic_Screen_edited.jpg rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxBasicScreenEdited.jpg diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Basic_Screen_edited.png b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxBasicScreenEdited.png similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Basic_Screen_edited.png rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxBasicScreenEdited.png diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/doxygen.png b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxDoxygen.png similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/doxygen.png rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxDoxygen.png diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Image_Loaded_Screen.jpg b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxImageLoadedScreen.jpg similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Image_Loaded_Screen.jpg rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxImageLoadedScreen.jpg diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Image_processed.jpg b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxImageProcessed.jpg similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Image_processed.jpg rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxImageProcessed.jpg diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Image_processed_Screen.jpg b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxImageProcessedScreen.jpg similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Image_processed_Screen.jpg rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxImageProcessedScreen.jpg diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/ImageStatistic_48.png b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxImageStatistic.png.png similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/ImageStatistic_48.png rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxImageStatistic.png.png diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Measurement_48.png b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxMeasurement.png similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Measurement_48.png rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxMeasurement.png diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/MeasurementFigureButtonline.jpg b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxMeasurementFigureButtonline.jpg similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/MeasurementFigureButtonline.jpg rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxMeasurementFigureButtonline.jpg diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/MeasurementFigureButtonline.png b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxMeasurementFigureButtonline.png similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/MeasurementFigureButtonline.png rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxMeasurementFigureButtonline.png diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/MeasurementGUI.png b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxMeasurementGUI.png similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/MeasurementGUI.png rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxMeasurementGUI.png diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/MeasurementIcon.png b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxMeasurementIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/MeasurementIcon.png rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxMeasurementIcon.png diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Measurement_View.jpg b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxMeasurementView.jpg similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Measurement_View.jpg rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxMeasurementView.jpg diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/OpenButton.png b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxOpenButton.png similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/OpenButton.png rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxOpenButton.png diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Screenshot1.png b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxScreenshot.png similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Screenshot1.png rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxScreenshot.png diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Workflow.png b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxWorkflow.png similarity index 100% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/Workflow.png rename to Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolboxWorkflow.png diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/files.cmake b/Plugins/org.mitk.gui.qt.measurementtoolbox/files.cmake deleted file mode 100644 index 0844fdcbb8..0000000000 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/files.cmake +++ /dev/null @@ -1,59 +0,0 @@ -set(SRC_CPP_FILES - -) - -set(INTERNAL_CPP_FILES - QmitkMeasurementView.cpp - QmitkPlanarFiguresTableModel.cpp - QmitkImageStatisticsView.cpp - QmitkImageStatisticsCalculationThread.cpp - mitkPluginActivator.cpp -) - -set(UI_FILES - src/internal/QmitkImageStatisticsViewControls.ui -) - -set(MOC_H_FILES - src/internal/QmitkMeasurementView.h - src/internal/QmitkPlanarFiguresTableModel.h - src/internal/QmitkImageStatisticsView.h - src/internal/QmitkImageStatisticsCalculationThread.h - src/internal/mitkPluginActivator.h - -) - -set(CACHED_RESOURCE_FILES - resources/angle.png - resources/arrow.png - resources/circle.png - resources/four-point-angle.png - resources/ImageStatistic_24.png - resources/ImageStatistic_48.png - resources/ImageStatistic_64.png - resources/lena.xpm - resources/line.png - resources/measurement.png - resources/path.png - resources/polygon.png - resources/rectangle.png - resources/stats.png - resources/text.png - plugin.xml -) - -set(QRC_FILES - resources/measurement.qrc - resources/QmitkImageStatisticsView.qrc -) - - -set(CPP_FILES ) - -foreach(file ${SRC_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/${file}) -endforeach(file ${SRC_CPP_FILES}) - -foreach(file ${INTERNAL_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/internal/${file}) -endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation.png b/Plugins/org.mitk.gui.qt.meshdecimation/documentation/UserManual/QmitkMeshDecimation.png similarity index 100% rename from Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation.png rename to Plugins/org.mitk.gui.qt.meshdecimation/documentation/UserManual/QmitkMeshDecimation.png diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation-manual.dox b/Plugins/org.mitk.gui.qt.meshdecimation/documentation/UserManual/QmitkMeshDecimationManual.dox similarity index 88% rename from Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation-manual.dox rename to Plugins/org.mitk.gui.qt.meshdecimation/documentation/UserManual/QmitkMeshDecimationManual.dox index 5cdc4fafa6..4efaf9ca85 100644 --- a/Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation-manual.dox +++ b/Plugins/org.mitk.gui.qt.meshdecimation/documentation/UserManual/QmitkMeshDecimationManual.dox @@ -1,33 +1,33 @@ /** \page org_mitk_views_meshdecimation The Mesh Decimation Plugin -\image html meshdecimation.png "Icon of the Plugin" +\image html QmitkMeshDecimation.png "Icon of the Plugin" Available sections: - \ref meshdecimationOverview - \ref meshdecimationFeatures - \ref meshdecimationUsage \section meshdecimationOverview Overview MeshDecimation is a user friendly tool to decimate a MITK surface. \section meshdecimationFeatures Features The view offers two basic procedures to decimate surfaces: One that reduces a surface with a possible loss of topology (quality), but with a garuanteed reduction rate that is expressed in terms of percent of the original mesh. The other variant preserves the topology and stops decimating when it detects heavy topological changes. \section meshdecimationUsage Usage -\image html meshdecimation-ui.png "The user interface of the Mesh Decimation View" +\image html QmitkMeshDecimationUI.png "The user interface of the Mesh Decimation View" The usage of the view should be straightforward, as shown in the screenshot. To decimate a MITK surface do the following: - Select a surface in the datamanager - Enter a target reduction rate - Select a decimation method (\ref meshdecimationFeatures) - Press the "Decimate" button - Repeat the process until you are satisfied with the decimation - Save the surface to disk */ diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation-ui.png b/Plugins/org.mitk.gui.qt.meshdecimation/documentation/UserManual/QmitkMeshDecimationUI.png similarity index 100% rename from Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation-ui.png rename to Plugins/org.mitk.gui.qt.meshdecimation/documentation/UserManual/QmitkMeshDecimationUI.png diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/files.cmake b/Plugins/org.mitk.gui.qt.meshdecimation/files.cmake deleted file mode 100644 index c8263e247d..0000000000 --- a/Plugins/org.mitk.gui.qt.meshdecimation/files.cmake +++ /dev/null @@ -1,37 +0,0 @@ -SET(SRC_CPP_FILES - -) - -SET(INTERNAL_CPP_FILES - QmitkMeshDecimationView.cpp - mitkPluginActivator.cpp -) - -SET(UI_FILES - src/internal/QmitkMeshDecimationView.ui -) - -SET(MOC_H_FILES - src/internal/QmitkMeshDecimationView.h - src/internal/mitkPluginActivator.h -) - -SET(CACHED_RESOURCE_FILES - resources/meshdecimation.png - plugin.xml -) - -SET(QRC_FILES - -) - -SET(CPP_FILES ) - -foreach(file ${SRC_CPP_FILES}) - SET(CPP_FILES ${CPP_FILES} src/${file}) -endforeach(file ${SRC_CPP_FILES}) - -foreach(file ${INTERNAL_CPP_FILES}) - SET(CPP_FILES ${CPP_FILES} src/internal/${file}) -endforeach(file ${INTERNAL_CPP_FILES}) - diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/plugin.xml b/Plugins/org.mitk.gui.qt.meshdecimation/plugin.xml deleted file mode 100644 index 13005afb6a..0000000000 --- a/Plugins/org.mitk.gui.qt.meshdecimation/plugin.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - - - - - - \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/icon.png b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMakerIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/icon.png rename to Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMakerIcon.png diff --git a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/icon.xpm b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMakerIcon.xpm similarity index 100% rename from Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/icon.xpm rename to Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMakerIcon.xpm diff --git a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/screenshot_maker_interface.png b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMakerScreenshotMakerInterface.png similarity index 100% rename from Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/screenshot_maker_interface.png rename to Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMakerScreenshotMakerInterface.png diff --git a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMakerUserManual.dox b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMakerUserManual.dox index 602f4243c5..a8239074f7 100644 --- a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMakerUserManual.dox +++ b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMakerUserManual.dox @@ -1,45 +1,45 @@ /** \page org_mitk_views_moviemaker The Movie Maker View -\image html icon.png "Icon of the View" +\image html QmitkMovieMakerIcon.png "Icon of the View" Available sections: - \ref QmitkMovieMakerUserManualOverview - \ref QmitkMovieMakerUserManualFeatures - \ref QmitkMovieMakerUserManualUsage \section QmitkMovieMakerUserManualOverview Overview MovieMaker is a functionality for easily creating fancy movies from scenes displayed in MITK widgets. It is also possible to slide through your data, automatically rotate 3D scenes and take screenshots of widgets. \section QmitkMovieMakerUserManualFeatures Features The Movie Maker allows you to create movies and screenshots from within MITK. It can automatically scroll thorugh timesteps and slices while recording a movie. This way, you can record visualizations like a beating heart or a rotating skull. \section QmitkMovieMakerUserManualUsage Usage \image html QmitkMovieMakerControlArea.png "A view of the command area of QmitkMovieMaker" \subsection QmitkMovieMakerUserManualWindowSelection Window selection With the first two drop down boxes, you can choose which window you want to step through and which window you want to record in. Left clicking inside a window will set both drop down boxes to that window, but you can choose different windows for stepping and recording. The first drop down box defines the window along which slices will be stepped through if stepping is set to spatial (see below). The second denotes the window from which the content will be recorded. \subsection QmitkMovieMakerUserManualRecordingOptions Recording Options The slider can be used to step through the slices manually while not recording. Start and stop control a preview of what a video would look like. The buttons in the bottom part of this section can be used to create movies (windows only) or screenshots. Clicking opens a file %dialog where a name can be selected. After confirmation, a screenshot or movie is created according to the playing options. \subsection QmitkMovieMakerUserManualPlayingOptions Playing Options The first section controls whether the movie steps through slices (if a 2D view is selected), rotate the shown scene (if a 3D view is selected), or step through time steps (if set to temporal and a time resolved dataset is selected). If set to combined, a combination of both above options is used, with their speed relation set via the S/T Relation Spinbox. In the second section the direction of stepping can be set. Options are: Forward, backward and Ping-Pong, which is back-and-forth.The stepping speed can be set via the spinbox(total time in seconds). Although stepping speed is a total time in sec., this can not always be achieved. As a minimal frame rate of 25 fps is assumed to provide smooth movies, a dataset with only 25 slices will always be stepped through in 1 sec or faster. */ diff --git a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkScreenshotMakerManual.dox b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkScreenshotMakerManual.dox index 688b614a55..6329610019 100644 --- a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkScreenshotMakerManual.dox +++ b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkScreenshotMakerManual.dox @@ -1,19 +1,19 @@ /** \page org_mitk_views_screenshotmaker The Screenshot Maker This view provides the functionality to create and save screenshots of the data. Available sections: - \ref QmitkScreenshotMakerUserManualUse -\image html screenshot_maker_interface.png The Screenshot Maker User Interface +\image html QmitkMovieMakerScreenshotMakerInterface.png The Screenshot Maker User Interface \section QmitkScreenshotMakerUserManualUse Usage The first section offers the option of creating a screenshot of the last activated render window (thus the one, which was last clicked into). Upon clicking the button, the Screenshot Maker asks for a filename in which the screenshot is to be stored. The multiplanar Screenshot button asks for a folder, where screenshots of the three 2D views will be stored with default names. The high resolution screenshot section works the same as the simple screenshot section, aside from the fact, that the user can choose a magnification factor. In the option section one can rotate the camera in the 3D view by using the buttons. Furthermore one can choose the background colour for the screenshots, default is black. */ diff --git a/Plugins/org.mitk.gui.qt.moviemaker/files.cmake b/Plugins/org.mitk.gui.qt.moviemaker/files.cmake deleted file mode 100644 index c4e28db992..0000000000 --- a/Plugins/org.mitk.gui.qt.moviemaker/files.cmake +++ /dev/null @@ -1,46 +0,0 @@ -set(SRC_CPP_FILES - -) - -set(INTERNAL_CPP_FILES - QmitkMovieMaker.cpp - mitkMovieMakerPluginActivator.cpp - QmitkScreenshotMaker.cpp - -) - -set(UI_FILES - src/internal/QmitkMovieMakerControls.ui - src/internal/QmitkScreenshotMakerControls.ui -) - -set(MOC_H_FILES - src/internal/mitkMovieMakerPluginActivator.h - src/internal/QmitkMovieMaker.h - src/internal/QmitkScreenshotMaker.h -) - -set(CACHED_RESOURCE_FILES - resources/icon.xpm - plugin.xml - resources/play.xpm - resources/stop.xpm - resources/pause.xpm - resources/screenshot_maker.png -) - -set(RES_FILES - resources/QmitkMovieMaker.qrc - resources/play.xpm - resources/stop.xpm - resources/pause.xpm -) - -foreach(file ${SRC_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/${file}) -endforeach(file ${SRC_CPP_FILES}) - -foreach(file ${INTERNAL_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/internal/${file}) -endforeach(file ${INTERNAL_CPP_FILES}) - diff --git a/Plugins/org.mitk.gui.qt.moviemaker/plugin.xml b/Plugins/org.mitk.gui.qt.moviemaker/plugin.xml deleted file mode 100644 index 6765494265..0000000000 --- a/Plugins/org.mitk.gui.qt.moviemaker/plugin.xml +++ /dev/null @@ -1,19 +0,0 @@ - - - - - - - - - - - - - diff --git a/Plugins/org.mitk.gui.qt.moviemaker/resources/QmitkMovieMaker.qrc b/Plugins/org.mitk.gui.qt.moviemaker/resources/QmitkMovieMaker.qrc index 8bdb515e34..d8bd752a2a 100644 --- a/Plugins/org.mitk.gui.qt.moviemaker/resources/QmitkMovieMaker.qrc +++ b/Plugins/org.mitk.gui.qt.moviemaker/resources/QmitkMovieMaker.qrc @@ -1,10 +1,10 @@ QmitkMovieMakerClasses.png QmitkMovieMakerGUI.png - icon.xpm + QmitkMovieMakerIcon.xpm pause.xpm play.xpm stop.xpm diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.png b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.png index 4ab561d095..dca1ede3fb 100644 Binary files a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.png and b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.png differ diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/AddPointSet.png b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteractionAddPointSet.png similarity index 100% rename from Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/AddPointSet.png rename to Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteractionAddPointSet.png diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/CurrentPointSetArea.png b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteractionCurrentPointSetArea.png similarity index 100% rename from Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/CurrentPointSetArea.png rename to Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteractionCurrentPointSetArea.png diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteractionUserManual.dox b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteractionUserManual.dox index 5151fea9ac..9374942e5b 100644 --- a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteractionUserManual.dox +++ b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteractionUserManual.dox @@ -1,38 +1,38 @@ /** \page org_mitk_views_pointsetinteraction The Point Set Interaction View -\image html pointset_interaction.png "Icon of the View" +\image html QmitkPointSetInteraction.png "Icon of the View" Available sections: - \ref QmitkPointSetInteractionUserManualOverview - \ref QmitkPointSetInteractionUserManualDetails \section QmitkPointSetInteractionUserManualOverview Overview This functionality allows you to define multiple sets of points, to fill them with points and to save them in so called PointSets. -\image html QmitkPointSetInteraction.png "MITK with the QmitkPointSetInteraction functionality" +\image html QmitkPointSetInteractionView.png "MITK with the QmitkPointSetInteraction functionality" This document will tell you how to use this functionality, but it is assumed that you already know how to navigate through the slices of an image using the four window view. Please read the application manual for more information. \section QmitkPointSetInteractionUserManualDetails Details First of all you have to select a PointSet to use this functionality. Therefore, you have to select the point set in the data manager. If there are currently no point sets in the data tree, you have to first add a new point set to the data tree. This is done by clicking the "Add pointset..." button. -\image html AddPointSet.png "The Add pointset... dialog" +\image html QmitkPointSetInteractionAddPointSet.png "The Add pointset... dialog" In the pop-up dialog, you have to specify a name for the new point set. This is also the node for the new data tree item. -\image html CurrentPointSetArea.png "The Current pointset area" +\image html QmitkPointSetInteractionCurrentPointSetArea.png "The Current pointset area" The "Current pointset" area contains a list of points. Within this area, all points for the current point set node are listed. To set points you have to toggle the "Set Points" button, the leftmost of the four buttons on the bottom of the view. Points can be defined by performing a left mouse button click while holding the "Shift"-key pressed in the four window view. To erase all points from the list press the next button. The user is prompted to confirm the decision. If you want to delete only a single point, left click on it in the list and then press delete on your keyboard. With the third button, a previously saved point set can be loaded and all of its points are shown in the list and the four window view. The user is prompted to select the file to be loaded. The file extension is ".mps". On the right of this button is the save button. With this function the entire point set can be saved to the harddrive. The user is prompted to select a filename. Pointsets are saved in XML fileformat but have to have a ".mps" file extension. You can select points in the render window, if the "Set Points" button is toggled, with a left mouse button click on them. If you keep the mouse button pressed, you can move the points by moving the mouse and then releasing the mouse button. With the delete key you can remove the selected points. */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.png b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteractionView.png similarity index 100% copy from Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.png copy to Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteractionView.png diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/pointset_interaction.png b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/pointset_interaction.png deleted file mode 100644 index dca1ede3fb..0000000000 Binary files a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/pointset_interaction.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/files.cmake b/Plugins/org.mitk.gui.qt.pointsetinteraction/files.cmake deleted file mode 100644 index 57c1329886..0000000000 --- a/Plugins/org.mitk.gui.qt.pointsetinteraction/files.cmake +++ /dev/null @@ -1,35 +0,0 @@ -set(SRC_CPP_FILES - -) - -set(INTERNAL_CPP_FILES - QmitkPointSetInteractionView.cpp - mitkPluginActivator.cpp -) - -set(UI_FILES - src/internal/QmitkPointSetInteractionViewControls.ui -) - -set(MOC_H_FILES - src/internal/mitkPluginActivator.h - src/internal/QmitkPointSetInteractionView.h -) - -set(CACHED_RESOURCE_FILES - resources/pointset_interaction.png - plugin.xml -) - -set(QRC_FILES - resources/QmitkPointSetInteractionView.qrc -) - -foreach(file ${SRC_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/${file}) -endforeach(file ${SRC_CPP_FILES}) - -foreach(file ${INTERNAL_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/internal/${file}) -endforeach(file ${INTERNAL_CPP_FILES}) - diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/plugin.xml b/Plugins/org.mitk.gui.qt.pointsetinteraction/plugin.xml deleted file mode 100644 index abd1ee41bd..0000000000 --- a/Plugins/org.mitk.gui.qt.pointsetinteraction/plugin.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - - - - - - diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/resources/QmitkPointSetInteractionView.qrc b/Plugins/org.mitk.gui.qt.pointsetinteraction/resources/QmitkPointSetInteractionView.qrc index 0cfb322fd2..2dc6c7a12e 100644 --- a/Plugins/org.mitk.gui.qt.pointsetinteraction/resources/QmitkPointSetInteractionView.qrc +++ b/Plugins/org.mitk.gui.qt.pointsetinteraction/resources/QmitkPointSetInteractionView.qrc @@ -1,6 +1,6 @@ - pointset_interaction.png + QmitkPointSetInteraction.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkDeformableRegistrationUserManual.dox b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkDeformableRegistrationUserManual.dox index fd11c761dc..fff8b10093 100644 --- a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkDeformableRegistrationUserManual.dox +++ b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkDeformableRegistrationUserManual.dox @@ -1,52 +1,52 @@ /** \page org_mitk_views_deformableregistration The Deformable Image Registration View Available sections: - \ref DeformableRegistrationUserManualOverview - \ref DeformableRegistrationUserManualDetails \section DeformableRegistrationUserManualOverview Overview This view allows you to register 2D as well as 3D images in a deformable manner. Register means to align two images, so that they become as similar as possible. Registration results will directly be applied to the Moving Image. \image html QmitkDeformableRegistration_small.png "MITK with the DeformableRegistration view" This document will tell you how to use this view, but it is assumed that you already know how to navigate through the slices of an image using the multi-widget. \section DeformableRegistrationUserManualDetails Details First of all you have to open the data sets which you want to register and select them in the Data Manager. You have to select exactly 2 images for registration. The image which was selected first will become the fixed image, the other one the moving image. The two selected images will remain for registration until exactly two images were selected in the Data Manager again. While there aren't two images for registration a message is viewed on top of the view saying that registration needs two images. If two images are selected the message disappears and the interaction areas for the fixed and moving data appears. On default only the fixed and moving image are shown in the render windows. If you want to have other images visible you have to set the visibility via the Data Manager. Also if you want to perform a reinit on a specific node or a global reinit for all nodes you have to use the Data Manager. -\image html ImageSelectionDeformable.png "The Image area" +\image html QmitkRegistrationImageSelectionDeformable.png "The Image area" The upper area is the "Image" area, where the selected images are shown. It is used for changing the colour of the images between grey values and red/green as well as for changing the opacity of the moving image. To do so, just use the "Moving Image Opacity:" slider. In the "Show Images Red/Green" you can switch the color from both datasets. If you check the box, the fixed dataset will be displayed in redvalues and the moving dataset in greenvalues to improve visibility of differences in the datasets. If you uncheck the "Show Images Red/Green" checkbox, both datasets will be displayed in greyvalues. -\image html RegistrationDeformable.png "The Registration area for Demons based registration" +\image html QmitkRegistrationRegistrationDeformable.png "The Registration area for Demons based registration" In the "Registration" area you have the choice between different Demonsbased deformable registration algorithms. There are available: \li Demons Registration \li Symmetric Forces Demons Registration For both methods you have to define the same set of parameters. First you have to decide whether you want to perform a histogram matching. This can be done by selecting "Use Histogram Matching". When it is selected the corresponding parameters are enabled and have to be set. These are the "Number of Histogram Levels", "Number of Match Points" and whether to use a "Threshold at Mean Intensity". For the registration method itself you have to specify the "Number of Iterations" and the "Standard Deviation" within the "Demons Registration" area. If all this is done, you can perform the registration by clicking the "Calculate Transformation" button. Finally, you will be asked where you want the result image and the resulting deformation field to be saved. Therefore you have to select the folder and enter a filename. The results will be added in the DataStorage and can be saved in the Data Manager. */ diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkPointBasedRegistrationUserManual.dox b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkPointBasedRegistrationUserManual.dox index cfc7e3be68..cafe45bc83 100644 --- a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkPointBasedRegistrationUserManual.dox +++ b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkPointBasedRegistrationUserManual.dox @@ -1,106 +1,106 @@ /** \page org_mitk_views_pointbasedregistration The Point Based Registration View -\image html pointBasedIcon.png "Icon of the View" +\image html QmitkRegistrationpointBasedIcon.png "Icon of the View" Available sections: - \ref PointBasedRegistrationUserManualOverview - \ref PointBasedRegistrationUserManualDetails \section PointBasedRegistrationUserManualOverview Overview This view allows you to register two datasets in a rigid and deformable manner via corresponding PointSets. Register means to align two datasets, so that they become as similar as possible. Therefore you have to set corresponding points in both datasets, which will be matched. The movement, which has to be performed on the points to align them, will be performed on the moving data as well. The result is shown in the multi-widget. -\image html PointBasedRegistration_small.png "MITK with the PointBasedRegistration view" +\image html QmitkRegistrationPointBasedRegistrationSmall.png "MITK with the PointBasedRegistration view" This document will tell you how to use this view, but it is assumed that you already know how to navigate through the slices of a dataset using the multi-widget. \section PointBasedRegistrationUserManualDetails Details First of all you have to open the data sets which you want to register and select them in the Data Manager. You have to select exactly 2 images for registration. The image which was selected first will become the fixed image, the other one the moving image. The two selected images will remain for registration until exactly two images were selected in the Data Manager again. While there aren't two images for registration a message is viewed on top of the view saying that registration needs two images. If two images are selected the message disappears and the interaction areas for the fixed and moving data appears. The upper area is for interaction with the fixed data. Beneath this area is the interaction area for the moving data. On default only the fixed and moving image with their corresponding pointsets are shown in the render windows. If you want to have other images visible you have to set the visibility via the Data Manager. Also if you want to perform a reinit on a specific node or a global reinit for all nodes you have to use the Data Manager. -\image html FixedDataPointBased.png "The Fixed Data area" +\image html QmitkRegistrationFixedDataPointBased.png "The Fixed Data area" The "Fixed Data" area contains a QmitkPointListWidget. Within this widget, all points for the fixed data are listed. The label above this list shows the number of points that are already set. To set points you have to toggle the "Set Points" button, the leftmost under the QmitkPointListWidget. The views in the QmitkStdMultiWidget were reinitialized to the fixed data. Points can be defined by performing a left click while holding the "Shift"-key pressed in the QmitkStdMultiWidget. You can remove the interactor which listens for left clicks while holding the "Shift"-key pressed by detoggle the "Set Points" button. The next button, "Clear Point Set", is for deleting all specified points from this dataset. The user is prompted to confirm the decision. With the most right button, a previously saved point set can be loaded and all of its points are shown in the QmitkPointListWidget and in the QmitkStdMultiWidget. The user is prompted to select the file to be loaded. The file extension is ".mps". On the left of this button is the save button. With this function all points specified for this dataset and shown in the QmitkPointListWidget are saved to harddisk. The user is prompted to select a filename. Pointsets were saved in XML fileformat but have to have a ".mps" file extension. You can select landmarks in the render window with a left mouse button click on them. If you keep the mouse button pressed you can move the landmark to an other position by moving the mouse and then release the mouse button. With the delete key you can remove the selected landmarks. You can also select landmarks by a double click on a landmark within the QmitkPointListWidget. Using the "Up-Arrow"-button or the "F2" key you can easily move a landmark upwards and bring it further downwards by pressing "F3" or using the "Down-Arrow"-button. Thus the landmark number can be changed. The QmitkStdMultiWidget changes its view to show the position of the landmark. -\image html MovingDataPointBased.png "The Moving Data area" +\image html QmitkRegistrationMovingDataPointBased.png "The Moving Data area" The "Moving Data" area contains a QmitkPointListWidget. Within this widget, all points for the moving data are listed. The label above this list shows the number of points that are already set. To set points you have to toggle the "Set Points" button, the leftmost under the QmitkPointListWidget. The views in the QmitkStdMultiWidget were reinitialized to the moving data. With the "Opacity:" slider you can change the opacity of the moving dataset. If the slider is leftmost the moving dataset is totally transparent, whereas if it is rightmost the moving dataset is totally opaque. Points can be defined by performing a left click while holding the "Shift"-key pressed in the QmitkStdMultiWidget. You can remove the interactor which listens for left mousebutton click while holding the "Shift"-key pressed by detoggle the "Set Points" button. The next button, "Clear Point Set", is for deleting all specified points from this dataset. The user is prompted to confirm the decision. With the button on your right hand side, a previously saved point set can be loaded and all of its points are shown in the QmitkPointListWidget and in the QmitkStdMultiWidget. The user is prompted to select the file to be loaded. The file extension is ".mps". On the left of this button is the save button. With this function all points specified for this dataset and shown in the QmitkPointListWidget are saved to harddisk. The user is prompted to select a filename. Pointsets were saved in XML fileformat but have to have a ".mps" file extension. You can select landmarks in the render window with a left click on them. If you keep the mouse button pressed you can move the landmark to an other position by moving the mouse and then release the mouse button. With the delete key you can remove the selected landmarks. You can also select landmarks by a double click on a landmark within the QmitkPointListWidget. Using the "Up-Arrow"-button or the "F2" key you can easily move a landmark upwards and bring it further downwards by pressing "F3" or using the "Down-Arrow"-button. Thus the landmark number can be changed.The QmitkStdMultiWidget changes its view to show the position of the landmark. -\image html DisplayOptionsPointBased.png "The Display Options area" +\image html QmitkRegistrationDisplayOptionsPointBased.png "The Display Options area" In this area you can find the "Show Images Red/Green" checkbox. Here you can switch the color from both datasets. If you check the box, the fixed dataset will be displayed in redvalues and the moving dataset in greenvalues to improve visibility of differences in the datasets. If you uncheck the "Show Images Red/Green" checkbox, both datasets will be displayed in greyvalues. Before you perform your transformation it is useful to see both images again. Therefore detoggle the "Set Points" button for the fixed data as well as for the moving data. -\image html RegistrationPointBased.png "The Registration area" +\image html QmitkRegistrationPointBased.png "The Registration area" The functions concerning the registration are displayed in the "Registration" area. It not only contains the registration method selection and the registration itself but also offers the possibility to save, undo or redo the results. Furthermore a display is implemented, which shows you how good the landmarks correspond. Those features will be explained in following paragraphs. Using the "Method"-selector, you can pick one of those transformations: Rigid, Similarity, Affine and LandmarkWarping. Depending on which one you chose, an additional specifier, "Use ICP" can be set, which leads to the following possibilities for registration: \li Rigid with ICP means only translation and rotation. The order of your landmarks will not be taken into account. E. g. landmark one in the fixed data can be mapped on landmark three in the moving data. You have to set at least one landmark in each dataset to enable the Register button which performs the transformation. \li Similarity with ICP means only translation, scaling and rotation. The order of your landmarks will not be taken into account. E. g. landmark one in the fixed data can be mapped on landmark three in the moving data. You have to set at least one landmark in each dataset to enable the Register button which performs the transformation. \li Affine with ICP means only translation, scaling, rotation and shearing. The order of your landmarks will not be taken into account. E. g. landmark one in the fixed data can be mapped on landmark three in the moving data. You have to set at least one landmark in each dataset to enable the Register button which performs the transformation. \li Rigid means only translation and rotation. The order of your landmarks will be taken into account. E. g. landmark one in the fixed data will be mapped on landmark one in the moving data. You have to set at least one landmark and the same number of landmarks in each dataset to enable the Register button which performs the transformation. \li Similarity means only translation, scaling and rotation. The order of your landmarks will be taken into account. E. g. landmark one in the fixed data will be mapped on landmark one in the moving data. You have to set at least one landmark and the same number of landmarks in each dataset to enable the Register button which performs the transformation. \li Affine means only translation, scaling, rotation and shearing. The order of your landmarks will be taken into account. E. g. landmark one in the fixed data will be mapped on landmark one in the moving data. You have to set at least one landmark and the same number of landmarks in each dataset to enable the Register button which performs the transformation. \li LandmarkWarping means a freeform deformation of the moving image, so that afterwards the landmarks are exactly aligned. The order of your landmarks will be taken into account. E. g. landmark one in the fixed data will be mapped on landmark one in the moving data. You have to set at least one landmark and the same number of landmarks in each dataset to enable the Register button which performs the transformation. The root mean squares difference between the landmarks will be displayed as number, so that you can check how good the landmarks correspond. The "Undo Transformation" button becomes enabled after performing a transformation and allows you to undo it. After doing this, the "Redo Transformation" button is enabled and lets you redo, the just undone transformation(no calculation needed) Saving of the transformed image can be done via the Data Manager. */ diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/DisplayOptionsPointBased.png b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationDisplayOptionsPointBased.png similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/DisplayOptionsPointBased.png rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationDisplayOptionsPointBased.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/FixedDataPointBased.png b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationFixedDataPointBased.png similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/FixedDataPointBased.png rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationFixedDataPointBased.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/ImageArea.png b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationImageArea.png similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/ImageArea.png rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationImageArea.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/ImageSelectionDeformable.png b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationImageSelectionDeformable.png similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/ImageSelectionDeformable.png rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationImageSelectionDeformable.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/ManualRegistrationArea.png b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationManualRegistrationArea.png similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/ManualRegistrationArea.png rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationManualRegistrationArea.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/RegistrationModuleOverview.dox b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationModuleOverview.dox similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/RegistrationModuleOverview.dox rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationModuleOverview.dox diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/MovingDataPointBased.png b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationMovingDataPointBased.png similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/MovingDataPointBased.png rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationMovingDataPointBased.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/RegistrationPointBased.png b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationPointBased.png similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/RegistrationPointBased.png rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationPointBased.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/PointBasedRegistration.png b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationPointBasedRegistration.png similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/PointBasedRegistration.png rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationPointBasedRegistration.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/PointBasedRegistration.xpm b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationPointBasedRegistration.xpm similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/PointBasedRegistration.xpm rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationPointBasedRegistration.xpm diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/PointBasedRegistration_small.png b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationPointBasedRegistrationSmall.png similarity index 100% rename from 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Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationRegistrationDeformable.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/RigidRegistration.png b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationRigidRegistration.png similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/RigidRegistration.png rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationRigidRegistration.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/RigidRegistration.xpm b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationRigidRegistration.xpm similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/RigidRegistration.xpm rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationRigidRegistration.xpm diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/rigidRegistrationIcon.png b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationRigidRegistrationIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/rigidRegistrationIcon.png rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationRigidRegistrationIcon.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/RigidRegistration_small.png b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationRigidRegistrationSmall.png similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/RigidRegistration_small.png rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationRigidRegistrationSmall.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/Tab2.png b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationTab2.png similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/Tab2.png rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationTab2.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/pointBasedIcon.png b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationpointBasedIcon.png similarity index 100% rename from Plugins/org.mitk.gui.qt.registration/documentation/UserManual/pointBasedIcon.png rename to Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRegistrationpointBasedIcon.png diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRigidRegistrationUserManual.dox b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRigidRegistrationUserManual.dox index 3d0c69fe8a..876b3eedaf 100644 --- a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRigidRegistrationUserManual.dox +++ b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkRigidRegistrationUserManual.dox @@ -1,214 +1,214 @@ /** \page org_mitk_views_rigidregistration The Rigid Registration View -\image html rigidRegistrationIcon.png "Icon of the View" +\image html QmitkRegistrationRigidRegistrationIcon.png "Icon of the View" Available sections: - \ref QmitkRigidRegistrationUserManualOverview - \ref QmitkRigidRegistrationUserManualIssues - \ref QmitkRigidRegistrationUserManualDetails - \ref QmitkRigidRegistrationUserManualReferences \section QmitkRigidRegistrationUserManualOverview Overview This view allows you to register 2D as well as 3D images in a rigid manner. If the Moving Image is an image with multiple timesteps you can select one timestep for registration. Register means to align two images, so that they become as similar as possible. Therefore you can select from different transforms, metrics and optimizers. Registration results will directly be applied to the Moving Image. Also binary images as image masks can be used to restrict the metric evaluation only to the masked area. -\image html RigidRegistration_small.png "MITK with the QmitkRigidRegistration view" +\image html QmitkRegistrationRigidRegistrationSmall.png "MITK with the QmitkRigidRegistration view" This document will tell you how to use this view, but it is assumed that you already know how to navigate through the slices of an image using the multi-widget. \section QmitkRigidRegistrationUserManualIssues Known Issues Depending on your system the registration can fail to allocate memory for calculating the gradient image for registration. In this case you can try to select another optimizer which is not based on a gradient image and uncheck the checkbox for "Compute Gradient". \section QmitkRigidRegistrationUserManualDetails Details First of all you have to open the data sets which you want to register and select them in the Data Manager. You have to select exactly 2 images for registration. The image which was selected first will become the fixed image, the other one the moving image. The two selected images will remain for registration until exactly two images were selected in the Data Manager again. -\image html ImageArea.png "The Image area" +\image html QmitkRegistrationImageArea.png "The Image area" While there aren't two images for registration a message is viewed on top of the view saying that registration needs two images. If two images are selected the message disappears and the interaction areas for the fixed and moving data appears. If both selected images have a binary image as childnode a selection box appears which allows, when checked, to use the binary images as image mask to restrict the registration on this certain area. If an image has more than one binary image as child, the upper one from the DataManager list is used. If the Moving Image is a dynamic images with several timesteps a slider appears to select a specific timestep for registration. On default only the fixed and moving image are shown in the render windows. If you want to have other images visible you have to set the visibility via the Data Manager. Also if you want to perform a reinit on a specific node or a global reinit for all nodes you have to use the Data Manager. The colour of the images can be changed between grey values and red/green and the opacity of the moving image can be changed. With the "Moving Image Opacity:" slider you can change the opacity of the moving dataset. In the "Show Images Red/Green" you can switch the color from both datasets. If you check the box, the fixed dataset will be displayed in red-values and the moving dataset in green-values to improve visibility of differences in the datasets. If you uncheck the "Show Images Red/Green" checkbox, both datasets will be displayed in grey-values. -\image html RegistrationArea.png "The Registration area" +\image html QmitkRegistrationRegistrationArea.png "The Registration area" In the "Register" area you can start the registration by clicking the "Calculate Transform" button. The optimizer value for every iteration step is diplayed as LCD number next to the "Optimizer Value:" label. Many of the registration methods can be canceled during their iteration steps by clicking the "Stop Optimization" button. During the calculation, a progress bar indicates the progress of the registration process. The render widgets are updated for every single iteration step, so that the user has the chance to supervise how good the registration process works with the selected methods and parameters. If the registration process does not lead to a sufficient result, it is possible to undo the transformation and restart the registration process with some changes in parameters. The differences in transformation due to the changed parameters can be seen in every iteration step and help the user understand the parameters. Also the optimizer value is updated for every single iteration step and shown in the GUI. The optimizer value is an indicator for the misalignment between the two images. The real time visualization of the registration as well as the optimizer value provides the user with information to trace the improvement through the optimization process. The "Undo Transformation" button becomes enabled when you have performed an transformation and you can undo the performed transformations. The "Redo Transformation" button becomes enabled when you have performed an undo to redo the transformation without to recalculate it. -\image html ManualRegistrationArea.png "The Manual Registration area" +\image html QmitkRegistrationManualQmitkRegistrationRegistrationArea.png "The Manual Registration area" In the "Manual Registration" area, shown by checking the checkbox Manual Registration, you can manually allign the images by moving sliders for translation and scaling in x-, y- and z-axis as well as for rotation around the x-, y- and z-Axis. Additionally you can automatically allign the image centers with the button "Automatic Allign Image Centers". -\image html Tab2.png "The Advanced Mode tab" +\image html QmitkRegistrationTab2.png "The Advanced Mode tab" In the "Advanced Mode" tab you can choose a transform, a metric, an optimizer and an interpolator and you have to set the corresponding parameters to specify the registration method you want to perform. With the topmost button you can also load testpresets. These presets contain all parametersets which were saved using the "Save as Testpreset" button. The "Save as Preset" button makes the preset available from the "Automatic Registration" tab. This button should be used when a preset is not intended for finding good parameters anymore but can be used as standard preset. To show the current transform and its parameters for the registration process, the Transform checkbox has to be checked. Currently, the following transforms are implemented (for detailed information see [1] and [2]): \li Translation: Transformation by a simple translation for every dimension. \li Scale: Transformation by a certain scale factor for each dimension. \li ScaleLogarithmic: Transformation by a certain scale factor for each dimension. The parameter factors are passed as logarithms. \li Affine: Represents an affine transform composed of rotation, scaling, shearing and translation. \li FixedCenterOfRotationAffine: Represents an affine transform composed of rotation around a user provided center, scaling, shearing and translation. \li Rigid3D: Represents a 3D rotation followed by a 3D translation. \li Euler3D: Represents a rigid rotation in 3D space. That is, a rotation followed by a 3D translation. \li CenteredEuler3D: Represents a rigid rotation in 3D space around a user provided center. That is, a rotation followed by a 3D translation. \li QuaternionRigid: Represents a 3D rotation and a 3D translation. The rotation is specified as a quaternion. \li Versor: Represents a 3D rotation. The rotation is specified by a versor or unit quaternion. \li VersorRigid3D: Represents a 3D rotation and a 3D translation. The rotation is specified by a versor or unit quaternion. \li ScaleSkewVersor3D: Represents a 3D translation, scaling, shearing and rotation. The rotation is specified by a versor or unit quaternion. \li Similarity3D: Represents a 3D rotation, a 3D translation and homogeneous scaling. \li Rigid2D: Represents a 2D rotation followed by a 2D translation. \li CenteredRigid2D: Represents a 2D rotation around a user provided center followed by a 2D translation. \li Euler2D: Represents a 2D rotation and a 2D translation. \li Similarity2D: Represents a 2D rotation, homogeneous scaling and a 2D translation. \li CenteredSimilarity2D: Represents a 2D rotation around a user provided center, homogeneous scaling and a 2D translation. The desired transform can be chosen from a combo box. All parameters defining the selected transform have to be specified within the line edits and checkboxes underneath the transform combo box. To show the current metric and its parameters for the registration process, the Metric checkbox has to be checked. Currently, the following metrics are implemented (for detailed information see [1] and [2]): \li MeanSquares: Computes the mean squared pixel-wise difference in intensity between image A and B. \li NormalizedCorrelation: Computes pixel-wise cross correlation and normalizes it by the square root of the autocorrelation of the images. \li GradientDifference: Evaluates the difference in the derivatives of the moving and fixed images. \li KullbackLeiblerCompareHistogram[3]: Measures the relative entropy between two discrete probability distributions. \li CorrelationCoefficientHistogram: Computes the cross correlation coefficient between the intensities. \li MeanSquaresHistogram: The joint histogram of the fixed and the mapped moving image is built first. Then the mean squared pixel-wise difference in intensity between image A and B is calculated. \li MutualInformationHistogram: Computes the mutual information between image A and image B. \li NormalizedMutualInformationHistogram: Computes the mutual information between image A and image B. \li MattesMutualInformation[4, 5]: The method of Mattes et al. is used to compute the mutual information between two images to be registered. \li MeanReciprocalSquareDifference: Computes pixel-wise differences and adds them after passing them through a bell-shaped function 1 / (1+x^2). \li MutualInformation[6]: Computes the mutual information between image A and image B. \li MatchCardinality: Computes cardinality of the set of pixels that match exactly between the moving and fixed images. \li KappaStatistic[7]: Computes spatial intersection of two binary images. The desired metric can be chosen from a combo box. All parameters defining the selected metric have to be specified within the line edits and checkboxes underneath the metric combo box. To show the current optimizer and its parameters for the registration process, the Optimizer checkbox has to be checked. Currently, the following optimizers are implemented (for detailed information see [1] and [2]): \li Exhaustive: Fully samples a grid on the parametric space. \li GradientDescent: A simple gradient descent optimizer. \li QuaternionRigidTransformGradientDescent: Variant of a gradient descent optimizer. \li LBFGSB[8, 9]: Limited memory Broyden Fletcher Goldfarb Shannon minimization with simple bounds. \li OnePlusOneEvolutionary[10]: 1+1 evolutionary strategy. \li Powell: Implements Powell optimization using Brent line search. \li FRPR: Fletch-Reeves & Polak-Ribiere optimization using dBrent line search. \li RegularStepGradientDescent: Variant of a gradient descent optimizer. \li VersorTransform: Variant of a gradient descent optimizer. \li Amoeba: Implementation of the Nelder-Meade downhill simplex algorithm. \li ConjugateGradient: Used to solve unconstrained optimization problems. \li LBFGS: Limited memory Broyden Fletcher Goldfarb Shannon minimization. \li SPSA[11]: Based on simultaneous perturbation. \li VersorRigid3DTransform: Variant of a gradient descent optimizer for the VersorRigid3DTransform parameter space. The desired optimizer can be chosen from a combo box. All parameters defining the selected optimizer have to be specified within the line edits and checkboxes underneath the optimizer combo box. To show the current interpolator for the registration process, just check the Interpolator checkbox. Currently, the following interpolators are implemented (for detailed information see [1] and [2]): \li Linear: Intensity varies linearly between grid positions. \li NearestNeighbor: Uses the intensity of the nearest grid position. You can show and hide the parameters for the selection by checking or unchecking the corresponding area. You can save the current sets of parameters with the "Save as Testpreset" or "Save as Preset" buttons. \section QmitkRigidRegistrationUserManualReferences References: 1. L. Ibanez, W. Schroeder and K. Ng, The ITK Software Guide, Kitware Inc, New York, 2005. 2. http://www.itk.org/Doxygen/ 3. Albert C.S. Chung, William M. Wells III, Alexander Norbash, and W. Eric L. Grimson, Multi-modal Image Registration by Minimising Kullback-Leibler Distance, In Medical Image Computing and Computer-Assisted Intervention - MICCAI 2002, LNCS 2489, pp. 525 - 532. 4. D. Mattes, D. R. Haynor, H. Vesselle, T. Lewellen and W. Eubank, "Nonrigid multimodality image registration", Medical Imaging 2001: Image Processing, 2001, pp. 1609-1620. 5. D. Mattes, D. R. Haynor, H. Vesselle, T. Lewellen and W. Eubank, "PET-CT Image Registration in the Chest Using Free-form Deformations", IEEE Transactions in Medical Imaging. Vol.22, No.1, January 2003, pp.120-128. 6. Viola, P. and Wells III, W. (1997). "Alignment by Maximization of Mutual Information" International Journal of Computer Vision, 24(2):137-154. 7. AP Zijdenbos, BM Dawant, RA Margolin , AC Palmer, Morphometric analysis of white matter lesions in MR images: Method and validation, IEEE Transactions on Medical Imaging, 13(4):716-724, Dec. 1994. 8. R. H. Byrd, P. Lu and J. Nocedal. A Limited Memory Algorithm for Bound Constrained Optimization, (1995), SIAM Journal on Scientific and Statistical Computing , 16, 5, pp. 1190-1208. 9. C. Zhu, R. H. Byrd and J. Nocedal. L-BFGS-B: Algorithm 778: L-BFGS-B, FORTRAN routines for large scale bound constrained optimization (1997), ACM Transactions on Mathematical Software, Vol 23, Num. 4, pp. 550 - 560. 10. Martin Styner, G. Gerig, Christian Brechbuehler, Gabor Szekely, "Parametric estimate of intensity inhomogeneities applied to MRI", IEEE TRANSACTIONS ON MEDICAL IMAGING; 19(3), pp. 153-165, 2000. 11. Spall, J.C. (1998), "An Overview of the Simultaneous Perturbation Method for Efficient Optimization," Johns Hopkins APL Technical Digest, vol. 19, pp. 482-492. */ diff --git a/Plugins/org.mitk.gui.qt.registration/files.cmake b/Plugins/org.mitk.gui.qt.registration/files.cmake deleted file mode 100644 index c2b2563a16..0000000000 --- a/Plugins/org.mitk.gui.qt.registration/files.cmake +++ /dev/null @@ -1,77 +0,0 @@ -set(SRC_CPP_FILES - -) - -set(INTERNAL_CPP_FILES - mitkPluginActivator.cpp - #DeformableRegistration - QmitkDeformableRegistrationView.cpp - # PointBasedRegistration - QmitkPointBasedRegistrationView.cpp - QmitkPointBasedRegistrationTesting.cpp - mitkLandmarkWarping.cpp - # RigidRegistration - QmitkRigidRegistrationView.cpp - QmitkLoadPresetDialog.cpp - QmitkRigidRegistrationSelectorView.cpp - -) - -set(UI_FILES - #DeformableRegistration - src/internal/QmitkDeformableRegistrationViewControls.ui - # PointBasedRegistration - src/internal/QmitkPointBasedRegistrationViewControls.ui - # RigidRegistration - src/internal/QmitkRigidRegistrationViewControls.ui - src/internal/QmitkRigidRegistrationSelector.ui -) - -set(MOC_H_FILES - src/internal/mitkPluginActivator.h - #DeformableRegistration - src/internal/QmitkDeformableRegistrationView.h - # PointBasedRegistration - src/internal/QmitkPointBasedRegistrationView.h - # RigidRegistration - src/internal/QmitkRigidRegistrationView.h - src/internal/QmitkLoadPresetDialog.h - src/internal/QmitkRigidRegistrationSelectorView.h - -) - -set(CACHED_RESOURCE_FILES -# list of resource files which can be used by the plug-in -# system without loading the plug-ins shared library, -# for example the icon used in the menu and tabs for the -# plug-in views in the workbench - plugin.xml - #DeformableRegistration - resources/DeformableRegistration.xpm - # PointBasedRegistration - resources/PointBasedRegistration.xpm - # RigidRegistration - resources/RigidRegistration.xpm -) - -set(QRC_FILES - #DeformableRegistration - resources/QmitkDeformableRegistrationView.qrc - # PointBasedRegistration - resources/QmitkPointBasedRegistrationView.qrc - # RigidRegistration - resources/QmitkRigidRegistrationView.qrc -) - -set(CPP_FILES - -) - -foreach(file ${SRC_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/${file}) -endforeach(file ${SRC_CPP_FILES}) - -foreach(file ${INTERNAL_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/internal/${file}) -endforeach(file ${INTERNAL_CPP_FILES}) - diff --git a/Plugins/org.mitk.gui.qt.registration/plugin.xml b/Plugins/org.mitk.gui.qt.registration/plugin.xml deleted file mode 100644 index 9f550dad2b..0000000000 --- a/Plugins/org.mitk.gui.qt.registration/plugin.xml +++ /dev/null @@ -1,25 +0,0 @@ - - - - - - - - - - - - - - - - diff --git a/Plugins/org.mitk.gui.qt.registration/resources/QmitkPointBasedRegistrationView.qrc b/Plugins/org.mitk.gui.qt.registration/resources/QmitkPointBasedRegistrationView.qrc index e45b28d80a..22a7d6be34 100644 --- a/Plugins/org.mitk.gui.qt.registration/resources/QmitkPointBasedRegistrationView.qrc +++ b/Plugins/org.mitk.gui.qt.registration/resources/QmitkPointBasedRegistrationView.qrc @@ -1,5 +1,5 @@ - PointBasedRegistration.xpm + QmitkRegistrationPointBasedRegistration.xpm diff --git a/Plugins/org.mitk.gui.qt.registration/resources/QmitkRigidRegistrationView.qrc b/Plugins/org.mitk.gui.qt.registration/resources/QmitkRigidRegistrationView.qrc index d9676153d7..de6d6339ae 100644 --- a/Plugins/org.mitk.gui.qt.registration/resources/QmitkRigidRegistrationView.qrc +++ b/Plugins/org.mitk.gui.qt.registration/resources/QmitkRigidRegistrationView.qrc @@ -1,5 +1,5 @@ - RigidRegistration.xpm + QmitkRegistrationRigidRegistration.xpm diff --git a/Plugins/org.mitk.gui.qt.registration/src/internal/QmitkPointBasedRegistrationViewControls.ui b/Plugins/org.mitk.gui.qt.registration/src/internal/QmitkPointBasedRegistrationViewControls.ui index 363106a05f..f95ce31242 100644 --- a/Plugins/org.mitk.gui.qt.registration/src/internal/QmitkPointBasedRegistrationViewControls.ui +++ b/Plugins/org.mitk.gui.qt.registration/src/internal/QmitkPointBasedRegistrationViewControls.ui @@ -1,619 +1,619 @@ QmitkPointBasedRegistrationControls 0 0 287 404 0 0 0 0 PointBasedRegistration 255 0 0 255 0 0 118 116 108 You have to select two images from Data Manager using CTRL + left click! Switch fixed and moving image 0 0 75 true Fixed Data true 0 50 false Dataset: false QFrame::HLine QFrame::Sunken 0 0 0 0 75 true Moving Data true 0 50 false Dataset: false 50 false Moving Image Opacity: false 50 false 0% 0 0 100 50 Qt::Horizontal 50 false 100% QFrame::HLine QFrame::Sunken 0 0 0 0 75 true Display Options true 0 0 0 50 false Show Images Red/Green 75 true Registration true 0 50 false Method: false 0 0 50 false Rigid Similarity Affine LandmarkWarping 50 false Use ICP (order of landmarks doesn't matter) false 0 0 150 0 50 false Register - :/QmitkPointBasedRegistrationView/PointBasedRegistration.xpm:/QmitkPointBasedRegistrationView/PointBasedRegistration.xpm + :/QmitkPointBasedRegistrationView/QmitkRegistrationPointBasedRegistration.xpm:/QmitkPointBasedRegistrationView/QmitkRegistrationPointBasedRegistration.xpm 0 0 50 false Error between Landmarks (RMS): false 0 0 50 false QFrame::NoFrame QFrame::Raised false 9 QLCDNumber::Flat 0.000000000000000 0 false 0 0 50 false Undo Transformation :/org.mitk.gui.qt.ext/edit-undo.png:/org.mitk.gui.qt.ext/edit-undo.png false 0 0 50 false Redo Transformation :/org.mitk.gui.qt.ext/edit-redo.png:/org.mitk.gui.qt.ext/edit-redo.png Qt::Vertical 1 1 QmitkPointListWidget QWidget
QmitkPointListWidget.h
 mitkDataNode.h mitkPointSet.h mitkStateEvent.h mitkEventMapper.h mitkInteractionConst.h mitkBaseData.h diff --git a/Plugins/org.mitk.gui.qt.registration/src/internal/QmitkRigidRegistrationViewControls.ui b/Plugins/org.mitk.gui.qt.registration/src/internal/QmitkRigidRegistrationViewControls.ui index 40f715a99f..7fd31f0c68 100644 --- a/Plugins/org.mitk.gui.qt.registration/src/internal/QmitkRigidRegistrationViewControls.ui +++ b/Plugins/org.mitk.gui.qt.registration/src/internal/QmitkRigidRegistrationViewControls.ui @@ -1,1030 +1,1030 @@ QmitkRigidRegistrationViewControls 0 0 417 932 0 0 RigidRegistrationControls 0 0 QTabWidget::South QTabWidget::Triangular 0 Qt::ElideNone Automatic Registration QFrame::StyledPanel QFrame::Raised 0 0 QFrame::StyledPanel QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 8 Fixed Image: 10 false 8 Moving Image : 10 false Switch fixed and moving image Use Fixed Image Mask Use Moving Image Mask 255 0 0 0 0 0 0 0 0 255 0 0 0 0 0 0 0 0 118 116 108 118 116 108 118 116 108 8 You have to select two images from Data Manager using CTRL + left click! 0% Moving Image Opacity: false 0 0 100 50 Qt::Horizontal 100% Show contour false Qt::Horizontal 0 0 0 Show Images Red/Green Load Preset false Stop false 0 0 0 0 Register - :/QmitkRigidRegistrationView/RigidRegistration.xpm:/QmitkRigidRegistrationView/RigidRegistration.xpm + :/QmitkRigidRegistrationView/QmitkRegistrationRigidRegistration.xpm:/QmitkRigidRegistrationView/QmitkRegistrationRigidRegistration.xpm false QFrame::StyledPanel QFrame::Raised Optimizer Value: false QFrame::Raised 10 QLCDNumber::Flat false 0 0 Undo Transformation :/org.mitk.gui.qt.ext/edit-undo.png:/org.mitk.gui.qt.ext/edit-undo.png false 0 0 Redo Transformation :/org.mitk.gui.qt.ext/edit-redo.png:/org.mitk.gui.qt.ext/edit-redo.png Manual Registration true QFrame::StyledPanel QFrame::Raised 0 50 false Align Image Centers 75 true Interactive Translations true false 6 0 50 false x-Direction (Frontal): false 50 false y-Direction (Sagittal): false 50 false z-Direction (Axial): false ArrowCursor -10000 10000 Qt::Horizontal -10000 10000 Qt::Horizontal -10000 10000 Qt::Horizontal 75 true Interactive Rotations true 0 50 false x-Axis (Frontal): false 50 false y-Axis (Sagittal): false 50 false z-Axis (Axial): false ArrowCursor -20 20 Qt::Horizontal -20 20 Qt::Horizontal -20 20 Qt::Horizontal 75 true Interactive Scaling true 0 50 false x-Direction (Frontal): false 50 false y-Direction (Sagittal): false 50 false z-Direction (Axial): false ArrowCursor -180 180 1 1 Qt::Horizontal false QSlider::NoTicks -180 180 1 Qt::Horizontal -180 180 1 Qt::Horizontal Qt::Vertical 20 40 Advanced Mode Load Testpresets QFrame::StyledPanel QFrame::Raised 10 10 505 712 0 0 Save as Testpreset Save as Preset QmitkRigidRegistrationSelectorView QWidget
src/internal/QmitkRigidRegistrationSelectorView.h
1 QmitkSliderNavigatorWidget QWidget
QmitkSliderNavigatorWidget.h
1 mitkDataNode.h mitkBaseData.h diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/segmentation.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.png.png similarity index 100% rename from Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/segmentation.png rename to Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.png.png diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/segmentationFromSurfaceAfter.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationFromSurfaceAfter.png similarity index 100% rename from Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/segmentationFromSurfaceAfter.png rename to Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationFromSurfaceAfter.png diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/segmentationFromSurfaceBefore.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationFromSurfaceBefore.png similarity index 100% rename from Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/segmentationFromSurfaceBefore.png rename to Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationFromSurfaceBefore.png diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/interactive_segmentation_classes.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationInteractiveClasses.png similarity index 100% rename from Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/interactive_segmentation_classes.png rename to Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationInteractiveClasses.png diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/interactive_segmentation_classes.xcf b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationInteractiveClasses.xcf similarity index 100% rename from Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/interactive_segmentation_classes.xcf rename to Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationInteractiveClasses.xcf diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationTechnical.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationTechnical.dox index c4145ac10e..28789e9777 100755 --- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationTechnical.dox +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationTechnical.dox @@ -1,101 +1,101 @@ /** \page QmitkSegmentationTechnicalPage Technical design of QmitkSegmentation \li \ref QmitkSegmentationTechnicalPage2 \li \ref QmitkSegmentationTechnicalPage3 \li \ref QmitkSegmentationTechnicalPage4 \section QmitkSegmentationTechnicalPage2 Introduction QmitkSegmentation was designed for the liver resection planning project "ReLiver". The goal was a stable, well-documented, extensible, and testable re-implementation of a functionality called "ERIS", which was used for manual segmentation in 2D slices of 3D or 3D+t images. Re-implementation was chosen because it seemed to be easier to write documentation and tests for newly developed code. In addition, the old code had some design weaknesses (e.g. a monolithic class), which would be hard to maintain in the future. By now Segmentation is a well tested and easily extensible vehicle for all kinds of interactive segmentation applications. A separate page describes how you can extend Segmentation with new tools in a shared object (DLL): \ref toolextensions. \section QmitkSegmentationTechnicalPage3 Overview of tasks We identified the following major tasks:
  1. Management of images: what is the original patient image, what images are the active segmentations?
  2. Management of drawing tools: there is a set of drawing tools, one at a time is active, that is, someone has to decide which tool will receive mouse (and other) events.
  3. Drawing tools: each tool can modify a segmentation in reaction to user interaction. To do so, the tools have to know about the relevant images.
  4. Slice manipulation: drawing tools need to have means to extract a single slice from an image volume and to write a single slice back into an image volume.
  5. Interpolation of unsegmented slices: some class has to keep track of all the segmentations in a volume and generate suggestions for missing slices. This should be possible in all three orthogonal slice direction.
  6. Undo: Slice manipulations should be undoable, no matter whether a tool or the interpolation mechanism changed something.
  7. GUI: Integration of everything.
\section QmitkSegmentationTechnicalPage4 Classes involved The above blocks correspond to a number of classes. Here is an overview of all related classes with their responsibilities and relations: -\image html interactive_segmentation_classes.png +\image html QmitkSegmentationInteractiveClasses.png
  1. Management of images: mitk::ToolManager has a set of reference data (original images) and a second set of working data (segmentations). mitk::Tool objects know a ToolManager and can ask the manager for the currently relevant images. There are two GUI elements that enable the user to modify the set of reference and working images (QmitkToolReferenceDataSelectionBox and QmitkToolWorkingDataSelectionBox). GUI and non-GUI classes are coupled by itk::Events (non-GUI to GUI) and direct method calls (GUI to non-GUI).
  2. Management of drawing tools: As a second task, ToolManager manages all available tools and makes sure that one at a time is able to receive MITK events. The GUI for selecting tools is implemented in QmitkToolSelectionBox.
  3. Drawing tools: Drawing tools all inherit from mitk::Tool, which is a mitk::StateMachine. There is a number of derivations from Tool, each offering some helper methods for specific sub-classes, like manipulation of 2D slices. Tools are instantiated through the itk::ObjectFactory, which means that there is also one factory for each tool (e.g. mitk::AddContourToolFactory). For the GUI representation, each tool has an identification, consisting of a name and an icon (XPM). The actual drawing methods are mainly implemented in mitk::SegTool2D (helper methods) and its sub-classes for region growing, freehand drawing, etc.
  4. Slice manipulation: There are two filters for manipulation of slices inside a 3D image volume. mitk::ExtractImageFilter retrieves a single 2D slice from a 3D volume. mitk::OverwriteSliceImageFilter replaces a slice inside a 3D volume with a second slice which is a parameter to the filter. These classes are used extensively by most of the tools to fulfill their task. mitk::OverwriteSliceImageFilter cooperates with the interpolation classes to inform them of single slice modifications.
  5. Interpolation of unsegmented slices: There are two classes involved in interpolation: mitk::SegmentationInterpolationController knows a mitk::Image (the segmentation) and scans its contents for slices with non-zero pixels. It keeps track of changes in the image and is always able to tell, which neighbors of a slice (in the three orthogonal slice directions) contain segmentations. The class also performs this interpolation for single slices on demand. Again, we have a second class responsible for the GUI: QmitkSlicesInterpolator enables/disables interpolation and offers to accept interpolations for one or all slices.
  6. Undo: Undo functionality is implemented in mitk::OverwriteSliceImageFilter, since this is the central place where all image modifications are made. The filter stores a binary difference image to the undo stack as a mitk::ApplyDiffImageOperation. When the user requests undo, this ApplyDiffImageOperation will be executed by a singleton class DiffImageApplier. The operation itself observes the image, which it refers to, for itk::DeleteEvent, so no undo operation will be executed on/for images that have already been destroyed.
  7. GUI: The top-level GUI is the functionality QmitkSegmentation, which is very thin in comparison to ERIS. There are separate widgets for image and tool selection, for interpolation. Additionaly, there are some methods to create, delete, crop, load and save segmentations.
**/ diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/ToolExtensionsGeneralOverview.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationToolExtensionsGeneralOverview.dox similarity index 100% rename from Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/ToolExtensionsGeneralOverview.dox rename to Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationToolExtensionsGeneralOverview.dox diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/org_mitk_gui_qt_segmentation.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/org_mitk_gui_qt_segmentation.dox index e087268bb7..88de2cb33e 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/org_mitk_gui_qt_segmentation.dox +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/org_mitk_gui_qt_segmentation.dox @@ -1,292 +1,292 @@ /** \page org_mitk_views_segmentation The Segmentation Plugin -\image html segmentation.png "Icon of the Plugin" +\image html QmitkSegmentation.png "Icon of the Plugin" Some of the features described below are closed source additions to the open source toolkit MITK and are not available in every application. Available sections: - \ref org_mitk_gui_qt_segmentationUserManualOverview - \ref org_mitk_gui_qt_segmentationUserManualTechnical - \ref org_mitk_gui_qt_segmentationUserManualImageSelection - \ref org_mitk_gui_qt_segmentationUserManualManualKringeling - \ref org_mitk_gui_qt_segmentationUserManualManualKringeling1 - \ref org_mitk_gui_qt_segmentationUserManualManualKringeling2 - \ref org_mitk_gui_qt_segmentationUserManualManualKringeling3 - \ref org_mitk_gui_qt_segmentationUserManualManualKringeling4 - \ref org_mitk_gui_qt_segmentationUserManualManualKringeling5 - \ref org_mitk_gui_qt_segmentationUserManualOrganSegmentation - \ref org_mitk_gui_qt_segmentationUserManualOrganSegmentation1 - \ref org_mitk_gui_qt_segmentationUserManualOrganSegmentation2 - \ref org_mitk_gui_qt_segmentationUserManualOrganSegmentation99 - \ref org_mitk_gui_qt_segmentationUserManualLesionSegmentation - \ref org_mitk_gui_qt_segmentationUserManualPostprocessing - \ref org_mitk_gui_qt_segmentationUserManualSurfaceMasking - \ref org_mitk_gui_qt_segmentationUserManualTechnicalDetail \section org_mitk_gui_qt_segmentationUserManualOverview Overview The Segmentation perspective allows you to create segmentations of anatomical and pathological structures in medical images of the human body. The perspective groups a number of tools which can be used for: \image html org_mitk_gui_qt_segmentationIMGapplication.png Segmentation perspective consisting of the Data Manager view and the Segmentation view If you wonder what segmentations are good for, we shortly revisit the concept of a segmentation here. A CT or MR image is made up of volume of physical measurements (volume elements are called voxels). In CT images, for example, the gray value of each voxel corresponds to the mass absorbtion coefficient for X-rays in this voxel, which is similar in many %parts of the human body. The gray value does not contain any further information, so the computer does not know whether a given voxel is part of the body or the background, nor can it tell a brain from a liver. However, the distinction between a foreground and a background structure is required when: Creating this distinction between foreground and background is called segmentation. The Segmentation perspective of the MITK Workbench uses a voxel based approach to segmentation, i.e. each voxel of an image must be completely assigned to either foreground or background. This is in contrast to some other applications which might use an approach based on contours, where the border of a structure might cut a voxel into two %parts. The remainder of this document will summarize the features of the Segmentation perspective and how they are used. \section org_mitk_gui_qt_segmentationUserManualTechnical Technical Issues The Segmentation perspective makes a number of assumptions. To know what this view can be used for, it will help you to know that: \section org_mitk_gui_qt_segmentationUserManualImageSelection Image Selection The Segmentation perspective makes use of the Data Manager view to give you an overview of all images and segmentations. \image html org_mitk_gui_qt_segmentationIMGselection.png Data Manager is used for selecting the current segmentation. The reference image is selected in the drop down box of the control area. To select the reference image (e.g. the original CT/MR image) use the drop down box in the control area of the Segmentation view. The segmentation image selected in the Data Manager is displayed below the drop down box. If no segmentation image exists or none is selected create a new segmentation image by using the "New segmentation" button. Some items of the graphical user interface might be disabled when no image is selected. In any case, the application will give you hints if a selection is needed. \section org_mitk_gui_qt_segmentationUserManualManualKringeling Manual Contouring With manual contouring you define which voxels are part of the segmentation and which are not. This allows you to create segmentations of any structeres that you may find in an image, even if they are not part of the human body. You might also use manual contouring to correct segmentations that result from sub-optimal automatic methods. The drawback of manual contouring is that you might need to define contours on many 2D slices. However, this is moderated by the interpolation feature, which will make suggestions for a segmentation. \subsection org_mitk_gui_qt_segmentationUserManualManualKringeling1 Creating New Segmentations Unless you want to edit existing segmentations, you have to create a new, empty segmentation before you can edit it. To do so, click the "New manual segmentation" button. Input fields will appear where you can choose a name for the new segmentation and a color for its display. Click the checkmark button to confirm or the X button to cancel the new segmentation. Notice that the input field suggests names once you %start typing and that it also suggests colors for known organ names. If you use names that are not yet known to the application, it will automatically remember these names and consider them the next time you create a new segmentation. Once you created a new segmentation, you can notice a new item with the "binary mask" icon in the Data Manager tree view. This item is automatically selected for you, allowing you to %start editing the new segmentation right away. \subsection org_mitk_gui_qt_segmentationUserManualManualKringeling2 Selecting Segmentations for Editing As you might want to have segmentations of multiple structures in a single patient image, the application needs to know which of them to use for editing. You select a segmenation by clicking it in the tree view of Data Manager. Note that segmentations are usually displayed as sub-items of "their" patient image. In the rare case, where you need to edit a segmentation that is not displayed as a a sub-item, you can click both the original image AND the segmentation while holding down CTRL or for Mac OS X the CMD on the keyboard. When a selection is made, the Segmentation View will hide all but the selected segmentation and the corresponding original image. When there are multiple segmentations, the unselected ones will remain in the Data Manager, you can make them visible at any time by selecting them. \subsection org_mitk_gui_qt_segmentationUserManualManualKringeling3 Selecting Editing Tools If you are familiar with the MITK Workbench, you know that clicking and moving the mouse in any of the 2D render windows will move around the crosshair that defines what part of the image is displayed. This behavior is disabled while any of the manual segmentation tools are active -- otherwise you might have a hard time concentrating on the contour you are drawing. To %start using one of the editing tools, click its button the the displayed toolbox. The selected editing tool will be active and its corresponding button will stay pressed until you click the button again. Selecting a different tool also deactivates the previous one. If you have to delineate a lot of images, you should try using shortcuts to switch tools. Just hit the first letter of each tool to activate it (A for Add, S for Subtract, etc.). \subsection org_mitk_gui_qt_segmentationUserManualManualKringeling4 Using Editing Tools All of the editing tools work by the same principle: you use the mouse (left button) to click anywhere in a 2D window (any of the orientations axial, sagittal, or frontal), move the mouse while holding the mouse button and release to finish the editing action. Multi-step undo and redo is fully supported by all editing tools. Use the application-wide undo button in the toolbar to revert erroneous %actions. \image html org_mitk_gui_qt_segmentationIMGiconAddSubtract.png Add and Subtract Tools Use the left mouse button to draw a closed contour. When releasing the mouse button, the contour will be added (Add tool) to or removed from (Subtract tool) the current segmentation. Hold down the CTRL / CMD key to invert the operation (this will switch tools temporarily to allow for quick corrections). \image html org_mitk_gui_qt_segmentationIMGiconPaintWipe.png Paint and Wipe Tools Use the slider below the toolbox to change the radius of these round paintbrush tools. Move the mouse in any 2D window and press the left button to draw or erase pixels. As the Add/Subtract tools, holding CTRL / CMD while drawing will invert the current tool's behavior. \image html org_mitk_gui_qt_segmentationIMGiconRegionGrowing.png Region Growing Tool Click at one point in a 2D slice widget to add an image region to the segmentation with the region growing tool. Moving up the cursor while holding the left mouse button widens the range for the included grey values; moving it down narrows it. When working on an image with a high range of grey values, the selection range can be influenced more strongly by moving the cursor at higher velocity. Region Growing selects all pixels around the mouse cursor that have a similar gray value as the pixel below the mouse cursor. This enables you to quickly create segmentations of structures that have a good contrast to surrounding tissue, e.g. the lungs. The tool will select more or less pixels (corresponding to a changing gray value interval width) when you move the mouse up or down while holding down the left mouse button. A common issue with region growing is the so called "leakage" which happens when the structure of interest is connected to other pixels, of similar gray values, through a narrow "bridge" at the border of the structure. The Region Growing tool comes with a "leakage detection/removal" feature. If leakage happens, you can left-click into the leakage region and the tool will try to automatically remove this region (see illustration below). \image html org_mitk_gui_qt_segmentationIMGleakage.png Leakage correction feature of the Region Growing tool
\image html org_mitk_gui_qt_segmentationIMGiconCorrection.png Correction Tool You do not have to draw a closed contour to use the Correction tool and do not need to switch between the Add and Substract tool to perform small corrective changes. The following figure shows the usage of this tool: \image html org_mitk_gui_qt_segmentationIMGcorrectionActions.png %Actions of the Correction tool illustrated.
\image html org_mitk_gui_qt_segmentationIMGiconFill.png Fill Tool Left-click inside a segmentation with holes to completely fill all holes. \image html org_mitk_gui_qt_segmentationIMGiconErase.png Erase Tool This tool removes a connected part of pixels that form a segmentation. You may use it to remove so called islands (see picture) or to clear a whole slice at once (hold CTRL while clicking). \subsection org_mitk_gui_qt_segmentationUserManualManualKringeling5 Interpolation Creating segmentations for modern CT volumes is very time-consuming, because structures of interest can easily cover a range of 50 or more slices. The Manual Segmentation View offers two helpful features for these cases:
The 3D interpolation is activated by default when using the manual segmentation tools. That means if you start contouring, from the second contour onwards, the surface of the segmented area will be interpolated based on the given contour information. The interpolation works with all available manual tools. Please note that this is currently a pure mathematical interpolation, i.e. image intensity information is not taken into account. With each further contour the interpolation result will be improved, but the more contours you provide the longer the recalculation will take. To achieve an optimal interpolation result and in this way a most accurate segmentation you should try to describe the surface with sparse contours by segmenting in arbitrary oriented planes. The 3D interpolation is not meant to be used for parallel slice-wise segmentation. \image html org_mitk_gui_qt_segmentation3DInterpolationWrongRight.png 3D Interpolation HowTo You can accept the interpolation result by clicking the "Accept" - button below the tool buttons. In this case the 3D interpolation will be deactivated automatically so that the result can be postprocessed without any interpolation running in background. During recalculation the interpolated surface is blinking yellow/white. When the interpolation has finished the surface is shown yellow with a small opacity. Additional to the surface, black contours are shown in the 3D render window. They mark the positions of all the drawn contours which were used for the interpolation. You can navigate between the drawn contours by clicking on the „Position“ - Nodes in the datamanager which are located below the selected segmentation. If you don't want to see these nodes just unckeck the „Show Position Nodes“ Checkbox and these nodes will be hidden. If you want to delete a drawn contour we recommend to use the Erase-Tool since Redo/Undo is not yet working for 3D interpolation.
The 2D Interpolation creates suggestions for a segmentation whenever you have a slice that Interpolated suggestions are displayed in a different way than manual segmentations are, until you "accept" them as part of the segmentation. To accept single slices, click the "Accept" button below the toolbox. If you have segmented a whole organ in every-x-slice, you may also review the interpolations and then accept all of them at once by clicking "... all slices". \section org_mitk_gui_qt_segmentationUserManualOrganSegmentation Organ Segmentation \note This feature is only available in our 3M3 Demo Application (http://www.mint-medical.de/productssolutions/mitk3m3/mitk3m3/#downloads) but not in the open source part of MITK The manual contouring described above is a fallback option that will work for any kind of images and structures of interest. However, manual contouring is very time-consuming and tedious. This is why a major part of image analysis research is working towards automatic segmentation methods. The Segmentation View comprises a number of easy-to-use tools for segmentation of CT images (Liver) and MR image (left ventricle and wall, left and right lung). \subsection org_mitk_gui_qt_segmentationUserManualOrganSegmentation1 Liver on CT Images On CT image volumes, preferrably with a contrast agent in the portal venous phase, the Liver tool will fully automatically analyze and segment the image. All you have to do is to load and select the image, then click the "Liver" button. During the process, which takes a minute or two, you will get visual progress feedback by means of a contour that moves closer and closer to the real liver boundaries. \subsection org_mitk_gui_qt_segmentationUserManualOrganSegmentation2 Heart, Lung, and Hippocampus on MRI While liver segmentation is performed fully automatic, the following tools for segmentation of the heart, the lungs, and the hippocampus need a minimum amount of guidance. Click one of the buttons on the "Organ segmentation" page to add an average %model of the respective organ to the image. This %model can be dragged to the right position by using the left mouse button while holding down the CTRL key. You can also use CTRL + middle mouse button to rotate or CTRL + right mouse button to scale the %model. Before starting the automatic segmentation process by clicking the "Start segmentation" button, try placing the %model closely to the organ in the MR image (in most cases, you do not need to rotate or scale the %model). During the segmentation process, a green contour that moves closer and closer to the real liver boundaries will provide you with visual feedback of the segmentation progress. The algorithms used for segmentation of the heart and lung are method which need training by a number of example images. They will not work well with other kind of images, so here is a list of the image types that were used for training: \subsection org_mitk_gui_qt_segmentationUserManualOrganSegmentation99 Other Organs As mentioned in the Heart/Lung section, most of the underlying methods are based on "training". The basic algorithm is versatile and can be applied on all kinds of segmentation problems where the structure of interest is topologically like a sphere (and not like a torus etc.). If you are interested in other organs than those offered by the current version of the Segmentation view, please contact our research team. \section org_mitk_gui_qt_segmentationUserManualLesionSegmentation Lesion Segmentation \note This feature is only available in our 3M3 Demo Application (http://www.mint-medical.de/productssolutions/mitk3m3/mitk3m3/#downloads) but not in the open source part of MITK Lesion segmentation is a little different from organ segmentation. Since lesions are not part of the healthy body, they sometimes have a diffused border, and are often found in varying places all over the body. The tools in this section offer efficient ways to create 3D segmentations of such lesions. The Segmentation View currently offers supoprt for enlarged lymph nodes. To segment an enlarged lymph node, find a more or less central slice of it, activate the "Lymph Node" tool and draw a rough contour on the inside of the lymph node. When releaseing the mouse button, a segmentation algorithm is started in a background task. The result will become visible after a couple of seconds, but you do not have to wait for it. If you need to segment several lymph nodes, you can continue to inspect the image right after closing the drawn contour. If the lymph node segmentation is not to your content, you can select the "Lymph Node Correction" tool and drag %parts of the lymph node surface towards the right position (works in 3D, not slice-by-slice). This kind of correction helps in many cases. If nothing else helps, you can still use the pure manual tools as a fallback. \section org_mitk_gui_qt_segmentationUserManualPostprocessing Things you can do with segmentations As mentioned in the introduction, segmentations are never an end in themselves. Consequently, the Segmentation view adds a couple of "post-processing" %actions to the Data Manager. These %actions are accessible through the context-menu of segmentations in Data Manager's list view \image html org_mitk_gui_qt_segmentationIMGDataManagerContextMenu.png Context menu items for segmentations. \section org_mitk_gui_qt_segmentationUserManualSurfaceMasking Surface Masking You can use the surface masking tool to create binary images from a surface which is used used as a mask on an image. This task is demonstrated below: -\image html segmentationFromSurfaceBefore.png Load an image and a surface. +\image html QmitkSegmentationFromSurfaceBefore.png Load an image and a surface. Select the image and the surface in the corresponding drop-down boxes (both are selected automatically if there is just one image and one surface) -\image html segmentationFromSurfaceAfter.png Create segmentation from surface +\image html QmitkSegmentationFromSurfaceAfter.png Create segmentation from surface After clicking "Create segmentation from surface" the newly created binary image is inserted in the DataManager and can be used for further processing \section org_mitk_gui_qt_segmentationUserManualTechnicalDetail Technical Information for Developers For technical specifications see \subpage QmitkSegmentationTechnicalPage and for information on the extensions of the tools system \subpage toolextensions . */ diff --git a/Plugins/org.mitk.gui.qt.segmentation/files.cmake b/Plugins/org.mitk.gui.qt.segmentation/files.cmake deleted file mode 100644 index bec23ea488..0000000000 --- a/Plugins/org.mitk.gui.qt.segmentation/files.cmake +++ /dev/null @@ -1,64 +0,0 @@ -set(SRC_CPP_FILES - QmitkSegmentationPreferencePage.cpp -) - -set(INTERNAL_CPP_FILES - mitkPluginActivator.cpp - QmitkSegmentationView.cpp - QmitkSegmentationPostProcessing.cpp - QmitkThresholdAction.cpp - QmitkCreatePolygonModelAction.cpp - QmitkStatisticsAction.cpp - QmitkAutocropAction.cpp - QmitkBooleanOperationsView.cpp - QmitkDeformableClippingPlaneView.cpp - regiongrowing/QmitkRegionGrowingView.cpp - QmitkOtsuAction.cpp -) - -set(UI_FILES - src/internal/QmitkSegmentationControls.ui - src/internal/QmitkBooleanOperationsView.ui - src/internal/QmitkDeformableClippingPlaneViewControls.ui - src/internal/regiongrowing/QmitkRegionGrowingViewControls.ui -) - -set(MOC_H_FILES - src/QmitkSegmentationPreferencePage.h - src/internal/mitkPluginActivator.h - src/internal/QmitkSegmentationView.h - src/internal/QmitkSegmentationPostProcessing.h - src/internal/QmitkThresholdAction.h - src/internal/QmitkCreatePolygonModelAction.h - src/internal/QmitkStatisticsAction.h - src/internal/QmitkAutocropAction.h - src/internal/QmitkBooleanOperationsView.h - src/internal/QmitkDeformableClippingPlaneView.h - src/internal/regiongrowing/QmitkRegionGrowingView.h - src/internal/QmitkOtsuAction.h -) - -set(CACHED_RESOURCE_FILES - resources/segmentation.png - resources/boolean.png - resources/deformablePlane.png - resources/regiongrowing.xpm - plugin.xml -) - -set(QRC_FILES - resources/segmentation.qrc - resources/boolean.qrc - resources/regiongrowing.qrc -) - - -set(CPP_FILES) - -foreach(file ${SRC_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/${file}) -endforeach(file ${SRC_CPP_FILES}) - -foreach(file ${INTERNAL_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/internal/${file}) -endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.segmentation/plugin.xml b/Plugins/org.mitk.gui.qt.segmentation/plugin.xml deleted file mode 100644 index efc274f7f5..0000000000 --- a/Plugins/org.mitk.gui.qt.segmentation/plugin.xml +++ /dev/null @@ -1,48 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Plugins/org.mitk.gui.qt.segmentation/resources/segmentation.qrc b/Plugins/org.mitk.gui.qt.segmentation/resources/segmentation.qrc index 94bb235e76..d1e9f843b2 100755 --- a/Plugins/org.mitk.gui.qt.segmentation/resources/segmentation.qrc +++ b/Plugins/org.mitk.gui.qt.segmentation/resources/segmentation.qrc @@ -1,10 +1,10 @@ btnReinit.xpm btnDelete.png btnNew.png - segmentation.png + QmitkSegmentation.png btnLoad.png btnSave.png diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationControls.ui b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationControls.ui index 892e83065a..4e96b7a31c 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationControls.ui +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationControls.ui @@ -1,729 +1,729 @@ QmitkSegmentationControls 0 0 246 591 0 0 MS Shell Dlg 2 8 50 false false false false QmitkSegmentation 0 0 0 0 16777215 16777215 Reference image 0 0 QComboBox::AdjustToMinimumContentsLength 200 0 0 200 0 0 200 0 0 200 0 0 200 0 0 200 0 0 84 82 78 84 82 78 84 82 78 50 false Please load an image! Segmentation image 0 0 0 259 316 - :/segmentation/segmentation.png:/segmentation/segmentation.png + :/segmentation/QmitkSegmentation.png:/segmentation/QmitkSegmentation.png Contouring 0 0 200 0 0 200 0 0 200 0 0 200 0 0 200 0 0 200 0 0 84 82 78 84 82 78 84 82 78 50 false You are now working with rotated planes 200 0 0 200 0 0 200 0 0 200 0 0 200 0 0 200 0 0 84 82 78 84 82 78 84 82 78 50 false Select or create a segmentation! false 1 0 50 false New segmentation New segmentation :/segmentation/btnNew.png:/segmentation/btnNew.png Qt::ToolButtonTextBesideIcon 75 true Editing tools 50 false 50 false 50 false Qt::Vertical 20 40 0 0 98 44 Organs 0 0 50 false 50 false Qt::Vertical 20 40 0 0 98 44 Lesions 0 0 50 false 50 false Qt::Vertical 20 40 0 0 273 116 Surface Masking Select Surface For Image Masking: false Create Segmentation From Surface Qt::Vertical 20 40 QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkToolSelectionBox QWidget
QmitkToolSelectionBox.h
 QmitkSlicesInterpolator QWidget
QmitkSlicesInterpolator.h
 QmitkToolGUIArea QWidget
QmitkToolGUIArea.h
 QmitkToolReferenceDataSelectionBox.h QmitkToolGUIArea.h QmitkToolSelectionBox.h QmitkSlicesInterpolator.h diff --git a/Plugins/org.mitk.gui.qt.toftutorial/documentation/Manual/Manual.dox b/Plugins/org.mitk.gui.qt.toftutorial/documentation/UserManual/QmitkTOFTutorial.dox similarity index 75% rename from Plugins/org.mitk.gui.qt.toftutorial/documentation/Manual/Manual.dox rename to Plugins/org.mitk.gui.qt.toftutorial/documentation/UserManual/QmitkTOFTutorial.dox index e8726726bb..aa5e849886 100644 --- a/Plugins/org.mitk.gui.qt.toftutorial/documentation/Manual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.toftutorial/documentation/UserManual/QmitkTOFTutorial.dox @@ -1,13 +1,13 @@ /** \page org_toftutorial ToFTutorial -\image html icon.png "Icon of ToFTutorial" +\image html QmitkTOFTutorial.png "Icon of ToFTutorial" Available sections: - \ref ToFTutorialOverview \section ToFTutorialOverview This is the description for the ToFTutorial. */ diff --git a/Plugins/org.mitk.gui.qt.toftutorial/documentation/Manual/icon.png b/Plugins/org.mitk.gui.qt.toftutorial/documentation/UserManual/QmitkTOFTutorial.png similarity index 100% rename from Plugins/org.mitk.gui.qt.toftutorial/documentation/Manual/icon.png rename to Plugins/org.mitk.gui.qt.toftutorial/documentation/UserManual/QmitkTOFTutorial.png diff --git a/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/QmitkUltrasound.dox similarity index 86% rename from Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/Manual.dox rename to Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/QmitkUltrasound.dox index 5f9dfdc00d..9527aac5d5 100644 --- a/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/QmitkUltrasound.dox @@ -1,19 +1,19 @@ /** \page org_mitk_gui_qt_ultrasound Ultrasound -\image html icon.xpm "Icon of Ultrasound" +\image html QmitkUltrasound.xpm "Icon of Ultrasound" Available sections: - \ref org_mitk_gui_qt_ultrasoundOverview \section org_mitk_gui_qt_ultrasoundOverview Describe the features of your awesome plugin here */ diff --git a/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/icon.xpm b/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/QmitkUltrasound.xpm similarity index 100% rename from Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/icon.xpm rename to Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/QmitkUltrasound.xpm diff --git a/Plugins/org.mitk.gui.qt.ultrasound/files.cmake b/Plugins/org.mitk.gui.qt.ultrasound/files.cmake deleted file mode 100644 index 35d6e9c9b2..0000000000 --- a/Plugins/org.mitk.gui.qt.ultrasound/files.cmake +++ /dev/null @@ -1,43 +0,0 @@ -set(SRC_CPP_FILES - -) - -set(INTERNAL_CPP_FILES - org_mitk_gui_qt_ultrasound_Activator.cpp - UltrasoundSupport.cpp -) - -set(UI_FILES - src/internal/UltrasoundSupportControls.ui -) - -set(MOC_H_FILES - src/internal/org_mitk_gui_qt_ultrasound_Activator.h - src/internal/UltrasoundSupport.h -) - -# list of resource files which can be used by the plug-in -# system without loading the plug-ins shared library, -# for example the icon used in the menu and tabs for the -# plug-in views in the workbench -set(CACHED_RESOURCE_FILES - resources/icon.xpm - plugin.xml -) - -# list of Qt .qrc files which contain additional resources -# specific to this plugin -set(QRC_FILES - -) - -set(CPP_FILES ) - -foreach(file ${SRC_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/${file}) -endforeach(file ${SRC_CPP_FILES}) - -foreach(file ${INTERNAL_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/internal/${file}) -endforeach(file ${INTERNAL_CPP_FILES}) - diff --git a/Plugins/org.mitk.gui.qt.ultrasound/plugin.xml b/Plugins/org.mitk.gui.qt.ultrasound/plugin.xml deleted file mode 100644 index 12e452b3d5..0000000000 --- a/Plugins/org.mitk.gui.qt.ultrasound/plugin.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - - - - - diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/icon.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.png similarity index 100% rename from Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/icon.png rename to Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.png diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/icon.xpm b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.xpm similarity index 100% rename from Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/icon.xpm rename to Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.xpm diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/bell.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationBell.png similarity index 100% rename from Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/bell.png rename to Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationBell.png diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/checkboxen.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationCheckboxen.png similarity index 100% rename from Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/checkboxen.png rename to Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationCheckboxen.png diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/color.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationColor.png similarity index 100% rename from Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/color.png rename to Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationColor.png diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/gradient.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationGradient.png similarity index 100% rename from Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/gradient.png rename to Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationGradient.png diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/mitkInternalPresets.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationInternalPresets.png similarity index 100% rename from Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/mitkInternalPresets.png rename to Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationInternalPresets.png diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/opacity.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationOpacity.png similarity index 100% rename from Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/opacity.png rename to Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationOpacity.png diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/vroverview.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationOverview.png similarity index 100% rename from Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/vroverview.png rename to Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationOverview.png diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/slider.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationSlider.png similarity index 100% rename from Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/slider.png rename to Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationSlider.png diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/threshold.png b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationThreshold.png similarity index 100% rename from Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/threshold.png rename to Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationThreshold.png diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationUserManual.dox b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationUserManual.dox index dbe3b81009..7a3fb6728d 100644 --- a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationUserManual.dox +++ b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualizationUserManual.dox @@ -1,150 +1,150 @@ /** \page org_mitk_views_volumevisualization The Volume Visualization Plugin -\image html icon.png "Icon of the Plugin" +\image html QmitkVolumeVisualization.png "Icon of the Plugin" Available sections: \section QVV_Overview Overview The Volume Visualization Plugin is a basic tool for visualizing three dimensional medical images. MITK provides generic transfer function presets for medical CT data. These functions, that map the gray-value to color and opacity, can be interactively edited. Additionally, there are controls to quickly generate common used transfer function shapes like the threshold and bell curve to help identify a range of grey-values. -\image html vroverview.png "" +\image html QmitkVolumeVisualizationOverview.png "" \section QVV_EnableVRPage Enable Volume Rendering \subsection QVV_LoadingImage Loading an image into the application Load an image into the application by Volume Visualization imposes following restrictions on images: \subsection QVV_EnableVR Enable Volumerendering -\image html checkboxen.png "" +\image html QmitkVolumeVisualizationCheckboxen.png "" Select an image in datamanager and click on the checkbox left of "Volumerendering". Please be patient, while the image is prepared for rendering, which can take up to a half minute. \subsection QVV_LODGPU The LOD & GPU checkboxes Volume Rendering requires a lot of computing resources including processor, memory and graphics card. To run volume rendering on smaller platforms, enable the LOD checkbox (level-of-detail rendering). Level-of-detail first renders a lower quality preview to increase interactivity. If the user stops to interact a normal quality rendering is issued. The GPU checkbox tries to use computing resources on the graphics card to accelerate volume rendering. It requires a powerful graphics card and OpenGL hardware support for shaders, but achieves much higher frame rates than software-rendering. \section QVV_PresetPage Applying premade presets \subsection QVV_Preset Internal presets There are some internal presets given, that can be used with normal CT data (given in Houndsfield units). A large set of medical data has been tested with that presets, but it may not suit on some special cases. Click on the "Preset" tab for using internal or custom presets. -\image html mitkInternalPresets.png "" +\image html QmitkVolumeVisualizationInternalPresets.png "" \subsection QVV_CustomPreset Saving and loading custom presets After creating or editing a transferfunction (see \ref QVV_Editing or \ref QVV_ThresholdBell), the custom transferfunction can be stored and later retrieved on the filesystem. Click "Save" (respectively "Load") button to save (load) the threshold-, color- and gradient function combined in a single .xml file. \section QVV_ThresholdBell Interactively create transferfunctions Beside the possibility to directly edit the transferfunctions (\ref QVV_Editing), a one-click generation of two commonly known shapes is given. Both generators have two parameters, that can be modified by first clicking on the cross and then moving the mouse up/down and left/right. The first parameter "center" (controlled by horizontal movement of the mouse) specifies the gravalue where the center of the shape will be located. The second parameter "width" (controlled by vertical movement of the mouse) specifies the width (or steepness) of the shape. \subsection Threshold Click on the "Threshold" tab to active the threshold function generator. -\image html threshold.png "" +\image html QmitkVolumeVisualizationThreshold.png "" A threshold shape begins with zero and raises to one across the "center" parameter. Lower widths results in steeper threshold functions. \subsection Bell Click on the "Bell" tab to active the threshold function generator. -\image html bell.png "" +\image html QmitkVolumeVisualizationBell.png "" A threshold shape begins with zero and raises to one at the "center" parameter and the lowers agains to zero. The "width" parameter correspondens to the width of the bell. \section QVV_Editing Customize transferfunctions in detail \subsection QVV_Navigate Choosing grayvalue interval to edit -\image html slider.png "" +\image html QmitkVolumeVisualizationSlider.png "" To navigate across the grayvalue range or to zoom in some ranges use the "range"-slider. All three function editors have in common following: There are three transferfunctions to customize: \subsection QVV_GO Grayvalue -> Opacity -\image html opacity.png "grayvalues will be mapped to opacity." +\image html QmitkVolumeVisualizationOpacity.png "grayvalues will be mapped to opacity." An opacity of 0 means total transparent, an opacity of 1 means total opaque. \subsection QVV_GC Grayvalue -> Color -\image html color.png "grayvalues will be mapped to color." +\image html QmitkVolumeVisualizationColor.png "grayvalues will be mapped to color." The color transferfunction editor also allows by double-clicking a point to change its color. \subsection QVV_GGO Grayvalue and Gradient -> Opacity -\image html gradient.png "" +\image html QmitkVolumeVisualizationGradient.png "" Here the influence of the gradient is controllable at specific grayvalues. */ diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/files.cmake b/Plugins/org.mitk.gui.qt.volumevisualization/files.cmake deleted file mode 100755 index 977a90ace5..0000000000 --- a/Plugins/org.mitk.gui.qt.volumevisualization/files.cmake +++ /dev/null @@ -1,37 +0,0 @@ -set(SRC_CPP_FILES - -) - -set(INTERNAL_CPP_FILES - mitkPluginActivator.cpp - QmitkVolumeVisualizationView.cpp -) - -set(UI_FILES - src/internal/QmitkVolumeVisualizationViewControls.ui -) - -set(MOC_H_FILES - src/internal/mitkPluginActivator.h - src/internal/QmitkVolumeVisualizationView.h -) - -set(CACHED_RESOURCE_FILES - plugin.xml - resources/icon.xpm -) - -set(QRC_FILES - -) - - -set(CPP_FILES ) - -foreach(file ${SRC_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/${file}) -endforeach(file ${SRC_CPP_FILES}) - -foreach(file ${INTERNAL_CPP_FILES}) - set(CPP_FILES ${CPP_FILES} src/internal/${file}) -endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/plugin.xml b/Plugins/org.mitk.gui.qt.volumevisualization/plugin.xml deleted file mode 100755 index 33ed061d6a..0000000000 --- a/Plugins/org.mitk.gui.qt.volumevisualization/plugin.xml +++ /dev/null @@ -1,15 +0,0 @@ - - - - - - - - \ No newline at end of file