diff --git a/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox b/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox index 06afcb812e..1487cb3947 100644 --- a/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox +++ b/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox @@ -1,16 +1,16 @@ /** \page org_blueberry_ui_qt_log The Logging Plugin -\imageMacro{Logging.png,"Icon of the Logging Plugin",2.00} +\imageMacro{logging.svg,"Icon of the Logging Plugin",2.00} This plug-in records all logging output of events and progress as specified in the source code with time of occurence, level of importance (Info, Warning, Error, Fatal, Debug), the message given and where it happens. The logging starts once the plug-is started. A screenshot of the provided Logging view is shown next. \imageMacro{LogView.png,"Screenshot of the Logging Module",16.00} There are different features available in the view. The filter text field allows for searching all log events containing a certain substring. Using the button "Copy to clipboard" on the bottom right you can copy the current content of the logging view to your clipboard. This enables you to insert the logging information to any text processing application. You can also show more information on every logging message by activating the two checkboxes. In the simple view, leaving both checkboxes unchecked, you'll see logging messages and logging levels. A brief description of the logging levels can be found in the \ref LoggingPage "logging concept documentation". The checkbox "Category" adds a column for the category. The checkbox "Show Advanced Field" shows method, filename and linenumber where the logging message was emitted as well as the running time of the application. The next figure shows all information which can be shown in the Logging Module. \imageMacro{LogViewExplain.png,"Details on the Vizualized Logging Information",16.00} */ diff --git a/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/logging.svg b/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/logging.svg new file mode 100644 index 0000000000..ccb549f8a6 --- /dev/null +++ b/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/logging.svg @@ -0,0 +1,80 @@ + + + + + + + image/svg+xml + + + + + + + + + + + + + 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 09ce1a4f48..08e636a260 100644 --- a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox +++ b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox @@ -1,109 +1,109 @@ /** \page org_mitk_views_datamanager The DataManager -\imageMacro{QmitkDatamanager_Icon.png,"Icon of the Data Manager",2.00} +\imageMacro{data-manager.svg,"Icon of the Data Manager",2.00} \tableofcontents \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". \imageMacro{QmitkDatamanager_Overview.png,"How MITK looks when started",16.00} \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. \imageMacro{QmitkDatamanager_ParentChild.png,"Screenshot1",9.61} 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). \imageMacro{QmitkDatamanager_ImageProperties.png,"Screenshot2: Properties for images",10.56} \imageMacro{QmitkDatamanager_SurfaceProperties.png,"Screenshot3: Properties for surfaces",11.01} \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". \imageMacro{QmitkDatamanager_Preferences.png,"Screenshot4",16.00} \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. \imageMacro{QmitkDatamanager_PropertyList.png,"Screenshot5: Property List",7.85} */ diff --git a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/data-manager.svg b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/data-manager.svg new file mode 100644 index 0000000000..7dd5c797d5 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/data-manager.svg @@ -0,0 +1,60 @@ + + + + + + + image/svg+xml + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox index fb81cee2d4..136c56e93d 100644 --- a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox +++ b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox @@ -1,118 +1,118 @@ /** \page org_mitk_gui_qt_dicom The Dicom Plugin -\imageMacro{QmitkDicom_Icon.png,"Icon of the DICOM Plugin",2.00} +\imageMacro{dicom.svg,"Icon of the DICOM Plugin",2.00} \note This article requires a basic knowledge of the DICOM Standard. \tableofcontents \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 \imageMacro{QmitkDicom_PluginControls.png,"The dicom Plugin controls",7.37} 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 \imageMacro{QmitkDicom_PluginExtended.png,"The DICOM data storage",16.00} 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. \imageMacro{QmitkDicom_DisplayDataManager.png,"Viewed image",16.00} \subsection org_mitk_gui_qt_dicomImport Data import \imageMacro{QmitkDicom_ImportDialog.png,"The import dialog checked",9.53} 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. \imageMacro{QmitkDicom_QueryRetrieve.png,"The query retrieve screen",16.00} \subsection org_mitk_gui_qt_dicomQuery Query \imageMacro{QmitkDicom_Nodes.png,"The DICOM network configuration",11.26} 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. \imageMacro{QmitkDicom_FilterWidget.png,"The DICOM search options",3.66} 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 \imageMacro{QmitkDicom_Retrieve.png,"The queried DICOM data.",15.22} 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/dicom.svg b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/dicom.svg new file mode 100644 index 0000000000..3d10f794ae --- /dev/null +++ b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/dicom.svg @@ -0,0 +1,85 @@ + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox index 70208b09c3..62658b5368 100644 --- a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox +++ b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox @@ -1,37 +1,37 @@ /** \page org_mitk_gui_qt_imagecropper Image Cropper Plugin -\imageMacro{QmitkImageCropper_Icon.png,"Icon of the Image Cropper Plugin.",20} +\imageMacro{crop.svg,"Icon of the Image Cropper Plugin.",20} \tableofcontents \section org_mitk_gui_qt_imagecropperUsage Usage The Image Cropper Plugin allows to crop subvolumes out of your original image volume by defining a cubic bounding box. This box can be placed at an arbitrary position in the volume and can be easily adjusted by using the handles on each of the faces. Touching the handles changes the size of the box whereas touching the box itself changes its position. As soon as the bounding box is placed at the desired position, pressing the button 'Crop' creates a new image assigned to the original image as child node containing only the selected subvolume. The size of the subvolume equals the size of the bounding box. Pressing the "Mask" button keeps the original image size but masks out the area not contained within the bounding box bounds. In case of 3D+t images the whole time series is cropped by default. \imageMacro{BoundingBox_ImageCropperView.png,"Bounding Box.",12.00} \imageMacro{Basic_ImageCropperView.png,"Basic Settings.",7.09} \section org_mitk_gui_qt_imagecropperAdvanced Advanced settings In the advanced settings view you find additional features to manipulate the bounding box. \imageMacro{Advanced_ImageCropperView.png,"Advanced Settings.",7.09} \subsection org_mitk_gui_qt_imagecropperAdvancedOverwrite Overwrite original image By enabling this checkbox the image is replaced by the cropped subvolume. Be careful to use this option since there is no undo action available. \subsection org_mitk_gui_qt_imagecropperAdvancedTimestep Crop current time step only If this checkbox is enabled the xD + t image is reduced to a xD image (e.g., 3D+t --> 3D) with the time step visible in the widget. This is useful if you want to extract a single image or its corresponding subvolume of the time series. The whole time series is cropped by default using the timeGeometry of the time step visible in the widget. \section org_mitk_gui_qt_imagecropperIssues Current issues Cropping 2D images is not supported unless the are 3D images containing only a single slice. The user will be notified by a warning and the input is handled as a single label image. Right now changing the shape or rotation of the bounding box is not supported but might be integrated in the future. */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/crop.svg b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/crop.svg new file mode 100644 index 0000000000..7abad89683 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/crop.svg @@ -0,0 +1,60 @@ + + + + + + + image/svg+xml + + + + + + + + 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 2267b623d2..e158d98694 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 -\imageMacro{QmtikImageNavigator_Slider.png,"Icon of the Image Navigator",2.00} +\imageMacro{image_navigator.svg,"Icon of the Image Navigator",2.00} \imageMacro{QmtikImageNavigator_ImageNavigator.png,"Image Navigator",7.47} 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/documentation/UserManual/image_navigator.svg b/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/image_navigator.svg new file mode 100644 index 0000000000..6bde98e8bc --- /dev/null +++ b/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/image_navigator.svg @@ -0,0 +1,90 @@ + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + 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 f9c2915943..0de797abdb 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 -\imageMacro{QmitkMeasurementToolbox_ImageStatisticsIcon.png,"Icon of the Image Statistics View",2.00} +\imageMacro{bar-chart.svg,"Icon of the Image Statistics View",2.00} \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. \imageMacro{QmitkMeasurementToolbox_Interface.png,"The interface",9.10} \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. For time data the current time step is used for the selected mask and the selected image. If the total number of time steps on the selected mask is less than the current time step, the last time step of the mask is used. If a mask is selected, its used time step will be displayed next to its name like this: (t=0). 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 613a057372..e7ea6bd729 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox @@ -1,126 +1,126 @@ /** \page org_mitk_views_measurement The Measurement View -\imageMacro{QmitkMeasurementToolbox_MeasurementIcon.png,"Icon of the Measurement View",2.00} +\imageMacro{measurement.svg,"Icon of the Measurement View",2.00} \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. \tableofcontents The workflow to use this view is: \imageMacro{QmitkMeasurementToolbox_Workflow.png,"",16.00} 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. \imageMacro{QmitkMeasurementToolbox_BasicScreenEdited.jpg,"",16.00} 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: \imageMacro{QmitkMeasurementToolbox_MeasurementView.jpg,"",7.60} 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.). \imageMacro{QmitkMeasurementToolbox_ImageProcessed.jpg,"",7.56} 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 \imageMacro{QmitkMeasurementToolbox_OpenButton.png,"",2.01} 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). \imageMacro{QmitkMeasurementToolbox_ImageLoadedScreen.jpg,"",16.00} 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. \imageMacro{QmitkMeasurementToolbox_MeasurementFigureButtonLine.jpg,"",7.22} 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. \imageMacro{QmitkMeasurementToolbox_ImageProcessedScreen.jpg,"",6.96} 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. ",16.00} */ diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/bar-chart.svg b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/bar-chart.svg new file mode 100644 index 0000000000..a756ada699 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/bar-chart.svg @@ -0,0 +1,65 @@ + + + + + + image/svg+xml + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/measurement.svg b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/measurement.svg new file mode 100644 index 0000000000..d5e6defc77 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/measurement.svg @@ -0,0 +1,196 @@ + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox index 2cfc3a9318..cc8f00e9a7 100644 --- a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox +++ b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox @@ -1,64 +1,64 @@ /** \page org_mitk_gui_qt_moviemaker The Movie Maker Plugin -\imageMacro{QmitkMovieMaker_Icon.png,"Icon of the Movie Maker Plugin.",2.00} +\imageMacro{video-camera.svg,"Icon of the Movie Maker Plugin.",2.00} \tableofcontents \section org_mitk_gui_qt_moviemakerOverview Overview The Movie Maker View allows you to create basic animations of your scene and to record them to video files. Individual animations are arranged in a timeline and can be played back sequential or in parallel. The Movie Maker View uses external FFmpeg/Libav command line utilities to write compressed video files. You have to manually install either FFmpeg or Libav and set the corresponding path in "External Programs" in the MITK Workbench Preferences (Ctrl+P) in order to record your movies to video files. \imageMacro{QmitkMovieMaker_Preferences.png,"The External Programs preferences page.",12.00} \section org_mitk_gui_qt_moviemakerUsage Usage \imageMacro{QmitkMovieMaker_MovieMakerView.png,"The Movie Maker View.",16.00} To create a movie you have to add an animation to the timeline by clicking the "Add animation" button. You can choose between the available types of animations, e.g., Orbit or Slice. The timeline surrounding bottons allow you to arrange, remove, or add further animations to your movie. Each animation can be set to either begin with the previous animation, i.e., run in parallel, or to start after the previous animation, i.e., run sequential. In combination with delays, rather complex animation arrangements are possible. To set animation specific parameters, select the corresponding animation in the timeline first. You can play back, pause and stop your movie with the according controls at the bottom of the Movie Maker View. Click the "Record" button to finally record your movie to a video file with the specified number of frames per second. You have to choose the render window which you want to record. \subsection org_mitk_gui_qt_moviemakerOrbitUsage Orbit Animation The Orbit animation rotates the camera in the 3D window around the scene. Align the camera directly in the 3D window and enter the number of degrees for the orbitting. If you are planning to have a specific view in the middle of your movie you can play the movie and pause it at the specific frame of interest. Adjust the camera in the 3D window and restart the animation. \imageMacro{QmitkMovieMaker_Orbit.png,"The Orbit animation.",12.00} \subsection org_mitk_gui_qt_moviemakerSliceUsage Slice Animation The Slice animation slices through an image. You can choose the image plane (axial, sagittal, or coronal), as well as the start and end points of the slicing. Use the image navigator in the bottom left of the Workbench to get an idea of the desired values. Check "Reverse" in order to slice from the higher slice number to the lower slice number. \imageMacro{QmitkMovieMaker_Slice.png,"The Slice animation.",12.00} \subsection org_mitk_gui_qt_moviemakerTimeUsage Time Animation The Time animation steps through the individual time steps of the current scene. You can specify the range of the animated time steps. Use the image navigator in the bottom left of the Workbench to get an idea of the desired values. Check "Reverse" in order to step from later time steps to previous time steps. \imageMacro{QmitkMovieMaker_Time.gif,"The Time animation.",12.00} */ diff --git a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/video-camera.svg b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/video-camera.svg new file mode 100644 index 0000000000..ebf0fd1bfd --- /dev/null +++ b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/video-camera.svg @@ -0,0 +1,60 @@ + + + + + + image/svg+xml + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/multilabelsegmentation.svg b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/multilabelsegmentation.svg new file mode 100644 index 0000000000..9b24feb3b2 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/multilabelsegmentation.svg @@ -0,0 +1,10683 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox index 77069cfa4b..a88b5f28fe 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox @@ -1,114 +1,114 @@ /** \page org_mitk_views_multilabelsegmentation The Multilabel Segmentation View -\imageMacro{"multilabelsegmentation.png", "html", 12} +\imageMacro{"multilabelsegmentation.svg", "Icon of the MultiLabelSegmentation Plugin", 12} Please reference \ref org_mitk_views_segmentation for the description of the general segmentation tools. \tableofcontents \section org_mitk_views_multilabelsegmentationUserManualCreateOpenSaveImportAdd Start Segmenting To start using the Segmentation Perspective you will have to either create a new segmentation session or load an existing one from disk. The Segmentation toolbar collects buttons for the these actions: \imageMacro{"org_mitk_views_multilabelsegmentationIMGtoolbar.png", "Segmentation toolbar", 12} \section org_mitk_views_multilabelsegmentationUserManualLabelTable The Label Table The following label properties are readily available to modify: The Label Table is shown below: \imageMacro{"org_mitk_views_multilabelsegmentationIMGlabeltable.png", "The Label Table showing all the labels in the current segmentation session", 12} \section org_mitk_views_multilabelsegmentationUserManualLabelCreation Creating a New Label Click the "New Label" button to add a new label. A dialog will show-up to enter the name and color. Preset organ names and corresponding colors are offered while you type in, but you can set any name. The new name if not known will be automatically remembered and made available the next time you create a new label. In the current implementation of the plugin, the maximum number of labels is restricted to 255. If you need more, you will have to create a new segmentation session. \section org_mitk_views_multilabelsegmentationUserManualLayerCreation Creating a New Layer A layer is a set of labels that occupy a non-overlapping anatomical space. The best way to describe them is by a real use case. Imagine you are working on a radiotherpay planning application. In the first layer of your segmentation session you would like to trace the contours of the liver and neighboring organs. You can accomodate all these segmentations in separate labels because they all occupy different anamical regions and do not overlap. Now say you would like to segment the arteries and veins inside the liver. If you don´t trace them in a different layer, you will overwrite the previous ones. You may also need a third layer for segmenting the different irrigation territories in the liver and a fourth layer to contain the lession you would like to treat. The next figure illustrates the Layer Manager . The buttons in it contained serve for adding a new layer, selecting the previous and the next one. The active layer is shown together with the buttons. \imageMacro{"org_mitk_views_multilabelsegmentationIMGlayerManager.png", "Correction Tool",12} \section org_mitk_views_multilabelsegmentationUserManualLabelSearch Searching a Label It may happen that many labels (e.g. > 200) are present in a segmentation session and therefore manual searching is time consuming. The Label Search edit box allows for quickly finding the label you want. Just start writing its name and and you will get assitance for completing its name. If the label you were searching is found, press enter and it will became the active one. \imageMacro{"org_mitk_views_multilabelsegmentationIMGsearchlabel.png", "Label search", 12} \section org_mitk_views_multilabelsegmentationUserManualLabelEditing Label Editing First of all, you have to select the active label by clicking on the corresponding row in the Label Table. Only one label can be active at the time. Then you can select an editing tool in the toolbox. \section org_mitk_views_multilabelsegmentationUserManualOperationsOnLabels Operations on Labels Depending on your selection in the Label Table , several actions are offered: \subsection org_mitk_views_multilabelsegmentationUserManualOperationsOnSingleSelection Single Label Selection If you right click on any label in the table, a menu will pop-up offering the following actions to be performed on the selected label: \imageMacro{"org_mitk_views_multilabelsegmentationIMGLabelTableSingleSelectionContextMenu.png", "Context menu for single label selection", 12} \subsection org_mitk_views_multilabelsegmentationUserManualOperationsOnMultipleSelection Multiple Label Selection If more than one label is selected, a different menu will show up: \imageMacro{"org_mitk_views_multilabelsegmentationIMGLabelTableMultipleSelectionContextMenu.png", "Context menu for multiple label selection", 12} */ diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.dox b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.dox index 012e67114d..a65d740abe 100644 --- a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.dox +++ b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.dox @@ -1,47 +1,47 @@ /** \page org_mitk_views_pointsetinteraction The Point Set Interaction View -\imageMacro{QmitkPointSetInteraction_Icon.png,"Icon of the Point Set Interaction View",2.00} +\imageMacro{pointset_interaction.svg,"Icon of the Point Set Interaction View",2.00} Available sections: - \ref QmitkPointSetInteractionUserManualOverview - \ref QmitkPointSetInteractionUserManualDetails \section QmitkPointSetInteractionUserManualOverview Overview This view allows you to define multiple sets of points, to fill them with points and to save them in so called PointSets. \imageMacro{QmitkPointSetInteraction_Screenshot.png,"MITK with the QmitkPointSetInteraction view",16.00} 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 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 view. 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. \imageMacro{QmitkPointSetInteraction_AddPointSet.png,"The Add pointset... dialog",8.64} 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. \imageMacro{QmitkPointSetInteraction_CurrentPointSetArea.png,"The Current pointset area",6.52} 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/pointset_interaction.svg b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/pointset_interaction.svg new file mode 100644 index 0000000000..969c6568aa --- /dev/null +++ b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/pointset_interaction.svg @@ -0,0 +1,77 @@ + + + + + + + + + + image/svg+xml + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox index b769e64cd1..82afd40d2f 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox @@ -1,317 +1,317 @@ /** \page org_mitk_views_segmentation The Segmentation Plugin -\imageMacro{QmitkSegmentation_Icon.png,"Icon of the Segmentation Plugin",2.00} +\imageMacro{segmentation.svg,"Icon of the Segmentation Plugin",2.00} Some of the features described below are closed source additions to the open source toolkit MITK and are not available in every application. \tableofcontents \section org_mitk_gui_qt_segmentationUserManualOverview Overview The Segmentation plugin allows you to create segmentations of anatomical and pathological structures in medical images of the human body. The plugin consists of a number of view which can be used for: \imageMacro{QmitkSegmentation_IMGApplication.png,"Segmentation Plugin consisting of the Segmentation View the Segmentation Utilities View and the Clipping Plane View", 16.00} The segmentation plugin offers a number of preferences which can be set via the MITK Workbench application preference dialog: \imageMacro{QmitkSegmentation_IMGPreferences.png,"Segmentation Plugin consisting of the Segmentation View the Segmentation Utilities View and the Clipping Plane View", 10.00} The following preferences can be set: 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. \imageMacro{QmitkSegmentation_IMGSelection.png,"Data Manager is used for selecting the current segmentation. The reference image is selected in the drop down box of the control area.",5.50} To select the reference image (e.g. the original CT/MR image) use the patient image drop down box in the control area of the Segmentation view. The segmentation image selected in the Data Manager is displayed below in the segmentation drop down box. By default the auto selection mode is enabled, which always keeps the selection of the segmentation drop down box in synch with the selection in the data manager. If you disable the auto selection mode the selection of the right segmentation image has to be done via the drop down box. If no segmentation image exists or none is selected create a new segmentation image by using the "New segmentation" button on the right of the Segmentation drop down box. Some items of the graphical user interface might be disabled when no image is selected or the selected image does not fit to the patient image's geoemtry. In any case, the application will give you hints if a selection is needed. \section org_mitk_gui_qt_segmentationUserManualToolOverview Tool overview MITK comes with a comprehensive set of segmentation tools. These tools can be differenciated between manual slice-based 2D segmentation tools and (semi-)automated 3D tools. The manual 2D tools require a big amount of user interaction and can only be applied to a single image slice whereas the 3D tools operate on the hole image. The 3D tools usually require a small amount of interaction like placin seedpoints of setting some parameters. You can switch between the different toolsets by switching the 2D/3D tab in the segmentation view. \imageMacro{QmitkSegmentation_ToolOverview.png,"An overview of the existing tools in MITK. There are interactive 2D tools as well as (semi-)automated 3D tools",5.50} \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. \imageMacro{QmitkSegmentation_IMGIconAddSubtract.png,"Add and Subtract Tools",7.70} 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). \imageMacro{QmitkSegmentation_IMGIconPaintWipe.png,"Paint and Wipe Tools",7.68} 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. \imageMacro{QmitkSegmentation_IMGIconRegionGrowing.png,"Region Growing Tool",3.81} 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. Moving the mouse left and right will shift the range. 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. \if THISISNOTIMPLEMENTEDATTHEMOMENT 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). \imageMacro{QmitkSegmentation_IMGLeakage.png,"Leakage correction feature of the Region Growing tool",11.28} \endif
\imageMacro{QmitkSegmentation_IMGIconCorrection.png,"Correction Tool",3.77} 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: \imageMacro{QmitkSegmentation_IMGCorrectionActions.png,"%Actions of the Correction tool illustrated.",13.50}
\imageMacro{QmitkSegmentation_IMGIconFill.png,"Fill Tool",3.81} Left-click inside a segmentation with holes to completely fill all holes (left-click outside a segmentation). \imageMacro{QmitkSegmentation_IMGIconErase.png,"Erase Tool",3.79} 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 (left-click outside a segmentation). \imageMacro{QmitkSegmentation_IMGIconLiveWire.png,"LiveWire Tool",3.01} The LiveWire Tool acts as a magnetic lasso with a contour snapping to edges of objects. \imageMacro{QmitkSegmentation_IMGLiveWireUsage.png,"Steps for using LiveWire Tool",16.00} The contour will be transfered to its binary image representation by deactivating the tool. \imageMacro{QmitkSegmentation_IMG2DFastMarchingUsage.png,"2D Fast Marching Tool",3.01} Provides a fast marching based 2D interaction segmentation tool. You start with setting seedpoints in an image slice. Via several sliders you can adapt parameters and see the fast marching result instantly. \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. \imageMacro{QmitkSegmentation_3DInterpolationWrongRight.png,"3D Interpolation HowTo",16.00} 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 current state of the 3D interpolation can be saved accross application restart. Therefor just click on save project during the interpolation is active. After restarting the application and load your project you can click on "Reinit Interpolation" within the 3D interpolation GUI area.
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_segmentationUserManual3DSegmentationTools 3D Segmenation tools The 3D tools operate on the hole image and require usually a small amount of interaction like placing seed-points or specifying certain parameters. All 3D tools provide an immediate segmentation feedback, which is displayed as a transparent green overlay. For accepting a preview you have to press the "Comfirm" button of the selected tool. The following 3D tools are at your disposal: \subsection org_mitk_gui_qt_segmentationUserManual3DThresholdTool 3D Threshold tool The Thresholding tool simply applies a 3D threshold to the patient image. All pixels with values equal or above the selected threshold are labeled. You can change the threshold by either moving the slider of setting a certain value in the spinbox. \imageMacro{QmitkSegmentation_3DThresholdTool.png,"3D Threshold tool",10.00} \subsection org_mitk_gui_qt_segmentationUserManual3DULTool 3D Upper/Lower Threshold tool The Upper/Lower Thresholding tool works similar to the simple 3D threshold tool but allows you to define an upper and lower threshold. All pixels with values within this threshold intervall will be labeled \imageMacro{QmitkSegmentation_3DULThresholdTool.png,"3D Upper/Lower Threshold tool",10.00} \subsection org_mitk_gui_qt_segmentationUserManual3DOtsuTool 3D Otsu tool The 3D Otsu tool provides a more sophisticated thresholding algorithm. It allows you to define a number of regions. Based on the image histogram the pixels will then divided into different regions. There more regions you define the longer will the calculation take. \imageMacro{QmitkSegmentation_3DOtsuTool.png,"3D Otsu tool",10.00} \subsection org_mitk_gui_qt_segmentationUserManual3DFMTool 3D Fast Marching tool The 3D Fast Marching tools works similar to the 2D pendant but on the hole image. Depending on you image's size the calculation will take some time. You can interactive set the parameters of the algorithm via the tool GUI. \imageMacro{QmitkSegmentation_3DFMTool.png,"3D Fast Marching tool",10.00} \subsection org_mitk_gui_qt_segmentationUserManual3DRGTool 3D Region Growing tool The 3D Region Growing tool works similar to the 2D pendant. At the beginning you have to place a seedpoint and define a threshold intervall. If you press "Run segmentation" a preview is calculated, if the "3D preview" box is checked you will also see the result in 3D. By moving the "Adapt region growing slider" you can interactively adapt the result to you image. \imageMacro{QmitkSegmentation_3DRGTool.png,"3D Region Growing tool",10.00} +\subsection org_mitk_gui_qt_segmentationUserManual3DWatershedTool 3D Watershed tool This tool provides a watershed based segmentation algorithm. \imageMacro{QmitkSegmentation_3DWatershedTool.png,"3D Watershed tool",10.00} \subsection org_mitk_gui_qt_segmentationUserManualPickingTool Picking tool The Picking tool allows you to select islands within your segmentation. This is especially usefull if e.g. a thresholding delivered your several areas within your image but you are just interested in one special region. \imageMacro{QmitkSegmentation_PickingTool.png,"Picking tool",10.00} \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 \imageMacro{QmitkSegmentation_IMGDataManagerContextMenu.png,"Context menu items for segmentations.",10.58} \section QmitkSegmentation_UserManualSurfaceMasking 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: \imageMacro{QmitkSegmentation_FromSurfaceBefore.png,"Load an image and a surface.",16.00} 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) \imageMacro{QmitkSegmentation_FromSurfaceAfter.png,"Create segmentation from surface",16.00} 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/documentation/UserManual/QmitkSegmentationUtilities.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities.dox index b60a39db80..65cf6d1b77 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities.dox +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities.dox @@ -1,62 +1,62 @@ /** \page org_mitk_views_segmentationutilities The Segmentation Utilities View -\imageMacro{SegmentationUtilities.png,"Icon of the Segmentation Utilities View",5.00} +\imageMacro{segmentation_utilities.svg,"Icon of the Segmentation Utilities View",5.00} \imageMacro{QmitkSegmentationUtilities_Overview.png,"The Segmentation Utilities view",16.00} \tableofcontents \section org_mitk_views_segmentationUtilitiesManualOverview Overview The Segmentation Utilities View allows you to postprocess existing segmentations \section org_mitk_views_segmentationUtilitiesImageSelection Image Selection Usually the data selection in the Segmentation Utilities View is done via drop down box which let you just select the appropriate data. \section org_mitk_views_segmentationUtilitiesBooleanOperations Boolean Operations Boolean operations allow you to create the of two segmentations. The selected segmentations must have the same geometry (size, spacing, ...) \imageMacro{QmitkSegmentationUtilities_IMGBooleanOperations.png,"Boolean operations of the SegmentationUtlitiesView",6.00} \section org_mitk_views_segmentationUtilitiesImageMasking Image masking You can mask your grey value image with either an existing segmentation or a surface. The result will be an image containing only the pixels that are cover by the respective mask. \imageMacro{QmitkSegmentationUtilities_IMGImageMasking.png,"Image masking widget of the Segmentation Utilities View",6.00} \section org_mitk_views_segmentationUtilitiesMorphologicalOperators Morphological Operators The morphological operators are applied to a single segmentation image. Based on a given structuring element the underlying segmentation will be modfied. MITK provides a ball and a cross as structuring elements. The follow operators are at your disposal: \imageMacro{QmitkSegmentationUtilities_IMGMorphologicalOperators.png,"Morphological operators widget of the Segmentation Utilities View",6.00} \section org_mitk_views_segmentationUtilitiesSurfaceToImage Surface to binary image This widget lets you fill you meshes into an empty binary image. It is required that a reference grey value image is present. The created binary image will have the same geometrical properties like the reference image \imageMacro{QmitkSegmentationUtilities_IMGSurfaceToImage.png,"Surface to image widget of the Segmentation Utilities View",6.00} **/ diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/segmentation.svg b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/segmentation.svg new file mode 100644 index 0000000000..54fb2e3178 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/segmentation.svg @@ -0,0 +1,2051 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/segmentation_utilities.svg b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/segmentation_utilities.svg new file mode 100644 index 0000000000..5689bc3f3c --- /dev/null +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/segmentation_utilities.svg @@ -0,0 +1,3481 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox index 45c93fb7c7..49360ff183 100644 --- a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox +++ b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox @@ -1,154 +1,154 @@ /** \page org_mitk_views_volumevisualization The Volume Visualization Plugin -\imageMacro{QmitkVolumeVisualization_Icon.png,"Icon of the Volume Visualization Plugin",2.00} +\imageMacro{volume_visualization.svg,"Icon of the Volume Visualization Plugin",2.00} \tableofcontents \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. \imageMacro{QmitkVolumeVisualization_Overview.png,"",16.00} \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 \imageMacro{QmitkVolumeVisualization_Checkboxen.png,"",8.21} 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 Dropdown menus for the rendering and blend modes Two dropdown menus allow selection of rendering mode (Default, RayCast, GPU) and the blend mode (Composite, Max, Min, Avg, Add). Any Volume Rendering mode requires a lot of computing resources including processor, memory and often also graphics card. The Default selection usually finds the best rendering mode for the available hardware. Alternatively, it is possible to manually specify the selections RayCast and GPU. The RayCast selection is based on CPU computation and therefore typically slow, but allows to render without hardware acceleration. The GPU selection uses 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. Blend modes define how the volume voxels intersected by the rendering rays are pooled. The composite mode specifies standard volume rendering, for which each voxel contributes equally with opacity and color. Other blend modes simply visualize the voxel of maximum / minimum intensity and average / add the intentities along the rendering ray. \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. \imageMacro{QmitkVolumeVisualization_InternalPresets.png,"",8.30} \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. \imageMacro{QmitkVolumeVisualization_Threshold.png,"",8.21} 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. \imageMacro{QmitkVolumeVisualization_Bell.png,"",8.23} 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 \imageMacro{QmitkVolumeVisualization_Slider.png,"",8.23} 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 \imageMacro{QmitkVolumeVisualization_Opacity.png,"grayvalues will be mapped to opacity.",8.04} An opacity of 0 means total transparent, an opacity of 1 means total opaque. \subsection QVV_GC Grayvalue -> Color \imageMacro{QmitkVolumeVisualization_Color.png,"grayvalues will be mapped to color.",8.81} The color transferfunction editor also allows by double-clicking a point to change its color. \subsection QVV_GGO Grayvalue and Gradient -> Opacity \imageMacro{QmitkVolumeVisualization_Gradient.png,"",8.85} Here the influence of the gradient is controllable at specific grayvalues. */ diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/volume_visualization.svg b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/volume_visualization.svg new file mode 100644 index 0000000000..26682d271e --- /dev/null +++ b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/volume_visualization.svg @@ -0,0 +1,65 @@ + + + + + + + + image/svg+xml + + + + + + + + +