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santos (Thiago dos Santos)
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Aug 1 2016, 12:10 PM (209 w, 5 d)
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Aug 2 2016

santos added projects to T12956: Selecting multiple DICOM files from the same series causes the series to be loaded multiple times: MITK, Bugzilla.
Aug 2 2016, 9:56 AM · Bugzilla, MITK
santos added projects to T11856: ITKv4 compatibility: itk::OStringStream does not exist anymore: MITK, Bugzilla.
Aug 2 2016, 9:53 AM · Bugzilla, MITK
santos added projects to T11855: ITKv4 compatibility: Number of Inputs and Outputs in the filter pipeline: MITK, Bugzilla.
Aug 2 2016, 9:53 AM · Bugzilla, MITK
santos added projects to T11484: TimeStamp in IGT classes are conflicting with the TimeStamp in ITKv4 itk::Object: MITK, Bugzilla.
Aug 2 2016, 9:52 AM · MITK (2013-03), Bugzilla
santos added a comment to T11130: Crash if mitkDicomSeriesReader misses Tag [0020,0032] ImagePositionPatient.

[cefe0c]: Merge branch 'bug-11130-crash-if-dicomTag-missing'

Merged commits:

2012-03-07 14:59:27 Markus Fangerau [15d965]
Checking the case when no valid images are found within a series

Aug 2 2016, 9:52 AM · Bugzilla, MITK
santos added a comment to T11130: Crash if mitkDicomSeriesReader misses Tag [0020,0032] ImagePositionPatient.

I've fixed the bug by checking if the volume has valid images before trying to load it. I've commited it in branch bug-11130-crash-if-dicomTag-missing.

Aug 2 2016, 9:52 AM · Bugzilla, MITK
santos added a comment to T11130: Crash if mitkDicomSeriesReader misses Tag [0020,0032] ImagePositionPatient.

There is a unit test. I need the core modification to push it.

Aug 2 2016, 9:52 AM · Bugzilla, MITK
santos added a comment to T11130: Crash if mitkDicomSeriesReader misses Tag [0020,0032] ImagePositionPatient.

[f5d8ce]: Merge branch 'bug-11130-MITK-Data-Conflict'

Merged commits:

2012-03-23 17:05:32 Thiago dos Santos [708183]
MITK-Data file was wrongly merged.

Aug 2 2016, 9:52 AM · Bugzilla, MITK
santos added projects to T10924: Bug in itk::LandmarkBasedTransformInitializer: MITK, Bugzilla.
Aug 2 2016, 9:51 AM · Bugzilla, MITK
santos added a comment to F781: itkLandmarkBasedTransformInitializer.h.patch.

Patch for itkLandmarkBasedTransformInitializer.h

Aug 2 2016, 9:51 AM
santos added a comment to T10743: DICOM reader fails if path contains UTF8 characters.

I've tested it on linux as well, and can confirm that it really works. I will look for an windows machine.

Aug 2 2016, 9:50 AM · Bugzilla, MITK
santos added a comment to T9423: Clean-up: executable bit removed from source files.

Hi Miklos,

Aug 2 2016, 9:48 AM · Bugzilla, MITK
santos added a comment to T9076: ImageCropper does not set outside value correctly.

[3abd4a]: Merge branch 'bug-9076-ImageCropper-outside-value'

Aug 2 2016, 9:47 AM · Bugzilla, MITK
santos added projects to T9076: ImageCropper does not set outside value correctly: MITK, Bugzilla.
Aug 2 2016, 9:47 AM · Bugzilla, MITK
santos added a comment to F705: Shifted_Cropping_BoundingBox.png.

Shifted bounding box

Aug 2 2016, 9:47 AM
santos added projects to T8905: ImageCropper does not work for rotated MR: MITK, Bugzilla.
Aug 2 2016, 9:47 AM · Bugzilla, MITK
santos added a comment to T8770: Add test for mitkSimpleHistogram and write some documentation for this class..

What is the status?

Aug 2 2016, 9:46 AM · Bugzilla, MITK
santos added a comment to T8628: Image selection does not work on Mac.

@Sasha: What is the status?

Aug 2 2016, 9:46 AM · Bugzilla, MITK
santos added a comment to T8571: [Dashboard] NavigationToolReaderAndWriterTest cannot write scene files.

Clearly an IGT issue!

Aug 2 2016, 9:46 AM · Bugzilla, MITK
santos added a comment to T8388: Remove dependency of mitk::ExtractDirectedPlaneImageFilter to pic2vtk module.

What is the status? Is someone going to fix it?

Aug 2 2016, 9:45 AM · Bugzilla, MITK
santos added a comment to T8219: Crash on DICOM loading if directory contains special images.

Do you have some secondary captures so I can reproduce the bug?

Aug 2 2016, 9:45 AM · Bugzilla, MITK
santos added a comment to T8108: DICOM tests fail on MacOS dart clients.

I do not have a solution for the bug. I only checked the dashboard and saw that the tests were passing, so I closed the bug.

Aug 2 2016, 9:45 AM · MITK (2013-03), Bugzilla
santos added a comment to T8108: DICOM tests fail on MacOS dart clients.

All DICOM tests are working correctly now.
If the issue appears again, please reopen the bug.

Aug 2 2016, 9:45 AM · MITK (2013-03), Bugzilla
santos added a comment to T7634: Extend unittest for PlanarPolygon.

@Markus: What is the status here?

Aug 2 2016, 9:44 AM · Bugzilla, MITK
santos added a comment to F666: 0001-Fix-for-package-dependencies.patch.

Patch with Marco's changes

Aug 2 2016, 9:43 AM
santos added projects to T7059: MBI-specific packages are not found by CMake: MITK, Bugzilla.
Aug 2 2016, 9:43 AM · Bugzilla, MITK
santos added projects to T7037: Compile error if BUILD_TESTING is off: MITK, Bugzilla.
Aug 2 2016, 9:43 AM · Bugzilla, MITK
santos added a comment to T6685: Port and redesign 3D Connexion Mouse support for linux.

What is the status?

Aug 2 2016, 9:42 AM · Bugzilla, MITK
santos added a comment to T6683: Tiny xml is not locale independent.

Whats the status here?
@Marco: did you post the patch to tiny xml?

Aug 2 2016, 9:42 AM · Bugzilla, MITK
santos added a comment to T6506: Sorting method in DicomSeriesReader makes wrong interpretation of image position attribute.

In order to load 4D datasets, both "sort" and "check_4d" parameters must be enabled.

Aug 2 2016, 9:42 AM · Bugzilla, MITK
santos added a comment to F653: DicomSeriesReader_sorting.patch.

Sorting with Image Poistion priority instead of acquisition time.

Aug 2 2016, 9:42 AM
santos added a comment to F652: dicom_sorting.patch.

Fix for the bug.

Aug 2 2016, 9:42 AM
santos added a comment to T6506: Sorting method in DicomSeriesReader makes wrong interpretation of image position attribute.

Fix for the bug.

Aug 2 2016, 9:42 AM · Bugzilla, MITK
santos added a comment to T6506: Sorting method in DicomSeriesReader makes wrong interpretation of image position attribute.

According to David Clunie (http://groups.google.com/group/comp.protocols.dicom/browse_thread/thread/4568635e083a3fba/e2a8ceec23032601?lnk=gst&q=sort+slices), the best way to sort is NOT the one I mentioned before, but to "sort along a vector normal to the plane of the image (determined from Image Orientation (Patient)) by the value of Image Position (Patient) projected onto that vector".

Aug 2 2016, 9:42 AM · Bugzilla, MITK
santos added projects to T6506: Sorting method in DicomSeriesReader makes wrong interpretation of image position attribute: MITK, Bugzilla.
Aug 2 2016, 9:42 AM · Bugzilla, MITK
santos added a comment to T6273: Loading of DICOM data without ending requires "trick".

This is because the option "all" shows all extensions that can be loaded with MITK. I agree that this is a bit confusing. Maybe we should change "all" to really show everything, and create another entry "known extensions" to show what "all"is currently showing.

Aug 2 2016, 9:41 AM · Bugzilla, MITK
santos added a comment to T6273: Loading of DICOM data without ending requires "trick".

[SVN revision 28011]
FIX (#6273): The entry "all" in the extensions menu is now showing all files, instead only the known extensions. A new entry "known extensions" was added.

Aug 2 2016, 9:41 AM · Bugzilla, MITK
santos added a comment to T6273: Loading of DICOM data without ending requires "trick".

Yes.

Aug 2 2016, 9:41 AM · Bugzilla, MITK
santos added a comment to T6264: Basic Image Processing crashes when processing large data sets.

@Caspar: What's the status?

Aug 2 2016, 9:41 AM · Bugzilla, MITK
santos added a comment to T6092: vtkUnstructuredGrid write support missing.

What is the status?

Aug 2 2016, 9:41 AM · Bugzilla, MITK
santos added a comment to T5739: Fix DICOM import with GDCM2.

[SVN revision 26833]
FIX (#5739): Instead of using time stamps to identify images belonging to the same time step in 3D+t data, it is now assumed that all time steps have the same initial slice position.

Aug 2 2016, 9:41 AM · Bugzilla, MITK
santos added a comment to T5719: mitkDicomSeriesReader interface should not depend on GDCM.

The problem of moving this method to .cpp is that a different implementation of this method would be required for each different pixel type.
I think the better solution would be to have an interface class (DicomSeriesReader) and an implementation class (GDCMDicomSeriesReader).
However, this is also a bit tricky, as the implementation is not purely GDCM based.

Aug 2 2016, 9:41 AM · Bugzilla, MITK
santos added a comment to T5608: Allow importing different volumes contained in one DICOM folder.

Sorry, didn't see that it is a diffusion DICOM images problem.
It does work only for regular DICOM data.

Aug 2 2016, 9:40 AM · Bugzilla, MITK
santos added a comment to T5608: Allow importing different volumes contained in one DICOM folder.

It is actually supposed to work if the volumes have different series UIDs.
I've tested it here and it worked fine. Can you send me some images that are not working correctly?

Aug 2 2016, 9:40 AM · Bugzilla, MITK
santos added a comment to T5551: Usability of vector-field visualization.

What is the status?

Aug 2 2016, 9:40 AM · Bugzilla, MITK
santos added a comment to T5249: 4D polygon models cannot be saved/loaded properly.

There are no 4D Polygon model classes in VTK / ITK. A Solution would be: Store single 3D polygon models for each timestep.

Aug 2 2016, 9:39 AM · Bugzilla, MITK
santos added projects to T4777: Warning in berry::StackTrace due to unused result: MITK, Bugzilla.
Aug 2 2016, 9:38 AM · Bugzilla, MITK
santos added a comment to T4648: Dicom Reader can only Read 4D Dicom Data.

[SVN revision 24574]
FIX (#4648): Instead of hard-setting the number dimensions to 4 in the itk image, it is checked if there are more then one time step. If there is only one, dimensions is set to 3.

Aug 2 2016, 9:38 AM · Bugzilla, MITK
santos added a comment to T4565: MITK does not recognize 4D DICOM volumes.

Recognition and loading of 4D data is working. More specific problems regarding this matter should discussed in more specific bugs. I am closing this one.

Aug 2 2016, 9:38 AM · Bugzilla, MITK
santos added a comment to T4565: MITK does not recognize 4D DICOM volumes.

[SVN revision 24215]
COMP (#4565): The solution for 4D volumes only works with GDCM>=2. It is now checked during compilation.

Aug 2 2016, 9:38 AM · Bugzilla, MITK
santos added a comment to T4565: MITK does not recognize 4D DICOM volumes.

[SVN revision 24210]
FIX (#4565): Image sorting according to acquisition time and position for the identification of 4D Dicom volumes. After sorting, the images with equal acquisition time are grouped together and loaded as separate volume. Each volume is put as a separate time step in the mitk::Image.

Aug 2 2016, 9:38 AM · Bugzilla, MITK
santos added projects to T4565: MITK does not recognize 4D DICOM volumes: MITK, Bugzilla.
Aug 2 2016, 9:38 AM · Bugzilla, MITK
santos added a comment to F551: mitkDicomSeriesReader.patch.

Modifications to DicomSeriesReader in order to make it 4D compatible.

Aug 2 2016, 9:38 AM
santos added a comment to T4565: MITK does not recognize 4D DICOM volumes.

Modifications to DicomSeriesReader in order to make it 4D compatible.

Aug 2 2016, 9:38 AM · Bugzilla, MITK
santos added a comment to T4525: Make DICOM IO Version configurable.

[SVN revision 24111]
ENH (#4525): Modification of the MITK DICOM series reader to look the at the MITK_USE_GDCMIO variable and to select the appropriate itk IO class accordingly.

Aug 2 2016, 9:38 AM · Bugzilla, MITK
santos added a comment to T4292: New DICOM IO do not use orientation info.

MITK loads the image correctly, if using GDCM 2.0, and having MITK_USE_GDCMIO variable enabled in CMake.

Aug 2 2016, 9:38 AM · Bugzilla, MITK
santos added a comment to T4234: SceneSerialization should be split up in Core/CoreExt dependent parts.

What is the status?

Aug 2 2016, 9:38 AM · Bugzilla, MITK
santos added a comment to T4033: Image cropper does not handle orientations correctly.

Works for me.

Aug 2 2016, 9:37 AM · Bugzilla, MITK
santos added a comment to T4000: IsInside function of boundingobjects seems to be broken.

Could not test it because of T8905.

Aug 2 2016, 9:37 AM · Bugzilla, MITK
santos added a comment to T4000: IsInside function of boundingobjects seems to be broken.

What is the status?

Aug 2 2016, 9:37 AM · Bugzilla, MITK
santos added a comment to T3984: PlanarFigureWriter/Reader need to store complete PlaneGeometry information.

What is the status?

Aug 2 2016, 9:37 AM · Bugzilla, MITK
santos added a comment to T3722: Some DICOM images are incorrectly loaded because of the PixelType.

[SVN revision 22555]
FIX (#3722): Same solution used for the Dicom browser was brought to the DataNodeFactory. A common class for loading Dicom files was created.

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added projects to T3722: Some DICOM images are incorrectly loaded because of the PixelType: MITK, Bugzilla.
Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to T3722: Some DICOM images are incorrectly loaded because of the PixelType.

[SVN revision 22384]
FIX (#3722): Used itk::DICOMImageIO2 to find out the pixel type before loading the whole image.

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to T3722: Some DICOM images are incorrectly loaded because of the PixelType.

[SVN revision 22385]
ENH (#3722): Added a default caso in order to cover the unknown pixel warnings and to get rid of the compiler warning.

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to T3722: Some DICOM images are incorrectly loaded because of the PixelType.

We should port this changes to mitkDataNodeFactory and adapt the DicomBrowser to use the load mechanism direct from there.

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added projects to T3698: Wrong dependence fromt QtDicomBrowser and QmitkDICOMBrowser view to DicomIndex: MITK, Bugzilla.
Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to T3698: Wrong dependence fromt QtDicomBrowser and QmitkDICOMBrowser view to DicomIndex.

[SVN revision 22291]
FIX (#3698): Dependencies to wrong module (DicomIndex) modified to the correct module (DicomIndexer).

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to T3698: Wrong dependence fromt QtDicomBrowser and QmitkDICOMBrowser view to DicomIndex.

[SVN revision 22363]
FIX (#3698): Dependencie is really DicomIndex. DicomIndexer does not exist.

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to T3684: Review and clean mbilog.

Clearly a core issue!

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to T3447: Import Error in DicomImport Bundle.

Chili found out that the image headers provided wrong information in the "Number of Frames" section of some series.

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to T3447: Import Error in DicomImport Bundle.

Apparently does ITK have more DICOM IO classes, than the GDCM-based one. Using the DICOMImageIO2, some of these images could be loaded correctly. However, some have wrong header information (image dimensions) and can not be loaded.

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to T3447: Import Error in DicomImport Bundle.

Some images could be opened after changing the ImageIO class. By others I think the headers are wrong in some series. For example, the images have different sizes within the same series.

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to T3447: Import Error in DicomImport Bundle.

[SVN revision 21987]
ENH (#3447): GDCMImageIO replaced by DICOMImageIO2.

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to T3447: Import Error in DicomImport Bundle.

Chili is also unable to load these images. It freezes.

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to T3447: Import Error in DicomImport Bundle.

Please look at the comments on bugs #3250 and #3146. There is not much I can do.

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to F488: mitkDicomSeriesReader.patch.

Modification in the DicomSeriesReader in order to allow progress callbacks.

Aug 2 2016, 9:36 AM
santos added a comment to F489: QmitkDicomBrowser.patch.

Modification in the DicomBrowser in order to update the progress bar in every progress callback from DicomSeriesReader.

Aug 2 2016, 9:36 AM
santos added a comment to T3440: There is no progress bar when loading DICOM images with the DICOM browser.

Modification in the DicomBrowser in order to update the progress bar in every progress callback from DicomSeriesReader.

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to T3440: There is no progress bar when loading DICOM images with the DICOM browser.

Modification in the DicomSeriesReader in order to allow progress callbacks.

Aug 2 2016, 9:36 AM · Bugzilla, MITK
santos added a comment to T3384: image cropper crops wrong region.

I added a patch that reverts all changes I made to the Image Cropper. Please apply it and try cropping your images.
It would be nice if you make the images you used available for tests. It may be a geometry problem.

Aug 2 2016, 9:35 AM · Bugzilla, MITK
santos added a comment to F476: ImageCropper.patch.

Patch that reverts all my changes.

Aug 2 2016, 9:35 AM
santos added a comment to T3384: image cropper crops wrong region.

We have tested the cropping with and without the changes we made, and in both cases the same result was achieved.
In order to evaluate if the cropped region is correct, we used synthetic images, such as wall (/lpic/synthetic), where we could easily check if the cropping region was correct.
The selected regions were successfully cropped. However, after cropping, the selected image always moves to the center of the original image. This effect can explain what happened in Jochen's screenshots. After cropping, and having the cropped region moved to the center, the red marker lies outside the cropped region. In summary, the marker set by Jochen is given in world coordinates, which before cropping lies inside the image, and does not lie inside the cropped image because its origin is moved to another world coordinate, so the image lies in the center.
I don't know if this a geometry problem, or if there is a problem at all. The behavior of the cropping tools was never specified before, and I don't know who implemented it that way.

Aug 2 2016, 9:35 AM · Bugzilla, MITK
santos added a comment to T3384: image cropper crops wrong region.

Patch that reverts all my changes.

Aug 2 2016, 9:35 AM · Bugzilla, MITK
santos added a comment to T3343: memcheck errors in mitkNavigationToolReaderAndWriterTest.

Some errors were suppressed. The errors that are still there can be fixed by the author. Valgrind gives very specific information about the location of the errors and what it is all about.

Aug 2 2016, 9:35 AM · Bugzilla, MITK
santos added a comment to T3343: memcheck errors in mitkNavigationToolReaderAndWriterTest.

There are no memory leaks. Valgrind is only pointing that there are operations with uninitialized variables.

Aug 2 2016, 9:35 AM · Bugzilla, MITK
santos added a comment to T3273: Add epsilon parameter to NavigationDataToMessageFilter.

Fixed in Commit: 25856. I used the wrong bug message in my history. Unfortunately it was commited as COMP.
The epsilons were added and are initialized with 0.0, in order to maintain the previous behavior.

Aug 2 2016, 9:35 AM · Bugzilla, MITK
santos added a comment to T3263: Autocropping segmentations produces offset (due to padding).

No, it is not a duplicate.

Aug 2 2016, 9:34 AM · Bugzilla, MITK
santos added a comment to T3250: DicomBrowser: Loading of dicom images does not work properly.

(In reply to comment #9)

Probably the cleanest solution would be to check in another way if the current
(reference?) geometry is not yet set, and therefore the extents cannot be
computed properly. The check for an index coordinate extent of <= 2 seems to be
a bit arbitrary to me (could it not be that the extent in some rare cases
suddenly becomes greate than 3.0, e.g.? At least then rounding would also not
work...)

Aug 2 2016, 9:34 AM · Bugzilla, MITK
santos added a comment to T3250: DicomBrowser: Loading of dicom images does not work properly.

The extents in the first run of GenerateData are computed through the norm of the axis vectors in index coordinate (lines 403-406). There are many operation involved:

  • Transformation of the vectors in world coordinates to index coordinates, which involves a few matrix transformations;
  • Computation of the norm from the transformed vectors.
Aug 2 2016, 9:34 AM · Bugzilla, MITK
santos added a comment to T3250: DicomBrowser: Loading of dicom images does not work properly.

In order to solve this warning problem, one can check if the world geometry was already initialized with a reference geometry. If not, it means the the planes are not there yet, and the method should return.

Aug 2 2016, 9:34 AM · Bugzilla, MITK
santos added a comment to T3250: DicomBrowser: Loading of dicom images does not work properly.

[SVN revision 22210]
FIX (#3250): Checking if the worldGeometry2D was correctly initialized before continuing.

Aug 2 2016, 9:34 AM · Bugzilla, MITK
santos added a comment to T3250: DicomBrowser: Loading of dicom images does not work properly.

I've checked the mitkImageMapper2D.

Aug 2 2016, 9:34 AM · Bugzilla, MITK
santos added a comment to T3250: DicomBrowser: Loading of dicom images does not work properly.

I think this bug is very similar to T3205. Since MITK relies on ITK (more specifically on gdcm) in order to load DICOM images, there is not much I can do about it.

Aug 2 2016, 9:34 AM · Bugzilla, MITK
santos added a comment to T3205: DicomBrowser: Usability "improveable".

[SVN revision 27934]
ENH (#3205): Warning fixed.

Aug 2 2016, 9:33 AM · Bugzilla, MITK
santos added a comment to T3205: DicomBrowser: Usability "improveable".

[SVN revision 27924]
ENH (#3205): Warning fixed.

Aug 2 2016, 9:33 AM · Bugzilla, MITK
santos added a comment to T3205: DicomBrowser: Usability "improveable".

[SVN revision 27922]
ENH (#3205): Status shows now "DB Ready" instead of "Connected". Update and Stop buttons are set visible or invisible, depending if they are needed.

Aug 2 2016, 9:33 AM · Bugzilla, MITK
santos added a comment to T3201: Linux: No file extension list visible while trying to save DataNodes out of DataManager.

The extensions are shown depending on the configuration of the linux environment (gnome, kde, etc.)

Aug 2 2016, 9:33 AM · Bugzilla, MITK
santos added a comment to T3193: Blank file extension line in File/Open dialog.

[SVN revision 21134]
FIX (#3193): Deleted unnecessary QT filter separation characters (;;), which were generating the empty line in the extension list of the load dialog.

Aug 2 2016, 9:33 AM · Bugzilla, MITK
santos added a comment to T3181: MIP in MITK.

What is the status?

Aug 2 2016, 9:33 AM · Bugzilla, MITK