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clitk.git
13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
David Sarrut [Mon, 26 Sep 2011 07:00:23 +0000 (09:00 +0200)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoinstallation of more scripts
dbcache [Thu, 22 Sep 2011 12:42:38 +0000 (14:42 +0200)]
installation of more scripts

13 years agomorphoMath tests
mpech [Wed, 21 Sep 2011 15:52:55 +0000 (17:52 +0200)]
morphoMath tests

13 years agotest for lung3d.mhd
mpech [Wed, 21 Sep 2011 14:31:21 +0000 (16:31 +0200)]
test for lung3d.mhd

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
mpech [Wed, 21 Sep 2011 09:29:06 +0000 (11:29 +0200)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
David Sarrut [Wed, 21 Sep 2011 07:51:29 +0000 (09:51 +0200)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agosupport for mha images
Romulo Pinho [Tue, 20 Sep 2011 16:47:52 +0000 (18:47 +0200)]
support for mha images

- another patch by Joël

13 years agocomparing raw files automatically. refFile can end with .mhd or not
mpech [Tue, 20 Sep 2011 15:28:53 +0000 (17:28 +0200)]
comparing raw files automatically. refFile can end with .mhd or not

13 years agoadd tests for imageArithm
mpech [Tue, 20 Sep 2011 13:53:11 +0000 (15:53 +0200)]
add tests for imageArithm

13 years agoundoing StructureSet-related patch
Romulo Pinho [Mon, 19 Sep 2011 11:56:11 +0000 (13:56 +0200)]
undoing StructureSet-related patch

- the one sent by Joël

13 years agoBug/issue 704
Romulo Pinho [Fri, 16 Sep 2011 09:23:42 +0000 (11:23 +0200)]
Bug/issue 704

- Made clitkPadImage generic (no support for 4D images for the moment).

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
David Sarrut [Fri, 16 Sep 2011 09:18:50 +0000 (11:18 +0200)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoreplacing \r\n by \n in generated mhd files when running toolTestRunner
mpech [Fri, 16 Sep 2011 09:12:43 +0000 (11:12 +0200)]
replacing \r\n by \n in generated mhd files when running toolTestRunner

13 years agoNo .gitignore file Joël! Put .gitignore in your .gitignore file.
Simon Rit [Wed, 14 Sep 2011 11:18:24 +0000 (13:18 +0200)]
No .gitignore file Joël! Put .gitignore in your .gitignore file.

13 years agofiner control over fusion transparency
Romulo Pinho [Tue, 13 Sep 2011 15:36:36 +0000 (17:36 +0200)]
finer control over fusion transparency

- addition of a spin box to set the values

13 years agoapplying another patch from Joel
Romulo Pinho [Tue, 13 Sep 2011 14:07:22 +0000 (16:07 +0200)]
applying another patch from Joel

13 years agopatches sent from Joel Schaerer
Romulo Pinho [Tue, 13 Sep 2011 08:39:33 +0000 (10:39 +0200)]
patches sent from Joel Schaerer

13 years agoitkv4 migration
Vivien Delmon [Mon, 12 Sep 2011 14:49:49 +0000 (16:49 +0200)]
itkv4 migration

- Add call to SetDirectionCollapseToSubmatrix needed by the
  ExtractImageFilter.

13 years agoitk4 Remove ITK_USE_OPTIMIZED_REGISTRATION_METHODS
Vivien Delmon [Mon, 12 Sep 2011 14:45:03 +0000 (16:45 +0200)]
itk4 Remove ITK_USE_OPTIMIZED_REGISTRATION_METHODS

- Bypass all ITK_USE_OPTIMIZED_REGISTRATION_METHODS with ITK 4. All
optimized version are now the normal version in itk4.
- Include itkImageToImageMetric.h instead of itkOptImageToImageMetric.h
- Rename GetJacobian to ComputeJacobianWithRespectToParameters.

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
David Sarrut [Mon, 12 Sep 2011 09:36:59 +0000 (11:36 +0200)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
Romulo Pinho [Fri, 9 Sep 2011 09:03:42 +0000 (11:03 +0200)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoerror in the install of segmentation tools
Romulo Pinho [Fri, 9 Sep 2011 09:03:00 +0000 (11:03 +0200)]
error in the install of segmentation tools

13 years agoitk4 Rename DeformationField to DisplacementField
Vivien Delmon [Tue, 6 Sep 2011 09:42:38 +0000 (11:42 +0200)]
itk4 Rename DeformationField to DisplacementField

13 years agoRevert "[BUG] Use POSIX local before call to GDCM"
Vivien Delmon [Mon, 5 Sep 2011 15:20:05 +0000 (17:20 +0200)]
Revert "[BUG] Use POSIX local before call to GDCM"

This reverts commit a1dbb1f955409410f9402f9f257482a03bb5d5d6.
Corrected by 98eb0c23b8066792d7a77e571fb7d48c9fe02db6.

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
Vivien Delmon [Mon, 5 Sep 2011 15:17:56 +0000 (17:17 +0200)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agolocale bug in vv with French
Romulo Pinho [Mon, 5 Sep 2011 15:16:02 +0000 (17:16 +0200)]
locale bug in vv with French

- An error when resetting the locale to its original value caused the previous setting to be undone...

13 years ago[BUG] Use POSIX local before call to GDCM
Vivien Delmon [Mon, 5 Sep 2011 15:15:45 +0000 (17:15 +0200)]
[BUG] Use POSIX local before call to GDCM

- Force the use of POSIX local to read dicom headers with gdcm

13 years agoRevert "itkv4 migration: Rename itkBSplineDeformableTransform to itkBSplineTransform"
Vivien Delmon [Mon, 5 Sep 2011 10:01:35 +0000 (12:01 +0200)]
Revert "itkv4 migration: Rename itkBSplineDeformableTransform to itkBSplineTransform"

This reverts commit ba207d8b674671e4e3e1ce6d4171e84474c4cfd9.

13 years agoitkv4 propagate Transform<*>::NumberOfParametersType
Vivien Delmon [Mon, 5 Sep 2011 09:34:19 +0000 (11:34 +0200)]
itkv4 propagate Transform<*>::NumberOfParametersType

- Propagate itk::Transform<*>::NumberOfParametersType typedef into our
homemade transforms.

13 years agoitkv4 Replace ITK_TYPENAME by typename
Vivien Delmon [Mon, 5 Sep 2011 09:06:10 +0000 (11:06 +0200)]
itkv4 Replace ITK_TYPENAME by typename

- ITK_TYPENAME disappeared in itkv4. It was in itkv3 to remove some warning
with MS VC++ 6.0 which is not supported by itk anymore.

13 years agoVTK 5.8.0 introduced a bug with overlay and fusion: default values for
Simon Rit [Fri, 2 Sep 2011 12:01:38 +0000 (14:01 +0200)]
VTK 5.8.0 introduced a bug with overlay and fusion: default values for
output origin and spacing of vtkImageReslice had changed and the proper
functions were not used for their initialization. Fixed.

13 years agoCompatibility with itk4, dont check image physical space (VerifyInputInformation)
David Sarrut [Fri, 2 Sep 2011 10:56:44 +0000 (12:56 +0200)]
Compatibility with itk4, dont check image physical space (VerifyInputInformation)

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
David Sarrut [Thu, 1 Sep 2011 14:21:45 +0000 (16:21 +0200)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoRemoved unused files
Simon Rit [Wed, 31 Aug 2011 12:49:38 +0000 (14:49 +0200)]
Removed unused files

13 years agoRemove clitkBSplineDeformableRegistration from CMakeLists also...
Simon Rit [Wed, 31 Aug 2011 12:21:57 +0000 (14:21 +0200)]
Remove clitkBSplineDeformableRegistration from CMakeLists also...

13 years agoRemoved clitkBSplineDeformableRegistration which was not supported
Simon Rit [Wed, 31 Aug 2011 12:11:36 +0000 (14:11 +0200)]
Removed clitkBSplineDeformableRegistration which was not supported
anymore. Prefer using clitkBLUTDIR --itkbspline.

13 years agoAdded option itkbspline to use itk::BSpline instead of multilabels BLUTs
Simon Rit [Wed, 31 Aug 2011 09:56:30 +0000 (11:56 +0200)]
Added option itkbspline to use itk::BSpline instead of multilabels BLUTs

13 years agoAdded Get function for the vector of transforms
Simon Rit [Wed, 31 Aug 2011 08:44:27 +0000 (10:44 +0200)]
Added Get function for the vector of transforms

13 years agouint compilation error on Windows
Simon Rit [Tue, 30 Aug 2011 16:27:45 +0000 (18:27 +0200)]
uint compilation error on Windows

13 years agoRemove /lib from INSTALL_RPATH properties
Vivien Delmon [Tue, 30 Aug 2011 13:36:27 +0000 (15:36 +0200)]
Remove /lib from INSTALL_RPATH properties

- only needed on my computer with itkv4

13 years agoMerge commit '488f24aa984ae24adc9458bf5fbf3b2351415742'
Vivien Delmon [Tue, 30 Aug 2011 13:24:27 +0000 (15:24 +0200)]
Merge commit '488f24aa984ae24adc9458bf5fbf3b2351415742'

Conflicts:
registration/clitkBSplineDeformableRegistrationGenericFilter.txx

13 years agomerge master
Vivien Delmon [Tue, 30 Aug 2011 11:34:16 +0000 (13:34 +0200)]
merge master

13 years agoAttempt to make clitkBSplineDeformableRegistration work
Simon Rit [Tue, 30 Aug 2011 10:59:42 +0000 (12:59 +0200)]
Attempt to make clitkBSplineDeformableRegistration work

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
David Sarrut [Tue, 30 Aug 2011 08:03:42 +0000 (10:03 +0200)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoitk4 Renaming
Vivien Delmon [Mon, 29 Aug 2011 16:08:01 +0000 (18:08 +0200)]
itk4 Renaming

- Rename GetJacobian to ComputeJacobianWithRespectToParameters
- Call Transform constructor without OutputDimension parameter
- Rename m_Jacobian to m_SharedDataBSplineJacobian and declare it

13 years agoitk4 Rename DeformationField to DisplacementField when necessary
Vivien Delmon [Mon, 29 Aug 2011 15:56:18 +0000 (17:56 +0200)]
itk4 Rename DeformationField to DisplacementField when necessary

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
David Sarrut [Mon, 29 Aug 2011 06:33:45 +0000 (08:33 +0200)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
Romulo Pinho [Wed, 24 Aug 2011 09:45:12 +0000 (11:45 +0200)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoBug in clitkMedianTemporalDimension
Romulo Pinho [Wed, 24 Aug 2011 09:42:49 +0000 (11:42 +0200)]
Bug in clitkMedianTemporalDimension

- median taken was one position before or after the real median. results were actually unpredictable...
- also optimized the code a bit...

13 years agoLimit uniformity test to first 3 dimensions (usually the spatial ones)
Simon Rit [Tue, 23 Aug 2011 17:16:48 +0000 (19:16 +0200)]
Limit uniformity test to first 3 dimensions (usually the spatial ones)
    to avoid problems when spacing was randomly assigned in 4th
    dimension

13 years agoAllow unlinking of window/level of overlay, enable ctrl+w for local
Simon Rit [Tue, 23 Aug 2011 17:05:58 +0000 (19:05 +0200)]
Allow unlinking of window/level of overlay, enable ctrl+w for local
windowing of fusion and overlay image

13 years agoAdded compression option to clitkImageConvert
Simon Rit [Tue, 23 Aug 2011 11:51:46 +0000 (13:51 +0200)]
Added compression option to clitkImageConvert

13 years ago[BUG] clitkImageInfo wasn't installed
Vivien Delmon [Tue, 16 Aug 2011 12:47:46 +0000 (14:47 +0200)]
[BUG] clitkImageInfo wasn't installed

- Replace clitkDicom2Image by clitkImageInfo CMakeLists

13 years agoclitkTransformLandmarks
Romulo Pinho [Tue, 9 Aug 2011 14:58:58 +0000 (16:58 +0200)]
clitkTransformLandmarks

- can now transform using a matrix (file) and/or spacing (cmd line)

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
Vivien Delmon [Tue, 9 Aug 2011 08:49:30 +0000 (10:49 +0200)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoitkv4 migration: Rename DifferenceImageFilter to ComparisonImageFilter
Vivien Delmon [Tue, 9 Aug 2011 08:41:41 +0000 (10:41 +0200)]
itkv4 migration: Rename DifferenceImageFilter to ComparisonImageFilter

13 years agoitkv4 migration: Rename itkBSplineDeformableTransform to itkBSplineTransform
Vivien Delmon [Tue, 9 Aug 2011 08:37:52 +0000 (10:37 +0200)]
itkv4 migration: Rename itkBSplineDeformableTransform to itkBSplineTransform

13 years agobug in create_mid_masks-2.0.sh
Romulo Pinho [Mon, 8 Aug 2011 12:51:51 +0000 (14:51 +0200)]
bug in create_mid_masks-2.0.sh

- "source ./variables" was in the wrong place

13 years agoregistration script more robust to parallelization
Romulo Pinho [Fri, 5 Aug 2011 11:09:21 +0000 (13:09 +0200)]
registration script more robust to parallelization

- elastix's parameter file is now created with a suffix

13 years agomore name conflicts
Romulo Pinho [Fri, 5 Aug 2011 10:51:45 +0000 (12:51 +0200)]
more name conflicts

13 years agoresolving script name conflicts
Romulo Pinho [Fri, 5 Aug 2011 09:37:04 +0000 (11:37 +0200)]
resolving script name conflicts

13 years agonew midP related scripts
Romulo Pinho [Fri, 5 Aug 2011 09:15:31 +0000 (11:15 +0200)]
new midP related scripts

- they are also installed when make-installing

13 years agosolved locale related bug
Romulo Pinho [Fri, 5 Aug 2011 07:43:39 +0000 (09:43 +0200)]
solved locale related bug

- problem appeared when opening dicom files in a "French" machine

13 years agoPut in this file all commands related to S2RL
David Sarrut [Fri, 29 Jul 2011 13:20:13 +0000 (15:20 +0200)]
Put in this file all commands related to S2RL

13 years agoAdd options for S3A
David Sarrut [Fri, 29 Jul 2011 13:19:44 +0000 (15:19 +0200)]
Add options for S3A

13 years agoAdd options for threshold
David Sarrut [Fri, 29 Jul 2011 13:19:36 +0000 (15:19 +0200)]
Add options for threshold

13 years agoAdd option for threshold
David Sarrut [Fri, 29 Jul 2011 13:19:30 +0000 (15:19 +0200)]
Add option for threshold

13 years agoAdd options for S3A
David Sarrut [Fri, 29 Jul 2011 13:18:10 +0000 (15:18 +0200)]
Add options for S3A

13 years agoFinish first step of S3A.
David Sarrut [Fri, 29 Jul 2011 13:17:54 +0000 (15:17 +0200)]
Finish first step of S3A.

13 years agorenaming filetest name
mpech [Fri, 29 Jul 2011 13:12:36 +0000 (15:12 +0200)]
renaming filetest name

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
David Sarrut [Fri, 29 Jul 2011 12:31:40 +0000 (14:31 +0200)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agotest for binarizeImage FG, lower 0.1556
mpech [Fri, 29 Jul 2011 09:11:01 +0000 (11:11 +0200)]
test for binarizeImage FG, lower 0.1556

13 years agotest --mode BG for binarizeImage
mpech [Thu, 28 Jul 2011 16:04:01 +0000 (18:04 +0200)]
test --mode BG for binarizeImage

13 years agoRemove unused variable
David Sarrut [Thu, 28 Jul 2011 13:41:16 +0000 (15:41 +0200)]
Remove unused variable

13 years agocorrect merge
David Sarrut [Thu, 28 Jul 2011 13:36:51 +0000 (15:36 +0200)]
correct merge

13 years agofirst trial
David Sarrut [Thu, 28 Jul 2011 10:59:47 +0000 (12:59 +0200)]
first trial

13 years ago first version of Image2DicomRT (dos not work)
David Sarrut [Thu, 28 Jul 2011 10:58:40 +0000 (12:58 +0200)]
 first version of Image2DicomRT (dos not work)

13 years agofirst version of UpdateDicomItem
David Sarrut [Thu, 28 Jul 2011 10:56:33 +0000 (12:56 +0200)]
first version of UpdateDicomItem

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
David Sarrut [Thu, 28 Jul 2011 10:55:11 +0000 (12:55 +0200)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoUse clitk version of the itkPasteImageFilter
David Sarrut [Thu, 28 Jul 2011 09:44:22 +0000 (11:44 +0200)]
Use clitk version of the itkPasteImageFilter

13 years agoI dont want to verify inputs information, override VerifyInputInformation
David Sarrut [Thu, 28 Jul 2011 09:44:03 +0000 (11:44 +0200)]
I dont want to verify inputs information, override VerifyInputInformation

13 years agoI dont want to verify inputs information, override VerifyInputInformation
David Sarrut [Thu, 28 Jul 2011 09:43:54 +0000 (11:43 +0200)]
I dont want to verify inputs information, override VerifyInputInformation

13 years agoAdd a clitk version of itkPasteImageFilter because, with itkv4, there is a new Verify...
David Sarrut [Thu, 28 Jul 2011 09:42:48 +0000 (11:42 +0200)]
Add a clitk version of itkPasteImageFilter because, with itkv4, there is a new VerifyInputInformation function that prevent filter to be used with images having different physical space, while I want to do that.

13 years agoChange reading. Add possibility to update dicom info (before writing dicom)
David Sarrut [Wed, 27 Jul 2011 09:49:05 +0000 (11:49 +0200)]
Change reading. Add possibility to update dicom info (before writing dicom)

13 years agoSimplify (!) DicomRT reading. Store Reader to be able to write later.
David Sarrut [Wed, 27 Jul 2011 09:48:30 +0000 (11:48 +0200)]
Simplify (!) DicomRT reading. Store Reader to be able to write later.

13 years agoReplace ListOfROI (vector) by MapOfROI to avoid ambiguity between the ROI number...
David Sarrut [Wed, 27 Jul 2011 09:44:13 +0000 (11:44 +0200)]
Replace ListOfROI (vector) by MapOfROI to avoid ambiguity between the ROI number and the index.
Remplace GetROI with GetROIFromROINumber

13 years agoReplace ListOfROI (vector) by MapOfROI to avoid ambiguity between the ROI number...
David Sarrut [Wed, 27 Jul 2011 09:43:33 +0000 (11:43 +0200)]
Replace ListOfROI (vector) by MapOfROI to avoid ambiguity between the ROI number and the index

13 years agoChange GetROI by GetROIFromROINumber
David Sarrut [Wed, 27 Jul 2011 09:42:43 +0000 (11:42 +0200)]
Change GetROI by GetROIFromROINumber

13 years agoIndicate that --radius option is multiple. User can set one radius by dimension
David Sarrut [Wed, 27 Jul 2011 09:41:47 +0000 (11:41 +0200)]
Indicate that --radius option is multiple. User can set one radius by dimension

13 years agoRemove fucking windows ^M
David Sarrut [Wed, 27 Jul 2011 09:41:03 +0000 (11:41 +0200)]
Remove fucking windows ^M

13 years agotmpnam_s for windows
mpech [Tue, 26 Jul 2011 14:14:14 +0000 (16:14 +0200)]
tmpnam_s for windows

13 years agodefinition of test_Tool_Path
mpech [Tue, 26 Jul 2011 09:33:55 +0000 (11:33 +0200)]
definition of test_Tool_Path

13 years agoremove toolsTest using google framework
mpech [Tue, 26 Jul 2011 09:06:47 +0000 (11:06 +0200)]
remove toolsTest using google framework

13 years agoremove vvTests because of google framework...
mpech [Tue, 26 Jul 2011 08:35:01 +0000 (10:35 +0200)]
remove vvTests because of google framework...

13 years agoremoving warnings: unused variable, tmpnam
mpech [Mon, 25 Jul 2011 14:22:15 +0000 (16:22 +0200)]
removing warnings: unused variable, tmpnam

13 years agoUpdate supports & stations 3A,3P
David Sarrut [Mon, 25 Jul 2011 12:49:25 +0000 (14:49 +0200)]
Update supports & stations 3A,3P

13 years agoAdd clitkDicomRTStruct2Image and clitkImage2DicomRTStruct
David Sarrut [Mon, 25 Jul 2011 12:48:46 +0000 (14:48 +0200)]
Add clitkDicomRTStruct2Image and clitkImage2DicomRTStruct

13 years agoAdd clitkImage2DicomRTStruct executable to convert a binary image into a dicom-rt...
David Sarrut [Mon, 25 Jul 2011 08:28:01 +0000 (10:28 +0200)]
Add clitkImage2DicomRTStruct executable to convert a binary image into a dicom-rt struct

13 years agoAdd clitkImage2DicomRTStructFilter to convert an image into a dicom-rt-struct
David Sarrut [Mon, 25 Jul 2011 08:27:28 +0000 (10:27 +0200)]
Add clitkImage2DicomRTStructFilter to convert an image into a dicom-rt-struct

13 years agoRename clitkDicomRT_ROI_ConvertToImageFilter into clitkDicomRTStruct2ImageFilter
David Sarrut [Mon, 25 Jul 2011 08:27:00 +0000 (10:27 +0200)]
Rename clitkDicomRT_ROI_ConvertToImageFilter into clitkDicomRTStruct2ImageFilter