tbaudier [Mon, 4 Mar 2019 15:47:12 +0000 (16:47 +0100)]
Change name of the button in Image Arithm tool
Before, it was QDialogButtonBox::Discard, but according to https://doc.qt.io/archives/qt-4.8/qdialogbuttonbox.html#StandardButton-enum
it can be displayed "Don't save".
For this tool, we want to select 1 image instead of 2, so the name of the button is not appropriate.
Moreover in skip function, the comparision to "Discard" can be complicated with another name.
So I prefer to use Ignore button because it's more appropriate
tbaudier [Mon, 4 Mar 2019 13:25:06 +0000 (14:25 +0100)]
Inverse VTK_VERSION VERSION_GREATER to VERSION_LESS
It seems that VERSION_GREATER is not granter and equal, so I prefer to use VERSION_LESS to include the version 8.2.0
tbaudier [Mon, 4 Mar 2019 10:44:02 +0000 (11:44 +0100)]
QVTKOpenGLNativeWidget is available from VTK8.2
Before this version (eg VTK8.1.1), use QVTKWidget
tbaudier [Thu, 28 Feb 2019 13:26:46 +0000 (14:26 +0100)]
Merge branch 'master' of https://github.com/open-vv/vv
tbaudier [Thu, 28 Feb 2019 13:25:04 +0000 (14:25 +0100)]
Add clitkImage2Dicom tool
The difference with clitkWriteDicomSerie is that the number of slice can be different between the input image and the input dicom
tbaudier [Thu, 28 Feb 2019 13:07:52 +0000 (14:07 +0100)]
Add reverse flag in clitkDicom2Image
Sometimes (eg: with MR from HEH), the basic algorithm is not sufficient to sort dicom slices
The sorting reverse the slice order
tbaudier [Thu, 28 Feb 2019 13:05:14 +0000 (14:05 +0100)]
Add instanceNumber sorting for clitkDicom2Image
Sometimes (eg: with MR from HEH), the basic algorithm is not sufficient to sort dicom slices
It is the case when multiples sequences are in the same image, the z position is the same for a same slice in all sequences, it creates conflict
In such a case, we can sort slices according instanceNumber
tbaudier [Thu, 28 Feb 2019 10:10:16 +0000 (11:10 +0100)]
Change header includion from .h to .cxx file
With ITK5, it was not possible to compile clitkAffineRegistrationGenericFilter with the included file clitkTransformUtilities.h
when the include were in the .h file
With include in the .cxx file it works
tbaudier [Fri, 15 Feb 2019 15:38:17 +0000 (16:38 +0100)]
Remove vnl_math dependency into registration codes
Necessary because ITK5 remove vnl_math dependency
tbaudier [Fri, 15 Feb 2019 15:51:35 +0000 (16:51 +0100)]
Remove itkMultiThreader dependency because it does not exist with ITK5
It still compile, does this inslude is necessary?
tbaudier [Fri, 15 Feb 2019 15:43:37 +0000 (16:43 +0100)]
Change itkSimpleFastMutexLock to std::mutex
This is mandatory with ITK5 and c++11
The filters created an itk::Image<itk::SimpleFastMutexLock, dim> but this procedure is not possible with itk::Image<std::mutex, dim>
(cannot copy a mutex)
So I created a mutex alone and lock/unlock it when it is necessary
tbaudier [Fri, 15 Feb 2019 14:05:11 +0000 (15:05 +0100)]
Change vnl_math_abs to std::
This changement is mandatory for ITKv5
All recent compiler are able to compile with std::
tbaudier [Fri, 15 Feb 2019 14:00:38 +0000 (15:00 +0100)]
With ITK 5.0, itk::ProcessObject::VerifyInputInformation are now declared const
tbaudier [Fri, 15 Feb 2019 12:27:02 +0000 (13:27 +0100)]
Change itk version for travis from v5.0b01 to v5.0rc01
The RC version is more actual than the beta version
tbaudier [Fri, 15 Feb 2019 12:23:42 +0000 (13:23 +0100)]
Remove vcl_math calls
In the early days of itk development, many c++ compilers treated
math functions inconsistently. The vcl_math routines provided a
platform independent interface. Now, with modern c++ compilers, math
functions are treated more uniformly. This patch removes the vcl_math
calls. The extra layer provided by vcl is no longer needed and may
even cause problems with newer compilers.
tbaudier [Wed, 13 Feb 2019 09:28:39 +0000 (10:28 +0100)]
Update ggo for clitkMergeSequence
Add version
Update purpose to give more information about the spacing option
tbaudier [Wed, 13 Feb 2019 08:46:50 +0000 (09:46 +0100)]
Add pixel type options for clitkMergeSequence (double and unsigned char)
Indent correctly
tbaudier [Wed, 13 Feb 2019 08:45:53 +0000 (09:45 +0100)]
Change tab to spaces
Indent correctly
tbaudier [Wed, 13 Feb 2019 08:45:08 +0000 (09:45 +0100)]
Change description for clitkMergeSequence
The previous one was a wrong copy of another filter
tbaudier [Thu, 17 Jan 2019 15:34:32 +0000 (16:34 +0100)]
Correct roi name into DicomRTStruct
Replace RoiName by RoiType because into the DicomRTStruct, before, it displayed the RoiName (name of the file) instead of the name of the ROI (RoiType)
tbaudier [Mon, 14 Jan 2019 12:21:02 +0000 (13:21 +0100)]
Add a watcher to file
vv reload automatically a file if it changed on the disk.
The watcher is on the mhd file, and when it send a signal:
we find the item in the data tree corresponding to that file (in the data tree the items are written with an extra 0 at the end of the pathname)
We reload all these items stored in a vector
tbaudier [Fri, 11 Jan 2019 12:43:06 +0000 (13:43 +0100)]
Cosmetic
Remove trailing spaces and indent correctly
tbaudier [Fri, 11 Jan 2019 12:36:24 +0000 (13:36 +0100)]
Comment snoutID
In clitkDicomRTPlan2Gate, I commented the part of code about snout ID because the variable snoutID is not used at all
tbaudier [Fri, 11 Jan 2019 10:58:58 +0000 (11:58 +0100)]
Change paradigm to find files
When we find the files to sort them with itk::GDCMSeriesFileNames, I just have to remove the first ./ if present
Moreover, sliceIndex has to be the sorting vector (it was not correct before)
tbaudier [Fri, 11 Jan 2019 10:56:39 +0000 (11:56 +0100)]
Do not use Series Details
The Serie UID got reading the file corresponds to the less detailed serie UID of the itk::GDCMSeriesFileNames
tbaudier [Fri, 11 Jan 2019 10:55:04 +0000 (11:55 +0100)]
Remove extract_series option
With the itk::GDCMSeriesFileNames, we automatically have the dicom sorted according series, so this option is not necessary anymore.
So I removed the option in the .ggo file and I remove the if conditions.
I add .c_str() to series_UID to remove trailling white spaces
tbaudier [Thu, 20 Dec 2018 12:53:01 +0000 (13:53 +0100)]
Add condition into clitkDicom2Image
The name return by GDCMSeriesFileNames starts by ./ if it is in the current folder or not if not. And the filenames never stat by ./
So I need to remove ./ only if it starts with ./
tbaudier [Thu, 20 Dec 2018 12:08:55 +0000 (13:08 +0100)]
Change dicom file sorting procedure in clitkDicom2Image
In clitkDicom2Image, the sorting of files was based on the slice position but it's not correct when a transformation matrix is set.
It's ok when you open a dicom serie with vv. So I used GDCMSeriesFileNames like with vv to sort filenames correctly
tbaudier [Thu, 20 Dec 2018 10:01:48 +0000 (11:01 +0100)]
Change serie number to serie UID
In clitkDicom2Image, change serie number to serie UID.
Serie UID is more restrictive and better to separate series
Change number to string because series UID is a string
Series UID is better to use itk::GDCMSeriesFileNames
tbaudier [Wed, 19 Dec 2018 14:54:09 +0000 (15:54 +0100)]
Open image, overlay, fusion taking into account the interpolation settings
It reads in vv_settings.txt the status of the interpolation
tbaudier [Wed, 19 Dec 2018 14:53:14 +0000 (15:53 +0100)]
Set vv settings if they are not present when the user open vv
tbaudier [Wed, 19 Dec 2018 14:52:35 +0000 (15:52 +0100)]
Add the use of user parameters in vv_settings
For now, just the interpolation is taken into account
But now, the user car save it's own settings modifying the vv_settings file
tbaudier [Wed, 19 Dec 2018 14:50:37 +0000 (15:50 +0100)]
Debug opening dicom with rotation matrix
With the introduction of the choose in the Image reader to open the dicom with or without the patient coordinate system, I need to pass the value of the patient flag to take into account the transformation matrix
tbaudier [Tue, 11 Dec 2018 08:47:15 +0000 (09:47 +0100)]
Prefer to use link instead of copy for ccIn2p3 data
Before, the job copied data into the temp calculation folder. We prefer to avoid copy of large data, so we use link now
David Sarrut [Tue, 4 Dec 2018 09:18:30 +0000 (10:18 +0100)]
add JOB_ID as alias
David Sarrut [Tue, 4 Dec 2018 07:46:52 +0000 (08:46 +0100)]
Merge branch 'master' of git.creatis.insa-lyon.fr:clitk
tbaudier [Thu, 29 Nov 2018 11:03:12 +0000 (12:03 +0100)]
Merge branch 'master' of https://github.com/open-vv/vv
tbaudier [Thu, 29 Nov 2018 11:02:47 +0000 (12:02 +0100)]
Add clitkScintivolStats
It use to compute statistics for Scintivol project
tbaudier [Tue, 27 Nov 2018 14:56:54 +0000 (15:56 +0100)]
Change N formula
N is the number of primaries and is determine using the value of std, edep and squared edep. If it is null, we look for the next line, etc...
tbaudier [Tue, 27 Nov 2018 14:54:54 +0000 (15:54 +0100)]
Add comment to precise the functionality of the inputs
tbaudier [Mon, 26 Nov 2018 15:49:25 +0000 (16:49 +0100)]
Add double image managment for clitkAffineTransform
By default, the image use Float and did not manage double images. I add a condition to handle double image
tbaudier [Thu, 22 Nov 2018 15:36:11 +0000 (16:36 +0100)]
Debug: correct wrong flag in condition
When the flag patientSystem was introduced in clitkDicom2Image to save the patient matrix, the flag to check the tool has to compute this matrix was not correct
tbaudier [Thu, 15 Nov 2018 15:59:55 +0000 (16:59 +0100)]
Cosmetic
Align all elements in clitkSUVPeak.ggo
tbaudier [Thu, 15 Nov 2018 15:57:53 +0000 (16:57 +0100)]
Add option to define the volume of the filter in clitkSUVPeak in cc
Before, the volume was fixed to 1cc
Now, if the volume option is set, multiply the given volume by 1000 to have in mc
tbaudier [Thu, 15 Nov 2018 15:50:13 +0000 (16:50 +0100)]
Check if mask and input have the same spacing to compute SUVPeak
Before, the output of the SUVPeak was unrealistic with a mask with a spacing different from the input.
Now, check if they have the same spacing. If not, the script raises an error.
I add an option (--allow_resize) to automatically resize the mask according to the input like in the clitkImageStatistics script
tbaudier [Thu, 15 Nov 2018 15:30:21 +0000 (16:30 +0100)]
Cosmetic
Align all elements in ggo file
tbaudier [Thu, 15 Nov 2018 15:25:10 +0000 (16:25 +0100)]
Precise the unite of the bounding box for clitkCropImageFilter
tbaudier [Thu, 15 Nov 2018 15:24:18 +0000 (16:24 +0100)]
Change behavior of clitkCropImage with like option
Before, if we cropped an image like another, the output's origin was set at the origin of the input.
But we prefer to keep the registration correctly, so we prefer to have an output's origin defined to still have the registration between the output and the input.
This is the normal behavior of the itk::PasteImageFilter.
I removed the SetNumberOfRequiredInputs to avoid this error: PasteImageFilter(0x1927770): At least 2 of the first 2 indexed inputs are required but only 1 are specified. The required inputs are expected to be the first inputs.
I add the updateOrigin flag to keep the previous behavior. If the flag is set to On (default is off), the origin of the output is set to the same origin than the input.
I update the description of the filte about this origin managment
tbaudier [Wed, 14 Nov 2018 12:28:25 +0000 (13:28 +0100)]
Merge dose by region uncertainties using Gate uncertainty calculation
Instead of using partial uncertainty, I use the total dose or edep and the square of the dose and edep like
I removed a bash function because it's useless
tbaudier [Tue, 13 Nov 2018 10:41:17 +0000 (11:41 +0100)]
Precise information about RTStruct statistics in comments and output
tbaudier [Tue, 13 Nov 2018 10:40:44 +0000 (11:40 +0100)]
Precise information about SUV peak in comments and output
tbaudier [Tue, 13 Nov 2018 10:07:54 +0000 (11:07 +0100)]
Remove trailing spaces and tab
tbaudier [Tue, 13 Nov 2018 08:21:54 +0000 (09:21 +0100)]
Allow compilation with ITK4.13.0
With initialisation of the smart pointer to NULL, it failed to compile (error of conversion from int to smart pointer). I removed the NULL
tbaudier [Tue, 13 Nov 2018 07:53:42 +0000 (08:53 +0100)]
Merge branch 'master' of git://git.creatis.insa-lyon.fr/clitk
tbaudier [Fri, 9 Nov 2018 08:49:28 +0000 (09:49 +0100)]
Modify mergeDoseByRegion
Before, it summed 2 files to write the result.
But I had to modify it to be able to sum partial std. So I created 3 functions:
-addToPartialResult with the previous code
- addWithoutPartialResult for the first file
- divideUncertaintyResult for the last step
tbaudier [Mon, 29 Oct 2018 13:46:09 +0000 (14:46 +0100)]
Change addition from bash bc to python
Before, with floating number, the script used bc to add numbers. But it failed with scientific notation. I chose to use python to compute it
tbaudier [Tue, 16 Oct 2018 08:42:15 +0000 (10:42 +0200)]
Reindentation of the ggo file
tbaudier [Tue, 16 Oct 2018 08:41:26 +0000 (10:41 +0200)]
Add like option in clitkExtrude tool
Before we had to set size, spacing and origin for the new dimension
But we could want to have the same size, spacing and origin than another image.
So I add the like option
I remove the required for the size option because if like is set , size is not mandatory
I controled that like and origin, size or spacing are not set at the same time
tbaudier [Mon, 15 Oct 2018 10:08:35 +0000 (12:08 +0200)]
Add clitkExtrude tool
With this tool, you can copy the image i N times along the last dimension
tbaudier [Thu, 4 Oct 2018 13:45:32 +0000 (15:45 +0200)]
Convert Drag/Drop opening file function to c++ < c++11
tbaudier [Thu, 4 Oct 2018 12:33:18 +0000 (14:33 +0200)]
Merge branch 'm-pilia-drop_files'
tbaudier [Thu, 4 Oct 2018 12:32:55 +0000 (14:32 +0200)]
Merge branch 'drop_files' of https://github.com/m-pilia/vv into m-pilia-drop_files
tbaudier [Fri, 21 Sep 2018 07:58:20 +0000 (09:58 +0200)]
Remove verbose for travis
When untar cmake
tbaudier [Fri, 21 Sep 2018 07:46:59 +0000 (09:46 +0200)]
Update QVTKWidget to QVTKOpenGLNativeWidget for VTK > 8.1
tbaudier [Wed, 19 Sep 2018 08:09:44 +0000 (10:09 +0200)]
Merge branch 'master' of https://github.com/open-vv/vv
tbaudier [Tue, 18 Sep 2018 13:55:24 +0000 (15:55 +0200)]
Ensure compatibility with ITK < 4.12 for throw exception
tbaudier [Tue, 18 Sep 2018 13:54:50 +0000 (15:54 +0200)]
Upgrade cmake version to >3.10 for ITK 5
tbaudier [Tue, 18 Sep 2018 09:40:39 +0000 (11:40 +0200)]
Add VTK 8.1.1 and ITK 5 beta
Clean travis script 4/n
tbaudier [Tue, 18 Sep 2018 06:48:35 +0000 (08:48 +0200)]
Add VTK 8.1.1 and ITK 5 beta
Clean travis script 3/n
tbaudier [Mon, 17 Sep 2018 15:00:39 +0000 (17:00 +0200)]
Add VTK 8.1.1 and ITK 5 beta
Clean travis script 2/n
tbaudier [Mon, 17 Sep 2018 14:49:43 +0000 (16:49 +0200)]
Add VTK 8.1.1 and ITK 5 beta
Clean travis script
Martino Pilia [Tue, 11 Sep 2018 18:47:09 +0000 (20:47 +0200)]
Open files by dropping them inside the window
Set the window to allow drag events entering it, and add an handler to
open files dropped within the window.
tbaudier [Fri, 7 Sep 2018 09:35:53 +0000 (11:35 +0200)]
Remove clitkAffineRegistrationLib compilation when CLTK_USE_REGISTRATION is OFF
tbaudier [Fri, 7 Sep 2018 09:18:45 +0000 (11:18 +0200)]
Ensure compatibility with newer version of VTK9
tbaudier [Fri, 7 Sep 2018 09:14:07 +0000 (11:14 +0200)]
VTK remove ImmediateModeRendering due to
Does not make sense for OpenGL2 and is not implemented
tbaudier [Fri, 7 Sep 2018 08:46:33 +0000 (10:46 +0200)]
Add AffineRegistration library to avoid compilation error
With a lot of cores, clitkElastixTransformToMatrix (that need clitkAffineTransform) can be compiled before clitkAffineTransform
And the gengetopt of clitkAffineTransform is not compiled leading to an error
tbaudier [Fri, 7 Sep 2018 08:44:20 +0000 (10:44 +0200)]
Remove throw to avoid warning with c++11
tbaudier [Fri, 7 Sep 2018 08:14:09 +0000 (10:14 +0200)]
Remove throw to avoid warnings with c++11
tbaudier [Tue, 7 Aug 2018 11:09:34 +0000 (13:09 +0200)]
Update to enable GDCMv3
tbaudier [Tue, 7 Aug 2018 08:26:42 +0000 (10:26 +0200)]
Ensure compatibility with ITK5
Change NumberOfThreads to NumberOfWorkUnits
tbaudier [Mon, 6 Aug 2018 14:18:26 +0000 (16:18 +0200)]
cosmetic
tbaudier [Fri, 3 Aug 2018 08:02:30 +0000 (10:02 +0200)]
Debug fusion display value for very small value
Use scientific representation
David Sarrut [Thu, 2 Aug 2018 06:01:56 +0000 (08:01 +0200)]
Merge branch 'master' of git.creatis.insa-lyon.fr:clitk
tbaudier [Wed, 1 Aug 2018 12:29:26 +0000 (14:29 +0200)]
cosmetic and remove useless part in clitkSpect2Dicom
tbaudier [Wed, 1 Aug 2018 09:24:05 +0000 (11:24 +0200)]
Remove ssh connection to creatis cluster from ccIn2p3
tbaudier [Tue, 31 Jul 2018 15:01:23 +0000 (17:01 +0200)]
Rename clitkImage2DicomSeries to clitkSpect2Dicom
tbaudier [Tue, 31 Jul 2018 14:46:22 +0000 (16:46 +0200)]
Functionnal version
tbaudier [Mon, 30 Jul 2018 09:58:51 +0000 (11:58 +0200)]
Ensure to have the correct name for dicom files
tbaudier [Mon, 30 Jul 2018 08:14:22 +0000 (10:14 +0200)]
Add description
tbaudier [Mon, 30 Jul 2018 07:54:33 +0000 (09:54 +0200)]
cosmetic
tbaudier [Mon, 30 Jul 2018 07:53:42 +0000 (09:53 +0200)]
cosmetic
tbaudier [Fri, 27 Jul 2018 12:22:03 +0000 (14:22 +0200)]
Merge branch 'master' of https://github.com/open-vv/vv
tbaudier [Fri, 27 Jul 2018 12:18:29 +0000 (14:18 +0200)]
Merge branch 'master' of https://github.com/open-vv/vv
tbaudier [Fri, 27 Jul 2018 12:01:08 +0000 (14:01 +0200)]
Merge branch 'clitkImage2Dicom'
tbaudier [Thu, 26 Jul 2018 12:46:52 +0000 (14:46 +0200)]
cosmetic
Remove tabs
tbaudier [Wed, 25 Jul 2018 09:13:20 +0000 (11:13 +0200)]
Add statistical tool to compute speed up for gate jobs
tbaudier [Fri, 13 Jul 2018 12:40:42 +0000 (14:40 +0200)]
Correct merger in gate_power_merge
tbaudier [Fri, 13 Jul 2018 08:33:17 +0000 (10:33 +0200)]
Add merger for DoseByRegions
tbaudier [Fri, 13 Jul 2018 08:32:39 +0000 (10:32 +0200)]
Change default value in clitkDicomRTStruct2ImageFilter for vtk mesh
tbaudier [Tue, 10 Jul 2018 13:27:03 +0000 (15:27 +0200)]
Add clitkChangeDicomTag tool