]> Creatis software - clitk.git/log
clitk.git
12 years agoMerge branch 'master' of git.creatis.insa-lyon.fr:clitk
Romulo Pinho [Fri, 27 Jan 2012 15:09:49 +0000 (16:09 +0100)]
Merge branch 'master' of git.creatis.insa-lyon.fr:clitk

12 years agocorrected bug in fusion opacity with double values
Romulo Pinho [Fri, 27 Jan 2012 15:09:09 +0000 (16:09 +0100)]
corrected bug in fusion opacity with double values

12 years agocorrected bug in fusion with double values
Romulo Pinho [Fri, 27 Jan 2012 15:05:06 +0000 (16:05 +0100)]
corrected bug in fusion with double values

12 years agobug in mhd 4D creation
Romulo Pinho [Thu, 26 Jan 2012 14:35:00 +0000 (15:35 +0100)]
bug in mhd 4D creation

12 years agoComposeVF with type 0 as default
Romulo Pinho [Thu, 26 Jan 2012 13:06:44 +0000 (14:06 +0100)]
ComposeVF with type 0 as default

12 years agocorrection in ComposeVF options
Romulo Pinho [Thu, 26 Jan 2012 13:05:51 +0000 (14:05 +0100)]
correction in ComposeVF options

12 years agoaccepts suffix for 4D mhd creation
Romulo Pinho [Thu, 26 Jan 2012 12:46:11 +0000 (13:46 +0100)]
accepts suffix for 4D mhd creation

12 years agochanges in CoeffsToDVF interface
Romulo Pinho [Wed, 25 Jan 2012 14:47:22 +0000 (15:47 +0100)]
changes in CoeffsToDVF interface

- affected tools...

12 years agonew tool: clitkCoeffsToDVF
Romulo Pinho [Wed, 25 Jan 2012 14:46:23 +0000 (15:46 +0100)]
new tool: clitkCoeffsToDVF

- converts a BLUT-coefficient image to a DVF

12 years agomore robust clitkExtractLung
Romulo Pinho [Tue, 24 Jan 2012 13:50:43 +0000 (14:50 +0100)]
more robust clitkExtractLung

- quits with exception when no seed is found for trachea

12 years agorefactoring...
Romulo Pinho [Thu, 19 Jan 2012 16:51:00 +0000 (17:51 +0100)]
refactoring...

- Put coeff to dvf function in separate file, as a global function
- Changed affected files/classes

12 years agoimage warping using B-Spline coefficients
Romulo Pinho [Thu, 19 Jan 2012 16:39:42 +0000 (17:39 +0100)]
image warping using B-Spline coefficients

- uses the resolution of the input image for the output

12 years agoInvert VF from B-Spline coefficients
Romulo Pinho [Wed, 18 Jan 2012 17:28:16 +0000 (18:28 +0100)]
Invert VF from B-Spline coefficients

- Interpolate VF first, from coeffs, using --like image

12 years agoVF composition with BSpline coefficients
Romulo Pinho [Wed, 18 Jan 2012 16:51:04 +0000 (17:51 +0100)]
VF composition with BSpline coefficients

- output resolution taken from --like image

12 years agoinvert Vf on given image grid with resampler
Romulo Pinho [Tue, 10 Jan 2012 15:36:21 +0000 (16:36 +0100)]
invert Vf on given image grid with resampler

- linear interpolation (itk resampler's default)
- undoes previous version

12 years agoinvert VF on given image grid
Romulo Pinho [Tue, 10 Jan 2012 14:18:12 +0000 (15:18 +0100)]
invert VF on given image grid

- with --like option

12 years agoAdapted crop for vector fields with partial specialization to generate
Simon Rit [Wed, 4 Jan 2012 15:48:10 +0000 (16:48 +0100)]
Adapted crop for vector fields with partial specialization to generate
exceptions for AutoCrop of VF

12 years agoProvide ADD_DEFAULT_VEC_IMAGE_TYPES for generic VF filters
Simon Rit [Wed, 4 Jan 2012 15:47:51 +0000 (16:47 +0100)]
Provide ADD_DEFAULT_VEC_IMAGE_TYPES for generic VF filters

12 years agoBUG Don't try to change the VF color on cancel.
Vivien Delmon [Wed, 28 Dec 2011 13:27:46 +0000 (14:27 +0100)]
BUG Don't try to change the VF color on cancel.

- Test the validity of the color returned by the QColorDialog before
  changing the VF color.

12 years agoAdd Overlay properties to SaveState / ReadState
Vivien Delmon [Tue, 27 Dec 2011 14:49:12 +0000 (15:49 +0100)]
Add Overlay properties to SaveState / ReadState

- Use vvSlicerManagers to Get/Set Overlay properties.

12 years agoAdd Fusion properties to SaveState / ReadState
Vivien Delmon [Tue, 27 Dec 2011 14:35:44 +0000 (15:35 +0100)]
Add Fusion properties to SaveState / ReadState

- Add constness on QTreeWidgetItem.
- Use vvSlicerManagers to Get/Set Fusion properties.

12 years agoAdd constness some getters
Vivien Delmon [Tue, 27 Dec 2011 14:30:50 +0000 (15:30 +0100)]
Add constness some getters

12 years agoRemove tmp files
Vivien Delmon [Tue, 27 Dec 2011 12:42:20 +0000 (13:42 +0100)]
Remove tmp files

- Remove tmp files after executing the script
- use mktemp instead of /tmp/$RANDOM

13 years agomidpP: combine VF's after inverting and composing
Romulo Pinho [Thu, 22 Dec 2011 16:50:48 +0000 (17:50 +0100)]
midpP: combine VF's after inverting and composing

13 years agouse of coefficient images in mid-P creation
Romulo Pinho [Thu, 22 Dec 2011 13:38:34 +0000 (14:38 +0100)]
use of coefficient images in mid-P creation

13 years ago--focal_origin works again
Romulo Pinho [Tue, 20 Dec 2011 17:24:36 +0000 (18:24 +0100)]
--focal_origin works again

13 years agoPossibility to add a VTK image to vvImage
Romulo Pinho [Tue, 20 Dec 2011 17:24:01 +0000 (18:24 +0100)]
Possibility to add a VTK image to vvImage

13 years agomore robust motion mask script
Romulo Pinho [Mon, 19 Dec 2011 13:22:17 +0000 (14:22 +0100)]
more robust motion mask script

13 years agodicom structure in cmd line
Romulo Pinho [Fri, 16 Dec 2011 10:55:00 +0000 (11:55 +0100)]
dicom structure in cmd line

- --contour <FILE>
- in the same way as overlay/fusion/vf

13 years agomotion masks with and without bands
Romulo Pinho [Thu, 15 Dec 2011 17:43:42 +0000 (18:43 +0100)]
motion masks with and without bands

13 years agoAdapt CMakeLists to include it from other projects
Vivien Delmon [Wed, 14 Dec 2011 13:18:40 +0000 (14:18 +0100)]
Adapt CMakeLists to include it from other projects

13 years agoRemove useless common.cmake inclusions
Simon Rit [Wed, 14 Dec 2011 12:50:13 +0000 (13:50 +0100)]
Remove useless common.cmake inclusions

13 years agoAdd VTK_LIBRARIES variable for vtk < 5.8.0
Vivien Delmon [Wed, 14 Dec 2011 09:07:24 +0000 (10:07 +0100)]
Add VTK_LIBRARIES variable for vtk < 5.8.0

Add VTK_LIBRARIES variable for vtk < 5.8.0 and use it.

13 years agomidp masks use new clitkExtractLung version
Romulo Pinho [Tue, 13 Dec 2011 16:38:53 +0000 (17:38 +0100)]
midp masks use new clitkExtractLung version

13 years agonew 4D files as output of midp script
Romulo Pinho [Tue, 13 Dec 2011 16:34:27 +0000 (17:34 +0100)]
new 4D files as output of midp script

13 years agoFactorize CMakeLists
Vivien Delmon [Tue, 13 Dec 2011 13:06:19 +0000 (14:06 +0100)]
Factorize CMakeLists

- Factorize CMakeLists to allow their use in other projects.

13 years agoitkv4 migration
Romulo Pinho [Tue, 13 Dec 2011 09:49:47 +0000 (10:49 +0100)]
itkv4 migration

13 years agoExtractLung - Small corrections in verbose mode
Romulo Pinho [Tue, 13 Dec 2011 09:35:10 +0000 (10:35 +0100)]
ExtractLung - Small corrections in verbose mode

13 years agoMerge branch 'master' of tux.creatis.insa-lyon.fr:clitk
Vivien Delmon [Mon, 12 Dec 2011 17:07:26 +0000 (18:07 +0100)]
Merge branch 'master' of tux.creatis.insa-lyon.fr:clitk

13 years agoRevert "itkv4 migration use itk::ThreadIdType"
Vivien Delmon [Mon, 12 Dec 2011 17:07:11 +0000 (18:07 +0100)]
Revert "itkv4 migration use itk::ThreadIdType"

This reverts commit a6957c4825e83c61b977ec316dd841878617ffbd.

13 years agoTrachea finding algorithm
Romulo Pinho [Mon, 12 Dec 2011 14:31:49 +0000 (15:31 +0100)]
Trachea finding algorithm

- version used in LOLA11
- preserved original version
- new "type" parameter to choose between algorithms
- algorithm-specific params

13 years agoworking version of new trachea finding algo
Romulo Pinho [Mon, 12 Dec 2011 12:33:21 +0000 (13:33 +0100)]
working version of new trachea finding algo

- the one used in LOLA11

13 years agoOptional options corrected
Gauthier Bouilhol [Mon, 12 Dec 2011 10:56:50 +0000 (11:56 +0100)]
Optional options corrected

13 years agoMerge branch 'master' of tux.creatis.insa-lyon.fr:clitk
Vivien Delmon [Thu, 8 Dec 2011 13:20:35 +0000 (14:20 +0100)]
Merge branch 'master' of tux.creatis.insa-lyon.fr:clitk

13 years agoFixed fusion panel size and change default threshold values
Vivien Delmon [Thu, 8 Dec 2011 13:16:33 +0000 (14:16 +0100)]
Fixed fusion panel size and change default threshold values

+ Span image value on more columns to avoid interface motion when values
  have more or less digits.
+ Use 1% as default threshold value and 30% as default transparency
  value.

13 years agoAdded patient mask resampling
dbcache [Thu, 8 Dec 2011 12:38:52 +0000 (13:38 +0100)]
Added patient mask resampling

- corrects problem when using clitkCombineImage in the mid-P calcs

13 years agoApplied clitk indentation
Simon Rit [Thu, 8 Dec 2011 10:05:30 +0000 (11:05 +0100)]
Applied clitk indentation

13 years agoGateAsciiImageIO is now cross-platform using itksys::RegularExpression
Simon Rit [Thu, 8 Dec 2011 10:03:15 +0000 (11:03 +0100)]
GateAsciiImageIO is now cross-platform using itksys::RegularExpression

13 years agoFixed MSVC warning
Simon Rit [Mon, 5 Dec 2011 07:58:31 +0000 (08:58 +0100)]
Fixed MSVC warning

13 years agoDefine mkstemp for MSVC. Not sure if it also works for other compilers
Simon Rit [Mon, 5 Dec 2011 07:57:38 +0000 (08:57 +0100)]
Define mkstemp for MSVC. Not sure if it also works for other compilers
on Windows

13 years agoGate text file I/O is not cross-platform due to regex, compile only on unix
Simon Rit [Mon, 5 Dec 2011 07:56:46 +0000 (08:56 +0100)]
Gate text file I/O is not cross-platform due to regex, compile only on unix

13 years agoAdd quotes in case variables are not defined
Simon Rit [Sun, 4 Dec 2011 17:18:08 +0000 (18:18 +0100)]
Add quotes in case variables are not defined

13 years agoUse the gnugetopt.h header part of gengetopt instead of cygwin's
Simon Rit [Sun, 4 Dec 2011 17:06:31 +0000 (18:06 +0100)]
Use the gnugetopt.h header part of gengetopt instead of cygwin's

13 years agoSubdirectory filters has been removed
Simon Rit [Sun, 4 Dec 2011 16:35:50 +0000 (17:35 +0100)]
Subdirectory filters has been removed

13 years agoRemoved warnings
Simon Rit [Sun, 4 Dec 2011 14:04:46 +0000 (15:04 +0100)]
Removed warnings

13 years agoitk4 migration
Vivien Delmon [Thu, 1 Dec 2011 10:49:01 +0000 (11:49 +0100)]
itk4 migration

- m_Parameters disapeared in itk4. Don't use it in our
  ImageToImageMetric.

13 years agoRemove warnings
Vivien Delmon [Wed, 30 Nov 2011 09:45:50 +0000 (10:45 +0100)]
Remove warnings

- Remove warnings with -Wall
  It remains some warning about gengetopt generated files
- Use ImageDimension instead of 3 in some filters

13 years agoBug #650 crash with --fusion and --overlay
Vivien Delmon [Tue, 29 Nov 2011 14:23:31 +0000 (15:23 +0100)]
Bug #650 crash with --fusion and --overlay

- Check if the file exists before opening it

13 years agoBUG seed_arg was used instead of seedRadius_arg
Vivien Delmon [Tue, 29 Nov 2011 12:56:33 +0000 (13:56 +0100)]
BUG seed_arg was used instead of seedRadius_arg

13 years agoAdd seedRadius option to clitkRegionGrowing
Vivien Delmon [Tue, 29 Nov 2011 11:03:49 +0000 (12:03 +0100)]
Add seedRadius option to clitkRegionGrowing

- Add seedRadius option to clitkRegionGrowing to allow ball of seeds
  instead of single pixel seed.

13 years agoreturned normal function to overlay menu origin/master
Romulo Pinho [Wed, 23 Nov 2011 15:45:22 +0000 (16:45 +0100)]
returned normal function to overlay menu

13 years agoitkv4 migration use itk::ThreadIdType
Vivien Delmon [Fri, 18 Nov 2011 16:37:54 +0000 (17:37 +0100)]
itkv4 migration use itk::ThreadIdType

- Add a typedef on unsigned int for itk 3.20 compatibility
- Use itk::ThreadIdType where needed

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
Vivien Delmon [Thu, 17 Nov 2011 15:39:00 +0000 (16:39 +0100)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoAdd missing basename call after.
Vivien Delmon [Thu, 17 Nov 2011 15:38:21 +0000 (16:38 +0100)]
Add missing basename call after.

13 years agoCorrected bug with button All: W/L was read from spin box which
Simon Rit [Thu, 17 Nov 2011 12:06:59 +0000 (13:06 +0100)]
Corrected bug with button All: W/L was read from spin box which
resolution is limited by text

13 years agoCorrected tab key bugs for one image and reverse order with shift
Simon Rit [Thu, 17 Nov 2011 12:02:32 +0000 (13:02 +0100)]
Corrected tab key bugs for one image and reverse order with shift

13 years agoMotion mask without resampling
Vivien Delmon [Thu, 17 Nov 2011 09:52:49 +0000 (10:52 +0100)]
Motion mask without resampling

- Remove resampling if create_midP_masks-2.0.sh is called without
  resampling arguments

13 years agoBLUT transform in threaded mode
Romulo Pinho [Wed, 16 Nov 2011 14:47:36 +0000 (15:47 +0100)]
BLUT transform in threaded mode

- Guarantees that the treaded version of the class will be invoked
+ obs: this change has no effect on the current version (of clitkBLUTDIR) yet, it's just for consistenty with similar changes made in clitkResampleImage

13 years agonew VV option: --linkall
Romulo Pinho [Wed, 16 Nov 2011 14:45:50 +0000 (15:45 +0100)]
new VV option: --linkall

- links all images given in the command line

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
Vivien Delmon [Wed, 16 Nov 2011 10:52:55 +0000 (11:52 +0100)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoBUG with gcc 4.1.2 unnecessary typename
Vivien Delmon [Wed, 16 Nov 2011 09:26:29 +0000 (10:26 +0100)]
BUG with gcc 4.1.2 unnecessary typename

- remove unnecessary typename

13 years agoMerge branch 'testblut'; commit 'c134c94'
Romulo Pinho [Wed, 16 Nov 2011 09:25:42 +0000 (10:25 +0100)]
Merge branch 'testblut'; commit 'c134c94'

13 years agochange in midP script to create 4D warped image
Romulo Pinho [Wed, 16 Nov 2011 09:22:37 +0000 (10:22 +0100)]
change in midP script to create 4D warped image

13 years agoCat image tool
Simon Rit [Thu, 10 Nov 2011 17:01:53 +0000 (18:01 +0100)]
Cat image tool

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
Simon Rit [Thu, 10 Nov 2011 15:11:58 +0000 (16:11 +0100)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoadded target image translation in gamma index
pierre gueth [Tue, 8 Nov 2011 10:17:55 +0000 (11:17 +0100)]
added target image translation in gamma index

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
Vivien Delmon [Mon, 7 Nov 2011 16:53:24 +0000 (17:53 +0100)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoBe compatible with itk 3.20 with debug on
Vivien Delmon [Mon, 7 Nov 2011 16:53:01 +0000 (17:53 +0100)]
Be compatible with itk 3.20 with debug on

13 years agoBLUT interpolation is really fast ... again!
Romulo Pinho [Mon, 7 Nov 2011 15:45:34 +0000 (16:45 +0100)]
BLUT interpolation is really fast ... again!

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
Simon Rit [Fri, 4 Nov 2011 09:44:56 +0000 (10:44 +0100)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoMerge branch 'master' of /home/dsarrut/clitk3.server
David Sarrut [Fri, 4 Nov 2011 09:36:31 +0000 (10:36 +0100)]
Merge branch 'master' of /home/dsarrut/clitk3.server

13 years agoremove gitignore
Vivien Delmon [Fri, 4 Nov 2011 09:35:09 +0000 (10:35 +0100)]
remove gitignore

13 years agoadd first version of LabelOverlapMeasuresImageFilter (dice computation)
David Sarrut [Fri, 4 Nov 2011 09:31:35 +0000 (10:31 +0100)]
add first version of LabelOverlapMeasuresImageFilter (dice computation)

13 years agoChange output display
David Sarrut [Fri, 4 Nov 2011 09:28:05 +0000 (10:28 +0100)]
Change output display

13 years agoComment CricoidCartilag limit (put in support)
David Sarrut [Fri, 4 Nov 2011 09:27:41 +0000 (10:27 +0100)]
Comment CricoidCartilag limit (put in support)

13 years agoNew way to extract support
David Sarrut [Fri, 4 Nov 2011 09:27:12 +0000 (10:27 +0100)]
New way to extract support

13 years agoSimplify 4R 4L seg
David Sarrut [Fri, 4 Nov 2011 09:26:51 +0000 (10:26 +0100)]
Simplify 4R 4L seg

13 years agoSecond version of rel pos analyzer
David Sarrut [Fri, 4 Nov 2011 09:26:11 +0000 (10:26 +0100)]
Second version of rel pos analyzer

13 years agoRemove old stuff
David Sarrut [Fri, 4 Nov 2011 09:25:41 +0000 (10:25 +0100)]
Remove old stuff

13 years agoNew ComputeOptimalThreshold
David Sarrut [Fri, 4 Nov 2011 09:25:29 +0000 (10:25 +0100)]
New ComputeOptimalThreshold

13 years agoCorrect angle units
David Sarrut [Fri, 4 Nov 2011 09:25:11 +0000 (10:25 +0100)]
Correct angle units

13 years agoTo be consistant, crop strictly above (not above or equal)
David Sarrut [Fri, 4 Nov 2011 09:24:59 +0000 (10:24 +0100)]
To be consistant, crop strictly above (not above or equal)

13 years agoSecond version of databse of rel pos
David Sarrut [Fri, 4 Nov 2011 09:24:20 +0000 (10:24 +0100)]
Second version of databse of rel pos

13 years agoFirst version of rel pos database builder
David Sarrut [Fri, 4 Nov 2011 09:23:03 +0000 (10:23 +0100)]
First version of rel pos database builder

13 years agoFirst version of the builder of relpos database
David Sarrut [Fri, 4 Nov 2011 09:22:45 +0000 (10:22 +0100)]
First version of the builder of relpos database

13 years agoExplicit units for Angle (rad or deg)
David Sarrut [Fri, 4 Nov 2011 09:21:58 +0000 (10:21 +0100)]
Explicit units for Angle (rad or deg)

13 years agocorrections in mid-P scripts
Romulo Pinho [Fri, 4 Nov 2011 08:32:30 +0000 (09:32 +0100)]
corrections in mid-P scripts

- when checking clitk tools' return values

13 years agoclitkExtractLung - new option
Romulo Pinho [Thu, 3 Nov 2011 17:07:31 +0000 (18:07 +0100)]
clitkExtractLung - new option

- doNotSeparateLungs

13 years agomore refined abort-on-exception mechanism
Romulo Pinho [Thu, 3 Nov 2011 15:56:52 +0000 (16:56 +0100)]
more refined abort-on-exception mechanism

- new macro defined in clitkCommon.h
- abort execution with a proper return code
- only used in tools related to mid-P calculation, for now
- mid-P scripts interpret return codes

13 years agoSecond version of clitkRelativePositionAnalyzer
David Sarrut [Thu, 27 Oct 2011 13:57:03 +0000 (15:57 +0200)]
Second version of clitkRelativePositionAnalyzer