Internal:PODM CNF - Revision history

Ctsolakis at 21:39, 10 May 2019

2019-05-10T21:39:34Z

← Older revision		Revision as of 16:39, 10 May 2019
Line 1:		Line 1:
	= Things TODO =		= Things TODO =
	# Create scripts to run the image easily. <span style="font-size:~~21px~~">✔</span>		# Create scripts to run the image easily. <span style="font-size:2px">✔</span>
	# Test:		# Test:
	## Linux <span style="font-size:21px">✔</span>		## Linux <span style="font-size:21px">✔</span>
Line 12:		Line 12:
	# add Volume grading command line option (ON and OFF for now) ( right now there is a macro, convert it to input flag OFF by default) <span style="font-size:21px">✔</span>		# add Volume grading command line option (ON and OFF for now) ( right now there is a macro, convert it to input flag OFF by default) <span style="font-size:21px">✔</span>
	# nrrd images do not visualize well in paraview -> add convert_image tool in the docker image. ( available at /RC/group/RC_NIKOS/Christos/convert_image.git ) so that the users can convert their raw data and visualize them in paraview, add runscript (or option in runscript) for that<span style="font-size:21px">✔</span>		# nrrd images do not visualize well in paraview -> add convert_image tool in the docker image. ( available at /RC/group/RC_NIKOS/Christos/convert_image.git ) so that the users can convert their raw data and visualize them in paraview, add runscript (or option in runscript) for that<span style="font-size:21px">✔</span>
	# ~~add~~ memory limit flag for docker inside the python script		# Add memory limit flag for docker inside the python script
			## The command --memory for docker =limits only physical memory not swap , using it make PODM to use swap. Constraning swap does not seem to work.
			# No (easy) way to kill the script and the docker instance (system signals ?)
			# Set up version tracking (on docker images ? , in code embed git sha in a header during compilation and print it during execution)
	# Create User Documentation <span style="font-size:21px">✔</span>		# Create User Documentation <span style="font-size:21px">✔</span>
	# explain better delta ?		# explain better delta ?
	# Clean up text output <span style="font-size:21px">✔</span>		# Clean up text output <span style="font-size:21px">✔</span>
	# segmentation can be easily be implemented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter] (maybe also linear interpolation ?) (low priority)		# segmentation can be easily be implemented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter] (maybe also linear interpolation ?) (low priority)

Ctsolakis at 21:36, 10 May 2019

2019-05-10T21:36:03Z

← Older revision		Revision as of 16:36, 10 May 2019
Line 1:		Line 1:
	= Things TODO =		= Things TODO =
	# Create scripts ~~native to the platform~~ to run the image easily.		# Create scripts to run the image easily. <span style="font-size:21px">✔</span>
	# Test on Linux, Windows ~~and~~ MacOS		# Test:
	# Add Linear Interpolation Code as default output		## Linux <span style="font-size:21px">✔</span>
	## Code is ready need to be integrated with PODM		## Windows <span style="font-size:21px">✔</span>
	# Segment automatically nrrd data		## MacOS
	## i.e. iterate with ITK Gajik's image and convert values !=0 -> 1		# Add Linear Interpolation Code as default output <span style="font-size:21px">✔</span>
	## Should be done as preproceccing step in PODM and it should be ON by default		## Code is ready need to be integrated with PODM <span style="font-size:21px">✔</span>
	# add Volume grading command line option (ON and OFF for now) ( right now there is a macro, convert it to input flag OFF by default)		# Segment automatically nrrd data <span style="font-size:21px">✔</span>
	# nrrd images do not visualize well in paraview -> add convert_image tool in the docker image. ( available at /RC/group/RC_NIKOS/Christos/convert_image.git ) so that the users can convert their raw data and visualize them in paraview, add runscript (or option in runscript) for that		## i.e. iterate with ITK Gajik's image and convert values !=0 -> 1 <span style="font-size:21px">✔</span>
			## Should be done as preproceccing step in PODM and it should be ON by default <span style="font-size:21px">✔</span>
			# add Volume grading command line option (ON and OFF for now) ( right now there is a macro, convert it to input flag OFF by default) <span style="font-size:21px">✔</span>
			# nrrd images do not visualize well in paraview -> add convert_image tool in the docker image. ( available at /RC/group/RC_NIKOS/Christos/convert_image.git ) so that the users can convert their raw data and visualize them in paraview, add runscript (or option in runscript) for that<span style="font-size:21px">✔</span>
	# add memory limit flag for docker inside the python script		# add memory limit flag for docker inside the python script
	# Create User Documentation		# Create User Documentation <span style="font-size:21px">✔</span>
	# explain better delta ?		# explain better delta ?
	# Clean up text output ~~(low priority)~~		# Clean up text output <span style="font-size:21px">✔</span>
	# segmentation can be easily be implemented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter] (maybe also linear interpolation ?) (low priority)		# segmentation can be easily be implemented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter] (maybe also linear interpolation ?) (low priority)

Ctsolakis at 22:34, 7 May 2019

2019-05-07T22:34:17Z

← Older revision		Revision as of 17:34, 7 May 2019
Line 9:		Line 9:
	# add Volume grading command line option (ON and OFF for now) ( right now there is a macro, convert it to input flag OFF by default)		# add Volume grading command line option (ON and OFF for now) ( right now there is a macro, convert it to input flag OFF by default)
	# nrrd images do not visualize well in paraview -> add convert_image tool in the docker image. ( available at /RC/group/RC_NIKOS/Christos/convert_image.git ) so that the users can convert their raw data and visualize them in paraview, add runscript (or option in runscript) for that		# nrrd images do not visualize well in paraview -> add convert_image tool in the docker image. ( available at /RC/group/RC_NIKOS/Christos/convert_image.git ) so that the users can convert their raw data and visualize them in paraview, add runscript (or option in runscript) for that
			# add memory limit flag for docker inside the python script
	# Create User Documentation		# Create User Documentation
	# explain better delta ?		# explain better delta ?
	# Clean up text output (low priority)		# Clean up text output (low priority)
	# segmentation can be easily be implemented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter] (maybe also linear interpolation ?) (low priority)		# segmentation can be easily be implemented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter] (maybe also linear interpolation ?) (low priority)

Ctsolakis at 15:48, 6 May 2019

2019-05-06T15:48:32Z

← Older revision		Revision as of 10:48, 6 May 2019
Line 8:		Line 8:
	## Should be done as preproceccing step in PODM and it should be ON by default		## Should be done as preproceccing step in PODM and it should be ON by default
	# add Volume grading command line option (ON and OFF for now) ( right now there is a macro, convert it to input flag OFF by default)		# add Volume grading command line option (ON and OFF for now) ( right now there is a macro, convert it to input flag OFF by default)
			# nrrd images do not visualize well in paraview -> add convert_image tool in the docker image. ( available at /RC/group/RC_NIKOS/Christos/convert_image.git ) so that the users can convert their raw data and visualize them in paraview, add runscript (or option in runscript) for that
	# Create User Documentation		# Create User Documentation
	# explain better delta ?		# explain better delta ?
	# Clean up text output (low priority)		# Clean up text output (low priority)
	# segmentation can be easily be implemented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter] (maybe also linear interpolation ?) (low priority)		# segmentation can be easily be implemented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter] (maybe also linear interpolation ?) (low priority)

Ctsolakis at 21:24, 3 May 2019

2019-05-03T21:24:30Z

← Older revision		Revision as of 16:24, 3 May 2019
Line 8:		Line 8:
	## Should be done as preproceccing step in PODM and it should be ON by default		## Should be done as preproceccing step in PODM and it should be ON by default
	# add Volume grading command line option (ON and OFF for now) ( right now there is a macro, convert it to input flag OFF by default)		# add Volume grading command line option (ON and OFF for now) ( right now there is a macro, convert it to input flag OFF by default)
	~~# linear interpolation and segmenetation can be easily be implemented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter]~~
	# Create User Documentation		# Create User Documentation
	# explain better delta ?		# explain better delta ?
	# Clean up text output (low priority)		# Clean up text output (low priority)
			# segmentation can be easily be implemented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter] (maybe also linear interpolation ?) (low priority)

Ctsolakis at 19:36, 2 May 2019

2019-05-02T19:36:09Z

← Older revision		Revision as of 14:36, 2 May 2019
Line 6:		Line 6:
	# Segment automatically nrrd data		# Segment automatically nrrd data
	## i.e. iterate with ITK Gajik's image and convert values !=0 -> 1		## i.e. iterate with ITK Gajik's image and convert values !=0 -> 1
	## ~~can~~ be done as preproceccing step in PODM ~~dhould~~ be on by default		## Should be done as preproceccing step in PODM and it should be ON by default
	# add Volume grading command line option (ON and OFF for now) ( right now there is a macro, convert it to input flag OFF by default)		# add Volume grading command line option (ON and OFF for now) ( right now there is a macro, convert it to input flag OFF by default)
	# linear interpolation and segmenetation can be easily be implemented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter]		# linear interpolation and segmenetation can be easily be implemented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter]

Ctsolakis at 18:14, 2 May 2019

2019-05-02T18:14:18Z

← Older revision		Revision as of 13:14, 2 May 2019
Line 1:		Line 1:
	= Things TODO =		= Things TODO =
			# Create scripts native to the platform to run the image easily.
			# Test on Linux, Windows and MacOS
	# Add Linear Interpolation Code as default output		# Add Linear Interpolation Code as default output
	## Code is ready need to be integrated with PODM		## Code is ready need to be integrated with PODM
	# Segment automatically nrrd data		# Segment automatically nrrd data
	## i.e. iterate with ITK Gajik's image and convert values !=0 -> 1		## i.e. iterate with ITK Gajik's image and convert values !=0 -> 1
	# add Volume grading command line option( ON and OFF for now)		## can be done as preproceccing step in PODM dhould be on by default
			# add Volume grading command line option (ON and OFF for now) ( right now there is a macro, convert it to input flag OFF by default)
			# linear interpolation and segmenetation can be easily be implemented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter]
			# Create User Documentation
	# explain better delta ?		# explain better delta ?
	~~# linear interpolation and segmenetation can be easily be implented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter]~~
	~~# Create scripts native to the platform to run the image easily.~~
	~~# Test on Linux, Windows and MacOS~~
	~~# Create User Documentation~~
	# Clean up text output (low priority)		# Clean up text output (low priority)

Ctsolakis at 18:10, 2 May 2019

2019-05-02T18:10:18Z

← Older revision		Revision as of 13:10, 2 May 2019
Line 6:		Line 6:
	# add Volume grading command line option( ON and OFF for now)		# add Volume grading command line option( ON and OFF for now)
	# explain better delta ?		# explain better delta ?
	# linear interpolation and segmenetation can be easily be ~~implemnted~~ in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter]		# linear interpolation and segmenetation can be easily be implented in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter]
	# Clean up text output		# Create scripts native to the platform to run the image easily.
			# Test on Linux, Windows and MacOS
			# Create User Documentation
			# Clean up text output (low priority)

Ctsolakis at 12:07, 2 May 2019

2019-05-02T12:07:10Z

← Older revision		Revision as of 07:07, 2 May 2019
Line 7:		Line 7:
	# explain better delta ?		# explain better delta ?
	# linear interpolation and segmenetation can be easily be implemnted in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter]		# linear interpolation and segmenetation can be easily be implemnted in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter]
			# Clean up text output

Ctsolakis at 11:50, 2 May 2019

2019-05-02T11:50:39Z

← Older revision		Revision as of 06:50, 2 May 2019
Line 3:		Line 3:
	## Code is ready need to be integrated with PODM		## Code is ready need to be integrated with PODM
	# Segment automatically nrrd data		# Segment automatically nrrd data
	## Ie iterate with ITK Gajik's image and convert values !=0 -> 1		## i.e. iterate with ITK Gajik's image and convert values !=0 -> 1
	# add Volume grading command line option( ON and OFF for now)		# add Volume grading command line option( ON and OFF for now)
	# explain better delta ?		# explain better delta ?
			# linear interpolation and segmenetation can be easily be implemnted in parallel just by using the Multithreaded ITK template [https://vtk.org/Wiki/ITK/Examples/Developer/MultiThreadedImageFilter]