Internal:PODM CNF: Difference between revisions
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= Things TODO = | = Things TODO = | ||
# Create scripts | # Create scripts to run the image easily. <span style="font-size:2px">✔</span> | ||
# Test | # 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> | ||
# Create User Documentation | # 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 | |||
## 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> | |||
# explain better delta ? | # explain better delta ? | ||
# Clean up text output | # 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) | ||
Latest revision as of 16:39, 10 May 2019
Things TODO
- Create scripts to run the image easily. ✔
- Test:
- Linux ✔
- Windows ✔
- MacOS
- Add Linear Interpolation Code as default output ✔
- Code is ready need to be integrated with PODM ✔
- Segment automatically nrrd data ✔
- i.e. iterate with ITK Gajik's image and convert values !=0 -> 1 ✔
- 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) ✔
- 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
- 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 ✔
- explain better delta ?
- Clean up text output ✔
- segmentation can be easily be implemented in parallel just by using the Multithreaded ITK template [1] (maybe also linear interpolation ?) (low priority)