imageguidedtherapylab/fileconversionscripts

MATLAB Code Repository

This repository stores various file conversion scripts

to run dicom server:

python DicomSeriesReadImageWrite.py --server=innovador.ini

• storescp obtained from Slicer4
• http://support.dcmtk.org/docs/storescp.html
• python vtk bindings obtained from EPD 7.3.1

python itk bindings build with

cmake -DCMAKE_CXX_COMPILER=/usr/bin/g++-4.4 -DCMAKE_C_COMPILER=/usr/bin/gcc-4.4 -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=Debug -DBUILD_EXAMPLES=ON -DBUILD_TESTING=OFF -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=$ITK_HOME -DITK_WRAP_PYTHON=ON -DINSTALL_WRAP_ITK_COMPATIBILITY=OFF -DITK_WRAP_double=ON -DITK_USE_SYSTEM_SWIG=ON -DPYTHON_EXECUTABLE=$EPD_ROOT/bin/python -DPYTHON_INCLUDE_DIR=$EPD_ROOT/include/python2.7 -DPYTHON_LIBRARY=$EPD_ROOT/lib/libpython2.7.so ../InsightToolkit-4.3.1

dicom transfer

findscu -P -k 0008,0052=STUDY -aet -aec IPAddress Port# -k 0010,0020= -k 0020,000d -k 0008,1030 -k 0008,0020 -k 0008,0050 findscu -S -k 0008,0052=SERIES -aet -aec IPAddress Port# -k 0020,000D= -k 0020,000E -k 0008,0060 -k 0010,0020= -k 0008,103e movescu -v -S -k 0008,0052=SERIES -aet -aec IPAddress Port# -k 0020,000D= -k 0020,000e=

simple file conversion:

python convertExodusToMatlab.py --ini_file=dog1.ini

all mesh file names, imaging parameters, and affine transformation parameters should be in the ini file

and example ini file is given in dog1.ini: adjust work_dir, mesh_filenames, etc accordingly

Standard prefixes for commit messages

following - http://www.itk.org/Wiki/ITK/Git/Develop

• BUG: Fix for runtime crash or incorrect result
• COMP: Compiler error or warning fix
• DOC: Documentation change
• ENH: New functionality
• PERF: Performance improvement
• STYLE: No logic impact (indentation, comments)
• WIP: Work In Progress not ready for merge

Naming Conventions

following - http://www.itk.org/Wiki/ITK/Coding_Style_Guide#Naming_Conventions

• Names are constructed by using case change to indicate separate words, as in TimeStamp (versus Time Stamp).
• Underscores are not used.
• Variable names are chosen carefully with the intention to convey the meaning behind the code.
• Names are generally spelled out
• Use of abbreviations is discouraged. (Abbreviation are allowable when in common use, and should be in uppercase as in RGB.) While this does result in long names, it self-documents the code.
• If you learn how to use name completion in your editor (e.g.,Vim, Emacs), this inconvenience can be minimized.

Submodules

http://git-scm.com/book/en/Git-Tools-Submodules http://stackoverflow.com/questions/3796927/how-to-git-clone-including-submodules

$ git submodule update --init --recursive
Submodule 'projects/CurveFit' ([email protected]:ImageGuidedTherapyLab/MatlabCurveFit.git) registered for path 'projects/CurveFit'
Cloning into 'projects/CurveFit'...
remote: Counting objects: 401, done.
remote: Total 401 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (401/401), 1.67 MiB | 1.72 MiB/s, done.
Resolving deltas: 100% (178/178), done.
Submodule path 'projects/CurveFit': checked out '109825540c0790b3a949f77661a59410fbafb133'

refresh all remotes' branches, adding new ones and deleting removed ones.

git remote update --prune

remove large file from history

https://help.github.com/articles/remove-sensitive-data/

• run from top of repo and push changes

  git filter-branch --force --index-filter 'git rm --cached --ignore-unmatch path/to/largefiles/*' --prune-empty --tag-name-filter cat -- --all git push origin --force --all

• other forks/branchnes need to rebase to the master... dangerous ? (http://git-scm.com/book/en/v2/Git-Branching-Rebasing)

  git pull --rebase origin master

extract a subdirectory as a new repo

https://help.github.com/articles/splitting-a-subfolder-out-into-a-new-repository/

• git filter-branch --prune-empty --subdirectory-filter YOUR_FOLDER_NAME master
• git push my-new-repo -f .

Merging Repos

http://stackoverflow.com/questions/13040958/merge-two-git-repositories-without-breaking-file-history

Here's a way that doesn't rewrite any history, so all commit IDs will remain valid. The end-result is that the second repo's files will end up in a subdirectory.

1. Add the second repo as a remote:

   cd firstgitrepo/ git remote add -f secondrepo username@servername:andsoon

2. Create a local branch from the second repo's branch:

   git branch branchfromsecondrepo secondrepo/master; git checkout branchfromsecondrepo

3. Move all its files into a subdirectory:

   mkdir subdir/ git ls-tree -z --name-only HEAD | xargs -0 -I {} git mv {} subdir/

4. Merge the second branch into the first repo's master branch:

git commit -m "STYLE: organizing files"; git checkout master; git merge branchfromsecondrepo

5. clean up

   git branch -D branchfromsecondrepo; git remote rm secondrepo

6. git log --follow file

   Continue listing the history of a file beyond renames (works only for a single file).

fileconversionscripts's Issues

Transfer Issue

Hey man,
The dicom files from PET and CT are put together in one folder for each patient, which makes them very hard to use. Is there a way to create a separate directory for each format?
Thanks,
D