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).