def make(commit=DEFAULT_HASH):
"""Downloads a lean version of tract_querier. Output is '$soft/tract_querier-<commit>'."""
if commit != 'master':
out = get_path(commit)
if checkExists(out):
return
with local.tempdir() as tmpdir, local.cwd(tmpdir):
repo = downloadGithubRepo(REPO, commit)
sha, date = getCommitInfo(repo)
out = get_path(sha)
if checkExists(out):
return
# save space
(repo / 'doc').delete()
(repo / '.git').delete()
log.info("Make '{out}'".format(**locals()))
repo.move(out)
with open(out / 'env.sh', 'w') as f:
f.write("export PATH={}:$PATH\n".format(out / 'scripts'))
f.write("export PYTHONPATH={}:$PYTHONPATH\n".format(out))
date_symlink = get_path(date)
date_symlink.unlink()
out.symlink(date_symlink)
def make(commit=DEFAULT_HASH):
softdir = getSoftDir()
if commit != 'master':
if checkExists(get_path(commit)):
return
blddir = softdir / "UKFTractography-build"
with local.cwd(softdir):
repo = downloadGithubRepo('pnlbwh/ukftractography', commit)
sha, date = getCommitInfo(repo)
outbinary = get_path(sha)
if checkExists(outbinary):
return
logging.info("Build code:")
blddir.mkdir()
with local.cwd(blddir):
cmake(repo)
import plumbum.cmd
plumbum.cmd.make['-j', psutil.cpu_count(logical=False)] & FG
binary1 = blddir / 'ukf/bin/UKFTractography'
binary2 = blddir / 'UKFTractography-build/UKFTractography/bin/UKFTractography' # later commits
binary = binary1 if binary1.exists() else binary2
outbinary.dirname.mkdir()
binary.move(outbinary)
# chmod('a-w', outbinary)
with open(outbinary.dirname / 'env.sh', 'w') as f:
f.write("export PATH={}:$PATH".format(outbinary.dirname))
symlink = get_path(date).dirname
print("Make symlink: {} -> {}".format(symlink, get_path(sha).dirname))
symlink.unlink()
get_path(sha).dirname.symlink(symlink)
blddir.delete()
logging.info("Made '{}'".format(outbinary))
logging.info("Made '{}'".format(get_path(date)))
def make(version=DEFAULT_VERSION):
if checkExists(get_path(version)):
return
with TemporaryDirectory() as tmpdir, local.cwd(tmpdir):
d = downloadGithubArchive(GITHUB_REPO, 'v' + version)
d.move(get_path(version))
log.info("Made '{}'".format(get_path(version)))
def make(hash=DEFAULT_HASH):
if hash != 'master':
if checkExists(get_path(hash)):
return
with local.tempdir() as tmpdir, local.cwd(tmpdir):
repo = downloadGithubRepo('reckbo/nrrdchecker', hash)
sha, date = getCommitInfo(repo)
with local.cwd(repo):
if on_partners_cluster():
import os
os.system('module load stack')
from plumbum.cmd import stack
stack['setup'] & FG
stack['build'] & FG
binary = stack('exec', 'which', 'nrrdchecker')[:-1]
get_path(sha).dirname.mkdir()
local.path(binary).move(get_path(sha))
symlink = get_path(date).dirname
print("Make symlink: {} -> {}".format(symlink, get_path(sha).dirname))
symlink.unlink()
get_path(sha).dirname.symlink(symlink)
logger.info("Made '{}'".format(get_path(sha)))
logger.info("Made '{}'".format(symlink))
def make(commit=DEFAULT_HASH):
softdir = getSoftDir()
if commit != 'master':
if checkExists(get_path(commit)):
return
blddir = softdir / "dcm2niix-build"
with local.cwd(softdir):
repo = downloadGithubRepo('rordenlab/dcm2niix', commit)
sha, date = getCommitInfo(repo)
outbinary = get_path(sha)
if checkExists(outbinary):
return
logging.info("Build code:")
blddir.mkdir()
with local.cwd(blddir):
cmake(repo, "-DUSE_STATIC_RUNTIME:BOOL=OFF")
import plumbum.cmd
plumbum.cmd.make['-j', psutil.cpu_count(logical=False)] & FG
binary = blddir / 'bin/dcm2niix'
outbinary.dirname.mkdir()
binary.move(outbinary)
# chmod('a-w', outbinary)
with open(outbinary.dirname / 'env.sh', 'w') as f:
f.write("export PATH={}:$PATH".format(outbinary.dirname))
symlink = get_path(date).dirname
print("Make symlink: {} -> {}".format(symlink, get_path(sha).dirname))
symlink.unlink()
get_path(sha).dirname.symlink(symlink)
blddir.delete()
logging.info("Made '{}'".format(outbinary))
logging.info("Made '{}'".format(get_path(date)))
def make(hash=DEFAULT_HASH):
if checkExists(get_path(hash)):
return
with TemporaryDirectory() as tmpdir, local.cwd(tmpdir):
tmpdir = local.path(tmpdir)
repo = downloadGithubRepo('MRtrix3/mrtrix3', hash)
sha, date = getCommitInfo(repo)
with local.cwd(repo):
os.system('./configure')
os.system('./build')
os.system('mv ./release {}'.format(get_path(hash)))
get_path(hash).symlink(get_path(date))
def make(version=DEFAULT_VERSION):
if not URL.get(version):
logging.error(
"No download link set for '{}' in pnlpipe_software/Slicer.py")
sys.exit(1)
if checkExists(get_path(version)):
return
with TemporaryDirectory() as tmpdir, local.cwd(tmpdir):
tmpdir = local.path(tmpdir)
wget[URL.get(version), '-O', 'slicer.tar.gz'] & FG
tar['zxvf', 'slicer.tar.gz'] & FG
(tmpdir // 'Slicer-*')[0].move(getDir(version))
logging.info("Made '{}'".format(get_path(version)))
def make(commit=DEFAULT_HASH):
"""Downloads whitematteranalysis. Output is '$soft/whitematteranalysis-<commit>'."""
dest = getSoftDir()
if commit != 'master':
out = get_path(commit)
if checkExists(out):
return
with local.tempdir() as tmpdir, local.cwd(tmpdir):
repo = downloadGithubRepo(REPO, commit)
sha, date = getCommitInfo(repo)
out = get_path(sha)
if checkExists(out):
return
# save space
(repo / 'tests').delete()
(repo / '.git').delete()
logging.info("Make '{out}'".format(**locals()))
repo.move(out)
# chmod('-R', 'a-w', out)
# chmod('a-w', out)
with open(out / 'env.sh', 'w') as f:
f.write("export PATH={}:$PATH\n".format(out / 'bin'))
f.write("export PYTHONPATH={}:$PYTHONPATH\n".format(out))
# compile cython files
with local.cwd(out):
from plumbum.cmd import python
python['setup.py', 'build_ext', '--inplace'] & FG
date_symlink = get_path(date)
date_symlink.unlink()
out.symlink(date_symlink)
def installTraining(repo, commit):
dest = getSoftDir()
if commit == 'master':
logging.error(
'installing master not implemented yet for training repos, specify github hash'
)
import sys
sys.exit(1)
out = local.path(dest / repo + '-' + commit)
if checkExists(out):
return
archive = downloadGithubArchive('pnlbwh/' + repo, commit)
archive.move(out)
with local.cwd(out):
from plumbum.cmd import bash
bash('./mktrainingcsv.sh', '.')
def make(commit=DEFAULT_HASH):
softdir = getSoftDir()
blddir = softdir / "ANTs-build"
with local.cwd(softdir):
repo = downloadGithubRepo('ANTsX/ANTs', commit)
sha, date = getCommitInfo(repo)
out = get_path(sha)
# if output binary directory already exists, then return
if checkExists(out):
return
logging.info("Build code:")
blddir.mkdir()
with local.cwd(blddir):
cmake(repo)
import plumbum.cmd
plumbum.cmd.make['-j', psutil.cpu_count(logical=False)] & FG
# copy ANTs scripts
cp('-a', (softdir / 'ANTs' / 'Scripts').list(),
blddir / 'ANTS-build' / 'Examples')
# move binary directory
(blddir / 'ANTS-build' / 'Examples').move(out)
# write PATH and ANTSPATH
with open(out / 'env.sh', 'w') as f:
f.write("export PATH={}:$PATH\n".format(out))
f.write("export ANTSPATH={}\n".format(out))
# generate symbolink links
symlink = get_path(date)
print("Make symlink: {} -> {}".format(symlink, get_path(sha)))
symlink.unlink()
get_path(sha).symlink(symlink)
logging.info("Made '{}'".format(out))
def make(commit=DEFAULT_HASH, delete=False):
"""Downloads and compiles BRAINSTools binaries. Output is '$soft/BRAINSTools-bin-<hash>'."""
if os.getenv("CONDA_PREFIX"):
# add CONDA_PREFIX paths to the compiler flags so we prefer conda's includes and libs
conda_prefix = os.getenv("CONDA_PREFIX")
build_flags = " -I{conda_prefix}/include -L{conda_prefix}/lib".format(conda_prefix=conda_prefix)
cflags = os.getenv("CFLAGS") + " " + build_flags
cxxflags = os.getenv("CXXFLAGS") + " " + build_flags
local.env["CFLAGS"] = cflags
local.env["CXXFLAGS"] = cxxflags
local.env["ICU_ROOT_DIR"] = conda_prefix
local.env["ICU_ROOT"] = conda_prefix
dest = getSoftDir()
if commit != 'master':
out = dest / ('BRAINSTools-bin-'+commit)
if checkExists(out):
return
blddir = dest / "BRAINSTools-build"
with local.cwd(dest):
repo = downloadGithubRepo('BRAINSia/BRAINSTools', commit)
sha, date = getCommitInfo(repo)
out = dest / ('BRAINSTools-bin-'+sha)
symlink = dest / ('BRAINSTools-bin-'+date)
symlink.unlink()
log.info("Make '{}'".format(out))
log.info("Make '{}'".format(symlink))
if checkExists(out):
return
logging.info("Build code:")
blddir.mkdir()
with local.cwd(blddir):
cmake(repo
,"-DBRAINSTools_INSTALL_DEVELOPMENT=OFF"
,"-DBRAINSTools_MAX_TEST_LEVEL=0"
,"-DBRAINSTools_SUPERBUILD=ON"
,"-DBRAINSTools_USE_QT=OFF"
,"-DBRAINS_DEBUG_IMAGE_WRITE=OFF"
,"-DBUILD_STYLE_UTILS=OFF"
,"-DBUILD_TESTING=OFF"
,"-DCMAKE_BUILD_TYPE=Release"
,"-DCMAKE_COLOR_MAKEFILE=ON"
,"-DCMAKE_EXE_LINKER_FLAGS=' '"
,"-DCMAKE_EXE_LINKER_FLAGS_DEBUG="
,"-DCMAKE_EXE_LINKER_FLAGS_MINSIZEREL="
,"-DCMAKE_EXE_LINKER_FLAGS_RELEASE="
,"-DCMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO="
,"-DCMAKE_EXPORT_COMPILE_COMMANDS=OFF"
,"-DCMAKE_INSTALL_PREFIX:PATH=/usr/local"
,"-DCMAKE_MODULE_LINKER_FLAGS=' '"
,"-DCMAKE_MODULE_LINKER_FLAGS_DEBUG="
,"-DCMAKE_MODULE_LINKER_FLAGS_MINSIZEREL="
,"-DCMAKE_MODULE_LINKER_FLAGS_RELEASE="
,"-DCMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO="
,"-DCMAKE_PROJECT_NAME:STATIC=SuperBuild_BRAINSTools"
,"-DCMAKE_SHARED_LINKER_FLAGS=' '"
,"-DCMAKE_SHARED_LINKER_FLAGS_DEBUG="
,"-DCMAKE_SHARED_LINKER_FLAGS_MINSIZEREL="
,"-DCMAKE_SHARED_LINKER_FLAGS_RELEASE="
,"-DCMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO="
,"-DCMAKE_SKIP_INSTALL_RPATH=NO"
,"-DCMAKE_SKIP_RPATH=NO"
,"-DCMAKE_STATIC_LINKER_FLAGS="
,"-DCMAKE_STATIC_LINKER_FLAGS_DEBUG="
,"-DCMAKE_STATIC_LINKER_FLAGS_MINSIZEREL="
,"-DCMAKE_STATIC_LINKER_FLAGS_RELEASE="
,"-DCMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO="
,"-DCMAKE_USE_RELATIVE_PATHS=OFF"
,"-DCMAKE_VERBOSE_MAKEFILE=FALSE"
,"-DCOVERAGE_EXTRA_FLAGS=-l"
,"-DCTEST_SUBMIT_RETRY_COUNT=3"
,"-DCTEST_SUBMIT_RETRY_DELAY=5"
,"-DDART_TESTING_TIMEOUT=1500"
,"-DEXTERNAL_PROJECT_BUILD_TYPE=Release"
,"-DFORCE_EXTERNAL_BUILDS=OFF"
,"-DITK_VERSION_MAJOR=4"
,"-DSuperBuild_BRAINSTools_BUILD_DICOM_SUPPORT=ON"
,"-DSuperBuild_BRAINSTools_USE_CTKAPPLAUNCHER=OFF"
,"-DSuperBuild_BRAINSTools_USE_GIT_PROTOCOL=ON"
,"-DUSE_ANTS=ON"
,"-DUSE_AutoWorkup=OFF"
,"-DUSE_BRAINSABC=OFF"
,"-DUSE_BRAINSConstellationDetector=OFF"
,"-DUSE_BRAINSContinuousClass=OFF"
,"-DUSE_BRAINSCreateLabelMapFromProbabilityMaps=OFF"
,"-DUSE_BRAINSCut=OFF"
,"-DUSE_BRAINSDWICleanup=OFF"
,"-DUSE_BRAINSDemonWarp=OFF"
,"-DUSE_BRAINSFit=OFF"
,"-DUSE_BRAINSInitializedControlPoints=OFF"
,"-DUSE_BRAINSLabelStats=OFF"
,"-DUSE_BRAINSLandmarkInitializer=OFF"
,"-DUSE_BRAINSMultiModeSegment=OFF"
,"-DUSE_BRAINSMultiSTAPLE=OFF"
,"-DUSE_BRAINSMush=OFF"
,"-DUSE_BRAINSPosteriorToContinuousClass=OFF"
,"-DUSE_BRAINSROIAuto=OFF"
,"-DUSE_BRAINSResample=OFF"
,"-DUSE_BRAINSSnapShotWriter=OFF"
,"-DUSE_BRAINSStripRotation=OFF"
,"-DUSE_BRAINSSurfaceTools=OFF"
,"-DUSE_BRAINSTalairach=OFF"
,"-DUSE_BRAINSTransformConvert=OFF"
,"-DUSE_ConvertBetweenFileFormats=ON"
,"-DUSE_DWIConvert=ON"
,"-DUSE_DebugImageViewer=OFF"
,"-DUSE_GTRACT=OFF"
,"-DUSE_ICCDEF=OFF"
,"-DUSE_ImageCalculator=OFF"
,"-DUSE_ReferenceAtlas=OFF"
,"-DUSE_SYSTEM_DCMTK=OFF"
,"-DUSE_SYSTEM_ITK=OFF"
,"-DUSE_SYSTEM_SlicerExecutionModel=OFF"
,"-DUSE_SYSTEM_VTK=OFF"
,"-DVTK_GIT_REPOSITORY=git://vtk.org/VTK.git"
)
import plumbum.cmd
plumbum.cmd.make['-j', psutil.cpu_count(logical=False)] & FG
(blddir / 'bin').move(out)
with open(blddir / 'ANTs/Scripts/antsRegistrationSyN.sh', 'r') as src:
with open(out / 'antsRegistrationSyN.sh', 'w') as dest:
for idx, line in enumerate(src):
if idx == 0:
dest.write('#!/usr/bin/env bash')
else:
dest.write(line)
st = os.stat(str(out / 'antsRegistrationSyN.sh'))
os.chmod(str(out / 'antsRegistrationSyN.sh'), st.st_mode | stat.S_IEXEC)
# (blddir / 'ANTs/Scripts/antsRegistrationSyN.sh').copy(out)
with open(out / 'env.sh', 'w') as f:
f.write("export PATH={}:$PATH\n".format(out))
f.write("export ANTSPATH={}\n".format(out))
# chmod('a-w', out.glob('*'))
# chmod('a-w', out)
symlink.unlink()
out.symlink(symlink)
if sys.flags.interactive:
if input("Delete build directory? [y/N]") == "y":
blddir.delete()
log.info("Made '{}'".format(get_path(sha)))
log.info("Made '{}'".format(symlink))
def make(commit=DEFAULT_HASH, delete=False):
"""Downloads and compiles BRAINSTools binaries. Output is '$soft/BRAINSTools-bin-<hash>'."""
dest = getSoftDir()
if commit != 'master':
out = dest / ('BRAINSTools-bin-' + commit)
if checkExists(out):
return
blddir = dest / "BRAINSTools-build"
with local.cwd(dest):
repo = downloadGithubRepo('BRAINSia/BRAINSTools', commit)
for line in fileinput.input(repo / 'SuperBuild' / 'External_ITKv5.cmake',
inplace=True):
print(line.replace('itk.org', 'github.com/InsightSoftwareConsortium'),
end='')
sha, date = getCommitInfo(repo)
out = dest / ('BRAINSTools-bin-' + sha)
symlink = dest / ('BRAINSTools-bin-' + date)
symlink.unlink()
log.info("Make '{}'".format(out))
log.info("Make '{}'".format(symlink))
if checkExists(out):
return
logging.info("Build code:")
blddir.mkdir()
with local.cwd(blddir):
cmake(
repo, "-DBRAINSTools_BUILD_DICOM_SUPPORT:BOOL=OFF",
"-DBRAINSTools_MAX_TEST_LEVEL:STRING=0",
"-DBRAINSTools_REQUIRES_VTK:BOOL=OFF",
"-DBRAINSTools_USE_CTKAPPLAUNCHER:BOOL=OFF",
"-DBUILD_TESTING:BOOL=OFF", "-DUSE_ANTS:BOOL=OFF",
"-DUSE_AutoWorkup:BOOL=OFF", "-DUSE_BRAINSABC:BOOL=OFF",
"-DUSE_BRAINSConstellationDetector:BOOL=OFF",
"-DUSE_BRAINSDWICleanup:BOOL=OFF", "-DUSE_BRAINSFit:BOOL=OFF",
"-DUSE_BRAINSInitializedControlPoints:BOOL=OFF",
"-DUSE_BRAINSLabelStats:BOOL=OFF",
"-DUSE_BRAINSLandmarkInitializer:BOOL=OFF",
"-DUSE_BRAINSROIAuto:BOOL=OFF", "-DUSE_BRAINSResample:BOOL=OFF",
"-DUSE_BRAINSSnapShotWriter:BOOL=OFF",
"-DUSE_BRAINSStripRotation:BOOL=OFF",
"-DUSE_BRAINSTransformConvert:BOOL=OFF",
"-DUSE_ImageCalculator:BOOL=OFF", "-DUSE_ReferenceAtlas:BOOL=OFF",
"-DCMAKE_SKIP_INSTALL_RPATH:BOOL=ON", "-DCMAKE_SKIP_RPATH:BOOL=ON")
import plumbum.cmd
plumbum.cmd.make['-j', psutil.cpu_count(logical=False)] & FG
(blddir / 'bin').move(out)
with open(out / 'env.sh', 'w') as f:
f.write("export PATH={}:$PATH\n".format(out))
symlink.unlink()
out.symlink(symlink)
log.info("Made '{}'".format(get_path(sha)))
log.info("Made '{}'".format(symlink))