def mainFunc():
parser = argparse.ArgumentParser(description='Run Elastix registration protocol for all images in the directory')
parser.add_argument('--refDir', '-r', dest='refDir', required = True, \
help='The directory containing the reference images.')
parser.add_argument('--floatFile', '-f', dest='floatFile', required = True, \
help='Path to the floating image.')
parser.add_argument('--outDir', '-o', dest='outDir', required = False, \
help='Path to store the output images/parameters (default: current dir)', default=os.getcwd())
parser.add_argument('--atlas', '-a', dest='atlas', required = False, \
help='Path to the atlas segmentation file which will be resampled with the CPP file from the registration.', default=None)
args = parser.parse_args()
refImgs = [join(args.refDir, File) for File in listdir(args.refDir)]
refImgs = [img for img in refImgs if isfile(img) and img.endswith('.nii')]
if not refImgs:
print('Couldn\'t find any reference images')
return
if not path.isfile(args.floatFile):
print('Coudln\'t find the float image')
refImgs.sort(key=str.lower)
refFloatPairs = [[refImg, args.floatFile] for refImg in refImgs]
f3dParStr = paramListToShortString(f3d_params)
aladinParStr = paramListToShortString(aladin_params)
for rfPair in refFloatPairs:
baseName = basename(rfPair[0])[:-4]+'_'+basename(rfPair[1])[:-4]
currOutDir = join(args.outDir,baseName)
mkdir(currOutDir)
elastixLogPath = join(currOutDir,basename+'_LOG.txt')
elastixCommand = elastixExec+' -f '+rfPair[0]+' -m '+rfPair[1]+' -p '.join(elastixParams)+' -o '+currOutDir
elastixLog = ''
try:
elastixLog = ccall(elastixCommand, shell=True, stderr=STDOUT)
except CalledProcessError as err:
writeAndDie(err.output, elastixLogPath)
with open(elastixLogPath, 'w') as f:
f.write(elastixLog)
transformParameterFiles = ['TransformParameters.0.txt', 'TransformParameters.1.txt']
transformParameterFiles = [join(currOutDir,tpFile) for tpFile in transformParameterFiles]
for tpFilePath in transformParameterFiles:
with open(tpFilePath,'r') as tpFile:
tpCont = tpFile.read()
tpCont = tpCont.replace('(FinalBSplineInterpolationOrder 3)', '(FinalBSplineInterpolationOrder 1)')
with open(tpFilePath,'w') as tpFile:
tpCont = tpFile.write(tpCont)
if args.atlas is not None:
atlasOutDir = join(currOutDir,'atlas')
mkdir(atlasOutDir)
trfxCmd = trfxExec+' -in '+args.atlas+' -out '+atlasOutDir+' tp '+transformParameterFiles[-1]
try:
resampleLog = ccall(trfxCmd, shell=True, stderr=STDOUT)
except CalledProcessError as err:
writeAndDie(err.output, join(atlasOutDir,'ERR.txt'))
def call(args):
cmd = ' '.join(flatten(args))
try:
if verbose == True:
print(cmd)
ccall(cmd, shell=True)
except:
print("Errors while compiling!")
sys.exit(1)
def call(args, env=None):
cmd = ' '.join(flatten(args))
if env != None:
env = to_env(env)
try:
if conf["VERBOSITY"] > 1:
print(cmd)
ccall(cmd, shell=True, env=env)
except:
print("Errors encountered while compiling!")
sys.exit(1)
def try_call(args, env=None):
cmd = ' '.join(flatten(args))
if env != None:
env = to_env(env)
try:
if conf["VERBOSITY"] > 1:
print(cmd)
ccall(cmd, shell=True, env=env)
return True
except:
return False
def try_call(args, env = None):
cmd = ' '.join(flatten(args))
if env != None:
env = to_env(env)
try:
if conf["VERBOSITY"] > 1:
print(cmd)
ccall(cmd, shell=True, env=env)
return True
except:
return False
def call(args, env = None):
cmd = ' '.join(flatten(args))
if env != None:
env = to_env(env)
try:
if conf["VERBOSITY"] > 1:
print(cmd)
ccall(cmd, shell=True, env = env)
except:
print("Errors encountered while compiling!")
sys.exit(1)
def mainFunc():
parser = argparse.ArgumentParser(
description=
'Run Elastix registration protocol for all images in the directory')
parser.add_argument('--refDir', '-r', dest='refDir', required = True, \
help='The directory containing the reference images.')
parser.add_argument('--floatFile', '-f', dest='floatFile', required = True, \
help='Path to the floating image.')
parser.add_argument('--outDir', '-o', dest='outDir', required = False, \
help='Path to store the output images/parameters (default: current dir)', default=os.getcwd())
parser.add_argument('--atlas', '-a', dest='atlas', required = False, \
help='Path to the atlas segmentation file which will be resampled with the CPP file from the registration.', default=None)
args = parser.parse_args()
refImgs = [join(args.refDir, File) for File in listdir(args.refDir)]
refImgs = [img for img in refImgs if isfile(img) and img.endswith('.nii')]
if not refImgs:
print('Couldn\'t find any reference images')
return
if not path.isfile(args.floatFile):
print('Coudln\'t find the float image')
refImgs.sort(key=str.lower)
refFloatPairs = [[refImg, args.floatFile] for refImg in refImgs]
f3dParStr = paramListToShortString(f3d_params)
aladinParStr = paramListToShortString(aladin_params)
for rfPair in refFloatPairs:
baseName = basename(rfPair[0])[:-4] + '_' + basename(rfPair[1])[:-4]
currOutDir = join(args.outDir, baseName)
mkdir(currOutDir)
elastixLogPath = join(currOutDir, basename + '_LOG.txt')
elastixCommand = elastixExec + ' -f ' + rfPair[0] + ' -m ' + rfPair[
1] + ' -p '.join(elastixParams) + ' -o ' + currOutDir
elastixLog = ''
try:
elastixLog = ccall(elastixCommand, shell=True, stderr=STDOUT)
except CalledProcessError as err:
writeAndDie(err.output, elastixLogPath)
with open(elastixLogPath, 'w') as f:
f.write(elastixLog)
transformParameterFiles = [
'TransformParameters.0.txt', 'TransformParameters.1.txt'
]
transformParameterFiles = [
join(currOutDir, tpFile) for tpFile in transformParameterFiles
]
for tpFilePath in transformParameterFiles:
with open(tpFilePath, 'r') as tpFile:
tpCont = tpFile.read()
tpCont = tpCont.replace('(FinalBSplineInterpolationOrder 3)',
'(FinalBSplineInterpolationOrder 1)')
with open(tpFilePath, 'w') as tpFile:
tpCont = tpFile.write(tpCont)
if args.atlas is not None:
atlasOutDir = join(currOutDir, 'atlas')
mkdir(atlasOutDir)
trfxCmd = trfxExec + ' -in ' + args.atlas + ' -out ' + atlasOutDir + ' tp ' + transformParameterFiles[
-1]
try:
resampleLog = ccall(trfxCmd, shell=True, stderr=STDOUT)
except CalledProcessError as err:
writeAndDie(err.output, join(atlasOutDir, 'ERR.txt'))
def mainFunc():
parser = argparse.ArgumentParser(
description=
'Run standard Registration protocol for all images in the directory')
parser.add_argument('--refDir', '-r', dest='refDir', required = True, \
help='The directory containing the reference images.')
parser.add_argument('--floatFile', '-f', dest='floatFile', required = True, \
help='Path to the floating image.')
parser.add_argument('--outDir', '-o', dest='outDir', required = False, \
help='Path to store the output images/parameters (default: current dir)', default=os.getcwd())
parser.add_argument('--atlas', '-a', dest='atlas', required = False, \
help='Path to the atlas segmentation file which will be resampled with the CPP file from the registration.', default=None)
parser.add_argument('--resOnly', '-m', dest='resOnly', required = False, action='store_true',\
help='Resample atlas only, relying on previous registration run.', default=False)
args = parser.parse_args()
refImgs = [join(args.refDir, File) for File in listdir(args.refDir)]
refImgs = [
img for img in refImgs
if isfile(img) and (img.endswith('.nii') or img.endswith('.nii.gz'))
]
if not refImgs:
print('Couldn\'t find any reference images')
return
if not path.isfile(args.floatFile):
print('Coudln\'t find the float image')
refImgs.sort(key=str.lower)
refFloatPairs = [[refImg, args.floatFile] for refImg in refImgs]
f3dParStr = paramListToShortString(f3d_params)
aladinParStr = paramListToShortString(aladin_params)
for rfPair in refFloatPairs:
baseName = basename(rfPair[0])[:nameEnd(rfPair[0])] + '_' + basename(
rfPair[1])[:nameEnd(rfPair[1])]
cppPath = join(args.outDir,
baseName + '_' + f3dParStr + '_CPP' + '.nii')
affPath = join(args.outDir,
baseName + '_' + aladinParStr + '_AFF' + '.txt')
imgsArg = ['-ref ' + rfPair[0], '-flo ' + rfPair[1]]
f3dArg = ['-cpp ' + cppPath]
affArg = ['-aff ' + affPath]
regAladinCommand = aladinExec + ' '.join(imgsArg + aladin_params +
affArg)
regF3dCommand = f3dExec + ' '.join(imgsArg + f3d_params + affArg +
f3dArg)
aladinLogPath = affPath[0:-4] + '_LOG.txt'
f3dLogPath = cppPath[0:-4] + '_LOG.txt'
aladinLog = ''
f3dLog = ''
if args.resOnly is False:
if not path.isfile(affPath):
try:
aladinLog = ccall(regAladinCommand,
shell=True,
stderr=STDOUT)
except CalledProcessError as err:
writeAndDie(err.output, aladinLogPath)
with open(aladinLogPath, 'w') as f:
f.write(aladinLog)
try:
print(regF3dCommand)
f3dLog = ccall(regF3dCommand, shell=True, stderr=STDOUT)
except CalledProcessError as err:
continue
writeAndDie(err.output, f3dLogPath)
with open(f3dLogPath, 'w') as f:
f.write(f3dLog)
if args.atlas is not None:
mapPath = join(args.outDir,
baseName + '_' + f3dParStr + '_MAP' + '.nii.gz')
resampleArgs = [
'-ref ' + rfPair[0], '-flo ' + args.atlas, '-trans ' + cppPath,
'-res ' + mapPath
]
resampleCommand = resampleExec + ' '.join(resampleArgs +
resample_params)
#print(resampleCommand)
try:
resampleLog = ccall(resampleCommand, shell=True, stderr=STDOUT)
except CalledProcessError as err:
writeAndDie(err.output, mapPath[0:-4] + 'ERR.txt')
def mainFunc():
parser = argparse.ArgumentParser(description='Run standard Registration protocol for all images in the directory')
parser.add_argument('--refDir', '-r', dest='refDir', required = True, \
help='The directory containing the reference images.')
parser.add_argument('--floatFile', '-f', dest='floatFile', required = True, \
help='Path to the floating image.')
parser.add_argument('--outDir', '-o', dest='outDir', required = False, \
help='Path to store the output images/parameters (default: current dir)', default=os.getcwd())
parser.add_argument('--atlas', '-a', dest='atlas', required = False, \
help='Path to the atlas segmentation file which will be resampled with the CPP file from the registration.', default=None)
parser.add_argument('--resOnly', '-m', dest='resOnly', required = False, action='store_true',\
help='Resample atlas only, relying on previous registration run.', default=False)
args = parser.parse_args()
refImgs = [join(args.refDir, File) for File in listdir(args.refDir)]
refImgs = [img for img in refImgs if isfile(img) and (img.endswith('.nii') or img.endswith('.nii.gz'))]
if not refImgs:
print('Couldn\'t find any reference images')
return
if not path.isfile(args.floatFile):
print('Coudln\'t find the float image')
refImgs.sort(key=str.lower)
refFloatPairs = [[refImg, args.floatFile] for refImg in refImgs]
f3dParStr = paramListToShortString(f3d_params)
aladinParStr = paramListToShortString(aladin_params)
for rfPair in refFloatPairs:
baseName = basename(rfPair[0])[:nameEnd(rfPair[0])]+'_'+basename(rfPair[1])[:nameEnd(rfPair[1])]
cppPath = join(args.outDir,baseName+'_'+f3dParStr+'_CPP'+'.nii')
affPath = join(args.outDir,baseName+'_'+aladinParStr+'_AFF'+'.txt')
imgsArg = ['-ref '+rfPair[0],'-flo '+rfPair[1]]
f3dArg = ['-cpp '+cppPath]
affArg = ['-aff '+affPath]
regAladinCommand = aladinExec+' '.join(imgsArg+aladin_params+affArg)
regF3dCommand = f3dExec+' '.join(imgsArg+f3d_params+affArg+f3dArg)
aladinLogPath = affPath[0:-4]+'_LOG.txt'
f3dLogPath = cppPath[0:-4]+'_LOG.txt'
aladinLog=''
f3dLog=''
if args.resOnly is False:
if not path.isfile(affPath):
try:
aladinLog = ccall(regAladinCommand, shell=True, stderr=STDOUT)
except CalledProcessError as err:
writeAndDie(err.output, aladinLogPath)
with open(aladinLogPath, 'w') as f:
f.write(aladinLog)
try:
print(regF3dCommand)
f3dLog = ccall(regF3dCommand, shell=True, stderr=STDOUT)
except CalledProcessError as err:
continue
writeAndDie(err.output, f3dLogPath)
with open(f3dLogPath, 'w') as f:
f.write(f3dLog)
if args.atlas is not None:
mapPath = join(args.outDir,baseName+'_'+f3dParStr+'_MAP'+'.nii.gz')
resampleArgs = ['-ref '+rfPair[0],'-flo '+args.atlas,'-trans '+cppPath,'-res '+mapPath]
resampleCommand = resampleExec+' '.join(resampleArgs+resample_params)
#print(resampleCommand)
try:
resampleLog = ccall(resampleCommand, shell=True, stderr=STDOUT)
except CalledProcessError as err:
writeAndDie(err.output, mapPath[0:-4]+'ERR.txt')
def install(packagename):
ccall(["pacman", "-Ss", "--noconfirm", packagename])
logging.info("installed {}".format(packagename))
