def __init__(
self,
inSource,
inTarget,
output=None, # ability to specify output transform when using strings for input
logFile=None,
maskFile=None,
defaultDir="transforms",
blur=0.56,
resample_step=4,
registration_step=10,
w_translations=8,
rotational_range=50,
rotational_interval=10,
mousedata=False):
CmdStage.__init__(self,
None) #don't do any arg processing in superclass
# handling of the input files
try:
if rf.isFileHandler(inSource, inTarget):
self.source = inSource.getBlur(fwhm=blur)
self.target = inTarget.getBlur(fwhm=blur)
if (output == None):
self.output = inSource.registerVolume(inTarget, defaultDir)
else:
self.output = output
if (logFile == None):
self.logFile = fh.logFromFile(inSource.logDir, self.output)
else:
self.logFile = logFile
else:
# TODO: fix this to work with string input files
self.source = inSource
self.target = inTarget
except:
print "Failed in putting together RotationalMinctracc command; unexpected error:"
raise
# The resolution is used to determine the step size and
# blurring kernels for the rotational minctracc call. This
# should be based on the target, not the input file (source)
highestResolution = rf.returnFinestResolution(inTarget)
# TODO: finish the following if clause... hahaha
#if(mousedata):
self.addDefaults(resample_step * highestResolution,
registration_step * highestResolution,
w_translations * highestResolution,
int(rotational_range), int(rotational_interval))
# potentially add a mask to the command
self.finalizeCommand(inTarget, maskFile)
self.setName()
self.colour = "green"
def __init__(self,
inSource,
inTarget,
output = None, # ability to specify output transform when using strings for input
logFile = None,
maskFile = None,
defaultDir="transforms",
blur=0.56,
resample_step=4,
registration_step=10,
w_translations=8,
rotational_range=50,
rotational_interval=10,
mousedata=False):
CmdStage.__init__(self, None) #don't do any arg processing in superclass
# handling of the input files
try:
if rf.isFileHandler(inSource, inTarget):
self.source = inSource.getBlur(fwhm=blur)
self.target = inTarget.getBlur(fwhm=blur)
if(output == None):
self.output = inSource.registerVolume(inTarget, defaultDir)
else:
self.output = output
if(logFile == None):
self.logFile = fh.logFromFile(inSource.logDir, self.output)
else:
self.logFile = logFile
else:
# TODO: fix this to work with string input files
self.source = inSource
self.target = inTarget
except:
print "Failed in putting together RotationalMinctracc command."
print "Unexpected error: ", sys.exc_info()
raise
highestResolution = rf.getFinestResolution(inSource)
# TODO: finish the following if clause... hahaha
#if(mousedata):
self.addDefaults(resample_step * highestResolution,
registration_step * highestResolution,
w_translations * highestResolution,
int(rotational_range),
int(rotational_interval))
# potentially add a mask to the command
self.finalizeCommand(inTarget, maskFile)
self.setName()
self.colour = "green"
def __init__(self,
inFile,
fwhm,
defaultDir="tmp",
gradient=False):
"""calls mincblur with the specified 3D Gaussian kernel
The inputs can be in one of two styles. The first argument can
be an instance of RegistrationPipeFH, in which case the last
volume in that instance (i.e. inFile.lastBasevol) will be
blurred and the output will be determined by its blurFile
method. Alternately, the inFile can be a string representing a
filename, in which case the output and logfile will be set based on
the inFile name. If the fwhm specified is -1, we do not construct
a command.
"""
if fwhm == -1:
return
CmdStage.__init__(self, None)
try:
if isFileHandler(inFile):
blurlist = inFile.blurFile(fwhm, gradient, defaultDir)
self.base = blurlist["base"]
self.inputFiles = [inFile.getLastBasevol()]
self.outputFiles = [blurlist["file"]]
self.logFile = blurlist["log"]
self.name = "mincblur " + str(fwhm) + " " + inFile.basename
if gradient:
self.outputFiles.append(blurlist["gradient"])
else:
self.base = str(inFile).replace(".mnc", "")
self.inputFiles = [inFile]
blurBase = "".join([self.base, "_fwhm", str(fwhm), "_blur"])
output = "".join([blurBase, ".mnc"])
self.outputFiles = [output]
self.logFile = fh.logFromFile(abspath(curdir), output)
self.name = "mincblur " + str(fwhm) + " " + basename(inFile)
if gradient:
gradientBase = blurBase.replace("blur", "dxyz")
self.outputFiles += ["".join([gradientBase, ".mnc"])]
except:
print "Failed in putting together blur command."
print "Unexpected error: ", sys.exc_info()
self.cmd = ["mincblur", "-clobber", "-no_apodize", "-fwhm", str(fwhm),
self.inputFiles[0], self.base]
if gradient:
self.cmd += ["-gradient"]
self.colour="blue"
def __init__(self, inFile, fwhm, defaultDir="tmp", gradient=False):
"""calls mincblur with the specified 3D Gaussian kernel
The inputs can be in one of two styles. The first argument can
be an instance of RegistrationPipeFH, in which case the last
volume in that instance (i.e. inFile.lastBasevol) will be
blurred and the output will be determined by its blurFile
method. Alternately, the inFile can be a string representing a
filename, in which case the output and logfile will be set based on
the inFile name. If the fwhm specified is -1, we do not construct
a command.
"""
if fwhm == -1:
return
CmdStage.__init__(self, None)
try:
if isFileHandler(inFile):
blurlist = inFile.blurFile(fwhm, gradient, defaultDir)
self.base = blurlist["base"]
self.inputFiles = [inFile.getLastBasevol()]
self.outputFiles = [blurlist["file"]]
self.logFile = blurlist["log"]
self.name = "mincblur " + str(fwhm) + " " + inFile.basename
if gradient:
self.outputFiles.append(blurlist["gradient"])
else:
self.base = str(inFile).replace(".mnc", "")
self.inputFiles = [inFile]
blurBase = "".join([self.base, "_fwhm", str(fwhm), "_blur"])
output = "".join([blurBase, ".mnc"])
self.outputFiles = [output]
self.logFile = fh.logFromFile(abspath(curdir), output)
self.name = "mincblur " + str(fwhm) + " " + basename(inFile)
if gradient:
gradientBase = blurBase.replace("blur", "dxyz")
self.outputFiles += ["".join([gradientBase, ".mnc"])]
except:
print "Failed in putting together blur command."
print "Unexpected error: ", sys.exc_info()
self.cmd = [
"mincblur", "-clobber", "-no_apodize", "-fwhm",
str(fwhm), self.inputFiles[0], self.base
]
if gradient:
self.cmd += ["-gradient"]
self.colour = "blue"
def __init__(self, inputFiles, outputFile, logFile=None):
CmdStage.__init__(self, None)
# in case there is a single input file... (it's actually possible)
if (not (type(inputFiles) is list)):
inputFiles = [inputFiles]
self.inputFiles = inputFiles
self.outputFiles = [outputFile]
self.logFile = logFile
self.cmd = ["xfmconcat", "-clobber"]
self.cmd += inputFiles
self.cmd += [outputFile]
self.name = "xfm-concat"
self.colour = "yellow"
def __init__(self,
inputFiles,
outputFile,
logFile=None):
CmdStage.__init__(self, None)
# in case there is a single input file... (it's actually possible)
if(not(type(inputFiles) is list)):
inputFiles = [inputFiles]
self.inputFiles = inputFiles
self.outputFiles = [outputFile]
self.logFile = logFile
self.cmd = ["xfmconcat", "-clobber"]
self.cmd += inputFiles
self.cmd += [outputFile]
self.name = "xfm-concat"
self.colour = "yellow"
def __init__(self, inputFH, outputFH, transform, defaultDir="tmp"):
CmdStage.__init__(self, None)
try:
if isFileHandler(inputFH, outputFH):
self.inFile = inputFH.getLastBasevol()
self.xfm = transform
self.outfile = createOutputFileName(outputFH, self.xfm, defaultDir, "_displacement.mnc")
self.logFile = fh.logFromFile(outputFH.logDir, self.outfile)
else:
print ("minc_displacement only works using file handlers. "
"Exception being raised.")
raise
except:
print "Failed in putting together minc_displacement command"
print "Unexpected error: ", sys.exc_info()
self.addDefaults()
self.finalizeCommand()
self.setName()
def __init__(self, inputFH, outputFH, transform, defaultDir="tmp"):
CmdStage.__init__(self, None)
try:
if isFileHandler(inputFH, outputFH):
self.inFile = inputFH.getLastBasevol()
self.xfm = transform
self.outfile = createOutputFileName(outputFH, self.xfm, defaultDir, "_displacement.mnc")
self.logFile = fh.logFromFile(outputFH.logDir, self.outfile)
else:
print ("minc_displacement only works using file handlers. "
"Exception being raised.")
raise
except:
print("Failed in putting together minc_displacement command")
print("Unexpected error: ", sys.exc_info())
self.addDefaults()
self.finalizeCommand()
self.setName()
def __init__(self, inputFH, targetFH, defaultDir="transforms"):
CmdStage.__init__(self, None)
try:
if isFileHandler(inputFH, targetFH):
self.inFile = inputFH.getLastBasevol()
self.mask = inputFH.getMask()
self.xfm = inputFH.getLastXfm(targetFH)
self.outfile = self.setOutputFile(inputFH, defaultDir)
self.logFile = fh.logFromFile(inputFH.logDir, self.outfile)
else:
print ("linear part of nlin currently only works using file handlers. "
"Exception being raised.")
raise
except:
print "Failed in putting together linearPartofNlin command"
print "Unexpected error: ", sys.exc_info()
self.addDefaults()
self.finalizeCommand()
self.setName()
def __init__(self, inputFH, targetFH, defaultDir="transforms"):
CmdStage.__init__(self, None)
try:
if isFileHandler(inputFH, targetFH):
self.inFile = inputFH.getLastBasevol()
self.mask = inputFH.getMask()
self.xfm = inputFH.getLastXfm(targetFH)
self.outfile = self.setOutputFile(inputFH, defaultDir)
self.logFile = fh.logFromFile(inputFH.logDir, self.outfile)
else:
print ("linear part of nlin currently only works using file handlers. "
"Exception being raised.")
raise
except:
print("Failed in putting together linearPartofNlin command")
print("Unexpected error: ", sys.exc_info())
self.addDefaults()
self.finalizeCommand()
self.setName()
def __init__(self, xfm, FH=None, logFile=None):
CmdStage.__init__(self, None)
try:
self.xfm = xfm
if isFileHandler(FH):
invXfmBase = fh.removeBaseAndExtension(
self.xfm).split(".xfm")[0]
self.output = fh.createBaseName(FH.transformsDir,
invXfmBase + "_inverted.xfm")
self.logFile = fh.logFromFile(FH.logDir, self.output)
else:
invXfmBase = splitext(self.xfm)[0]
self.output = invXfmBase + "_inverted.xfm"
if logFile:
self.logFile = logFile
except:
print "Failed in putting together xfminvert command"
print "Unexpected error: ", sys.exc_info()
self.finalizeCommand()
self.setName()
def __init__(self,
resolution,
inFile,
output=None,
logFile=None,
defaultDir="resampled"):
"""Resamples the input file to the resolution specified
using autocrop. The -resample flag forces the use of
mincresample.
Resolutions should be specified in mm.
e.g. 56 microns should be specified as 0.056
"""
CmdStage.__init__(self, None)
self.resolution = str(resolution)
try:
if isFileHandler(inFile):
self.inFile = inFile.getLastBasevol()
self.outfile = self.setOutputFile(inFile, defaultDir)
self.logFile = fh.logFromFile(inFile.logDir, self.outfile)
else:
self.inFile = inFile
self.outfile = output
if not logFile:
self.logFile = fh.logFromFile(abspath(curdir), output)
else:
self.logFile = logFile
except:
print "Failed in putting together autocrop command"
print "Unexpected error: ", sys.exc_info()
self.addDefaults()
self.finalizeCommand()
self.setName()
def __init__(self,
xfm,
FH=None,
logFile=None):
CmdStage.__init__(self, None)
try:
self.xfm = xfm
if isFileHandler(FH):
invXfmBase = fh.removeBaseAndExtension(self.xfm).split(".xfm")[0]
self.output = fh.createBaseName(FH.transformsDir, invXfmBase + "_inverted.xfm")
self.logFile = fh.logFromFile(FH.logDir, self.output)
else:
invXfmBase = splitext(self.xfm)[0]
self.output = invXfmBase + "_inverted.xfm"
if logFile:
self.logFile = logFile
except:
print "Failed in putting together xfminvert command"
print "Unexpected error: ", sys.exc_info()
self.finalizeCommand()
self.setName()
def __init__(self,
inputArray,
outputAvg,
output=None,
logFile=None,
defaultDir="tmp"):
CmdStage.__init__(self, None)
try:
"""If output is fileHandler, we assume input array is as well"""
if isFileHandler(outputAvg):
self.filesToAvg = []
for i in range(len(inputArray)):
self.filesToAvg.append(inputArray[i].getLastBasevol())
"""If no output file is specified, create default, using file handler
otherwise use what is specified."""
if not output:
self.output = self.setOutputFile(outputAvg, defaultDir)
else:
self.output = output
self.logFile = fh.logFromFile(outputAvg.logDir, self.output)
else:
self.filesToAvg = inputArray
self.output = outputAvg
if not logFile:
self.logFile = fh.logFromFile(abspath(curdir), outputAvg)
else:
self.logFile = logFile
except:
print "Failed in putting together mincaverage command"
print "Unexpected error: ", sys.exc_info()
self.addDefaults()
self.finalizeCommand()
self.setName()
def __init__(self,
resolution,
inFile,
output=None,
logFile=None,
defaultDir="resampled"):
"""Resamples the input file to the resolution specified
using autocrop. The -resample flag forces the use of
mincresample.
Resolutions should be specified in mm.
e.g. 56 microns should be specified as 0.056
"""
CmdStage.__init__(self, None)
self.resolution = str(resolution)
try:
if isFileHandler(inFile):
self.inFile = inFile.getLastBasevol()
self.outfile = self.setOutputFile(inFile, defaultDir)
self.logFile = fh.logFromFile(inFile.logDir, self.outfile)
else:
self.inFile = inFile
self.outfile = output
if not logFile:
self.logFile = fh.logFromFile(abspath(curdir), output)
else:
self.logFile = logFile
except:
print "Failed in putting together autocrop command"
print "Unexpected error: ", sys.exc_info()
self.addDefaults()
self.finalizeCommand()
self.setName()
def __init__(self,
inputArray,
outputAvg,
output=None,
logFile=None,
defaultDir="tmp"):
CmdStage.__init__(self, None)
try:
"""If output is fileHandler, we assume input array is as well"""
if isFileHandler(outputAvg):
self.filesToAvg = []
for i in range(len(inputArray)):
self.filesToAvg.append(inputArray[i].getLastBasevol())
"""If no output file is specified, create default, using file handler
otherwise use what is specified."""
if not output:
self.output = self.setOutputFile(outputAvg, defaultDir)
else:
self.output = output
self.logFile = fh.logFromFile(outputAvg.logDir, self.output)
else:
self.filesToAvg = inputArray
self.output = outputAvg
if not logFile:
self.logFile = fh.logFromFile(abspath(curdir), outputAvg)
else:
self.logFile = logFile
except:
print "Failed in putting together mincaverage command"
print "Unexpected error: ", sys.exc_info()
self.addDefaults()
self.finalizeCommand()
self.setName()
def __init__(self,
inSource,
inTarget,
output=None,
logFile=None,
defaultDir="transforms",
blur=None,
gradient=False,
linearparam="nlin",
source_mask=None,
target_mask=None,
iterations=40,
step=0.5,
transform=None,
weight=0.8,
stiffness=0.98,
similarity=0.8,
w_translations=0.4,
w_rotations=0.0174533,
w_scales=0.02,
w_shear=0.02,
simplex=1,
optimization="-use_simplex",
useMask=True):
#MF TODO: Specify different w_translations, rotations, scales shear in each direction?
# Now assumes same in all directions
# Go to more general **kwargs?
"""an efficient way to add a minctracc call to a pipeline
The constructor needs two inputFile arguments, the source and the
target for the registration, and multiple optional arguments
for specifying parameters. The source and the target can be
specified as either RegistrationPipeFH instances or as strings
representing filenames. In the latter case an output and a
logfile filename are required as well (these are filled in
automatically in the case of RegistrationPipeFH instances.)
"""
CmdStage.__init__(self, None) #don't do any arg processing in superclass
try:
if isFileHandler(inSource, inTarget):
""" if blur = None, getBlur returns lastblur
if gradient is true, getBlur returns gradient instead of blur
if blur = -1, lastBaseVol is returned and gradient is ignored.
self.transform will be None if there is no previous transform
between input and target. If this is the case, lsq6 and lsq12
defaults are added in the setTransforms function
"""
self.source = inSource.getBlur(blur, gradient)
self.target = inTarget.getBlur(blur, gradient)
self.transform = inSource.getLastXfm(inTarget)
"""If no output transform is specified, use registerVolume to create a default.
If an output transform name is specified, use this as the output, and add it as the last xfm between source and target.
Note: The output file passed in must be a full path."""
if not output:
outputXfm = inSource.registerVolume(inTarget, defaultDir)
self.output = outputXfm
else:
self.output = output
inSource.addAndSetXfmToUse(inTarget, self.output)
outputXfm = output
self.logFile = fh.logFromFile(inSource.logDir, outputXfm)
self.useMask = useMask
if self.useMask:
self.source_mask = inSource.getMask()
self.target_mask = inTarget.getMask()
else:
self.source = inSource
self.target = inTarget
self.output = output
if not logFile:
self.logFile = fh.logFromFile(abspath(curdir), output)
else:
self.logFile = logFile
self.transform = transform
self.useMask = useMask
if self.useMask:
self.source_mask = source_mask
self.target_mask = target_mask
except:
print "Failed in putting together minctracc command."
print "Unexpected error: ", sys.exc_info()
self.linearparam = linearparam
self.iterations = str(iterations)
self.lattice_diameter = str(step*3.0)
self.step = str(step)
self.weight = str(weight)
self.stiffness = str(stiffness)
self.similarity = str(similarity)
self.w_translations = str(w_translations)
self.w_rotations = str(w_rotations)
self.w_scales = str(w_scales)
self.w_shear = str(w_shear)
self.simplex = str(simplex)
self.optimization = str(optimization)
self.addDefaults()
self.finalizeCommand()
self.setTransform()
self.setName()
self.colour = "red"
def __init__(self,
inSource,
inTarget,
output=None,
logFile=None,
defaultDir="transforms",
blur=None,
gradient=False,
linearparam="nlin",
source_mask=None,
target_mask=None,
iterations=40,
step=0.5,
transform=None,
weight=0.8,
stiffness=0.98,
similarity=0.8,
w_translations=0.4,
w_rotations=0.0174533,
w_scales=0.02,
w_shear=0.02,
simplex=1,
optimization="-use_simplex",
useMask=True):
#MF TODO: Specify different w_translations, rotations, scales shear in each direction?
# Now assumes same in all directions
# Go to more general **kwargs?
"""an efficient way to add a minctracc call to a pipeline
The constructor needs two inputFile arguments, the source and the
target for the registration, and multiple optional arguments
for specifying parameters. The source and the target can be
specified as either RegistrationPipeFH instances or as strings
representing filenames. In the latter case an output and a
logfile filename are required as well (these are filled in
automatically in the case of RegistrationPipeFH instances.)
"""
CmdStage.__init__(self,
None) #don't do any arg processing in superclass
try:
if isFileHandler(inSource, inTarget):
""" if blur = None, getBlur returns lastblur
if gradient is true, getBlur returns gradient instead of blur
if blur = -1, lastBaseVol is returned and gradient is ignored.
self.transform will be None if there is no previous transform
between input and target. If this is the case, lsq6 and lsq12
defaults are added in the setTransforms function
"""
self.source = inSource.getBlur(blur, gradient)
self.target = inTarget.getBlur(blur, gradient)
self.transform = inSource.getLastXfm(inTarget)
"""If no output transform is specified, use registerVolume to create a default.
If an output transform name is specified, use this as the output, and add it as the last xfm between source and target.
Note: The output file passed in must be a full path."""
if not output:
outputXfm = inSource.registerVolume(inTarget, defaultDir)
self.output = outputXfm
else:
self.output = output
inSource.addAndSetXfmToUse(inTarget, self.output)
outputXfm = output
self.logFile = fh.logFromFile(inSource.logDir, outputXfm)
self.useMask = useMask
if self.useMask:
self.source_mask = inSource.getMask()
self.target_mask = inTarget.getMask()
else:
self.source = inSource
self.target = inTarget
self.output = output
if not logFile:
self.logFile = fh.logFromFile(abspath(curdir), output)
else:
self.logFile = logFile
self.transform = transform
self.useMask = useMask
if self.useMask:
self.source_mask = source_mask
self.target_mask = target_mask
except:
print "Failed in putting together minctracc command."
print "Unexpected error: ", sys.exc_info()
self.linearparam = linearparam
self.iterations = str(iterations)
self.lattice_diameter = str(step * 3.0)
self.step = str(step)
self.weight = str(weight)
self.stiffness = str(stiffness)
self.similarity = str(similarity)
self.w_translations = str(w_translations)
self.w_rotations = str(w_rotations)
self.w_scales = str(w_scales)
self.w_shear = str(w_shear)
self.simplex = str(simplex)
self.optimization = str(optimization)
self.addDefaults()
self.finalizeCommand()
self.setTransform()
self.setName()
self.colour = "red"
def __init__(
self,
inSource,
inTarget,
output=None,
logFile=None,
defaultDir="transforms",
blur=[-1, 0.056],
gradient=[False, True],
target_mask=None, #ANTS only uses one mask
similarity_metric=["CC", "CC"],
weight=[1, 1],
iterations="100x100x100x150",
radius_or_histo=[3, 3],
transformation_model="SyN[0.1]",
regularization="Gauss[2,1]",
useMask=True):
CmdStage.__init__(self,
None) #don't do any arg processing in superclass
try:
if isFileHandler(inSource, inTarget):
"""Same defaults as minctracc class:
blur = None --> return lastblur
gradient = True --> return gradient instead of blur
if blur = -1 --> lastBaseVol returned and gradient ignored"""
self.source = []
self.target = []
# Need to check that length of blur, gradient, similarity, weight
# and radius_or_histo are the same
self.checkArrayLengths(blur, gradient, similarity_metric,
weight, radius_or_histo)
for i in range(len(blur)):
self.source.append(inSource.getBlur(blur[i], gradient[i]))
self.target.append(inTarget.getBlur(blur[i], gradient[i]))
"""If no output transform is specified, use registerVolume to create a default.
If an output transform name is specified, use this as the output, and add it as the last xfm between source and target.
Note: The output file passed in must be a full path."""
if not output:
outputXfm = inSource.registerVolume(inTarget, defaultDir)
self.output = outputXfm
else:
self.output = output
inSource.addAndSetXfmToUse(inTarget, self.output)
self.logFile = fh.logFromFile(inSource.logDir, self.output)
self.useMask = useMask
if self.useMask:
self.target_mask = inTarget.getMask()
else:
self.source = inSource
self.target = inTarget
#MF TODO: Need to find a way to specify multiple source and targets
#based on blur and gradient
self.output = output
if not logFile:
self.logFile = fh.logFromFile(abspath(curdir), output)
else:
self.logFile = logFile
self.useMask = useMask
if self.useMask:
self.target_mask = target_mask
except:
print "Failed in putting together mincANTS command."
print "Unexpected error: ", sys.exc_info()
self.similarity_metric = similarity_metric
self.weight = weight
self.iterations = iterations
self.radius_or_histo = radius_or_histo
"""Single quotes needed on the command line for
transformation_model and regularization
"""
self.transformation_model = "'" + transformation_model + "'"
self.regularization = "'" + regularization + "'"
self.addDefaults()
self.finalizeCommand()
self.setName()
self.colour = "red"
def __init__(self,
inFile,
targetFile,
**kwargs):
"""calls mincresample with the specified options
The inFile and likeFile can be in one of two styles.
The first argument can be an instance of RegistrationPipeFH.
In this case the last volume in that instance (i.e. inFile.lastBasevol)
will be resampled and the output will be determined accordingly.
Alternatively, the inFile can be a string representing a
filename, in which case the output and logfile will be set based on
the inFile name.
inFile is required, everything else optional
This class assuming use of the most commonly used flags (-2, -clobber, -like, -transform)
Any commands above and beyond the standard will be read in from argarray
argarray could contain inFile and/or output files
"""
argArray = kwargs.pop("argArray", None)
if not argArray:
CmdStage.__init__(self, ["mincresample"])
else:
CmdStage.__init__(self, ["mincresample"] + argArray)
try:
#MF TODO: What if we don't want to use lastBasevol?
if isFileHandler(inFile, targetFile):
self.inFile = self.getFileToResample(inFile, **kwargs)
self.targetFile = targetFile.getLastBasevol()
likeFile=kwargs.pop("likeFile", None)
if likeFile:
if isFileHandler(likeFile):
self.likeFile = likeFile.getLastBasevol()
else:
print "likeFile must be RegistrationPipeFH or RegistrationFHBase."
raise
invert = False
for cmd in self.cmd:
if fnmatch.fnmatch(cmd, "*-invert*"):
invert = True
break
xfm = kwargs.pop("transform", None)
if xfm:
self.cxfm = xfm
else:
if invert:
self.cxfm = targetFile.getLastXfm(inFile)
else:
self.cxfm = inFile.getLastXfm(targetFile)
self.outputLocation=kwargs.pop("outputLocation", None)
if not self.outputLocation:
self.outputLocation=inFile
else:
if not isFileHandler(self.outputLocation):
print "outputLocation must be RegistrationPipeFH or RegistrationFHBase."
raise
default = kwargs.pop("defaultDir", None)
if not default:
defaultDir = "resampled"
else:
defaultDir = default
"""If an output file is specified, then use it, else create a default file name.
Note: The output file passed in must be a full path."""
output = kwargs.pop("output", None)
if not output:
self.outfile = self.setOutputFile(self.outputLocation, defaultDir)
else:
self.outfile = output
self.logFile = fh.logFromFile(self.outputLocation.logDir, self.outfile)
else:
self.inFile = inFile
self.targetFile = targetFile
self.likeFile = kwargs.pop("likeFile", None)
self.cxfm = kwargs.pop("transform", None)
self.outfile=kwargs.pop("output", None)
logFile=kwargs.pop("logFile", None)
if not logFile:
self.logFile = fh.logFromFile(abspath(curdir), self.outfile)
else:
self.logFile = logFile
except:
print "Failed in putting together resample command"
print "Unexpected error: ", sys.exc_info()
self.addDefaults()
self.finalizeCommand()
self.setName()
if isFileHandler(inFile, targetFile):
self.setLastResampledFile()
def __init__(self, inFile, targetFile, **kwargs):
"""calls mincresample with the specified options
The inFile and likeFile can be in one of two styles.
The first argument can be an instance of RegistrationPipeFH.
In this case the last volume in that instance (i.e. inFile.lastBasevol)
will be resampled and the output will be determined accordingly.
Alternatively, the inFile can be a string representing a
filename, in which case the output and logfile will be set based on
the inFile name.
inFile is required, everything else optional
This class assuming use of the most commonly used flags (-2, -clobber, -like, -transform)
Any commands above and beyond the standard will be read in from argarray
argarray could contain inFile and/or output files
"""
argArray = kwargs.pop("argArray", None)
if not argArray:
CmdStage.__init__(self, ["mincresample"])
else:
CmdStage.__init__(self, ["mincresample"] + argArray)
try:
#MF TODO: What if we don't want to use lastBasevol?
if isFileHandler(inFile, targetFile):
self.inFile = self.getFileToResample(inFile, **kwargs)
self.targetFile = targetFile.getLastBasevol()
likeFile = kwargs.pop("likeFile", None)
if likeFile:
if isFileHandler(likeFile):
self.likeFile = likeFile.getLastBasevol()
else:
print "likeFile must be RegistrationPipeFH or RegistrationFHBase."
raise
invert = False
for cmd in self.cmd:
if fnmatch.fnmatch(cmd, "*-invert*"):
invert = True
break
xfm = kwargs.pop("transform", None)
if xfm:
self.cxfm = xfm
else:
if invert:
self.cxfm = targetFile.getLastXfm(inFile)
else:
self.cxfm = inFile.getLastXfm(targetFile)
self.outputLocation = kwargs.pop("outputLocation", None)
if not self.outputLocation:
self.outputLocation = inFile
else:
if not isFileHandler(self.outputLocation):
print "outputLocation must be RegistrationPipeFH or RegistrationFHBase."
raise
default = kwargs.pop("defaultDir", None)
if not default:
defaultDir = "resampled"
else:
defaultDir = default
"""If an output file is specified, then use it, else create a default file name.
Note: The output file passed in must be a full path."""
output = kwargs.pop("output", None)
if not output:
self.outfile = self.setOutputFile(self.outputLocation,
defaultDir)
else:
self.outfile = output
self.logFile = fh.logFromFile(self.outputLocation.logDir,
self.outfile)
else:
self.inFile = inFile
self.targetFile = targetFile
self.likeFile = kwargs.pop("likeFile", None)
self.cxfm = kwargs.pop("transform", None)
self.outfile = kwargs.pop("output", None)
logFile = kwargs.pop("logFile", None)
if not logFile:
self.logFile = fh.logFromFile(abspath(curdir),
self.outfile)
else:
self.logFile = logFile
except:
print "Failed in putting together resample command"
print "Unexpected error: ", sys.exc_info()
self.addDefaults()
self.finalizeCommand()
self.setName()
if isFileHandler(inFile, targetFile):
self.setLastResampledFile()
def __init__(self,
inSource,
inTarget,
output=None,
logFile=None,
defaultDir="transforms",
blur=[-1, 0.056],
gradient=[False, True],
target_mask=None, #ANTS only uses one mask
similarity_metric=["CC", "CC"],
weight=[1,1],
iterations="100x100x100x150",
radius_or_histo=[3,3],
transformation_model="SyN[0.1]",
regularization="Gauss[2,1]",
useMask=True):
CmdStage.__init__(self, None) #don't do any arg processing in superclass
try:
if isFileHandler(inSource, inTarget):
"""Same defaults as minctracc class:
blur = None --> return lastblur
gradient = True --> return gradient instead of blur
if blur = -1 --> lastBaseVol returned and gradient ignored"""
self.source = []
self.target = []
# Need to check that length of blur, gradient, similarity, weight
# and radius_or_histo are the same
self.checkArrayLengths(blur,
gradient,
similarity_metric,
weight,
radius_or_histo)
for i in range(len(blur)):
self.source.append(inSource.getBlur(blur[i], gradient[i]))
self.target.append(inTarget.getBlur(blur[i], gradient[i]))
"""If no output transform is specified, use registerVolume to create a default.
If an output transform name is specified, use this as the output, and add it as the last xfm between source and target.
Note: The output file passed in must be a full path."""
if not output:
outputXfm = inSource.registerVolume(inTarget, defaultDir)
self.output = outputXfm
else:
self.output = output
inSource.addAndSetXfmToUse(inTarget, self.output)
self.logFile = fh.logFromFile(inSource.logDir, self.output)
self.useMask=useMask
if self.useMask:
self.target_mask = inTarget.getMask()
else:
self.source = inSource
self.target = inTarget
#MF TODO: Need to find a way to specify multiple source and targets
#based on blur and gradient
self.output = output
if not logFile:
self.logFile = fh.logFromFile(abspath(curdir), output)
else:
self.logFile = logFile
self.useMask=useMask
if self.useMask:
self.target_mask = target_mask
except:
print "Failed in putting together mincANTS command."
print "Unexpected error: ", sys.exc_info()
self.similarity_metric = similarity_metric
self.weight = weight
self.iterations = iterations
self.radius_or_histo = radius_or_histo
"""Single quotes needed on the command line for
transformation_model and regularization
"""
self.transformation_model = "'" + transformation_model + "'"
self.regularization = "'" + regularization + "'"
self.addDefaults()
self.finalizeCommand()
self.setName()
self.colour = "red"
def __init__(self, inFile, fwhm, defaultDir="tmp", gradient=False):
"""calls mincblur with the specified 3D Gaussian kernel
The inputs can be in one of two styles. The first argument can
be an instance of RegistrationPipeFH, in which case the last
volume in that instance (i.e. inFile.lastBasevol) will be
blurred and the output will be determined by its blurFile
method. Alternately, the inFile can be a string representing a
filename, in which case the output and logfile will be set based on
the inFile name. If the fwhm specified is -1, we do not construct
a command.
"""
if fwhm == -1:
return
CmdStage.__init__(self, None)
try:
if isFileHandler(inFile):
blurlist = inFile.blurFile(fwhm, gradient, defaultDir)
self.base = blurlist["base"]
self.inputFiles = [inFile.getLastBasevol()]
self.outputFiles = [blurlist["file"]]
self.logFile = blurlist["log"]
self.name = "mincblur " + str(fwhm) + " " + inFile.basename
if gradient:
self.outputFiles.append(blurlist["gradient"])
else:
self.base = str(inFile).replace(".mnc", "")
self.inputFiles = [inFile]
blurBase = "".join([self.base, "_fwhm", str(fwhm), "_blur"])
output = "".join([blurBase, ".mnc"])
self.outputFiles = [output]
self.logFile = fh.logFromFile(abspath(curdir), output)
self.name = "mincblur " + str(fwhm) + " " + basename(inFile)
if gradient:
gradientBase = blurBase.replace("blur", "dxyz")
self.outputFiles += ["".join([gradientBase, ".mnc"])]
except:
print "Failed in putting together blur command; unexpected error: "
raise
self.cmd = [
"mincblur", "-clobber", "-no_apodize", "-fwhm",
str(fwhm), self.inputFiles[0], self.base
]
if gradient:
self.cmd += ["-gradient"]
self.colour = "blue"
# this is a temporary solution, but it's better to at least catch it
# somewhere... In the mincblur code, there is a hardcoded limit for
# the length of the output file: full_outfilename[256]; (blur_volume.c)
# This is a limit for the basename. Added to that will be: _dxyz.mnc
# or _blur.mnc. In total the output file names can not be longer than 264
# characters. Given that we don't know which version of mincblur is installed
# (this should and will be fixed at some point in the future), we'll exit here
if len(self.outputFiles[0]) > 264:
raise Exception(
"mincblur (potentially) has a hardcoded limit for the allowed length of the output file. The following command will not be able to run: \n\n%s\n\nPlease rename your input files/paths to make sure the filenames become shorter.\n"
% self.cmd)
