def deformationField(sink=[],
transformParameterFile=None,
transformDirectory=None,
resultDirectory=None):
"""Create the deformation field T(x) - x
The map determined by elastix is
:math:`T \\mathrm{fixed} \\rightarrow \\mathrm{moving}`
Arguments:
sink (str, [] or None): image sink to save the transformation field; if [] return the default name of the data file generated by transformix.
transformParameterFile (str or None): parameter file for the primary transformation, if None, the file is determined from the transformDirectory.
transformDirectory (str or None): result directory of elastix alignment, if None the transformParameterFile has to be given.
resultDirectory (str or None): the directorty for the transformix results
Returns:
array or str: array or file name of the transformed data
"""
global TransformixBinary
if resultDirectory == None:
resultdirname = os.path.join(tempfile.gettempdir(), 'elastix_output')
else:
resultdirname = resultDirectory
if not os.path.exists(resultdirname):
os.makedirs(resultdirname)
if transformParameterFile == None:
if transformDirectory == None:
raise RuntimeError(
'neither alignment directory and transformation parameter file specified!'
)
transformparameterdir = transformDirectory
transformParameterFile = getTransformParameterFile(
transformparameterdir)
else:
transformparameterdir = os.path.split(transformParameterFile)
transformparameterdir = transformparameterdir[0]
#transform
#make path in parameterfiles absolute
setPathTransformParameterFiles(transformparameterdir)
#transformix -in inputImage.ext -out outputDirectory -tp TransformParameters.txt
cmd = TransformixBinary + ' -threads 8 -def all -out ' + resultdirname + ' -tp ' + transformParameterFile
res = os.system(cmd)
if res != 0:
raise RuntimeError('deformationField: failed executing: ' + cmd)
if sink == []:
return getResultDataFile(resultdirname)
elif sink is None:
resultfile = getResultDataFile(resultdirname)
data = io.readData(resultfile)
if resultDirectory is None:
shutil.rmtree(resultdirname)
return data
elif isinstance(sink, basestring):
resultfile = getResultDataFile(resultdirname)
data = io.convertData(resultfile, sink)
if resultDirectory is None:
shutil.rmtree(resultdirname)
return data
else:
raise RuntimeError('deformationField: sink not valid!')
def deformationField(sink = [], transformParameterFile = None, transformDirectory = None, resultDirectory = None):
"""Create the deformation field T(x) - x
The map determined by elastix is
:math:`T \\mathrm{fixed} \\rightarrow \\mathrm{moving}`
Arguments:
sink (str, [] or None): image sink to save the transformation field; if [] return the default name of the data file generated by transformix.
transformParameterFile (str or None): parameter file for the primary transformation, if None, the file is determined from the transformDirectory.
transformDirectory (str or None): result directory of elastix alignment, if None the transformParameterFile has to be given.
resultDirectory (str or None): the directorty for the transformix results
Returns:
array or str: array or file name of the transformed data
"""
global TransformixBinary;
if resultDirectory == None:
resultdirname = os.path.join(tempfile.tempdir, 'elastix_output');
else:
resultdirname = resultDirectory;
if not os.path.exists(resultdirname):
os.makedirs(resultdirname);
if transformParameterFile == None:
if transformDirectory == None:
raise RuntimeError('neither alignment directory and transformation parameter file specified!');
transformparameterdir = transformDirectory
transformParameterFile = getTransformParameterFile(transformparameterdir);
else:
transformparameterdir = os.path.split(transformParameterFile);
transformparameterdir = transformparameterdir[0];
#transform
#make path in parameterfiles absolute
setPathTransformParameterFiles(transformparameterdir);
#transformix -in inputImage.ext -out outputDirectory -tp TransformParameters.txt
cmd = TransformixBinary + ' -def all -out ' + resultdirname + ' -tp ' + transformParameterFile;
res = os.system(cmd);
if res != 0:
raise RuntimeError('deformationField: failed executing: ' + cmd);
if sink == []:
return getResultDataFile(resultdirname);
elif sink is None:
resultfile = getResultDataFile(resultdirname);
data = io.readData(resultfile);
if resultDirectory is None:
shutil.rmtree(resultdirname);
return data;
elif isinstance(sink, basestring):
resultfile = getResultDataFile(resultdirname);
data = io.convertData(resultfile, sink);
if resultDirectory is None:
shutil.rmtree(resultdirname);
return data;
else:
raise RuntimeError('deformationField: sink not valid!');
def transformData(source,
sink=[],
transformParameterFile=None,
transformDirectory=None,
resultDirectory=None):
"""Transform a raw data set to reference using the elastix alignment results
If the map determined by elastix is
:math:`T \\mathrm{fixed} \\rightarrow \\mathrm{moving}`,
transformix on data works as :math:`T^{-1}(\\mathrm{data})`.
Arguments:
source (str or array): image source to be transformed
sink (str, [] or None): image sink to save transformed image to. if [] return the default name of the data file generated by transformix.
transformParameterFile (str or None): parameter file for the primary transformation, if None, the file is determined from the transformDirectory.
transformDirectory (str or None): result directory of elastix alignment, if None the transformParameterFile has to be given.
resultDirectory (str or None): the directorty for the transformix results
Returns:
array or str: array or file name of the transformed data
"""
global TransformixBinary
if isinstance(source, numpy.ndarray):
imgname = os.path.join(tempfile.gettempdir(), 'elastix_input.tif')
io.writeData(source, imgname)
elif isinstance(source, basestring):
if io.dataFileNameToType(source) == "TIF":
imgname = source
else:
imgname = os.path.join(tempfile.gettempdir(), 'elastix_input.tif')
io.transformData(source, imgname)
else:
raise RuntimeError('transformData: source not a string or array')
if resultDirectory == None:
resultdirname = os.path.join(tempfile.gettempdir(), 'elastix_output')
else:
resultdirname = resultDirectory
if not os.path.exists(resultdirname):
os.makedirs(resultdirname)
if transformParameterFile == None:
if transformDirectory == None:
raise RuntimeError(
'neither alignment directory and transformation parameter file specified!'
)
transformparameterdir = transformDirectory
transformParameterFile = getTransformParameterFile(
transformparameterdir)
else:
transformparameterdir = os.path.split(transformParameterFile)
transformparameterdir = transformparameterdir[0]
#transform
#make path in parameterfiles absolute
setPathTransformParameterFiles(transformparameterdir)
#transformix -in inputImage.ext -out outputDirectory -tp TransformParameters.txt
cmd = TransformixBinary + ' -threads 8 -in ' + imgname + ' -out ' + resultdirname + ' -tp ' + transformParameterFile
res = os.system(cmd)
if res != 0:
raise RuntimeError('transformData: failed executing: ' + cmd)
if not isinstance(source, basestring):
os.remove(imgname)
if sink == []:
return getResultDataFile(resultdirname)
elif sink is None:
resultfile = getResultDataFile(resultdirname)
return io.readData(resultfile)
elif isinstance(sink, basestring):
resultfile = getResultDataFile(resultdirname)
return io.convertData(resultfile, sink)
else:
raise RuntimeError('transformData: sink not valid!')
def transformData(source, sink = [], transformParameterFile = None, transformDirectory = None, resultDirectory = None):
"""Transform a raw data set to reference using the elastix alignment results
If the map determined by elastix is
:math:`T \\mathrm{fixed} \\rightarrow \\mathrm{moving}`,
transformix on data works as :math:`T^{-1}(\\mathrm{data})`.
Arguments:
source (str or array): image source to be transformed
sink (str, [] or None): image sink to save transformed image to. if [] return the default name of the data file generated by transformix.
transformParameterFile (str or None): parameter file for the primary transformation, if None, the file is determined from the transformDirectory.
transformDirectory (str or None): result directory of elastix alignment, if None the transformParameterFile has to be given.
resultDirectory (str or None): the directorty for the transformix results
Returns:
array or str: array or file name of the transformed data
"""
global TransformixBinary;
if isinstance(source, numpy.ndarray):
imgname = os.path.join(tempfile.gettempdir(), 'elastix_input.tif');
io.writeData(source, imgname);
elif isinstance(source, basestring):
if io.dataFileNameToType(source) == "TIF":
imgname = source;
else:
imgname = os.path.join(tempfile.gettempdir(), 'elastix_input.tif');
io.transformData(source, imgname);
else:
raise RuntimeError('transformData: source not a string or array');
if resultDirectory == None:
resultdirname = os.path.join(tempfile.tempdir, 'elastix_output');
else:
resultdirname = resultDirectory;
if not os.path.exists(resultdirname):
os.makedirs(resultdirname);
if transformParameterFile == None:
if transformDirectory == None:
raise RuntimeError('neither alignment directory and transformation parameter file specified!');
transformparameterdir = transformDirectory
transformParameterFile = getTransformParameterFile(transformparameterdir);
else:
transformparameterdir = os.path.split(transformParameterFile);
transformparameterdir = transformparameterdir[0];
#transform
#make path in parameterfiles absolute
setPathTransformParameterFiles(transformparameterdir);
#transformix -in inputImage.ext -out outputDirectory -tp TransformParameters.txt
cmd = TransformixBinary + ' -in ' + imgname + ' -out ' + resultdirname + ' -tp ' + transformParameterFile;
res = os.system(cmd);
if res != 0:
raise RuntimeError('transformData: failed executing: ' + cmd);
if not isinstance(source, basestring):
os.remove(imgname);
if sink == []:
return getResultDataFile(resultdirname);
elif sink is None:
resultfile = getResultDataFile(resultdirname);
return io.readData(resultfile);
elif isinstance(sink, basestring):
resultfile = getResultDataFile(resultdirname);
return io.convertData(resultfile, sink);
else:
raise RuntimeError('transformData: sink not valid!');
