def runResampling(parameter):
"""Resample data"""
rp = parameter.Resampling;
im = rp.Source;
if im is None:
im = parameter.DataSource.ImageFile;
resampleData(im, outputFile = rp.ResampledFile,
resolutionData = rp.ResolutionData, resolutionReference = rp.ResolutionReference,
processingDirectory = None, processes = rp.Processes, cleanup = True, orientation = rp.Orientation);
return rp.ResampledFile;
def runResampling(parameter):
"""Resample data"""
rp = parameter.Resampling
im = rp.Source
if im is None:
im = parameter.DataSource.ImageFile
resampleData(im,
outputFile=rp.ResampledFile,
resolutionData=rp.ResolutionData,
resolutionReference=rp.ResolutionReference,
processingDirectory=None,
processes=rp.Processes,
cleanup=True,
orientation=rp.Orientation)
return rp.ResampledFile
#Resolution of the raw data (in um / pixel) as (x,y,z)
"resolutionSource" : (5, 5, 3),
#Resolution of the Reference / Atlas (in um/ pixel) as (x,y,z)
"resolutionSink" : (12, 15, 5),
#Orientation of the Data set wrt reference as (x=1,y=2,z=3)
#(-axis will invert the orientation, for other hemisphere use (-1, 2, 3), to exchnge x,y use (2,1,3) etc)
"orientation" : (1,2,3),
#number of processes to use in parallel:
"processes" : 4,
};
resampledImage = resampleData(**resamplingParameter)
print("Resampled image saved as %s" % resampledImage)
# create reference for further tests
#import shutil
#shutil.copyfile(resampledImage, os.path.join(baseDirectory, 'Synthetic/test_iDISCO_reference.tif'))
resamplingParameter["sink"] = os.path.join(baseDirectory, 'Synthetic/test_iDISCO_reference.tif');
resamplingParameter["resolutionSink"] = (12, 12, 5);
referenceImage = resampleData(**resamplingParameter);
print("Reference image saved as %s" % referenceImage)
# use None as sink to get the numpy array
resamplingParameter["sink"] = None
referenceImage = resampleData(**resamplingParameter);
#Resolution of the raw data (in um / pixel) as (x,y,z)
"resolutionSource" : (5, 5, 3),
#Resolution of the Reference / Atlas (in um/ pixel) as (x,y,z)
"resolutionSink" : (12, 15, 5),
#Orientation of the Data set wrt reference as (x=1,y=2,z=3)
#(-axis will invert the orientation, for other hemisphere use (-1, 2, 3), to exchnge x,y use (2,1,3) etc)
"orientation" : (1,2,3),
#number of processes to use in parallel:
"processes" : 4,
};
resampledImage = resampleData(**resamplingParameter)
print "Resampled image saved as %s" % resampledImage
# create reference for further tests
#import shutil
#shutil.copyfile(resampledImage, os.path.join(baseDirectory, 'Synthetic/test_iDISCO_reference.tif'))
resamplingParameter["sink"] = os.path.join(baseDirectory, 'Synthetic/test_iDISCO_reference.tif');
resamplingParameter["resolutionSink"] = (12, 12, 5);
referenceImage = resampleData(**resamplingParameter);
print "Reference image saved as %s" % referenceImage
# use None as sink to get the numpy array
resamplingParameter["sink"] = None
referenceImage = resampleData(**resamplingParameter);
