def runCellCoordinateTransformationToReference(parameter):
"""Transform points by resampling and applying the elastix transformation in the reference data"""
im = parameter.Resampling.DataFiles;
if im is None:
im = parameter.DataSource.ImageFile;
cf = parameter.ImageProcessing.CellCoordinateFile;
pa = parameter.Alignment;
pr = parameter.Resampling;
# downscale points to referenece image size
points = resamplePoints(cf, im, resolutionData = pr.ResolutionData, resolutionReference = pr.ResolutionReference, orientation = pr.Orientation);
# transform points
#points = points[:,[1,0,2]];
points = transformPoints(points, alignmentdirectory = pa.AlignmentDirectory, transformparameterfile = None, read = True, tmpfile = None, outdirectory = None, indices = True);
#points = points[:,[1,0,2]];
tf = parameter.ImageProcessing.CellTransformedCoordinateFile;
if tf is None:
return points;
else:
io.writePoints(tf, points);
return tf;
def runCellCoordinateTransformation(parameter):
"""Transform points by resampling applying the elastix transformation and then re-resample again"""
im = parameter.Resampling.DataFiles;
if im is None:
im = parameter.DataSource.ImageFile;
cf = parameter.ImageProcessing.CellCoordinateFile;
pa = parameter.Alignment;
pr = parameter.Resampling;
# downscale points to referenece image size
points = resamplePoints(cf, im, resolutionData = pr.ResolutionData, resolutionReference = pr.ResolutionReference, orientation = pr.Orientation);
# transform points
points = points[:,[1,0,2]]; # account for (y,x, z) array representaton here
points = transformPoints(points, alignmentdirectory = pa.AlignmentDirectory, transformparameterfile = None, read = True, tmpfile = None, outdirectory = None, indices = False);
points = points[:,[1,0,2]]; # account for (y,x, z) array representaton here
# upscale ppints back to original size
points = resamplePointsInverse(points, im, resolutionData = pr.ResolutionData, resolutionReference = pr.ResolutionReference, orientation = pr.Orientation);
tf = parameter.ImageProcessing.CellTransformedCoordinateFile;
if tf is None:
return points;
else:
io.writePoints(tf, points);
return tf;
def runCellCoordinateTransformationToReference(parameter):
"""Transform points by resampling and applying the elastix transformation in the reference data"""
im = parameter.Resampling.DataFiles
if im is None:
im = parameter.DataSource.ImageFile
cf = parameter.ImageProcessing.CellCoordinateFile
pa = parameter.Alignment
pr = parameter.Resampling
# downscale points to referenece image size
points = resamplePoints(cf,
im,
resolutionData=pr.ResolutionData,
resolutionReference=pr.ResolutionReference,
orientation=pr.Orientation)
# transform points
#points = points[:,[1,0,2]];
points = transformPoints(points,
alignmentdirectory=pa.AlignmentDirectory,
transformparameterfile=None,
read=True,
tmpfile=None,
outdirectory=None,
indices=True)
#points = points[:,[1,0,2]];
tf = parameter.ImageProcessing.CellTransformedCoordinateFile
if tf is None:
return points
else:
io.writePoints(tf, points)
return tf
def runCellCoordinateTransformation(parameter):
"""Transform points by resampling applying the elastix transformation and then re-resample again"""
im = parameter.Resampling.DataFiles
if im is None:
im = parameter.DataSource.ImageFile
cf = parameter.ImageProcessing.CellCoordinateFile
pa = parameter.Alignment
pr = parameter.Resampling
# downscale points to referenece image size
points = resamplePoints(cf,
im,
resolutionData=pr.ResolutionData,
resolutionReference=pr.ResolutionReference,
orientation=pr.Orientation)
# transform points
points = points[:, [1, 0, 2]]
# account for (y,x, z) array representaton here
points = transformPoints(points,
alignmentdirectory=pa.AlignmentDirectory,
transformparameterfile=None,
read=True,
tmpfile=None,
outdirectory=None,
indices=False)
points = points[:, [1, 0, 2]]
# account for (y,x, z) array representaton here
# upscale ppints back to original size
points = resamplePointsInverse(points,
im,
resolutionData=pr.ResolutionData,
resolutionReference=pr.ResolutionReference,
orientation=pr.Orientation)
tf = parameter.ImageProcessing.CellTransformedCoordinateFile
if tf is None:
return points
else:
io.writePoints(tf, points)
return tf
#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)
};
alignmentDirectory = os.path.join(baseDirectory, 'Synthetic/elastix');
# downscale points to referenece image size
points = resamplePoints(pointsFile, dataFile, **resamplingParameter);
# transform points
points = transformPoints(points, transformDirectory = alignmentDirectory, indices = False, resultDirectory = None);
# save
io.writePoints(transformedPointsFile, points);
if verbose:
refdata = io.readData(os.path.join(baseDirectory, 'Synthetic/test_iDISCO_reference.tif'));
plot.plotOverlayPoints(0.01 * refdata, points)
#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)
};
alignmentDirectory = os.path.join(baseDirectory, 'Synthetic/elastix');
# downscale points to referenece image size
points = resamplePoints(pointsFile, dataFile, **resamplingParameter);
# transform points
points = transformPoints(points, transformDirectory = alignmentDirectory, indices = False, resultDirectory = None);
# save
io.writePoints(transformedPointsFile, points);
if verbose:
refdata = io.readData(os.path.join(baseDirectory, 'Synthetic/test_iDISCO_reference.tif'));
plot.plotOverlayPoints(0.01 * refdata, points)