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 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
respoints = resamplePoints(points, dataSize, shiftPoints = True, **resamplingParameter);
print("Reshaped centers shape: (%d, %d)" % respoints.shape)
if verbose:
dataraw = io.readData(os.path.join(baseDirectory, 'Data/Synthetic/test_iDISCO_\d{3}.tif'));
datares = io.readData(os.path.join(baseDirectory, 'Synthetic/test_iDISCO_resample.tif'));
print("Shape raw: " + str(dataraw.shape))
print("Shape res: " + str(datares.shape))
plot.plotOverlayPoints(dataraw*0.01, points);
plot.plotOverlayPoints(datares*0.01, respoints);
#check inverse:
resipoints = resamplePointsInverse(respoints, dataSize, **resamplingParameter);
diff = points - resipoints;
print (diff.max(), diff.min());
##############################################################################
# Test Transform Points on Corners
##############################################################################
import numpy
import iDISCO.Alignment.Elastix as elx;
verbose = True;
respoints = resamplePoints(points, dataSize, shiftPoints = True, **resamplingParameter);
print "Reshaped centers shape: (%d, %d)" % respoints.shape
if verbose:
dataraw = io.readData(os.path.join(baseDirectory, 'Data/Synthetic/test_iDISCO_\d{3}.tif'));
datares = io.readData(os.path.join(baseDirectory, 'Synthetic/test_iDISCO_resample.tif'));
print "Shape raw: " + str(dataraw.shape)
print "Shape res: " + str(datares.shape)
plot.plotOverlayPoints(dataraw*0.01, points);
plot.plotOverlayPoints(datares*0.01, respoints);
#check inverse:
resipoints = resamplePointsInverse(respoints, dataSize, **resamplingParameter);
diff = points - resipoints;
print (diff.max(), diff.min());
##############################################################################
# Test Transform Points on Corners
##############################################################################
import numpy
import iDISCO.Alignment.Elastix as elx;
verbose = True;
