def runVoxelization(parameter): """Voxelize a set of points""" cf = parameter.ImageProcessing.CellTransformedCoordinateFile; if cf is None: cf = parameter.ImageProcessing.CellCoordinateFile; points = io.readPoints(cf); pv = parameter.Voxelization; si = pv.Size; if si is None: si = parameter.Alignment.MovingImage; if si is None: si = parameter.Resampling.ResampledFile; if isinstance(si, basestring): si = dataSize(si); print si vox = voxelize(points, si, average = pv.AveragingDiameter, mode = pv.Mode); vf = pv.File; if vf is None: return vox; else: io.writeDataStack(vf, vox.astype('int32')); return vf;
def runVoxelization(parameter): """Voxelize a set of points""" cf = parameter.ImageProcessing.CellTransformedCoordinateFile if cf is None: cf = parameter.ImageProcessing.CellCoordinateFile points = io.readPoints(cf) pv = parameter.Voxelization si = pv.Size if si is None: si = parameter.Alignment.MovingImage if si is None: si = parameter.Resampling.ResampledFile if isinstance(si, str): si = dataSize(si) print(si) vox = voxelize(points, si, average=pv.AveragingDiameter, mode=pv.Mode) vf = pv.File if vf is None: return vox else: io.writeDataStack(vf, vox.astype('int32')) return vf
# Voxelization weigths (e/g intensities) "voxelizationWeights" : None }; #Points transformedPointsFile = os.path.join(baseDirectory, 'Synthetic/cells_transformed_to_reference.csv') #Reference file referenceFile = os.path.join(baseDirectory, 'Synthetic/test_iDISCO_reference.tif'); #voxelization file voxelizationFile = None; voxdata = voxelize(transformedPointsFile, dataSize = referenceFile, sink = voxelizationFile, **voxelizationParameter) if verbose: #voxdata = io.readData(parameter.Alignment.FixedImage); voxdata = io.readData(voxdata); points = io.readPoints(transformedPointsFile) plot.plotOverlayPoints(voxdata.astype('float') / voxdata.max(), points) ## with weights import numpy points = io.readPoints(transformedPointsFile) voxelizationParameter["voxelizationSize"] = (9,9,9);