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
parameter.Resampling.Processes = 4; resampledImage = runResampling(parameter); print "Resampled image saved as %s" % resampledImage # voxelize result voximg = vox.voxelizePixel(acenters, referencedata.shape); io.writeDataStack(os.path.join(basedirectory, 'Synthetic/points_transformed_pixel.tif'), 5000* voximg) if verbose: transformdata = io.readData(os.path.join(transformdir, 'result.mhd')); referencedata = io.readData(os.path.join(basedirectory, 'Synthetic/test_iDISCO_resample.tif')) Plot.plotOverlayPoints(transformdata * 0.01, acenters); Plot.plotOverlayPoints(referencedata * 0.01, acenters);
runInitializeElastix(parameter) pts = runCellCoordinateTransformation(parameter) io.writePoints(os.path.join(basedirectory, 'cells_to_autofluo.csv'), pts) ## Visualize cfos to auto points parameter.ImageProcessing.CellCoordinateFile = pts parameter.ImageProcessing.CellTransformedCoordinateFile = None pts2 = runCellCoordinateResampling(parameter) ds = dataSize(os.path.join(basedirectory, 'autofluo_for_cfos_resample.tif')) voximg = vox.voxelizePixel(pts2, ds) io.writeDataStack( os.path.join(basedirectory, 'points_transformed_cfos_to_auto.tif'), voximg) #pts0 = io.readPoints(os.path.join(basedirectory, 'cells.csv')); ############################################################################## # Transform Points matched to Autofluorescence to Atlas Reference ############################################################################## import os from iDISCO.Parameter import * from iDISCO.Run import runInitializeElastix, runCellCoordinateTransformationToReference import iDISCO.Visualization.Plot as Plot import iDISCO.IO.IO as io
pts = runCellCoordinateTransformation(parameter); io.writePoints(os.path.join(basedirectory, 'cells_to_autofluo.csv'), pts); ## Visualize cfos to auto points parameter.ImageProcessing.CellCoordinateFile = pts; parameter.ImageProcessing.CellTransformedCoordinateFile = None; pts2 = runCellCoordinateResampling(parameter) ds = dataSize(os.path.join(basedirectory, 'autofluo_for_cfos_resample.tif')); voximg = vox.voxelizePixel(pts2, ds); io.writeDataStack(os.path.join(basedirectory, 'points_transformed_cfos_to_auto.tif'), voximg) #pts0 = io.readPoints(os.path.join(basedirectory, 'cells.csv')); ############################################################################## # Transform Points matched to Autofluorescence to Atlas Reference ############################################################################## import os from iDISCO.Parameter import * from iDISCO.Run import runInitializeElastix, runCellCoordinateTransformationToReference import iDISCO.Visualization.Plot as Plot
parameter.Resampling.Processes = 4; resampledImage = runResampling(parameter); print("Resampled image saved as %s" % resampledImage) # voxelize result voximg = vox.voxelizePixel(acenters, referencedata.shape); io.writeDataStack(os.path.join(basedirectory, 'Synthetic/points_transformed_pixel.tif'), 5000* voximg) if verbose: transformdata = io.readData(os.path.join(transformdir, 'result.mhd')); referencedata = io.readData(os.path.join(basedirectory, 'Synthetic/test_iDISCO_resample.tif')) Plot.plotOverlayPoints(transformdata * 0.01, acenters); Plot.plotOverlayPoints(referencedata * 0.01, acenters);