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.Alignment.MovingImage = os.path.join(basedirectory, 'Synthetic/test_iDISCO_resample.tif'); parameter.Alignment.FixedImage = os.path.join(basedirectory, 'Synthetic/test_iDISCO_reference.tif'); parameter.Alignment.FixedImageMask = None; #elastix parameter files for alignment parameter.Alignment.AffineParameterFile = os.path.join(parameter.Alignment.AlignmentDirectory, 'ElastixParameterAffine.txt'); #parameter.Alignment.BSplineParameterFile = os.path.join(parameter.Alignment.AlignmentDirectory, 'ElastixParameterBSpline.txt'); parameter.Alignment.BSplineParameterFile = None; runInitializeElastix(parameter) runCellCoordinateTransformationToReference(parameter) if verbose: refdata = io.readData(parameter.Alignment.FixedImage); pts = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile); Plot.plotOverlayPoints(0.01 * refdata, pts) ############################################################################## # Test Voxelization ############################################################################## import os from iDISCO.Parameter import * from iDISCO.Run import runVoxelization import iDISCO.Visualization.Plot as Plot
#pts[0,:] = [0,0,0]; #pts = pts[:, [1,0,2]]; runCellCoordinateTransformationToReference(parameter) #pts2 = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile); #pts2 = pts2[:,[1,0,2]]; if verbose: refdata = io.readData(parameter.Alignment.FixedImage) #pts = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile); Plot.plotOverlayPoints(0.1 * refdata, pts2) refdata.shape pts2 = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile) #pts2 = pts2[:,[1,0,2]]; voximg = vox.voxelizePixel(pts2, refdata.shape) io.writeDataStack(os.path.join(basedirectory, 'points_transformed_pixel.tif'), voximg) ############################################################################## # Test Resample Points ############################################################################## import os import numpy from iDISCO.Parameter import * from iDISCO.Run import runResampling import iDISCO.IO.IO as io
runCellCoordinateTransformationToReference(parameter) #pts2 = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile); #pts2 = pts2[:,[1,0,2]]; if verbose: refdata = io.readData(parameter.Alignment.FixedImage); #pts = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile); Plot.plotOverlayPoints(0.1 * refdata, pts2) refdata.shape pts2 = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile); #pts2 = pts2[:,[1,0,2]]; voximg = vox.voxelizePixel(pts2, refdata.shape); io.writeDataStack(os.path.join(basedirectory, 'points_transformed_pixel.tif'), voximg) ############################################################################## # Test Resample Points ############################################################################## import os import numpy;
allParameter = joinParameter(stackProcessingParameter, spotDetectionParameter, {'x' : (100,160), 'y' : (10,140), 'z' : (2,38)}) #allParameter = joinParameter(stackProcessingParameter, spotDetectionParameter, {'x' : all, 'y' : all, 'z' : all}) result = detectCells(**allParameter); print(result) verbose = True; if verbose: import iDISCO.IO.IO as io import iDISCO.Visualization.Plot as plot dataraw = io.readData(spotDetectionParameter["source"]); dataraw[dataraw > 50] = 50; dataraw = dataraw.astype('float') / dataraw.max(); points = io.readPoints(spotDetectionParameter["sink"][0]); plot.plotOverlayPoints(dataraw, points, pointColor = [1,0,0]); dataraw = io.readData(spotDetectionParameter["source"], x = (100,160), y = (10,140), z = (2,38)); io.writeData( os.path.join(baseDirectory, 'Synthetic/raw.tif'), dataraw) ############################################################################## # Test Resample Points ############################################################################## import os import iDISCO.Settings as settings import iDISCO.IO.IO as io import iDISCO.Visualization.Plot as plot
allParameter = joinParameter(stackProcessingParameter, spotDetectionParameter, {'x' : (100,160), 'y' : (10,140), 'z' : (2,38)}) #allParameter = joinParameter(stackProcessingParameter, spotDetectionParameter, {'x' : all, 'y' : all, 'z' : all}) result = detectCells(**allParameter); print result verbose = True; if verbose: import iDISCO.IO.IO as io import iDISCO.Visualization.Plot as plot dataraw = io.readData(spotDetectionParameter["source"]); dataraw[dataraw > 50] = 50; dataraw = dataraw.astype('float') / dataraw.max(); points = io.readPoints(spotDetectionParameter["sink"][0]); plot.plotOverlayPoints(dataraw, points, pointColor = [1,0,0]); dataraw = io.readData(spotDetectionParameter["source"], x = (100,160), y = (10,140), z = (2,38)); io.writeData( os.path.join(baseDirectory, 'Synthetic/raw.tif'), dataraw) ############################################################################## # Test Resample Points ############################################################################## import os import iDISCO.Settings as settings import iDISCO.IO.IO as io import iDISCO.Visualization.Plot as plot