def _cropParallel(arg):
"""Cropping helper function to use for parallel cropping of image slices"""
fileSource = arg[0]
fileSink = arg[1]
x = arg[2]
y = arg[3]
ii = arg[4]
nn = arg[5]
if ii is not None:
pw = ProcessWriter(ii)
pw.write("cropData: corpping image %d / %d" % (ii, nn))
# pw.write('%s -> %s' % (fileSource, fileSink));
data = io.readData(fileSource, x=x, y=y)
io.writeData(fileSink, data)
def _resampleXYParallel(arg):
"""Resampling helper function to use for parallel resampling of image slices"""
fileSource = arg[0];
fileSink = arg[1];
dataSizeSink = arg[2];
interpolation = arg[3];
ii = arg[4];
nn = arg[5];
verbose = arg[6];
pw = ProcessWriter(ii);
if verbose:
pw.write("resampleData: resampling in XY: image %d / %d" % (ii, nn))
data = numpy.squeeze(io.readData(fileSource, z = ii));
resampleXY(data, sink = fileSink, dataSizeSink = dataSizeSink, interpolation = interpolation, out = pw, verbose = verbose);
def _resampleXYParallel(arg):
"""Resampling helper function to use for parallel resampling of image slices"""
fileSource = arg[0];
fileSink = arg[1];
dataSizeSink = arg[2];
interpolation = arg[3];
ii = arg[4];
nn = arg[5];
verbose = arg[6];
pw = ProcessWriter(ii);
if verbose:
pw.write("resampleData: resampling in XY: image %d / %d" % (ii, nn))
data = numpy.squeeze(io.readData(fileSource, z = ii));
resampleXY(data, sink = fileSink, dataSizeSink = dataSizeSink, interpolation = interpolation, out = pw, verbose = verbose);
def _processSubStack(dsr):
"""Helper to process stack in parallel"""
sf = dsr[0];
pp = dsr[1];
sub = dsr[2];
verbose = dsr[3];
timer = Timer();
pw = ProcessWriter(sub["stackId"]);
if verbose:
pw.write("processing substack " + str(sub["stackId"]) + "/" + str(sub["nStacks"]));
pw.write("file = " + sub["source"]);
pw.write("segmentation = " + str(sf));
pw.write("ranges: x,y,z = " + str(sub["x"]) + "," + str(sub["y"]) + "," + str(sub["z"]));
img = io.readData(sub["source"], x = sub["x"], y = sub["y"], z = sub["z"]);
if verbose:
pw.write(timer.elapsedTime(head = 'Reading data of size ' + str(img.shape)));
timer.reset();
seg = sf(img, subStack = sub, out = pw, **pp);
if verbose:
pw.write(timer.elapsedTime(head = 'Processing substack of size ' + str(img.shape)));
return seg;
def _processSubStack(dsr):
"""Helper to process stack in parallel"""
sf = dsr[0];
pp = dsr[1];
sub = dsr[2];
verbose = dsr[3];
timer = Timer();
pw = ProcessWriter(sub["stackId"]);
if verbose:
pw.write("processing substack " + str(sub["stackId"]) + "/" + str(sub["nStacks"]));
pw.write("file = " + sub["source"]);
pw.write("segmentation = " + str(sf));
pw.write("ranges: x,y,z = " + str(sub["x"]) + "," + str(sub["y"]) + "," + str(sub["z"]));
img = io.readData(sub["source"], x = sub["x"], y = sub["y"], z = sub["z"]);
if verbose:
pw.write(timer.elapsedTime(head = 'Reading data of size ' + str(img.shape)));
timer.reset();
seg = sf(img, subStack = sub, out = pw, **pp);
if verbose:
pw.write(timer.elapsedTime(head = 'Processing substack of size ' + str(img.shape)));
return seg;