vessel_filling#

This module uses a convolutional neuronal network to fill empty tubes and vessels.

downsample(data, resample, maxpool, verbose)[source]#

fill_vessels(source, sink, resample=None, threshold=0.5, network=None, dtype='float16', cuda=None, processing_parameter=None, verbose=False)[source]#

Fill hollow tubes via a neural network.

Arguments

sourcestr or Source: The binary data source to fill hollow tubes in.
sinkstr or Source.: The binary sink to write data to. sink is created if it does not exists.
resampleint or None: If int, downsample the data by this factor, apply network and upsample.
thresholdfloat or None: Apply a threshold to the result of the cnn. If None, the probability of being foreground is returned.
networkstr, Model or None: The network specification. If None, the default trained network is used.
dtypestr: The dtype to use for the network. See ClearMap.ImageProcessing.machine_learning.Torch.to() for details.
cudabool or None: If True, use gpu processing. If None, automatically detect gpu.
processing_parameterdict or None: Parameter to use for block processing.
verbosebool: If True, print progress.

Returns

networkModel: The neural network model.

load_data(data, cuda, dtype, verbose)[source]#

print_array_shape(step, array, verbose)[source]#

train(network, data)[source]#

vessel_filling_network(network=None, dtype='float16', cuda=None)[source]#

Initialize vessel filling network.

Arguments

networkstr, Model or None: The network specification. If None the default trained network is used.
dtypestr: The dtype to use for the network. See ClearMap.ImageProcessing.machine_learning.Torch.to() for details.
cudabool or None: If True, use gpu processing. If None, automatically detect gpu.

Returns

networkModel: The neural network model.

network_binary_vessel_filling_filename = '/home/charly.rousseau/code/icm/ClearMap2/ClearMap/ImageProcessing/machine_learning/vessel_filling/resources/cnn_binary_vessel_filling.pth'#: Filename of the default neuronal network to use for binary hollow vessel filling.

resources_path = '/home/charly.rousseau/code/icm/ClearMap2/ClearMap/ImageProcessing/machine_learning/vessel_filling/resources'#: Path to the trained neuronal networks.