inferno.io.volumetric package

Submodules

inferno.io.volumetric.lazy_volume_loader module

class inferno.io.volumetric.lazy_volume_loader.LazyHDF5VolumeLoader(path, path_in_h5_dataset=None, data_slice=None, transforms=None, name=None, **slicing_config)

Bases: inferno.io.volumetric.lazy_volume_loader.LazyVolumeLoader

class inferno.io.volumetric.lazy_volume_loader.LazyVolumeLoader(file_impl, path, path_in_file=None, data_slice=None, transforms=None, name=None, **slicing_config)

Bases: inferno.io.volumetric.lazy_volume_loader.LazyVolumeLoaderBase

validate_data_slice(data_slice)

class inferno.io.volumetric.lazy_volume_loader.LazyVolumeLoaderBase(dataset, window_size, stride, downsampling_ratio=None, padding=None, padding_mode='reflect', transforms=None, return_index_spec=False, name=None, data_slice=None)

Bases: inferno.io.core.base.SyncableDataset

clone(dataset=None, transforms=None, name=None)

get_shape()

make_sliding_windows()

normalize_slice(data_slice)

class inferno.io.volumetric.lazy_volume_loader.N5VolumeLoader(path, path_in_file=None, data_slice=None, transforms=None, name=None, **slicing_config)

Bases: inferno.io.volumetric.lazy_volume_loader.LazyVolumeLoader

class inferno.io.volumetric.lazy_volume_loader.ZarrVolumeLoader(path, path_in_file=None, data_slice=None, transforms=None, name=None, **slicing_config)

Bases: inferno.io.volumetric.lazy_volume_loader.LazyVolumeLoader

inferno.io.volumetric.volume module

class inferno.io.volumetric.volume.HDF5VolumeLoader(path, path_in_h5_dataset=None, data_slice=None, transforms=None, name=None, **slicing_config)

Bases: inferno.io.volumetric.volume.VolumeLoader

class inferno.io.volumetric.volume.TIFVolumeLoader(path, data_slice=None, transforms=None, name=None, **slicing_config)

Bases: inferno.io.volumetric.volume.VolumeLoader

Loader for volumes stored in .tif files.

class inferno.io.volumetric.volume.VolumeLoader(volume, window_size, stride, downsampling_ratio=None, padding=None, padding_mode='reflect', transforms=None, return_index_spec=False, name=None)

Bases: inferno.io.core.base.SyncableDataset

clone(volume=None, transforms=None, name=None)

make_sliding_windows()

pad_volume(padding=None)

inferno.io.volumetric.volumetric_utils module

inferno.io.volumetric.volumetric_utils.parse_data_slice(data_slice)

Parse a dataslice as a list of slice objects.

inferno.io.volumetric.volumetric_utils.slidingwindowslices(shape, window_size, strides, ds=1, shuffle=True, rngseed=None, dataslice=None, add_overhanging=True)

inferno.io.volumetric.volumetric_utils.slidingwindowslices_depr(shape, nhoodsize, stride=1, ds=1, window=None, ignoreborder=True, shuffle=True, rngseed=None, startmins=None, startmaxs=None, dataslice=None)

Returns a generator yielding (shuffled) sliding window slice objects. :type shape: int or list of int :param shape: Shape of the input data :type nhoodsize: int or list of int :param nhoodsize: Window size of the sliding window. :type stride: int or list of int :param stride: Stride of the sliding window. :type shuffle: bool :param shuffle: Whether to shuffle the iterator.

Module contents