Resampling

This module provides methods to resample and reorient data.

Resampling the data is usually necessary as the first step to match the resolution and orientation of the reference object.

format_orientation(orientation, inverse=False, default=None)

Convert orientation to standard format.

Arguments

orientationtuple or str

The orientation specification.

inversebool

If True, invert orientation.

defaultobject

The default value if orientation is None;

Returns

orientationtuple of ints

The orientation sequence.

See also

None()

inverse_orientation(orientation)

Returns the inverse orientation taking axis inversions into account.

Arguments

orientationtuple or str

The orientation specification.

Returns

orientationtuple

The inverse orientation sequence.

See also

None()

orient_resolution(resolution, orientation, inverse=False)

Permutes a resolution tuple according to the given orientation.

Arguments

resolutiontuple

The resolution specification.

orientationtuple or str

The orientation specification.

inversebool

If True, invert the orientation.

Returns

resolutiontuple

The re-oriented resolution sequence.

See also

None()

orient_shape(shape, orientation, inverse=False)

Permutes a shape according to the given orientation.

Arguments

shapetuple

The shape specification.

orientationtuple or str

The orientation specification.

inversebool

If True, invert the orientation.

Returns

shapetuple

The oriented shape tuple.

See also

None()

orientation_to_permuation(orientation, inverse=False)

Extracts the permuation from an orientation.

Arguments

orientationtuple or str

The orientation specification.

inversebool

If True, return inverse permutation.

Returns

permuationtuple of ints

The premutation sequence.

See also

None()

resample(source, sink=None, orientation=None, sink_shape=None, source_resolution=None, sink_resolution=None, interpolation='linear', axes_order=None, method='shared', processes=None, verbose=True)

Resample data of source in new shape/resolution and orientation.

Arguments

sourcestr or array

The source to be resampled.

sinkstr or None

The sink for the resampled image.

orientationtuple or None:

The orientation specified by permuation and change in sign of (1,2,3).

sink_shapetuple or None

The target shape of the resampled sink.

source_resolutiontuple or None

The resolution of the source (in length per pixel).

sink_resolutiontuple or None

The resolution of the resampled source (in length per pixel).

interpolationstr

The method to use for interpolating to the resmapled array.

axis_orderstr, list of tuples of int or None

The axes pairs along which to resample the data at each step. If None, this is detertmined automatically. For a FileList source, setting the first tuple should point to axis not indicating files. If ‘size’ the axis order is determined automatically to maximally reduce the size of the array in each resmapling step. If ‘order’ the axis order is chosed automatically to optimize io speed.

method‘shared’ or ‘memmap’

Method to handle intermediate resampling results. If ‘shared’ use shared memory, otherwise use a memory map on disk.

processesint, None or ‘serial’

Number of processes to use for parallel resampling, if None use maximal processes avaialable, if ‘serial’ process in serial.

verbosebool

If True, display progress information.

Returns

sinkarray or str

The data or filename of resampled sink.

Notes

• Resolutions are assumed to be given for the axes of the intrinsic orientation of the data and reference (as when viewed by ImageJ).

• Orientation: permuation of 1,2,3 with potential sign, indicating which axes map onto the reference axes, a negative sign indicates reversal of that particular axes.

• Only a minimal set of information to determine the resampling parameter has to be given, e.g. source_shape and sink_shape.

• The resampling is done by iterating two dimensional resampling steps.

resample_factor(source_shape, sink_shape=None, source_resolution=None, sink_resolution=None, orientation=None)

Calculate scaling factors for resampling.

Arguments

source_shapetuple

The shape the source.

sink_shapetuple or None

The shape of the resmapled sink.

source_resolutiontuple or None

The resolution of the source.

sink_resolutiontuple or None

The resolution of the sink.

orientationtuple or str

The re-orientation specification.

Returns

factortuple

The resampling factor along the axes of the source.

See also

None()

resample_inverse(source, sink=None, resample_source=None, resample_sink=None, orientation=None, source_shape=None, source_resolution=None, sink_shape=None, sink_resolution=None, axes_order=None, method='memmap', interpolation='linear', processes=None, verbose=True, **args)

Resample data inversely to resample() routine.

Arguments

sourcestr, array

Source to be inversly resampled (e.g. sink in resample()).

sinkstr or None

Sink to write the inversly resampled image to.

resample_sourcestr, array or None

Optional source in resample().

resmaple_sink: str, array or None

Optional sink used in resample().

orientationtuple

Orientation as specified as in resample().

source_shapetuple or None

Optional value of source_shape as in resample().

source_resolutiontuple or None

Optional value of source_resolution as in resample().

sink_resolutiontuple or None

Optional value of sink_resolution as in resample().

processing_directorystr or None

Optional directory in which to perform resmapling in parallel. If None, a temporary directry will be created.

axis_orderlist of tuples of int or None

The axes pairs along which to resample the data as in resample().

method‘shared’ or ‘memmap’

Method to handle intermediate resampling results. If ‘shared’ use shared memory, otherwise use a memory map on disk.

interpolationstr

Method to use for interpolating to the resmapled image.

processes int or None

Number of processes to use for parallel resampling.

verbosebool

If True, print progress information.

Returns

resampledarray or str

Data or file name of inversly resampled image.

Notes

• All arguments, except source and sink should be passed as resample() to invert the resmapling.

resample_points(source, sink=None, resample_source=None, resample_sink=None, orientation=None, source_shape=None, sink_shape=None, source_resolution=None, sink_resolution=None, **args)

Resample points from original coordiantes to resampled ones.

Arguments

sourcestr or array

Points to be resampled.

sinkstr or None

Sink for the resmapled point coordinates.

orientationtuple

Orientation as specified in resample().

resample_sourcestr, array or None

Optional source as in resample().

resample_sink: str, array or None

Optional sink used in resample().

source_shapetuple or None

Optional value of source_shape as in resample().

source_resolutiontuple or None

Optional value of source_resolution as in resample().

sink_resolutiontuple or None

Optional value of sink_resolution as in resample().

Returns

resmapledarray or str

Sink for the resampled point coordinates.

Notes

• The resampling of points here corresponds to he resampling of an image in resample().

• The arguments should be passed exactly as in resample() except soure and sink that point to the point sources. Use resample_source and resmaple_sink to pass the source and sink values used in resample().

resample_points_inverse(source, sink=None, resample_source=None, resample_sink=None, orientation=None, source_shape=None, sink_shape=None, source_resolution=None, sink_resolution=None, **args)

Resample points from original coordiantes to resampled ones.

Arguments

sourcestr or array

Points to be resampled inversely.

sinkstr or None

Sink for the inversly resmapled points.

resample_sourcestr, array or None

Optional source as in resample().

resample_sink: str, array or None

Optional sink used in resample().

orientationtuple

Orientation as specified in resample().

source_shapetuple or None

Optional value of source_shape as in resample().

source_resolutiontuple or None

Optional value of source_resolution as in resample().

sink_resolutiontuple or None

Optional value of sink_resolution as in resample().

Returns

resmapledarray or str

Sink for the inversly resampled point coordinates.

Notes

• The resampling of points here corresponds to the inverse resampling of an image in resample(), i.e. to func:resample_inverse

• The arguments should be passed exactly as in resample() except source and sink that point to the point sources. Use resample_source and resmaple_sink to pass the source and sink values used in resample().

resample_shape(source_shape, sink_shape=None, source_resolution=None, sink_resolution=None, orientation=None)

Calculate scaling factors and data shapes for resampling.

Arguments

source_shapetuple

The shape the source.

sink_shapetuple or None

The shape of the resmapled sink.

source_resolutiontuple or None

The resolution of the source.

sink_resolutiontuple or None

The resolution of the sink.

orientationtuple or str

The re-orientation specification.

Returns

source_shapetuple

The shape of the source.

sink_shapetuple

The shape of the sink.

source_resolutiontuple or None

The resolution of the source.

sink_resolutiontuple or None

The resolution of the sink.

See also

None()