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datasources

ngtools.local.datasources

Objects that represent local multidimensional arrays.

BabelVolumeInfo 

BabelVolumeInfo(fileobj)

Bases: VolumeInfo

Generic NiBabel metadata.

getDataType 

getDataType()

TODO.

getShape 

getShape(level=0)

TODO.

getInputNames 

getInputNames()

TODO.

getOutputNames 

getOutputNames()

TODO.

getInputScales 

getInputScales()

TODO.

getOutputScales 

getOutputScales()

TODO.

getUnits 

getUnits()

TODO.

getMatrix 

getMatrix()

TODO.

getNbLevels 

getNbLevels()

Compute number of dimensions.

getRank 

getRank()

Compute number of dimensions.

getSlopeInter 

getSlopeInter()

Affine intensity scaling.

getInputDimensions 

getInputDimensions()

Compute input dimensions.

getOutputDimensions 

getOutputDimensions()

Compute output dimensions.

getTransform 

getTransform()

Compute neuroglancer transform.

BabelDataSource 

BabelDataSource(*args, **kwargs)

Bases: LocalVolumeDataSource

A local volume read using nibabel.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

local_volume property 

local_volume

Points to the underlying LocalVolume, if any.

LocalVolume

Bases: LocalVolume

LocalVolume that knows it is in a BabelDataSource.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

MGHDataSource 

MGHDataSource(*args, **kwargs)

Bases: BabelDataSource

Wrapper for MGH/MGZ volume sources.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

local_volume property 

local_volume

Points to the underlying LocalVolume, if any.

LocalVolume

Bases: LocalVolume

LocalVolume that knows it is in a MGHDataSource.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

TiffVolumeInfo 

TiffVolumeInfo(url, fileobj=None)

Bases: VolumeInfo

Wrapper for local tiff volumes.

getShape 

getShape(level=0)

TODO.

getDataType 

getDataType()

TODO.

getScales 

getScales()

TODO.

getUnits 

getUnits()

TODO.

getNames 

getNames()

TODO.

getDimensions 

getDimensions()

TODO.

getTransform 

getTransform()

TODO.

getZoomsOME staticmethod 

getZoomsOME(omexml, series=None)

Extract zoom factors (i.e., voxel size) from OME metadata.

This function returns the zoom levels at the highest resolution. Zooms at subsequent resolution (in the in-plane direction only) can be obtained by multiplying the zooms at the previous resolution by 2. (This assumes that pyramid levels are built using a sliding window).

If more than one series is requested, the returned variables are wrapped in a tuple E.g.: 

>>> zooms, units, axes = ome_zooms(omexml)
>>> zooms_series1 = zooms[1]
>>> zooms_series1
(10., 10., 5.)
>>> units_series1 = units[1]
>>> units_series1
('mm', 'mm', 'mm')

Parameters:

Name Type Description Default
omexml str or bytes

OME-XML metadata

 required
series int or list[int] or None

Series ID(s)

 all

Returns:

Name Type Description
zooms tuple[float]
units tuple[str]
axes str

getNbLevels 

getNbLevels()

Compute number of dimensions.

getRank 

getRank()

Compute number of dimensions.

getSlopeInter 

getSlopeInter()

Affine intensity scaling.

getMatrix 

getMatrix()

Compute transformation matrix.

TiffDataSource 

TiffDataSource(*args, **kwargs)

Bases: LocalVolumeDataSource

A local tiff volume, read with tifffile.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

local_volume property 

local_volume

Points to the underlying LocalVolume, if any.

LocalVolume

Bases: LocalVolume

LocalVolume that knows it is in a TiffDataSource.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.