Imagedata packages

Module Axis

Axis defines a dimension of an images Series.

class imagedata.axis.UniformAxis(name: str, start: type[SupportsFloat], stop: type[SupportsFloat], step: type[SupportsFloat] = 1)

Define axis by giving start, stop and step (optional). Start, stop and step are given in actual values

Examples

>>> ax = UniformAxis('row', 0, 128)

append(axis: Axis)

Append another axis

copy(name: str = None, start: type[SupportsFloat] = None, stop: type[SupportsFloat] = None, step: type[SupportsFloat] = None, n: int = None) → UniformAxis

Return a copy of the axis, where the length n can be different.

class imagedata.axis.UniformLengthAxis(name: str, start: type[SupportsFloat], n: int, step: type[SupportsFloat] = 1)

Define axis by giving start, length and step (optional). Start and step are given in actual values.

Examples

>>> ax = UniformLengthAxis('row', 0, 128)

append(axis: Axis)

Append another axis

copy(name: str = None, start: type[SupportsFloat] = None, n: type[SupportsFloat] = None, step: type[SupportsFloat] = None) → UniformLengthAxis

Return a copy of the axis, where the length n can be different.

class imagedata.axis.VariableAxis(name: str, values: Sequence)

Define axis by giving an array of values. values are actual values.

Examples

>>> ax = VariableAxis('time', [0, 1, 4, 9, 11, 13])

append(axis: Axis)

Append another axis

copy(name: str = None, n: type[SupportsFloat] = None) → VariableAxis

Return a copy of the axis, where the length n can be different.

imagedata.axis.to_namedtuple(axes) → namedtuple

Convert iterable (list, tuple, etc.) to namedtuple of Axes.

Module cmdline

Add standard command line options.

class imagedata.cmdline.CommaSepAction(option_strings, dest, nargs=None, **kwargs)

class imagedata.cmdline.DictAction(option_strings, dest, nargs=None, **kwargs)

class imagedata.cmdline.DtypeAction(option_strings, dest, nargs=None, **kwargs)

class imagedata.cmdline.InputOrderAction(option_strings, dest, nargs=None, **kwargs)

class imagedata.cmdline.OutputFormatAction(option_strings, dest, nargs=None, **kwargs)

class imagedata.cmdline.SortOnAction(option_strings, dest, nargs=None, **kwargs)

Module imagedata.header

Image series header

class imagedata.header.Header

Image header object.

Variables:

• input_order

• sort_on

• input_format

• dicomTemplate

• seriesNumber

• seriesDescription

• imageType

• frameOfReferenceUID

• studyInstanceUID

• studyID

• seriesInstanceUID

• SOPClassUID

• accessionNumber

• patientName

• patientID

• patientBirthDate

• input_sort

• sliceLocations (#)

• tags

• spacing

• imagePositions

• orientation

• transformationMatrix

• photometricInterpretation

• axes (collections.namedtuple)

• __uid_generator

add_geometry(geometry)

Add geometry data to obj header.

Parameters:

• self – header or dict

• geometry – geometry template header or dict. Can be None.

add_template(template) → None

Add template data to this header. Does not add geometry data.

Parameters:

template – template header. Can be None.

new_uid() → str

Return the next available UID from the UID generator.

set_default_values(axes: namedtuple) → None

Set default values.

property shape: tuple

Return matrix shape as given by axes properties.

Module imagedata.readdata

Read/Write image files, calling appropriate transport, archive and format plugins

exception imagedata.readdata.NoArchiveError

exception imagedata.readdata.NoTransportError

exception imagedata.readdata.UnknownOptionType

imagedata.readdata.read(urls, order=None, opts=None, input_format=None)

Read image data, calling appropriate transport, archive and format plugins

Parameters:

• urls – list of urls or url to read (list of str, or str)

• order – determine how to sort the images (default: auto-detect)

• opts – input options (argparse.Namespace or dict)

• input_format – specify a particular input format (default: auto-detect)

Returns:

tuple of

• hdr: header instance

• si[tag,slice,rows,columns]: numpy array

Raises:

• ValueError – When no sources are given.

• UnknownOptionType – When opts cannot be made into a dict.

• FileNotFoundError – When specified URL cannot be opened.

• UnknownInputError – When the input format could not be determined.

• CannotSort – When input data cannot be sorted.

imagedata.readdata.sorted_plugins_dicom_first(plugins, input_format)

Sort plugins such that any Nifti plugin is used early.

imagedata.readdata.str_to_dtype(s)

Convert dtype string to numpy dtype.

imagedata.readdata.write(si, url, opts=None, formats=None)

Write image data, calling appropriate format plugins

Parameters:

• si[tag – Series array

• slice – Series array

• rows – Series array

• columns] – Series array

• url – output destination url

• opts – Output options (argparse.Namespace or dict)

• formats – list of output formats, overriding opts.output_format (list or str)

Raises:

• UnknownOptionType – When opts cannot be made into a dict.

• TypeError – List of output format is not list().

• ValueError – Wrong number of destinations given, or no way to write multidimensional image.

• imagedata.formats.WriteNotImplemented – Cannot write this image format.