Imagedata packages

Module Axis

Axis defines a dimension of an images Series.

class imagedata.axis.UniformAxis(name, start, stop, step=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)

class imagedata.axis.UniformLengthAxis(name, start, n, step=1)

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

Examples

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

class imagedata.axis.VariableAxis(name, values)

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

Examples

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

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 –

• DicomHeaderDict –

• seriesNumber –

• seriesDescription –

• imageType –

• frameOfReferenceUID –

• studyInstanceUID –

• studyID –

• seriesInstanceUID –

• SOPClassUID –

• accessionNumber –

• patientName –

• patientID –

• patientBirthDate –

• input_sort –

• sliceLocations –

• tags –

• spacing –

• imagePositions –

• orientation –

• transformationMatrix –

• color –

• photometricInterpretation –

• axes –

• __uid_generator –

• studyInstanceUID –

• seriesInstanceUID –

• frameOfReferenceUID –

• DicomHeaderDict –

• tags –

• axes –

add_geometry(template, geometry)

Add geometry data to obj header.

Parameters

• self – header or dict

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

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

add_template(template)

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)

Set default values.

imagedata.header.deepcopy_DicomHeaderDict(source, filename=None)

Deepcopy contents of DicomHeaderDict.

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)

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)

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.

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

• imagedata.formats.CannotSort – When input data cannot be sorted.

imagedata.readdata.sorted_plugins_dicom_first(plugins)

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.