Imagedata packages

Module Axis

Axis defines a dimension of an images Series.

class imagedata.axis.UniformAxis(name, start, stop, step=1)[source]

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)[source]

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)[source]

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)[source]
class imagedata.cmdline.DictAction(option_strings, dest, nargs=None, **kwargs)[source]
class imagedata.cmdline.DtypeAction(option_strings, dest, nargs=None, **kwargs)[source]
class imagedata.cmdline.InputOrderAction(option_strings, dest, nargs=None, **kwargs)[source]
class imagedata.cmdline.OutputFormatAction(option_strings, dest, nargs=None, **kwargs)[source]
class imagedata.cmdline.SortOnAction(option_strings, dest, nargs=None, **kwargs)[source]

Module imagedata.header

Image series header

class imagedata.header.Header[source]

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

  • __uid_generator

add_geometry(geometry)[source]

Add geometry data to obj header.

Parameters:
  • self – header or dict

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

add_template(template) None[source]

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

Parameters:

template – template header. Can be None.

find_axis(name)[source]

Find axis with given name

Parameters:

name – Axis name to search for

Returns:

axis object with given name

Raises:

ValueError – when no axis object has given name

Usage:
>>> from imagedata.series import Series
>>> si = Series(np.array([3, 3, 3]))
>>> axis = si.find_axis('slice')
new_uid() str[source]

Return the next available UID from the UID generator.

set_default_values(axes) None[source]

Set default values.

Module imagedata.readdata

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

exception imagedata.readdata.NoArchiveError[source]
exception imagedata.readdata.NoTransportError[source]
exception imagedata.readdata.UnknownOptionType[source]
imagedata.readdata.read(urls, order=None, opts=None)[source]

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.

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

  • CannotSort – When input data cannot be sorted.

imagedata.readdata.sorted_plugins_dicom_first(plugins)[source]

Sort plugins such that any Nifti plugin is used early.

imagedata.readdata.str_to_dtype(s)[source]

Convert dtype string to numpy dtype.

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

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.