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)
Module cmdline
Add standard command line options.
Module imagedata.header
Image series header
- class imagedata.header.Header[source]
Image header object.
- Variables
~Header.input_order –
~Header.sort_on –
~Header.input_format –
~Header.DicomHeaderDict –
~Header.seriesNumber –
~Header.seriesDescription –
~Header.imageType –
~Header.frameOfReferenceUID –
~Header.studyInstanceUID –
~Header.studyID –
~Header.seriesInstanceUID –
~Header.SOPClassUID –
~Header.accessionNumber –
~Header.patientName –
~Header.patientID –
~Header.patientBirthDate –
~Header.input_sort –
~Header.sliceLocations –
~Header.tags –
~Header.spacing –
~Header.imagePositions –
~Header.orientation –
~Header.transformationMatrix –
~Header.color –
~Header.photometricInterpretation –
~Header.axes –
~Header.__uid_generator –
~Header.studyInstanceUID –
~Header.seriesInstanceUID –
~Header.frameOfReferenceUID –
~Header.DicomHeaderDict –
~Header.tags –
- add_geometry(template, geometry)[source]
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.
Module imagedata.readdata
Read/Write image files, calling appropriate transport, archive and format plugins
- 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.
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)[source]
Sort plugins such that any Nifti plugin is used early.
- 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.