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:
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')
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.
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.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.