Collections Class

class imagedata.Study(data, opts=None)

Study – Read and sort images into a collection of Series objects.

Study(data, opts=None)

Examples

>>> from imagedata import Study
>>> study = Study('directory/')
>>> for uid in study:
>>>     series = study[uid]

Parameters:

• data – URL to input data, or list of Series instances

• opts – Dict of input options, mostly for format specific plugins (argparse.Namespace or dict) * ‘strict_values’: Whether study attributes should match in each series (bool)

Returns:

Study instance

write(url, opts=None, formats=None)

Write image data, calling appropriate format plugins

Parameters:

• self – Study instance

• url – output destination url

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

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

Raises:

• imagedata.collections.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.

class imagedata.Patient(data, opts=None)

Patient – Read and sort images into a collection of Study objects.

Patient(data, opts=None)

Examples

>>> from imagedata import Patient
>>> patient = Patient('directory/')
>>> for uid in patient:
>>>     study = patient[uid]

Parameters:

• data – URL to input data, or list of Study instances

• opts – Dict of input options, mostly for format specific plugins (argparse.Namespace or dict) * ‘strict_values’: Whether attributes should match in each study (bool)

Returns:

Patient instance

write(url, opts=None, formats=None)

Write image data, calling appropriate format plugins

Parameters:

• self – Patient instance

• url – output destination url

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

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

Raises:

• imagedata.collections.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.

class imagedata.Cohort(data, opts=None)

Cohort – Read and sort images into a collection of Patient objects.

Cohort(data, opts=None)

Examples

>>> from imagedata import Cohort
>>> cohort = Cohort('directory/')
>>> for id in cohort:
>>>     patient = cohort[id]

Parameters:

• data – URL to input data, or list of Patient instances

• opts – Dict of input options, mostly for format specific plugins (argparse.Namespace or dict) * ‘strict_values’: Whether attributes should match in each study (bool)

Returns:

Cohort instance

write(url, opts=None, formats=None)

Write image data, calling appropriate format plugins

Parameters:

• self – Cohort instance

• url – output destination url

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

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

Raises:

• imagedata.collections.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.