src.imagedata package

Subpackages

• src.imagedata.apps package
  • Subpackages
    • src.imagedata.apps.Siemens package
      • Submodules
      • src.imagedata.apps.Siemens.ROI module
      • src.imagedata.apps.Siemens.draw_antialiased module
      • src.imagedata.apps.Siemens.evidence2mask module
      • src.imagedata.apps.Siemens.evidence_main module
      • Module contents
  • Submodules
  • src.imagedata.apps.diffusion module
  • Module contents
• src.imagedata.archives package
  • Submodules
  • src.imagedata.archives.abstractarchive module
    • AbstractArchive
      • AbstractArchive.add_localfile()
      • AbstractArchive.authors
      • AbstractArchive.base
      • AbstractArchive.basename()
      • AbstractArchive.close()
      • AbstractArchive.construct_filename()
      • AbstractArchive.description
      • AbstractArchive.exists()
      • AbstractArchive.getmembers()
      • AbstractArchive.getnames()
      • AbstractArchive.is_file()
      • AbstractArchive.mimetypes
      • AbstractArchive.name
      • AbstractArchive.new_local_file()
      • AbstractArchive.open()
      • AbstractArchive.path
      • AbstractArchive.plugin_type
      • AbstractArchive.root
      • AbstractArchive.set_member_naming_scheme()
      • AbstractArchive.to_localfile()
      • AbstractArchive.transport
      • AbstractArchive.url
      • AbstractArchive.use_query()
      • AbstractArchive.version
      • AbstractArchive.writedata()
    • Member
      • Member.name
    • NoOtherInstance
    • WriteMultipleArchives
  • src.imagedata.archives.filesystemarchive module
    • FilesystemArchive
      • FilesystemArchive.add_localfile()
      • FilesystemArchive.authors
      • FilesystemArchive.base
      • FilesystemArchive.basename()
      • FilesystemArchive.close()
      • FilesystemArchive.construct_filename()
      • FilesystemArchive.description
      • FilesystemArchive.exists()
      • FilesystemArchive.extensions
      • FilesystemArchive.getmembers()
      • FilesystemArchive.getnames()
      • FilesystemArchive.is_file()
      • FilesystemArchive.level
      • FilesystemArchive.mimetypes
      • FilesystemArchive.name
      • FilesystemArchive.new_local_file()
      • FilesystemArchive.open()
      • FilesystemArchive.path
      • FilesystemArchive.root
      • FilesystemArchive.to_localfile()
      • FilesystemArchive.url
      • FilesystemArchive.use_query()
      • FilesystemArchive.version
      • FilesystemArchive.writedata()
    • NoSuchFile
    • ReadOnlyError
    • WriteOnFile
  • src.imagedata.archives.zipfilearchive module
    • WriteFileIO
      • WriteFileIO.close()
      • WriteFileIO.local_file
    • ZipfileArchive
      • ZipfileArchive.add_localfile()
      • ZipfileArchive.authors
      • ZipfileArchive.base
      • ZipfileArchive.basename()
      • ZipfileArchive.close()
      • ZipfileArchive.construct_filename()
      • ZipfileArchive.description
      • ZipfileArchive.exists()
      • ZipfileArchive.getmembers()
      • ZipfileArchive.getnames()
      • ZipfileArchive.is_file()
      • ZipfileArchive.mimetypes
      • ZipfileArchive.name
      • ZipfileArchive.new_local_file()
      • ZipfileArchive.open()
      • ZipfileArchive.path
      • ZipfileArchive.root
      • ZipfileArchive.to_localfile()
      • ZipfileArchive.url
      • ZipfileArchive.use_query()
      • ZipfileArchive.version
      • ZipfileArchive.writedata()
    • list_files()
  • Module contents
    • ArchivePluginNotFound
    • FileAlreadyExistsError
    • find_mimetype_plugin()
    • find_plugin()
    • get_archiver_list()
• src.imagedata.formats package
  • Subpackages
    • src.imagedata.formats.dicomlib package
      • Submodules
      • src.imagedata.formats.dicomlib.uid module
      • Module contents
  • Submodules
  • src.imagedata.formats.abstractplugin module
  • src.imagedata.formats.dicomplugin module
  • src.imagedata.formats.itkplugin module
  • src.imagedata.formats.matplugin module
  • src.imagedata.formats.niftiplugin module
  • Module contents
    • CannotSort
    • EmptyImageError
    • FormatPluginNotFound
    • NotImageError
    • NotTimeOrder
    • SOPInstanceUIDNotFound
    • UnknownInputError
    • UnknownTag
    • WriteNotImplemented
    • find_plugin()
    • get_plugins_list()
    • get_size()
    • get_uid()
    • shape_to_str()
    • sort_on_to_str()
    • str_to_dtype()
    • str_to_sort_on()
• src.imagedata.transports package
  • Submodules
  • src.imagedata.transports.abstracttransport module
    • AbstractTransport
      • AbstractTransport.authors
      • AbstractTransport.close()
      • AbstractTransport.description
      • AbstractTransport.exists()
      • AbstractTransport.info()
      • AbstractTransport.isfile()
      • AbstractTransport.mimetype
      • AbstractTransport.name
      • AbstractTransport.open()
      • AbstractTransport.plugin_type
      • AbstractTransport.schemes
      • AbstractTransport.url
      • AbstractTransport.version
      • AbstractTransport.walk()
    • NoOtherInstance
  • src.imagedata.transports.dicomtransport module
    • AssociationFailed
    • AssociationNotEstablished
    • DicomTransport
      • DicomTransport.authors
      • DicomTransport.close()
      • DicomTransport.description
      • DicomTransport.exists()
      • DicomTransport.info()
      • DicomTransport.isfile()
      • DicomTransport.name
      • DicomTransport.open()
      • DicomTransport.schemes
      • DicomTransport.store()
      • DicomTransport.url
      • DicomTransport.version
      • DicomTransport.walk()
  • src.imagedata.transports.filetransport module
    • FileTransport
      • FileTransport.authors
      • FileTransport.close()
      • FileTransport.description
      • FileTransport.exists()
      • FileTransport.info()
      • FileTransport.isfile()
      • FileTransport.name
      • FileTransport.netloc
      • FileTransport.open()
      • FileTransport.opts
      • FileTransport.path
      • FileTransport.schemes
      • FileTransport.url
      • FileTransport.version
      • FileTransport.walk()
  • src.imagedata.transports.xnattransport module
    • XnatTransport
      • XnatTransport.authors
      • XnatTransport.close()
      • XnatTransport.description
      • XnatTransport.exists()
      • XnatTransport.info()
      • XnatTransport.isfile()
      • XnatTransport.mimetype
      • XnatTransport.name
      • XnatTransport.netloc
      • XnatTransport.open()
      • XnatTransport.opts
      • XnatTransport.read_directory_only
      • XnatTransport.schemes
      • XnatTransport.url
      • XnatTransport.version
      • XnatTransport.walk()
  • Module contents
    • FunctionNotSupported
    • RootIsNotDirectory
    • Transport()
    • TransportPluginNotFound
    • get_transporter_list()

Submodules

src.imagedata.axis module

src.imagedata.cmdline module

src.imagedata.collections module

src.imagedata.header module

src.imagedata.image_data module

src.imagedata.list_plugins module

src.imagedata.readdata module

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

exception src.imagedata.readdata.NoArchiveError

Bases: Exception

exception src.imagedata.readdata.NoTransportError

Bases: Exception

exception src.imagedata.readdata.UnknownOptionType

Bases: Exception

src.imagedata.readdata.read(urls, order=None, opts=None, input_format=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)

• input_format – specify a particular input format (default: auto-detect)

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.

src.imagedata.readdata.sorted_plugins_dicom_first(plugins, input_format)

Sort plugins such that any Nifti plugin is used early.

src.imagedata.readdata.str_to_dtype(s)

Convert dtype string to numpy dtype.

src.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.

src.imagedata.series module

src.imagedata.viewer module

Module contents