nornir_volumecontroller API

nornir_volumecontroller.CreateVolumeController(vol_model)[source]: Given a volume model create a controller for the model

class nornir_volumecontroller.Volume(volumeModel=None)[source]

Bases: VolumeInterface

Concrete volume controller wrapping a Volume model.

Lazily builds per-section transform maps and channel lists on first access so loading a large volume does not incur upfront I/O costs.

property Bounds: Bounding box of the entire volume :return: (minZ, minY, minX, maxZ, maxY, maxX)

Calculate2DBoundingBox()[source]

property Channels: List of all channels in the volume

GetData(region, resolution, channel_names)[source]: Return data for the specified region :param ndarray region: (minZ, minY, minX, maxZ, maxY, maxX) :param float resolution: resolution of output data :param list channels: channels to include in output :returns: list of ndarray images

GetHighestResolution(region=None, channel_names=None)[source]: Return the highest resolution of data within the bounding box

property Name

property transform_path_map

nornir_volumecontroller.base_objects.GetChannels(channelmap, channelnames)[source]

class nornir_volumecontroller.base_objects.Scale(scale_model=None)[source]

Bases: object

Physical scale of a volume channel on each spatial axis (units per pixel).

Wraps the volumemodel Scale object so callers can read X, Y, and Z units-per-pixel as plain floats rather than navigating the model hierarchy.

classmethod MinAxisScales(scale_model_A, scale_model_B)[source]: Given two scale models, return a scale object describing the highest resolution available for each axis

property X

property Y

property Z

class nornir_volumecontroller.base_objects.Volume(volumeModel=None)[source]

Bases: VolumeInterface

Concrete volume controller wrapping a Volume model.

Lazily builds per-section transform maps and channel lists on first access so loading a large volume does not incur upfront I/O costs.

property Bounds: Bounding box of the entire volume :return: (minZ, minY, minX, maxZ, maxY, maxX)

Calculate2DBoundingBox()[source]

property Channels: List of all channels in the volume

GetData(region, resolution, channel_names)[source]: Return data for the specified region :param ndarray region: (minZ, minY, minX, maxZ, maxY, maxX) :param float resolution: resolution of output data :param list channels: channels to include in output :returns: list of ndarray images

GetHighestResolution(region=None, channel_names=None)[source]: Return the highest resolution of data within the bounding box

property Name

property transform_path_map

class nornir_volumecontroller.base_objects.VolumeInterface[source]

Bases: object

Abstract interface for any volume controller.

Concrete subclasses (e.g. Volume) must implement Bounds, Channels, and GetData().

property Bounds: Bounding box of the entire volume

property Channels: List of all channels available in the volume

GetData(region, resolution, channels)[source]: Get the raw data inside the boundaries :param box region: Data within the region is returned :param ndarray resolution: The resolution to return data in :param list channels: List of channels to assign to the output array :returns: 4D Matrix with Channel,Z,Y,X axes :rtype: ndarray

class nornir_volumecontroller.base_objects.VolumeRegisteredChannel(channelModel=None)[source]

Bases: object

Wraps a single imaging channel together with its channel-to-volume registration transform.

Provides convenient access to the channel’s Name, Scale, and tile-pyramid file paths at a given downsample level.

GetTilesPath(filtername, level)[source]

property Name

property Scale

property Transform

Created on Apr 10, 2014

@author: u0490822

nornir_volumecontroller.factory.CreateVolumeController(vol_model)[source]: Given a volume model create a controller for the model

nornir_volumecontroller.spatial.BuildSectionChannelMap(section)[source]

Build a mapping from channel name to VolumeRegisteredChannel for one section.

Only channels that have a ChannelToVolume transform are included.

Parameters:: section – A Section model object.
Returns:: {channel_name: VolumeRegisteredChannel}
Return type:: dict

nornir_volumecontroller.spatial.BuildVolumeTransformMap(volume)[source]

Build a two-level map from section number → channel name → VolumeRegisteredChannel.

Only sections that contain at least one channel with a ChannelToVolume transform are included.

Parameters:: volume – A Volume model object.
Returns:: {section_number: {channel_name: VolumeRegisteredChannel}}
Return type:: dict

nornir_volumecontroller.spatial.SectionsInBoundingBox(boundingbox)[source]

Yield every integer section number whose Z-coordinate falls within boundingbox.

Parameters:: boundingbox – A bounding-box object with a BoundingBox attribute indexed by nornir_imageregistration.iBox constants.
Yields:: int — section numbers from MinZ to MaxZ inclusive.