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Package bar :: Package rec :: Module index_holder :: Class barReconstructorIndexer
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Class barReconstructorIndexer

Nested Classes [hide private]
class _slideElement
class of objects representing 'slide' elements

Inherited from atlas_indexer.barIndexer (private): _groupElement, _indexerElement, _propertyElement, _structureElement

Inherited from base.barObject (private): _clsBoundingBox, _clsBregmaMetadataElement, _clsCommentLabel, _clsGenericStructure, _clsMetadataElement, _clsPath, _clsRegularLabel, _clsSpotLabel, _clsStructureLabel, _clsTransfMatrixMetadataElement

Instance Methods [hide private]
 
__init__(self)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
None
_createMappings(self)
Creates set of mappings for convinient processing by reconstruction procedures.
None
__defineSpan(self)
Defines span of all slides.
None
__defineAxesFlips(self)
Checks if the rasterized slided will be flipped during the reconstruction.
 
getUIDsForGivenGroupName(self, topStructureName)
Returns: List of UIDs covered by topStructureID GID.
[str, str, ... ]
getStructureList(self, HierarchyRootElementName)
Returns: List of of structures (not groups!) covered by given hierarchy element.
(int, int)
getSlidesSpan(self, HierarchyRootElementName)
Returns: Returns tuple if integers containing first and last containing structures covered by given hierarhy elemnt.
 
_structList2SlideSpan(self, structuresList, rawIndexes=False)
Returns: (tuple of two integers) (min.
 
getZOriginAndExtent(self, slideIdxSpan, zRes, margin, eqSpacing=False)
Calculates span of the given set of slides in plane perpendicular to the slide plane.
barBoundingBox

Merges bounding boxes of all provided structures one after another.
getStructuresListBbx(self, structuresList)
Returns: Merged bounding boxes for all provied structures.
float
getDefaultZres(self)
Calculate distance between central slide in the stack and the next one.
 
__getRefCords(self)
 
__setRefCords(self, value)

Inherited from atlas_indexer.barIndexer: clearProperties, fixOrphanStructures, getXMLelement, indexSingleSlide, normaliseIDs, setParentsFromFile, unfoldSubtrees, updateProperties, visibleGroups

Inherited from atlas_indexer.barIndexer (private): _validateInternalData

Inherited from base.barObject: __str__, getElementById, writeXMLtoFile

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

    color_mappings

Inherited from atlas_indexer.barIndexer: setColorMappingFromFile

    fullname_mappings

Inherited from atlas_indexer.barIndexer: setNameMappingFromFile

    hierarchy
 
getHierarchyTree(self, root, depth=100)

Inherited from atlas_indexer.barIndexer: createFlatHierarchy

Inherited from atlas_indexer.barIndexer (private): _setHierarchyRelation

Class Methods [hide private]
cls
fromXML(cls, filename)
__fromXML method bound to the class as its classmethod.
Static Methods [hide private]

Inherited from atlas_indexer.barIndexer (private): _fromXML

Inherited from base.barObject (private): _getAttributesDict

Class Variables [hide private]

Inherited from atlas_indexer.barIndexer (private): _elementsList, _initialIDs, _requiredInternalData

Instance Variables [hide private]

Inherited from atlas_indexer.barIndexer: cafDirectory

Inherited from atlas_indexer.barIndexer (private): _colorMapping, _gid, _hierarchyGroups, _hierarchyRootElementName, _properties, _slides, _structures, _uid

    fullname_mappings

Inherited from atlas_indexer.barIndexer (private): _fullNameMapping

Properties [hide private]
  refCords

Inherited from atlas_indexer.barIndexer: colorMapping, gid, groups, hierarchy, hierarchyRootElementName, properties, slides, structures, uid, uidList

Inherited from object: __class__

    fullname_mappings

Inherited from atlas_indexer.barIndexer: fullNameMapping

Method Details [hide private]

__init__(self)
(Constructor)

 

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Parameters:
  • hierarchyRootElementName - Name of the root element of the hierarchy. The root element is the superior group of the hierarhy gathering all structures. CONF_HIERARCHY_ROOT_NAME by default.
Overrides: object.__init__
(inherited documentation)

fromXML(cls, filename)
Class Method

 

__fromXML method bound to the class as its classmethod.

Parameters:
  • sourceXMLElement - XML representation of the barIndexerObject on which the object is based
Returns: cls
created object
Overrides: atlas_indexer.barIndexerObject.fromXML
(inherited documentation)

_createMappings(self)

 

Creates set of mappings for convinient processing by reconstruction procedures.

Returns: None
None

__defineSpan(self)

 

Defines span of all slides. Checks, if all slides have the same thickness.

Returns: None
None

__defineAxesFlips(self)

 

Checks if the rasterized slided will be flipped during the reconstruction.

Returns: None
None

getUIDsForGivenGroupName(self, topStructureName)

 
Parameters:
  • topStructureID (int) - GID of structure element for which UID's will be be collected.
Returns:
List of UIDs covered by topStructureID GID.

Extracts set of regular structures ID's (UID's) for given topStructureID.

In other words: topstructure GID -> list of substructures UIDs for topStructureID and its child.

getStructureList(self, HierarchyRootElementName)

 
Parameters:
  • HierarchyRootElementName (str) - Name of root structure
Returns: [str, str, ... ]
List of of structures (not groups!) covered by given hierarchy element.

getSlidesSpan(self, HierarchyRootElementName)

 
Parameters:
  • HierarchyRootElementName (str) - Name of root structure
Returns: (int, int)
Returns tuple if integers containing first and last containing structures covered by given hierarhy elemnt.

_structList2SlideSpan(self, structuresList, rawIndexes=False)

 
Parameters:
  • structuresList (list of strings) - list of structure's names for which slide span will be calculated.
Returns:
(tuple of two integers) (min. slide number, max. slide number)

Function has self explaining name :). Purpose of this function is to define slide span (indexes of slides) for set of passed structures.

getZOriginAndExtent(self, slideIdxSpan, zRes, margin, eqSpacing=False)

 

Calculates span of the given set of slides in plane perpendicular to the slide plane.

Parameters:
  • slideIdxSpan ((int, int)) - tuple containing boundary slides indexes.
  • zRes (float) - Quantification unit of the reconstruction
  • margin (int) - Number of margin voxels (voxels not filled with the reconstruction) in the z plane.
  • eqSpacing (bool) - Flag determining if the provided zRes is equal to the spacing of the all slides. Implies that all the slides are qualy spaced.

getStructuresListBbx(self, structuresList)

 
Parameters:
  • structuresList ([str, str, ... ]) - List of structure names for which global bounding box will be calculated.
Returns: barBoundingBox

Merges bounding boxes of all provided structures one after another.

Merged bounding boxes for all provied structures.

getDefaultZres(self)

 

Calculate distance between central slide in the stack and the next one. This value is considered as default interplane resolution.

Returns: float
Default interplane distance (default z resolution)

Property Details [hide private]

refCords

Get Method:
__getRefCords(self)
Set Method:
__setRefCords(self, value)

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