Index

A

accumulateSegDict() (in module pyshepseg.tilingstats) accumulateSegSpatial() (in module pyshepseg.tilingstats) addOverviews() (in module pyshepseg.utils) addressStr() (pyshepseg.tiling.NetworkDataChannel method) addResult() (pyshepseg.tiling.SegmentationResultCache method)

addTile() (pyshepseg.tiling.TileInfo method) addTwoHistograms() (pyshepseg.tiling.HistogramAccumulator static method) append() (pyshepseg.shepseg.RowColArray method) applySpectralClusters() (in module pyshepseg.shepseg) autoMaxSpectralDiff() (in module pyshepseg.shepseg)

B

buildSegmentSpectra() (in module pyshepseg.shepseg)

C

calcHistogramTiled() (in module pyshepseg.tiling) calcPerSegmentSpatialStats_riosFunc() (in module pyshepseg.tilingstats) calcPerSegmentSpatialStatsRIOS() (in module pyshepseg.tilingstats) calcPerSegmentSpatialStatsTiled() (in module pyshepseg.tilingstats) calcPerSegmentStats_riosFunc() (in module pyshepseg.tilingstats) calcPerSegmentStatsRIOS() (in module pyshepseg.tilingstats) calcPerSegmentStatsTiled() (in module pyshepseg.tilingstats) calcStatsForCompletedSegs() (in module pyshepseg.tilingstats) calcStatsForCompletedSegsSpatial() (in module pyshepseg.tilingstats) checkColType() (pyshepseg.tilingstats.OpenRatContainer method) checkForEmptySegments() (pyshepseg.tiling.SegmentationConcurrencyMgr method) checkSegComplete() (in module pyshepseg.tilingstats) checkSegCompleteSpatial() (in module pyshepseg.tilingstats) checkTaskErrors() (pyshepseg.tiling.SegFargateMgr method) checkWorkerExceptions() (pyshepseg.tiling.SegmentationConcurrencyMgr method) (pyshepseg.tiling.SegNoConcurrencyMgr method) close() (pyshepseg.tilingstats.OpenRatContainer method) (pyshepseg.tilingstats.StatsReadManager method) clump() (in module pyshepseg.shepseg)

colExists() (pyshepseg.tilingstats.OpenRatContainer method) concurrencyType (pyshepseg.tiling.SegFargateMgr attribute) (pyshepseg.tiling.SegmentationConcurrencyMgr attribute) (pyshepseg.tiling.SegNoConcurrencyMgr attribute) (pyshepseg.tiling.SegSubprocMgr attribute) (pyshepseg.tiling.SegThreadsMgr attribute) convertPtsInto2DArray() (in module pyshepseg.tilingstats) convertPtsInto2DMaskArray() (in module pyshepseg.tilingstats) copyColumns() (in module pyshepseg.subset) copyRatCols() (in module pyshepseg.tilingstats) copySubsettedSegmentsToNew() (in module pyshepseg.subset) CreateColumn() (pyshepseg.tilingstats.OpenRatContainer method) createNoDataDict() (in module pyshepseg.tilingstats) createPagedRat() (in module pyshepseg.tilingstats) createSegDict() (in module pyshepseg.tilingstats) createSegSpatialDataDict() (in module pyshepseg.tilingstats) createStatColumns() (in module pyshepseg.tilingstats) createUserColumnsSpatial() (in module pyshepseg.tilingstats) crossesMidline() (pyshepseg.tiling.SegmentationConcurrencyMgr static method)

D

deprecationWarning() (in module pyshepseg.utils) diagonalClusterCentres() (in module pyshepseg.shepseg) doHistAccum() (pyshepseg.tiling.HistogramAccumulator method)

doImageChecks() (in module pyshepseg.tilingstats) doMerge() (in module pyshepseg.shepseg) doShepherdSegmentation() (in module pyshepseg.shepseg) doTiledShepherdSegmentation() (in module pyshepseg.tiling)

E

eliminateSinglePixels() (in module pyshepseg.shepseg) eliminateSmallSegments() (in module pyshepseg.shepseg)

equalProjection() (in module pyshepseg.tilingstats) estimateStatsFromHisto() (in module pyshepseg.utils)

F

FargateConfig (class in pyshepseg.tiling) findMergeSegment() (in module pyshepseg.shepseg) findNearestNeighbourPixel() (in module pyshepseg.shepseg)

fitSpectralClusters() (in module pyshepseg.shepseg) fitSpectralClustersWholeFile() (in module pyshepseg.tiling) formatTimingRpt() (in module pyshepseg.utils)

G

getClusterTaskCount() (pyshepseg.tiling.SegFargateMgr method) getColNdx() (pyshepseg.tilingstats.OpenRatContainer method) getImgNullValue() (in module pyshepseg.tiling) getIndexInPage() (pyshepseg.tilingstats.RatPage method) getNumTiles() (pyshepseg.tiling.TileInfo method) getPercentile() (pyshepseg.tilingstats.SegmentStats method) getRatPageId() (in module pyshepseg.tilingstats) getRatVal() (pyshepseg.tilingstats.RatPage method)

getSegmentComplete() (pyshepseg.tilingstats.RatPage method) getSegmentIndices() (pyshepseg.shepseg.RowColArray method) getSortedKeysAndValuesForDict() (in module pyshepseg.tilingstats) getStat() (pyshepseg.tilingstats.SegmentStats method) getTile() (pyshepseg.tiling.TileInfo method) getTileSegmentation() (pyshepseg.tiling.SegmentationConcurrencyMgr method) (pyshepseg.tiling.SegNoConcurrencyMgr method) getTilesForFile() (in module pyshepseg.tiling)

H

HistogramAccumulator (class in pyshepseg.tiling)

I

initialize() (pyshepseg.tiling.SegmentationConcurrencyMgr method)

L

loadOverlap() (pyshepseg.tiling.SegmentationConcurrencyMgr method) (pyshepseg.tiling.SegNoConcurrencyMgr method)

M

makeFastStatsSelection() (in module pyshepseg.tilingstats) makeOutRatKea() (in module pyshepseg.tilingstats) makeSegmentLocations() (in module pyshepseg.shepseg) makeSegSize() (in module pyshepseg.shepseg) mergeSinglePixels() (in module pyshepseg.shepseg)

module pyshepseg.shepseg pyshepseg.subset pyshepseg.tiling pyshepseg.tilingstats pyshepseg.utils

N

NetworkDataChannel (class in pyshepseg.tiling)

O

openEverything() (in module pyshepseg.tilingstats) OpenRatContainer (class in pyshepseg.tilingstats)

overlapCacheFilename() (pyshepseg.tiling.SegNoConcurrencyMgr method) overlapCacheKey() (pyshepseg.tiling.SegmentationConcurrencyMgr static method)

P

pageComplete() (pyshepseg.tilingstats.RatPage method) popFromQue() (pyshepseg.tiling.SegmentationConcurrencyMgr static method) popNextTile() (pyshepseg.tilingstats.StatsReadManager method) processSubsetTile() (in module pyshepseg.subset) pyshepseg.shepseg module pyshepseg.subset module

pyshepseg.tiling module pyshepseg.tilingstats module pyshepseg.utils module PyShepSegStatsError PyShepSegSubsetError PyShepSegTilingError

R

RatPage (class in pyshepseg.tilingstats) readColDataIntoPage() (in module pyshepseg.subset) readRATIntoPage() (in module pyshepseg.subset) readSubsampledImageBand() (in module pyshepseg.tiling) readTile() (pyshepseg.tilingstats.StatsReadManager method)

recodeSharedSegments() (pyshepseg.tiling.SegmentationConcurrencyMgr static method) recodeTile() (pyshepseg.tiling.SegmentationConcurrencyMgr method) relabelSegments() (in module pyshepseg.shepseg) (pyshepseg.tiling.SegmentationConcurrencyMgr static method) reportWorkerException() (in module pyshepseg.utils) RowColArray (class in pyshepseg.shepseg)

S

saveOverlap() (pyshepseg.tiling.SegmentationConcurrencyMgr method) (pyshepseg.tiling.SegNoConcurrencyMgr method) SegFargateMgr (class in pyshepseg.tiling) segmentAllTiles() (pyshepseg.tiling.SegmentationConcurrencyMgr method) (pyshepseg.tiling.SegNoConcurrencyMgr method) SegmentationConcurrencyConfig (class in pyshepseg.tiling) SegmentationConcurrencyMgr (class in pyshepseg.tiling) SegmentationResult (class in pyshepseg.shepseg) SegmentationResultCache (class in pyshepseg.tiling) SegmentStats (class in pyshepseg.tilingstats) SegNoConcurrencyMgr (class in pyshepseg.tiling) SegPoint (class in pyshepseg.tilingstats) SegSubprocMgr (class in pyshepseg.tiling) SegThreadsMgr (class in pyshepseg.tiling) selectConcurrencyClass() (in module pyshepseg.tiling) setHistogramFromDictionary() (in module pyshepseg.subset) setRatVal() (pyshepseg.tilingstats.RatPage method) SetRowCount() (pyshepseg.tilingstats.OpenRatContainer method) setSegmentComplete() (pyshepseg.tilingstats.RatPage method)

setSubsetRecodeFromDictionary() (in module pyshepseg.subset) setupNetworkComms() (pyshepseg.tiling.SegmentationConcurrencyMgr method) (pyshepseg.tiling.SegThreadsMgr method) setupOverviews() (pyshepseg.tiling.SegmentationConcurrencyMgr method) shutdown() (pyshepseg.tiling.NetworkDataChannel method) (pyshepseg.tiling.SegFargateMgr method) (pyshepseg.tiling.SegmentationConcurrencyMgr method) (pyshepseg.tiling.SegThreadsMgr method) specificChecks() (pyshepseg.tiling.SegFargateMgr method) (pyshepseg.tiling.SegmentationConcurrencyMgr method) (pyshepseg.tiling.SegThreadsMgr method) startReadWorkers() (pyshepseg.tilingstats.StatsReadManager method) startWorkers() (pyshepseg.tiling.SegFargateMgr method) (pyshepseg.tiling.SegmentationConcurrencyMgr method) (pyshepseg.tiling.SegSubprocMgr method) (pyshepseg.tiling.SegThreadsMgr method) StatsReadConfig (class in pyshepseg.tilingstats) StatsReadManager (class in pyshepseg.tilingstats) stitchTiles() (pyshepseg.tiling.SegmentationConcurrencyMgr method) subsetImage() (in module pyshepseg.subset)

T

TiledSegmentationResult (class in pyshepseg.tiling)

TiledStatsResult (class in pyshepseg.tilingstats) TileInfo (class in pyshepseg.tiling)

U

updateCounts() (in module pyshepseg.tiling) updateHist() (pyshepseg.tiling.HistogramAccumulator method)

userFuncMeanCoord() (in module pyshepseg.tilingstats) userFuncNumEdgePixels() (in module pyshepseg.tilingstats) userFuncVariogram() (in module pyshepseg.tilingstats)

W

waitClusterTasksFinished() (pyshepseg.tiling.SegFargateMgr method) waitForTile() (pyshepseg.tiling.SegmentationResultCache method) worker() (pyshepseg.tiling.SegThreadsMgr method) (pyshepseg.tilingstats.StatsReadManager method) WorkerErrorRecord (class in pyshepseg.utils) WriteArray() (pyshepseg.tilingstats.OpenRatContainer method)

writeColorTableFromRatColumns() (in module pyshepseg.utils) writeCompletedPagesForSubset() (in module pyshepseg.subset) writeCompletePages() (in module pyshepseg.tilingstats) writeHistogramToFile() (pyshepseg.tiling.SegmentationConcurrencyMgr static method) writeOverviews() (pyshepseg.tiling.SegmentationConcurrencyMgr method) writeRandomColourTable() (in module pyshepseg.utils) writeTileToTemp() (pyshepseg.tiling.SegNoConcurrencyMgr method)