def pysegPostRec(self, outStar):
# Generate output subtomo dir
outDir = self._getExtraPath(POST_REC_OUT)
makePath(outDir)
# Script called
Plugin.runPySeg(self, PYTHON, self._getCommand(outDir, outStar))
def pysegPicking(self):
# Generate output dir
outDir = self._getExtraPath()
makePath(outDir)
# Generate slices xml
self._createPickingXmlFile(Plugin.getHome(PICKING_SLICES), outDir)
# Script called
Plugin.runPySeg(self, PYTHON, self._getPickingCommand(outDir))
def pysegGraphs(self):
# Generate output dir
outDir = self._getExtraPath()
makePath(outDir)
# Script called
Plugin.runPySeg(self, PYTHON, self._getGraphsCommand(outDir))
# Remove Disperse program intermediate result directories if requested
if self.keepOnlyreqFiles.get():
disperseDirs = glob(self._getExtraPath('disperse_*'))
[shutil.rmtree(disperseDir) for disperseDir in disperseDirs]
def pysegFils(self):
# Generate output dir
outDir = self._getExtraPath()
makePath(outDir)
# Generate sources xml
self._createFilsXmlFile(Plugin.getHome(FILS_SOURCES), outDir)
# Generate targets xml
self._createFilsXmlFile(Plugin.getHome(FILS_TARGETS),
outDir,
isSource=False)
# Script called
Plugin.runPySeg(self, PYTHON, self._getFilsCommand(outDir))
def _getCommand(self):
alg = self.clusteringAlg.get()
classCmd = ' '
classCmd += '%s ' % Plugin.getHome(PLANE_ALIGN_CLASS_SCRIPT)
classCmd += '--inRootDir scipion '
classCmd += '--inStar %s ' % self._getExtraPath(self.inStarName)
classCmd += '--inMask %s ' % getFinalMaskFileName(self.inMask.get())
classCmd += '--outDir %s ' % self._outDir
classCmd += '--filterSize %s ' % self.filterSize.get()
classCmd += '--procLevel %s ' % (FULL_CLASSIFICATION + 1) # Numbered from 1 in pyseg
classCmd += '--doCC3d %s ' % self.doCC3d.get()
classCmd += '--ccMetric %s ' % self._decodeCCMetric()
classCmd += '--clusteringAlg %s ' % self._decodeClusteringAlg()
classCmd += '--distanceMetric %s ' % self._decodeDistanceMetric()
if alg == AFFINITY_PROP:
classCmd += '--apPref %s ' % self.apPref.get()
classCmd += '--apDumping %s ' % self.apDumping.get()
classCmd += '--apMaxIter %s ' % self.apMaxIter.get()
classCmd += '--apConvIter %s ' % self.apConvIter.get()
classCmd += '--apCCRefFilter %s ' % self.apCCRefFilter.get()
else:
classCmd += '--pcaComps %s ' % self._estimatePCAComps()
if alg == AGGLOMERATIVE:
classCmd += '--aggNClusters %s ' % self.aggNClusters.get()
else:
classCmd += '--kmeansNClusters %s ' % self.aggNClusters.get()
classCmd += '--apPartSizeFilter %s ' % self.apPartSizeFilter.get()
classCmd += '-j %s ' % self.numberOfThreads.get()
return classCmd
def _getPickingCommand(self, outDir):
pickingCmd = ' '
pickingCmd += '%s ' % Plugin.getHome(PICKING_SCRIPT)
pickingCmd += '--inStar %s ' % self._getFilsStarFileName()
pickingCmd += '--outDir %s ' % outDir
pickingCmd += '--slicesFile %s ' % self._xmlSlices
pickingCmd += '--peakTh %s ' % self.peakTh.get()
pickingCmd += '--peakNs %s ' % self.peakNs.get()
return pickingCmd
def _getFilsCommand(self, outDir):
filsCmd = ' '
filsCmd += '%s ' % Plugin.getHome(FILS_SCRIPT)
filsCmd += '--inStar %s ' % self._getGraphsStarFile()
filsCmd += '--outDir %s ' % outDir
filsCmd += '--inSources %s ' % abspath(self._xmlSources)
filsCmd += '--inTargets %s ' % abspath(self._xmlTargets)
filsCmd += '--thMode %s ' % self._parseThModeSelection()
filsCmd += '--gRgLen %s ' % self.gRgLen.get()
filsCmd += '--gRgSin %s ' % self.gRgSin.get()
filsCmd += '--gRgEud %s ' % self.gRgEud.get()
return filsCmd
def _getGraphsCommand(self, outDir):
pixSize = self._getSamplingRate() / 10
graphsCmd = ' '
graphsCmd += '%s ' % Plugin.getHome(GRAPHS_SCRIPT)
graphsCmd += '--inStar %s ' % self._getPreSegStarFile(
) # self.inStar.get()
graphsCmd += '--outDir %s ' % outDir
graphsCmd += '--pixelSize %s ' % pixSize # PySeg requires it in nm
graphsCmd += '--sSig %s ' % self.sSig.get()
graphsCmd += '--vDen %s ' % self.vDen.get()
graphsCmd += '--veRatio %s ' % self.vRatio.get()
graphsCmd += '--maxLen %s ' % self.maxLen.get()
graphsCmd += '-j %s ' % self.numberOfThreads.get()
return graphsCmd
def _getPreSegCmd(self, inStar, outDir):
preSegCmd = ' '
preSegCmd += '%s ' % Plugin.getHome(PRESEG_SCRIPT)
preSegCmd += '--inStar %s ' % inStar
preSegCmd += '--outDir %s ' % outDir
preSegCmd += '--spSplit %s ' % self.spSplit.get()
preSegCmd += '--spOffVoxels %s ' % self.spOffVoxels.get()
preSegCmd += '--sgVoxelSize %s ' % (float(self._getSamplingRate()) / 10
) # required in nm
preSegCmd += '--sgThreshold %s ' % self.sgThreshold.get()
preSegCmd += '--sgSizeThreshold %s ' % self.sgSizeThreshold.get()
preSegCmd += '--sgMembThk %s ' % self._checkValue4PySeg(
self.sgMembThk.get()) # required in nm
preSegCmd += '--sgMembNeigh %s ' % self._checkValue4PySeg(
self.sgMembNeigh.get()) # required in nm
return preSegCmd
def _getCommand(self, outDir, outStar):
doGaussianLPFilter = self.doGaussLowPassFilter.get()
cutOffRes = 0
ampCutOff = 0
if doGaussianLPFilter:
cutOffRes = self.cutOffRes.get()
ampCutOff = self.ampCutOff.get()
posRecCmd = ' '
posRecCmd += '%s ' % Plugin.getHome(POST_REC_SCRIPT_MEMB_ATT)
posRecCmd += '--inStar %s ' % self._getExtraPath(self.inStarName)
posRecCmd += '--inMask %s ' % getFinalMaskFileName(self.inMask.get())
posRecCmd += '--inMaskMbSup %s ' % (getFinalMaskFileName(self.mbMask.get()) if self.mbMask.get() else 'None')
posRecCmd += '--mbSupFactor %s ' % (self.mbSupFactor.get() if self.mbSupFactor.get() else '0')
posRecCmd += '--doGaussLowPass %s ' % doGaussianLPFilter
posRecCmd += '--resolution %s ' % (float(self.inputSubtomos.get().getSamplingRate()) / 10) # in nm
posRecCmd += '--cutOffRes %s ' % cutOffRes
posRecCmd += '--ampCutOff %s ' % ampCutOff
posRecCmd += '--filterCTF %s ' % self.filterCTF.get()
posRecCmd += '--outDir %s ' % outDir
posRecCmd += '--outStar %s ' % outStar
posRecCmd += '-j %s ' % self.numberOfThreads.get()
return posRecCmd
def pysegPlaneAlignClassification(self):
# Script called
Plugin.runPySeg(self, PYTHON, self. _getCommand())
def pysegPreSegCenteredStep(self):
inStar = abspath(self.getVesiclesCenteredStarFile())
outDir = self._getExtraPath()
# Script called
Plugin.runPySeg(self, PYTHON, self._getPreSegCmd(inStar, outDir))
def pysegPreSegStep(self):
outDir = self._getExtraPath()
# Script called
Plugin.runPySeg(self, PYTHON,
self._getPreSegCmd(self._starFile, outDir))