def createOutputStep(self):
# PARTICLES
cleanPattern(self._getPath("*.sqlite"))
partSet = self._createSetOfParticles()
readSetOfParticles(self._getPath("particles.xmd"), partSet)
inputSampling = self.inputCoordinates[0].get().getMicrographs(
).getSamplingRate()
partSet.setSamplingRate(self._getDownFactor() * inputSampling)
boxSize = self._getBoxSize()
# COORDINATES
writeSet = False
if self.checkIfPrevRunIsCompatible("coords_"):
writeSet = True
if not "OR" in self.coordinatesDict:
self.loadCoords(self._getExtraPath(
self.CONSENSUS_COOR_PATH_TEMPLATE % 'TRUE'),
'OR',
writeSet=False)
coordSet = SetOfCoordinates(
filename=self._getPath("coordinates.sqlite"))
coordSet.copyInfo(self.coordinatesDict['OR'])
coordSet.setBoxSize(boxSize)
coordSet.setMicrographs(self.coordinatesDict['OR'].getMicrographs())
downFactor = self._getDownFactor()
for part in partSet:
coord = part.getCoordinate().clone()
coord.scale(downFactor)
deepZscoreLabel = '_xmipp_%s' % xmipp.label2Str(
MD.MDL_ZSCORE_DEEPLEARNING1)
setattr(coord, deepZscoreLabel, getattr(part, deepZscoreLabel))
coordSet.append(coord)
coordSet.write()
partSet.write()
self._defineOutputs(outputCoordinates=coordSet)
self._defineOutputs(outputParticles=partSet)
for inSetOfCoords in self.inputCoordinates:
self._defineSourceRelation(inSetOfCoords.get(), coordSet)
self._defineSourceRelation(inSetOfCoords.get(), partSet)
def readSetOfCoordsFromPosFnames(posDir, setOfInputCoords, sqliteOutName,
write=True):
"""
posDir: path where there are .pos files with coordinates
setOfInputCoords. Set to find micrographs
sqliteOutName. Path where sqlite map will be created. Warning, it overwrites
content
"""
inputMics = setOfInputCoords.getMicrographs()
cleanPath(sqliteOutName)
setOfOutputCoordinates= SetOfCoordinates(filename= sqliteOutName)
setOfOutputCoordinates.setMicrographs(inputMics)
setOfOutputCoordinates.setBoxSize(setOfInputCoords.getBoxSize())
readSetOfCoordinates(posDir, micSet=inputMics,
coordSet=setOfOutputCoordinates,
readDiscarded=False)
if write:
setOfOutputCoordinates.write()
return setOfOutputCoordinates
def _visualizeCoordinates(self, e=None):
views = []
outCoords = self.protocol.getOutput()
if not outCoords: print(" > Not output found, yet."); return
coordsViewerFn = self.protocol._getExtraPath('coordsViewer.sqlite')
mdLabel = emlib.MDL_GOOD_REGION_SCORE
if not getXmippAttribute(outCoords.getFirstItem(), mdLabel):
print(" > outputCoordinates do NOT have 'MDL_GOOD_REGION_SCORE'!"); return
cleanPath(coordsViewerFn)
newOutput = SetOfCoordinates(filename=coordsViewerFn)
newOutput.copyInfo(outCoords)
newOutput.setMicrographs(outCoords.getMicrographs())
thres = self.visualizeCoordinates.get()
for coord in outCoords:
if getXmippAttribute(coord, mdLabel).get() > thres:
newOutput.append(coord.clone())
newOutput.write()
newOutput.close() #SetOfCoordinates does not implement __exit__, required for with
micSet = newOutput.getMicrographs() # accessing mics to provide metadata file
if micSet is None:
raise Exception('visualize: SetOfCoordinates has no micrographs set.')
fn = self.protocol._getExtraPath("allMics.xmd")
xmipp3.convert.writeSetOfMicrographs(micSet, fn)
tmpDir = self.protocol._getExtraPath('manualThresholding_%03d'%int(thres*100))
cleanPath(tmpDir)
makePath(tmpDir)
xmipp3.convert.writeSetOfCoordinates(tmpDir, newOutput)
views.append(CoordinatesObjectView(self._project, fn, tmpDir,
self.protocol, inTmpFolder=True))
return views