def _insertAllSteps(self):
"""Insert all steps to calculate the resolution of a 3D reconstruction. """
self.inputVol = locationToXmipp(*self.inputVolume.get().getLocation())
self.refVol = locationToXmipp(*self.referenceVolume.get().getLocation())
if self.doFSC:
self._insertFunctionStep('calculateFscStep')
if self.doStructureFactor:
self._insertFunctionStep('structureFactorcStep')
self._insertFunctionStep('createSummaryStep')
def updateItem(self, item, row):
from convert import locationToXmipp
# ToDo: uncomment this lines when the output metadata has ITEM_ID
# if item.getObjId() != row.getValue(xmipp.MDL_ITEM_ID):
# raise Exception("The objId is not equal to ITEM_ID. Please, sort the metadata.")
if isinstance(item, Class2D):
img = item.getRepresentative()
index, fn = img.getLocation()
else:
index, fn = item.getLocation()
objLoc = locationToXmipp(index, fn)
mdLoc = row.getValue(xmipp.MDL_IMAGE)
if objLoc != mdLoc:
print objLoc+" "+mdLoc
raise Exception("The image isn't the same. Please, sort the metadata.")
item._xmipp_maxCC = Float(row.getValue(xmipp.MDL_MAXCC))
item._xmipp_zScoreResCov = Float(row.getValue(xmipp.MDL_ZSCORE_RESCOV))
item._xmipp_zScoreResMean = Float(row.getValue(xmipp.MDL_ZSCORE_RESMEAN))
item._xmipp_zScoreResVar = Float(row.getValue(xmipp.MDL_ZSCORE_RESVAR))
if isinstance(item, Class2D):
particle = item.getRepresentative()
else:
particle = item
particle.setTransform(rowToAlignment(row, alignType=ALIGN_PROJ))
def compareVolumeStep(self, volLoc, i):
fnRef = self._getExtraPath("reference.vol")
sampling = self.referenceVolume.get().getSamplingRate()
fnRoot = self._getExtraPath("volume_%02d" % i)
fnVol = fnRoot + ".vol"
self.runJob("xmipp_image_convert","-i %s -o %s -t vol"%(locationToXmipp(volLoc[0],volLoc[1]),fnVol))
# Resize if the volume has different size than the reference
self._resizeVolume(fnVol)
if self.doAlign: # Align against the reference if selected
self.runJob('xmipp_volume_align',
"--i1 %s --i2 %s --apply --local" % (fnRef, fnVol))
if self.mask.hasValue(): # Mask volume if input mask
self._maskVolume(fnVol)
# Finally compute the FSC
args = "--ref %s -i %s -o %s_fsc.xmd --sampling_rate %f" % (fnRef, fnVol,
fnRoot, sampling)
self.runJob("xmipp_resolution_fsc", args)
def compareVolumeStep(self, volLoc, i):
fnRef = self._getExtraPath("reference.vol")
sampling = self.referenceVolume.get().getSamplingRate()
fnRoot = self._getExtraPath("volume_%02d" % i)
fnVol = fnRoot + ".vol"
self.runJob(
"xmipp_image_convert", "-i %s -o %s -t vol" %
(locationToXmipp(volLoc[0], volLoc[1]), fnVol))
# Resize if the volume has different size than the reference
self._resizeVolume(fnVol)
if self.doAlign: # Align against the reference if selected
self.runJob('xmipp_volume_align',
"--i1 %s --i2 %s --apply --local" % (fnRef, fnVol))
if self.mask.hasValue(): # Mask volume if input mask
self._maskVolume(fnVol)
# Finally compute the FSC
args = "--ref %s -i %s -o %s_fsc.xmd --sampling_rate %f" % (
fnRef, fnVol, fnRoot, sampling)
self.runJob("xmipp_resolution_fsc", args)
