def _preprocessImageRow(self, img, imgRow):
from convert import setupCTF, copyOrLinkFileName
if self._imgPath is not None:
copyOrLinkFileName(imgRow, self._imgPath, self.protocol._getExtraPath())
setupCTF(imgRow, self.protocol.samplingRate.get())
if self._micIdOrName:
micId = imgRow.getValue('rlnMicrographId', None)
micName = imgRow.getValue('rlnMicrographName', None)
# Check which is the key to identify micrographs (id or name)
if micId is not None:
micKey = micId
else:
micKey = micName
mic = self.micDict.get(micKey, None)
# First time I found this micrograph (either by id or name)
if mic is None:
mic = Micrograph()
mic.setObjId(micId)
if micName is None:
micName = self.protocol._getExtraPath('fake_micrograph%6d' % micId)
mic.setFileName(micName)
self.micSet.append(mic)
# Update dict with new Micrograph
self.micDict[micKey] = mic
# Update the row to set a MDL_MICROGRAPH_ID
imgRow.setValue('rlnMicrographId', long(mic.getObjId()))
def _preprocessImageRow(self, img, imgRow):
from convert import setupCTF, copyOrLinkFileName
if self._imgPath is not None:
copyOrLinkFileName(imgRow, self._imgPath,
self.protocol._getExtraPath())
setupCTF(imgRow, self.protocol.samplingRate.get())
if self._micIdOrName:
micId = imgRow.getValue('rlnMicrographId', None)
micName = imgRow.getValue('rlnMicrographName', None)
# Check which is the key to identify micrographs (id or name)
if micId is not None:
micKey = micId
else:
micKey = micName
mic = self.micDict.get(micKey, None)
# First time I found this micrograph (either by id or name)
if mic is None:
mic = Micrograph()
mic.setObjId(micId)
if micName is None:
micName = self.protocol._getExtraPath(
'fake_micrograph%6d' % micId)
mic.setFileName(micName)
mic.setMicName(os.path.basename(micName))
self.micSet.append(mic)
# Update dict with new Micrograph
self.micDict[micKey] = mic
# Update the row to set a MDL_MICROGRAPH_ID
imgRow.setValue('rlnMicrographId', long(mic.getObjId()))
def _checkNewMics(self, micSet):
""" Check for already computed CTF and update the output set. """
micDict = {}
newMic = False
for mic in micSet:
micDict[mic.getFileName()] = True
if micDict:
if micSet.getSize():
micSet.enableAppend()
micSet.loadAllProperties()
else:
micSet.setStreamState(micSet.STREAM_OPEN)
acquisition = Acquisition()
acquisition.setMagnification(self._magnification)
acquisition.setVoltage(self._voltage)
acquisition.setSphericalAberration(self._sphericalAberration)
acquisition.setAmplitudeContrast(self._amplitudeContrast)
micSet.setAcquisition(acquisition)
micSet.setSamplingRate(self.samplingRate.get())
mic = Micrograph()
counter = 0
for k, v in self.xmippMic.iteritems():
counter += 1
if (k not in micDict):
mic.setFileName(k)
mic.setMicName(basename(k))
mic.setObjId(counter)
micSet.append(mic)
newMic = True
return micSet, newMic #why a dictionary, a boolean may be enought
def _preprocessParticleRow(self, img, imgRow):
if self._imgPath:
# Create a link or copy files to extraPath
# and update the Row properly
index, fn = xmippToLocation(imgRow.getValue(md.MDL_IMAGE))
imgBase = basename(fn)
imgDst = self.protocol._getExtraPath(imgBase)
if not exists(imgDst):
self.copyOrLink(join(self._imgPath, fn), imgDst)
imgRow.setValue(md.MDL_IMAGE, locationToXmipp(index, imgDst))
if self._micIdOrName:
micId = imgRow.getValue(md.MDL_MICROGRAPH_ID, None)
micName = imgRow.getValue(md.MDL_MICROGRAPH, None)
# Check which is the key to identify micrographs (id or name)
if micId is not None:
micKey = micId
else:
micKey = micName
mic = self.micDict.get(micKey, None)
# First time I found this micrograph (either by id or name)
if mic is None:
mic = Micrograph()
mic.setObjId(micId)
if micName is None:
micName = self.protocol._getExtraPath(
'fake_micrograph%6d' % micId)
mic.setFileName(micName)
self.micSet.append(mic)
# Update dict with new Micrograph
self.micDict[micKey] = mic
# Update the row to set a MDL_MICROGRAPH_ID
imgRow.setValue(md.MDL_MICROGRAPH_ID, long(mic.getObjId()))
# JMRT: This means that the metadata contains MDL_CTF_MODEL
# and the files path were found from some root
# In Xmipp 3.1 the ctfparam metadata in particles
# was replaced with directly seeting the CTF values
# so we need to fill those in the particle row
if self._ctfPath:
ctfModel = imgRow.getValue(md.MDL_CTF_MODEL)
if ctfModel in self._ctfDict:
ctfRow = self._ctfDict[ctfModel]
else:
ctfRow = md.Row()
ctfRow.readFromFile(join(self._ctfPath, ctfModel))
self._ctfDict[ctfModel] = ctfRow
imgRow.copyFromRow(ctfRow)
def _preprocessParticleRow(self, img, imgRow):
if self._imgPath:
# Create a link or copy files to extraPath
# and update the Row properly
index, fn = xmippToLocation(imgRow.getValue(md.MDL_IMAGE))
imgBase = basename(fn)
imgDst = self.protocol._getExtraPath(imgBase)
if not exists(imgDst):
self.copyOrLink(join(self._imgPath, fn), imgDst)
imgRow.setValue(md.MDL_IMAGE, locationToXmipp(index, imgDst))
if self._micIdOrName:
micId = imgRow.getValue(md.MDL_MICROGRAPH_ID, None)
micName = imgRow.getValue(md.MDL_MICROGRAPH, None)
# Check which is the key to identify micrographs (id or name)
if micId is not None:
micKey = micId
else:
micKey = micName
mic = self.micDict.get(micKey, None)
# First time I found this micrograph (either by id or name)
if mic is None:
mic = Micrograph()
mic.setObjId(micId)
if micName is None:
micName = self.protocol._getExtraPath('fake_micrograph%6d'
% micId)
mic.setFileName(micName)
self.micSet.append(mic)
# Update dict with new Micrograph
self.micDict[micKey] = mic
# Update the row to set a MDL_MICROGRAPH_ID
imgRow.setValue(md.MDL_MICROGRAPH_ID, long(mic.getObjId()))
# JMRT: This means that the metadata contains MDL_CTF_MODEL
# and the files path were found from some root
# In Xmipp 3.1 the ctfparam metadata in particles
# was replaced with directly seeting the CTF values
# so we need to fill those in the particle row
if self._ctfPath:
ctfModel = imgRow.getValue(md.MDL_CTF_MODEL)
if ctfModel in self._ctfDict:
ctfRow = self._ctfDict[ctfModel]
else:
ctfRow = md.Row()
ctfRow.readFromFile(join(self._ctfPath, ctfModel))
self._ctfDict[ctfModel] = ctfRow
imgRow.copyFromRow(ctfRow)
def _preprocessParticleRow(self, img, imgRow):
if self._imgPath:
# Create a link or copy files to extraPath
# and update the Row properly
index, fn = xmippToLocation(imgRow.getValue(md.MDL_IMAGE))
imgBase = basename(fn)
imgDst = self.protocol._getExtraPath(imgBase)
if not exists(imgDst):
self.copyOrLink(join(self._imgPath, fn), imgDst)
imgRow.setValue(md.MDL_IMAGE, locationToXmipp(index, imgDst))
if self._micIdOrName:
micId = imgRow.getValue(md.MDL_MICROGRAPH_ID, None)
micName = imgRow.getValue(md.MDL_MICROGRAPH, None)
# Check which is the key to identify micrographs (id or name)
if micId is not None:
micKey = micId
else:
micKey = micName
mic = self.micDict.get(micKey, None)
# First time I found this micrograph (either by id or name)
if mic is None:
mic = Micrograph()
mic.setObjId(micId)
if micName is None:
micName = self.protocol._getExtraPath('fake_micrograph%6d' % micId)
mic.setFileName(micName)
self.micSet.append(mic)
# Update dict with new Micrograph
self.micDict[micKey] = mic
# Update the row to set a MDL_MICROGRAPH_ID
imgRow.setValue(md.MDL_MICROGRAPH_ID, long(mic.getObjId()))
