def __createTemporaryCtfs(self, obj, setOfMics):
""" Create a temporary .sqlite file to visualize CTF while the
protocol has not finished yet.
"""
cleanPath(obj._getPath("ctfs_temporary.sqlite"))
ctfSet = self.protocol._createSetOfCTF("_temporary")
for mic in setOfMics:
micFn = mic.getFileName()
micDir = obj._getExtraPath(removeBaseExt(mic.getFileName()))
samplingRate = mic.getSamplingRate() * self.protocol.ctfDownFactor.get()
mic.setSamplingRate(samplingRate)
out = self.protocol._getCtfOutPath(micDir)
psdFile = self.protocol._getPsdPath(micDir)
if exists(out) and exists(psdFile):
ctfModel = em.CTFModel()
readCtfModel(ctfModel, out,
ctf4=self.protocol.useCtffind4.get())
ctfModel.setPsdFile(psdFile)
ctfModel.setMicrograph(mic)
ctfSet.append(ctfModel)
if not ctfSet.isEmpty():
ctfSet.write()
ctfSet.close()
return ctfSet
def _createOutputStep(self):
ctfSet = self._createSetOfCTF()
ctfSet.setMicrographs(self.inputMics)
defocusList = []
for _, micDir, mic in self._iterMicrographs():
samplingRate = mic.getSamplingRate() * self.ctfDownFactor.get()
mic.setSamplingRate(samplingRate)
psdFile = self._getPsdPath(micDir)
out = self._getCtfOutPath(micDir)
ctfModel = em.CTFModel()
if not self.useCftfind4:
readCtfModel(ctfModel, out)
else:
readCtfModel(ctfModel, out, True)
ctfModel.setPsdFile(psdFile)
ctfModel.setMicrograph(mic)
defocusList.append(ctfModel.getDefocusU())
defocusList.append(ctfModel.getDefocusV())
ctfSet.append(ctfModel)
self._defocusMaxMin(defocusList)
self._defineOutputs(outputCTF=ctfSet)
self._defineCtfRelation(self.inputMics, ctfSet)
def visualizeObjs(obj, setOfMics):
if exists(obj._getPath("ctfs_temporary.sqlite")):
os.remove(obj._getPath("ctfs_temporary.sqlite"))
ctfSet = self.protocol._createSetOfCTF("_temporary")
for fn, micDir, mic in iterMicrographs(setOfMics):
samplingRate = mic.getSamplingRate() * self.protocol.ctfDownFactor.get()
mic.setSamplingRate(samplingRate)
out = self.protocol._getCtfOutPath(micDir)
psdFile = self.protocol._getPsdPath(micDir)
if exists(out) and exists(psdFile):
ctfModel = em.CTFModel()
if not self.protocol.useCftfind4:
readCtfModel(ctfModel, out)
else:
readCtfModel(ctfModel, out, True)
ctfModel.setPsdFile(psdFile)
ctfModel.setMicrograph(mic)
ctfSet.append(ctfModel)
if ctfSet.getSize() < 1:
raise Exception("Has not been completed the CTF estimation of any micrograph")
else:
ctfSet.write()
ctfSet.close()
self._visualize(ctfSet)
def __createTemporaryCtfs(self, obj, setOfMics):
""" Create a temporary .sqlite file to visualize CTF while the
protocol has not finished yet.
"""
cleanPath(obj._getPath("ctfs_temporary.sqlite"))
ctfSet = self.protocol._createSetOfCTF("_temporary")
for mic in setOfMics:
micFn = mic.getFileName()
micDir = obj._getExtraPath(removeBaseExt(mic.getFileName()))
samplingRate = mic.getSamplingRate(
) * self.protocol.ctfDownFactor.get()
mic.setSamplingRate(samplingRate)
out = self.protocol._getCtfOutPath(micDir)
psdFile = self.protocol._getPsdPath(micDir)
if exists(out) and exists(psdFile):
ctfModel = em.CTFModel()
readCtfModel(ctfModel,
out,
ctf4=self.protocol.useCtffind4.get())
ctfModel.setPsdFile(psdFile)
ctfModel.setMicrograph(mic)
ctfSet.append(ctfModel)
if not ctfSet.isEmpty():
ctfSet.write()
ctfSet.close()
return ctfSet
def visualizeObjs(obj, setOfMics):
if exists(obj._getPath("ctfs_temporary.sqlite")):
os.remove(obj._getPath("ctfs_temporary.sqlite"))
ctfSet = self.protocol._createSetOfCTF("_temporary")
for fn, micDir, mic in iterMicrographs(setOfMics):
samplingRate = mic.getSamplingRate(
) * self.protocol.ctfDownFactor.get()
mic.setSamplingRate(samplingRate)
out = self.protocol._getCtfOutPath(micDir)
psdFile = self.protocol._getPsdPath(micDir)
if exists(out) and exists(psdFile):
ctfModel = em.CTFModel()
readCtfModel(ctfModel, out)
ctfModel.setPsdFile(psdFile)
ctfModel.setMicrograph(mic)
ctfSet.append(ctfModel)
if ctfSet.getSize() < 1:
raise Exception(
"Has not been completed the CTF estimation of any micrograph"
)
else:
ctfSet.write()
ctfSet.close()
self._visualize(ctfSet)
def _createNewCtfModel(self, mic):
micDir = self._getMicrographDir(mic)
out = self._getCtfOutPath(micDir)
psdFile = self._getPsdPath(micDir)
ctfModel2 = em.CTFModel()
readCtfModel(ctfModel2, out, ctf4=self.useCtffind4.get())
ctfModel2.setPsdFile(psdFile)
ctfModel2.setMicrograph(mic)
return ctfModel2
def importCTF(self, mic, fileName):
ctf = CTFModel()
ctf.setMicrograph(mic)
readCtfModel(ctf, fileName, ctf4=ctffindOutputVersion(fileName) == 4)
for suffix in ["_psd.mrc", ".mrc"]:
if os.path.exists(pwutils.removeExt(fileName) + suffix):
ctf.setPsdFile(pwutils.removeExt(fileName) + suffix)
return ctf
def _createNewCtfModel(self, mic):
micDir = self._getMicrographDir(mic)
out = self._getCtfOutPath(micDir)
psdFile = self._getPsdPath(micDir)
ctfModel2 = em.CTFModel()
if not self.useCftfind4:
readCtfModel(ctfModel2, out)
else:
readCtfModel(ctfModel2, out, True)
ctfModel2.setPsdFile(psdFile)
ctfModel2.setMicrograph(mic)
return ctfModel2
def importCTF(self, mic, fileName):
ctf = CTFModel()
ctf.setMicrograph(mic)
readCtfModel(ctf, fileName, ctf4=ctffindOutputVersion(fileName) == 4)
# Try to find the given PSD file associated with the cttfind log file
# we handle special cases of .ctf extension and _ctffindX prefix for Relion runs
fnBase = pwutils.removeExt(fileName)
for suffix in ["_psd.mrc", ".mrc", ".ctf"]:
psdPrefixes = [fnBase, fnBase.replace("_ctffind3", ""), fnBase.replace("_ctffind4", "")]
for prefix in psdPrefixes:
psdFile = prefix + suffix
if os.path.exists(psdFile):
if psdFile.endswith(".ctf"):
psdFile += ":mrc"
ctf.setPsdFile(psdFile)
return ctf
def _createCtfModel(self, mic, updateSampling=True):
# When downsample option is used, we need to update the
# sampling rate of the micrograph associated with the CTF
# since it could be downsampled
if updateSampling:
newSampling = mic.getSamplingRate() * self.ctfDownFactor.get()
mic.setSamplingRate(newSampling)
micDir = self._getMicrographDir(mic)
out = self._getCtfOutPath(micDir)
psdFile = self._getPsdPath(micDir)
ctfModel2 = em.CTFModel()
readCtfModel(ctfModel2, out)
ctfModel2.setPsdFile(psdFile)
ctfModel2.setMicrograph(mic)
return ctfModel2
def _createCtfModel(self, mic, updateSampling=True):
# When downsample option is used, we need to update the
# sampling rate of the micrograph associeted with the CTF
# since it could be downsampled
if updateSampling:
newSampling = mic.getSamplingRate() * self.ctfDownFactor.get()
mic.setSamplingRate(newSampling)
micDir = self._getMicrographDir(mic)
out = self._getCtfOutPath(micDir)
psdFile = self._getPsdPath(micDir)
ctfModel = em.CTFModel()
readCtfModel(ctfModel, out, ctf4=self.useCtffind4.get())
ctfModel.setPsdFile(psdFile)
ctfModel.setMicrograph(mic)
return ctfModel
def importCTF(self, mic, fileName):
ctf = CTFModel()
ctf.setMicrograph(mic)
readCtfModel(ctf, fileName, ctf4=False)
# Try to find the given PSD file associated with the cttfind log file
# we handle special cases of .ctf extension and _ctffindX prefix for Relion runs
fnBase = pwutils.removeExt(fileName)
for suffix in ['_psd.mrc', '.mrc', '.ctf']:
psdPrefixes = [fnBase,
fnBase.replace('_ctffind3', ''),
fnBase.replace('_gctf', '')]
for prefix in psdPrefixes:
psdFile = prefix + suffix
if os.path.exists(psdFile):
if psdFile.endswith('.ctf'):
psdFile += ':mrc'
ctf.setPsdFile(psdFile)
return ctf
def importCTF(self, mic, fileName):
ctf = CTFModel()
ctf.setMicrograph(mic)
readCtfModel(ctf, fileName, ctf4=False)
# Try to find the given PSD file associated with the cttfind log file
# we handle special cases of .ctf extension and _ctffindX prefix for Relion runs
fnBase = pwutils.removeExt(fileName)
for suffix in ['_psd.mrc', '.mrc', '.ctf']:
psdPrefixes = [
fnBase,
fnBase.replace('_ctffind3', ''),
fnBase.replace('_gctf', '')
]
for prefix in psdPrefixes:
psdFile = prefix + suffix
if os.path.exists(psdFile):
if psdFile.endswith('.ctf'):
psdFile += ':mrc'
ctf.setPsdFile(psdFile)
return ctf
def _createOutputStep(self):
ctfSet = self._createSetOfCTF()
ctfSet.setMicrographs(self.inputMics)
defocusList = []
for _, micDir, mic in self._iterMicrographs():
samplingRate = mic.getSamplingRate() * self.ctfDownFactor.get()
mic.setSamplingRate(samplingRate)
psdFile = self._getPsdPath(micDir)
out = self._getCtfOutPath(micDir)
ctfModel = em.CTFModel()
readCtfModel(ctfModel, out, ctf4=self.useCtffind4.get())
ctfModel.setPsdFile(psdFile)
ctfModel.setMicrograph(mic)
defocusList.append(ctfModel.getDefocusU())
defocusList.append(ctfModel.getDefocusV())
ctfSet.append(ctfModel)
self._defocusMaxMin(defocusList)
self._defineOutputs(outputCTF=ctfSet)
self._defineCtfRelation(self.inputMics, ctfSet)
