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 importCTF(self, mic, fileName):
defocusU, defocusV, defocusAngle = parseCtffindOutput(fileName)
ctf = CTFModel()
ctf.copyObjId(mic)
ctf.setStandardDefocus(defocusU, defocusV, defocusAngle)
ctf.setMicrograph(mic)
ctf.setPsdFile(removeExt(fileName) + "_psd.mrc")
return ctf
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 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 importCtfStep(self, micsId, pattern):
""" Copy movies matching the filename pattern
Register other parameters.
"""
inputMics = self.inputMicrographs.get()
ctfSet = self._createSetOfCTF()
ctfSet.setMicrographs(inputMics)
ctfFiles = self._getFilePaths(pattern)
ctfDict = {}
for fn in ctfFiles:
# Try to match the micrograph id from filename
# this is set by the user by using #### format in the pattern
match = self._idRegex.match(fn)
if match is None:
raise Exception("File '%s' doesn't match the pattern '%s'" %
(fn, self.pattern.get()))
ctfId = int(match.group(1))
ctfDict[ctfId] = fn
from pyworkflow.em.packages.grigoriefflab.convert import parseCtffindOutput
for mic in inputMics:
if mic.getObjId() in ctfDict:
defocusU, defocusV, defocusAngle = parseCtffindOutput(
ctfDict[mic.getObjId()])
else:
self.warning("CTF for micrograph id %d was not found." %
mic.getObjId())
defocusU, defocusV, defocusAngle = -999, -1, -999
# save the values of defocus for each micrograph in a list
ctf = CTFModel()
ctf.copyObjId(mic)
ctf.setStandardDefocus(defocusU, defocusV, defocusAngle)
ctf.setMicrograph(mic)
ctfSet.append(ctf)
self._defineOutputs(outputCTF=ctfSet)
self._defineCtfRelation(inputMics, ctfSet)
def importCtfStep(self, micsId, pattern):
""" Copy movies matching the filename pattern
Register other parameters.
"""
inputMics = self.inputMicrographs.get()
ctfSet = self._createSetOfCTF()
ctfSet.setMicrographs(inputMics)
ctfFiles = self._getFilePaths(pattern)
ctfDict = {}
for fn in ctfFiles:
# Try to match the micrograph id from filename
# this is set by the user by using #### format in the pattern
match = self._idRegex.match(fn)
if match is None:
raise Exception("File '%s' doesn't match the pattern '%s'" % (fn, self.pattern.get()))
ctfId = int(match.group(1))
ctfDict[ctfId] = fn
from pyworkflow.em.packages.grigoriefflab.convert import parseCtffindOutput
for mic in inputMics:
if mic.getObjId() in ctfDict:
defocusU, defocusV, defocusAngle = parseCtffindOutput(ctfDict[mic.getObjId()])
else:
self.warning("CTF for micrograph id %d was not found." % mic.getObjId())
defocusU, defocusV, defocusAngle = -999, -1, -999
# save the values of defocus for each micrograph in a list
ctf = CTFModel()
ctf.copyObjId(mic)
ctf.setStandardDefocus(defocusU, defocusV, defocusAngle)
ctf.setMicrograph(mic)
ctfSet.append(ctf)
self._defineOutputs(outputCTF=ctfSet)
self._defineCtfRelation(inputMics, ctfSet)
def importCTF(self, mic, fileName):
ctf = CTFModel()
ctf.setMicrograph(mic)
readCTFModel(ctf, fileName)
return ctf