def _getCTFModel(self, defocusU, defocusV, defocusAngle, resol, psdFile):
ctf = CTFModel()
ctf.setStandardDefocus(defocusU, defocusV, defocusAngle)
ctf.setResolution(resol)
ctf.setPsdFile(psdFile)
return ctf
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 _getCTFModel(self, defocusU, defocusV, defocusAngle, psdFile):
ctf = CTFModel()
ctf.setStandardDefocus(defocusU, defocusV, defocusAngle)
ctf.setPsdFile(psdFile)
return ctf
