コード例 #1
0
    def _getCTFModel(self, defocusU, defocusV, defocusAngle, resol, psdFile):
        ctf = CTFModel()
        ctf.setStandardDefocus(defocusU, defocusV, defocusAngle)
        ctf.setResolution(resol)
        ctf.setPsdFile(psdFile)

        return ctf
コード例 #2
0
ファイル: dataimport.py プロジェクト: josegutab/scipion
    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


    

                
コード例 #3
0
    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)
コード例 #4
0
ファイル: protocol_import.py プロジェクト: coocoky/scipion
    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)            
コード例 #5
0
    def _getCTFModel(self, defocusU, defocusV, defocusAngle, psdFile):
        ctf = CTFModel()
        ctf.setStandardDefocus(defocusU, defocusV, defocusAngle)
        ctf.setPsdFile(psdFile)

        return ctf