def _ctfToMd(self, ctf, ctfMd):
""" Write the proper metadata for Xmipp from a given CTF """
ctfMd.clear()
ctfRow = Row()
convert.ctfModelToRow(ctf, ctfRow)
convert.micrographToRow(ctf.getMicrograph(), ctfRow,
alignType=convert.ALIGN_NONE)
ctfRow.addToMd(ctfMd)
def _pickMicrograph(self, mic, *args):
""" This method should be invoked only when working in streaming mode.
"""
micRow = md.Row()
self._preprocessMicrographRow(mic, micRow)
micrographToRow(mic, micRow)
self._postprocessMicrographRow(mic, micRow)
self._pickMicrographsFromStar(self._getMicStarFile(mic), *args)
def _pickMicrograph(self, mic, params, threshold, minDistance, fom):
""" This method should be invoked only when working in streaming mode.
"""
micRow = md.Row()
self._preprocessMicrographRow(mic, micRow)
micrographToRow(mic, micRow)
self._postprocessMicrographRow(mic, micRow)
self._pickMicrographsFromStar(self._getMicStarFile(mic), params,
threshold, minDistance, fom)
def _pickMicrograph(self, mic, params, threshold, minDistance, fom):
""" This method should be invoked only when working in streaming mode.
"""
micRow = md.Row()
self._preprocessMicrographRow(mic, micRow)
micrographToRow(mic, micRow)
self._postprocessMicrographRow(mic, micRow)
self._pickMicrographsFromStar(self._getMicStarFile(mic), params,
threshold, minDistance, fom)
def _ctfToMd(self, ctf, ctfMd):
""" Write the proper metadata for Xmipp from a given CTF """
ctfMd.clear()
ctfRow = Row()
convert.ctfModelToRow(ctf, ctfRow)
convert.micrographToRow(ctf.getMicrograph(),
ctfRow,
alignType=convert.ALIGN_NONE)
ctfRow.addToMd(ctfMd)
def _computeCTFDiscrepancyStep(self, ctfId, method1, method2):
#TODO must be same micrographs
#convert to md
mdList = [MetaData(), MetaData()]
ctfList = [self.inputCTFs[method1].get()[ctfId], self.inputCTFs[method2].get()[ctfId]]
ctfRow = Row()
for md, ctf in izip(mdList, ctfList):
objId = md.addObject()
convert.ctfModelToRow(ctf, ctfRow)
convert.micrographToRow(ctf.getMicrograph(), ctfRow, alignType=convert.ALIGN_NONE)
ctfRow.writeToMd(md, objId)
self._freqResol[(method1, method2, ctfId)] = xmipp.errorMaxFreqCTFs2D(*mdList)
def _pickMicrograph(self, mic, params, threshold, minDistance, fom):
""" This method should be invoked only when working in streaming mode.
"""
# We need to write the needed star files
# TODO: We need to check when working in real streaming, not all
# TODO: CTF will be available and this needs to be taken into account
micRow = md.Row()
self._preprocessMicrographRow(mic, micRow)
micrographToRow(mic, micRow)
self._postprocessMicrographRow(mic, micRow)
print micRow
self._pickMicrographsFromStar(self._getMicStarFile(mic), params,
threshold, minDistance, fom)
def _computeCTFDiscrepancyStep(self, ctfId, method1, method2):
#TODO must be same micrographs
#convert to md
mdList = [MetaData(), MetaData()]
ctfList = [
self.inputCTFs[method1].get()[ctfId],
self.inputCTFs[method2].get()[ctfId]
]
ctfRow = Row()
for md, ctf in izip(mdList, ctfList):
objId = md.addObject()
convert.ctfModelToRow(ctf, ctfRow)
convert.micrographToRow(ctf.getMicrograph(),
ctfRow,
alignType=convert.ALIGN_NONE)
ctfRow.writeToMd(md, objId)
self._freqResol[(method1, method2,
ctfId)] = xmipp.errorMaxFreqCTFs2D(*mdList)