def createOutputStep(self):
inputMovies = self.inputMovies.get()
micSet = self._createSetOfMicrographs()
micSet.copyInfo(inputMovies)
# Also create a Set of Movies with the alignment parameters
movieSet = self._createSetOfMovies()
movieSet.copyInfo(inputMovies)
for movie in inputMovies:
movieId = movie.getObjId()
micName = self._getMicName(movieId)
movieFolder = self._getMovieFolder(movieId)
mic = micSet.ITEM_TYPE()
mic.setObjId(movieId)
mic.setFileName(self._getExtraPath(micName))
micSet.append(mic)
# Parse the alignment parameters and store the log files
alignedMovie = movie.clone()
logFile = self._getExtraPath(self._getLogFile(movieId))
alignment = parseMovieAlignment(logFile)
alignedMovie.setAlignment(alignment)
movieSet.append(alignedMovie)
self._defineOutputs(outputMicrographs=micSet)
self._defineTransformRelation(inputMovies, micSet)
self._defineOutputs(outputMovies=movieSet)
self._defineTransformRelation(inputMovies, movieSet)
def importAlignmentStep(self, micsId, pattern):
""" Copy alignment matching the filename pattern
"""
inputMovies = self.inputMovies.get()
# Also create a Set of Movies with the alignment parameters
movieSet = self._createSetOfMovies()
movieSet.copyInfo(inputMovies)
alignmentFiles = self._getFilePaths(pattern)
movieDict = {}
for fn in alignmentFiles:
# 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()))
movieId = int(match.group(1))
movieDict[movieId] = fn
for movie in inputMovies:
movieId = movie.getObjId()
if movieId in movieDict:
# Parse the alignment parameters and store the log files
alignedMovie = movie.clone()
logFileSrc = movieDict[movieId]
alignment = parseMovieAlignment(logFileSrc)
alignedMovie.setAlignment(alignment)
movieSet.append(alignedMovie)
else:
self.warning("Alignment for movie with id %d was not found. DISCARDED!!!" % movieId)
self._defineOutputs(outputMovies=movieSet)
self._defineTransformRelation(inputMovies, movieSet)
def createOutputStep(self):
inputMovies = self.inputMovies.get()
micSet = self._createSetOfMicrographs()
micSet.copyInfo(inputMovies)
# Also create a Set of Movies with the alignment parameters
movieSet = self._createSetOfMovies()
movieSet.copyInfo(inputMovies)
for movie in inputMovies:
movieId = movie.getObjId()
micName = self._getMicName(movieId)
movieFolder = self._getMovieFolder(movieId)
mic = micSet.ITEM_TYPE()
mic.setObjId(movieId)
mic.setFileName(self._getExtraPath(micName))
micSet.append(mic)
# Parse the alignment parameters and store the log files
alignedMovie = movie.clone()
logFile = self._getExtraPath(self._getLogFile(movieId))
alignment = parseMovieAlignment(logFile)
alignedMovie.setAlignment(alignment)
movieSet.append(alignedMovie)
self._defineOutputs(outputMicrographs=micSet)
self._defineTransformRelation(inputMovies, micSet)
self._defineOutputs(outputMovies=movieSet)
self._defineTransformRelation(inputMovies, movieSet)
def _getMovieShifts(self, movie):
""" Returns the x and y shifts for the alignment of this movie.
The shifts should refer to the original micrograph without any binning.
In case of a binning greater than 1, the shifts should be scaled.
"""
logPath = self._getExtraPath(self._getMovieLogFile(movie))
binning = self.binFactor.get()
if not self.useMotioncor2:
xShifts, yShifts = parseMovieAlignment(logPath)
else:
xShifts, yShifts = parseMovieAlignment2(logPath)
xSfhtsCorr = [x * binning for x in xShifts]
ySfhtsCorr = [y * binning for y in yShifts]
return xSfhtsCorr, ySfhtsCorr
def _getMovieShifts(self, movie):
""" Returns the x and y shifts for the alignment of this movie.
The shifts should refer to the original micrograph without any binning.
In case of a binning greater than 1, the shifts should be scaled.
"""
logPath = self._getExtraPath(self._getMovieLogFile(movie))
binning = self.binFactor.get()
if not self.useMotioncor2:
xShifts, yShifts = parseMovieAlignment(logPath)
else:
xShifts, yShifts = parseMovieAlignment2(logPath)
# ROB: this is wrong, shifts are given in "original pixels"
# even if bin is requested
# xSfhtsCorr = [x * binning for x in xShifts]
# ySfhtsCorr = [y * binning for y in yShifts]
# return xSfhtsCorr, ySfhtsCorr
return xShifts, yShifts
def importAlignmentStep(self, micsId, pattern):
""" Copy alignment matching the filename pattern
"""
inputMovies = self.inputMovies.get()
# Also create a Set of Movies with the alignment parameters
movieSet = self._createSetOfMovies()
movieSet.copyInfo(inputMovies)
alignmentFiles = self._getFilePaths(pattern)
movieDict = {}
for fn in alignmentFiles:
# 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()))
movieId = int(match.group(1))
movieDict[movieId] = fn
for movie in inputMovies:
movieId = movie.getObjId()
if movieId in movieDict:
# Parse the alignment parameters and store the log files
alignedMovie = movie.clone()
logFileSrc = movieDict[movieId]
alignment = parseMovieAlignment(logFileSrc)
alignedMovie.setAlignment(alignment)
movieSet.append(alignedMovie)
else:
self.warning(
"Alignment for movie with id %d was not found. DISCARDED!!!"
% movieId)
self._defineOutputs(outputMovies=movieSet)
self._defineTransformRelation(inputMovies, movieSet)
