def polishStep(self, params):
""" Create the input file in STAR format as expected by Relion.
If the input particles comes from Relion, just link the file.
"""
from pyworkflow.utils.path import copyTree
copyTree(self.refineRun.get()._getExtraPath(), self._getExtraPath())
self.runJob(self._getProgram('relion_particle_polish'), params, env=getEnviron(self.refineRun.get().useRelion14))
def __init__(self, inputFile, **kwargs):
# Small trick to handle .vol Spider volumes
if inputFile.endswith('.vol'):
inputFile += ":spi"
CommandView.__init__(self, 'bshow "%s" &' % inputFile,
env=getEnviron(), **kwargs)
def __init__(self, inputFile, **kwargs):
# Small trick to handle .vol Spider volumes
if inputFile.endswith('.vol'):
inputFile += ":spi"
CommandView.__init__(self,
'bshow "%s" &' % inputFile,
env=getEnviron(),
**kwargs)
This sub-package contains data and protocol classes
wrapping Kai Zhang's GCTF program
"""
import os
_logo = "gctf_logo.png"
GCTF_HOME = 'GCTF_HOME'
from bibtex import _bibtex # Load bibtex dict with references
from convert import getEnviron
from protocol_gctf import ProtGctf
# Wizards
from wizard import GctfCTFWizard
_environ = getEnviron()
# We need this import to register the specific viewing command
# when visualizing Gctf results
from viewer import GctfViewer
def validateInstallation():
""" This function will be used to check if package is properly installed."""
missingPaths = [
"%s: %s" % (var, _environ[var]) for var in [GCTF_HOME]
if not os.path.exists(_environ[var])
]
if missingPaths:
return ["Missing variables:"] + missingPaths
This sub-package contains cryoMethods protocols and tools.
"""
# from bibtex import _bibtex # Load bibtex dict with references
_logo = "cryomethods_logo.png"
_references = []
import os
from convert import getSupportedVersions, getVersion, getEnviron
from protocol_volume_selector import ProtInitialVolumeSelector
# Wizards
from wizard import (TargetFilterWizard, InitialPassFilterWizard,
MaskDiameterWizard)
#Viewer
from viewer import VolumeSelectorViewer
_environ = getEnviron()
def validateInstallation():
""" This function will be used to check if RELION is properly installed. """
missingPaths = ["%s: %s" % (var, _environ[var])
for var in ['RELION_HOME']
if not os.path.exists(_environ[var])]
if missingPaths:
return ["Missing variables:"] + missingPaths
else:
return [] # No errors
def _processMovie(self, movie):
inputMovies = self.inputMovies.get()
movieFolder = self._getOutputMovieFolder(movie)
outputMicFn = self._getRelPath(self._getOutputMicName(movie),
movieFolder)
outputMovieFn = self._getRelPath(self._getOutputMovieName(movie),
movieFolder)
movieBaseName = pwutils.removeExt(movie.getFileName())
aveMicFn = movieBaseName + '_uncorrected_avg.mrc'
logFile = self._getRelPath(self._getMovieLogFile(movie), movieFolder)
a0, aN = self._getRange(movie, 'align')
if not self.useMotioncor2:
# Get the number of frames and the range to be used
# for alignment and sum
s0, sN = self._getRange(movie, 'sum')
argsDict = {
'-crx': self.cropOffsetX.get(),
'-cry': self.cropOffsetY.get(),
'-cdx': self.cropDimX.get(),
'-cdy': self.cropDimY.get(),
'-bin': self.binFactor.get(),
'-nst': '%d' % a0,
'-ned': '%d' % aN,
'-nss': '%d' % s0,
'-nes': '%d' % sN,
'-gpu': self.GPUIDs.get(),
'-flg': logFile,
}
args = '"%s" ' % movie.getBaseName()
args += ' '.join(
['%s %s' % (k, v) for k, v in argsDict.iteritems()])
if inputMovies.getGain():
args += ' -fgr "%s"' % inputMovies.getGain()
if inputMovies.getDark():
args += ' -fdr "%s"' % inputMovies.getDark()
if self.doSaveAveMic:
args += ' -fcs "%s" ' % outputMicFn
if self.doSaveMovie:
args += ' -fct "%s" -ssc 1' % outputMovieFn
args += ' ' + self.extraParams.get()
program = MOTIONCORR_PATH
else:
logFileBase = (logFile.replace('0-Full.log',
'').replace('0-Patch-Full.log', ''))
# default values for motioncor2 are (1, 1)
cropDimX = self.cropDimX.get() or 1
cropDimY = self.cropDimY.get() or 1
numbOfFrames = self._getNumberOfFrames(movie)
if self.doApplyDoseFilter:
preExp, dose = self._getCorrectedDose(inputMovies)
else:
preExp, dose = 0.0, 0.0
# reset values = 1 to 0 (motioncor2 does it automatically,
# but we need to keep this for consistency)
if self.patchX.get() == 1:
self.patchX.set(0)
if self.patchY.get() == 1:
self.patchY.set(0)
argsDict = {
'-OutMrc': '"%s"' % outputMicFn,
'-Patch': '%d %d' % (self.patchX, self.patchY),
'-MaskCent': '%d %d' % (self.cropOffsetX, self.cropOffsetY),
'-MaskSize': '%d %d' % (cropDimX, cropDimY),
'-FtBin': self.binFactor.get(),
'-Tol': self.tol.get(),
'-Group': self.group.get(),
'-FmDose': dose,
'-Throw': '%d' % a0,
'-Trunc': '%d' % (abs(aN - numbOfFrames + 1)),
'-PixSize': inputMovies.getSamplingRate(),
'-kV': inputMovies.getAcquisition().getVoltage(),
'-Gpu': self.GPUIDs.get(),
'-LogFile': logFileBase,
}
if getVersion('MOTIONCOR2') != '03162016':
argsDict['-InitDose'] = preExp
argsDict['-OutStack'] = 1 if self.doSaveMovie else 0
if self.isSemVersion():
if self.defectFile.get():
argsDict['-DefectFile'] = self.defectFile.get()
if self.versionGE(
'1.0.1'): # Patch overlap was introduced in 1.0.1
patchOverlap = self.getAttributeValue('patchOverlap', None)
if patchOverlap: # 0 or None is False
argsDict['-Patch'] += " %d" % patchOverlap
if self._supportsMagCorrection() and self.doMagCor:
if self.useEst:
inputEst = self.inputEst.get().getOutputLog()
if getVersion('MOTIONCOR2') == '01302017':
input_params = parseMagCorrInput(inputEst)
# this version uses stretch parameters as following:
# 1/maj, 1/min, -angle
argsDict['-Mag'] = '%0.3f %0.3f %0.3f' % (
1.0 / input_params[1], 1.0 / input_params[2],
-1 * input_params[0])
else:
# While motioncor2 >=1.0.0 uses estimation params AS IS
input_params = parseMagEstOutput(inputEst)
argsDict['-Mag'] = '%0.3f %0.3f %0.3f' % (
input_params[1], input_params[2], input_params[0])
else:
argsDict['-Mag'] = '%0.3f %0.3f %0.3f' % (
self.scaleMaj, self.scaleMin, self.angDist)
ext = pwutils.getExt(movie.getFileName()).lower()
if ext in ['.mrc', '.mrcs']:
args = ' -InMrc "%s" ' % movie.getBaseName()
elif ext in ['.tif', '.tiff']:
args = ' -InTiff "%s" ' % movie.getBaseName()
else:
raise Exception("Unsupported format: %s" % ext)
args += ' '.join(
['%s %s' % (k, v) for k, v in argsDict.iteritems()])
if inputMovies.getGain():
args += ' -Gain "%s" ' % inputMovies.getGain()
if inputMovies.getDark():
args += ' -Dark "%s"' % inputMovies.getDark()
args += ' ' + self.extraParams2.get()
program = MOTIONCOR2_PATH
try:
self.runJob(program,
args,
cwd=movieFolder,
env=getEnviron(self.useMotioncor2))
self._fixMovie(movie)
# Compute PSDs
outMicFn = self._getExtraPath(self._getOutputMicName(movie))
if not os.path.exists(outMicFn):
# if only DW mic is saved
outMicFn = self._getExtraPath(self._getOutputMicWtName(movie))
if self.doComputePSD:
# Compute uncorrected avg mic
roi = [
self.cropOffsetX.get(),
self.cropOffsetY.get(),
self.cropDimX.get(),
self.cropDimY.get()
]
fakeShiftsFn = self.writeZeroShifts(movie)
self.averageMovie(movie,
fakeShiftsFn,
aveMicFn,
binFactor=self.binFactor.get(),
roi=roi,
dark=inputMovies.getDark(),
gain=inputMovies.getGain())
self.computePSDs(movie,
aveMicFn,
outMicFn,
outputFnCorrected=self._getPsdJpeg(movie))
self._saveAlignmentPlots(movie)
if self._doComputeMicThumbnail():
self.computeThumbnail(
outMicFn, outputFn=self._getOutputMicThumbnail(movie))
except:
print("ERROR: Movie %s failed\n" % movie.getName())
def _processMovie(self, movie):
inputMovies = self.inputMovies.get()
movieFolder = self._getOutputMovieFolder(movie)
outputMicFn = self._getRelPath(self._getOutputMicName(movie),
movieFolder)
outputMovieFn = self._getRelPath(self._getOutputMovieName(movie),
movieFolder)
movieBaseName = pwutils.removeExt(movie.getFileName())
aveMicFn = movieBaseName + '_uncorrected_avg.mrc'
logFile = self._getRelPath(self._getMovieLogFile(movie),
movieFolder)
a0, aN = self._getRange(movie, 'align')
if not self.useMotioncor2:
# Get the number of frames and the range to be used
# for alignment and sum
s0, sN = self._getRange(movie, 'sum')
argsDict = {'-crx': self.cropOffsetX.get(),
'-cry': self.cropOffsetY.get(),
'-cdx': self.cropDimX.get(),
'-cdy': self.cropDimY.get(),
'-bin': self.binFactor.get(),
'-nst': '%d' % a0,
'-ned': '%d' % aN,
'-nss': '%d' % s0,
'-nes': '%d' % sN,
'-flg': logFile,
}
args = '"%s" ' % movie.getBaseName()
args += ' '.join(
['%s %s' % (k, v) for k, v in argsDict.iteritems()])
if inputMovies.getGain():
args += ' -fgr "%s"' % inputMovies.getGain()
if inputMovies.getDark():
args += ' -fdr "%s"' % inputMovies.getDark()
if self.doSaveAveMic:
args += ' -fcs "%s" ' % outputMicFn
if self.doSaveMovie:
args += ' -fct "%s" -ssc 1' % outputMovieFn
args += ' -gpu %(GPU)s'
args += ' ' + self.extraParams.get()
program = MOTIONCORR_PATH
else:
logFileBase = (logFile.replace('0-Full.log', '').replace(
'0-Patch-Full.log', ''))
# default values for motioncor2 are (1, 1)
cropDimX = self.cropDimX.get() or 1
cropDimY = self.cropDimY.get() or 1
numbOfFrames = self._getNumberOfFrames(movie)
if self.doApplyDoseFilter:
preExp, dose = self._getCorrectedDose(inputMovies)
else:
preExp, dose = 0.0, 0.0
# reset values = 1 to 0 (motioncor2 does it automatically,
# but we need to keep this for consistency)
if self.patchX.get() == 1:
self.patchX.set(0)
if self.patchY.get() == 1:
self.patchY.set(0)
argsDict = {'-OutMrc': '"%s"' % outputMicFn,
'-Patch': '%d %d' % (self.patchX, self.patchY),
'-MaskCent': '%d %d' % (self.cropOffsetX,
self.cropOffsetY),
'-MaskSize': '%d %d' % (cropDimX, cropDimY),
'-FtBin': self.binFactor.get(),
'-Tol': self.tol.get(),
'-Group': self.group.get(),
'-FmDose': dose,
'-Throw': '%d' % a0,
'-Trunc': '%d' % (abs(aN - numbOfFrames + 1)),
'-PixSize': inputMovies.getSamplingRate(),
'-kV': inputMovies.getAcquisition().getVoltage(),
'-LogFile': logFileBase,
}
if getVersion('MOTIONCOR2') != '03162016':
argsDict['-InitDose'] = preExp
argsDict['-OutStack'] = 1 if self.doSaveMovie else 0
if self.isSemVersion():
if self.defectFile.get():
argsDict['-DefectFile'] = self.defectFile.get()
if self.versionGE('1.0.1'): # Patch overlap was introduced in 1.0.1
patchOverlap = self.getAttributeValue('patchOverlap', None)
if patchOverlap: # 0 or None is False
argsDict['-Patch'] += " %d" % patchOverlap
if self._supportsMagCorrection() and self.doMagCor:
if self.useEst:
inputEst = self.inputEst.get().getOutputLog()
if getVersion('MOTIONCOR2') == '01302017':
input_params = parseMagCorrInput(inputEst)
# this version uses stretch parameters as following:
# 1/maj, 1/min, -angle
argsDict['-Mag'] = '%0.3f %0.3f %0.3f' % (
1.0 / input_params[1],
1.0 / input_params[2],
-1 * input_params[0])
else:
# While motioncor2 >=1.0.0 uses estimation params AS IS
input_params = parseMagEstOutput(inputEst)
argsDict['-Mag'] = '%0.3f %0.3f %0.3f' % (
input_params[1],
input_params[2],
input_params[0])
else:
argsDict['-Mag'] = '%0.3f %0.3f %0.3f' % (self.scaleMaj,
self.scaleMin,
self.angDist)
ext = pwutils.getExt(movie.getFileName()).lower()
if ext in ['.mrc', '.mrcs']:
args = ' -InMrc "%s" ' % movie.getBaseName()
elif ext in ['.tif', '.tiff']:
args = ' -InTiff "%s" ' % movie.getBaseName()
else:
raise Exception("Unsupported format: %s" % ext)
args += ' '.join(['%s %s' % (k, v)
for k, v in argsDict.iteritems()])
if inputMovies.getGain():
args += ' -Gain "%s" ' % inputMovies.getGain()
if inputMovies.getDark():
args += ' -Dark "%s"' % inputMovies.getDark()
args += ' -Gpu %(GPU)s'
args += ' ' + self.extraParams2.get()
program = MOTIONCOR2_PATH
try:
self.runJob(program, args, cwd=movieFolder,
env=getEnviron(self.useMotioncor2))
self._fixMovie(movie)
# Compute PSDs
outMicFn = self._getExtraPath(self._getOutputMicName(movie))
if not os.path.exists(outMicFn):
# if only DW mic is saved
outMicFn = self._getExtraPath(self._getOutputMicWtName(movie))
def _extraWork():
if self.doComputePSD:
# Compute uncorrected avg mic
roi = [self.cropOffsetX.get(), self.cropOffsetY.get(),
self.cropDimX.get(), self.cropDimY.get()]
fakeShiftsFn = self.writeZeroShifts(movie)
self.averageMovie(movie, fakeShiftsFn, aveMicFn,
binFactor=self.binFactor.get(),
roi=roi, dark=inputMovies.getDark(),
gain=inputMovies.getGain())
self.computePSDs(movie, aveMicFn, outMicFn,
outputFnCorrected=self._getPsdJpeg(movie))
self._saveAlignmentPlots(movie)
if self._doComputeMicThumbnail():
self.computeThumbnail(outMicFn,
outputFn=self._getOutputMicThumbnail(
movie))
# This protocols takes control of clean up the temporary movie folder
# which is required mainly when using a thread for this extra work
self._cleanMovieFolder(movieFolder)
if self._useWorkerThread():
thread = Thread(target=_extraWork)
thread.start()
else:
_extraWork()
except:
print("ERROR: Movie %s failed\n" % movie.getName())
def _processMovie(self, movie):
inputMovies = self.inputMovies.get()
movieFolder = self._getOutputMovieFolder(movie)
outputMicFn = self._getRelPath(self._getOutputMicName(movie),
movieFolder)
outputMovieFn = self._getRelPath(self._getOutputMovieName(movie),
movieFolder)
movieBaseName = pwutils.removeExt(movie.getFileName())
aveMicFn = movieBaseName + '_uncorrected_avg.mrc'
logFile = self._getRelPath(self._getMovieLogFile(movie), movieFolder)
a0, aN = self._getRange(movie, 'align')
if not self.useMotioncor2:
# Get the number of frames and the range to be used
# for alignment and sum
s0, sN = self._getRange(movie, 'sum')
argsDict = {
'-crx': self.cropOffsetX.get(),
'-cry': self.cropOffsetY.get(),
'-cdx': self.cropDimX.get(),
'-cdy': self.cropDimY.get(),
'-bin': self.binFactor.get(),
'-nst': '%d' % a0,
'-ned': '%d' % aN,
'-nss': '%d' % s0,
'-nes': '%d' % sN,
'-gpu': self.GPUIDs.get(),
'-flg': logFile,
}
args = '"%s" ' % movie.getBaseName()
args += ' '.join(
['%s %s' % (k, v) for k, v in argsDict.iteritems()])
if inputMovies.getGain():
args += ' -fgr "%s"' % inputMovies.getGain()
if inputMovies.getDark():
args += ' -fdr "%s"' % inputMovies.getDark()
if self.doSaveAveMic:
args += ' -fcs "%s" ' % outputMicFn
if self.doSaveMovie:
args += ' -fct "%s" -ssc 1' % outputMovieFn
args += ' ' + self.extraParams.get()
program = MOTIONCORR_PATH
else:
logFileBase = (logFile.replace('0-Full.log',
'').replace('0-Patch-Full.log', ''))
# default values for motioncor2 are (1, 1)
cropDimX = self.cropDimX.get() or 1
cropDimY = self.cropDimY.get() or 1
numbOfFrames = self._getNumberOfFrames(movie)
if self.doApplyDoseFilter:
preExp, dose = self._getCorrectedDose(inputMovies)
else:
preExp, dose = 0.0, 0.0
argsDict = {
'-OutMrc': '"%s"' % outputMicFn,
'-Patch': '%d %d' % (self.patchX, self.patchY),
'-MaskCent': '%d %d' % (self.cropOffsetX, self.cropOffsetY),
'-MaskSize': '%d %d' % (cropDimX, cropDimY),
'-FtBin': self.binFactor.get(),
'-Tol': self.tol.get(),
'-Group': self.group.get(),
'-FmDose': dose,
'-Throw': '%d' % a0,
'-Trunc': '%d' % (abs(aN - numbOfFrames + 1)),
'-PixSize': inputMovies.getSamplingRate(),
'-kV': inputMovies.getAcquisition().getVoltage(),
'-Gpu': self.GPUIDs.get(),
'-LogFile': logFileBase,
}
if getVersion('MOTIONCOR2') != '03162016':
argsDict['-InitDose'] = preExp
argsDict['-OutStack'] = 1 if self.doSaveMovie else 0
if self._supportsMagCorrection() and self.doMagCor:
if self.useEst:
inputEst = self.inputEst.get().getOutputLog()
input_params = parseMagCorrInput(inputEst)
# mag dist angle is inverted due to a different convention
argsDict['-Mag'] = '%0.2f %0.2f %0.2f' % (
input_params[1], input_params[2], -1 * input_params[0])
else:
argsDict['-Mag'] = '%0.2f %0.2f %0.2f' % (
self.scaleMaj.get(), self.scaleMin.get(),
self.angDist.get())
args = ' -InMrc "%s" ' % movie.getBaseName()
args += ' '.join(
['%s %s' % (k, v) for k, v in argsDict.iteritems()])
if inputMovies.getGain():
args += ' -Gain "%s" ' % inputMovies.getGain()
args += ' ' + self.extraParams2.get()
program = MOTIONCOR2_PATH
try:
self.runJob(program,
args,
cwd=movieFolder,
env=getEnviron(self.useMotioncor2))
self._fixMovie(movie)
# Compute PSDs
outMicFn = self._getExtraPath(self._getOutputMicName(movie))
if not os.path.exists(outMicFn):
# if only DW mic is saved
outMicFn = self._getExtraPath(self._getOutputMicWtName(movie))
if self.doComputePSD:
uncorrectedPSD = movieBaseName + '_uncorrected'
correctedPSD = movieBaseName + '_corrected'
# Compute uncorrected avg mic
roi = [
self.cropOffsetX.get(),
self.cropOffsetY.get(),
self.cropDimX.get(),
self.cropDimY.get()
]
fakeShiftsFn = self.writeZeroShifts(movie)
self.averageMovie(movie,
fakeShiftsFn,
aveMicFn,
binFactor=self.binFactor.get(),
roi=roi,
dark=None,
gain=inputMovies.getGain())
self.computePSD(aveMicFn, uncorrectedPSD)
self.computePSD(outMicFn, correctedPSD)
self.composePSD(uncorrectedPSD + ".psd", correctedPSD + ".psd",
self._getPsdCorr(movie))
self._saveAlignmentPlots(movie)
if self._doComputeMicThumbnail():
self.computeThumbnail(
outMicFn, outputFn=self._getOutputMicThumbnail(movie))
except:
print("ERROR: Movie %s failed\n" % movie.getName())
# * GNU General Public License for more details. # * # * You should have received a copy of the GNU General Public License # * along with this program; if not, write to the Free Software # * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA # * 02111-1307 USA # * # * All comments concerning this program package may be sent to the # * e-mail address '*****@*****.**' # * # ************************************************************************** """ This sub-package contains data and protocol classes wrapping Pytom programs http://www.pytom.org """ from bibtex import _bibtex # Load bibtex dict with references _logo = 'pytomLogo.jpg' import convert _environ = convert.getEnviron() from protocol_import import ProtPyTomImport from protocol_autofocus_classify import ProtAutofocusClassify from protocol_frm_alignment import ProtFrmAlign from viewer import PyTomAutofocusViewer, PyTomFrmAlignmentViewer