def _insertMicStep(mic):
localDeps = [firstStepId]
fnLast = mic.getFileName()
micName = pwutils.removeBaseExt(mic.getFileName())
def getMicTmp(suffix):
return self._getTmpPath(micName + suffix)
# Create a list with micrographs operations (programs in xmipp) and
# the required command line parameters (except input/ouput files)
micOps = []
# Check if it is required to downsample your micrographs
downFactor = self.downFactor.get()
if self.notOne(downFactor):
fnDownsampled = getMicTmp("_downsampled.xmp")
args = "-i %s -o %s --step %f --method fourier"
micOps.append(('xmipp_transform_downsample',
args % (fnLast, fnDownsampled, downFactor)))
fnLast = fnDownsampled
if self.doRemoveDust:
fnNoDust = getMicTmp("_noDust.xmp")
args = " -i %s -o %s --bad_pixels outliers %f"
micOps.append(('xmipp_transform_filter',
args % (fnLast, fnNoDust, self.thresholdDust)))
fnLast = fnNoDust
if self._useCTF() and self.ctfDict[mic] is not None:
# We need to write a Xmipp ctfparam file
# to perform the phase flip on the micrograph
fnCTF = self._getTmpPath("%s.ctfParam" % micName)
mic.setCTF(self.ctfDict[mic])
micrographToCTFParam(mic, fnCTF)
# Insert step to flip micrograph
if self.doFlip:
fnFlipped = getMicTmp('_flipped.xmp')
args = " -i %s -o %s --ctf %s --sampling %f"
micOps.append(
('xmipp_ctf_phase_flip', args %
(fnLast, fnFlipped, fnCTF, self._getNewSampling())))
fnLast = fnFlipped
else:
fnCTF = None
# Actually extract
deps.append(
self._insertFunctionStep('extractParticlesStep',
mic.getObjId(),
micName,
fnCTF,
fnLast,
micOps,
self.doInvert.get(),
self._getNormalizeArgs(),
self.doBorders.get(),
prerequisites=localDeps))
def preprocessMicsStep(self):
for i in range(len(self.inputCoordinatesTrue)):
coordTrue = self.inputCoordinatesTrue[i].get()
coordFalse = self.inputCoordinatesFalse[i].get()
mics_ = coordTrue.getMicrographs()
samplingRate = mics_.getSamplingRate()
micIds = self.getMicsIds(i)
micsFnameSet = {
mics_[micId].getMicName(): mics_[micId].getFileName()
for micId in micIds
}
if self.ignoreCTF.get():
preproMicsContent = "#mics\n"
for micName in micsFnameSet:
preproMicsContent += "%s\n" % (micsFnameSet[micName])
else:
preproMicsContent = "#mics ctfs\n"
setOfMicCtf = self.ctfRelations[i].get()
if setOfMicCtf.getSize() < len(micsFnameSet):
raise ValueError(
"Error, there are different number of CTFs compared to "
+
"the number of micrographs where particles were picked"
)
else:
assert setOfMicCtf is not None, "Error, CTFs must be provided to compute phase flip"
for ctf in setOfMicCtf:
ctf_mic = ctf.getMicrograph()
ctfMicName = ctf_mic.getMicName()
if ctfMicName in micsFnameSet:
ctf_mic.setCTF(ctf)
ctfMicName = micsFnameSet[ctfMicName]
fnCTF = self._getTmpPath(
"%s.ctfParam" % os.path.basename(ctfMicName))
micrographToCTFParam(ctf_mic, fnCTF)
preproMicsContent += "%s %s\n" % (ctfMicName,
fnCTF)
inputsFname = self._getExtraPath("preprocMic_inputs_%d.txt" % i)
ouputDir = self._getExtraPath(self.PRE_PROC_MICs_PATH % i)
nThrs = self.numberOfThreads.get()
with open(inputsFname, "w") as f:
f.write(preproMicsContent)
downFactor = self._getDownFactor()
args = "-i %s -s %s -d %s -o %s -t %d" % (
inputsFname, samplingRate, downFactor, ouputDir, nThrs)
if self.doInvert.get():
args += " --invert_contrast"
if not self.ignoreCTF.get():
args += " --phase_flip"
self.runJob('xmipp_preprocess_mics', args, numberOfMpi=1)
def _extractMicrograph(self, mic, doInvert, normalizeArgs, doBorders):
""" Extract particles from one micrograph """
fnLast = mic.getFileName()
baseMicName = pwutils.removeBaseExt(fnLast)
outputRoot = str(self._getExtraPath(baseMicName))
fnPosFile = self._getMicPos(mic)
boxSize = self.boxSize.get()
downFactor = self.downFactor.get()
patchSize = self.patchSize.get() if self.patchSize.get() > 0 \
else int(boxSize*1.5*downFactor)
particlesMd = 'particles@%s' % fnPosFile
# If it has coordinates extract the particles
if exists(fnPosFile):
# Create a list with micrographs operations (programs in xmipp) and
# the required command line parameters (except input/ouput files)
micOps = []
# Compute the variance and Gini coeff. of the part. and mic., resp.
args = '--pos %s' % fnPosFile
args += ' --mic %s' % fnLast
args += ' --patchSize %d' % patchSize
self.runJob('xmipp_coordinates_noisy_zones_filter', args)
def getMicTmp(suffix):
return self._getTmpPath(baseMicName + suffix)
# Check if it is required to downsample our micrographs
if self.notOne(downFactor):
fnDownsampled = getMicTmp("_downsampled.xmp")
args = "-i %s -o %s --step %f --method fourier"
self.runJob('xmipp_transform_downsample',
args % (fnLast, fnDownsampled, downFactor))
fnLast = fnDownsampled
if self.doRemoveDust:
fnNoDust = getMicTmp("_noDust.xmp")
args = " -i %s -o %s --bad_pixels outliers %f"
self.runJob('xmipp_transform_filter',
args % (fnLast, fnNoDust, self.thresholdDust))
fnLast = fnNoDust
if self._useCTF():
# We need to write a Xmipp ctfparam file
# to perform the phase flip on the micrograph
fnCTF = self._getTmpPath("%s.ctfParam" % baseMicName)
micrographToCTFParam(mic, fnCTF)
# Insert step to flip micrograph
if self.doFlip:
fnFlipped = getMicTmp('_flipped.xmp')
args = " -i %s -o %s --ctf %s --sampling %f"
self.runJob(
'xmipp_ctf_phase_flip', args %
(fnLast, fnFlipped, fnCTF, self._getNewSampling()))
fnLast = fnFlipped
else:
fnCTF = None
args = " -i %s --pos %s" % (fnLast, particlesMd)
args += " -o %s --Xdim %d" % (outputRoot, boxSize)
if doInvert:
args += " --invert"
if fnCTF:
args += " --ctfparam " + fnCTF
if doBorders:
args += " --fillBorders"
self.runJob("xmipp_micrograph_scissor", args)
# Normalize
if normalizeArgs:
self.runJob('xmipp_transform_normalize',
'-i %s.stk %s' % (outputRoot, normalizeArgs))
else:
self.warning("The micrograph %s hasn't coordinate file! " %
baseMicName)
self.warning("Maybe you picked over a subset of micrographs")
# Let's clean the temporary mrc micrographs
if not pwutils.envVarOn("SCIPION_DEBUG_NOCLEAN"):
pwutils.cleanPattern(self._getTmpPath(baseMicName) + '*')