def applyAlignmentStep(self, tsObjId):
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
path.makePath(extraPrefix)
outputTsFileName = os.path.join(extraPrefix, "%s.mrc" % tsId)
ts.applyTransform(outputTsFileName)
outputInterpolatedSetOfTiltSeries = self.getOutputInterpolatedSetOfTiltSeries()
newTs = tomoObj.TiltSeries(tsId=tsId)
newTs.copyInfo(ts)
outputInterpolatedSetOfTiltSeries.append(newTs)
for index, tiltImage in enumerate(ts):
newTi = tomoObj.TiltImage()
newTi.copyInfo(tiltImage, copyId=True)
newTi.setLocation(index + 1, outputTsFileName)
newTs.append(newTi)
ih = ImageHandler()
x, y, z, _ = ih.getDimensions(newTs.getFirstItem().getFileName())
newTs.setDim((x, y, z))
newTs.write()
outputInterpolatedSetOfTiltSeries.update(newTs)
outputInterpolatedSetOfTiltSeries.updateDim()
outputInterpolatedSetOfTiltSeries.write()
self._store()
def assignTransformationMatricesStep(self, tsObjId):
outputAssignedTransformSetOfTiltSeries = self.getOutputAssignedTransformSetOfTiltSeries(
)
setTMTS = self.setTMSetOfTiltSeries.get()[tsObjId]
getTMTS = self.getTMSetOfTiltSeries.get()[tsObjId]
tsId = getTMTS.getTsId()
newTs = tomoObj.TiltSeries(tsId=tsId)
newTs.copyInfo(setTMTS)
outputAssignedTransformSetOfTiltSeries.append(newTs)
for tiltImageGetTM, tiltImageSetTM in zip(getTMTS, setTMTS):
newTi = tomoObj.TiltImage()
newTi.copyInfo(tiltImageSetTM, copyId=True)
newTi.setLocation(tiltImageSetTM.getLocation())
newTi.setTransform(tiltImageGetTM.getTransform())
newTs.append(newTi)
newTs.setDim(setTMTS.getDim())
newTs.write()
outputAssignedTransformSetOfTiltSeries.update(newTs)
outputAssignedTransformSetOfTiltSeries.updateDim()
outputAssignedTransformSetOfTiltSeries.write()
self._store()
def interpolateTiltSeries(self, tsObjId):
missAliTs = self.outputMisalignedSetOfTiltSeries[tsObjId]
tsId = missAliTs.getTsId()
outputInterpolatedSetOfTiltSeries = self.getOutputInterpolatedSetOfTiltSeries(
)
extraPrefix = self._getExtraPath(tsId)
outputTsFileName = os.path.join(extraPrefix, "%s_missAli.st" % tsId)
"""Apply the transformation form the input tilt-series"""
missAliTs.applyTransform(outputTsFileName)
missAliInterTs = tomoObj.TiltSeries(tsId=tsId)
missAliInterTs.copyInfo(missAliTs)
outputInterpolatedSetOfTiltSeries.append(missAliInterTs)
for index, tiltImage in enumerate(missAliTs):
missAliInterTi = tomoObj.TiltImage()
missAliInterTi.copyInfo(tiltImage, copyId=True)
missAliInterTi.setLocation(index + 1, outputTsFileName)
missAliInterTs.append(missAliInterTi)
missAliInterTs.write()
outputInterpolatedSetOfTiltSeries.update(missAliInterTs)
outputInterpolatedSetOfTiltSeries.write()
self._store()
def introduceRandomMisalignment(self, tsObjId):
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
outputMisalignedSetOfTiltSeries = self.getOutputMisalignedSetOfTiltSeries(
)
missAliTs = tomoObj.TiltSeries(tsId=tsId)
missAliTs.copyInfo(ts)
outputMisalignedSetOfTiltSeries.append(missAliTs)
for index, ti in enumerate(ts):
missAliTi = tomoObj.TiltImage()
missAliTi.copyInfo(ti, copyId=True)
missAliTi.setLocation(ti.getLocation())
if ti.hasTransform():
transformMat = ti.getTransform().getMatrix()
else:
transformMat = np.identity(3)
newTransformMat = self.modifyTransformMatrix(
transformMat, index, ts.getSize(), tsId)
newTransform = data.Transform()
newTransform.setMatrix(newTransformMat)
missAliTi.setTransform(newTransform)
missAliTs.append(missAliTi)
missAliTs.write()
outputMisalignedSetOfTiltSeries.update(missAliTs)
outputMisalignedSetOfTiltSeries.write()
self._store()
def assignTransformationMatricesStep(self):
self.getOutputAssignedTransformSetOfTiltSeries()
inputSetOfTiltSeries = self.inputSetOfTiltSeries.get()
for ts in inputSetOfTiltSeries:
tsId = ts.getTsId()
tsFileName = ts.getFirstItem().parseFileName(extension='')
for tmFilePath, _ in self.iterFiles():
tmFileName = os.path.basename(os.path.splitext(tmFilePath)[0])
if tsFileName == tmFileName:
alignmentMatrix = utils.formatTransformationMatrix(
tmFilePath)
newTs = tomoObj.TiltSeries(tsId=tsId)
newTs.copyInfo(ts)
self.outputAssignedTransformSetOfTiltSeries.append(newTs)
for index, tiltImage in enumerate(ts):
newTi = tomoObj.TiltImage()
newTi.copyInfo(tiltImage, copyId=True)
newTi.setLocation(tiltImage.getLocation())
transform = data.Transform()
if tiltImage.hasTransform():
previousTransform = tiltImage.getTransform(
).getMatrix()
newTransform = alignmentMatrix[:, :, index]
previousTransformArray = np.array(
previousTransform)
newTransformArray = np.array(newTransform)
outputTransformMatrix = np.matmul(
previousTransformArray, newTransformArray)
transform.setMatrix(outputTransformMatrix)
newTi.setTransform(transform)
else:
transform.setMatrix(alignmentMatrix[:, :, index])
newTi.setTransform(transform)
newTs.append(newTi)
ih = ImageHandler()
x, y, z, _ = ih.getDimensions(
newTs.getFirstItem().getFileName())
newTs.setDim((x, y, z))
newTs.write(properties=False)
self.outputAssignedTransformSetOfTiltSeries.update(newTs)
self.outputAssignedTransformSetOfTiltSeries.updateDim()
self.outputAssignedTransformSetOfTiltSeries.write()
self._store()
def generateOutputStackStep(self, tomoObjId):
tomo = self.inputSetOfTomograms.get()[tomoObjId]
tomoId = os.path.splitext(os.path.basename(tomo.getFileName()))[0]
extraPrefix = self._getExtraPath(tomoId)
outputProjectedSetOfTiltSeries = self.getOutputProjectedSetOfTiltSeries(
)
newTs = tomoObj.TiltSeries(tsId=tomoId)
newTs.copyInfo(tomo)
newTs.setTsId(tomoId)
# Add origin to output tilt-series
origin = Transform()
outputProjectedSetOfTiltSeries.append(newTs)
tiltAngleList = self.getTiltAngleList()
for index in range(self.getProjectionRange()):
newTi = tomoObj.TiltImage()
newTi.setTiltAngle(tiltAngleList[index])
newTi.setTsId(tomoId)
newTi.setLocation(
index + 1,
os.path.join(extraPrefix,
os.path.basename(tomo.getFileName())))
newTi.setSamplingRate(
self.inputSetOfTomograms.get().getSamplingRate())
newTs.append(newTi)
ih = ImageHandler()
x, y, z, _ = ih.getDimensions(newTs.getFirstItem().getFileName())
newTs.setDim((x, y, z))
# Set origin to output tilt-series
origin.setShifts(
x / -2. * self.inputSetOfTomograms.get().getSamplingRate(),
y / -2. * self.inputSetOfTomograms.get().getSamplingRate(), 0)
newTs.setOrigin(origin)
newTs.write(properties=False)
outputProjectedSetOfTiltSeries.update(newTs)
outputProjectedSetOfTiltSeries.updateDim()
outputProjectedSetOfTiltSeries.write()
self._store()
def createOutputStep(self, tsObjId):
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
outputSetOfTiltSeries = self.getOutputSetOfTiltSeries()
newTs = tomoObj.TiltSeries(tsId=tsId)
newTs.copyInfo(ts)
outputSetOfTiltSeries.append(newTs)
newTs.setSamplingRate(self.samplingRate)
fileName = ts.getFirstItem().parseFileName()
for index, ti in enumerate(ts):
newTi = tomoObj.TiltImage()
newTi.copyInfo(ti, copyId=True)
newTi.setLocation(index + 1, os.path.join(extraPrefix, fileName))
if ti.hasTransform():
newTi.setTransform(ti.getTransform())
newTi.setSamplingRate(self.samplingRate)
newTs.append(newTi)
ih = ImageHandler()
x, y, z, _ = ih.getDimensions(newTs.getFirstItem().getFileName())
newTs.setDim((x, y, z))
newTs.write(properties=False)
outputSetOfTiltSeries.update(newTs)
outputSetOfTiltSeries.updateDim()
outputSetOfTiltSeries.write()
self._store()
def createOutputStep(self, tsObjId):
outputXraysErasedSetOfTiltSeries = self.getOutputSetOfXraysErasedTiltSeries(
)
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
newTs = tomoObj.TiltSeries(tsId=tsId)
newTs.copyInfo(ts)
outputXraysErasedSetOfTiltSeries.append(newTs)
for index, tiltImage in enumerate(ts):
newTi = tomoObj.TiltImage()
newTi.copyInfo(tiltImage, copyId=True)
newTi.setLocation(
index + 1,
(os.path.join(extraPrefix, tiltImage.parseFileName())))
newTs.append(newTi)
newTs.write(properties=False)
outputXraysErasedSetOfTiltSeries.update(newTs)
outputXraysErasedSetOfTiltSeries.write()
self._store()
def generateOutputStackStep(self, tsObjId):
outputNormalizedSetOfTiltSeries = self.getOutputNormalizedSetOfTiltSeries(
)
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
tmpPrefix = self._getTmpPath(tsId)
paramsNewstack = {
'input': os.path.join(tmpPrefix,
ts.getFirstItem().parseFileName()),
'output': os.path.join(extraPrefix,
ts.getFirstItem().parseFileName()),
'bin': int(self.binning.get()),
'imagebinned': 1.0,
}
argsNewstack = "-input %(input)s " \
"-output %(output)s " \
"-bin %(bin)d " \
"-imagebinned %(imagebinned)s "
if self.floatDensities.get() != 0:
argsNewstack += " -FloatDensities " + str(
self.floatDensities.get())
if self.floatDensities.get() == 2:
if self.meanSdToggle.get() == 0:
argsNewstack += " -MeanAndStandardDeviation " + str(self.scaleMean.get()) + "," + \
str(self.scaleSd.get())
elif self.floatDensities.get() == 4:
argsNewstack += " -ScaleMinAndMax " + str(
self.scaleMax.get()) + "," + str(self.scaleMin.get())
else:
if self.scaleRangeToggle.get() == 0:
argsNewstack += " -ScaleMinAndMax " + str(self.scaleRangeMax.get()) + "," + \
str(self.scaleRangeMin.get())
if self.getModeToOutput() is not None:
argsNewstack += " -ModeToOutput " + str(self.getModeToOutput())
Plugin.runImod(self, 'newstack', argsNewstack % paramsNewstack)
newTs = tomoObj.TiltSeries(tsId=tsId)
newTs.copyInfo(ts)
outputNormalizedSetOfTiltSeries.append(newTs)
if self.binning > 1:
newTs.setSamplingRate(ts.getSamplingRate() *
int(self.binning.get()))
for index, tiltImage in enumerate(ts):
newTi = tomoObj.TiltImage()
newTi.copyInfo(tiltImage, copyId=True)
newTi.setLocation(
index + 1,
(os.path.join(extraPrefix, tiltImage.parseFileName())))
if self.binning > 1:
newTi.setSamplingRate(tiltImage.getSamplingRate() *
int(self.binning.get()))
newTs.append(newTi)
ih = ImageHandler()
x, y, z, _ = ih.getDimensions(newTs.getFirstItem().getFileName())
newTs.setDim((x, y, z))
newTs.write(properties=False)
outputNormalizedSetOfTiltSeries.update(newTs)
outputNormalizedSetOfTiltSeries.updateDim()
outputNormalizedSetOfTiltSeries.write()
self._store()
def convertInputStep(self, ts):
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
tmpPrefix = self._getTmpPath(tsId)
path.makePath(tmpPrefix)
path.makePath(extraPrefix)
firstItem = ts.getFirstItem()
outputTsFileName = self.getFilePath(ts, extension=".st")
"""Apply transformation matrices and remove excluded views"""
if self.excludeList.get() == '':
"""Apply the transformation form the input tilt-series"""
ts.applyTransform(outputTsFileName)
"""Generate angle file"""
angleFilePath = self.getFilePath(ts, extension=".rawtlt")
ts.generateTltFile(angleFilePath)
else:
interpolatedTsFileName = os.path.join(tmpPrefix,
firstItem.parseFileName())
angleFilePath = self.getFilePath(ts, extension=".rawtlt")
"""Apply the transformation form the input tilt-series and generate a new ts object"""
ts.applyTransform(interpolatedTsFileName)
interpolatedSetOfTiltSeries = self._createSetOfTiltSeries(
suffix='Interpolated')
interpolatedSetOfTiltSeries.copyInfo(ts)
interpolatedSetOfTiltSeries.setDim(ts.getDim())
interpolatedTs = tomoObj.TiltSeries(tsId=tsId)
interpolatedTs.copyInfo(ts)
interpolatedSetOfTiltSeries.append(interpolatedTs)
for index, tiltImage in enumerate(ts):
newTi = tomoObj.TiltImage()
newTi.copyInfo(tiltImage, copyId=True)
newTi.setLocation(index + 1, interpolatedTsFileName)
interpolatedTs.append(newTi)
interpolatedTs.write()
"""Write a new stack discarding excluded tilts"""
excludeList = [int(i) for i in self.excludeList.get().split()]
tiList = [ti.clone() for ti in interpolatedTs]
tiList.sort(key=lambda ti: ti.getTiltAngle())
writeTiStack(tiList,
outputStackFn=outputTsFileName,
outputTltFn=angleFilePath,
excludeList=excludeList)
"""Generate etomo config file"""
args = '-name %s ' % firstItem.parseFileName(extension="")
args += '-gold %0.3f ' % self.markersDiameter
# Imod use the pixel size in NM
pixelSizeNm = ts.getSamplingRate() / 10.
args += '-pixel %0.3f ' % pixelSizeNm
args += '-rotation %0.3f ' % self.rotationAngle
args += '-userawtlt '
# 0 for output image files to have descriptive extensions like ".preali", 1 for extension ".mrc", or 2 for
# extension ".hdf". In the latter two cases the usual descriptive text is put before the extension, and command
# files will contain an environment variable setting to make programs generate files of the corresponding type.
# From: https://bio3d.colorado.edu/imod/doc/man/copytomocoms.html
args += '-NamingStyle 0 '
# Extension of raw stack excluding the period. If this is not specified, the program will assume the extension
# ".st" unless the -style option is entered. With a -style option and no specified stack extension, it will
# look for ".st", ".mrc", ".hdf",".tif", and ".tiff" and require that only one of those types is present. With
# this entry, which could in principle be arbitrary, it will not care if files with other extensions are
# present.
# From: https://bio3d.colorado.edu/imod/doc/man/copytomocoms.html
args += '-StackExtension ""'
Plugin.runImod(self, 'copytomocoms', args, cwd=extraPrefix)
edfFn = self.getFilePath(ts, extension=".edf")
minTilt = min(
utils.formatAngleList(self.getFilePath(ts, extension=".rawtlt")))
self._writeEtomoEdf(
edfFn, {
'date': pw.utils.prettyTime(),
'name': firstItem.parseFileName(extension=''),
'pixelSize': pixelSizeNm,
'version': pw.__version__,
'minTilt': minTilt,
'markerDiameter': self.markersDiameter,
'rotationAngle': self.rotationAngle
})
def generateOutputStackStep(self, tsObjId):
outputInterpolatedSetOfTiltSeries = self.getOutputInterpolatedSetOfTiltSeries(
)
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
firstItem = ts.getFirstItem()
paramsAlignment = {
'input':
firstItem.getFileName(),
'output':
os.path.join(extraPrefix, firstItem.parseFileName()),
'xform':
os.path.join(extraPrefix,
firstItem.parseFileName(extension=".prexg")),
'bin':
int(self.binning.get()),
'imagebinned':
1.0
}
argsAlignment = "-input %(input)s " \
"-output %(output)s " \
"-xform %(xform)s " \
"-bin %(bin)d " \
"-imagebinned %(imagebinned)s "
rotationAngleAvg = utils.calculateRotationAngleFromTM(ts)
# Check if rotation angle is greater than 45º. If so, swap x and y dimensions to adapt output image sizes to
# the final sample disposition.
if rotationAngleAvg > 45 or rotationAngleAvg < -45:
paramsAlignment.update(
{'size': "%d,%d" % (firstItem.getYDim(), firstItem.getXDim())})
argsAlignment += "-size %(size)s "
Plugin.runImod(self, 'newstack', argsAlignment % paramsAlignment)
newTs = tomoObj.TiltSeries(tsId=tsId)
newTs.copyInfo(ts)
outputInterpolatedSetOfTiltSeries.append(newTs)
if self.binning > 1:
newTs.setSamplingRate(ts.getSamplingRate() *
int(self.binning.get()))
for index, tiltImage in enumerate(ts):
newTi = tomoObj.TiltImage()
newTi.copyInfo(tiltImage, copyId=True)
newTi.setLocation(
index + 1,
(os.path.join(extraPrefix, tiltImage.parseFileName())))
if self.binning > 1:
newTi.setSamplingRate(tiltImage.getSamplingRate() *
int(self.binning.get()))
newTs.append(newTi)
ih = ImageHandler()
x, y, z, _ = ih.getDimensions(newTs.getFirstItem().getFileName())
newTs.setDim((x, y, z))
newTs.write(properties=False)
outputInterpolatedSetOfTiltSeries.update(newTs)
outputInterpolatedSetOfTiltSeries.updateDim()
outputInterpolatedSetOfTiltSeries.write()
self._store()
def computeInterpolatedStackStep(self, tsObjId):
outputInterpolatedSetOfTiltSeries = self.getOutputInterpolatedSetOfTiltSeries(
)
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
tmpPrefix = self._getTmpPath(tsId)
paramsAlignment = {
'input':
os.path.join(tmpPrefix,
ts.getFirstItem().parseFileName()),
'output':
os.path.join(extraPrefix,
ts.getFirstItem().parseFileName()),
'xform':
os.path.join(extraPrefix,
ts.getFirstItem().parseFileName(extension=".prexg")),
'bin':
int(self.binning.get()),
'imagebinned':
1.0
}
argsAlignment = "-input %(input)s " \
"-output %(output)s " \
"-xform %(xform)s " \
"-bin %(bin)d " \
"-imagebinned %(imagebinned)s"
Plugin.runImod(self, 'newstack', argsAlignment % paramsAlignment)
newTs = tomoObj.TiltSeries(tsId=tsId)
newTs.copyInfo(ts)
outputInterpolatedSetOfTiltSeries.append(newTs)
if self.binning > 1:
newTs.setSamplingRate(ts.getSamplingRate() *
int(self.binning.get()))
for index, tiltImage in enumerate(ts):
newTi = tomoObj.TiltImage()
newTi.copyInfo(tiltImage, copyId=True)
newTi.setLocation(
index + 1,
(os.path.join(extraPrefix, tiltImage.parseFileName())))
if self.binning > 1:
newTi.setSamplingRate(tiltImage.getSamplingRate() *
int(self.binning.get()))
newTs.append(newTi)
ih = ImageHandler()
x, y, z, _ = ih.getDimensions(newTs.getFirstItem().getFileName())
newTs.setDim((x, y, z))
newTs.write(properties=False)
outputInterpolatedSetOfTiltSeries.update(newTs)
outputInterpolatedSetOfTiltSeries.updateDim()
outputInterpolatedSetOfTiltSeries.write()
self._store()
def computeXcorrStep(self, tsObjId):
"""Compute transformation matrix for each tilt series"""
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
tmpPrefix = self._getTmpPath(tsId)
paramsXcorr = {
'input':
os.path.join(tmpPrefix,
ts.getFirstItem().parseFileName()),
'output':
os.path.join(extraPrefix,
ts.getFirstItem().parseFileName(extension=".prexf")),
'tiltfile':
os.path.join(tmpPrefix,
ts.getFirstItem().parseFileName(extension=".tlt")),
'rotationAngle':
self.rotationAngle.get(),
'filterSigma1':
self.filterSigma1.get(),
'filterSigma2':
self.filterSigma2.get(),
'filterRadius1':
self.filterRadius1.get(),
'filterRadius2':
self.filterRadius2.get()
}
argsXcorr = "-input %(input)s " \
"-output %(output)s " \
"-tiltfile %(tiltfile)s " \
"-RotationAngle %(rotationAngle)f " \
"-FilterSigma1 %(filterSigma1)f " \
"-FilterSigma2 %(filterSigma2)f " \
"-FilterRadius1 %(filterRadius1)f " \
"-FilterRadius2 %(filterRadius2)f "
Plugin.runImod(self, 'tiltxcorr', argsXcorr % paramsXcorr)
paramsXftoxg = {
'input':
os.path.join(extraPrefix,
ts.getFirstItem().parseFileName(extension=".prexf")),
'goutput':
os.path.join(extraPrefix,
ts.getFirstItem().parseFileName(extension=".prexg")),
}
argsXftoxg = "-input %(input)s " \
"-goutput %(goutput)s"
Plugin.runImod(self, 'xftoxg', argsXftoxg % paramsXftoxg)
"""Generate output tilt series"""
outputSetOfTiltSeries = self.getOutputSetOfTiltSeries()
alignmentMatrix = utils.formatTransformationMatrix(
os.path.join(extraPrefix,
ts.getFirstItem().parseFileName(extension=".prexg")))
newTs = tomoObj.TiltSeries(tsId=tsId)
newTs.copyInfo(ts)
outputSetOfTiltSeries.append(newTs)
for index, tiltImage in enumerate(ts):
newTi = tomoObj.TiltImage()
newTi.copyInfo(tiltImage, copyId=True)
newTi.setLocation(tiltImage.getLocation())
transform = data.Transform()
transform.setMatrix(alignmentMatrix[:, :, index])
newTi.setTransform(transform)
newTs.append(newTi)
newTs.write(properties=False)
outputSetOfTiltSeries.update(newTs)
outputSetOfTiltSeries.write()
self._store()