def generateFiducialModelStep(self, tsObjId):
# TODO: check si es el landmark model correcto
lm = self.inputSetOfLandmarkModels.get()[tsObjId]
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
tmpPrefix = self._getTmpPath(tsId)
path.makePath(extraPrefix)
path.makePath(tmpPrefix)
landmarkTextFilePath = os.path.join(
extraPrefix,
ts.getFirstItem().parseFileName(suffix="_fid", extension=".txt"))
landmarkModelPath = os.path.join(
extraPrefix,
ts.getFirstItem().parseFileName(suffix="_fid", extension=".mod"))
# Generate the IMOD file containing the information from the landmark model
utils.generateIMODFiducialTextFile(landmarkModel=lm,
outputFilePath=landmarkTextFilePath)
# Convert IMOD file into IMOD model
paramsPoint2Model = {
'inputFile': landmarkTextFilePath,
'outputFile': landmarkModelPath,
}
argsPoint2Model = "-InputFile %(inputFile)s " \
"-OutputFile %(outputFile)s"
Plugin.runImod(self, 'point2model',
argsPoint2Model % paramsPoint2Model)
def pickGoldBeadsStep(self, tsObjId):
tomo = self.inputSetOfTomograms.get()[tsObjId]
location = tomo.getLocation()[1]
fileName, _ = os.path.splitext(location)
extraPrefix = self._getExtraPath(os.path.basename(fileName))
path.makePath(extraPrefix)
""" Run findbeads3d IMOD program """
paramsFindbeads3d = {
'inputFile':
location,
'outputFile':
os.path.join(extraPrefix, "%s.mod" % os.path.basename(fileName)),
'beadSize':
self.beadDiameter.get(),
'minRelativeStrength':
self.minRelativeStrength.get(),
'minSpacing':
self.minSpacing.get(),
}
argsFindbeads3d = "-InputFile %(inputFile)s " \
"-OutputFile %(outputFile)s " \
"-BeadSize %(beadSize)d " \
"-MinRelativeStrength %(minRelativeStrength)f " \
"-MinSpacing %(minSpacing)d "
if self.beadsColor.get() == 1:
argsFindbeads3d += "-LightBeads "
Plugin.runImod(self, 'findbeads3d',
argsFindbeads3d % paramsFindbeads3d)
def projectTomogram(self, tomoObjId):
tomo = self.inputSetOfTomograms.get()[tomoObjId]
tomoId = os.path.splitext(os.path.basename(tomo.getFileName()))[0]
extraPrefix = self._getExtraPath(tomoId)
tmpPrefix = self._getTmpPath(tomoId)
path.makePath(tmpPrefix)
path.makePath(extraPrefix)
paramsXYZproj = {
'input':
tomo.getFileName(),
'output':
os.path.join(extraPrefix, os.path.basename(tomo.getFileName())),
'axis':
self.getRotationAxis(),
'angles':
str(self.minAngle.get()) + ',' + str(self.maxAngle.get()) + ',' +
str(self.stepAngle.get()),
}
argsXYZproj = "-input %(input)s " \
"-output %(output)s " \
"-axis %(axis)s " \
"-angles %(angles)s "
Plugin.runImod(self, 'xyzproj', argsXYZproj % paramsXYZproj)
def runEtomo(self, ts):
self.convertInputStep(ts)
if ts is not None:
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
args = '--fg '
args += ts.getFirstItem().parseFileName(extension=".edf")
Plugin.runImod(self, 'etomo', args, cwd=extraPrefix)
def ctfCorrection(self, tsObjId):
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
tmpPrefix = self._getTmpPath(tsId)
"""Run ctfphaseflip IMOD program"""
paramsCtfPhaseFlip = {
'inputStack':
os.path.join(tmpPrefix,
ts.getFirstItem().parseFileName()),
'angleFile':
os.path.join(tmpPrefix,
ts.getFirstItem().parseFileName(extension=".tlt")),
'outputFileName':
os.path.join(extraPrefix,
ts.getFirstItem().parseFileName()),
'defocusFile':
os.path.join(
extraPrefix,
ts.getFirstItem().parseFileName(extension=".defocus")),
'voltage':
self.inputSetOfTiltSeries.get().getAcquisition().getVoltage(),
'sphericalAberration':
self.inputSetOfTiltSeries.get().getAcquisition(
).getSphericalAberration(),
'defocusTol':
self.defocusTol.get(),
'pixelSize':
self.inputSetOfTiltSeries.get().getSamplingRate() / 10,
'amplitudeContrast':
self.inputSetOfTiltSeries.get().getAcquisition().
getAmplitudeContrast(),
'interpolationWidth':
self.interpolationWidth.get(),
}
argsCtfPhaseFlip = "-InputStack %(inputStack)s " \
"-AngleFile %(angleFile)s " \
"-OutputFileName %(outputFileName)s " \
"-DefocusFile %(defocusFile)s " \
"-Voltage %(voltage)d " \
"-SphericalAberration %(sphericalAberration)f " \
"-DefocusTol %(defocusTol)d " \
"-PixelSize %(pixelSize)f " \
"-AmplitudeContrast %(amplitudeContrast)f " \
"-InterpolationWidth %(interpolationWidth)d "
if self.usesGpu():
paramsCtfPhaseFlip.update({"useGPU": self.getGpuList()[0]})
argsCtfPhaseFlip += "-UseGPU %(useGPU)d "
Plugin.runImod(self, 'ctfphaseflip',
argsCtfPhaseFlip % paramsCtfPhaseFlip)
class ImodViewer(pwviewer.Viewer):
""" Wrapper to visualize different type of objects
with the Imod program 3dmod
"""
_environments = [pwviewer.DESKTOP_TKINTER, Plugin.getEnviron()]
_targets = [
tomo.objects.TiltSeries,
tomo.objects.Tomogram,
tomo.objects.SetOfTomograms,
tomo.objects.SetOfTiltSeries,
tomo.objects.SetOfLandmarkModels,
tomo.objects.LandmarkModel
]
def _visualize(self, obj, **kwargs):
env = Plugin.getEnviron()
cls = type(obj)
if issubclass(cls, tomo.objects.TiltSeries):
view = ImodObjectView(obj.getFirstItem())
elif issubclass(cls, tomo.objects.Tomogram):
view = ImodObjectView(obj)
elif issubclass(cls, tomo.objects.LandmarkModel):
view = ImodObjectView(obj)
else:
view = ImodGenericViewer(self.getTkRoot(), self.protocol, obj)
view._env = env
return [view]
def __init__(self, set, **kwargs):
fn = ""
for item in set:
# Remove :mrc if present
fn += " " + item.getFirstItem().getFileName().split(':')[0]
pwviewer.CommandView.__init__(
self, "%s %s" % (Plugin.getImodCmd('3dmod'), fn))
self.show()
def doseFilterStep(self, tsObjId):
"""Apply the dose fitler to every tilt series"""
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
tmpPrefix = self._getTmpPath(tsId)
path.makePath(tmpPrefix)
path.makePath(extraPrefix)
firstItem = ts.getFirstItem()
paramsMtffilter = {
'input': firstItem.getFileName(),
'output': os.path.join(extraPrefix, firstItem.parseFileName()),
'voltage': ts.getAcquisition().getVoltage(),
}
argsMtffilter = "-input %(input)s " \
"-output %(output)s " \
"-Voltage %(voltage)d "
if self.inputDoseType.get() == SCIPION_IMPORT:
outputDefocusFilePath = os.path.join(
extraPrefix, firstItem.parseFileName(extension=".dose"))
utils.generateDoseFileFromTS(ts, outputDefocusFilePath)
paramsMtffilter.update({
'typeOfDoseFile': 1,
'doseWeightingFile': outputDefocusFilePath,
})
argsMtffilter += "-TypeOfDoseFile %(typeOfDoseFile)d " \
"-DoseWeightingFile %(doseWeightingFile)s "
if self.inputDoseType.get() == FIXED_DOSE:
paramsMtffilter.update(
{'fixedImageDose': self.fixedImageDose.get()})
argsMtffilter += "-FixedImageDose %(fixedImageDose)f"
Plugin.runImod(self, 'mtffilter', argsMtffilter % paramsMtffilter)
def convertModelToCoordinatesStep(self, tsObjId):
tomo = self.inputSetOfTomograms.get()[tsObjId]
location = tomo.getLocation()[1]
fileName, _ = os.path.splitext(location)
extraPrefix = self._getExtraPath(os.path.basename(fileName))
""" Run model2point IMOD program """
paramsModel2Point = {
'inputFile':
os.path.join(extraPrefix, "%s.mod" % os.path.basename(fileName)),
'outputFile':
os.path.join(extraPrefix, "%s.xyz" % os.path.basename(fileName)),
}
argsModel2Point = "-InputFile %(inputFile)s " \
"-OutputFile %(outputFile)s " \
Plugin.runImod(self, 'model2point',
argsModel2Point % paramsModel2Point)
def __init__(self, obj, **kwargs):
# Remove :mrc if present
if isinstance(obj, tomo.objects.LandmarkModel):
tsId = os.path.basename(obj.getFileName()).split('_')[0]
if os.path.exists(os.path.join(os.path.split(obj.getModelName())[0],
"%s_preali.st" % tsId)):
prealiTSPath = os.path.join(os.path.split(obj.getModelName())[0],
"%s_preali.st" % tsId)
elif os.path.exists(os.path.join(os.path.split(obj.getModelName())[0],
"%s.preali" % tsId)):
prealiTSPath = os.path.join(os.path.split(obj.getModelName())[0],
"%s.preali" % tsId)
else:
prealiTSPath = ""
fn = Plugin.getImodCmd('3dmod') + " -m " + prealiTSPath + " " + obj.getModelName() + " ; "
else:
fn = Plugin.getImodCmd('3dmod') + ' ' + obj.getFileName().split(':')[0]
pwviewer.CommandView.__init__(self, fn)
def eraseXraysStep(self, tsObjId):
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
tmpPrefix = self._getTmpPath(tsId)
paramsCcderaser = {
'inputFile':
os.path.join(tmpPrefix,
ts.getFirstItem().parseFileName()),
'outputFile':
os.path.join(extraPrefix,
ts.getFirstItem().parseFileName()),
'modelFile':
os.path.join(
extraPrefix,
ts.getFirstItem().parseFileName(suffix="_fid",
extension=".mod")),
'betterRadius':
self.betterRadius.get(),
'polynomialOrder':
0,
'circleObjects':
"/"
}
argsCcderaser = "-InputFile %(inputFile)s " \
"-OutputFile %(outputFile)s " \
"-ModelFile %(modelFile)s " \
"-BetterRadius %(betterRadius)d " \
"-PolynomialOrder %(polynomialOrder)d " \
"-CircleObjects %(circleObjects)s " \
"-MergePatches " \
"-ExcludeAdjacent"
Plugin.runImod(self, 'ccderaser', argsCcderaser % paramsCcderaser)
def _visualize(self, obj, **kwargs):
env = Plugin.getEnviron()
cls = type(obj)
if issubclass(cls, tomo.objects.TiltSeries):
view = ImodObjectView(obj.getFirstItem())
elif issubclass(cls, tomo.objects.Tomogram):
view = ImodObjectView(obj)
elif issubclass(cls, tomo.objects.LandmarkModel):
view = ImodObjectView(obj)
else:
view = ImodGenericViewer(self.getTkRoot(), self.protocol, obj)
view._env = env
return [view]
def __init__(self, set, **kwargs):
fn = ""
for item in set:
tsId = os.path.basename(item.getFileName()).split('_')[0]
if os.path.exists(
os.path.join(
os.path.split(item.getModelName())[0],
"%s_preali.st" % tsId)):
prealiTSPath = os.path.join(
os.path.split(item.getModelName())[0],
"%s_preali.st" % tsId)
elif os.path.exists(
os.path.join(
os.path.split(item.getModelName())[0],
"%s.preali" % tsId)):
prealiTSPath = os.path.join(
os.path.split(item.getModelName())[0], "%s.preali" % tsId)
else:
prealiTSPath = ""
fn += Plugin.getImodCmd(
'3dmod') + " -m " + prealiTSPath + " " + item.getModelName(
) + " ; "
pwviewer.CommandView.__init__(self, fn)
self.show()
def computeReconstructionStep(self, tsObjId):
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
tmpPrefix = self._getTmpPath(tsId)
paramsTilt = {
'InputProjections': os.path.join(tmpPrefix, ts.getFirstItem().parseFileName()),
'OutputFile': os.path.join(tmpPrefix, ts.getFirstItem().parseFileName(extension=".rec")),
'TiltFile': os.path.join(tmpPrefix, ts.getFirstItem().parseFileName(extension=".tlt")),
'Thickness': self.tomoThickness.get(),
'FalloffIsTrueSigma': 1,
'Radial': str(self.radialFirstParameter.get()) + "," + str(self.radialSecondParameter.get()),
'Shift': str(self.tomoShiftX.get()) + " " + str(self.tomoShiftZ.get()),
'Offset': str(self.angleOffset.get()) + " " + str(self.tiltAxisOffset.get()),
}
argsTilt = "-InputProjections %(InputProjections)s " \
"-OutputFile %(OutputFile)s " \
"-TILTFILE %(TiltFile)s " \
"-THICKNESS %(Thickness)d " \
"-FalloffIsTrueSigma %(FalloffIsTrueSigma)d " \
"-RADIAL %(Radial)s " \
"-SHIFT %(Shift)s " \
"-OFFSET %(Offset)s "
if self.fakeInteractionsSIRT.get() != 0:
paramsTilt.update({
'FakeSIRTInteractions': self.fakeInteractionsSIRT.get()
})
argsTilt += "-FakeSIRTiterations %(FakeSIRTInteractions)d "
if self.usesGpu():
paramsTilt.update({
"useGPU": self.getGpuList()[0],
"actionIfGPUFails": "2,2",
})
argsTilt += "-UseGPU %(useGPU)d " \
"-ActionIfGPUFails %(actionIfGPUFails)s "
Plugin.runImod(self, 'tilt', argsTilt % paramsTilt)
paramsNewstack = {
'input': os.path.join(tmpPrefix, ts.getFirstItem().parseFileName(extension=".rec")),
'output': os.path.join(tmpPrefix, ts.getFirstItem().parseFileName(suffix="_flipped", extension=".mrc")),
}
argsNewstack = "-input %(input)s " \
"-output %(output)s"
Plugin.runImod(self, 'newstack', argsNewstack % paramsNewstack)
paramsTrimVol = {
'input': os.path.join(tmpPrefix, ts.getFirstItem().parseFileName(suffix="_flipped", extension=".mrc")),
'output': os.path.join(extraPrefix, ts.getFirstItem().parseFileName(extension=".mrc")),
'rotation': "-yz "
}
argsTrimvol = "%(input)s " \
"%(output)s " \
"%(rotation)s "
Plugin.runImod(self, 'trimvol', argsTrimvol % paramsTrimVol)
def __init__(self, set, **kwargs):
fn = " -s 0,0 "
for item in set:
fn += " " + item.getLocation()[1]
pwviewer.CommandView.__init__(self, Plugin.getImodCmd('3dmod') + fn)
self.show()
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 generateOutputStackStep(self, tsObjId):
tomo = self.inputSetOfTomograms.get()[tsObjId]
location = tomo.getLocation()[1]
fileName, fileExtension = os.path.splitext(location)
extraPrefix = self._getExtraPath(os.path.basename(fileName))
tmpPrefix = self._getTmpPath(os.path.basename(fileName))
path.makePath(extraPrefix)
path.makePath(tmpPrefix)
runNewstack = False
paramsNewstack = {
'input': location,
'output': os.path.join(extraPrefix, os.path.basename(location)),
'imagebinned': 1.0,
}
argsNewstack = "-input %(input)s " \
"-output %(output)s " \
"-imagebinned %(imagebinned)s "
if self.floatDensities.get() != 0:
runNewstack = True
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:
runNewstack = True
argsNewstack += " -ModeToOutput " + str(self.getModeToOutput())
if runNewstack:
Plugin.runImod(self, 'newstack', argsNewstack % paramsNewstack)
if self.binning.get() != 1:
if runNewstack:
path.moveFile(
os.path.join(extraPrefix, os.path.basename(location)),
os.path.join(tmpPrefix, os.path.basename(location)))
inputTomoPath = os.path.join(tmpPrefix,
os.path.basename(location))
else:
inputTomoPath = location
paramsBinvol = {
'input': inputTomoPath,
'output': os.path.join(extraPrefix,
os.path.basename(location)),
'binning': self.binning.get(),
}
argsBinvol = "-input %(input)s " \
"-output %(output)s " \
"-binning %(binning)d "
Plugin.runImod(self, 'binvol', argsBinvol % paramsBinvol)
outputNormalizedSetOfTomograms = self.getOutputNormalizedSetOfTomograms(
)
newTomogram = Tomogram()
newTomogram.copyInfo(tomo)
newTomogram.copyAttributes(tomo, '_origin')
if not runNewstack and self.binning.get() == 1:
newTomogram.setLocation(location)
else:
newTomogram.setLocation(
os.path.join(extraPrefix, os.path.basename(location)))
if self.binning > 1:
newTomogram.setSamplingRate(tomo.getSamplingRate() *
int(self.binning.get()))
outputNormalizedSetOfTomograms.append(newTomogram)
outputNormalizedSetOfTomograms.update(newTomogram)
outputNormalizedSetOfTomograms.write()
self._store()
def createOutput(self):
outputPrealiSetOfTiltSeries = None
outputAliSetOfTiltSeries = None
outputSetOfLandmarkModelsNoGaps = None
outputSetOfCoordinates3D = None
outputSetOfFullTomograms = None
outputSetOfPostProcessTomograms = None
for ts in self.inputSetOfTiltSeries.get():
self.inputTiltSeries = ts
tsId = ts.getTsId()
"""Prealigned tilt-series"""
prealiFilePath = self.getFilePath(ts, extension=".preali")
if os.path.exists(prealiFilePath):
if outputPrealiSetOfTiltSeries is None:
outputPrealiSetOfTiltSeries = self._createSetOfTiltSeries(
suffix='Preali')
outputPrealiSetOfTiltSeries.copyInfo(self.inputTiltSeries)
outputPrealiSetOfTiltSeries.setDim(
self.inputTiltSeries.getDim())
self._defineOutputs(outputPrealignedSetOfTiltSeries=
outputPrealiSetOfTiltSeries)
self._defineSourceRelation(self.inputTiltSeries,
outputPrealiSetOfTiltSeries)
newTs = ts.clone()
newTs.copyInfo(ts)
outputPrealiSetOfTiltSeries.append(newTs)
ih = ImageHandler()
index = 0
for index, tiltImage in enumerate(ts.iterItems(iterate=False)):
newTi = tiltImage.clone()
newTi.copyInfo(tiltImage, copyId=True)
newTi.setLocation(index + 1, prealiFilePath)
index += 1
xPreali, _, _, _ = ih.getDimensions(newTi.getFileName() +
":mrc")
newTi.setSamplingRate(
self.getPixSizeFromDimensions(xPreali))
newTs.append(newTi)
xPreali, yPreali, zPreali, _ = ih.getDimensions(
newTs.getFirstItem().getFileName() + ":mrc")
newTs.setDim((xPreali, yPreali, zPreali))
newTs.write(properties=False)
outputPrealiSetOfTiltSeries.setSamplingRate(
self.getPixSizeFromDimensions(xPreali))
outputPrealiSetOfTiltSeries.write()
self._store(outputPrealiSetOfTiltSeries)
"""Aligned tilt-series"""
aligFilePath = self.getFilePath(ts, extension=".ali")
if os.path.exists(aligFilePath):
if outputAliSetOfTiltSeries is None:
outputAliSetOfTiltSeries = self._createSetOfTiltSeries(
suffix='Ali')
outputAliSetOfTiltSeries.copyInfo(self.inputTiltSeries)
outputAliSetOfTiltSeries.setDim(
self.inputTiltSeries.getDim())
self._defineOutputs(
outputAlignedSetOfTiltSeries=outputAliSetOfTiltSeries)
self._defineSourceRelation(self.inputSetOfTiltSeries,
outputAliSetOfTiltSeries)
newTs = ts.clone()
newTs.copyInfo(ts)
outputAliSetOfTiltSeries.append(newTs)
ih = ImageHandler()
tltFilePath = self.getFilePath(ts,
suffix='_fid',
extension=".tlt")
if os.path.exists(tltFilePath):
tltList = utils.formatAngleList(tltFilePath)
else:
tltList = None
index = 0
for index, tiltImage in enumerate(ts.iterItems(iterate=False)):
newTi = tiltImage.clone()
newTi.copyInfo(tiltImage, copyId=True)
newTi.setLocation(index + 1, aligFilePath)
if tltList is not None:
newTi.setTiltAngle(float(tltList[index]))
xAli, _, _, _ = ih.getDimensions(newTi.getFileName() +
":mrc")
newTi.setSamplingRate(self.getPixSizeFromDimensions(xAli))
newTs.append(newTi)
xAli, yAli, zAli, _ = ih.getDimensions(
newTs.getFirstItem().getFileName() + ":mrc")
newTs.setDim((xAli, yAli, zAli))
newTs.write(properties=False)
outputAliSetOfTiltSeries.setSamplingRate(
self.getPixSizeFromDimensions(xAli))
outputAliSetOfTiltSeries.write()
self._store(outputAliSetOfTiltSeries)
"""Output set of coordinates 3D (associated to the aligned tilt-series)"""
coordFilePath = self.getFilePath(ts,
suffix='fid',
extension=".xyz")
if os.path.exists(coordFilePath):
if outputSetOfCoordinates3D is None:
outputSetOfCoordinates3D = self._createSetOfCoordinates3D(
volSet=outputAliSetOfTiltSeries,
suffix='LandmarkModel')
outputSetOfCoordinates3D.setSamplingRate(
self.inputTiltSeries.getSamplingRate())
outputSetOfCoordinates3D.setPrecedents(
outputAliSetOfTiltSeries)
self._defineOutputs(
outputSetOfCoordinates3D=outputSetOfCoordinates3D)
self._defineSourceRelation(self.inputSetOfTiltSeries,
outputSetOfCoordinates3D)
coordList = utils.format3DCoordinatesList(coordFilePath)
for element in coordList:
newCoord3D = tomoObj.Coordinate3D()
newCoord3D.setVolume(ts)
newCoord3D.setX(element[0], constants.BOTTOM_LEFT_CORNER)
newCoord3D.setY(element[1], constants.BOTTOM_LEFT_CORNER)
newCoord3D.setZ(element[2], constants.BOTTOM_LEFT_CORNER)
newCoord3D.setVolId(ts.getObjId())
outputSetOfCoordinates3D.append(newCoord3D)
outputSetOfCoordinates3D.update(newCoord3D)
outputSetOfCoordinates3D.write()
self._store(outputSetOfCoordinates3D)
"""Landmark models with no gaps"""
if (os.path.exists(
self.getFilePath(ts, suffix="_nogaps", extension=".fid"))
and os.path.exists(self.getFilePath(ts,
extension=".resid"))):
paramsNoGapPoint2Model = {
'inputFile':
self.getFilePath(ts, suffix="_nogaps", extension=".fid"),
'outputFile':
self.getFilePath(ts,
suffix="_nogaps_fid",
extension=".txt")
}
argsNoGapPoint2Model = "-InputFile %(inputFile)s " \
"-OutputFile %(outputFile)s"
Plugin.runImod(self, 'model2point',
argsNoGapPoint2Model % paramsNoGapPoint2Model)
if outputSetOfLandmarkModelsNoGaps is None:
outputSetOfLandmarkModelsNoGaps = self._createSetOfLandmarkModels(
suffix='NoGaps')
outputSetOfLandmarkModelsNoGaps.copyInfo(
self.inputTiltSeries)
self._defineOutputs(outputSetOfLandmarkModelsNoGaps=
outputSetOfLandmarkModelsNoGaps)
self._defineSourceRelation(
self.inputSetOfTiltSeries,
outputSetOfLandmarkModelsNoGaps)
fiducialNoGapFilePath = self.getFilePath(ts,
suffix="_nogaps_fid",
extension=".txt")
fiducialNoGapList = utils.formatFiducialList(
fiducialNoGapFilePath)
fiducialModelNoGapPath = self.getFilePath(ts,
suffix="_nogaps",
extension=".fid")
landmarkModelNoGapsFilePath = self.getFilePath(
ts, suffix="_nogaps", extension=".sfid")
landmarkModelNoGapsResidPath = self.getFilePath(
ts, extension=".resid")
fiducialNoGapsResidList = utils.formatFiducialResidList(
landmarkModelNoGapsResidPath)
landmarkModelNoGaps = tomoObj.LandmarkModel(
tsId, landmarkModelNoGapsFilePath, fiducialModelNoGapPath)
prevTiltIm = 0
chainId = 0
indexFake = 0
for fiducial in fiducialNoGapList:
if int(float(fiducial[2])) <= prevTiltIm:
chainId += 1
prevTiltIm = int(float(fiducial[2]))
if (indexFake < len(fiducialNoGapsResidList)
and fiducial[2]
== fiducialNoGapsResidList[indexFake][2]):
landmarkModelNoGaps.addLandmark(
xCoor=fiducial[0],
yCoor=fiducial[1],
tiltIm=fiducial[2],
chainId=chainId,
xResid=fiducialNoGapsResidList[indexFake][3],
yResid=fiducialNoGapsResidList[indexFake][4])
indexFake += 1
else:
landmarkModelNoGaps.addLandmark(xCoor=fiducial[0],
yCoor=fiducial[1],
tiltIm=fiducial[2],
chainId=chainId,
xResid='0',
yResid='0')
outputSetOfLandmarkModelsNoGaps.append(landmarkModelNoGaps)
outputSetOfLandmarkModelsNoGaps.write()
self._store(outputSetOfLandmarkModelsNoGaps)
"""Full reconstructed tomogram"""
reconstructTomoFilePath = self.getFilePath(ts,
suffix="_full",
extension=".rec")
if os.path.exists(reconstructTomoFilePath):
if outputSetOfFullTomograms is None:
outputSetOfFullTomograms = self._createSetOfTomograms(
suffix='Full')
outputSetOfFullTomograms.copyInfo(self.inputTiltSeries)
self._defineOutputs(
outputSetOfFullTomograms=outputSetOfFullTomograms)
self._defineSourceRelation(self.inputSetOfTiltSeries,
outputSetOfFullTomograms)
newTomogram = tomoObj.Tomogram()
newTomogram.setLocation(reconstructTomoFilePath)
newTomogram.setSamplingRate(ts.getSamplingRate())
outputSetOfFullTomograms.append(newTomogram)
outputSetOfFullTomograms.write()
self._store(outputSetOfFullTomograms)
"""Post-processed reconstructed tomogram"""
posprocessedRecTomoFilePath = self.getFilePath(ts,
extension=".rec")
if os.path.exists(posprocessedRecTomoFilePath):
if outputSetOfPostProcessTomograms is None:
outputSetOfPostProcessTomograms = self._createSetOfTomograms(
)
outputSetOfPostProcessTomograms.copyInfo(
self.inputTiltSeries)
self._defineOutputs(outputSetOfPostProcessTomograms=
outputSetOfPostProcessTomograms)
self._defineSourceRelation(
self.inputSetOfTiltSeries,
outputSetOfPostProcessTomograms)
newTomogram = tomoObj.Tomogram()
newTomogram.setLocation(posprocessedRecTomoFilePath)
outputSetOfPostProcessTomograms.append(newTomogram)
outputSetOfPostProcessTomograms.write()
self._store(outputSetOfPostProcessTomograms)
self.closeMappers()
def ctfEstimation(self, tsObjId):
"""Run ctfplotter IMOD program"""
ts = self._getTiltSeries(tsObjId)
tsSet = self._getSetOfTiltSeries()
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
tmpPrefix = self._getTmpPath(tsId)
paramsCtfPlotter = {
'inputStack':
os.path.join(tmpPrefix,
ts.getFirstItem().parseFileName()),
'angleFile':
os.path.join(tmpPrefix,
ts.getFirstItem().parseFileName(extension=".tlt")),
'defocusFile':
os.path.join(
extraPrefix,
ts.getFirstItem().parseFileName(extension=".defocus")),
'axisAngle':
self.axisAngle.get(),
'pixelSize':
tsSet.getSamplingRate() / 10,
'expectedDefocus':
self.getExpectedDefocus(tsId),
'autoFitRangeAndStep':
str(self.angleRange.get()) + "," + str(self.angleStep.get()),
'voltage':
tsSet.getAcquisition().getVoltage(),
'sphericalAberration':
tsSet.getAcquisition().getSphericalAberration(),
'amplitudeContrast':
tsSet.getAcquisition().getAmplitudeContrast(),
'defocusTol':
self.defocusTol.get(),
'psResolution':
101,
'leftDefTol':
self.leftDefTol.get(),
'rightDefTol':
self.rightDefTol.get(),
'tileSize':
self.tileSize.get(),
}
argsCtfPlotter = "-InputStack %(inputStack)s " \
"-AngleFile %(angleFile)s " \
"-DefocusFile %(defocusFile)s " \
"-AxisAngle %(axisAngle)f " \
"-PixelSize %(pixelSize)f " \
"-ExpectedDefocus %(expectedDefocus)f " \
"-AutoFitRangeAndStep %(autoFitRangeAndStep)s " \
"-Voltage %(voltage)d " \
"-SphericalAberration %(sphericalAberration)f " \
"-AmplitudeContrast %(amplitudeContrast)f " \
"-DefocusTol %(defocusTol)d " \
"-PSResolution %(psResolution)d " \
"-LeftDefTol %(leftDefTol)f " \
"-RightDefTol %(rightDefTol)f " \
"-tileSize %(tileSize)d "
if self.startFreq.get() != 0 or self.endFreq.get() != 0:
paramsCtfPlotter.update({
'startFreq': self.startFreq.get(),
'endFreq': self.endFreq.get(),
})
argsCtfPlotter += "-FrequencyRangeToFit %(startFreq)f,%(endFreq)f "
if self.extraZerosToFit.get() != 0:
paramsCtfPlotter.update({
'extraZerosToFit':
self.extraZerosToFit.get(),
})
argsCtfPlotter += "-ExtraZerosToFit %(extraZerosToFit)f "
if self.skipAstigmaticViews.get() == 0:
argsCtfPlotter += "-SkipOnlyForAstigPhase "
if self.searchAstigmatism.get() == 0:
paramsCtfPlotter.update({
'maximumAstigmatism':
self.maximumAstigmatism.get(),
'numberOfSectors':
self.numberSectorsAstigmatism.get(),
'minimumViewsAstigmatism':
self.minimumViewsAstigmatism.get()
})
argsCtfPlotter += "-SearchAstigmatism " \
"-MaximumAstigmatism %(maximumAstigmatism)f " \
"-NumberOfSectors %(numberOfSectors)d "
if self.searchPhaseShift.get() == 0:
paramsCtfPlotter.update(
{'minimumViewsPhaseShift': self.minimumViewsPhaseShift.get()})
argsCtfPlotter += "-SearchPhaseShift "
if self.searchAstigmatism.get() == 0 and self.searchPhaseShift.get(
) == 0:
argsCtfPlotter += "-MinViewsAstigAndPhase %(minimumViewsAstigmatism)d,%(minimumViewsPhaseShift)d "
elif self.searchAstigmatism.get() == 0:
argsCtfPlotter += "-MinViewsAstigAndPhase %(minimumViewsAstigmatism)d,0 "
elif self.searchPhaseShift.get() == 0:
argsCtfPlotter += "-MinViewsAstigAndPhase 0,%(minimumViewsPhaseShift)d "
if self.searchCutOnFreq.get() == 0:
if self.maximumCutOnFreq.get() == -1:
argsCtfPlotter += "-SearchCutonFrequency "
else:
paramsCtfPlotter.update({
'maximumCutOnFreq':
self.maximumCutOnFreq.get(),
})
argsCtfPlotter += "-SearchCutonFrequency " \
"-MaxCutOnToSearch %(maximumCutOnFreq)f "
if not self._interactiveMode:
argsCtfPlotter += "-SaveAndExit "
Plugin.runImod(self, 'ctfplotter', argsCtfPlotter % paramsCtfPlotter)
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 eraseXraysStep(self, tsObjId):
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
tmpPrefix = self._getTmpPath(tsId)
paramsCcderaser = {
'input':
os.path.join(tmpPrefix,
ts.getFirstItem().parseFileName()),
'output':
os.path.join(extraPrefix,
ts.getFirstItem().parseFileName()),
'findPeaks':
1,
'peakCriterion':
self.peakCriterion.get(),
'diffCriterion':
self.diffCriterion.get(),
'growCriterion':
4,
'scanCriterion':
3,
'maximumRadius':
self.maximumRadius.get(),
'giantCriterion':
12,
'extraLargeRadius':
8,
'bigDiffCriterion':
self.bigDiffCriterion.get(),
'annulusWidth':
2.0,
'xyScanSize':
100,
'edgeExclusionWidth':
4,
'pointModel':
os.path.join(
extraPrefix,
ts.getFirstItem().parseFileName(suffix="_fid",
extension=".mod")),
'borderSize':
2,
'polynomialOrder':
2,
}
argsCcderaser = "-InputFile %(input)s " \
"-OutputFile %(output)s " \
"-FindPeaks %(findPeaks)d " \
"-PeakCriterion %(peakCriterion).2f " \
"-DiffCriterion %(diffCriterion).2f " \
"-GrowCriterion %(growCriterion)d " \
"-ScanCriterion %(scanCriterion)d " \
"-MaximumRadius %(maximumRadius).2f " \
"-GiantCriterion %(giantCriterion)d " \
"-ExtraLargeRadius %(extraLargeRadius)d " \
"-BigDiffCriterion %(bigDiffCriterion)d " \
"-AnnulusWidth %(annulusWidth).2f " \
"-XYScanSize %(xyScanSize)d " \
"-EdgeExclusionWidth %(edgeExclusionWidth)d " \
"-BorderSize %(borderSize)d " \
"-PolynomialOrder %(polynomialOrder)d "
Plugin.runImod(self, 'ccderaser', argsCcderaser % paramsCcderaser)
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 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 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()