Source code for imod.protocols.protocol_tomoReconstruction

# **************************************************************************
# *
# * Authors:     Federico P. de Isidro Gomez (fp.deisidro@cnb.csic.es) [1]
# *
# * [1] Centro Nacional de Biotecnologia, CSIC, Spain
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# * 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 'scipion@cnb.csic.es'
# *
# **************************************************************************

import os

from pwem.objects import Transform
from pyworkflow import BETA
from pyworkflow.object import Set
import pyworkflow.protocol.params as params
import pyworkflow.utils.path as path
from pwem.protocols import EMProtocol
from tomo.protocols import ProtTomoBase
from tomo.objects import Tomogram
from tomo.objects import TomoAcquisition
from imod import Plugin


[docs]class ProtImodTomoReconstruction(EMProtocol, ProtTomoBase): """ Tomogram reconstruction procedure based on the IMOD procedure. More info: https://bio3d.colorado.edu/imod/doc/man/tilt.html """ _label = 'tomo reconstruction' _devStatus = BETA # -------------------------- DEFINE param functions ----------------------- def _defineParams(self, form): form.addSection('Input') form.addParam('inputSetOfTiltSeries', params.PointerParam, pointerClass='SetOfTiltSeries', important=True, label='Input set of tilt-series') form.addParam('tomoThickness', params.FloatParam, default=100, label='Tomogram thickness (voxels)', important=True, display=params.EnumParam.DISPLAY_HLIST, help='Size in voxels of the tomogram in the z axis (beam direction).') form.addParam('tomoShiftX', params.FloatParam, default=0, label='Tomogram shift in X', important=True, display=params.EnumParam.DISPLAY_HLIST, help='This entry allows one to shift the reconstructed slice in X before it is output. If ' 'the X shift is positive, the slice will be shifted to the right, and the output will ' 'contain the left part of the whole potentially reconstructable area.') form.addParam('tomoShiftZ', params.FloatParam, default=0, label='Tomogram shift in Z', important=True, display=params.EnumParam.DISPLAY_HLIST, help='This entry allows one to shift the reconstructed slice in Z before it is output. If the Z ' 'shift is positive, the slice is shifted upward. The Z entry is optional and defaults to 0 ' 'when omitted.') form.addParam('angleOffset', params.FloatParam, default=0, label='Angle offset', important=True, display=params.EnumParam.DISPLAY_HLIST, help='Apply an angle offset in degrees to all tilt angles. This offset positively rotates the ' 'reconstructed sections anticlockwise.') form.addParam('tiltAxisOffset', params.FloatParam, default=0, label='Tilt axis offset', important=True, display=params.EnumParam.DISPLAY_HLIST, help='Apply an offset to the tilt axis in a stack of full-sized projection images, cutting the ' 'X-axis at NX/2. + offset instead of NX/2. The DELXX entry is optional and defaults to 0 ' 'when omitted.') form.addParam('fakeInteractionsSIRT', params.IntParam, default=0, label='Iterations of a SIRT-like equivalent filter', display=params.EnumParam.DISPLAY_HLIST, expertLevel=params.LEVEL_ADVANCED, help='Modify the radial filter to produce a reconstruction equivalent to the one produced by the ' 'given number of iterations of SIRT. The Gaussian filter is applied at the high-frequency ' 'end of the filter. The functioning of this filter is described in: \n\t' 'https://bio3d.colorado.edu/imod/doc/man/tilt.html') groupRadialFrequencies = form.addGroup('Radial filtering', help='This entry controls low-pass filtering with the radial weighting ' 'function. The radial weighting function is linear away from the ' 'origin out to the distance in reciprocal space specified by the ' 'first value, followed by a Gaussian fall-off determined by the ' 'second value.', expertLevel=params.LEVEL_ADVANCED) groupRadialFrequencies.addParam('radialFirstParameter', params.FloatParam, default=0.35, label='First parameter', help='Linear region value') groupRadialFrequencies.addParam('radialSecondParameter', params.FloatParam, default=0.035, label='Second parameter', help='Gaussian fall-off parameter') form.addHidden(params.USE_GPU, params.BooleanParam, default=True, label="Use GPU for execution", help="This protocol has both CPU and GPU implementation.\ Select the one you want to use.") form.addHidden(params.GPU_LIST, params.StringParam, default='0', expertLevel=params.LEVEL_ADVANCED, label="Choose GPU IDs", help="GPU ID. To pick the best available one set 0. For a specific GPU set its number ID.") # -------------------------- INSERT steps functions --------------------- def _insertAllSteps(self): for ts in self.inputSetOfTiltSeries.get(): self._insertFunctionStep('convertInputStep', ts.getObjId()) self._insertFunctionStep('computeReconstructionStep', ts.getObjId()) self._insertFunctionStep('createOutputStep', ts.getObjId()) self._insertFunctionStep('closeOutputSetsStep') # --------------------------- STEPS functions ----------------------------
[docs] def convertInputStep(self, tsObjId): ts = self.inputSetOfTiltSeries.get()[tsObjId] tsId = ts.getTsId() extraPrefix = self._getExtraPath(tsId) tmpPrefix = self._getTmpPath(tsId) path.makePath(tmpPrefix) path.makePath(extraPrefix) """Apply the transformation form the input tilt-series""" outputTsFileName = os.path.join(tmpPrefix, ts.getFirstItem().parseFileName()) ts.applyTransform(outputTsFileName) """Generate angle file""" angleFilePath = os.path.join(tmpPrefix, ts.getFirstItem().parseFileName(extension=".tlt")) ts.generateTltFile(angleFilePath)
[docs] 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)
[docs] def createOutputStep(self, tsObjId): ts = self.inputSetOfTiltSeries.get()[tsObjId] tsId = ts.getTsId() extraPrefix = self._getExtraPath(tsId) outputSetOfTomograms = self.getOutputSetOfTomograms() newTomogram = Tomogram() newTomogram.setLocation(os.path.join(extraPrefix, ts.getFirstItem().parseFileName(extension=".mrc"))) # Set tomogram origin origin = Transform() sr = self.inputSetOfTiltSeries.get().getSamplingRate() origin.setShifts(ts.getFirstItem().getXDim() / -2. * sr, ts.getFirstItem().getYDim() / -2. * sr, self.tomoThickness.get() / -2 * sr) newTomogram.setOrigin(origin) # Set tomogram acquisition acquisition = TomoAcquisition() acquisition.setAngleMin(ts.getFirstItem().getTiltAngle()) acquisition.setAngleMax(ts[ts.getSize()].getTiltAngle()) acquisition.setStep(self.getAngleStepFromSeries(ts)) newTomogram.setAcquisition(acquisition) outputSetOfTomograms.append(newTomogram) outputSetOfTomograms.update(newTomogram) outputSetOfTomograms.write() self._store()
[docs] def closeOutputSetsStep(self): self.getOutputSetOfTomograms().setStreamState(Set.STREAM_CLOSED) self._store()
# --------------------------- UTILS functions ----------------------------
[docs] def getOutputSetOfTomograms(self): if hasattr(self, "outputSetOfTomograms"): self.outputSetOfTomograms.enableAppend() else: outputSetOfTomograms = self._createSetOfTomograms() outputSetOfTomograms.copyInfo(self.inputSetOfTiltSeries.get()) outputSetOfTomograms.setStreamState(Set.STREAM_OPEN) self._defineOutputs(outputSetOfTomograms=outputSetOfTomograms) self._defineSourceRelation(self.inputSetOfTiltSeries, outputSetOfTomograms) return self.outputSetOfTomograms
[docs] @staticmethod def getAngleStepFromSeries(ts): """ This method return the average angles step from a series. """ angleStepAverage = 0 for i in range(1, ts.getSize()): angleStepAverage += abs(ts[i].getTiltAngle()-ts[i+1].getTiltAngle()) angleStepAverage /= ts.getSize()-1 return angleStepAverage
# --------------------------- INFO functions ---------------------------- def _summary(self): summary = [] if hasattr(self, 'outputSetOfTomograms'): summary.append("Input Tilt-Series: %d.\nTomograms reconstructed: %d.\n" % (self.inputSetOfTiltSeries.get().getSize(), self.outputSetOfTomograms.getSize())) else: summary.append("Output classes not ready yet.") return summary def _methods(self): methods = [] if hasattr(self, 'outputSetOfTomograms'): methods.append("The reconstruction has been computed for %d " "Tilt-series using the IMOD procedure.\n" % (self.outputSetOfTomograms.getSize())) else: methods.append("Output classes not ready yet.") return methods