Source code for dynamo.protocols.protocol_extraction

# **************************************************************************
# *
# * Authors:    David Herreros Calero (dherreros@cnb.csic.es)
# *
# *  BCU, Centro Nacional de Biotecnologia, CSIC
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# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
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import os
import glob

import pyworkflow.utils as pwutils
import pyworkflow.protocol.params as params
from pwem.emlib.image import ImageHandler
from pwem.objects import Transform
from pwem.protocols import EMProtocol

from tomo.protocols import ProtTomoBase
from tomo.objects import SetOfSubTomograms, SubTomogram, TomoAcquisition

from dynamo import Plugin
from dynamo.convert import matrix2eulerAngles


# Tomogram type constants for particle extraction
SAME_AS_PICKING = 0
OTHER = 1


[docs]class DynamoExtraction(EMProtocol, ProtTomoBase): """Extraction of subtomograms using Dynamo""" _label = 'vectorial extraction' def __init__(self, **kwargs): EMProtocol.__init__(self, **kwargs) # --------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputCoordinates', params.PointerParam, label="Input Coordinates", important=True, pointerClass='SetOfCoordinates3D', help='Select the SetOfCoordinates3D.') form.addParam('tomoSource', params.EnumParam, choices=['same as picking', 'other'], default=0, display=params.EnumParam.DISPLAY_HLIST, label='Tomogram source', help='By default the subtomograms will be extracted ' 'from the tomogram used in the picking ' 'step ( _same as picking_ option ). \n' 'If you select _other_ option, you must provide ' 'a different tomogram to extract from. \n' '*Note*: In the _other_ case, ensure that provided ' 'tomogram and coordinates are related ') form.addParam('inputTomograms', params.PointerParam, pointerClass='SetOfTomograms', condition='tomoSource != %s' % SAME_AS_PICKING, label='Input tomogram', help='Select the tomogram from which to extract.') form.addParam('boxSize', params.FloatParam, label='Box size', help='The subtomograms are extracted as a cubic box of this size.\n' 'The wizard selects same box size as picking.\n' 'Dynamo only accepts even numbers as box sizes. Otherwise, an exception will ' 'be returned.') form.addParam('downFactor', params.FloatParam, default=1.0, label='Downsampling factor', help='If 1.0 is used, no downsample is applied. ' 'Non-integer downsample factors are possible. ') form.addSection(label='Preprocess') form.addParam('doInvert', params.BooleanParam, default=False, label='Invert contrast?', help='Invert the contrast if your tomogram is black ' 'over a white background. Xmipp, Spider, Relion ' 'and Eman require white particles over a black ' 'background.') # --------------------------- INSERT steps functions ---------------------- def _insertAllSteps(self): self._insertFunctionStep('writeSetOfCoordinates3D') self._insertFunctionStep('launchDynamoExtractStep') if self.doInvert: self._insertFunctionStep('invertContrastStep') self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions -----------------------------
[docs] def writeSetOfCoordinates3D(self): samplingRateCoord = self.inputCoordinates.get().getSamplingRate() samplingRateTomo = self.getInputTomograms().getFirstItem().getSamplingRate() self.factor = float(samplingRateCoord / samplingRateTomo) self.lines = [] inputSet = self.getInputTomograms().getFiles() self.coordsFileName = self._getExtraPath('coords.txt') self.anglesFileName = self._getExtraPath('angles.txt') outC = open(self.coordsFileName, "w") outA = open(self.anglesFileName, 'w') for idt, item in enumerate(inputSet): coordDict = [] for coord3DSet in self.inputCoordinates.get().iterCoordinates(): if pwutils.removeBaseExt(item) == pwutils.removeBaseExt(coord3DSet.getVolName()): angles_coord = matrix2eulerAngles(coord3DSet.getMatrix()) x = round(self.factor * coord3DSet.getX()) y = round(self.factor * coord3DSet.getY()) z = round(self.factor * coord3DSet.getZ()) outC.write("%d\t%d\t%d\t%d\n" % (x, y, z, idt+1)) outA.write("%f\t%f\t%f\n" % (angles_coord[0], angles_coord[1], angles_coord[2])) coordDict.append(coord3DSet.getObjId()) if coordDict: self.lines.append(coordDict) outC.close() outA.close()
[docs] def launchDynamoExtractStep(self): codeFilePath = self.writeMatlabCode() args = ' %s' % codeFilePath self.runJob(Plugin.getDynamoProgram(), args, env=Plugin.getEnviron()) pwutils.cleanPattern('*.m')
[docs] def invertContrastStep(self): import xmipp3 program = 'xmipp_image_operate' for ind, tomoFile in enumerate(self.tomoFiles): cropPath = os.path.join(self._getExtraPath('Crop%d' % (ind + 1)), '') pattern = os.path.join(cropPath, '*.mrc') for subTomoFile in glob.glob(pattern): args = "-i %s --mult -1" % subTomoFile self.runJob(program, args, env=xmipp3.Plugin.getEnviron())
[docs] def createOutputStep(self): self.outputSubTomogramsSet = self._createSetOfSubTomograms(self._getOutputSuffix(SetOfSubTomograms)) self.outputSubTomogramsSet.setSamplingRate(self.getInputTomograms().getSamplingRate() * self.downFactor.get()) self.outputSubTomogramsSet.setCoordinates3D(self.inputCoordinates) acquisition = TomoAcquisition() acquisition.setAngleMin(self.getInputTomograms().getFirstItem().getAcquisition().getAngleMin()) acquisition.setAngleMax(self.getInputTomograms().getFirstItem().getAcquisition().getAngleMax()) acquisition.setStep(self.getInputTomograms().getFirstItem().getAcquisition().getStep()) self.outputSubTomogramsSet.setAcquisition(acquisition) for ind, tomoFile in enumerate(self.tomoFiles): cropPath = os.path.join(self._getExtraPath('Crop%d' % (ind+1)), '') if os.path.isdir(cropPath): coordSet = self.lines[ind] outputSet = self.readSetOfSubTomograms(cropPath, self.outputSubTomogramsSet, coordSet) self._defineOutputs(outputSetOfSubtomogram=outputSet) self._defineSourceRelation(self.inputCoordinates, outputSet)
# --------------------------- DEFINE utils functions ----------------------
[docs] def getInputTomograms(self): """ Return the tomogram associated to the 'SetOfCoordinates3D' or 'Other' tomograms. """ if self.tomoSource.get() == SAME_AS_PICKING: return self.inputCoordinates.get().getPrecedents() else: return self.inputTomograms.get()
[docs] def writeMatlabCode(self): # Initialization params codeFilePath = os.path.join(os.getcwd(), "DynamoExtraction.m") listTomosFile = self._getTmpPath("tomos.vll") catalogue = os.path.abspath(self._getExtraPath("tomos")) self.tomoFiles = sorted(self.getInputTomograms().getFiles()) # Create list of tomos file tomoFid = open(listTomosFile, 'w') for tomoFile in self.tomoFiles: tomoPath = os.path.abspath(tomoFile) tomoFid.write(tomoPath + '\n') tomoFid.close() # Check of box size is an even number (as required by Dynamo) boxSize = round(self.factor * self.boxSize.get()) if boxSize % 2 != 0: boxSize += 1 # Write code to Matlab code file codeFid = open(codeFilePath, 'w') content = "path='%s'\n" \ "savePath = '%s'\n" \ "catalogue_name='%s'\n" \ "box=%d\n" \ "dcm -create %s -fromvll %s\n" \ "c=dread(strcat(catalogue_name,'.ctlg'))\n" \ "aux=readmatrix('%s')\n" \ "angles=readmatrix('%s')\n" \ "coords=aux(:,1:3)\n" \ "tags=aux(:,4)'\n" \ "for tag=unique(tags)\n" \ "tomoCoords=coords(tags==tag,:)\n" \ "tomoAngles=angles(tags==tag,:)\n" \ "t=dynamo_table_blank(size(tomoCoords,1),'r',tomoCoords,'angles',rad2deg(tomoAngles))\n" \ "dtcrop(c.volumes{tag}.fullFileName,t,strcat(savePath,num2str(tag)),box,'ext','mrc')\n" \ "end\n" \ % (os.path.abspath(os.getcwd()), self._getExtraPath('Crop'), catalogue,boxSize, catalogue, listTomosFile, os.path.abspath(self.coordsFileName), os.path.abspath(self.anglesFileName)) codeFid.write(content) codeFid.close() return codeFilePath
[docs] def readSetOfSubTomograms(self, workDir, outputSubTomogramsSet, coordSet): coords = self.inputCoordinates.get() for ids, subTomoFile in enumerate(sorted(glob.glob(os.path.join(workDir, '*' + '.mrc')))): subtomogram = SubTomogram() subtomogram.cleanObjId() subtomogram.setLocation(subTomoFile) dfactor = self.downFactor.get() if dfactor != 1: fnSubtomo = self._getExtraPath(os.path.basename(workDir.strip("/")) + "_downsampled_subtomo%d.mrc" % (ids+1)) ImageHandler.scaleSplines(subtomogram.getFileName() + ':mrc', fnSubtomo, dfactor) subtomogram.setLocation(fnSubtomo) subtomogram.setCoordinate3D(coords[coordSet[ids]]) subtomogram.setVolName(coords[coordSet[ids]].getVolName()) transform = Transform() transform.setMatrix(coords[coordSet[ids]].getMatrix()) subtomogram.setTransform(transform) outputSubTomogramsSet.append(subtomogram) return outputSubTomogramsSet
# --------------------------- DEFINE info functions ---------------------- def _validate(self): errors = [] if not self.boxSize.get() % 2 == 0: errors.append('The box size provided to Dynamo is an odd number. ' 'This will rise an execption when Dynamo is invoked.\n' 'Please, provide an even number to continue with the extraction.') return errors def _tomosOther(self): """ Return True if other tomograms are used for extract. """ return self.tomoSource == OTHER def _methods(self): methodsMsgs = [] if self.getOutputsSize() >= 1: msg = ("A total of %s subtomograms of size %s were extracted" % (str(self.inputCoordinates.get().getSize()), self.boxSize.get())) if self._tomosOther(): msg += (" from another set of tomograms: %s" % self.getObjectTag('inputTomogram')) msg += " using coordinates %s" % self.getObjectTag('inputCoordinates') msg += self.methodsVar.get('') methodsMsgs.append(msg) else: methodsMsgs.append("Set of Subtomograms not ready yet") if self.downFactor.get() != 1: methodsMsgs.append("Subtomograms downsample by factor %d." % self.downFactor.get()) return methodsMsgs def _summary(self): summary = [] summary.append("Tomogram source: *%s*" % self.getEnumText("tomoSource")) if self.getOutputsSize() >= 1: summary.append("Particle box size: *%s*" % self.boxSize.get()) summary.append("Subtomogram extracted: *%s*" % self.inputCoordinates.get().getSize()) else: summary.append("Output subtomograms not ready yet.") if self.doInvert: summary.append('*White over black.*') else: summary.append('*Black over white.*') return summary