Source code for xmipp3.viewers.viewer_projmatch

# **************************************************************************
# *
# * Authors:     Roberto Marabini (roberto@cnb.csic.es)
# *              J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
# *              Josue Gomez Blanco (josue.gomez-blanco@mcgill.ca)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * 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'
# *
# **************************************************************************
"""
This module implement the wrappers aroung Xmipp ML2D protocol
visualization program.
"""

from pyworkflow.protocol.executor import StepExecutor
from pyworkflow.viewer import ProtocolViewer, DESKTOP_TKINTER, WEB_DJANGO
from pwem.viewers import (DataView, EmPlotter, showj, ChimeraClientView,
                          ChimeraView, ObjectView, ChimeraAngDist)
import pwem.objects as emobj
from pyworkflow.utils import createUniqueFileName, cleanPattern, cleanPath
from pyworkflow.protocol.constants import LEVEL_ADVANCED
from pyworkflow.protocol.params import (LabelParam, IntParam, FloatParam,
                                        StringParam, EnumParam,
                                        NumericRangeParam, BooleanParam)
from xmipp3.convert import *
from xmipp3.viewers.plotter import XmippPlotter
from xmipp3.protocols import XmippProtProjMatch


ITER_LAST = 0
ITER_SELECTION = 1

ANGDIST_2DPLOT = 0
ANGDIST_CHIMERA = 1

VOLUME_SLICES = 0
VOLUME_CHIMERA = 1

DISPLAY_LIBRARY = 0

REF_ALL = 0
REF_SEL = 1

CLASSES_ALL = 0
CLASSES_SEL = 1

[docs]class XmippProjMatchViewer(ProtocolViewer): """ Wrapper to visualize different type of data objects with the Xmipp program xmipp_showj """ _targets = [XmippProtProjMatch] _environments = [DESKTOP_TKINTER, WEB_DJANGO] _label = 'viewer projection matching' # _plotVars = ['doShowLL', 'doShowPmax', 'doShowSignalChange', 'doShowMirror'] def _defineParams(self, form): form.addSection(label='Visualization') group = form.addGroup('Overall results') form.addParam('viewIter', EnumParam, choices=['last', 'selection'], default=ITER_LAST, display=EnumParam.DISPLAY_HLIST, label="Iteration to visualize", help=""" *last*: only the last iteration will be visualized. *selection*: you may specify a range of iterations. Examples: "1,5-8,10" -> [1,5,6,7,8,10] "2,6,9-11" -> [2,6,9,10,11] "2 5, 6-8" -> [2,5,6,7,8] """) form.addParam('iterSelection', NumericRangeParam, condition='viewIter==%d' % ITER_SELECTION, label="Iteration list", help="Write the iteration list to visualize.") group = form.addGroup('Particles') group.addParam('displayLibraryOrClasses', EnumParam, choices=['projections', 'classes', 'projections and classes'], default=DISPLAY_LIBRARY, display=EnumParam.DISPLAY_COMBO, label='Display', help='Displays images with angular assignment') group.addParam('showProjectionMatchingLibraryAndImages', LabelParam, default=False, label='Display projections and particles', help="Display projections and particles") group.addParam('showExperimentalImages', LabelParam, default=False, label='Display particles', help="""Display particles with alignment and classification information WARNING: the angles and shifts are the adequate for reconstruction but not for 2D aligment. """) group.addParam('showDiscardedImages', LabelParam, default=False, label='Display discarded particles', help='Display discarded particles.') group = form.addGroup('Volumes') group.addParam('showRef3DNo', EnumParam, choices=['all', 'selection'], default=REF_ALL, display=EnumParam.DISPLAY_HLIST, label='3D Class to visualize', help='All: Display all 3D classes for each iteration' 'that you selected.\n' 'Selection: You may specify which 3D class (or classes)' ' to visualize') group.addParam('ref3DSelection', NumericRangeParam, default='1', condition='showRef3DNo == %d' % REF_SEL, label='Classes list', help='Write the 3d classes list to visualize.') group.addParam('matrixWidth', FloatParam, default=-1, expertLevel=LEVEL_ADVANCED, label='Width of projection galleries', help='Usually a multiple of 2 is the right value. -1 => authomatic') group.addParam('showAngDist', EnumParam, choices=['2D plot', 'chimera'], display=EnumParam.DISPLAY_HLIST, default=ANGDIST_2DPLOT, label='Display angular distribution', help='*2D plot*: display angular distribution as interative 2D in matplotlib.\n' '*chimera*: display angular distribution using Chimera with red spheres.') group.addParam('displayVolWith', EnumParam, choices=['slices', 'chimera'], display=EnumParam.DISPLAY_HLIST, default=VOLUME_SLICES, label='Display volume with', help='*slices*: display volumes as 2D slices along z axis.\n' '*chimera*: display volumes as surface with Chimera.') group.addParam('displayVolume', EnumParam, choices=['Reference', 'Reconstructed', 'Filtered', 'bfactor corrected'], default=1, display=EnumParam.DISPLAY_COMBO, label='Display volume', help='Displays selected volume') group.addParam('spheresScale', IntParam, default=-1, expertLevel=LEVEL_ADVANCED, label='Spheres size', help='') group.addParam('maxRes', FloatParam, default=5, condition='displayVolume==3', label='Maximum resolution to apply B-factor (in Angstroms)') group.addParam('correctBfactorExtraCommand', StringParam, default='--auto', condition='displayVolume==3', label='User defined flags for the correct_bfactor program', help=""" See http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Correct_bfactor for details. DEFAULT behaviour is --auto """) group = form.addGroup('Resolution') group.addParam('showResolutionPlots', LabelParam, default=True, label='Display resolution plots (FSC)', help='') group.addParam('resolutionThreshold', FloatParam, default=0.5, expertLevel=LEVEL_ADVANCED, label='Threshold in resolution plots', help='') form.addSection(label='Convergence') group = form.addGroup('Convergence') group.addParam('plotHistogramAngularMovement', LabelParam, default=False, label='Plot histogram with angular/shift changes', help=""" Plot histogram with angular changes from one iteration to next. Iteration 0 -> initial values """) group.addParam('numberOfBins', IntParam, default=50, condition='plotHistogramAngularMovement', label='Number of bins (for histogram)', help='Number of bins in histograms') group.addParam('usePsi', BooleanParam, default=False, label='Use Psi to compute angular distances', help='Use Psi') group.addParam('angleSort', BooleanParam, default=False, label='Sort assigned angles', help='Sort by angles the experimental images.') group.addParam('shiftSort', BooleanParam, default=False, label='Sort shift', help='Sort by shift the experimental images.') def _getVisualizeDict(self): self._load() return { 'displayVolume' : self._showVolume, 'displayLibraryOrClasses' : self._showLibraryOrClasses, 'showProjectionMatchingLibraryAndImages' : self._showProjMatchLibAndImages, 'showDiscardedImages' : self._showDiscardedImages, 'showExperimentalImages' : self._showExperimentalImages, 'plotHistogramAngularMovement' : self._plotHistogramAngularMovement, 'showAngDist': self._showAngularDistribution, 'showResolutionPlots': self._showFSC } def _viewAll(self, *args): pass def _validate(self): if self.lastIter is None: return ['There are not iterations completed.']
[docs] def createDataView(self, filename, viewParams={}): return DataView(filename, viewParams)
# def createScipionView(self, filename, extraParams=''): # inputParticlesId = self.protocol.inputParticles.get().strId() # return Classes3DView(self._project, # self.protocol.strId(), filename, other=inputParticlesId, # env=self._env) def _load(self): """ Load selected iterations and classes 3D for visualization mode. """ self._refsList = [1] self.protocol._initialize() # Load filename templates if self.showRef3DNo == REF_ALL: self._refsList = range(1, self.protocol.numberOfReferences+1) else: self._refsList = self._getListFromRangeString(self.ref3DSelection.get()) # ToDo: enhance this self.firstIter = 1 #self.lastIter = self.protocol.numberOfIterations.get() self.lastIter = self.protocol.getLastIter() if self.viewIter.get() == ITER_LAST: self._iterations = [self.lastIter] else: self._iterations = self._getListFromRangeString(self.iterSelection.get()) from matplotlib.ticker import FuncFormatter self._plotFormatter = FuncFormatter(self._formatFreq) def _formatFreq(self, value, pos): """ Format function for Matplotlib formatter. """ inv = 999 if value: inv = 1/value return "1/%0.2f" % inv def _getGridSize(self, n=None): """ Figure out the layout of the plots given the number of references. """ if n is None: n = len(self._refsList) if n == 1: gridsize = [1, 1] elif n == 2: gridsize = [2, 1] else: gridsize = [(n+1)/2, 2] return gridsize #=============================================================================== # Show Volumes #=============================================================================== def _showVolume(self, paramName=None): choice = self.displayVolume.get() if choice == 0: return self._showRefs(paramName) elif choice == 1: return self._showRecons(paramName) elif choice == 2: return self._showFilVols(paramName) else: return self._showBfactorVols(paramName) def _createVolumesMd(self, volumes): """ Write a metadata with all volumes selected for visualization. """ mdPath = self.protocol._getExtraPath('viewer_volumes.xmd') md = emlib.MetaData() for volFn in volumes: md.clear() md.setValue(emlib.MDL_IMAGE, volFn, md.addObject()) blockName = volFn.split("/")[3] # print("Volume: %s %s" %(volFn, blockName)) md.write("%s@%s"% (blockName, mdPath), emlib.MD_APPEND) return [self.createDataView(mdPath)]
[docs] def createVolumesSqlite(self, files, path, samplingRate, updateItemCallback=None): cleanPath(path) volSet = emobj.SetOfVolumes(filename=path) volSet.setSamplingRate(samplingRate) for volFn in files: vol = emobj.Volume() vol.setFileName(volFn) if updateItemCallback: updateItemCallback(vol) volSet.append(vol) volSet.write() volSet.close() return volSet
[docs] def viewVolumesSqlite(self, volumes): path = self.protocol._getExtraPath('viewer_volumes.sqlite') samplingRate = self.protocol.inputParticles.get().getSamplingRate() self.createVolumesSqlite(volumes, path, samplingRate) return [ObjectView(self._project, self.protocol.strId(), path)]
def _showVolumesChimera(self, volumes): """ Create a chimera script to visualize selected volumes. """ if len(volumes) > 1: cmdFile = self.protocol._getExtraPath('chimera_volumes.cxc') f = open(cmdFile, 'w+') f.write('windowsize 800 600\n') for volFn in volumes: vol = os.path.relpath(volFn, self.protocol._getExtraPath()) f.write("open %s\n" % vol) f.write('tile\n') f.close() view = ChimeraView(cmdFile) else: #view = CommandView('xmipp_chimera_client --input "%s" --mode projector 256 &' % volumes[0]) view = ChimeraClientView(volumes[0], showProjection=True) return [view] def _showVolumes(self, volumes): if self.displayVolWith == VOLUME_CHIMERA: return self._showVolumesChimera(volumes) elif self.displayVolWith == VOLUME_SLICES: #return self._createVolumesMd(volumes) return self.viewVolumesSqlite(volumes) def _volFileNames(self, volTemplate): volumes = [] for it in self._iterations: for ref3d in self._refsList: volFn = self.protocol._getFileName(volTemplate, iter=it, ref=ref3d) if exists(volFn): volumes.append(volFn) else: print("Volume %s does not exist" % volFn) return volumes def _showRefs(self, paramName=None): volumes = self._volFileNames('maskedFileNamesIters') return self._showVolumes(volumes) def _showRecons(self, paramName=None): volumes = self._volFileNames('reconstructedFileNamesIters') return self._showVolumes(volumes) def _showFilVols(self, paramName=None): volumes = self._volFileNames('reconstructedFilteredFileNamesIters') return self._showVolumes(volumes) def _showBfactorVols(self, paramName=None): volsBfactor = [] guinierPlots = [] volumes = self._volFileNames('reconstructedFileNamesIters') for vol in volumes: volBfactor = vol + '.bfactor' volsBfactor.append(volBfactor) args = '-i %(vol)s --sampling %(samplingRate)s --maxres %(maxRes)s -o %(volBfactor)s ' + self.correctBfactorExtraCommand.get() maxRes = self.maxRes.get() samplingRate = self.protocol.resolSam args = args % locals() hostConfig = self.protocol.getHostConfig() # Create the steps executor executor = StepExecutor(hostConfig) self.protocol.setStepsExecutor(executor) # Finally run the protocol self.protocol.runJob("xmipp_volume_correct_bfactor", args, numberOfMpi=1) guinierPlots.append(self._showGuinier(volBfactor)) return self._showVolumes(volsBfactor) + guinierPlots #=============================================================================== # Show Library, Classes and Images #=============================================================================== def _showLibraryOrClasses(self, paramName=None): choice = self.displayLibraryOrClasses.get() if choice == DISPLAY_LIBRARY: return self._showProjMatchLibrary(paramName) elif choice == 1: return self._showProjMatchClasses(paramName) else: return self._showProjMatchLibAndClasses(paramName) def _showProjMatchLibrary(self, paramName=None): #map stack position with ref number list = [] mdIn = emlib.MetaData() mdOut = emlib.MetaData() cleanPattern(self.protocol._getExtraPath('references_library*')) for ref3d in self._refsList: for it in self._iterations: convert_refno_to_stack_position = {} file_name = self.protocol._getFileName('projectLibrarySampling', iter=it, ref=ref3d) file_nameReferences = 'projectionDirections@' + file_name #last reference name if exists(file_name): mdReferences = emlib.MetaData(file_nameReferences) mdReferencesSize = mdReferences.size() for id in mdReferences: convert_refno_to_stack_position[mdReferences.getValue(emlib.MDL_NEIGHBOR,id)]=id file_nameAverages = self.protocol._getFileName('outClassesXmd', iter=it, ref=ref3d) if exists(file_nameAverages): # print("OutClassesXmd %s" % OutClassesXmd) mdIn.read(file_nameAverages) mdOut.clear() for i in mdIn: # id1=mdOut.addObject() # mdOut.setValue(MDL_IMAGE,mdIn.getValue(MDL_IMAGE,i),id1) ref2D = mdIn.getValue(emlib.MDL_REF,i) file_references = self.protocol._getFileName('projectLibraryStk', iter=it, ref=ref3d) file_reference = emlib.FileName() file_reference.compose(convert_refno_to_stack_position[ref2D],file_references) id2=mdOut.addObject() mdOut.setValue(emlib.MDL_IMAGE, file_reference, id2) if mdOut.size() == 0: print("Empty metadata: ", file_nameReferences) else: file_nameReferences = self.protocol._getExtraPath('references_library.xmd') sfn = createUniqueFileName(file_nameReferences) file_nameReferences = 'projectionDirections@' + sfn mdOut.write(file_nameReferences) list.append(self.createDataView(file_nameReferences)) else: print("File %s does not exist" % file_name) return list def _showProjMatchClasses(self, paramName=None): classes = [] for ref3d in self._refsList: for it in self._iterations: classesFn = self.protocol._getFileName('outClassesXmd', iter=it, ref=ref3d) if exists(classesFn): _, _, _, _, size = emlib.MetaDataInfo(classesFn) if size == 0: print("Empty metadata: ", classesFn) else: classes.append(self.createDataView(classesFn)) else: print("File %s does not exist" % classesFn) return classes def _showProjMatchLibAndClasses(self, paramName=None): #map stack position with ref number list = [] mdIn = emlib.MetaData() mdOut = emlib.MetaData() for ref3d in self._refsList: for it in self._iterations: convert_refno_to_stack_position = {} file_name = self.protocol._getFileName('projectLibrarySampling', iter=it, ref=ref3d) file_nameReferences = 'projectionDirections@' + file_name if exists(file_name): mdReferences = emlib.MetaData(file_nameReferences) mdReferencesSize = mdReferences.size() for id in mdReferences: convert_refno_to_stack_position[mdReferences.getValue(emlib.MDL_NEIGHBOR,id)]=id file_nameAverages = self.protocol._getFileName('outClassesXmd', iter=it, ref=ref3d) file_references = self.protocol._getFileName('projectLibraryStk', iter=it, ref=ref3d) if exists(file_nameAverages): mdIn.read(file_nameAverages) mdOut.clear() for i in mdIn: ref2D = mdIn.getValue(emlib.MDL_REF, i) file_reference = emlib.FileName() file_reference.compose(convert_refno_to_stack_position[ref2D],file_references) id1 = mdOut.addObject() mdOut.setValue(emlib.MDL_IMAGE, mdIn.getValue(emlib.MDL_IMAGE,i), id1) mdOut.setValue(emlib.MDL_IMAGE2, file_reference, id1) if mdOut.size() == 0: print("Empty metadata: ", file_nameReferences) else: file_nameReferences = self.protocol._getFileName('projectLibrarySampling', iter=it, ref=ref3d) sfn = createUniqueFileName(file_nameReferences) file_nameReferences = 'projectionDirections@' + sfn mdOut.merge(mdIn) mdOut.write(file_nameReferences) # ToDo: show the metadata in "metadata" form. list.append(self.createDataView(file_nameReferences)) else: print("File %s does not exist" % file_name) return list def _showProjMatchLibAndImages(self, paramName=None): from numpy import (array, dot) #map stack position with ref number imgAndClasses = [] mdIn = emlib.MetaData() mdOut = emlib.MetaData() mdTmp = emlib.MetaData() for ref3d in self._refsList: for it in self._iterations: convert_refno_to_stack_position = {} file_name = self.protocol._getFileName('projectLibrarySampling', iter=it, ref=ref3d) file_nameReferences = 'projectionDirections@' + file_name if exists(file_name): #last reference name mdReferences = emlib.MetaData(file_nameReferences) mdReferencesSize = mdReferences.size() for id in mdReferences: convert_refno_to_stack_position[mdReferences.getValue(emlib.MDL_NEIGHBOR,id)]=id file_nameImages = "ctfGroup[0-9][0-9][0-9][0-9][0-9][0-9]@" + self.protocol._getFileName('docfileInputAnglesIters', iter=it) mdTmp.read(file_nameImages)#query with ref3D mdIn.importObjects(mdTmp, emlib.MDValueEQ(emlib.MDL_REF3D, ref3d)) mdOut.clear() for i in mdIn: id1 = mdOut.addObject() mdOut.setValue(emlib.MDL_IMAGE, mdIn.getValue(emlib.MDL_IMAGE,i), id1) psi = -1. * mdIn.getValue(emlib.MDL_ANGLE_PSI, i) flip = mdIn.getValue(emlib.MDL_FLIP, i) if(flip): psi = -psi eulerMatrix = emlib.Euler_angles2matrix(0., 0., psi) x = mdIn.getValue(emlib.MDL_SHIFT_X, i) y = mdIn.getValue(emlib.MDL_SHIFT_Y, i) shift = array([x, y, 0]) shiftOut = dot(eulerMatrix, shift) [x,y,z] = shiftOut if flip: x = -x mdOut.setValue(emlib.MDL_ANGLE_PSI, psi, id1) mdOut.setValue(emlib.MDL_SHIFT_X, x, id1) mdOut.setValue(emlib.MDL_SHIFT_Y, y, id1) mdOut.setValue(emlib.MDL_FLIP, flip, id1) ref2D = mdIn.getValue(emlib.MDL_REF,i) file_references = self.protocol._getFileName('projectLibraryStk', iter=it, ref=ref3d) file_reference = emlib.FileName() file_reference.compose(convert_refno_to_stack_position[ref2D], file_references) id2 = mdOut.addObject() mdOut.setValue(emlib.MDL_IMAGE, file_reference, id2) mdOut.setValue(emlib.MDL_ANGLE_PSI, 0., id2) if mdOut.size() == 0: print("Empty metadata") else: file_nameReferences = self.protocol._getFileName('projectLibrarySampling', iter=it, ref=ref3d) sfn = createUniqueFileName(file_nameReferences) file_nameReferences = 'projectionDirections@' + sfn mdOut.write(file_nameReferences) imgAndClasses.append(self.createDataView(file_nameReferences)) else: print("File %s does not exist" % file_name) return imgAndClasses def _showDiscardedImages(self, paramName=None): md = emlib.MetaData() for it in self._iterations: file_name = self.protocol._getFileName('outClassesDiscarded', iter=it) if exists(file_name): md.read(file_name) if md.size() == 0: print("Empty metadata: ", file_name) else: return [self.createDataView(file_name)] else: print("File %s does not exist" % file_name) return [] def _showExperimentalImages(self, paramName=None): views = [] for ref3d in self._refsList: for it in self._iterations: partSet = self.protocol._getIterParticles(it) v = self.createScipionPartView(partSet) views.append(v) return views #=============================================================================== # Convergence #=============================================================================== def _plotHistogramAngularMovement(self, paramName=None): #from numpy import arange #from matplotlib.ticker import FormatStrFormatter plots = [] colors = ['g', 'b', 'r', 'y', 'c', 'm', 'k'] lenColors=len(colors) numberOfBins = self.numberOfBins.get() md = emlib.MetaData() for it in self._iterations: mdFn = self.protocol._mdDevitationsFn(it) if emlib.existsBlockInMetaDataFile(mdFn): md.read(mdFn) if not self.usePsi: md.fillConstant(emlib.MDL_ANGLE_PSI,0.) nrefs = len(self._refsList) gridsize = self._getGridSize(nrefs) xplotterShift = XmippPlotter(*gridsize, mainTitle='Iteration_%d\n' % it, windowTitle="ShiftDistribution") xplotter = XmippPlotter(*gridsize, mainTitle='Iteration_%d' % it, windowTitle="AngularDistribution") for ref3d in self._refsList: mDoutRef3D = emlib.MetaData() mDoutRef3D.importObjects(md, emlib.MDValueEQ(emlib.MDL_REF3D, ref3d)) _frequency = "Frequency (%d)" % mDoutRef3D.size() xplotterShift.createSubPlot("%s_ref3D_%d"%(emlib.label2Str(emlib.MDL_SHIFT_DIFF),ref3d), "pixels", _frequency) xplotter.createSubPlot("%s_ref3D_%d"%(emlib.label2Str(emlib.MDL_ANGLE_DIFF),ref3d), "degrees", _frequency) #mDoutRef3D.write("afterimportObject@mdIter.sqlite",MD_APPEND) xplotter.plotMd(mDoutRef3D, emlib.MDL_ANGLE_DIFF, emlib.MDL_ANGLE_DIFF, color=colors[ref3d%lenColors], #nbins=50 nbins=int(numberOfBins) )#if nbins is present do an histogram xplotterShift.plotMd(mDoutRef3D, emlib.MDL_SHIFT_DIFF, emlib.MDL_SHIFT_DIFF, color=colors[ref3d%lenColors], nbins=int(numberOfBins) )#if nbins is present do an histogram if self.angleSort: mDoutRef3D.sort(emlib.MDL_ANGLE_DIFF) fn = emlib.FileName() baseFileName = self.protocol._getExtraPath("angle_sort.xmd") fn = self.protocol._getRefBlockFileName("angle_iter", it, "ref3D", ref3d, baseFileName) mDoutRef3D.write(fn, emlib.MD_APPEND) print("File with sorted angles saved in:", fn) if self.shiftSort: mDoutRef3D.sort(emlib.MDL_SHIFT_DIFF) fn = emlib.FileName() baseFileName = self.protocol._getExtraPath("angle_sort.xmd") fn = self.protocol._getRefBlockFileName("shift_iter", it, "ref3D", ref3d, baseFileName) mDoutRef3D.write(fn, emlib.MD_APPEND) print("File with sorted shifts saved in:", fn) plots.append(xplotterShift) plots.append(xplotter) else: print("File %s does not exist" % mdFn) return plots #=============================================================================== # showAngularDistribution #=============================================================================== def _showAngularDistribution(self, paramName=None): views = [] if self.showAngDist == ANGDIST_CHIMERA: for it in self._iterations: angDist = self._createAngDistChimera(it) if angDist is not None: views.append(angDist) elif self.showAngDist == ANGDIST_2DPLOT: for it in self._iterations: angDist = self._createAngDist2D(it) if angDist is not None: views.append(angDist) return views def _createAngDistChimera(self, it): radius = self.spheresScale.get() if len(self._refsList) == 1: ref3d = self._refsList[0] classesFn = self.protocol._getFileName('outClassesXmd', iter=it, ref=ref3d) vol = self.protocol._getFileName('reconstructedFilteredFileNamesIters', iter=it, ref=ref3d) if exists(classesFn): tmpFilesPath = self.protocol._getExtraPath() volOrigin = self.protocol.outputVolume.getShiftsFromOrigin() return ChimeraAngDist(vol, tmpFilesPath, angularDistFile=classesFn, spheresDistance=radius, voxelSize=self.protocol.outputVolume.getSamplingRate(), volOrigin=volOrigin) else: print("File %s does not exist" % classesFn) return None else: return self.infoMessage('Please select only one class to display angular distribution') def _createAngDist2D(self, it): # Common variables to use nrefs = len(self._refsList) gridsize = self._getGridSize(nrefs) xplotter = XmippPlotter(*gridsize, mainTitle='Iteration %d' % it, windowTitle="Angular Distribution") for ref3d in self._refsList: classesFn = self.protocol._getFileName('outClassesXmd', iter=it, ref=ref3d) if exists(classesFn): md = emlib.MetaData(classesFn) title = 'Ref3D_%d' % ref3d xplotter.plotMdAngularDistribution(title, md) else: print("File %s does not exist" % classesFn) return None return xplotter #=============================================================================== # plotFSC #=============================================================================== def _showFSC(self, paramName=None): threshold = self.resolutionThreshold.get() nrefs = len(self._refsList) gridsize = self._getGridSize(nrefs) emlib.activateMathExtensions() for ref3d in self._refsList: xplotter = XmippPlotter(*gridsize, windowTitle='Resolution FSC') legends = [] show = False plot_title = 'Ref3D_%s' % ref3d a = xplotter.createSubPlot(plot_title, 'frequency(1/A)', 'FSC', yformat=False) legends = [] for it in self._iterations: file_name = self.protocol._getFileName('resolutionXmdFile', iter=it, ref=ref3d) if exists(file_name): show = True legends.append('iter %d' % it) self._plotFSC(a, file_name) xplotter.showLegend(legends) if show: if threshold < self.maxFrc: a.plot([self.minInv, self.maxInv],[threshold, threshold], color='black', linestyle='--') a.grid(True) else: raise Exception("Set a valid iteration to show its FSC") return [xplotter] def _plotFSC(self, a, mdFn): md = emlib.MetaData(mdFn) resolution_inv = [md.getValue(emlib.MDL_RESOLUTION_FREQ, id) for id in md] frc = [md.getValue(emlib.MDL_RESOLUTION_FRC, id) for id in md] self.maxFrc = max(frc) self.minInv = min(resolution_inv) self.maxInv = max(resolution_inv) a.plot(resolution_inv, frc) a.xaxis.set_major_formatter(self._plotFormatter) a.set_ylim([-0.1, 1.1]) #=============================================================================== # plotBfactor #=============================================================================== def _showGuinier(self, volume): nrefs = len(self._refsList) gridsize = self._getGridSize(nrefs) guinierFn = volume + ".guinier" d2 = self._getGuinierValue(guinierFn, 0) legends = ["lnFweighted ln(F)", "corrected ln(F)", "model"] xplotter = EmPlotter(*gridsize, windowTitle='Guinier Plots') subPlot = xplotter.createSubPlot(basename(volume), 'd^-2(A^-2)', 'ln(F)', yformat=False) for i, legend in enumerate(legends): y = self._getGuinierValue(guinierFn, i+2) subPlot.plot(d2, y) xplotter.showLegend(legends) subPlot.grid(True) return xplotter def _getGuinierValue(self, guinierFn, col): f1 = open(guinierFn) value = [] for l in f1: if not "#" in l: valList = l.split() val = float(valList[col]) value.append(val) f1.close() return value #=============================================================================== # Utils Functions #===============================================================================
[docs] def createScipionPartView(self, partSet, viewParams={}): inputParticlesId = self.protocol.inputParticles.get().strId() filename = partSet.getFileName() labels = 'enabled id _size _filename _transform._matrix' viewParams = {showj.ORDER:labels, showj.VISIBLE: labels, showj.RENDER:'_filename', 'labels': 'id', } return ObjectView(self._project, self.protocol.strId(), filename, other=inputParticlesId, # env=self._env, viewParams=viewParams)