def _visualize(self, obj, **kwargs):
cls = type(obj)
if issubclass(cls, SetOfNormalModes):
fn = obj.getFileName()
from .viewer_nma import OBJCMD_NMA_PLOTDIST, OBJCMD_NMA_VMD
objCommands = "'%s' '%s'" % (OBJCMD_NMA_PLOTDIST, OBJCMD_NMA_VMD)
self._views.append(
ObjectView(self._project,
self.protocol.strId(),
fn,
obj.strId(),
viewParams={OBJCMDS: objCommands},
**kwargs))
elif issubclass(cls, XmippProtCTFMicrographs):
if obj.hasAttribute('outputCTF'):
ctfSet = obj.outputCTF
else:
mics = obj.inputMicrographs.get()
ctfSet = self.__createTemporaryCtfs(obj, mics)
if ctfSet.isEmpty():
self._views.append(
self.infoMessage("No CTF estimation has finished yet"))
else:
self.getCTFViews(ctfSet)
elif (issubclass(cls, XmippProtExtractParticles)
or issubclass(cls, XmippProtScreenParticles)):
particles = obj.outputParticles
self._visualize(particles)
fn = obj._getPath('images.xmd')
if os.path.exists(fn): # it doesnt unless cls is Xmipp
md = xmippLib.MetaData(fn)
# If Zscore on output images plot Zscore particle sorting
if md.containsLabel(xmippLib.MDL_ZSCORE):
from plotter import XmippPlotter
xplotter = XmippPlotter(
windowTitle="Zscore particles sorting")
xplotter.createSubPlot("Particle sorting",
"Particle number", "Zscore")
xplotter.plotMd(md, False, mdLabelY=xmippLib.MDL_ZSCORE)
self._views.append(xplotter)
# If VARscore on output images plot VARscore particle sorting
if md.containsLabel(xmippLib.MDL_SCORE_BY_VAR):
from plotter import XmippPlotter
xplotter = XmippPlotter(
windowTitle="Variance particles sorting")
xplotter.createSubPlot("Variance Histogram", "Variance",
"Number of particles")
xplotter.plotMd(md,
False,
mdLabelY=xmippLib.MDL_SCORE_BY_VAR,
nbins=100)
self._views.append(xplotter)
elif issubclass(cls, XmippProtDeepDenoising):
fn = obj.outputParticles.getFileName()
self._views.append(
ObjectView(self._project,
obj.outputParticles.strId(),
fn,
viewParams={
VISIBLE:
'enabled id _filename '
'_xmipp_corrDenoisedProjection '
'_xmipp_corrDenoisedNoisy '
'_xmipp_imageOriginal _xmipp_imageRef',
SORT_BY:
'id',
MODE:
MODE_MD
}))
elif issubclass(cls, XmippProtMovieGain):
self._visualize(obj.outputMovies)
movieGainMonitor = MonitorMovieGain(
obj,
workingDir=obj.workingDir.get(),
samplingInterval=60,
monitorTime=300,
stddevValue=0.04,
ratio1Value=1.15,
ratio2Value=4.5)
self._views.append(MovieGainMonitorPlotter(movieGainMonitor))
elif issubclass(cls, XmippProtRotSpectra):
self._visualize(
obj.outputClasses,
viewParams={
'columns': obj.SomXdim.get(),
RENDER: ' spectraPlot._filename average._filename',
ZOOM: 30,
VISIBLE:
'enabled id _size average._filename spectraPlot._filename',
'labels': 'id _size',
SORT_BY: 'id'
})
elif issubclass(cls, XmippProtKerdensom):
self._visualize(obj.outputClasses,
viewParams={
'columns': obj.SomXdim.get(),
'render':
'average._filename _representative._filename',
'labels': '_size',
'sortby': 'id'
})
elif issubclass(cls, XmippProtCompareReprojections):
fn = obj.outputParticles.getFileName()
labels = 'id enabled _index _xmipp_image._filename _xmipp_imageRef._filename _xmipp_imageResidual._filename _xmipp_imageCovariance._filename _xmipp_cost _xmipp_zScoreResCov _xmipp_zScoreResMean _xmipp_zScoreResVar _xmipp_continuousA _xmipp_continuousB _xmipp_continuousX _xmipp_continuousY'
labelRender = "_xmipp_image._filename _xmipp_imageRef._filename _xmipp_imageResidual._filename _xmipp_imageCovariance._filename"
self._views.append(
ObjectView(self._project,
obj.outputParticles.strId(),
fn,
viewParams={
ORDER: labels,
VISIBLE: labels,
SORT_BY: '_xmipp_cost asc',
RENDER: labelRender,
MODE: MODE_MD
}))
elif issubclass(cls, XmippProtCompareAngles):
fn = obj.outputParticles.getFileName()
labels = 'id enabled _index _filename _xmipp_shiftDiff _xmipp_angleDiff'
labelRender = "_filename"
self._views.append(
ObjectView(self._project,
obj.outputParticles.strId(),
fn,
viewParams={
ORDER: labels,
VISIBLE: labels,
SORT_BY: '_xmipp_angleDiff asc',
RENDER: labelRender,
MODE: MODE_MD
}))
elif issubclass(cls, XmippParticlePickingAutomatic):
micSet = obj.getInputMicrographs()
mdFn = getattr(micSet, '_xmippMd', None)
inTmpFolder = False
if mdFn:
micsfn = mdFn.get()
else: # happens if protocol is not an xmipp one
micsfn = self._getTmpPath(micSet.getName() +
'_micrographs.xmd')
writeSetOfMicrographs(micSet, micsfn)
inTmpFolder = True
posDir = obj._getExtraPath()
memory = showj.getJvmMaxMemory()
launchSupervisedPickerGUI(micsfn,
posDir,
obj,
mode='review',
memory=memory,
inTmpFolder=inTmpFolder)
elif issubclass(cls, XmippProtParticleBoxsize):
""" Launching a Coordinates viewer with only one coord in the center
with the estimated boxsize.
"""
micSet = obj.inputMicrographs.get()
coordsFn = self._getTmpPath(micSet.getName() +
'_coords_to_view.sqlite')
if not os.path.exists(coordsFn):
# Just creating the coords once
coordsSet = SetOfCoordinates(filename=coordsFn)
coordsSet.setBoxSize(obj.boxsize)
for mic in micSet:
coord = Coordinate()
coord.setMicrograph(mic)
coord.setPosition(mic.getXDim() / 2, mic.getYDim() / 2)
coordsSet.append(coord)
coordsSet.write()
else:
coordsSet = SetOfCoordinates(filename=coordsFn)
coordsSet.loadAllProperties()
coordsSet.setMicrographs(micSet)
coordsSet.setName(micSet.getName())
self._visualize(coordsSet)
# We need this case to happens before the ProtParticlePicking one
elif issubclass(cls, XmippProtAssignmentTiltPair):
if obj.getOutputsSize() >= 1:
coordsSet = obj.getCoordsTiltPair()
self._visualize(coordsSet)
elif issubclass(cls, XmippProtValidateNonTilt):
outputVols = obj.outputVolumes
labels = 'id enabled comment _filename weight'
self._views.append(
ObjectView(self._project,
outputVols.strId(),
outputVols.getFileName(),
viewParams={
MODE: MODE_MD,
VISIBLE: labels,
ORDER: labels,
SORT_BY: 'weight desc',
RENDER: '_filename'
}))
elif issubclass(cls, XmippProtMultiRefAlignability):
outputVols = obj.outputVolumes
labels = 'id enabled comment _filename weightAlignabilityPrecision weightAlignabilityAccuracy'
self._views.append(
ObjectView(self._project,
outputVols.strId(),
outputVols.getFileName(),
viewParams={
MODE: MODE_MD,
VISIBLE: labels,
ORDER: labels,
SORT_BY: 'weightAlignabilityAccuracy desc',
RENDER: '_filename'
}))
fn = obj.outputParticles.getFileName()
labels = 'id enabled _index _filename _xmipp_scoreAlignabilityAccuracy _xmipp_scoreAlignabilityPrecision'
labelRender = "_filename"
self._views.append(
ObjectView(self._project,
obj.outputParticles.strId(),
fn,
viewParams={
ORDER: labels,
VISIBLE: labels,
SORT_BY:
'_xmipp_scoreAlignabilityAccuracy desc',
RENDER: labelRender,
MODE: MODE_MD
}))
fn = obj._getExtraPath('vol001_pruned_particles_alignability.xmd')
md = xmippLib.MetaData(fn)
from .plotter import XmippPlotter
plotter = XmippPlotter()
plotter.createSubPlot('Soft-alignment validation plot',
'Angular Precision', 'Angular Accuracy')
plotter.plotMdFile(md,
xmippLib.MDL_SCORE_BY_ALIGNABILITY_PRECISION,
xmippLib.MDL_SCORE_BY_ALIGNABILITY_ACCURACY,
marker='.',
markersize=.55,
color='red',
linestyle='')
self._views.append(plotter)
elif issubclass(cls, XmippProtExtractParticlesPairs):
self._visualize(obj.outputParticlesTiltPair)
else:
# Use default visualization defined in base class
DataViewer._visualize(self, obj, **kwargs)
return self._views
def _visualize(self, obj, **args):
cls = type(obj)
if issubclass(cls, Volume):
fn = getImageLocation(obj)
self._views.append(ObjectView(self._project, obj.strId(), fn,
viewParams={RENDER: 'image',
SAMPLINGRATE: obj.getSamplingRate()}))
elif issubclass(cls, Image):
fn = getImageLocation(obj)
self._views.append(ObjectView(self._project, obj.strId(), fn))
elif issubclass(cls, SetOfNormalModes):
fn = obj.getFileName()
objCommands = "'%s' '%s'" % (OBJCMD_NMA_PLOTDIST, OBJCMD_NMA_VMD)
self._views.append(ObjectView(self._project, self.protocol.strId(),
fn, obj.strId(),
viewParams={OBJCMDS: objCommands}, **args))
elif issubclass(cls, SetOfMovies):
fn = obj.getFileName()
# Enabled for the future has to be available
labels = 'id _filename _samplingRate '
self._views.append(ObjectView(self._project, obj.strId(), fn,
viewParams={ORDER: labels,
VISIBLE: labels,
MODE: MODE_MD, RENDER: "no"}))
elif issubclass(cls, SetOfMicrographs):
fn = obj.getFileName()
self._views.append(ObjectView(self._project, obj.strId(), fn, **args))
elif issubclass(cls, MicrographsTiltPair):
labels = 'id enabled _untilted._filename _tilted._filename'
self._views.append(ObjectView(self._project, obj.strId(), obj.getFileName(),
viewParams={ORDER: labels,
VISIBLE: labels,
MODE: MODE_MD,
RENDER: '_untilted._filename _tilted._filename'}))
elif issubclass(cls, ParticlesTiltPair):
labels = 'id enabled _untilted._filename _tilted._filename'
self._views.append(ObjectView(self._project, obj.strId(), obj.getFileName(),
viewParams={ORDER: labels,
VISIBLE: labels,
RENDER:'_untilted._filename _tilted._filename',
MODE: MODE_MD}))
elif issubclass(cls, SetOfCoordinates):
micSet = obj.getMicrographs() # accessing mics to provide metadata file
if micSet is None:
raise Exception('visualize: SetOfCoordinates has no micrographs set.')
mdFn = getattr(micSet, '_xmippMd', None)
if mdFn:
fn = mdFn.get()
else: # happens if protocol is not an xmipp one
fn = self._getTmpPath(micSet.getName() + '_micrographs.xmd')
writeSetOfMicrographs(micSet, fn)
tmpDir = self._getTmpPath(obj.getName())
cleanPath(tmpDir)
makePath(tmpDir)
# FIXME: (JMRT) We are always writing the SetOfCoordinates and removing
# the tmpDir, we need to take into account if the user have pick
# some particles in the tmpDir and have not save them, that now
# will loose all picked particles.
# A possible solution could be to alert that changes have not been
# written during modification of tmpDir or create a new Xmipp picking
# protocol to continue picking later without loosing the coordinates.
writeSetOfCoordinates(tmpDir, obj)
self._views.append(CoordinatesObjectView(self._project, fn, tmpDir, self.protocol, inTmpFolder=True))
elif issubclass(cls, SetOfParticles):
fn = obj.getFileName()
labels = 'id enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling '
labels += '_ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle _transform._matrix'
self._views.append(ObjectView(self._project, obj.strId(), fn,
viewParams={ORDER: labels,
VISIBLE: labels,
'sortby': '_xmipp_zScore asc',
RENDER:'_filename'}))
elif issubclass(cls, SetOfVolumes):
fn = obj.getFileName()
labels = 'id enabled comment _filename '
self._views.append(ObjectView(self._project, obj.strId(), fn,
viewParams={MODE: MODE_MD,
ORDER: labels,
VISIBLE: labels,
RENDER: '_filename'}))
elif issubclass(cls, SetOfClasses2D):
fn = obj.getFileName()
self._views.append(ClassesView(self._project, obj.strId(), fn, **args))
elif issubclass(cls, SetOfClasses3D):
fn = obj.getFileName()
self._views.append(Classes3DView(self._project, obj.strId(), fn))
if issubclass(cls, XmippProtCTFMicrographs):
if obj.hasAttribute('outputCTF'):
ctfSet = obj.outputCTF
else:
mics = obj.inputMicrographs.get()
ctfSet = self.__createTemporaryCtfs(obj, mics)
if ctfSet.isEmpty():
self._views.append(self.infoMessage("No CTF estimation has finished yet"))
else:
self._views.append(CtfView(self._project, ctfSet))
elif issubclass(cls, SetOfCTF):
self._views.append(CtfView(self._project, obj))
elif issubclass(cls, CoordinatesTiltPair):
tmpDir = self._getTmpPath(obj.getName())
makePath(tmpDir)
mdFn = join(tmpDir, 'input_micrographs.xmd')
writeSetOfMicrographsPairs(obj.getUntilted().getMicrographs(),
obj.getTilted().getMicrographs(),
mdFn)
parentProtId = obj.getObjParentId()
parentProt = self.getProject().mapper.selectById(parentProtId)
extraDir = parentProt._getExtraPath()
# extraDir = parentProt._getExtraPath()
#TODO: Review this if ever a non Xmipp CoordinatesTiltPair is available
writeSetOfCoordinates(tmpDir, obj.getUntilted())
writeSetOfCoordinates(tmpDir, obj.getTilted())
launchTiltPairPickerGUI(mdFn, tmpDir, self.protocol)
elif issubclass(cls, XmippProtExtractParticles) or issubclass(cls, XmippProtScreenParticles):
particles = obj.outputParticles
self._visualize(particles)
fn = obj._getPath('images.xmd')
md = xmipp.MetaData(fn)
# If Zscore on output images plot Zscore particle sorting
if md.containsLabel(xmipp.MDL_ZSCORE):
from plotter import XmippPlotter
xplotter = XmippPlotter(windowTitle="Zscore particles sorting")
xplotter.createSubPlot("Particle sorting", "Particle number", "Zscore")
xplotter.plotMd(md, False, mdLabelY=xmipp.MDL_ZSCORE)
self._views.append(xplotter)
elif issubclass(cls, XmippProtRotSpectra):
self._visualize(obj.outputClasses,
viewParams={'columns': obj.SomXdim.get(),
RENDER: ' spectraPlot._filename average._filename',
ZOOM: 30,
VISIBLE: 'enabled id _size average._filename spectraPlot._filename',
'labels': 'id _size',
SORT_BY: 'id'})
elif issubclass(cls, XmippProtKerdensom):
self._visualize(obj.outputClasses, viewParams={'columns': obj.SomXdim.get(),
'render': 'average._filename _representative._filename',
'labels': '_size',
'sortby': 'id'})
elif issubclass(cls, XmippProtCompareReprojections):
fn = obj.outputParticles.getFileName()
labels = 'id enabled _index _xmipp_image._filename _xmipp_imageRef._filename _xmipp_imageResidual._filename _xmipp_imageCovariance._filename _xmipp_cost _xmipp_zScoreResCov _xmipp_zScoreResMean _xmipp_zScoreResVar _xmipp_continuousA _xmipp_continuousB _xmipp_continuousX _xmipp_continuousY'
labelRender = "_xmipp_image._filename _xmipp_imageRef._filename _xmipp_imageResidual._filename _xmipp_imageCovariance._filename"
self._views.append(ObjectView(self._project, obj.outputParticles.strId(), fn,
viewParams={ORDER: labels,
VISIBLE: labels,
SORT_BY: '_xmipp_cost asc', RENDER:labelRender,
MODE: MODE_MD}))
elif issubclass(cls, XmippParticlePickingAutomatic):
micSet = obj.getInputMicrographs()
mdFn = getattr(micSet, '_xmippMd', None)
inTmpFolder = False
if mdFn:
micsfn = mdFn.get()
else: # happens if protocol is not an xmipp one
micsfn = self._getTmpPath(micSet.getName() + '_micrographs.xmd')
writeSetOfMicrographs(micSet, micsfn)
inTmpFolder = True
posDir = obj._getExtraPath()
memory = '%dg'%obj.memory.get(),
launchSupervisedPickerGUI(micsfn, posDir, obj, mode='review', memory=memory, inTmpFolder=inTmpFolder)
# We need this case to happens before the ProtParticlePicking one
elif issubclass(cls, XmippProtAssignmentTiltPair):
if obj.getOutputsSize() >= 1:
coordsSet = obj.getCoordsTiltPair()
self._visualize(coordsSet)
elif issubclass(cls, ProtParticlePicking):
if obj.getOutputsSize() >= 1:
coordsSet = obj.getCoords()
self._visualize(coordsSet)
elif issubclass(cls, ProtMovieAlignment):
outputMics = obj.outputMicrographs
plotLabels = 'psdCorr._filename plotPolar._filename plotCart._filename'
labels = plotLabels + ' _filename '
objCommands = "'%s'" % (OBJCMD_MOVIE_ALIGNCARTESIAN)
self._views.append(ObjectView(self._project, self.protocol.strId(), outputMics.getFileName(),
viewParams={MODE: MODE_MD, ORDER: labels, VISIBLE: labels,
RENDER: plotLabels, ZOOM: 50,
OBJCMDS: objCommands}))
elif issubclass(cls, XmippProtValidateNonTilt):
outputVols = obj.outputVolumes
labels = 'id enabled comment _filename weight'
self._views.append(ObjectView(self._project, outputVols.strId(), outputVols.getFileName(),
viewParams={MODE: MODE_MD, VISIBLE:labels, ORDER: labels,
SORT_BY: 'weight desc', RENDER: '_filename'}))
elif issubclass(cls, XmippProtExtractParticlesPairs):
self._visualize(obj.outputParticlesTiltPair)
return self._views
def _visualize(self, obj, **kwargs):
cls = type(obj)
if issubclass(cls, Volume):
fn = getImageLocation(obj)
self._views.append(
ObjectView(self._project,
obj.strId(),
fn,
viewParams={
RENDER: 'image',
SAMPLINGRATE: obj.getSamplingRate()
}))
elif issubclass(cls, Image):
fn = getImageLocation(obj)
self._views.append(ObjectView(self._project, obj.strId(), fn))
elif issubclass(cls, SetOfNormalModes):
fn = obj.getFileName()
from nma.viewer_nma import OBJCMD_NMA_PLOTDIST, OBJCMD_NMA_VMD
objCommands = "'%s' '%s'" % (OBJCMD_NMA_PLOTDIST, OBJCMD_NMA_VMD)
self._views.append(
ObjectView(self._project,
self.protocol.strId(),
fn,
obj.strId(),
viewParams={OBJCMDS: objCommands},
**kwargs))
elif issubclass(cls, SetOfMovies):
fn = obj.getFileName()
# Enabled for the future has to be available
labels = 'id _filename _samplingRate '
self._views.append(
ObjectView(self._project,
obj.strId(),
fn,
viewParams={
ORDER: labels,
VISIBLE: labels,
MODE: MODE_MD,
RENDER: "no"
}))
elif issubclass(cls, SetOfMicrographs):
self._views.append(MicrographsView(self._project, obj, **kwargs))
elif issubclass(cls, MicrographsTiltPair):
labels = 'id enabled _untilted._filename _tilted._filename'
self._views.append(
ObjectView(self._project,
obj.strId(),
obj.getFileName(),
viewParams={
ORDER: labels,
VISIBLE: labels,
MODE: MODE_MD,
RENDER: '_untilted._filename _tilted._filename'
}))
elif issubclass(cls, ParticlesTiltPair):
labels = 'id enabled _untilted._filename _tilted._filename'
self._views.append(
ObjectView(self._project,
obj.strId(),
obj.getFileName(),
viewParams={
ORDER: labels,
VISIBLE: labels,
RENDER: '_untilted._filename _tilted._filename',
MODE: MODE_MD
}))
elif issubclass(cls, SetOfCoordinates):
micSet = obj.getMicrographs(
) # accessing mics to provide metadata file
if micSet is None:
raise Exception(
'visualize: SetOfCoordinates has no micrographs set.')
mdFn = getattr(micSet, '_xmippMd', None)
if mdFn:
fn = mdFn.get()
else: # happens if protocol is not an xmipp one
fn = self._getTmpPath(micSet.getName() + '_micrographs.xmd')
writeSetOfMicrographs(micSet, fn)
tmpDir = self._getTmpPath(obj.getName())
cleanPath(tmpDir)
makePath(tmpDir)
# FIXME: (JMRT) We are always writing the SetOfCoordinates and removing
# the tmpDir, we need to take into account if the user have pick
# some particles in the tmpDir and have not save them, that now
# will loose all picked particles.
# A possible solution could be to alert that changes have not been
# written during modification of tmpDir or create a new Xmipp picking
# protocol to continue picking later without loosing the coordinates.
writeSetOfCoordinates(tmpDir, obj)
self._views.append(
CoordinatesObjectView(self._project,
fn,
tmpDir,
self.protocol,
inTmpFolder=True))
elif issubclass(cls, SetOfParticles):
fn = obj.getFileName()
labels = 'id enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling '
labels += '_ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle _transform._matrix'
self._views.append(
ObjectView(self._project,
obj.strId(),
fn,
viewParams={
ORDER: labels,
VISIBLE: labels,
'sortby': '_xmipp_zScore asc',
RENDER: '_filename'
}))
elif issubclass(cls, SetOfVolumes):
fn = obj.getFileName()
labels = 'id enabled comment _filename '
self._views.append(
ObjectView(self._project,
obj.strId(),
fn,
viewParams={
MODE: MODE_MD,
ORDER: labels,
VISIBLE: labels,
RENDER: '_filename'
}))
elif issubclass(cls, SetOfClasses2D):
fn = obj.getFileName()
self._views.append(
ClassesView(self._project, obj.strId(), fn, **kwargs))
elif issubclass(cls, SetOfClasses3D):
fn = obj.getFileName()
self._views.append(Classes3DView(self._project, obj.strId(), fn))
elif issubclass(cls, SetOfImages):
fn = obj.getFileName()
self._views.append(
ObjectView(self._project, obj.strId(), fn, **kwargs))
if issubclass(cls, XmippProtCTFMicrographs):
if obj.hasAttribute('outputCTF'):
ctfSet = obj.outputCTF
else:
mics = obj.inputMicrographs.get()
ctfSet = self.__createTemporaryCtfs(obj, mics)
if ctfSet.isEmpty():
self._views.append(
self.infoMessage("No CTF estimation has finished yet"))
else:
self._views.append(CtfView(self._project, ctfSet))
elif issubclass(cls, SetOfCTF):
self._views.append(CtfView(self._project, obj))
elif issubclass(cls, CoordinatesTiltPair):
tmpDir = self._getTmpPath(obj.getName())
makePath(tmpDir)
mdFn = join(tmpDir, 'input_micrographs.xmd')
writeSetOfMicrographsPairs(obj.getUntilted().getMicrographs(),
obj.getTilted().getMicrographs(), mdFn)
parentProtId = obj.getObjParentId()
parentProt = self.getProject().mapper.selectById(parentProtId)
extraDir = parentProt._getExtraPath()
# extraDir = parentProt._getExtraPath()
#TODO: Review this if ever a non Xmipp CoordinatesTiltPair is available
writeSetOfCoordinates(tmpDir, obj.getUntilted())
writeSetOfCoordinates(tmpDir, obj.getTilted())
launchTiltPairPickerGUI(mdFn, tmpDir, self.protocol)
elif (issubclass(cls, XmippProtExtractParticles)
or issubclass(cls, XmippProtScreenParticles)):
particles = obj.outputParticles
self._visualize(particles)
fn = obj._getPath('images.xmd')
if os.path.exists(fn): # it doesnt unless cls is Xmipp
md = xmipp.MetaData(fn)
# If Zscore on output images plot Zscore particle sorting
if md.containsLabel(xmipp.MDL_ZSCORE):
from plotter import XmippPlotter
xplotter = XmippPlotter(
windowTitle="Zscore particles sorting")
xplotter.createSubPlot("Particle sorting",
"Particle number", "Zscore")
xplotter.plotMd(md, False, mdLabelY=xmipp.MDL_ZSCORE)
self._views.append(xplotter)
elif issubclass(cls, XmippProtRotSpectra):
self._visualize(
obj.outputClasses,
viewParams={
'columns': obj.SomXdim.get(),
RENDER: ' spectraPlot._filename average._filename',
ZOOM: 30,
VISIBLE:
'enabled id _size average._filename spectraPlot._filename',
'labels': 'id _size',
SORT_BY: 'id'
})
elif issubclass(cls, XmippProtKerdensom):
self._visualize(obj.outputClasses,
viewParams={
'columns': obj.SomXdim.get(),
'render':
'average._filename _representative._filename',
'labels': '_size',
'sortby': 'id'
})
elif issubclass(cls, XmippProtCompareReprojections):
fn = obj.outputParticles.getFileName()
labels = 'id enabled _index _xmipp_image._filename _xmipp_imageRef._filename _xmipp_imageResidual._filename _xmipp_imageCovariance._filename _xmipp_cost _xmipp_zScoreResCov _xmipp_zScoreResMean _xmipp_zScoreResVar _xmipp_continuousA _xmipp_continuousB _xmipp_continuousX _xmipp_continuousY'
labelRender = "_xmipp_image._filename _xmipp_imageRef._filename _xmipp_imageResidual._filename _xmipp_imageCovariance._filename"
self._views.append(
ObjectView(self._project,
obj.outputParticles.strId(),
fn,
viewParams={
ORDER: labels,
VISIBLE: labels,
SORT_BY: '_xmipp_cost asc',
RENDER: labelRender,
MODE: MODE_MD
}))
elif issubclass(cls, XmippParticlePickingAutomatic):
micSet = obj.getInputMicrographs()
mdFn = getattr(micSet, '_xmippMd', None)
inTmpFolder = False
if mdFn:
micsfn = mdFn.get()
else: # happens if protocol is not an xmipp one
micsfn = self._getTmpPath(micSet.getName() +
'_micrographs.xmd')
writeSetOfMicrographs(micSet, micsfn)
inTmpFolder = True
posDir = obj._getExtraPath()
memory = '%dg' % obj.memory.get(),
launchSupervisedPickerGUI(micsfn,
posDir,
obj,
mode='review',
memory=memory,
inTmpFolder=inTmpFolder)
# We need this case to happens before the ProtParticlePicking one
elif issubclass(cls, XmippProtAssignmentTiltPair):
if obj.getOutputsSize() >= 1:
coordsSet = obj.getCoordsTiltPair()
self._visualize(coordsSet)
elif issubclass(cls, ProtParticlePicking):
if obj.getOutputsSize() >= 1:
coordsSet = obj.getCoords()
self._visualize(coordsSet)
elif issubclass(cls, XmippProtValidateNonTilt):
outputVols = obj.outputVolumes
labels = 'id enabled comment _filename weight'
self._views.append(
ObjectView(self._project,
outputVols.strId(),
outputVols.getFileName(),
viewParams={
MODE: MODE_MD,
VISIBLE: labels,
ORDER: labels,
SORT_BY: 'weight desc',
RENDER: '_filename'
}))
elif issubclass(cls, XmippProtMultiRefAlignability):
outputVols = obj.outputVolumes
labels = 'id enabled comment _filename weightAlignabilityPrecision weightAlignabilityAccuracy'
self._views.append(
ObjectView(self._project,
outputVols.strId(),
outputVols.getFileName(),
viewParams={
MODE: MODE_MD,
VISIBLE: labels,
ORDER: labels,
SORT_BY: 'weightAlignabilityAccuracy desc',
RENDER: '_filename'
}))
fn = obj.outputParticles.getFileName()
labels = 'id enabled _index _filename _xmipp_scoreAlignabilityAccuracy _xmipp_scoreAlignabilityPrecision'
labelRender = "_filename"
self._views.append(
ObjectView(self._project,
obj.outputParticles.strId(),
fn,
viewParams={
ORDER: labels,
VISIBLE: labels,
SORT_BY:
'_xmipp_scoreAlignabilityAccuracy desc',
RENDER: labelRender,
MODE: MODE_MD
}))
fn = obj._getExtraPath('vol001_pruned_particles_alignability.xmd')
md = xmipp.MetaData(fn)
from plotter import XmippPlotter
from pyworkflow.em.plotter import EmPlotter
plotter = XmippPlotter()
plotter.createSubPlot('Soft-alignment validation plot',
'Angular Precision', 'Angular Accuracy')
plotter.plotMdFile(md,
xmipp.MDL_SCORE_BY_ALIGNABILITY_PRECISION,
xmipp.MDL_SCORE_BY_ALIGNABILITY_ACCURACY,
marker='.',
markersize=.55,
color='red',
linestyle='')
self._views.append(plotter)
elif issubclass(cls, XmippProtExtractParticlesPairs):
self._visualize(obj.outputParticlesTiltPair)
return self._views
def _visualize(self, obj, **args):
cls = type(obj)
def _getMicrographDir(mic):
""" Return an unique dir name for results of the micrograph. """
return obj._getExtraPath(removeBaseExt(mic.getFileName()))
def iterMicrographs(mics):
""" Iterate over micrographs and yield
micrograph name and a directory to process.
"""
for mic in mics:
micFn = mic.getFileName()
micDir = _getMicrographDir(mic)
yield (micFn, micDir, mic)
def visualizeCTFObjs(obj, setOfMics):
if exists(obj._getPath("ctfs_temporary.sqlite")):
os.remove(obj._getPath("ctfs_temporary.sqlite"))
self.protocol._createFilenameTemplates()
ctfSet = self.protocol._createSetOfCTF("_temporary")
for fn, micDir, mic in iterMicrographs(setOfMics):
ctfparam = self.protocol._getFileName('ctfparam', micDir=micDir)
if exists(ctfparam) or exists('xmipp_default_ctf.ctfparam'):
if not os.path.exists(ctfparam):
ctfparam = 'xmipp_default_ctf.ctfparam'
ctfModel = readCTFModel(ctfparam, mic)
self.protocol._setPsdFiles(ctfModel, micDir)
ctfSet.append(ctfModel)
if ctfSet.getSize() < 1:
raise Exception("Has not been completed the CTT estimation of any micrograph")
else:
ctfSet.write()
ctfSet.close()
self._visualize(ctfSet)
if issubclass(cls, Volume):
fn = getImageLocation(obj)
self._views.append(DataView(fn, viewParams={RENDER: 'image', SAMPLINGRATE: obj.getSamplingRate()}))
elif issubclass(cls, Image):
fn = getImageLocation(obj)
self._views.append(ObjectView(self._project, obj.strId(), fn))
elif issubclass(cls, SetOfNormalModes):
fn = obj.getFileName()
objCommands = "'%s' '%s'" % (OBJCMD_NMA_PLOTDIST, OBJCMD_NMA_VMD)
self._views.append(ObjectView(self._project, self.protocol.strId(), fn, viewParams={OBJCMDS: objCommands}, **args))
elif issubclass(cls, SetOfMovies):
fn = obj.getFileName()
# Enabled for the future has to be available
labels = 'id _filename _samplingRate '
self._views.append(ObjectView(self._project, obj.strId(), fn,
viewParams={ORDER: labels,
VISIBLE: labels,
MODE: MODE_MD, RENDER: "no"}))
elif issubclass(cls, SetOfMicrographs):
fn = obj.getFileName()
self._views.append(ObjectView(self._project, obj.strId(), fn, **args))
elif issubclass(cls, MicrographsTiltPair):
# fnU = obj.getUntilted().getFileName()
# fnT = obj.getTilted().getFileName()
# self._views.append(ObjectView(self._project.getName(), obj.strId(), fnU, **args))
# self._views.append(ObjectView(self._project.getName(), obj.strId(), fnT, **args))
labels = 'id enabled _untilted._filename _tilted._filename'
self._views.append(ObjectView(self._project, obj.strId(), obj.getFileName(),
viewParams={ORDER: labels,
VISIBLE: labels,
MODE: MODE_MD,
RENDER: '_untilted._filename _tilted._filename'}))
elif issubclass(cls, ParticlesTiltPair):
labels = 'id enabled _untilted._filename _tilted._filename'
self._views.append(ObjectView(self._project, obj.strId(), obj.getFileName(),
viewParams={ORDER: labels,
VISIBLE: labels, RENDER:'_untilted._filename _tilted._filename',
MODE: MODE_MD}))
elif issubclass(cls, SetOfCoordinates):
micSet = obj.getMicrographs() # accessing mics to provide metadata file
if micSet is None:
raise Exception('visualize: SetOfCoordinates has no micrographs set.')
mdFn = getattr(micSet, '_xmippMd', None)
tmpDir = self._getTmpPath(obj.getName())
makePath(tmpDir)
if mdFn:
fn = mdFn.get()
else: # happens if protocol is not an xmipp one
fn = self._getTmpPath(micSet.getName() + '_micrographs.xmd')
writeSetOfMicrographs(micSet, fn)
posDir = getattr(obj, '_xmippMd', None) # extra dir istead of md file for SetOfCoordinates
if posDir:
copyTree(posDir.get(), tmpDir)
else:
writeSetOfCoordinates(tmpDir, obj)
self._views.append(CoordinatesObjectView(self._project, fn, tmpDir))
elif issubclass(cls, SetOfParticles):
fn = obj.getFileName()
labels = 'id enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling '
labels += '_ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle _transform._matrix'
self._views.append(ObjectView(self._project, obj.strId(), fn,
viewParams={ORDER: labels,
VISIBLE: labels,
'sortby': '_xmipp_zScore asc', RENDER:'_filename'}))
elif issubclass(cls, SetOfVolumes):
fn = obj.getFileName()
labels = 'id enabled comment _filename '
self._views.append(ObjectView(self._project, obj.strId(), fn,
viewParams={MODE: MODE_MD, ORDER: labels, VISIBLE: labels, RENDER: '_filename'}))
elif issubclass(cls, SetOfClasses2D):
fn = obj.getFileName()
self._views.append(ClassesView(self._project, obj.strId(), fn, **args))
elif issubclass(cls, SetOfClasses3D):
fn = obj.getFileName()
self._views.append(Classes3DView(self._project, obj.strId(), fn))
if issubclass(cls, XmippProtCTFMicrographs) and not obj.hasAttribute("outputCTF"):
mics = obj.inputMicrographs.get()
visualizeCTFObjs(obj, mics)
elif obj.hasAttribute("outputCTF"):
self._visualize(obj.outputCTF)
elif issubclass(cls, SetOfCTF):
fn = obj.getFileName()
# self._views.append(DataView(fn, viewParams={MODE: 'metadata'}))
psdLabels = '_psdFile _xmipp_enhanced_psd _xmipp_ctfmodel_quadrant _xmipp_ctfmodel_halfplane'
labels = 'id enabled label %s _defocusU _defocusV _defocusAngle _defocusRatio ' \
'_xmipp_ctfCritFirstZero _xmipp_ctfCritCorr13 _xmipp_ctfCritFitting _xmipp_ctfCritNonAstigmaticValidity ' \
'_xmipp_ctfCritCtfMargin _micObj._filename' % psdLabels #TODO:CHECK IF _xmipp_ctfCritNonAstigmaticValidity AND _xmipp_ctfCritCtfMargin exist sometimes.
self._views.append(ObjectView(self._project, obj.strId(), fn,
viewParams={MODE: MODE_MD, ORDER: labels, VISIBLE: labels, ZOOM: 50, RENDER: psdLabels}))
elif issubclass(cls, CoordinatesTiltPair):
tmpDir = self._getTmpPath(obj.getName())
makePath(tmpDir)
mdFn = join(tmpDir, 'input_micrographs.xmd')
writeSetOfMicrographsPairs(obj.getUntilted().getMicrographs(),
obj.getTilted().getMicrographs(),
mdFn)
parentProtId = obj.getObjParentId()
parentProt = self.getProject().mapper.selectById(parentProtId)
extraDir = parentProt._getExtraPath()
extraDir = parentProt._getExtraPath()
#TODO: Review this if ever a non Xmipp CoordinatesTiltPair is available
# writeSetOfCoordinates(tmpDir, obj.getUntilted())
# writeSetOfCoordinates(tmpDir, obj.getTilted())
scipion = "%s \"%s\" %s" % (self.getProject().port, self.getProject().getDbPath(), obj.strId())
app = "xmipp.viewer.particlepicker.tiltpair.TiltPairPickerRunner"
args = " --input %(mdFn)s --output %(extraDir)s --mode readonly --scipion %(scipion)s"%locals()
runJavaIJapp("2g", app, args)
elif issubclass(cls, XmippProtExtractParticles) or issubclass(cls, XmippProtScreenParticles):
particles = obj.outputParticles
self._visualize(particles)
fn = obj._getPath('images.xmd')
md = xmipp.MetaData(fn)
# If Zscore on output images plot Zscore particle sorting
if md.containsLabel(xmipp.MDL_ZSCORE):
from plotter import XmippPlotter
xplotter = XmippPlotter(windowTitle="Zscore particles sorting")
xplotter.createSubPlot("Particle sorting", "Particle number", "Zscore")
xplotter.plotMd(md, False, mdLabelY=xmipp.MDL_ZSCORE)
self._views.append(xplotter)
elif issubclass(cls, XmippProtRotSpectra):
self._visualize(obj.outputClasses, viewParams={#'mode': 'rotspectra',
'columns': obj.SomXdim.get(),
RENDER: 'average._filename spectraPlot._filename',
VISIBLE: 'enabled id _size average._filename spectraPlot._filename',
'labels': '_size',
SORT_BY: 'id'})
elif issubclass(cls, XmippProtKerdensom):
self._visualize(obj.outputClasses, viewParams={'columns': obj.SomXdim.get(),
'render': 'average._filename _representative._filename',
'labels': '_size',
'sortby': 'id'})
elif issubclass(cls, XmippProtScreenClasses):
if isinstance(obj.inputSet.get(), SetOfClasses2D):
fn = obj.outputClasses
labels = 'id enabled _size _representative._filename _xmipp_imageRef _xmipp_image1 _xmipp_maxCC'
labelRender = "_representative._filename _xmipp_imageRef _xmipp_image1"
self._visualize(fn, viewParams={ORDER: labels,
VISIBLE: labels,
SORT_BY: '_xmipp_maxCC desc', RENDER:labelRender,
MODE: MODE_MD})
else:
fn = obj.outputAverages.getFileName()
labels = 'id enabled _filename _xmipp_imageRef _xmipp_image1 _xmipp_maxCC'
labelRender = "_filename _xmipp_imageRef _xmipp_image1"
self._views.append(ObjectView(self._project, obj.outputAverages.strId(), fn,
viewParams={ORDER: labels,
VISIBLE: labels,
SORT_BY: '_xmipp_maxCC desc', RENDER:labelRender,
MODE: MODE_MD}))
elif issubclass(cls, XmippProtProjectionOutliers):
if isinstance(obj.inputSet.get(), SetOfClasses2D):
fn = obj.outputClasses
labels = 'id enabled _size _representative._index _representative._filename _xmipp_maxCC _xmipp_zScoreResCov _xmipp_zScoreResMean _xmipp_zScoreResVar'
labelRender = "_representative._filename"
self._visualize(fn, viewParams={ORDER: labels,
VISIBLE: labels,
SORT_BY: '_xmipp_zScoreResCov desc', RENDER:labelRender})
else:
fn = obj.outputAverages.getFileName()
labels = 'id enabled _index _filename _xmipp_maxCC _xmipp_zScoreResCov _xmipp_zScoreResMean _xmipp_zScoreResVar _transform._matrix'
labelRender = "_filename"
self._views.append(ObjectView(self._project, obj.outputAverages.strId(), fn,
viewParams={ORDER: labels,
VISIBLE: labels,
SORT_BY: '_xmipp_zScoreResCov desc', RENDER:labelRender}))
elif issubclass(cls, XmippProtParticlePicking):
if obj.getOutputsSize() >= 1:
self._visualize(obj.getCoords())
elif issubclass(cls, XmippParticlePickingAutomatic):
micSet = obj.getInputMicrographs()
mdFn = getattr(micSet, '_xmippMd', None)
if mdFn:
micsfn = mdFn.get()
else: # happens if protocol is not an xmipp one
micsfn = self._getTmpPath(micSet.getName() + '_micrographs.xmd')
writeSetOfMicrographs(micSet, micsfn)
posDir = getattr(obj.getCoords(), '_xmippMd').get() # extra dir istead of md file for SetOfCoordinates
launchSupervisedPickerGUI(2, micsfn, posDir, 'review', obj)
elif issubclass(cls, XmippProtParticlePickingPairs):
tmpDir = self._getTmpPath(obj.getName())
makePath(tmpDir)
mdFn = join(tmpDir, 'input_micrographs.xmd')
writeSetOfMicrographsPairs(obj.outputCoordinatesTiltPair.getUntilted().getMicrographs(),
obj.outputCoordinatesTiltPair.getTilted().getMicrographs(),
mdFn)
extraDir = obj._getExtraPath()
launchTiltPairPickerGUI(obj.memory.get(), mdFn, extraDir, 'readonly', obj)
elif issubclass(cls, ProtMovieAlignment):
outputMics = obj.outputMicrographs
plotLabels = 'psdCorr._filename plotPolar._filename plotCart._filename'
labels = plotLabels + ' _filename '
objCommands = "'%s' '%s' '%s'" % (OBJCMD_MOVIE_ALIGNPOLAR, OBJCMD_MOVIE_ALIGNCARTESIAN, OBJCMD_MOVIE_ALIGNPOLARCARTESIAN)
self._views.append(ObjectView(self._project, outputMics.strId(), outputMics.getFileName(), viewParams={MODE: MODE_MD,
ORDER: labels, VISIBLE: labels, RENDER: plotLabels, 'zoom': 50,
OBJCMDS: objCommands}))
elif issubclass(cls, XmippProtValidateNonTilt):
outputVols = obj.outputVolumes
labels = 'id enabled comment _filename weight'
self._views.append(ObjectView(self._project, outputVols.strId(), outputVols.getFileName(), viewParams={MODE: MODE_MD,
VISIBLE:labels, ORDER: labels, SORT_BY: 'weight desc', RENDER: '_filename'}))
elif issubclass(cls, XmippProtExtractParticlesPairs):
self._visualize(obj.outputParticlesTiltPair)
return self._views
