def _loadVisualizeItersAndRefs(self):
""" Load selected iterations and classes 3D for visualization mode. """
DisplayRef3DNo = self.parser.getTkValue('DisplayRef3DNo')
VisualizeIter = self.parser.getTkValue('VisualizeIter')
if DisplayRef3DNo == 'all':
self._visualizeRef3Ds = range(1, self.NumberOfClasses + 1)
else:
self._visualizeRef3Ds = getListFromRangeString(self.parser.getTkValue('SelectedRef3DNo'))
self._visualizeNrefs = len(self._visualizeRef3Ds)
lastIteration = self.lastIter()
firstIter = self.firstIter()
if VisualizeIter == 'last':
self._visualizeIterations = [lastIteration]
else:
self._visualizeIterations = getListFromRangeString(self.parser.getTkValue('SelectedIters'))
self._visualizeLastIteration = self._visualizeIterations[-1]
self._visualizeLastRef3D = self._visualizeRef3Ds[-1]
self._visualizeVolumesMode = self.parser.getTkValue('DisplayReconstruction')
from matplotlib.ticker import FuncFormatter
self._plotFormatter = FuncFormatter(self._formatFreq)
def validate(self):
errors = []
classSelection = getListFromRangeString(self.SelectedClasses)
blocks = getBlocksInMetaDataFile(self.ClassifMd)
self.ExtractDir = getWorkingDirFromRunName(self.ExtractionRun)
for classNo in classSelection:
blockName = "class%06d_images" % classNo
if not blockName in blocks:
errors.append("%s cannot be found at %s" % (blockName, self.ClassifMd))
if self.CenterMaxShift > 100 or self.CenterMaxShift < 0:
errors.append("Maximum shift must be in the range 0-100")
if self.LowPassFilter > 0.5 or self.LowPassFilter < 0:
errors.append("Low pass filter must be in the range 0-0.5")
files = [getImagesFilename(self.ExtractDir, s) for s in ["", "untilted", "tilted"]]
fnMicrographs = getProtocolFilename("micrographs", WorkingDir=self.ExtractDir)
files.append(fnMicrographs)
for f in files:
if not exists(f):
errors.append("Cannot find file: %s" % f)
if exists(fnMicrographs):
blocks = getBlocksInMetaDataFile(fnMicrographs)
if not "micrographPairs" in blocks:
errors.append("Cannot find block micrographPairs@" + fnMicrographs)
return errors
def visualize(self):
from protlib_utils import runShowJ
fnSubset=""
if self.WhatToShow=="Classes":
fnSubset=""
elif self.WhatToShow=="Class Cores":
fnSubset="_core"
elif self.WhatToShow=="Class Stable Cores":
fnSubset="_stable_core"
levelFiles=glob.glob(os.path.join(self.ExtraDir,"level_??/level_classes%s.xmd"%fnSubset))
if levelFiles:
levelFiles.sort()
lastLevelFile=levelFiles[-1]
if self.DoShowLast:
runShowJ("classes@"+lastLevelFile)
else:
listOfLevels = getListFromRangeString(self.LevelsToShow)
lastLevel=int(re.search('level_(\d\d)',lastLevelFile).group(1))
if max(listOfLevels)<=lastLevel:
files = "";
for level in listOfLevels:
fn=os.path.join(self.ExtraDir,"level_%02d/level_classes%s.xmd"%(level,fnSubset))
if os.path.exists(fn):
files+="classes_sorted@"+fn+" "
if files!="":
runShowJ(files)
if self.DoShowHierarchy:
fnHierarchy=self.getFilename("hierarchy",subset=fnSubset)
if os.path.exists(fnHierarchy):
from protlib_gui_ext import showTextfileViewer
showTextfileViewer(fnHierarchy,[fnHierarchy])
def visualize(self):
if self.DoShowList:
fnVolumes = self.workingDirPath('proposedVolumes.xmd')
runShowJ(fnVolumes)
if self.VolumesToShow!="":
listOfVolumes = getListFromRangeString(self.VolumesToShow)
for volume in listOfVolumes:
fnRoot=os.path.join(WorkingDir,'Structure00000_core_extended','proposedVolume%05d'%volume)
os.system("xmipp_chimera_client -i %s.vol --mode projector 256 --angulardist %s.xmd"%(fnRoot,fnRoot))
def visualize(self):
if self.DoShowList:
fnVolumes = self.workingDirPath('volumesProposed.xmd')
runShowJ(fnVolumes)
if self.VolumesToShow!="":
listOfVolumes = getListFromRangeString(self.VolumesToShow)
for volume in listOfVolumes:
fnRoot=self.workingDirPath('volumeProposed%05d'%int(volume))
os.system("xmipp_chimera_client -i %s.vol --mode projector 256 --angulardist %s.xmd"%(fnRoot,fnRoot))
def summary(self):
message = []
classSelection = getListFromRangeString(self.SelectedClasses)
message.append(
"Random conical tilt reconstruction of %d classes of [%s]" % (len(classSelection), self.ClassifMd)
)
import glob
reconstructedFiles = glob.glob(self.WorkingDir + "/rct_??????.vol")
if not reconstructedFiles:
message.append("No reconstruction has been generated")
else:
message.append(str(len(reconstructedFiles)) + " reconstructions have finished")
return message
def defineSteps(self):
self.insertStep("createDir", path=self.ExtraDir)
pickingDir = getWorkingDirFromRunName(self.ExtractionRun)
self.insertStep("createLink2", filename="acquisition_info.xmd", dirSrc=pickingDir, dirDest=self.WorkingDir)
classSelection = getListFromRangeString(self.SelectedClasses)
fnRCTClasses = self.extraPath("rct_classes.xmd")
self.insertStep(
"gatherPairs",
verifyfiles=[fnRCTClasses],
WorkingDir=self.WorkingDir,
ExtraDir=self.ExtraDir,
ClassSelection=classSelection,
ClassFile=self.ClassifMd,
ExtractDir=self.ExtractDir,
PickingDir=pickingDir,
)
mdClasses = MetaData("classes@" + self.ClassifMd)
hasImage = mdClasses.containsLabel(MDL_IMAGE)
for classId in mdClasses:
classNo = mdClasses.getValue(MDL_REF, classId)
if classNo in classSelection:
# Locate class representative
classImage = ""
if hasImage:
classImage = mdClasses.getValue(MDL_IMAGE, classId)
classNameIn = "class%06d_images@%s" % (classNo, fnRCTClasses)
classNameOut = self.extraPath("rct_images_%06d.xmd" % classNo)
classVolumeOut = self.workingDirPath("rct_%06d.vol" % classNo)
self.insertParallelStep(
"reconstructClass",
verifyfiles=[classNameOut, classVolumeOut],
WorkingDir=self.WorkingDir,
ExtraDir=self.ExtraDir,
ClassNameIn=classNameIn,
ClassNameOut=classNameOut,
ClassImage=classImage,
CenterMaxShift=self.CenterMaxShift,
ThinObject=self.ThinObject,
SkipTiltedTranslations=self.SkipTiltedTranslations,
ClassVolumeOut=classVolumeOut,
ReconstructAdditionalParams=self.ReconstructAdditionalParams,
DoLowPassFilter=self.DoLowPassFilter,
LowPassFilter=self.LowPassFilter,
parent_step_id=XmippProjectDb.FIRST_STEP,
)
def visualize(self):
classSelection = getListFromRangeString(self.SelectedClasses)
for classNo in classSelection:
fnVol = self.workingDirPath("rct_%06d.vol" % classNo)
if exists(fnVol):
runShowJ(fnVol)
