def visualize(self):
summaryFile = self.getFilename('micrographs')
if not exists(summaryFile): # Try to create partial summary file
summaryFile = summaryFile.replace(self.WorkingDir, self.TmpDir)
buildSummaryMetadata(self.WorkingDir, self.Input['micrographs'], summaryFile, self.MDL_TYPE)
if exists(summaryFile):
self.regenerateSummary(summaryFile)
runShowJ(summaryFile, extraParams = "--mode metadata --render psd psdEnhanced image1 image2 --order psd psdEnhanced image1 image2 --zoom 50")
else:
showWarning('Warning', 'There are not results yet',self.master)
def buildSummaryMetadata(WorkingDir,importMicrographs,summaryFile,MDL_TYPE):
md = xmipp.MetaData()
importMd = xmipp.MetaData(importMicrographs)
importMd.removeDisabled()
for id in importMd:
inputFile = importMd.getValue(MDL_TYPE,id)
micrographName = os.path.basename(inputFile)
shortname = replaceFilenameExt(micrographName, '')
micrographDir = join(WorkingDir, 'extra', shortname)
objId = md.addObject()
md.setValue(MDL_TYPE, inputFile, objId)
ctfparam = _getFilename('ctfparam', micrographDir=micrographDir)
labels = [xmipp.MDL_PSD, xmipp.MDL_PSD_ENHANCED, xmipp.MDL_CTF_MODEL,xmipp.MDL_IMAGE1, xmipp.MDL_IMAGE2]
if exists(ctfparam): # Get filenames
keys = ['psd', 'enhanced_psd', 'ctfparam', 'ctfmodel_quadrant', 'ctfmodel_halfplane']
values = [_getFilename(key, micrographDir=micrographDir) for key in keys]
else: # No files
values = ['NA'] * len(labels)
# Set values in metadata
for label, value in zip(labels, values):
md.setValue(label, value, objId)
if not md.isEmpty():
md.sort(MDL_TYPE)
md.write(summaryFile)
def gatherResults(log,
WorkingDir,
extraDir,
currProtMicrographClass,
currProtMicrograph,
currProtMicroscope,
currProtAcquisitionInfo,
prevProtMicrograph,
prevProtMicroscope,
prevProtAcquisitionInfo
):
import glob
#fnList=glob.glob(os.path.join(extraDir,'*_aligned.spi'))
copyFile(log,prevProtMicrograph,currProtMicrograph)
copyFile(log,prevProtMicroscope,currProtMicroscope)
copyFile(log,prevProtAcquisitionInfo,currProtAcquisitionInfo)
md=xmipp.MetaData(currProtMicrograph)
for id in md:
inputMovie = md.getValue(xmipp.MDL_MICROGRAPH, id)
movieNameList = os.path.basename(inputMovie)
movieName = os.path.splitext(movieNameList)[0]
file = _getFilename('movieAverage',movieDir=extraDir,baseName=movieName)
md.setValue(xmipp.MDL_MICROGRAPH,file,id)
if exists(file):
enabled = 1
else:
enabled = -1
md.setValue(xmipp.MDL_ENABLED,enabled)
md.sort(xmipp.MDL_MICROGRAPH)
md.write(currProtMicrographClass,xmipp.MD_APPEND)
def visualize(self):
summaryFile = self.getFilename('micrographs')
if exists(summaryFile):
runShowJ(summaryFile, extraParams = "--mode metadata")
else:
showWarning('Warning', 'There are not results yet',self.master)