def checkResult(self, testfiles, outDir, random):
error = ""
try:
from xmipp import FileName, Image, compareTwoFiles, compareTwoMetadataFiles
for file in testfiles:
file = join(outDir, file)
fileGoldStd = file.replace(self.fnDir, 'goldStandard')
result = True
if not exists(file):
error += file + " was NOT produced\n"
else:
if (random):
self.warning += file + " was created using a random seed, check skipped\n"
self.warningFlag = True
else:
fnGoldStd = FileName(fileGoldStd)
if fnGoldStd.isImage():
im1 = Image(fileGoldStd)
im2 = Image(file)
result = im1.equal(im2, 0.001)
elif fnGoldStd.isMetaData():
result = compareTwoMetadataFiles(file, fileGoldStd)
else:
result = compareTwoFiles(file, fileGoldStd, 0)
if not result:
error += " file '%s' and '%s' are NOT identical\n" % (
file, fileGoldStd)
except KeyboardInterrupt:
raise
except Exception, ex:
error += " Error checking results: '%s'\n" % str(ex)
def createMetaDataFromPattern(pattern, isStack=False, label="image"):
''' Create a metadata from files matching pattern'''
import glob
files = glob.glob(pattern)
files.sort()
from xmipp import MetaData, FileName, getImageSize, MDL_ENABLED, str2Label
label = str2Label(label) #Check for label value
mD = MetaData()
inFile = FileName()
nSize = 1
for file in files:
fileAux=file
if isStack:
if file.endswith(".mrc"):
fileAux=file+":mrcs"
x, x, x, nSize = getImageSize(fileAux)
if nSize != 1:
counter = 1
for jj in range(nSize):
inFile.compose(counter, fileAux)
objId = mD.addObject()
mD.setValue(label, inFile, objId)
mD.setValue(MDL_ENABLED, 1, objId)
counter += 1
else:
objId = mD.addObject()
mD.setValue(label, fileAux, objId)
mD.setValue(MDL_ENABLED, 1, objId)
return mD
def checkResult(self, testfiles, outDir, random):
error = ""
try:
from xmipp import FileName, Image, compareTwoFiles, compareTwoMetadataFiles
for file in testfiles:
file = join(outDir, file)
fileGoldStd = file.replace(self.fnDir, 'goldStandard')
result = True
if not exists(file):
error += file + " was NOT produced\n"
else:
if (random):
self.warning += file + " was created using a random seed, check skipped\n"
self.warningFlag = True
else:
fnGoldStd = FileName(fileGoldStd)
if fnGoldStd.isImage():
im1 = Image(fileGoldStd)
im2 = Image(file)
result = im1.equal(im2, 0.001)
elif fnGoldStd.isMetaData():
result = compareTwoMetadataFiles(file, fileGoldStd)
else:
result = compareTwoFiles(file, fileGoldStd, 0)
if not result:
error += " file '%s' and '%s' are NOT identical\n" % (file, fileGoldStd)
except KeyboardInterrupt:
raise
except Exception, ex:
error += " Error checking results: '%s'\n" % str(ex)
def estimateImageSize(input):
memory = 0
input = FileName(input)
if input.exists() and input.isImage():
(Xdim, Ydim, Zdim, Ndim) = xmipp.getImageSize(input)
memory = Xdim * Ydim * Zdim * Ndim * 8
return memory
def estimateFileNameSize(input):
from xmipp import FileName
if '@' in input:
trueFn = input.split('@')[1]
else:
trueFn = input
fn = FileName(trueFn);
if fn.isMetaData():
return estimateMDSize(fn)
elif fn.isImage():
return estimateImageSize(fn)
else:
return 0
def estimateMDSize(input):
from xmipp import FileName
memory = 0
fn = FileName(input);
if fn.exists():
MD = xmipp.MetaData(input)
if(MD.containsLabel(xmipp.MDL_IMAGE)):
for id in MD:
fnImg = MD.getValue(xmipp.MDL_IMAGE, id)
idMemory = estimateImageSize(fnImg)
memory = max(memory, idMemory)
return memory
def run(self):
xmdFileName = FileName(self.getParam('-i'))
emxFileName = self.getParam('-o')
if (emxFileName=='metadataXMIPP.emx'):
emxFileName = xmdFileName.withoutExtension()+'.emx'
mode = self.getParam('-m')
if exists(emxFileName):
remove(emxFileName)
emxData = EmxData()
#create emx files with mic CTF information
if mode == 'micCTF':
ctfMicXmippToEmx(emxData,xmdFileName)
elif mode == 'micCTFChallenge':
ctfMicXmippToEmxChallenge(emxData,xmdFileName)
elif mode == 'coordinates':
coorrXmippToEmx(emxData,xmdFileName)
elif mode == 'alignment':
alignXmippToEmx(emxData,xmdFileName)
emxData.write(emxFileName)
def importImages(log, InputFile, WorkingDir, DoCopy, ImportAll, SubsetMode, Nsubset):
imagesFn = getImagesFilename(WorkingDir)
fnInput = FileName(InputFile)
md = MetaData(InputFile)
#check if micrographs or ctfparam exists
doMic=False
doCTFParam=False
if md.containsLabel(MDL_MICROGRAPH):
doMic = True
if md.containsLabel(MDL_CTF_MODEL):
doCTFParam = True
if fnInput.isMetaData():
inputRelativePath = dirname(relpath(InputFile, '.'))
projectPath = findProjectPath(InputFile)
for id in md:
imgFn = md.getValue(MDL_IMAGE, id)
imgNo, imgFn = splitFilename(imgFn)
imgFn = xmippRelpath(fixPath(imgFn, projectPath, inputRelativePath, '.'))
if imgNo != None:
imgFn = "%s@%s" % (imgNo, imgFn)
md.setValue(MDL_IMAGE, imgFn, id)
#micrograph
if doMic:
imgFn = md.getValue(MDL_MICROGRAPH, id)
imgNo, imgFn = splitFilename(imgFn)
imgFn = xmippRelpath(fixPath(imgFn, projectPath, inputRelativePath, '.'))
if imgNo != None:
imgFn = "%s@%s" % (imgNo, imgFn)
md.setValue(MDL_MICROGRAPH, imgFn, id)
#ctf param
if doCTFParam:
ctfFn = md.getValue(MDL_CTF_MODEL, id)
ctfFn = xmippRelpath(fixPath(ctfFn, projectPath, inputRelativePath, '.'))
md.setValue(MDL_CTF_MODEL, ctfFn, id)
outExt = '.stk'
else:
outExt = '.%s' % fnInput.getExtension()
imagesStk = imagesFn.replace('.xmd', outExt)
writeImagesMd(log, md, ImportAll, SubsetMode, Nsubset, imagesFn, imagesStk, DoCopy)
def actionsToBePerformedInsideLoop(self):
_log = self.Log
_dataBase = self.Db
for indexCTFInsideLoop in range(1, self.defocusGroupNo+1):
if(self.doScaleImages):
inputSelfile = self.scaledImages +'.xmd'
else:
inputSelfile = self.getFilename('SubCurrentAnglesAllExpImgs')
if(self.DocFileExp == ''):
DocFileExpAux = self.getFilename('SubCurrentAnglesCftGroups', ctf=indexCTFInsideLoop)
else:
DocFileExpAux = self.DocFileExp
if(self.defocusGroupNo > 1):
if(self.doScaleImages):
_VerifyFiles = []
auxFilename = FileName(self.getFilename('SubCurrentAnglesCftGroups', ctf=indexCTFInsideLoop))
_VerifyFiles.append(auxFilename.removeBlockName())
id = self.Db.insertStep('joinImageCTFscale', verifyfiles = _VerifyFiles
, CTFgroupName = self.getFilename('DocCTFsBlocks', ctf=indexCTFInsideLoop)
, DocFileExp = DocFileExpAux
, inputSelfile = inputSelfile
)
else: #No scale
_VerifyFiles = []
auxFilename = FileName(self.getFilename('SubCurrentAnglesCftGroups', ctf=indexCTFInsideLoop))
_VerifyFiles.append(auxFilename.removeBlockName())
id = self.Db.insertStep('joinImageCTF', verifyfiles = _VerifyFiles
, CTFgroupName = self.getFilename('DocCTFsBlocks', ctf=indexCTFInsideLoop)
, DocFileExp = DocFileExpAux
, inputSelfile = inputSelfile
)
else: # No Ctf correction in ProjMatch
if(self.doScaleImages):
_VerifyFiles = []
id = self.Db.insertStep('joinImageCTFscale', verifyfiles = _VerifyFiles
, CTFgroupName = self.localFilenameCurrentAngles
, DocFileExp = DocFileExpAux
, inputSelfile = inputSelfile
)
else:
_VerifyFiles = []
id = self.Db.insertStep('joinImageCTF', verifyfiles = _VerifyFiles
, CTFgroupName = self.localFilenameCurrentAngles
, DocFileExp = DocFileExpAux
, inputSelfile = inputSelfile
)
#reconstruct each CTF group
_VerifyFiles = []
_VerifyFiles.append(self.getFilename('ReconstructedFileNamesIters', ctf=indexCTFInsideLoop))
id = self.Db.insertStep('reconstructVolume', verifyfiles = _VerifyFiles
, DocFileExp = DocFileExpAux
, MpiJobSize = self.MpiJobSize
, NumberOfMpi = self.NumberOfMpi
, NumberOfThreads = self.NumberOfThreads
, reconstructedVolume = self.getFilename('ReconstructedFileNamesIters', ctf=indexCTFInsideLoop)
, SymmetryGroup = self.SymmetryGroup)
#mask volume before projection
_VerifyFiles = []
auxFilename = FileName(self.getFilename('SubCurrentAnglesCftGroups', ctf=indexCTFInsideLoop))
_VerifyFiles.append(self.getFilename('ReconstructedMaskedFileNamesIters', ctf=indexCTFInsideLoop))
id = self.Db.insertStep('maskVolume', verifyfiles = _VerifyFiles
, dRradiusMax = self.dRradiusMax
, dRradiusMin = self.dRradiusMin
, maskReconstructedVolume = self.getFilename('ReconstructedMaskedFileNamesIters', ctf=indexCTFInsideLoop)
, reconstructedVolume = self.getFilename('ReconstructedFileNamesIters', ctf=indexCTFInsideLoop)
, NumberOfMpi = self.NumberOfMpi
, NumberOfThreads = self.NumberOfThreads)
#project reconstructe4d volumes
_VerifyFiles = []
_VerifyFiles.append(self.getFilename('ReferenceStack', ctf=indexCTFInsideLoop))
_VerifyFiles.append(self.getFilename('ReferenceStackDoc', ctf=indexCTFInsideLoop))
_VerifyFiles.append(self.getFilename('ReferenceStackSampling', ctf=indexCTFInsideLoop))
id = self.Db.insertStep('createProjections', verifyfiles = _VerifyFiles
, AngSamplingRateDeg = self.AngSamplingRateDeg
, DocFileExp = DocFileExpAux
, maskReconstructedVolume = self.getFilename('ReconstructedMaskedFileNamesIters', ctf=indexCTFInsideLoop)
, MaxChangeInAngles = self.MaxChangeInAngles
, MpiJobSize = self.MpiJobSize
, NumberOfMpi = self.NumberOfMpi
, NumberOfThreads = self.NumberOfThreads
, referenceStack = self.getFilename('ReferenceStack', ctf=indexCTFInsideLoop)
, SymmetryGroup = self.SymmetryGroup)
#project reconstructe4d volumes
_VerifyFiles = []
_VerifyFiles.append(self.getFilename('SubtractedStack', ctf=indexCTFInsideLoop))
_VerifyFiles.append(self.getFilename('SubtractedStack', ctf=indexCTFInsideLoop)+'ref')
_VerifyFiles.append(self.getFilename('SubtractedStack', ctf=indexCTFInsideLoop)+'exp')
id = self.Db.insertStep('subtractionScript', verifyfiles = _VerifyFiles
, DocFileExp = DocFileExpAux
, referenceStackDoc = self.getFilename('ReferenceStackDoc', ctf=indexCTFInsideLoop)
, subtractedStack = self.getFilename('SubtractedStack', ctf=indexCTFInsideLoop)
, resultsImagesName = self.resultsImagesName)
self.Db.connection.commit()