def summary(self):
message = []
from protlib_xmipp import getMdSize
size = getMdSize(self.Input['micrographs'])
message.append("Movies aligned <%d>" % (size))
message.append("Input directory: [%s]" % self.PrevRun.WorkingDir)
return message
def validate(self):
errors = []
N1=getMdSize(self.Operand1)
Operation=self.Operation
checkDimensions=False
if Operation=='column' or Operation=='slice' or Operation=='row':
if not self.Operand2.isdigit():
errors.append('You should give a number for the column, slice or row')
elif Operation=='dot product':
if self.Operand2.isdigit():
errors.append('Second operand cannot be a number')
else:
checkDimensions=True
elif Operation=='plus' or Operation=='minus' or Operation=='multiply' or Operation=='divide' or Operation=='minimum' or \
Operation=='maximum':
if not self.Operand2.isdigit():
checkDimensions=True
if checkDimensions:
md1=MetaData(self.Operand1)
md2=MetaData(self.Operand2)
x1, y1, z1, _, _ = MetaDataInfo(md1)
x2, y2, z2, _, _ = MetaDataInfo(md2)
if x1!=x2 or y1!=y2 or z1!=z2:
errors.append("Image/Volume sizes in the two operands are not the same")
if md2.size()>1:
if md2.size()!=md1.size():
errors.append("The number of images/volumes in the two operands are not the same")
return errors
def getBestVolumes(log,WorkingDir,NRansac,NumVolumes,UseAll):
volumes = []
inliers = []
for n in range(NRansac):
fnAngles = os.path.join(WorkingDir,"tmp/angles_ransac%05d"%n+".xmd")
md=MetaData("inliers@"+fnAngles)
numInliers=md.getValue(MDL_WEIGHT,md.firstObject())
volumes.append(fnAngles)
inliers.append(numInliers)
index = sorted(range(inliers.__len__()), key=lambda k: inliers[k])
fnBestAngles = ''
threshold=getCCThreshold(WorkingDir)
i=NRansac-1
indx = 0
while i>=0 and indx<NumVolumes:
fnBestAngles = volumes[index[i]]
fnBestAnglesOut=os.path.join(WorkingDir,"volumeProposed%05d"%indx+".xmd")
copyFile(log,fnBestAngles,fnBestAnglesOut)
print("Best volume "+str(indx)+" = "+fnBestAngles)
if not UseAll:
runJob(log,"xmipp_metadata_utilities","-i %s -o %s --query select \"maxCC>%f \" --mode append" %(fnBestAnglesOut,fnBestAnglesOut,threshold))
if getMdSize(fnBestAnglesOut) > 0:
indx += 1
else:
indx += 1
i -= 1
# Remove unnecessary files
for n in range(NRansac):
fnAngles = os.path.join(WorkingDir,"tmp/angles_ransac%05d"%n+".xmd")
deleteFile(log, fnAngles)
def summary(self):
message=[]
if self.DoGenerateReferences:
N=self.NumberOfReferences
else:
from protlib_xmipp import getMdSize
N = getMdSize(self.RefMd)
message.append("MLTomo on [%s] with %d references" % (self.VolumeList, N))
return message
def summary(self):
message=[]
message.append(("Classification of [%s]"%self.InSelFile)+" into "+str(self.NumberOfReferences)+" classes")
levelFiles=glob.glob(self.WorkingDir+"/extra/level_??/level_classes.xmd")
if not levelFiles:
message.append("No class file has been generated")
else:
import time
levelFiles.sort()
lastLevelFile=levelFiles[-1]
date=time.ctime(os.path.getmtime(lastLevelFile))
lastLevel=int(re.search('level_(\d\d)',lastLevelFile).group(1))
iteration = getMdSize("info@"+lastLevelFile)
try:
size = getMdSize("classes@"+lastLevelFile)
message.append("Last iteration is %s from level %d with %d classes (at %s)"%(iteration,lastLevel, size,date))
except:
pass
return message
def postCl2d(log, WorkingDir, NumberOfReferences):
levelDirs=glob.glob(os.path.join(WorkingDir,"extra/level_??"))
createLink(log,os.path.join(WorkingDir,"extra/images.xmd"),os.path.join(WorkingDir,"images.xmd"))
if levelDirs:
levelDirs.sort()
lastLevelDir=levelDirs[-1]
fnLastLevelFile=os.path.join(lastLevelDir,"level_classes.xmd")
from protlib_xmipp import getMdSize
size = getMdSize("classes@"+fnLastLevelFile)
if size == NumberOfReferences:
createLink(log, fnLastLevelFile, os.path.join(WorkingDir,"classes.xmd"))
def summary(self):
micrographs, particles = countParticles(self.ExtraDir)
if self.TiltPairs:
suffix = "tilt pairs"
items = "pairs"
micrographs /= 2
particles /= 2
else:
suffix = "micrographs"
items = "particles"
from protlib_xmipp import getMdSize
size = getMdSize(self.MicrographsMd)
summary = ["Input: [%s] with <%u> %s" % (self.importDir, size, suffix),
"Number of %(items)s manually picked: <%(particles)d> (from <%(micrographs)d> micrographs)" % locals()]
md=xmipp.MetaData(self.MicrographsMd)
if not md.containsLabel(xmipp.MDL_CTF_MODEL):
summary.append(redStr("There is no CTF information in the input micrographs: "))
summary.append("[%s]"%self.MicrographsMd)
return summary
def preprocess(self):
import launch_job,xmipp
if self.DoFilter:
slope=max(self.Highpass/2,0.01)
fnOut=self.WorkingDir+'/preprocessedImages.stk'
self.selFileToUse=fnOut
if not self.doStep1 and os.path.exists(fnOut):
numberOfImages=xmipp.getImageSize(fnOut)[3]
from protlib_xmipp import getMdSize
size = getMdSize(self.InSelFile)
if size != numberOfImages:
self.doStep1 = True
if not stepPerformed("Step 1",self.WorkingDir + "/status.txt"):
self.doStep1 = True
if self.doStep1:
params= '-i '+str(self.InSelFile)+\
' --fourier_mask raised_cosine '+str(slope)+\
' -o '+fnOut
if self.Highpass>0 and self.Lowpass>0:
params+=" --band_pass "+str(self.Highpass)+" "+str(self.Lowpass)
elif self.Highpass>0:
params+=" --high_pass "+str(self.Highpass)
elif self.Lowpass>0:
params+=" --low_pass "+str(self.Lowpass)
launchJob("xmipp_fourier_filter",
params,
self.log,
False,
1,
1,
self.SystemFlavour)
# Update status
if os.path.exists(self.WorkingDir+'/preprocessedImages.stk'):
fh=open(self.WorkingDir + "/status.txt", "a")
fh.write("Step 1: Preprocessing finished at " + time.asctime() + "\n")
fh.close()
else:
self.selFileToUse=self.InSelFile
def subtractionScript(_log
,DocFileExp
,referenceStackDoc
,subtractedStack
,resultsImagesName
):
md = MetaData(DocFileExp)#experimental images
mdRotations = MetaData(md) #rotations
# Save Metadata with just rotations (shifts will be applied when reading)
mdRotations.setValueCol(MDL_SHIFT_X, 0.)
mdRotations.setValueCol(MDL_SHIFT_Y, 0.)
mdRotations.operate('anglePsi=-anglePsi')
mdResults = MetaData(mdRotations)
mdResults.operate('anglePsi=0')
#reference projection for a given defocus group
mdRef = MetaData(referenceStackDoc) #reference library
imgExp = Image()
imgRef = Image()
imgSub = Image()
stackResults = resultsImagesName+'.stk'
if (os.path.exists(stackResults)):
from protlib_xmipp import getMdSize
idResults = getMdSize(stackResults)
else:
idResults = 0
xmdResults = resultsImagesName+'.xmd'
if (os.path.exists(xmdResults)):
xmdOldResults = MetaData(xmdResults)
xmdOldResults.unionAll(mdResults)
mdResults = MetaData(xmdOldResults)
for id in md:
angRot = md.getValue(MDL_ANGLE_ROT, id)
angTilt = md.getValue(MDL_ANGLE_TILT, id)
psi = md.getValue(MDL_ANGLE_PSI, id)
# Search for the closest idRef
dist = -1.
distMin = 999.
for idRef in mdRef:
angRotRef = mdRef.getValue(MDL_ANGLE_ROT, idRef)
angTiltRef = mdRef.getValue(MDL_ANGLE_TILT, idRef)
dist = abs(float(angRotRef) - float(angRot)) + abs(float(angTiltRef) - float(angTilt))
if(dist < distMin or dist == -1):
refNum = idRef
distMin = dist
# Apply alignment as follows: shifts firt (while reading), then rotations
imgExp.readApplyGeo(md, id, True, DATA, ALL_IMAGES, False) # only_apply_shifts = true
imgExp.applyGeo(mdRotations, id, False, False)
imgRef.readApplyGeo(mdRef,refNum, False, DATA, ALL_IMAGES,False)
imgSub = imgExp - imgRef
imgSub.write('%06d@%s'%(id,subtractedStack))
imgExp.write('%06d@%s'%(id,subtractedStack+'exp'))
imgRef.write('%06d@%s'%(id,subtractedStack+'ref'))
mdRotations.setValue(MDL_IMAGE, '%06d@%s'%(id,subtractedStack), id)
# write protocols results
imgSub.write('%06d@%s'%(id + idResults, stackResults))
mdResults.setValue(MDL_IMAGE, '%06d@%s'%(id + idResults, stackResults), id + idResults)
mdRotations.operate('anglePsi=0')
mdRotations.write(subtractedStack.replace('.stk','.xmd'))
mdResults.write(xmdResults)