def processAndSaveAllImages(self):
sys.stderr.write("Pre-processing images before picking\n")
count = 0
total = len(self.imgtree)
# if we are masking based on a previous mask run, and only want to process images with rejected masks,
# remove any images with accepted masks from the imgtree.
newImageTree = []
for imgdata in self.imgtree:
count += 1
# useAccecepted mask is true when the assess flag is used, and an
# accepted mask is found in the indicated mask run that should be retained
self.useAcceptedMask = False
# check to see if this image
# 1. Does not have a mask region
# 2. Has only mask regions that have been rejected
# If both are true, continue, otherwise we do not need to display this image.
filename = imgdata['filename']
maskAssessRunName = self.params['assessname']
sessiondata = apDatabase.getSessionDataFromSessionName(
self.params['sessionname'])
maskimg, maskbin = apMask.makeInspectedMask(
sessiondata, maskAssessRunName, imgdata)
if maskimg is not None and maskimg.size:
apDisplay.printMsg("Skipping image with accepted mask region.")
maskimg = apMask.reshapeMask(imgdata['image'], maskimg)
self.maskimg = maskimg
self.image = imgdata['image']
self.useAcceptedMask = True
self.commitToDatabase(imgdata)
continue
imgpath = os.path.join(self.params['rundir'],
imgdata['filename'] + '.dwn.mrc')
if self.params['continue'] is True and os.path.isfile(imgpath):
sys.stderr.write(".")
#print "already processed: ",apDisplay.short(imgdata['filename'])
else:
if os.path.isfile(imgpath):
os.remove(imgpath)
sys.stderr.write("#")
apFindEM.processAndSaveImage(imgdata, params=self.params)
newImageTree.append(imgdata)
if count % 60 == 0:
sys.stderr.write(" %d left\n" % (total - count))
self.imgtree = newImageTree
def loopProcessImage(self, imgdata):
"""
Over-writes the particleLoop processImage and uses the appionLoop processImage
"""
#GET THE TILT PAIR
tiltdata = apTiltPair.getTiltPair(imgdata)
if tiltdata is None:
return
### process images
procimgpath = os.path.join(self.params['rundir'],
imgdata['filename'] + '.dwn.mrc')
if not os.path.isfile(procimgpath):
apDisplay.printMsg("processing mrc for first image")
apFindEM.processAndSaveImage(imgdata, params=self.params)
procimg1 = apImage.mrcToArray(procimgpath, msg=False)
procimgpath = os.path.join(self.params['rundir'],
tiltdata['filename'] + '.dwn.mrc')
if not os.path.isfile(procimgpath):
apDisplay.printMsg("processing mrc for second image")
apFindEM.processAndSaveImage(tiltdata, params=self.params)
procimg2 = apImage.mrcToArray(procimgpath, msg=False)
#RUN THE ALIGNER GUI
result = self.runTiltAligner(imgdata, tiltdata)
if self.badprocess is True:
return
numpeaks = len(self.peaktree1)
#apDisplay.printMsg("Found "+str(numpeaks)+" particles for "+apDisplay.shortenImageName(imgdata['filename']))
self.stats['lastpeaks'] = numpeaks
### mask the images
procimg1, procimg2 = apTiltTransform.maskOverlapRegion(
procimg1, procimg2, self.data)
#CREATE PEAK JPEG
if self.threadJpeg is True:
threading.Thread(target=apPeaks.createTiltedPeakJpeg,
args=(imgdata, tiltdata, self.peaktree1,
self.peaktree2, self.params, procimg1,
procimg2)).start()
else:
apPeaks.createTiltedPeakJpeg(imgdata, tiltdata, self.peaktree1,
self.peaktree2, self.params, procimg1,
procimg2)
#EXTRA DONE DICT CALL
self._writeDoneDict(tiltdata['filename'])
def processAndSaveAllImages(self):
sys.stderr.write("Pre-processing images before picking\n")
count = 0
total = len(self.imgtree)
# if we are masking based on a previous mask run, and only want to process images with rejected masks,
# remove any images with accepted masks from the imgtree.
newImageTree = []
for imgdata in self.imgtree:
count += 1
# useAccecepted mask is true when the assess flag is used, and an
# accepted mask is found in the indicated mask run that should be retained
self.useAcceptedMask = False
# check to see if this image
# 1. Does not have a mask region
# 2. Has only mask regions that have been rejected
# If both are true, continue, otherwise we do not need to display this image.
filename = imgdata['filename']
maskAssessRunName = self.params['assessname']
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
maskimg,maskbin = apMask.makeInspectedMask( sessiondata, maskAssessRunName, imgdata )
if maskimg is not None and maskimg.size:
apDisplay.printMsg("Skipping image with accepted mask region.")
maskimg = apMask.reshapeMask( imgdata['image'], maskimg )
self.maskimg = maskimg
self.image = imgdata['image']
self.useAcceptedMask = True
self.commitToDatabase(imgdata)
continue
imgpath = os.path.join(self.params['rundir'], imgdata['filename']+'.dwn.mrc')
if self.params['continue'] is True and os.path.isfile(imgpath):
sys.stderr.write(".")
#print "already processed: ",apDisplay.short(imgdata['filename'])
else:
if os.path.isfile(imgpath):
os.remove(imgpath)
sys.stderr.write("#")
apFindEM.processAndSaveImage(imgdata, params=self.params)
newImageTree.append(imgdata)
if count % 60 == 0:
sys.stderr.write(" %d left\n" % (total-count))
self.imgtree = newImageTree
def processAndSaveAllImages(self):
sys.stderr.write("Pre-processing images before picking\n")
#print self.params
count = 0
total = len(self.imgtree)
for imgdata in self.imgtree:
count += 1
imgpath = os.path.join(self.params['rundir'], imgdata['filename']+'.dwn.mrc')
if self.params['continue'] is True and os.path.isfile(imgpath):
sys.stderr.write(".")
#print "already processed: ",apDisplay.short(imgdata['filename'])
else:
if os.path.isfile(imgpath):
os.remove(imgpath)
sys.stderr.write("#")
apFindEM.processAndSaveImage(imgdata, params=self.params)
if count % 60 == 0:
sys.stderr.write(" %d left\n" % (total-count))
def loopProcessImage(self, imgdata):
"""
Over-writes the particleLoop processImage and uses the appionLoop processImage
"""
#GET THE TILT PAIR
tiltdata = apTiltPair.getTiltPair(imgdata)
if tiltdata is None:
return
### process images
procimgpath = os.path.join(self.params['rundir'], imgdata['filename']+'.dwn.mrc')
if not os.path.isfile(procimgpath):
apDisplay.printMsg("processing mrc for first image")
apFindEM.processAndSaveImage(imgdata, params=self.params)
procimg1 = apImage.mrcToArray(procimgpath, msg=False)
procimgpath = os.path.join(self.params['rundir'], tiltdata['filename']+'.dwn.mrc')
if not os.path.isfile(procimgpath):
apDisplay.printMsg("processing mrc for second image")
apFindEM.processAndSaveImage(tiltdata, params=self.params)
procimg2 = apImage.mrcToArray(procimgpath, msg=False)
#RUN THE ALIGNER GUI
result = self.runTiltAligner(imgdata, tiltdata)
if self.badprocess is True:
return
numpeaks = len(self.peaktree1)
#apDisplay.printMsg("Found "+str(numpeaks)+" particles for "+apDisplay.shortenImageName(imgdata['filename']))
self.stats['lastpeaks'] = numpeaks
### mask the images
procimg1, procimg2 = apTiltTransform.maskOverlapRegion(procimg1, procimg2, self.data)
#CREATE PEAK JPEG
if self.threadJpeg is True:
threading.Thread(target=apPeaks.createTiltedPeakJpeg, args=(imgdata, tiltdata, self.peaktree1,
self.peaktree2, self.params, procimg1, procimg2)).start()
else:
apPeaks.createTiltedPeakJpeg(imgdata, tiltdata, self.peaktree1, self.peaktree2, self.params,
procimg1, procimg2)
#EXTRA DONE DICT CALL
self._writeDoneDict(tiltdata['filename'])
def processAndSaveAllImages(self):
print "Pre-processing images before picking\nNow is a good time to go get a candy bar"
count = 0
total = len(self.imgtree)
for imgdata in self.imgtree:
count += 1
tiltdata = apTiltPair.getTiltPair(imgdata)
if tiltdata is None:
#reject it
apDatabase.insertImgAssessmentStatus(imgdata, "notiltpair", False)
continue
#First the image
imgpath = os.path.join(self.params['rundir'], imgdata['filename']+'.dwn.mrc')
if os.path.isfile(imgpath):
sys.stderr.write(".")
#print "already processed: ",apDisplay.short(imgdata['filename'])
else:
sys.stderr.write("#")
#print "processing: ",apDisplay.short(imgdata['filename'])
apFindEM.processAndSaveImage(imgdata, params=self.params)
#Now for its tilt pair
tiltpath = os.path.join(self.params['rundir'], tiltdata['filename']+'.dwn.mrc')
if os.path.isfile(tiltpath):
sys.stderr.write(".")
#print "already processed: ",apDisplay.short(tiltdata['filename'])
else:
sys.stderr.write("#")
#print "processing: ",apDisplay.short(tiltdata['filename'])
apFindEM.processAndSaveImage(tiltdata, params=self.params)
if count % 30 == 0:
sys.stderr.write(" %d left\n" % (total-count))
### check if automation was already run
outname1 = os.path.basename(imgdata['filename'])+"."+self.getExtension()
outname2 = os.path.basename(tiltdata['filename'])+"."+self.getExtension()
outfile1 = os.path.join(self.params['pickdatadir'], outname1)
outfile2 = os.path.join(self.params['pickdatadir'], outname2)
if os.path.isfile(outfile1):
sys.stderr.write(",")
else:
### set important parameters
picks1 = self.getParticlePicks(imgdata, False)
picks2 = self.getParticlePicks(tiltdata, False)
pixdiam = self.params['diam']/self.params['apix']/self.params['bin']
tilt1 = apDatabase.getTiltAngleDeg(imgdata)
tilt2 = apDatabase.getTiltAngleDeg(tiltdata)
tiltdiff = abs(tilt2) - abs(tilt1)
tiltaxis = self.params['inittiltaxis']
### run tilt automation
if self.params['autopick'] is True and self.params['importalign'] is False:
if len(picks1) > 0 and len(picks2) > 0:
autotilter = autotilt.autoTilt()
result = autotilter.processTiltPair(imgpath, tiltpath, picks1, picks2,
tiltdiff, outfile1, pixdiam, tiltaxis, msg=False)
if os.path.isfile(outfile1):
if os.path.exists(outfile2):
os.remove(outfile2)
os.symlink(os.path.basename(outfile1), outfile2)
sys.stderr.write("%")
apDisplay.printMsg("done")
return
def processImage(self, imgdata, filterarray):
if self.params['sessionname'] is not None:
apFindEM.processAndSaveImage(imgdata, params=self.params)
self.runManualPicker(imgdata)
def runFindEM(imgdict, params, thread=False):
"""
runs a separate thread of findem.exe for each template
to get cross-correlation maps
"""
### check image
apFindEM.processAndSaveImage(imgdict, params)
dwnimgname = imgdict['filename'] + ".dwn.mrc"
if not os.path.isfile(dwnimgname):
apDisplay.printError("cound not find image to process: " + dwnimgname)
### check template
if len(params['templatelist']) < 1:
apDisplay.printError("templatelist == 0; there are no templates")
joblist = []
ccmapfilelist = []
t0 = time.time()
for i, templatename in enumerate(params['templatelist']):
classavg = i + 1
#DETERMINE OUTPUT FILE NAME
#CHANGE THIS TO BE 00%i in future
numstr = "%03d" % classavg
#numstr = str(classavg%10)+"00"
ccmapfile = "cccmaxmap" + numstr + ".mrc"
apFile.removeFile(ccmapfile)
#GET FINDEM RUN COMMANDS
feed = findEMString(classavg, templatename, dwnimgname, ccmapfile,
params)
#RUN THE PROGRAM
if thread is True:
job = findemjob(feed)
joblist.append(job)
job.start()
else:
execFindEM(feed)
#TO REMOVE LATER: Fake output
fakeOutput(dwnimgname, ccmapfile, params)
#STORE OUTPUT FILE
ccmapfilelist.append(ccmapfile)
### WAIT FOR THREADS TO COMPLETE
if thread is True:
apDisplay.printMsg("waiting for " + str(len(joblist)) +
" findem threads to complete")
for i, job in enumerate(joblist):
while job.isAlive():
sys.stderr.write(".")
time.sleep(1.5)
sys.stderr.write("\n")
apDisplay.printMsg("FindEM finished in " +
apDisplay.timeString(time.time() - t0))
for ccmapfile in ccmapfilelist:
if not os.path.isfile(ccmapfile):
apDisplay.printError("findem.exe did not run or crashed.\n")
return ccmapfilelist
def runFindEM(imgdict, params, thread=False):
"""
runs a separate thread of findem.exe for each template
to get cross-correlation maps
"""
### check image
apFindEM.processAndSaveImage(imgdict, params)
dwnimgname = imgdict['filename']+".dwn.mrc"
if not os.path.isfile(dwnimgname):
apDisplay.printError("cound not find image to process: "+dwnimgname)
### check template
if len(params['templatelist']) < 1:
apDisplay.printError("templatelist == 0; there are no templates")
joblist = []
ccmapfilelist = []
t0 = time.time()
for i,templatename in enumerate(params['templatelist']):
classavg = i + 1
#DETERMINE OUTPUT FILE NAME
#CHANGE THIS TO BE 00%i in future
numstr = "%03d" % classavg
#numstr = str(classavg%10)+"00"
ccmapfile="cccmaxmap"+numstr+".mrc"
apFile.removeFile(ccmapfile)
#GET FINDEM RUN COMMANDS
feed = findEMString(classavg, templatename, dwnimgname, ccmapfile, params)
#RUN THE PROGRAM
if thread is True:
job = findemjob(feed)
joblist.append(job)
job.start()
else:
execFindEM(feed)
#TO REMOVE LATER: Fake output
fakeOutput(dwnimgname,ccmapfile,params)
#STORE OUTPUT FILE
ccmapfilelist.append(ccmapfile)
### WAIT FOR THREADS TO COMPLETE
if thread is True:
apDisplay.printMsg("waiting for "+str(len(joblist))+" findem threads to complete")
for i,job in enumerate(joblist):
while job.isAlive():
sys.stderr.write(".")
time.sleep(1.5)
sys.stderr.write("\n")
apDisplay.printMsg("FindEM finished in "+apDisplay.timeString(time.time()-t0))
for ccmapfile in ccmapfilelist:
if not os.path.isfile(ccmapfile):
apDisplay.printError("findem.exe did not run or crashed.\n")
return ccmapfilelist
def processImage(self, imgdata,filterarray): if self.params['sessionname'] is not None: apFindEM.processAndSaveImage(imgdata, params=self.params) self.runManualLocalMasker(imgdata)
