def loopCommitToDatabase(self, imgdata):
"""
Over-writes the particleLoop commit and uses the appionLoop commit
"""
tiltdata = apTiltPair.getTiltPair(imgdata)
if tiltdata is None:
apDisplay.printWarning("Tilt data not found; not commiting data")
return False
### insert the runid
self.commitRunToDatabase(imgdata['session'], True)
if self.assess is not None:
#note runid is overrided to be 'run1'
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runname'], self.assess)
apDatabase.insertImgAssessmentStatus(tiltdata, self.params['runname'], self.assess)
if len(self.peaktree1) < 3 or len(self.peaktree1) < 3:
apDisplay.printWarning("Not enough particle picks; not commiting transform or particle data")
return False
### insert the transform
transdata = apTiltPair.insertTiltTransform(imgdata, tiltdata, self.tiltparams, self.params)
### insert the particles
self.insertParticlePeakPairs(imgdata, tiltdata, transdata)
def commitToDatabase(self, imgdata):
# if a kept mask was created in a previous mask run and the
# assess flag was used (basically combining the 2 runs) there is
# nothing new to commit.
if self.useAcceptedMask: return
sessiondata = imgdata['session']
rundir = self.params['rundir']
maskname = self.params['runname']
assessname = self.params['assessname']
bin = self.params['bin']
maskdir = os.path.join(rundir, "masks")
maskrundata, maskparamsdata = apMask.getMaskParamsByRunName(
maskname, sessiondata)
if not maskrundata:
apMask.insertManualMaskRun(sessiondata, rundir, maskname, bin)
maskrundata, maskparamsdata = apMask.getMaskParamsByRunName(
maskname, sessiondata)
try:
apParam.createDirectory(maskdir)
except:
apDisplay.printWarning('can not create mask directory')
massessrundata, exist = apMask.insertMaskAssessmentRun(
sessiondata, maskrundata, assessname)
mask = self.maskimg
maskfilename = imgdata['filename'] + '_mask.png'
image = self.image
labeled_regions, clabels = nd.label(mask)
testlog = [False, 0, ""]
infos = {}
infos, testlog = apCrud.getLabeledInfo(image, mask, labeled_regions,
range(1, clabels + 1), False,
infos, testlog)
offset = 1
for l1 in range(0, len(infos)):
l = l1 + offset
info = infos[l]
info.append(l)
regiondata = apMask.insertMaskRegion(maskrundata, imgdata, info)
print "Inserting mask region in database"
# PIL alpha channel read does not work
#apImage.arrayMaskToPngAlpha(mask, os.path.join(maskdir,maskfilename))
apImage.arrayMaskToPng(mask, os.path.join(maskdir, maskfilename))
allregiondata = apMask.getMaskRegions(maskrundata, imgdata)
for regiondata in allregiondata:
apMask.insertMaskAssessment(massessrundata, regiondata, 1)
print "Inserting mask assessment in database."
if self.assess != self.assessold and self.assess is not None:
#imageaccessor run is always named run1
apDatabase.insertImgAssessmentStatus(imgdata, 'run1', self.assess)
return
def commitToDatabase(self,imgdata):
# if a kept mask was created in a previous mask run and the
# assess flag was used (basically combining the 2 runs) there is
# nothing new to commit.
if self.useAcceptedMask: return
sessiondata = imgdata['session']
rundir = self.params['rundir']
maskname = self.params['runname']
assessname = self.params['assessname']
bin = self.params['bin']
maskdir=os.path.join(rundir,"masks")
maskrundata,maskparamsdata = apMask.getMaskParamsByRunName(maskname,sessiondata)
if not maskrundata:
apMask.insertManualMaskRun(sessiondata,rundir,maskname,bin)
maskrundata,maskparamsdata = apMask.getMaskParamsByRunName(maskname,sessiondata)
try:
apParam.createDirectory(maskdir)
except:
apDisplay.printWarning('can not create mask directory')
massessrundata,exist = apMask.insertMaskAssessmentRun(sessiondata,maskrundata,assessname)
mask = self.maskimg
maskfilename = imgdata['filename']+'_mask.png'
image = self.image
labeled_regions,clabels=nd.label(mask)
testlog = [False,0,""]
infos={}
infos,testlog=apCrud.getLabeledInfo(image,mask,labeled_regions,range(1,clabels+1),False,infos,testlog)
offset=1
for l1 in range(0,len(infos)):
l=l1+offset
info=infos[l]
info.append(l)
regiondata= apMask.insertMaskRegion(maskrundata,imgdata,info)
print "Inserting mask region in database"
# PIL alpha channel read does not work
#apImage.arrayMaskToPngAlpha(mask, os.path.join(maskdir,maskfilename))
apImage.arrayMaskToPng(mask, os.path.join(maskdir,maskfilename))
allregiondata = apMask.getMaskRegions(maskrundata,imgdata)
for regiondata in allregiondata:
apMask.insertMaskAssessment(massessrundata,regiondata,1)
print "Inserting mask assessment in database."
if self.assess != self.assessold and self.assess is not None:
#imageaccessor run is always named run1
apDatabase.insertImgAssessmentStatus(imgdata, 'run1', self.assess)
return
def commitToDatabase(self, imgdata):
"""
Uses the appionLoop commit
"""
msg = not self.params['background']
### insert False values
if self.imgassess is False:
time.sleep(0.1)
self.reject += 1
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runname'], False, msg=True)
f = open("imageRejectList-"+self.timestamp+".txt", "a")
f.write(imgdata['filename']+"\n")
f.close()
def commitToDatabase(self, imgdata):
"""
Uses the appionLoop commit
"""
msg = not self.params['background']
### insert False values
if self.imgassess is False:
time.sleep(0.1)
self.reject += 1
apDatabase.insertImgAssessmentStatus(imgdata,
self.params['runname'],
False,
msg=True)
f = open("imageRejectList-" + self.timestamp + ".txt", "a")
f.write(imgdata['filename'] + "\n")
f.close()
def commitToDatabase(self, imgdata):
"""
Uses the appionLoop commit
"""
imgassess = apDatabase.getImgCompleteStatus(imgdata)
tiltdata = apTiltPair.getTiltPair(imgdata)
msg = not self.params['background']
if tiltdata is None:
if imgassess is not False:
apDisplay.printColor("\nrejecting unpaired image: "+apDisplay.short(imgdata['filename']), "red")
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runid'], False, msg=msg)
self.reject+=1
return
if self.params['background'] is False:
apDisplay.printMsg("tiltpair: "+apDisplay.short(tiltdata['filename']))
tiltassess = apDatabase.getImgCompleteStatus(tiltdata)
if imgassess is False or tiltassess is False:
if imgassess is not False:
apDisplay.printColor("\nrejecting bad tilt images: "+apDisplay.short(imgdata['filename']), "magenta")
if tiltassess is not False:
apDisplay.printColor("\nrejecting bad tilt images: "+apDisplay.short(tiltdata['filename']), "magenta")
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runid'], False, msg=msg)
apDatabase.insertImgAssessmentStatus(tiltdata, self.params['runid'], False, msg=msg)
self.reject+=2
if self.params['background'] is False:
print "Assessment:", imgassess, tiltassess
return
def commitToDatabase(self, imgdata):
"""
Uses the appionLoop commit
"""
imgassess = apDatabase.getImgCompleteStatus(imgdata)
tiltdata = apTiltPair.getTiltPair(imgdata)
msg = not self.params['background']
if tiltdata is None:
if imgassess is not False:
apDisplay.printColor("\nrejecting unpaired image: "+apDisplay.short(imgdata['filename']), "red")
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runid'], False, msg=msg)
self.reject+=1
return
if self.params['background'] is False:
apDisplay.printMsg("tiltpair: "+apDisplay.short(tiltdata['filename']))
tiltassess = apDatabase.getImgCompleteStatus(tiltdata)
if imgassess is False or tiltassess is False:
if imgassess is not False:
apDisplay.printColor("\nrejecting bad tilt images: "+apDisplay.short(imgdata['filename']), "magenta")
if tiltassess is not False:
apDisplay.printColor("\nrejecting bad tilt images: "+apDisplay.short(tiltdata['filename']), "magenta")
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runid'], False, msg=msg)
apDatabase.insertImgAssessmentStatus(tiltdata, self.params['runid'], False, msg=msg)
self.reject+=2
if self.params['background'] is False:
print "Assessment:", imgassess, tiltassess
return
def commitToDatabase(self, imgdata, rundata): if self.assess != self.assessold and self.assess is not None: #imageaccessor run is always named run1 apDatabase.insertImgAssessmentStatus(imgdata, 'run1', self.assess) return
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
