def processImage(self, imgdata, filtarray):
if abs(self.params['apix'] - self.params['templateapix']) > 0.01:
#rescale templates, apix has changed
apTemplate.getTemplates(self.params)
### RUN FindEM
### save filter image to .dwn.mrc
imgpath = os.path.join(self.params['rundir'], imgdata['filename']+".dwn.mrc")
apImage.arrayToMrc(filtarray, imgpath, msg=False)
### run FindEM
looptdiff = time.time()-self.proct0
self.proct0 = time.time()
proctdiff = time.time()-self.proct0
f = open("template_image_timing.dat", "a")
datstr = "%d\t%.5f\t%.5f\n"%(self.stats['count'], proctdiff, looptdiff)
f.write(datstr)
f.close()
### run Template Correlation program
cclist = self.runTemplateCorrelator(imgdata)
### find peaks in map
peaktree = self.findPeaks(imgdata, cclist)
return peaktree
def processImage(self, imgdata, filtarray):
if abs(self.params['apix'] - self.params['templateapix']) > 0.01:
#rescale templates, apix has changed
apTemplate.getTemplates(self.params)
### RUN Signature
### save filter image to .dwn.mrc
imgpath = os.path.join(self.params['rundir'],
imgdata['filename'] + ".dwn.mrc")
apImage.arrayToMrc(filtarray, imgpath, msg=False)
### run Signature
looptdiff = time.time() - self.proct0
self.proct0 = time.time()
plist = apSignature.runSignature(imgdata, self.params)
proctdiff = time.time() - self.proct0
f = open("template_image_timing.dat", "a")
datstr = "%d\t%.5f\t%.5f\n" % (self.stats['count'], proctdiff,
looptdiff)
f.write(datstr)
f.close()
# convert list of particles to peaktree
peaktree = apSignature.partToPeakTree(plist, self.params['bin'])
return peaktree
def processImage(self, imgdata, filtarray):
if abs(self.params['apix'] - self.params['templateapix']) > 0.01:
#rescale templates, apix has changed
apTemplate.getTemplates(self.params)
### RUN FindEM
### save filter image to .dwn.mrc
imgpath = os.path.join(self.params['rundir'],
imgdata['filename'] + ".dwn.mrc")
apImage.arrayToMrc(filtarray, imgpath, msg=False)
### run FindEM
looptdiff = time.time() - self.proct0
self.proct0 = time.time()
proctdiff = time.time() - self.proct0
f = open("template_image_timing.dat", "a")
datstr = "%d\t%.5f\t%.5f\n" % (self.stats['count'], proctdiff,
looptdiff)
f.write(datstr)
f.close()
### run Template Correlation program
cclist = self.runTemplateCorrelator(imgdata)
### find peaks in map
peaktree = self.findPeaks(imgdata, cclist)
return peaktree
def preLoopFunctions(self):
if len(self.imgtree) > 0:
self.params['apix'] = apDatabase.getPixelSize(self.imgtree[0])
# CREATES TEMPLATES
# SETS params['templatelist'] AND self.params['templateapix']
apTemplate.getTemplates(self.params)
apDisplay.printColor("Template list: "+str(self.params['templatelist']), "cyan")
self.checkPreviousTemplateRun()
def preLoopFunctions(self):
if len(self.imgtree) > 0:
self.params['apix'] = apDatabase.getPixelSize(self.imgtree[0])
# CREATES TEMPLATES
# SETS params['templatelist'] AND self.params['templateapix']
apTemplate.getTemplates(self.params)
apDisplay.printColor(
"Template list: " + str(self.params['templatelist']), "cyan")
self.checkPreviousTemplateRun()
def createTemplateStack(self):
"""
takes the spider file and creates an average template of all particles
"""
templatestack = os.path.join(self.params['rundir'], "templatestack00.spi")
apFile.removeFile(templatestack, warn=True)
### hack to use standard filtering library
templateparams = {}
templateparams['apix'] = self.stack['apix']
templateparams['rundir'] = os.path.join(self.params['rundir'], "templates")
templateparams['templateIds'] = self.templatelist
templateparams['bin'] = self.params['bin']
templateparams['lowpass'] = self.params['lowpass']
templateparams['median'] = None
templateparams['pixlimit'] = None
print templateparams
apParam.createDirectory(os.path.join(self.params['rundir'], "templates"))
filelist = apTemplate.getTemplates(templateparams)
for mrcfile in filelist:
emancmd = ("proc2d templates/"+mrcfile+" "+templatestack
+" clip="+str(self.boxsize)+","+str(self.boxsize)
+" spider ")
if self.params['inverttemplates'] is True:
emancmd += " invert "
apEMAN.executeEmanCmd(emancmd, showcmd=False)
return templatestack
def createTemplateStack(self):
"""
takes the spider file and creates an average template of all particles
"""
templatestack = os.path.join(self.params['rundir'], "templatestack00.spi")
apFile.removeFile(templatestack, warn=True)
### hack to use standard filtering library
templateparams = {}
templateparams['apix'] = self.stack['apix']
templateparams['rundir'] = os.path.join(self.params['rundir'], "templates")
templateparams['templateIds'] = self.templatelist
templateparams['bin'] = self.params['bin']
templateparams['lowpass'] = self.params['lowpass']
templateparams['median'] = None
templateparams['pixlimit'] = None
print templateparams
apParam.createDirectory(os.path.join(self.params['rundir'], "templates"))
filelist = apTemplate.getTemplates(templateparams)
for mrcfile in filelist:
emancmd = ("proc2d templates/"+mrcfile+" "+templatestack
+" clip="+str(self.boxsize)+","+str(self.boxsize)
+" spider ")
if self.params['inverttemplates'] is True:
emancmd += " invert "
apEMAN.executeEmanCmd(emancmd, showcmd=False)
return templatestack
def createTemplateStack(self):
"""
convert spider template stack
"""
templatestack = os.path.join(self.params['rundir'],
"templatestack.spi")
apFile.removeFile(templatestack, warn=True)
### hack to use standard filtering library
templateparams = {}
templateparams['apix'] = self.stack['apix']
templateparams['rundir'] = os.path.join(self.params['rundir'],
"templates")
templateparams['templateIds'] = self.templatelist
templateparams['bin'] = self.params['bin']
templateparams['lowpass'] = self.params['lowpass']
templateparams['median'] = None
templateparams['pixlimit'] = None
print 'Converting reference templates:\n', templateparams
apParam.createDirectory(
os.path.join(self.params['rundir'], "templates"))
filelist = apTemplate.getTemplates(templateparams)
localclip = self.clipsize / self.params['bin']
for mrcfile in filelist:
emancmd = ("proc2d templates/" + mrcfile + " " + templatestack +
" clip=" + str(localclip) + "," + str(localclip) +
" edgenorm spiderswap ")
if self.params['inverttemplates'] is True:
emancmd += " invert "
apEMAN.executeEmanCmd(emancmd, showcmd=False)
return templatestack
def createOrientationReference(self):
"""
convert spider orientation reference
"""
orientref = os.path.join(self.params['rundir'], "orient.spi")
apFile.removeFile(orientref, warn=True)
#templatedata = apTemplate.getTemplateFromId(self.params['orientref'])
#templatefile = os.path.join(templatedata['path']['path'], templatedata['templatename'])
### hack to use standard filtering library
templateparams = {}
templateparams['apix'] = self.stack['apix']
templateparams['rundir'] = os.path.join(self.params['rundir'], "templates")
templateparams['templateIds'] = [self.params['orientref'],]
templateparams['bin'] = self.params['bin']
templateparams['lowpass'] = self.params['lowpass']
templateparams['median'] = None
templateparams['pixlimit'] = None
print 'Converting orientation reference:\n', templateparams
apParam.createDirectory(os.path.join(self.params['rundir'], "templates"))
filelist = apTemplate.getTemplates(templateparams)
mrcfile = filelist[0]
localclip = self.clipsize/self.params['bin']
emancmd = ("proc2d templates/"+mrcfile+" "+orientref
+" clip="+str(localclip)+","+str(localclip)
+" edgenorm spiderswap-single ")
if self.params['inverttemplates'] is True:
emancmd += " invert "
apEMAN.executeEmanCmd(emancmd, showcmd=False)
return orientref
def createTemplateStack(self):
"""
convert spider template stack
"""
templatestack = os.path.join(self.params['rundir'], "templatestack.spi")
apFile.removeFile(templatestack, warn=True)
### hack to use standard filtering library
templateparams = {}
templateparams['apix'] = self.stack['apix']
templateparams['rundir'] = os.path.join(self.params['rundir'], "templates")
templateparams['templateIds'] = self.templatelist
templateparams['bin'] = self.params['bin']
templateparams['lowpass'] = self.params['lowpass']
templateparams['median'] = None
templateparams['pixlimit'] = None
print 'Converting reference templates:\n', templateparams
apParam.createDirectory(os.path.join(self.params['rundir'], "templates"))
filelist = apTemplate.getTemplates(templateparams)
localclip = self.clipsize/self.params['bin']
for mrcfile in filelist:
emancmd = ("proc2d templates/"+mrcfile+" "+templatestack
+" clip="+str(localclip)+","+str(localclip)
+" edgenorm spiderswap ")
if self.params['inverttemplates'] is True:
emancmd += " invert "
apEMAN.executeEmanCmd(emancmd, showcmd=False)
return templatestack
def preLoopFunctions(self):
if len(self.imgtree) > 0:
self.params['apix'] = apDatabase.getPixelSize(self.imgtree[0])
# CREATES TEMPLATES
# SETS params['templatelist'] AND self.params['templateapix']
apTemplate.getTemplates(self.params)
apDisplay.printColor("Template list: "+str(self.params['templatelist']), "cyan")
self.checkPreviousTemplateRun()
# convert templates to single mrc stack for signature
tstack="templatestack.mrc"
twods=[]
for t in self.params['templatelist']:
twods.append(mrc.read(t))
imgar=numpy.array(twods)
mrc.write(imgar, tstack)
self.params['templatename']=tstack
def preLoopFunctions(self):
if len(self.imgtree) > 0:
self.params['apix'] = apDatabase.getPixelSize(self.imgtree[0])
# CREATES TEMPLATES
# SETS params['templatelist'] AND self.params['templateapix']
apTemplate.getTemplates(self.params)
apDisplay.printColor(
"Template list: " + str(self.params['templatelist']), "cyan")
self.checkPreviousTemplateRun()
# convert templates to single mrc stack for signature
tstack = "templatestack.mrc"
twods = []
for t in self.params['templatelist']:
twods.append(mrc.read(t))
imgar = numpy.array(twods)
mrc.write(imgar, tstack)
self.params['templatename'] = tstack
def processImage(self, imgdata, filtarray):
if abs(self.params['apix'] - self.params['templateapix']) > 0.01:
#rescale templates, apix has changed
apTemplate.getTemplates(self.params)
### RUN Signature
### save filter image to .dwn.mrc
imgpath = os.path.join(self.params['rundir'], imgdata['filename']+".dwn.mrc")
apImage.arrayToMrc(filtarray, imgpath, msg=False)
### run Signature
looptdiff = time.time()-self.proct0
self.proct0 = time.time()
plist = apSignature.runSignature(imgdata, self.params)
proctdiff = time.time()-self.proct0
f = open("template_image_timing.dat", "a")
datstr = "%d\t%.5f\t%.5f\n"%(self.stats['count'], proctdiff, looptdiff)
f.write(datstr)
f.close()
# convert list of particles to peaktree
peaktree = apSignature.partToPeakTree(plist,self.params['bin'])
return peaktree
def initializeTemplates(self):
"""
creates initial templates
"""
templatetime = time.time()
templatedir = os.path.join(self.params['rundir'], "templates")
apParam.createDirectory(templatedir)
### hack to use standard filtering library
templateparams = {}
templateparams['apix'] = self.stack['apix']
templateparams['rundir'] = templatedir
templateparams['templateIds'] = self.templatelist
templateparams['bin'] = self.params['bin']
templateparams['lowpass'] = self.params['lowpass']
templateparams['median'] = None
templateparams['pixlimit'] = None
filelist = apTemplate.getTemplates(templateparams)
templateselfile = os.path.join(self.params['rundir'], "templates.sel")
f = open(templateselfile, "w")
for mrcfile in filelist:
spifile = mrcfile[:-4] + ".xmp"
emancmd = ("proc2d templates/" + mrcfile + " templates/" +
spifile + " clip=" + str(self.clipsize) + "," +
str(self.clipsize) + " spiderswap-single ")
if self.params['inverttemplates'] is True:
emancmd += " invert "
apEMAN.executeEmanCmd(emancmd, showcmd=False)
if not os.path.isfile("templates/" + spifile):
apDisplay.printError("Template conversion failed")
temppath = os.path.join(self.params['rundir'],
"templates/" + spifile)
f.write(temppath + " 1\n")
f.close()
templatetime = time.time() - templatetime
apDisplay.printMsg("Template time: " +
apDisplay.timeString(templatetime))
return templateselfile
def initializeTemplates(self):
"""
creates initial templates
"""
templatetime = time.time()
templatedir = os.path.join(self.params['rundir'], "templates")
apParam.createDirectory(templatedir)
### hack to use standard filtering library
templateparams = {}
templateparams['apix'] = self.stack['apix']
templateparams['rundir'] = templatedir
templateparams['templateIds'] = self.templatelist
templateparams['bin'] = self.params['bin']
templateparams['lowpass'] = self.params['lowpass']
templateparams['median'] = None
templateparams['pixlimit'] = None
filelist = apTemplate.getTemplates(templateparams)
templateselfile = os.path.join(self.params['rundir'], "templates.sel")
f = open(templateselfile, "w")
for mrcfile in filelist:
spifile = mrcfile[:-4]+".xmp"
emancmd = ("proc2d templates/"+mrcfile+" templates/"+spifile
+" clip="+str(self.clipsize)+","+str(self.clipsize)
+" spiderswap-single ")
if self.params['inverttemplates'] is True:
emancmd += " invert "
apEMAN.executeEmanCmd(emancmd, showcmd=False)
if not os.path.isfile("templates/"+spifile):
apDisplay.printError("Template conversion failed")
temppath = os.path.join(self.params['rundir'], "templates/"+spifile)
f.write(temppath+" 1\n")
f.close()
templatetime = time.time() - templatetime
apDisplay.printMsg("Template time: "+apDisplay.timeString(templatetime))
return templateselfile
def createOrientationReference(self):
"""
convert spider orientation reference
"""
orientref = os.path.join(self.params['rundir'], "orient.spi")
apFile.removeFile(orientref, warn=True)
#templatedata = apTemplate.getTemplateFromId(self.params['orientref'])
#templatefile = os.path.join(templatedata['path']['path'], templatedata['templatename'])
### hack to use standard filtering library
templateparams = {}
templateparams['apix'] = self.stack['apix']
templateparams['rundir'] = os.path.join(self.params['rundir'],
"templates")
templateparams['templateIds'] = [
self.params['orientref'],
]
templateparams['bin'] = self.params['bin']
templateparams['lowpass'] = self.params['lowpass']
templateparams['median'] = None
templateparams['pixlimit'] = None
print 'Converting orientation reference:\n', templateparams
apParam.createDirectory(
os.path.join(self.params['rundir'], "templates"))
filelist = apTemplate.getTemplates(templateparams)
mrcfile = filelist[0]
localclip = self.clipsize / self.params['bin']
emancmd = ("proc2d templates/" + mrcfile + " " + orientref + " clip=" +
str(localclip) + "," + str(localclip) +
" edgenorm spiderswap-single ")
if self.params['inverttemplates'] is True:
emancmd += " invert "
apEMAN.executeEmanCmd(emancmd, showcmd=False)
return orientref
