def printHelp(xmldict, exit=True):
"""
print out help info for a function with XML file
"""
paramlist = xmldict.keys()
paramlist.sort()
maxlen = 0
maxlentype = 0
for param in paramlist:
if len(param) > maxlen:
maxlen = len(param)
if 'type' in xmldict[param] and len(
xmldict[param]['type']) > maxlentype:
maxlentype = len(xmldict[param]['type'])
for param in paramlist:
if not 'alias' in xmldict[param] and \
(not 'modify' in xmldict[param] or str2bool(xmldict[param]['modify']) == True):
outstr = " "
outstr += apDisplay.color(apDisplay.rightPadString(param, maxlen),
"green")
outstr += " :"
if 'type' in xmldict[param] and xmldict[param]['type'] != None:
outstr += " (" + apDisplay.rightPadString(
xmldict[param]['type'] + ")", maxlentype + 1)
outstr += " :"
if 'required' in xmldict[param] and str2bool(
xmldict[param]['required']) == True:
outstr += apDisplay.color(" REQ", "red")
if 'description' in xmldict[
param] and xmldict[param]['description'] != None:
outstr += " " + xmldict[param]['description']
elif 'name' in xmldict[param] and xmldict[param]['name'] != None:
outstr += " " + xmldict[param]['name']
if 'default' in xmldict[
param] and xmldict[param]['default'] != None:
if 'nargs' in xmldict[param] and xmldict[param][
'nargs'] is not None and xmldict[param]['nargs'] > 1:
defstr = " (default: "
for i in range(len(xmldict[param]['default'])):
defstr += str(xmldict[param]['default'][i]) + ","
defstr = defstr[:-1] + ")"
outstr += apDisplay.color(defstr, "cyan")
else:
outstr += apDisplay.color(
" (default: " + str(xmldict[param]['default']) + ")",
"cyan")
if 'example' in xmldict[
param] and xmldict[param]['example'] != None:
outstr += " (example: " + str(xmldict[param]['example']) + ")"
print outstr
if exit is True:
sys.exit(1)
def printHelp(xmldict, exit=True):
"""
print out help info for a function with XML file
"""
paramlist = xmldict.keys()
paramlist.sort()
maxlen = 0
maxlentype = 0
for param in paramlist:
if len(param) > maxlen:
maxlen = len(param)
if 'type' in xmldict[param] and len(xmldict[param]['type']) > maxlentype:
maxlentype = len(xmldict[param]['type'])
for param in paramlist:
if not 'alias' in xmldict[param] and \
(not 'modify' in xmldict[param] or str2bool(xmldict[param]['modify']) == True):
outstr = " "
outstr += apDisplay.color(apDisplay.rightPadString(param,maxlen),"green")
outstr += " :"
if 'type' in xmldict[param] and xmldict[param]['type'] != None:
outstr += " ("+apDisplay.rightPadString(xmldict[param]['type']+")",maxlentype+1)
outstr += " :"
if 'required' in xmldict[param] and str2bool(xmldict[param]['required']) == True:
outstr += apDisplay.color(" REQ","red")
if 'description' in xmldict[param] and xmldict[param]['description'] != None:
outstr += " "+xmldict[param]['description']
elif 'name' in xmldict[param] and xmldict[param]['name'] != None:
outstr += " "+xmldict[param]['name']
if 'default' in xmldict[param] and xmldict[param]['default'] != None:
if 'nargs' in xmldict[param] and xmldict[param]['nargs'] is not None and xmldict[param]['nargs'] > 1:
defstr = " (default: "
for i in range(len(xmldict[param]['default'])):
defstr += str(xmldict[param]['default'][i])+","
defstr = defstr[:-1]+")"
outstr += apDisplay.color(defstr,"cyan")
else:
outstr += apDisplay.color(" (default: "+str(xmldict[param]['default'])+")","cyan")
if 'example' in xmldict[param] and xmldict[param]['example'] != None:
outstr += " (example: "+str(xmldict[param]['example'])+")"
print outstr
if exit is True:
sys.exit(1)
def printCtfSummary(params, imgtree):
"""
prints a histogram of the best ctfvalues for the session
"""
# if there are no images in the imgtree, there was no new processing done, so exit this function early.
if not imgtree:
apDisplay.printWarning("There are no new results to summarize.")
return
sys.stderr.write("processing CTF histogram...\n")
### get best ctf values for each image
ctfhistconf = []
ctfhistval = []
for imgdata in imgtree:
if params[
'norejects'] is True and apDatabase.getSiblingImgAssessmentStatus(
imgdata) is False:
continue
ctfq = appiondata.ApCtfData()
ctfq['image'] = imgdata
ctfvalues = ctfq.query()
### check if it has values
if ctfvalues is None:
continue
### find the best values
bestconf = 0.0
bestctfvalue = None
for ctfvalue in ctfvalues:
conf = calculateConfidenceScore(ctfvalue, False)
if conf > bestconf:
bestconf = conf
bestctfvalue = ctfvalue
ctfhistconf.append(bestconf)
ctfhistval.append(bestctfvalue)
ctfhistconf.sort()
confhist = {}
yspan = 20.0
minconf = ctfhistconf[0]
maxconf = ctfhistconf[len(ctfhistconf) - 1]
maxcount = 0
for conf in ctfhistconf:
c2 = round(conf * yspan, 0) / float(yspan)
if c2 in confhist:
confhist[c2] += 1
if confhist[c2] > maxcount:
maxcount = confhist[c2]
else:
confhist[c2] = 1
if maxcount > 70:
scale = 70.0 / float(maxcount)
sys.stderr.write(" * = " + str(round(scale, 1)) + " images\n")
else:
scale = 1.0
colorstr = {}
for i in range(int(yspan + 1)):
j = float(i) / yspan
if j < 0.5:
colorstr[j] = "red"
elif j < 0.8:
colorstr[j] = "yellow"
else:
colorstr[j] = "green"
sys.stderr.write("Confidence histogram:\n")
for i in range(int(yspan + 1)):
j = float(i) / yspan
if j < minconf - 1.0 / yspan:
continue
jstr = "%1.2f" % j
jstr = apDisplay.rightPadString(jstr, 5)
sys.stderr.write(jstr + "> ")
if j in confhist:
for k in range(int(confhist[j] * scale)):
sys.stderr.write(apDisplay.color("*", colorstr[j]))
sys.stderr.write("\n")
def printCtfSummary(params, imgtree):
"""
prints a histogram of the best ctfvalues for the session
"""
# if there are no images in the imgtree, there was no new processing done, so exit this function early.
if not imgtree:
apDisplay.printWarning("There are no new results to summarize.")
return
sys.stderr.write("processing CTF histogram...\n")
### get best ctf values for each image
ctfhistconf = []
ctfhistval = []
for imgdata in imgtree:
if params['norejects'] is True and apDatabase.getSiblingImgAssessmentStatus(imgdata) is False:
continue
ctfq = appiondata.ApCtfData()
ctfq['image'] = imgdata
ctfvalues = ctfq.query()
### check if it has values
if ctfvalues is None:
continue
### find the best values
bestconf = 0.0
bestctfvalue = None
for ctfvalue in ctfvalues:
conf = calculateConfidenceScore(ctfvalue,False)
if conf > bestconf:
bestconf = conf
bestctfvalue = ctfvalue
ctfhistconf.append(bestconf)
ctfhistval.append(bestctfvalue)
ctfhistconf.sort()
confhist = {}
yspan = 20.0
minconf = ctfhistconf[0]
maxconf = ctfhistconf[len(ctfhistconf)-1]
maxcount = 0
for conf in ctfhistconf:
c2 = round(conf*yspan,0)/float(yspan)
if c2 in confhist:
confhist[c2] += 1
if confhist[c2] > maxcount:
maxcount = confhist[c2]
else:
confhist[c2] = 1
if maxcount > 70:
scale = 70.0/float(maxcount)
sys.stderr.write(" * = "+str(round(scale,1))+" images\n")
else:
scale = 1.0
colorstr = {}
for i in range(int(yspan+1)):
j = float(i)/yspan
if j < 0.5:
colorstr[j] = "red"
elif j < 0.8:
colorstr[j] = "yellow"
else:
colorstr[j] = "green"
sys.stderr.write("Confidence histogram:\n")
for i in range(int(yspan+1)):
j = float(i)/yspan
if j < minconf-1.0/yspan:
continue
jstr = "%1.2f" % j
jstr = apDisplay.rightPadString(jstr,5)
sys.stderr.write(jstr+"> ")
if j in confhist:
for k in range(int(confhist[j]*scale)):
sys.stderr.write(apDisplay.color("*",colorstr[j]))
sys.stderr.write("\n")
