def printCtfData(self, ctfvalue):
if ctfvalue is None:
return
defocusratio = ctfvalue['defocus2']/ctfvalue['defocus1']
if 'acerun' in ctfvalue:
method = getCtfMethod(ctfvalue)
runname = ctfvalue['acerun']['name']
sys.stderr.write("[%s] method: %s | runname %s\n"%
(apDisplay.colorString("CTF run", "blue"), method, runname))
sys.stderr.write("[%s] def1: %.2e | def2: %.2e | angle: %.1f | ampcontr %.2f | defratio %.3f\n"%
(apDisplay.colorString("CTF param", "blue"), ctfvalue['defocus1'],
ctfvalue['defocus2'], ctfvalue['angle_astigmatism'],
ctfvalue['amplitude_contrast'], defocusratio))
if 'resolution_80_percent' in ctfvalue.keys() and ctfvalue['resolution_80_percent'] is not None:
sys.stderr.write("[%s] conf_30-10: %s | conf_5peak: %s | res_0.8: %.1fA | res_0.5 %.1fA\n"%
(apDisplay.colorString("CTF stats", "blue"),
apDisplay.colorProb(ctfvalue['confidence_30_10']),
apDisplay.colorProb(ctfvalue['confidence_5_peak']),
ctfvalue['resolution_80_percent'], ctfvalue['resolution_50_percent']))
#sys.stderr.write("[%s] conf: %s | conf_d: %s\n"%
# (apDisplay.colorString("CTF stats", "blue"), apDisplay.colorProb(ctfvalue['confidence']),
# apDisplay.colorProb(ctfvalue['confidence_d'])))
#apDisplay.colorProb(numlist[i])
#time.sleep(3)
return
def runCommand(self, cmd):
t0 = time.time()
if self.params['showcmd'] is True:
apDisplay.printColor("###################################", "magenta")
sys.stderr.write(
apDisplay.colorString("COMMAND: \n","magenta")
+apDisplay.colorString(cmd, "cyan")+"\n")
apDisplay.printColor("###################################", "cyan")
try:
if self.params['verbose'] is False:
logf = open('testsuite-programs.log' ,'a')
proc = subprocess.Popen(cmd, shell=True,
stdout=logf, stderr=logf)
else:
proc = subprocess.Popen(cmd, shell=True)
proc.wait()
except:
apDisplay.printError("could not run command: "+cmd)
runtime = time.time() - t0
if self.params['showcmd'] is True:
apDisplay.printColor("###################################", "cyan")
apDisplay.printColor("command ran in "+apDisplay.timeString(runtime), "cyan")
if runtime < 1:
apDisplay.printError("command runtime was too short: "
+apDisplay.timeString(runtime))
elif runtime < 10:
apDisplay.printWarning("command runtime was very short: "
+apDisplay.timeString(runtime))
return False
if self.params['verbose'] is False:
logf.close()
return True
def runCommand(self, cmd):
t0 = time.time()
if self.params['showcmd'] is True:
apDisplay.printColor("###################################", "magenta")
sys.stderr.write(
apDisplay.colorString("COMMAND: \n","magenta")
+apDisplay.colorString(cmd, "cyan")+"\n")
apDisplay.printColor("###################################", "cyan")
try:
if self.params['verbose'] is False:
proc = subprocess.Popen(cmd, shell=True,
stdout=subprocess.PIPE)#, stderr=subprocess.PIPE)
else:
proc = subprocess.Popen(cmd, shell=True)
proc.wait()
except:
apDisplay.printWarning("could not run command: "+cmd)
sys.exit(1)
return False
runtime = time.time() - t0
if self.params['showcmd'] is True:
apDisplay.printColor("###################################", "cyan")
apDisplay.printColor("command ran in "+apDisplay.timeString(runtime), "cyan")
if runtime < 10:
apDisplay.printWarning("command runtime was very short: "
+apDisplay.timeString(runtime))
sys.exit(1)
return False
#self.timestamp = apParam.makeTimestamp()
return True
def setImgViewerStatus(imgdata, status=None, msg=True):
"""
Function that sets the image status in the viewer
False: Image was hidden
True: Image is an exemplar
None: Image is visible
see 'ViewerImageStatus' table in dbemdata
"""
if status is False:
statusVal = 'hidden'
elif status is True:
statusVal = 'exemplar'
else:
print "skipping set viewer status"
return
currentstatus = getImgViewerStatus(imgdata)
if currentstatus is None:
#insert new
statusq = leginon.leginondata.ViewerImageStatus()
statusq['image'] = imgdata
statusq['status'] = statusVal
statusq.insert()
elif currentstatus != status:
#update column
dbconf=sinedon.getConfig('leginondata')
db=sinedon.sqldb.sqlDB(**dbconf)
q= ( "UPDATE "+dbconf['db']+".`ViewerImageStatus` "
+"SET status = '"+statusVal
+ ("' WHERE `REF|AcquisitionImageData|image`=%d" % (imgdata.dbid,)))
db.execute(q)
#check assessment
if msg is True:
finalassess = getImgViewerStatus(imgdata)
imgname = apDisplay.short(imgdata['filename'])
if finalassess is True:
astr = apDisplay.colorString("exemplar", "green")
elif finalassess is False:
astr = apDisplay.colorString("hidden", "red")
elif finalassess is None:
astr = apDisplay.colorString("none", "yellow")
apDisplay.printMsg("Final image assessment: "+astr+" ("+imgname+")")
return
def getSymmetryFromReconRunId(reconrunid, msg=True):
"""
get the symmetry from the last iteration of a refinement
"""
refrundata = appiondata.ApRefineRunData.direct_query(reconrunid)
refdataq = appiondata.ApRefineIterData()
refdataq['refineRun'] = refrundata
refdata = refdataq.query()
uniqsym = refdata[0]['symmetry']
if uniqsym is None:
apDisplay.printWarning("symmetry is not saved during reconstruction!")
apDisplay.printWarning("Using the symmetry of the initial model")
modeldata = refrundata['initialModel']
uniqsym = modeldata['symmetry']
else:
for data in refdata:
if uniqsym != data['symmetry']:
apDisplay.printWarning("symmetry is not consistent throughout reconstruction!")
apDisplay.printWarning("Using symmetry of last iteration")
uniqsym = data['symmetry']
if msg is True:
apDisplay.printMsg("selected symmetry group: "
+apDisplay.colorString("'"+uniqsym['eman_name']+"'", "cyan")
+" for recon run: "+str(reconrunid))
return uniqsym
def executeAce2Cmd(self, ace2cmd, verbose=False, showcmd=True, logfile=None):
"""
executes an EMAN command in a controlled fashion
"""
waited = False
if showcmd is True:
os.sys.stderr.write(apDisplay.colorString("ACE2: ","magenta")+ace2cmd+"\n")
t0 = time.time()
try:
if logfile is not None:
logf = open(logfile, 'a')
ace2proc = subprocess.Popen(ace2cmd, shell=True, stdout=logf, stderr=logf)
elif verbose is False:
ace2proc = subprocess.Popen(ace2cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
else:
ace2proc = subprocess.Popen(ace2cmd, shell=True)
if verbose is True:
ace2proc.wait()
else:
### continuous check
waittime = 2.0
while ace2proc.poll() is None:
if waittime > 10:
waited = True
os.sys.stderr.write(".")
waittime *= 1.1
time.sleep(waittime)
except:
apDisplay.printWarning("could not run ace2 command: "+ace2cmd)
raise
tdiff = time.time() - t0
if tdiff > 20:
apDisplay.printMsg("completed in "+apDisplay.timeString(tdiff))
elif waited is True:
print ""
def getSymmetryDataFromID(symid, msg=True):
symdata = appiondata.ApSymmetryData.direct_query(int(symid))
if not symdata:
printSymmetries()
apDisplay.printError("no symmetry associated with this id: "+str(symid))
if msg is True:
apDisplay.printMsg("Selected symmetry group: "
+apDisplay.colorString("%s -- %s"%(symdata['eman_name'].upper(), symdata['symmetry']), "cyan"))
return symdata
def executeEmanCmd(emancmd, verbose=False, showcmd=True, logfile=None, fail=False):
"""
executes an EMAN command in a controlled fashion
"""
waited = False
if showcmd is True:
sys.stderr.write(apDisplay.colorString("EMAN: ","magenta")+emancmd+"\n")
t0 = time.time()
try:
if logfile is not None:
logf = open(logfile, 'a')
emanproc = subprocess.Popen(emancmd, shell=True,
stdout=logf, stderr=logf)
elif verbose is False:
devnull = open('/dev/null', 'w')
emanproc = subprocess.Popen(emancmd, shell=True,
stdout=devnull, stderr=devnull)
else:
emanproc = subprocess.Popen(emancmd, shell=True)
if verbose is True:
#emanproc.wait()
out, err = emanproc.communicate()
if out is not None and err is not None:
print "EMAN error", out, err
else:
out, err = emanproc.communicate()
### continuous check
waittime = 2.0
while emanproc.poll() is None:
if waittime > 10:
waited = True
sys.stderr.write(".")
waittime *= 1.1
time.sleep(waittime)
except:
apDisplay.printWarning("could not run eman command: "+emancmd)
raise
tdiff = time.time() - t0
if tdiff > 20:
apDisplay.printMsg("completed in "+apDisplay.timeString(tdiff))
elif waited is True:
print ""
proc_code = emanproc.returncode
if proc_code != 0:
if proc_code == -11:
if fail is True:
apDisplay.printError("EMAN failed with Segmentation Fault")
else:
apDisplay.printWarning("EMAN failed with Segmentation Fault")
else:
if fail is True:
apDisplay.printError("EMAN failed with subprocess error code %d" % proc_code)
else:
apDisplay.printWarning("EMAN failed with subprocess error code %d" % proc_code)
def getSymmetryDataFromID(symid, msg=True):
symdata = appiondata.ApSymmetryData.direct_query(int(symid))
if not symdata:
printSymmetries()
apDisplay.printError("no symmetry associated with this id: " +
str(symid))
if msg is True:
apDisplay.printMsg("Selected symmetry group: " + apDisplay.colorString(
"%s -- %s" %
(symdata['eman_name'].upper(), symdata['symmetry']), "cyan"))
return symdata
def insertImgAssessmentStatus(imgdata,
runname="run1",
assessment=None,
msg=True):
"""
Insert the assessment status
keep = True
reject = False
unassessed = None
"""
if assessment is True or assessment is False:
assessrun = appiondata.ApAssessmentRunData()
assessrun['session'] = imgdata['session']
#override to ALWAYS be 'run1'
#assessrun['name'] = runname
assessrun['name'] = "run1"
assessquery = appiondata.ApAssessmentData()
assessquery['image'] = imgdata
assessquery['assessmentrun'] = assessrun
assessquery['selectionkeep'] = assessment
assessquery.insert()
else:
apDisplay.printWarning("No image assessment made, invalid data: " +
str(assessment))
#check assessment
if msg is True:
finalassess = getImgAssessmentStatus(imgdata)
imgname = apDisplay.short(imgdata['filename'])
if finalassess is True:
astr = apDisplay.colorString("keep", "green")
elif finalassess is False:
astr = apDisplay.colorString("reject", "red")
elif finalassess is None:
astr = apDisplay.colorString("none", "yellow")
apDisplay.printMsg("Final image assessment: " + astr + " (" + imgname +
")")
return True
def printSymmetries():
symq = appiondata.ApSymmetryData()
syms = symq.query()
sys.stderr.write("ID NAME DESCRIPTION\n")
sys.stderr.write("-- ---- -----------\n")
syms.sort(compSymm)
for s in syms:
name = s['eman_name']
name = re.sub('Icosahedral', 'Icos', name)
sys.stderr.write(
apDisplay.colorString(apDisplay.rightPadString(s.dbid, 3), "green")
+ " " + apDisplay.rightPadString(name, 5) + " " +
apDisplay.rightPadString(s['description'], 60) + "\n")
def printSymmetries():
symq = appiondata.ApSymmetryData()
syms = symq.query()
sys.stderr.write("ID NAME DESCRIPTION\n")
sys.stderr.write("-- ---- -----------\n")
syms.sort(compSymm)
for s in syms:
name = s['eman_name']
name = re.sub('Icosahedral', 'Icos', name)
sys.stderr.write(
apDisplay.colorString(apDisplay.rightPadString(s.dbid,3),"green")+" "
+apDisplay.rightPadString(name,5)+" "
+apDisplay.rightPadString(s['description'],60)+"\n"
)
def insertImgAssessmentStatus(imgdata, runname="run1", assessment=None, msg=True):
"""
Insert the assessment status
keep = True
reject = False
unassessed = None
"""
if assessment is True or assessment is False:
assessrun = appiondata.ApAssessmentRunData()
assessrun['session'] = imgdata['session']
#override to ALWAYS be 'run1'
#assessrun['name'] = runname
assessrun['name'] = "run1"
assessquery = appiondata.ApAssessmentData()
assessquery['image'] = imgdata
assessquery['assessmentrun'] = assessrun
assessquery['selectionkeep'] = assessment
assessquery.insert()
else:
apDisplay.printWarning("No image assessment made, invalid data: "+str(assessment))
#check assessment
if msg is True:
finalassess = getImgAssessmentStatus(imgdata)
imgname = apDisplay.short(imgdata['filename'])
if finalassess is True:
astr = apDisplay.colorString("keep", "green")
elif finalassess is False:
astr = apDisplay.colorString("reject", "red")
elif finalassess is None:
astr = apDisplay.colorString("none", "yellow")
apDisplay.printMsg("Final image assessment: "+astr+" ("+imgname+")")
return True
def runCmd(cmd,
package="",
verbose=False,
showcmd=True,
logfile=None,
fail=False):
"""
executes a command from any processing package in a controlled fashion
"""
waited = False
if showcmd is True:
sys.stderr.write(
apDisplay.colorString(str(package) + ": ", "magenta") + cmd + "\n")
t0 = time.time()
try:
if logfile is not None:
logf = open(logfile, 'a')
proc = subprocess.Popen(cmd, shell=True, stdout=logf, stderr=logf)
elif verbose is False:
devnull = open('/dev/null', 'w')
proc = subprocess.Popen(cmd,
shell=True,
stdout=devnull,
stderr=devnull)
else:
proc = subprocess.Popen(cmd, shell=True)
if verbose is True:
out, err = proc.communicate()
if out is not None and err is not None:
print "error", out, err
else:
out, err = proc.communicate()
### continuous check
waittime = 2.0
while proc.poll() is None:
if waittime > 10:
waited = True
sys.stderr.write(".")
waittime *= 1.1
time.sleep(waittime)
except:
apDisplay.printWarning("could not run command: " + cmd)
raise
tdiff = time.time() - t0
if tdiff > 20:
apDisplay.printMsg("completed in " + apDisplay.timeString(tdiff))
elif waited is True:
print ""
def getSymmetryDataFromName(symtext='c1', msg=True):
# find the symmetry entry (full symmetry name) in the database
if len(symtext.split()) > 1:
symdataq = appiondata.ApSymmetryData(symmetry=symtext.strip())
else:
# based on the text version from EMAN
# first convert to lower case
symtext = symtext.lower().strip()
if symtext == "i":
symtext = "icos"
symdataq = appiondata.ApSymmetryData(eman_name=symtext)
symdatas = symdataq.query()
if not symdatas:
apDisplay.printError("No symmetry named %s was found"%(symtext))
# select oldest match
symdata = symdatas[len(symdatas)-1]
if msg is True:
apDisplay.printMsg("Selected symmetry group: "
+apDisplay.colorString("%s -- %s"%(symdata['eman_name'].upper(), symdata['symmetry']), "cyan"))
return symdata
def getSymmetryDataFromName(symtext='c1', msg=True):
# find the symmetry entry (full symmetry name) in the database
if len(symtext.split()) > 1:
symdataq = appiondata.ApSymmetryData(symmetry=symtext.strip())
else:
# based on the text version from EMAN
# first convert to lower case
symtext = symtext.lower().strip()
if symtext == "i":
symtext = "icos"
symdataq = appiondata.ApSymmetryData(eman_name=symtext)
symdatas = symdataq.query()
if not symdatas:
apDisplay.printError("No symmetry named %s was found"%(symtext))
# select oldest match
symdata = symdatas[len(symdatas)-1]
if msg is True:
apDisplay.printMsg("Selected symmetry group: "
+apDisplay.colorString("%s -- %s"%(symdata['eman_name'].upper(), symdata['symmetry']), "cyan"))
return symdata
def runCmd(cmd, package="", verbose=False, showcmd=True, logfile=None, fail=False):
"""
executes a command from any processing package in a controlled fashion
"""
waited = False
if showcmd is True:
sys.stderr.write(apDisplay.colorString(str(package)+": ","magenta")+cmd+"\n")
t0 = time.time()
try:
if logfile is not None:
logf = open(logfile, 'a')
proc = subprocess.Popen(cmd, shell=True,
stdout=logf, stderr=logf)
elif verbose is False:
devnull = open('/dev/null', 'w')
proc = subprocess.Popen(cmd, shell=True,
stdout=devnull, stderr=devnull)
else:
proc = subprocess.Popen(cmd, shell=True)
if verbose is True:
out, err = proc.communicate()
if out is not None and err is not None:
print "error", out, err
else:
out, err = proc.communicate()
### continuous check
waittime = 2.0
while proc.poll() is None:
if waittime > 10:
waited = True
sys.stderr.write(".")
waittime *= 1.1
time.sleep(waittime)
except:
apDisplay.printWarning("could not run command: "+cmd)
raise
tdiff = time.time() - t0
if tdiff > 20:
apDisplay.printMsg("completed in "+apDisplay.timeString(tdiff))
elif waited is True:
print ""
def executeEmanCmd(emancmd,
verbose=False,
showcmd=True,
logfile=None,
fail=False):
"""
executes an EMAN command in a controlled fashion
"""
waited = False
if showcmd is True:
sys.stderr.write(
apDisplay.colorString("EMAN: ", "magenta") + emancmd + "\n")
t0 = time.time()
try:
if logfile is not None:
logf = open(logfile, 'a')
emanproc = subprocess.Popen(emancmd,
shell=True,
stdout=logf,
stderr=logf)
elif verbose is False:
devnull = open('/dev/null', 'w')
emanproc = subprocess.Popen(emancmd,
shell=True,
stdout=devnull,
stderr=devnull)
else:
emanproc = subprocess.Popen(emancmd, shell=True)
if verbose is True:
#emanproc.wait()
out, err = emanproc.communicate()
if out is not None and err is not None:
print "EMAN error", out, err
else:
out, err = emanproc.communicate()
### continuous check
waittime = 2.0
while emanproc.poll() is None:
if waittime > 10:
waited = True
sys.stderr.write(".")
waittime *= 1.1
time.sleep(waittime)
except:
apDisplay.printWarning("could not run eman command: " + emancmd)
raise
tdiff = time.time() - t0
if tdiff > 20:
apDisplay.printMsg("completed in " + apDisplay.timeString(tdiff))
elif waited is True:
print ""
proc_code = emanproc.returncode
if proc_code != 0:
if proc_code == -11:
if fail is True:
apDisplay.printError("EMAN failed with Segmentation Fault")
else:
apDisplay.printWarning("EMAN failed with Segmentation Fault")
else:
if fail is True:
apDisplay.printError(
"EMAN failed with subprocess error code %d" % proc_code)
else:
apDisplay.printWarning(
"EMAN failed with subprocess error code %d" % proc_code)
