def visualizeReferences(self):
refs = self.getFilename('iter_refs', iter=lastIteration(self))
if xmippExists(refs):
try:
runShowJ(refs, extraParams="--mode metadata --render first")
except Exception, e:
showError("Error launching java app", str(e), self.master)
def launchProjSubPlots(self, selectedPlots):
''' Launch some plots for a Projection Matching protocol run '''
import numpy as np
_log = self.Log
xplotter=None
self._plot_count = 0
def doPlot(plotName):
return plotName in selectedPlots
file_name_tmp = join(self.CtfGroupDirectoryName, self.CtfGroupRootName) +'Info.xmd'
file_name = join(self.PrevRun.WorkingDir, file_name_tmp)
if exists(file_name):
auxMD = MetaData("numberGroups@"+file_name)
self.NumberOfCtfGroups = auxMD.getValue(MDL_COUNT,auxMD.firstObject())
else:
self.NumberOfCtfGroups = 1
if doPlot('DisplayReference'):
for indexCtf in range(1, self.NumberOfCtfGroups+1):
file_name = self.getFilename('SubtractedStack', ctf=indexCtf)+'ref'
if exists(file_name):
try:
runShowJ(file_name)
except Exception, e:
showError("Error launching java app", str(e), self.master)
def display2D(self,fn, extraParams=''):
if xmippExists(fn):
try:
# We use os.system to load the relion labels through showj
os.system('xmipp_showj %(fn)s %(extraParams)s --dont_wrap &' % locals())
#runShowJ(fn, extraParams=extraParams + ' --dont_wrap')
except Exception, e:
showError("Error launching java app", str(e), self.master)
def getFilename():
if len(fileList) == 0:
showError("Input error", "File list is empty", parent=gui.master)
return None
fn = FileName(fileList[0])
if not xmippExists(fn):
showError("Input error", "Filename <%s> doesn't exists" % str(fn),parent=gui.master)
return None
return fn
def _checkIterData(self):
""" check that for last visualized iteration, the data is produced. """
dataStar = self.getFilename('data', iter=self._visualizeLastIteration)
if not xmippExists(dataStar):
message = "No data available for <iteration %d>, file <%s> not found." % (self._visualizeLastIteration, dataStar)
showError("File not Found", message, self.master)
return False
return True
def display3D(self, filename):
if xmippExists(filename):
#Chimera
if self._visualizeVolumesMode == 'chimera':
runChimeraClient(filename)
else:
try:
runShowJ(filename, extraParams=' --dont_wrap ')
except Exception, e:
showError("Error launching xmipp_showj: ", str(e), self.master)
def wizardHelperSetRadii(gui, inputVarName, outerVarName, innerVarName=None, unit='pixel', sampling=1.):
fileList = gui.getVarValue(inputVarName).split()
showInner = innerVarName is not None
innerRadius = 0
try:
if showInner:
innerRadius = int(gui.getVarValue(innerVarName))
outerRadius = int(gui.getVarValue(outerVarName))
except Exception, e:
showError("Conversion error", "Error trying to parse integer value from \ninnerRadius: <%(innerVarName)s> or\n outerRadius: <%(outerVarName)s>" % locals()
,parent=gui.master)
return
def _checkIterData(self):
""" check that for last visualized iteration, the data is produced. """
volumes = []
for prefix in self._getPrefixes():
volumes.append(self.getFilename(prefix + 'volume',
iter=self._visualizeLastIteration,
ref3d=self._visualizeLastRef3D))
for v in volumes:
if not xmippExists(v):
message = "No data available for <iteration %d> and <class %d>" % (self._visualizeLastIteration, self._visualizeLastRef3D)
message += '\nVolume <%s> not found. ' % v
showError("File not Found", message, self.master)
return False
return True
def runExternalAppWithResponse(cmd):
#Create a simple socket server to wait for response
HOST = '' # Symbolic name meaning the local host
PORT = 14321
if cmd[-1]=="&":
cmd=cmd.replace("&"," -port %d &" % PORT)
else:
cmd += " -port %d" % PORT
#Launch the plugin that will send the data response over a socket
print cmd
os.system(cmd)
#os.system('java SocketsTest 54321 &')
#Create the socket server
msg = ''
try:
import socket
s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
s.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
s.settimeout(5.0)
s.bind((HOST, PORT))
s.listen(1)
conn = s.accept()[0]
#Read the awake message
data = conn.recv(256)
if not data or data.strip() != '__STARTED__':
raise Exception('Invalid START message received')
else:
conn.close()
s.settimeout(None) # reset timeout
conn = s.accept()[0]
#Read len of message (max 4 bytes)
while True:
data = conn.recv(1024)
msg += data
if not data or msg.find('__END__') !=-1: break
conn.close()
except Exception, e:
from protlib_gui_ext import showError
showError("Error waiting for response", "No reponse, returning empty string. ERROR: " + str(e))
def wizardNotFound(gui, var):
showError("Wizard not found", "The wizard <%s> for this parameter has not been found" % var.tags['wizard']
, parent=gui.master)
if exists(file_name):
try:
runShowJ(file_name)
except Exception, e:
showError("Error launching java app", str(e), self.master)
if doPlot('DisplaySubtracted'):
for indexCtf in range(1, self.NumberOfCtfGroups+1):
file_name = self.getFilename('SubtractedStack', ctf=indexCtf)
print "DisplaySubtracted file_name: ", file_name
if exists(file_name):
try:
runShowJ(file_name)
except Exception, e:
showError("Error launching java app", str(e), self.master)
if xplotter:
xplotter.show()
def createFilenameTemplates(self):
extraParams = {'ReferenceVolumeName': 'reference_volume.vol',
'ProjSubDir': "ProjSub",
'LocalCurrentAngles': 'sub_current_angles.doc',
'LocalCurrentAnglesCtfGroups': 'sub_current_angles_ctfgroups.doc',
'CtfGroupDirectory': "CtfGroups",
'CtfGroupRootName': "ctf",
'CtfGroupRecRootName':'rec_ctfg',
'VolsDir': 'Vols',
#
# if xplotter:
# xplotter.show()
def display3D(self, filename):
if xmippExists(filename):
#Chimera
if self._visualizeVolumesMode == 'chimera':
runChimeraClient(filename)
else:
try:
runShowJ(filename, extraParams=' --dont_wrap ')
except Exception, e:
showError("Error launching xmipp_showj: ", str(e), self.master)
else:
showError("Can not visualize volume file <%s>\nit does not exists." % filename, self.master)
def display2D(self,fn, extraParams=''):
if xmippExists(fn):
try:
# We use os.system to load the relion labels through showj
os.system('xmipp_showj %(fn)s %(extraParams)s --dont_wrap &' % locals())
#runShowJ(fn, extraParams=extraParams + ' --dont_wrap')
except Exception, e:
showError("Error launching java app", str(e), self.master)
else:
showError("Can not visualize file <%s>\nit does not exists." % fn, self.master)
def imagesAssignedToClass2(self,firstIter, lastIteration):
inputMetadatas = []
for it in range (firstIter,lastIteration+1): #always list all iterations
