def __init_memory(self,options):
'''
This function assigns critical attributes
'''
# print "init ",options
from EMAN2PAR import image_range
shrink = None
if "shrink" in options and options["shrink"] != None and options["shrink"] > 1:
shrink = options["shrink"]
ref_data_name=self.data["references"][1]
ref_indices = image_range(*self.data["references"][2:])
if "colmasks" in self.data :
ref_masks_name=self.data["colmasks"][1]
else : ref_masks_name=None
if "mask" in self.data :
mask=EMData(self.data["mask"][1],self.data["mask"][2])
if shrink != None : mask.process_inplace("math.fft.resample",{"n":shrink})
else : mask=None
# print self.data["references"][2:]
refs = {}
for idx in ref_indices:
datareaderror=True
for datareadid in range(20):
try: image = EMData(ref_data_name,idx)
except:
print("Failed to read %s. Wait for 5s and try again."%(str(idx)))
time.sleep(5)
else:
datareaderror=False
break
if datareaderror:
print("Cannot read image. Give up.")
raise Exception("Couldn't read data in init_memory")
if shrink != None:
image.process_inplace("math.fft.resample",{"n":shrink})
if ref_masks_name==None :
refs[idx] = (image,None)
else :
mask=EMData(ref_masks_name,idx)
if shrink != None:
mask.process_inplace("math.fft.resample",{"n":shrink})
refs[idx] = (image,mask)
ptcl_data_name=self.data["particles"][1]
ptcl_indices = image_range(*self.data["particles"][2:])
ptcls = {}
for idx in ptcl_indices:
datareaderror=True
for datareadid in range(20):
try: image = EMData(ptcl_data_name,idx)
except:
print("Failed to read %s in %s from range %s. Wait for 5s and try again."%(str(idx),ptcl_data_name,str(ptcl_indices)))
time.sleep(5)
else:
datareaderror=False
break
if datareaderror:
print("Cannot read image. Give up.")
raise Exception("Couldn't read data in init_memory")
if shrink != None:
image.process_inplace("math.fft.resample",{"n":options["shrink"]})
# removed 8/2/12 stevel. Don't want to apply mask before alignment
# if mask!=None : image.mult(mask)
ptcls[idx] = image
# Note that 'refs' is now a dictionary of tuples: (reference,mask) or (reference,None)
return refs,ptcls,shrink,mask
def __init_memory(self,options):
'''
This function assigns critical attributes
'''
# print "init ",options
from EMAN2PAR import image_range
shrink = None
if options.has_key("shrink") and options["shrink"] != None and options["shrink"] > 1:
shrink = options["shrink"]
ref_data_name=self.data["references"][1]
ref_indices = image_range(*self.data["references"][2:])
if self.data.has_key("colmasks") :
ref_masks_name=self.data["colmasks"][1]
else : ref_masks_name=None
if self.data.has_key("mask") :
mask=EMData(self.data["mask"][1],self.data["mask"][2])
if shrink != None : mask.process_inplace("math.meanshrink",{"n":options["shrink"]})
else : mask=None
# print self.data["references"][2:]
refs = {}
for idx in ref_indices:
datareaderror=True
for datareadid in range(20):
try: image = EMData(ref_data_name,idx)
except:
print "Failed to read %s. Wait for 5s and try again."%(str(idx))
time.sleep(5)
else:
datareaderror=False
break
if datareaderror:
print "Cannot read image. Give up."
raise Exception,"Couldn't read data in init_memory"
if shrink != None:
image.process_inplace("math.meanshrink",{"n":options["shrink"]})
if ref_masks_name==None :
refs[idx] = (image,None)
else :
mask=EMData(ref_masks_name,idx)
if shrink != None:
mask.process_inplace("math.meanshrink",{"n":options["shrink"]})
refs[idx] = (image,mask)
ptcl_data_name=self.data["particles"][1]
ptcl_indices = image_range(*self.data["particles"][2:])
ptcls = {}
for idx in ptcl_indices:
datareaderror=True
for datareadid in range(20):
try: image = EMData(ptcl_data_name,idx)
except:
print "Failed to read %s in %s from range %s. Wait for 5s and try again."%(str(idx),ptcl_data_name,str(ptcl_indices))
time.sleep(5)
else:
datareaderror=False
break
if datareaderror:
print "Cannot read image. Give up."
raise Exception,"Couldn't read data in init_memory"
if shrink != None:
image.process_inplace("math.meanshrink",{"n":options["shrink"]})
# removed 8/2/12 stevel. Don't want to apply mask before alignment
# if mask!=None : image.mult(mask)
ptcls[idx] = image
# Note that 'refs' is now a dictionary of tuples: (reference,mask) or (reference,None)
return refs,ptcls,shrink,mask