def __getitem__(self,key):
self.realopen(self.rohint)
try: r=loads(self.bdb.get(dumps(key,-1),txn=self.txn))
except: return None
if isinstance(r,dict) and r.has_key("is_complex_x") :
pkey="%s/%s_"%(self.path,self.name)
fkey="%dx%dx%d"%(r["nx"],r["ny"],r["nz"])
# print "r",fkey
ret=EMData(r["nx"],r["ny"],r["nz"])
if r.has_key("data_path"):
p,l=r["data_path"].split("*")
# print "read ",os.getcwd(),self.path,p,l
if p[0]=='/' : ret.read_data(p,int(l))
else : ret.read_data(self.path+"/"+p,int(l))
else:
try: n=loads(self.bdb.get(fkey+dumps(key,-1))) # this is the index for this binary data item in the image-dimensions-specific binary data file
except: raise KeyError,"Undefined data location key for : %s"%key
ret.read_data(pkey+fkey,n*4*r["nx"]*r["ny"]*r["nz"])
k=set(r.keys())
k-=DBDict.fixedkeys
for i in k:
if i not in ('nx', 'ny', 'nz'):
ret.set_attr(i,r[i])
ret["source_path"]=pkey[:-1]
ret["source_n"]=key
return ret
return r
def get(self,key,dfl=None,txn=None,target=None,nodata=0,region=None,idx=0):
"""Alternate method for retrieving records. Permits specification of an EMData 'target'
object in which to place the read object"""
self.realopen(self.rohint)
try: r=loads(self.bdb.get(dumps(key,-1),txn=txn))
except: return dfl
if isinstance(r,dict) and r.has_key("is_complex_x") :
pkey="%s/%s_"%(self.path,self.name)
rnx,rny,rnz = r["nx"],r["ny"],r["nz"]
fkey="%dx%dx%d"%(rnx,rny,rnz)
# print "r",fkey
if region != None:
size = region.get_size()
# zeros are annoyingly necessary
for i in range(len(size)):
if size[i] == 0: size[i] = 1
nx,ny,nz = int(size[0]),int(size[1]),int(size[2])
else:
nx,ny,nz = rnx,rny,rnz
if target : ret = target
else: ret = EMData()
# metadata
k=set(r.keys())
# k-=DBDict.fixedkeys
for i in k:
if i not in ('nx', 'ny', 'nz'):
ret.set_attr(i,r[i])
ret["source_path"]=pkey[:-1]
ret["source_n"]=key
# binary data
ret.set_size(nx,ny,nz,nodata)
if not nodata:
if region != None: ret.to_zero() # this has to occur in situations where the clip region goes outside the image
if r.has_key("data_path"):
p,l=r["data_path"].split("*")
if p[0]=='/' or p[0]=='\\' or p[1]==':': ret.read_data(p,int(l),region,rnx,rny,rnz) # absolute path
else :
ret.read_data(self.path+"/"+p,int(l),region,rnx,rny,rnz) # relative path
else:
try: n=loads(self.bdb.get(fkey+dumps(key,-1))) # this is the index for this binary data item in the image-dimensions-specific binary data file
except: raise KeyError,"Undefined data location key %s for %s"%(key,pkey+fkey)
try: ret.read_data(pkey+fkey,n*4*rnx*rny*rnz,region,rnx,rny,rnz) # note that this uses n, NOT 'key'. Images cannot be located in the binary file based on their numerical key
except :
import socket
print "Data read error (%s) on %s (%d)"%(socket.gethostname(),pkey+fkey,key*4*rnx*rny*rnz)
traceback.print_exc()
sys.stderr.flush()
sys.stdout.flush()
os._exit(1)
return ret
return r