def setval(self, key, val, deferupdate=False):
'''Alternative to assignment operator. Permits deferred writing to improve performance.'''
# ok, decided to permit non-string keys to pass through and get converted to strings
# if not isinstance(key,str) : raise Exception,"JSONDB keys must be strings"
key = str(key)
if key in self.delkeys: self.delkeys.remove(key)
# for EMData objects we need to figure out what file they will get stored in
if isinstance(val, EMData):
# Changing an image triggers an actual read of the old image
try:
if isinstance(self.data[key], tmpimg):
self.data[key] = self.data[key].image()
except:
pass
try:
val["json_path"] = self.changes[key]["json_path"]
val["json_n"] = self.changes[key]["json_n"]
except:
try:
val["json_path"] = self.data[key]["json_path"]
val["json_n"] = self.data[key]["json_n"]
except:
val["json_path"] = self.path.replace(
".json", "_jsonimg.hdf")
try:
val["json_n"] = EMUtil.get_image_count(
val["json_path"])
except:
val["json_n"] = 0
# print key,val["json_path"],val["json_n"]
self.changes[key] = val
if not deferupdate: self.sync()
def setval(self,key,val,deferupdate=False):
'''Alternative to assignment operator. Permits deferred writing to improve performance.'''
# ok, decided to permit non-string keys to pass through and get converted to strings
# if not isinstance(key,str) : raise Exception,"JSONDB keys must be strings"
key=str(key)
if key in self.delkeys : self.delkeys.remove(key)
# for EMData objects we need to figure out what file they will get stored in
if isinstance(val,EMData) :
# Changing an image triggers an actual read of the old image
try:
if isinstance(self.data[key],tmpimg):
self.data[key]=self.data[key].image()
except: pass
try:
val["json_path"]=self.changes[key]["json_path"]
val["json_n"]=self.changes[key]["json_n"]
except:
try:
val["json_path"]=self.data[key]["json_path"]
val["json_n"]=self.data[key]["json_n"]
except:
val["json_path"] = self.path.replace(".json","_jsonimg.hdf")
try:
val["json_n"] = EMUtil.get_image_count(val["json_path"])
except: val["json_n"] = 0
# print key,val["json_path"],val["json_n"]
self.changes[key]=val
if not deferupdate : self.sync()
def db_get_image_info(fsp):
"""get_image_info(path)
Takes a bdb: specifier and returns the number of images and image dimensions."""
if fsp[:4].lower()=="bdb:" :
path,dictname,keys=db_parse_path(fsp)
if keys==None :
# This dictionary contains image counts for the others in this directory
db2=db_open_dict("bdb:%s#%s"%(path,"00image_counts"))
# If this is true, we need to update the dictionary
if (db2.has_key(dictname) and os.path.getmtime("%s/EMAN2DB/%s.bdb"%(path,dictname))>db2[dictname][0]) or not db2.has_key(dictname) or db2[dictname][2][0]==0:
# print "update ",dictname,os.path.getmtime("%s/EMAN2DB/%s.bdb"%(path,dictname)),db2[dictname][0],db2.has_key(dictname)
db=db_open_dict(fsp,True)
try:
im=db[0]
sz=(im["nx"],im["ny"],im["nz"])
except :
sz=(0,0,0)
db2[dictname]=(time.time(),len(db),sz)
return db2[dictname][1:]
else : # if the user specifies the key in fsp, we ignore parms
db=db_open_dict(fsp,True)
n=0
for i in keys:
if i in db : n+=1
sz=db[keys[0]]
sz=(sz["nx"],sz["ny"],sz["nz"])
return (n,sz)
img=EMData(fsp,0,True)
return (EMUtil.get_image_count_c(fsp),(img["nx"],img["ny"],img["nz"]))
def db_get_image_count(fsp):
"""get_image_count(path)
Takes a path or bdb: specifier and returns the number of images in the referenced stack."""
if fsp[:4].lower()=="bdb:" :
path,dictname,keys=db_parse_path(fsp)
if keys==None :
# This dictionary contains image counts for the others in this directory
db2=db_open_dict("bdb:%s#%s"%(path,"00image_counts"))
# If this is true, we need to update the dictionary
if (db2.has_key(dictname) and os.path.getmtime("%s/EMAN2DB/%s.bdb"%(path,dictname))>db2[dictname][0]) or not db2.has_key(dictname) :
db=db_open_dict(fsp,True)
try:
im=db[0]
sz=(im["nx"],im["ny"],im["nz"])
except : sz=(0,0,0)
db2[dictname]=(time.time(),len(db),sz)
return db2[dictname][1]
else : # if the user specifies the key in fsp, we ignore parms
db=db_open_dict(fsp,True)
n=0
for i in keys:
if i in db : n+=1
return n
return EMUtil.get_image_count_c(fsp)
def db_get_all_attributes(fsp,*parms):
if fsp[:4].lower()=="bdb:" :
db=db_open_dict(fsp,True)
attr_name = parms[-1]
if "?" in fsp:
keys=fsp[fsp.rfind("?")+1:].split(",")
for i in range(len(keys)):
try: keys[i]=int(keys[i])
except: pass
return [db.get_attr(i, attr_name) for i in keys]
else :
if len(parms)==1 : keys=range(0,len(db))
else : keys=parms[0]
return [db.get_attr(i, attr_name) for i in keys]
return EMUtil.get_all_attributes_c(fsp,*parms)