#/*########################################################################## # Copyright (C) 2004-2014 European Synchrotron Radiation Facility # # This file is part of the PyMca X-ray Fluorescence Toolkit developed at # the ESRF by the Software group. # # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by the # Free Software Foundation; either version 2 of the License, or (at your option) # any later version. # # This file is distributed in the hope that it will be useful, but WITHOUT ANY # WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more # details. # #############################################################################*/ __author__ = "V.A. Sole - ESRF Data Analysis" from PyMca import DataObject from PyMca.PyMcaIO import EdfFile import types import sys import os import numpy SOURCE_TYPE = "EdfFile" DEBUG = 0 class EdfFileDataSource(object): def __init__(self,nameInput, fastedf=False): if type(nameInput) == list: nameList = nameInput else: nameList = [nameInput] if sys.version < '3.0': stringTypes = [types.StringType, types.UnicodeType] else: stringTypes = [type("a"), type(eval('b"a"'))] for name in nameList: if type(name) not in stringTypes: raise TypeError("Constructor needs string as first argument") self.sourceName = nameInput self.sourceType = SOURCE_TYPE self.__sourceNameList = nameList #this is to be added #self._fastedf = True self._fastedf = fastedf if fastedf: print("fastedf is unsafe!") self.refresh() def refresh(self): self._sourceObjectList=[] for name in self.__sourceNameList: self._sourceObjectList.append(EdfFile.EdfFile(name, access='rb', fastedf=self._fastedf)) self.__lastKeyInfo = {} def getSourceInfo(self): """ Returns information about the EdfFile object created by SetSource, to give application possibility to know about it before loading. Returns a dictionary with the key "KeyList" (list of all available keys in this source). Each element in "KeyList" has the form 'n1.n2' where n1 is the source number and n2 image number in file starting at 1. """ return self.__getSourceInfo() def __getSourceInfo(self): SourceInfo={} SourceInfo["SourceType"]=SOURCE_TYPE SourceInfo["KeyList"]=[] i = 0 for sourceObject in self._sourceObjectList: i+=1 nimages = sourceObject.GetNumImages() for n in range(nimages): SourceInfo["KeyList"].append("%d.%d" % (i,n+1)) SourceInfo["Size"]=len(SourceInfo["KeyList"]) return SourceInfo def getKeyInfo(self,key): if key in self.getSourceInfo()['KeyList']: return self.__getKeyInfo(key) else: #should we raise a KeyError? if DEBUG: print("Error key not in list ") return {} def __getKeyInfo(self,key): try: index,image = key.split(".") index = int(index)-1 image = int(image)-1 except: #should we rise an error? if DEBUG: print("Error trying to interpret key =",key) return {} sourceObject = self._sourceObjectList[index] info= sourceObject.GetStaticHeader(image) info.update(sourceObject.GetHeader(image)) info["SourceType"] = SOURCE_TYPE #doubts about if refer to the list or to the individual file info["SourceName"] = self.sourceName info["Key"] = key #specific info of interest info['FileName'] = sourceObject.FileName info["rows"] = info['Dim_2'] info["cols"] = info['Dim_1'] info["type"] = info['DataType'] if 'MCA start ch' in info: info['Channel0'] = int(info['MCA start ch']) else: info['Channel0'] = 0 if not ( 'McaCalib' in info): if ('MCA a' in info) and\ ('MCA b' in info) and\ ('MCA c' in info): info['McaCalib'] = [float(info['MCA a']), float(info['MCA b']), float(info['MCA c'])] else: info['McaCalib'] = [ 0.0, 1.0, 0.0] else: if type(info['McaCalib']) in [type(" ")]: info['McaCalib'] = info['McaCalib'].replace("[","") info['McaCalib'] = info['McaCalib'].replace("]","") cala, calb, calc = info['McaCalib'].split(",") info['McaCalib'] = [float(cala), float(calb), float(calc)] self.__lastKeyInfo[key] = os.path.getmtime(sourceObject.FileName) return info def getDataObject(self,key,selection=None): """ selection: a dictionnary with the keys pos and size: (x), (x,y) or (x,y,z) tuples defining a roi If not defined, takes full array """ sourcekeys = self.getSourceInfo()['KeyList'] #a key corresponds to an image key_split= key.split(".") image_key= key_split[0]+"."+key_split[1] if image_key not in sourcekeys: #if image_key == "0.0": # #this is in fact a special selection: The SUM # pass #else: raise KeyError("Key %s not in source keys" % image_key) #create data object data = DataObject.DataObject() data.info = self.__getKeyInfo(image_key) data.info ['selection'] = selection data.info['selectiontype'] = "2D" index = key_split[0] image = key_split[1] index = int(index)-1 image = int(image)-1 MCAIMP = 0 if len(key_split) == 4: if DEBUG: print("mca like selection") #print data.info if 1: MCAIMP = 1 if key_split[2].upper() == 'R': pos = (0, int(key_split[3])) size = (int(data.info['Dim_1']), 1) elif key_split[2].upper() == 'C': pos = (int(key_split[3]), 0) size = (1,int(data.info['Dim_2'])) data.info['selectiontype'] = "1D" else: if DEBUG: print("mca like selection not yet implemented") pos = None size = None data.info['selectiontype'] = "1D" elif selection is None: pos = None size = None else: if "pos" in selection: data.info["pos"]=selection['pos'] else: data.info['pos']=None if "size" in selection: data.info["size"]=selection['size'] else: data.info['size']=None pos = data.info['pos'] size = data.info['size'] sourceObject = self._sourceObjectList[index] data.data=sourceObject.GetData(image,Pos=pos,Size=size) data.info['rows'], data.info['cols'] = data.data.shape[0:2] if data.info['selectiontype'] == "1D": if MCAIMP: data.y = [numpy.ravel(data.data[:]).astype(numpy.float)] else: if key_split[2].upper() == 'C': data.y=[data.data[:,int(key_split[3])-1].astype(numpy.float)] elif key_split[2].upper() == 'R': data.y=[data.data[int(key_split[3])-1, :].astype(numpy.float)] else: raise ValueError("Unknown key %s" % key) ch0 = int(data.info['Channel0']) data.x = [ch0+numpy.arange(len(data.y[0])).astype(numpy.float)] data.m = None data.data = None #print "data.x.shape ", data.x[0].shape #print "data.y.shape ", data.y[0].shape return data def isUpdated(self, sourceName, key): #sourceName is redundant? index,image = key.split(".") index = int(index)-1 lastmodified = os.path.getmtime(self.__sourceNameList[index]) if lastmodified != self.__lastKeyInfo[key]: self.__lastKeyInfo[key] = lastmodified return True else: return False source_types = { SOURCE_TYPE: EdfFileDataSource} def DataSource(name="", source_type=SOURCE_TYPE): try: sourceClass = source_types[source_type] except KeyError: #ERROR invalid source type raise TypeError("Invalid Source Type, source type should be one of %s" %\ source_types.keys()) return sourceClass(name) if __name__ == "__main__": import time try: sourcename=sys.argv[1] key =sys.argv[2] except: print("Usage: EdfFileDataSource ") sys.exit() #one can use this: obj = EdfFileDataSource(sourcename) #or this: obj = DataSource(sourcename) #data = obj.getData(key,selection={'pos':(10,10),'size':(40,40)}) #data = obj.getDataObject(key,selection={'pos':None,'size':None}) t0 = time.time() data = obj.getDataObject(key,selection=None) print("elapsed = ",time.time() - t0) print("info = ",data.info) if data.data is not None: print("data shape = ",data.data.shape) print(numpy.ravel(data.data)[0:10]) else: print(data.y[0].shape) print(numpy.ravel(data.y[0])[0:10]) data = obj.getDataObject('1.1',selection=None) r = int(key.split('.')[-1]) print(" data[%d,0:10] = " % (r-1),data.data[r-1 ,0:10]) print(" data[0:10,%d] = " % (r-1),data.data[0:10, r-1])