Source code for PyMca5.PyMcaCore.EdfFileDataSource

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# The PyMca X-Ray Fluorescence Toolkit
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# Copyright (c) 2004-2014 European Synchrotron Radiation Facility
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__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
from . import DataObject
from PyMca5.PyMcaIO import EdfFile
import types
import sys
import os
import numpy

SOURCE_TYPE = "EdfFile"
DEBUG = 0

[docs]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()
[docs] def refresh(self): self._sourceObjectList=[] for name in self.__sourceNameList: self._sourceObjectList.append(EdfFile.EdfFile(name, access='rb', fastedf=self._fastedf)) self.__lastKeyInfo = {}
[docs] 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
[docs] 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
[docs] 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
[docs] 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}
[docs]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 <file> <key>") 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])