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#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2004-2019 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#############################################################################*/
__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
import logging
SOURCE_TYPE = "EdfFile"
_logger = logging.getLogger(__name__)
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:
_logger.warning("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?
_logger.debug("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?
_logger.debug("Error trying to interpret key = %s", 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 dictionary 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:
_logger.debug("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:
_logger.debug("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.float64)]
else:
if key_split[2].upper() == 'C':
data.y=[data.data[:,int(key_split[3])-1].astype(numpy.float64)]
elif key_split[2].upper() == 'R':
data.y=[data.data[int(key_split[3])-1, :].astype(numpy.float64)]
else:
raise ValueError("Unknown key %s" % key)
ch0 = int(data.info['Channel0'])
data.x = [ch0+numpy.arange(len(data.y[0])).astype(numpy.float64)]
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:
_logger.error("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])
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