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#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# 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.
#
# 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"
import numpy
import sys
import os
from PyMca5 import DataObject
SOURCE_TYPE = "EdfFileStack"
DEBUG = 0
class TextImageStack(DataObject.DataObject):
def __init__(self, filelist = None, imagestack=None, dtype=None):
DataObject.DataObject.__init__(self)
self.incrProgressBar=0
self.__keyList = []
if imagestack is None:
self.__imageStack = True
else:
self.__imageStack = imagestack
self.__dtype = dtype
if filelist is not None:
if type(filelist) != type([]):
filelist = [filelist]
if len(filelist) == 1:
self.loadIndexedStack(filelist)
else:
self.loadFileList(filelist)
def loadFileList(self, filelist, fileindex=0):
if type(filelist) == type(''):
filelist = [filelist]
self.__keyList = []
self.sourceName = filelist
self.__indexedStack = True
self.sourceType = SOURCE_TYPE
self.info = {}
self.__nFiles=len(filelist)
#read first file
arrRet = numpy.loadtxt(filelist[0])
if self.__dtype is None:
self.__dtype = arrRet.dtype
self.__nImagesPerFile = 1
#try to allocate the memory
shape = self.__nFiles, arrRet.shape[0], arrRet.shape[1]
samplingStep = 1
try:
self.data = numpy.zeros(shape, self.__dtype)
except (MemoryError, ValueError):
for i in range(3):
print("\7")
samplingStep = None
i = 2
while samplingStep is None:
print("**************************************************")
print(" Memory error!, attempting %dx%d sampling reduction ") % (i,i)
print("**************************************************")
s1, s2 = arrRet[::i, ::i].shape
try:
self.data = numpy.zeros((self.__nFiles, s1, s2),
self.__dtype)
samplingStep = i
except (MemoryError, ValueError):
i += 1
#fill the array
self.onBegin(self.__nFiles)
self.__imageStack = True
self.incrProgressBar=0
if samplingStep == 1:
for tempFileName in filelist:
self.data[self.incrProgressBar]=numpy.loadtxt(tempFileName,
dtype=self.__dtype)
self.incrProgressBar += 1
self.onProgress(self.incrProgressBar)
else:
for tempFileName in filelist:
pieceOfStack=numpy.loadtxt(tempFileName, dtype=self.__dtype)
self.data[self.incrProgressBar] = pieceOfStack[::samplingStep,
::samplingStep]
self.incrProgressBar += 1
self.onProgress(self.incrProgressBar)
self.onEnd()
if self.__imageStack:
self.info["McaIndex"] = 0
self.info["FileIndex"] = 1
else:
self.info["McaIndex"] = 2
self.info["FileIndex"] = 0
self.info["SourceType"] = SOURCE_TYPE
self.info["SourceName"] = self.sourceName
self.info["NumberOfFiles"] = self.__nFiles * 1
self.info["Size"] = self.__nFiles * self.__nImagesPerFile
def onBegin(self, n):
pass
def onProgress(self, n):
pass
def onEnd(self):
pass
def loadIndexedStack(self,filename,begin=None,end=None, skip = None, fileindex=0):
#if begin is None: begin = 0
if type(filename) == type([]):
filename = filename[0]
if not os.path.exists(filename):
raise IOError("File %s does not exists" % filename)
name = os.path.basename(filename)
n = len(name)
i = 1
numbers = ['0', '1', '2', '3', '4', '5',
'6', '7', '8','9']
while (i <= n):
c = name[n-i:n-i+1]
if c in ['0', '1', '2',
'3', '4', '5',
'6', '7', '8',
'9']:
break
i += 1
suffix = name[n-i+1:]
if len(name) == len(suffix):
#just one file, one should use standard widget
#and not this one.
self.loadFileList(filename, fileindex=fileindex)
else:
nchain = []
while (i<=n):
c = name[n-i:n-i+1]
if c not in ['0', '1', '2',
'3', '4', '5',
'6', '7', '8',
'9']:
break
else:
nchain.append(c)
i += 1
number = ""
nchain.reverse()
for c in nchain:
number += c
fformat = "%" + "0%dd" % len(number)
if (len(number) + len(suffix)) == len(name):
prefix = ""
else:
prefix = name[0:n-i+1]
prefix = os.path.join(os.path.dirname(filename),prefix)
if not os.path.exists(prefix + number + suffix):
print("Internal error in EDFStack")
print("file should exist: %s " % (prefix + number + suffix))
return
i = 0
if begin is None:
begin = 0
testname = prefix+fformat % begin+suffix
while not os.path.exists(prefix+fformat % begin+suffix):
begin += 1
testname = prefix+fformat % begin+suffix
if len(testname) > len(filename):break
i = begin
else:
i = begin
if not os.path.exists(prefix+fformat % i+suffix):
raise ValueError("Invalid start index file = %s" % \
(prefix+fformat % i+suffix))
f = prefix+fformat % i+suffix
filelist = []
while os.path.exists(f):
filelist.append(f)
i += 1
if end is not None:
if i > end:
break
f = prefix+fformat % i+suffix
self.loadFileList(filelist, fileindex=fileindex)
def getSourceInfo(self):
sourceInfo = {}
sourceInfo["SourceType"]=SOURCE_TYPE
if self.__keyList == []:
for i in range(1, self.__nFiles + 1):
for j in range(1, self.__nImages + 1):
self.__keyList.append("%d.%d" % (i,j))
sourceInfo["KeyList"]= self.__keyList
def getKeyInfo(self, key):
print("Not implemented")
return {}
def isIndexedStack(self):
return self.__indexedStack
def getZSelectionArray(self,z=0):
return (self.data[:,:,z]).astype(numpy.float)
def getXYSelectionArray(self,coord=(0,0)):
x,y=coord
return (self.data[y,x,:]).astype(numpy.float)
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