/usr/lib/python2.7/dist-packages/PyMca/TiffStack.py is in pymca 4.7.1+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# Copyright (C) 2004-2012 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"
import sys
import os
import numpy
from PyMca import DataObject
from PyMca import TiffIO
if sys.version > '2.9':
long = int
SOURCE_TYPE = "TiffStack"
class TiffArray(object):
def __init__(self, filelist, shape, dtype, imagestack=True):
self.__fileList = filelist
self.__shape = shape
self.__dtype = dtype
self.__imageStack = imagestack
if imagestack:
self.__nImagesPerFile = int(shape[0]/len(filelist))
else:
self.__nImagesPerFile = int(shape[-1]/len(filelist))
self.__oldFileNumber = -1
def __getitem__(self, args0):
standardSlice = True
indices = []
outputShape = []
scalarArgs = []
args = []
if not hasattr(args0, "__len__"):
args0 = [args0]
for i in range(len(self.__shape)):
if i < len(args0):
args.append(args0[i])
else:
args.append(slice(None, None, None))
for i in range(len(args)):
if isinstance(args[i], slice):
start = args[i].start
stop = args[i].stop
step = args[i].step
if start is None:
start = 0
if stop is None:
stop = self.__shape[i]
if step is None:
step = 1
if step < 1:
raise ValueError("Step must be >= 1 (got %d)" % step)
if start is None:
start = 0
if start < 0:
start = self.__shape[i]-start
if stop < 0:
stop = self.__shape[i]-stop
if stop == start:
raise ValueError("Zero-length selections are not allowed")
indices.append(list(range(start, stop, step)))
elif type(args[i]) == type([]):
if len(args[i]):
indices.append([int(x) for x in args[i]])
else:
standardSlice = False
elif type(args[i]) in [type(1), type(long(1))]:
start = args[i]
if start < 0:
start = self.__shape[i] - start
stop = start + 1
step = 1
start = args[i]
args[i] = slice(start, stop, step)
indices.append(list(range(start, stop, step)))
scalarArgs.append(i)
else:
standardSlice = False
if not standardSlice:
print("args = ", args)
raise NotImplemented("__getitem__(self, args) only works on slices")
if len(indices) < 3:
print("input args = ", args0)
print("working args = ", args)
print("indices = ", indices)
raise NotImplemented("__getitem__(self, args) only works on slices")
outputShape = [len(indices[0]), len(indices[1]), len(indices[2])]
outputArray = numpy.zeros(outputShape, dtype=self.__dtype)
# nbFiles = len(self.__fileList)
nImagesPerFile = self.__nImagesPerFile
if self.__imageStack:
i = 0
rowMin = min(indices[1])
rowMax = max(indices[1])
for imageIndex in indices[0]:
fileNumber = int(imageIndex/nImagesPerFile)
if fileNumber != self.__oldFileNumber:
self.__tmpInstance = TiffIO.TiffIO(self.__fileList[fileNumber],
mode='rb+')
self.__oldFileNumber = fileNumber
imageNumber = imageIndex % nImagesPerFile
imageData = self.__tmpInstance.getData(imageNumber,
rowMin=rowMin,
rowMax=rowMax)
try:
outputArray[i,:,:] = imageData[args[1],args[2]]
except:
print("outputArray[i,:,:].shape =",outputArray[i,:,:].shape)
print("imageData[args[1],args[2]].shape = " , imageData[args[1],args[2]].shape)
print("input args = ", args0)
print("working args = ", args)
print("indices = ", indices)
print("scalarArgs = ", scalarArgs)
raise
i += 1
else:
i = 0
rowMin = min(indices[0])
rowMax = max(indices[0])
for imageIndex in indices[-1]:
fileNumber = int(imageIndex/nImagesPerFile)
if fileNumber != self.__oldFileNumber:
self.__tmpInstance = TiffIO.TiffIO(self.__fileList[fileNumber],
mode='rb+')
self.__oldFileNumber = fileNumber
imageNumber = imageIndex % nImagesPerFile
imageData = self.__tmpInstance.getData(imageNumber,
rowMin=rowMin,
rowMax=rowMax)
outputArray[:,:, i] = imageData[args[0],args[1]]
i += 1
if len(scalarArgs):
finalShape = []
for i in range(len(outputShape)):
if i in scalarArgs:
continue
finalShape.append(outputShape[i])
outputArray.shape = finalShape
return outputArray
def getShape(self):
return self.__shape
shape = property(getShape)
def getDtype(self):
return self.__dtype
dtype = property(getDtype)
def getSize(self):
s = 1
for item in self.__shape:
s *= item
return s
size = property(getSize)
class TiffStack(DataObject.DataObject):
def __init__(self, filelist=None, imagestack=None, dtype=None):
DataObject.DataObject.__init__(self)
self.sourceType = SOURCE_TYPE
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, dynamic=False, fileindex=0):
if type(filelist) != type([]):
filelist = [filelist]
#retain the file list
self.sourceName = filelist
#the number of files
nbFiles=len(filelist)
#the intance to access the first file
fileInstance = TiffIO.TiffIO(filelist[0])
#the number of images per file
nImagesPerFile = fileInstance.getNumberOfImages()
#get the dimensions from the image itself
tmpImage = fileInstance.getImage(0)
if self.__dtype is None:
self.__dtype = tmpImage.dtype
nRows, nCols = tmpImage.shape
#stack shape
if self.__imageStack:
shape = (nbFiles * nImagesPerFile, nRows, nCols)
else:
shape = (nRows, nCols, nbFiles * nImagesPerFile)
#we can create the stack
if not dynamic:
try:
data = numpy.zeros(shape,
self.__dtype)
except (MemoryError, ValueError):
dynamic = True
if not dynamic:
imageIndex = 0
self.onBegin(nbFiles * nImagesPerFile)
for i in range(nbFiles):
tmpInstance =TiffIO.TiffIO(filelist[i])
for j in range(nImagesPerFile):
tmpImage = tmpInstance.getImage(j)
if self.__imageStack:
data[imageIndex,:,:] = tmpImage
else:
data[:,:,imageIndex] = tmpImage
imageIndex += 1
self.incrProgressBar = imageIndex
self.onProgress(imageIndex)
self.onEnd()
if dynamic:
data = TiffArray(filelist,
shape,
self.__dtype,
imagestack=self.__imageStack)
self.info = {}
self.data = data
shape = self.data.shape
for i in range(len(shape)):
key = 'Dim_%d' % (i+1,)
self.info[key] = shape[i]
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
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 numbers:
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 numbers:
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 TIFFStack")
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 onBegin(self, n):
pass
def onProgress(self, n):
pass
def onEnd(self):
pass
def test():
from PyMca import StackBase
testFileName = "TiffTest.tif"
nrows = 2000
ncols = 2000
#create a dummy stack with 100 images
nImages = 100
imagestack = True
a = numpy.ones((nrows, ncols), numpy.float32)
if not os.path.exists(testFileName):
print("Creating test filename %s" % testFileName)
tif = TiffIO.TiffIO(testFileName, mode = 'wb+')
for i in range(nImages):
data = (a * i).astype(numpy.float32)
if i == 1:
tif = TiffIO.TiffIO(testFileName, mode = 'rb+')
tif.writeImage(data,
info={'Title':'Image %d of %d' % (i+1, nImages)})
tif = None
stackData = TiffStack(imagestack=imagestack)
stackData.loadFileList([testFileName], dynamic=True)
if 0:
stack = StackBase.StackBase()
stack.setStack(stackData)
print("This should be 0 = %f" % stack.calculateROIImages(0, 0)['ROI'].sum())
print("This should be %f = %f" %\
(a.sum(),stack.calculateROIImages(1, 2)['ROI'].sum()))
if imagestack:
print("%f should be = %f" %\
(stackData.data[0:10,:,:].sum(),
stack.calculateROIImages(0, 10)['ROI'].sum()))
print("Test small ROI 10 should be = %f" %\
stackData.data[10:11,[10],11].sum())
print("Test small ROI 40 should be = %f" %\
stackData.data[10:11,[10,12,14,16],11].sum())
else:
print("%f should be = %f" %\
(stackData.data[:,:, 0:10].sum(),
stack.calculateROIImages(0, 10)['ROI'].sum()))
print("Test small ROI %f" %\
stackData.data[10:11,[29],:].sum())
else:
from PyMca import PyMcaQt as qt
from PyMca import QStackWidget
app = qt.QApplication([])
w = QStackWidget.QStackWidget()
print("Setting stack")
w.setStack(stackData)
w.show()
app.exec_()
if __name__ == "__main__":
test()
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