/usr/lib/python2.7/dist-packages/PyMca/SpecFileStack.py is in pymca 4.7.4+dfsg-1.
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 toolkit is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the Free
# Software Foundation; either version 2 of the License, or (at your option)
# any later version.
#
# PyMca 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 General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# PyMca; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# PyMca follows the dual licensing model of Riverbank's PyQt and cannot be
# used as a free plugin for a non-free program.
#
# Please contact the ESRF industrial unit (industry@esrf.fr) if this license
# is a problem for you.
#############################################################################*/
import sys
import os
import numpy
from PyMca import DataObject
from PyMca.PyMcaIO import specfilewrapper as specfile
from PyMca import SpecFileDataSource
HDF5 = False
try:
import h5py
HDF5 = True
except:
pass
SOURCE_TYPE = "SpecFileStack"
DEBUG = 0
X_AXIS=0
Y_AXIS=1
Z_AXIS=2
class SpecFileStack(DataObject.DataObject):
def __init__(self, filelist = None):
DataObject.DataObject.__init__(self)
self.incrProgressBar=0
self.__keyList = []
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, shape=None):
if type(filelist) == type(''):
filelist = [filelist]
self.__keyList = []
self.sourceName = filelist
self.__indexedStack = True
self.sourceType = SOURCE_TYPE
self.info = {}
self.nbFiles=len(filelist)
#read first file
#get information
tempInstance=SpecFileDataSource.SpecFileDataSource(filelist[0])
keylist = tempInstance.getSourceInfo()['KeyList']
nscans = len(keylist) #that is the number of scans
nmca = 0
numberofdetectors = 0
for key in keylist:
info = tempInstance.getKeyInfo(key)
numberofmca = info['NbMca']
if numberofmca > 0:
numberofdetectors = info['NbMcaDet']
scantype = info["ScanType"]
if numberofmca:
nmca += numberofmca
if numberofdetectors == 0:
raise ValueError("No MCA found in file %s" % filelist[0])
if (nscans > 1) and ((nmca/numberofdetectors) == nscans):
SLOW_METHOD = True
else:
SLOW_METHOD = False
#get last mca of first point
key = "%s.1.%s" % (keylist[-1], numberofmca)
dataObject = tempInstance._getMcaData(key)
self.info.update(dataObject.info)
arrRet = dataObject.data
self.onBegin(self.nbFiles*nmca/numberofdetectors)
self.incrProgressBar= 0
if info['NbMcaDet'] > 1:
#Should I generate a map for each mca and not just for the last one as I am doing?
iterlist = range(info['NbMcaDet'],info['NbMca']+1,info['NbMcaDet'])
else:
iterlist = [1]
if SLOW_METHOD and shape is None:
self.data = numpy.zeros((self.nbFiles,
nmca/numberofdetectors,
arrRet.shape[0]),
arrRet.dtype.char)
filecounter = 0
for tempFileName in filelist:
tempInstance=SpecFileDataSource.SpecFileDataSource(tempFileName)
mca_number = -1
for keyindex in keylist:
info = tempInstance.getKeyInfo(keyindex)
numberofmca = info['NbMca']
if numberofmca <= 0:
continue
key = "%s.1.%s" % (keyindex, numberofmca)
dataObject = tempInstance._getMcaData(key)
arrRet = dataObject.data
mca_number += 1
for i in iterlist:
#mcadata = scan_obj.mca(i)
self.data[filecounter,
mca_number,
:] = arrRet[:]
self.incrProgressBar += 1
self.onProgress(self.incrProgressBar)
filecounter += 1
elif shape is None and (self.nbFiles == 1) and (iterlist == [1]):
#it can only be here if there is one file
#it can only be here if there is only one scan
#it can only be here if there is only one detector
self.data = numpy.zeros((1,
numberofmca,
arrRet.shape[0]),
arrRet.dtype.char)
for tempFileName in filelist:
tempInstance=specfile.Specfile(tempFileName)
#it can only be here if there is one scan per file
#prevent problems if the scan number is different
#scan = tempInstance.select(keylist[-1])
scan = tempInstance[-1]
iterationList = range(scan.nbmca())
for i in iterationList:
#mcadata = scan_obj.mca(i)
self.data[0,
i,
:] = scan.mca(i+1)[:]
self.incrProgressBar += 1
self.onProgress(self.incrProgressBar)
filecounter = 1
elif shape is None:
#it can only be here if there is one scan per file
try:
self.data = numpy.zeros((self.nbFiles,
numberofmca/numberofdetectors,
arrRet.shape[0]),
arrRet.dtype.char)
filecounter = 0
for tempFileName in filelist:
tempInstance=specfile.Specfile(tempFileName)
#it can only be here if there is one scan per file
#prevent problems if the scan number is different
#scan = tempInstance.select(keylist[-1])
scan = tempInstance[-1]
for i in iterlist:
#mcadata = scan_obj.mca(i)
self.data[filecounter,
0,
:] = scan.mca(i)[:]
self.incrProgressBar += 1
self.onProgress(self.incrProgressBar)
filecounter += 1
except MemoryError:
qtflag = False
if ('PyQt4.QtCore' in sys.modules) or\
('PyMcaQt' in sys.modules) or\
('PyMca.PyMcaQt' in sys.modules):
qtflag = True
hdf5done = False
if HDF5 and qtflag:
import PyMcaQt as qt
import ArraySave
msg=qt.QMessageBox.information( None,
"Memory error\n",
"Do you want to convert your data to HDF5?\n",
qt.QMessageBox.Yes,qt.QMessageBox.No)
if msg != qt.QMessageBox.No:
hdf5file = qt.QFileDialog.getSaveFileName(None,
"Please select output file name",
os.path.dirname(filelist[0]),
"HDF5 files *.h5")
if not len(hdf5file):
raise IOError("Invalid output file")
hdf5file = qt.safe_str(hdf5file)
if not hdf5file.endswith(".h5"):
hdf5file += ".h5"
#get the final shape
from PyMca.RGBCorrelatorWidget import ImageShapeDialog
stackImageShape = self.nbFiles,\
int(numberofmca/numberofdetectors)
dialog = ImageShapeDialog(None, shape =stackImageShape)
dialog.setModal(True)
ret = dialog.exec_()
if ret:
stackImageShape= dialog.getImageShape()
dialog.close()
del dialog
hdf, self.data = ArraySave.getHDF5FileInstanceAndBuffer(hdf5file,
(stackImageShape[0],
stackImageShape[1],
arrRet.shape[0]),
compression=None,
interpretation="spectrum")
nRow = 0
nCol = 0
for tempFileName in filelist:
tempInstance=specfile.Specfile(tempFileName)
#it can only be here if there is one scan per file
#prevent problems if the scan number is different
#scan = tempInstance.select(keylist[-1])
scan = tempInstance[-1]
nRow = int(self.incrProgressBar/stackImageShape[1])
nCol = self.incrProgressBar%stackImageShape[1]
for i in iterlist:
#mcadata = scan_obj.mca(i)
self.data[nRow,
nCol,
:] = scan.mca(i)[:]
self.incrProgressBar += 1
self.onProgress(self.incrProgressBar)
hdf5done = True
hdf.flush()
self.onEnd()
self.info["SourceType"] = "HDF5Stack1D"
self.info["McaIndex"] = 2
self.info["FileIndex"] = 0
self.info["SourceName"] = [hdf5file]
self.info["NumberOfFiles"] = 1
self.info["Size"] = 1
return
else:
raise
else:
sampling_order = 1
s0 = shape[0]
s1 = shape[1]
MEMORY_ERROR = False
try:
self.data = numpy.zeros((shape[0],
shape[1],
arrRet.shape[0]),
arrRet.dtype.char)
except MemoryError:
try:
self.data = numpy.zeros((shape[0],
shape[1],
arrRet.shape[0]),
numpy.float32)
except MemoryError:
MEMORY_ERROR = True
while MEMORY_ERROR:
try:
for i in range(5):
print("\7")
sampling_order += 1
print("**************************************************")
print(" Memory error!, attempting %dx%d sub-sampling " %\
(sampling_order, sampling_order))
print("**************************************************")
s0 = int(shape[0]/sampling_order)
s1 = int(shape[1]/sampling_order)
#if shape[0] % sampling_order:
# s0 = s0 + 1
#if shape[1] % sampling_order:
# s1 = s1 + 1
self.data = numpy.zeros((s0, s1,
arrRet.shape[0]),
numpy.float32)
MEMORY_ERROR = False
except MemoryError:
pass
filecounter = 0
for j in range(s0):
filecounter = (j * sampling_order) * shape[1]
for k in range(s1):
tempFileName = filelist[filecounter]
tempInstance=specfile.Specfile(tempFileName)
if tempInstance is None:
if not os.path.exists(tempFileName):
print("File %s does not exists" % tempFileName)
raise IOError(\
"File %s does not exists" % tempFileName)
scan = tempInstance.select(keylist[-1])
for i in iterlist:
#sum the present mcas
self.data[j,
k,
:] += scan.mca(i)[:]
self.incrProgressBar += 1
self.onProgress(self.incrProgressBar)
filecounter += sampling_order
self.nbFiles = s0 * s1
self.onEnd()
"""
# Scan types
# ----------
#SF_EMPTY = 0 # empty scan
#SF_SCAN = 1 # non-empty scan
#SF_MESH = 2 # mesh scan
#SF_MCA = 4 # single mca
#SF_NMCA = 8 # multi mca (more than 1 mca per acq)
case = None
if scantype == (SpecFileDataSource.SF_MESH + \
SpecFileDataSource.SF_MCA):
# SINGLE MESH + SINGLE MCA
# nfiles = 1
# nscans = 1
# nmca = 1
# there is a danger if it can be considered an indexed file ...
pass
elif scantype == (SpecFileDataSource.SF_MESH + \
SpecFileDataSource.SF_NMCA):
# SINGLE MESH + MULTIPLE MCA
# nfiles = 1
# nscans = 1
# nmca > 1
# there is a danger if it can be considered an indexed file ...
#for the time being I take last mca
pass
elif scantype == (SpecFileDataSource.SF_SCAN+ \
SpecFileDataSource.SF_MCA):
#Assumed scans containing always 1 detector
pass
elif scantype == (SpecFileDataSource.SF_MCA):
#Assumed scans containing always 1 detector
pass
elif scantype == (SpecFileDataSource.SF_SCAN+ \
SpecFileDataSource.SF_NMCA):
#Assumed scans containing the same number of detectors
#for the time being I take last mca
pass
elif scantype == (SpecFileDataSource.SF_NMCA):
#Assumed scans containing the same number of detectors
#for the time being I take last mca
pass
else:
raise ValueError, "Unhandled scan type = %s" % scantype
"""
self.__nFiles = self.nbFiles
self.__nImagesPerFile = 1
shape = self.data.shape
for i in range(len(shape)):
key = 'Dim_%d' % (i+1,)
self.info[key] = shape[i]
self.info["SourceType"] = SOURCE_TYPE
self.info["SourceName"] = self.sourceName
self.info["Size"] = self.__nFiles * self.__nImagesPerFile
self.info["NumberOfFiles"] = self.__nFiles * 1
self.info["FileIndex"] = fileindex
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)
if __name__ == "__main__":
import time
import sys
t0= time.time()
stack = SpecFileStack()
#stack.loadIndexedStack("Z:\COTTE\ch09\ch09__mca_0005_0000_0070.edf")
if len(sys.argv) > 1:
stack.loadIndexedStack(sys.argv[1])
else:
stack.loadIndexedStack("..\..\mca3\c449b01_001.mca")
shape = stack.data.shape
print("elapsed = %f" % (time.time() - t0))
#guess the MCA
imax = 0
for i in range(len(shape)):
if shape[i] > shape[imax]:
imax = i
print("selections ")
print("getZSelectionArray shape = ", stack.getZSelectionArray().shape)
print("getXYSelectionArray shape = ", stack.getXYSelectionArray().shape)
from PyMca import PyMcaQt as qt
app = qt.QApplication([])
qt.QObject.connect(app, qt.SIGNAL("lastWindowClosed()"),
app, qt.SLOT("quit()"))
if 1:
from PyMca import RGBCorrelatorGraph
w = RGBCorrelatorGraph.RGBCorrelatorGraph()
graph = w.graph
else:
from PyMca import QtBlissGraph
w = QtBlissGraph.QtBlissGraph()
graph = w
print("shape sum 0 = ", numpy.sum(stack.data, 0).shape)
print("shape sum 1 = ", numpy.sum(stack.data, 1).shape)
print("shape sum 2 = ", numpy.sum(stack.data, 2).shape)
a = numpy.sum(stack.data, imax)
print(a.shape)
graph.setX1AxisLimits(0, a.shape[0])
if 0:
w.setY1AxisLimits(0, a.shape[1])
w.setY1AxisInverted(True)
else:
graph.setY1AxisInverted(True)
graph.setY1AxisLimits(0, a.shape[1])
graph.imagePlot(a, ymirror=0)
if imax == 0:
graph.x1Label('Column Number')
else:
graph.x1Label('Row Number')
graph.ylabel('File Number')
w.show()
if imax == 0:
mcaData0 = numpy.sum(numpy.sum(stack.data, 2),1)
else:
mcaData0 = numpy.sum(numpy.sum(stack.data, 2),0)
from PyMca import McaWindow
mca = McaWindow.McaWidget()
sel = {}
sel['SourceName'] = "Specfile Stack"
sel['Key'] = "SUM"
sel['legend'] = "EDF Stack SUM"
mcaData = DataObject.DataObject()
mcaData.info = {'McaCalib': [0 , 2.0 ,0],
"selectiontype":"1D",
"SourceName":"Specfile Stack",
"Key":"SUM"}
mcaData.x = [numpy.arange(len(mcaData0)).astype(numpy.float)]
mcaData.y = [mcaData0]
sel['dataobject'] = mcaData
mca.show()
mca._addSelection([sel])
graph.enableSelection(True)
def graphSlot(ddict):
if ddict['event'] == "MouseSelection":
ix1 = int(ddict['xmin'])
ix2 = int(ddict['xmax'])+1
iy1 = int(ddict['xmin'])
iy2 = int(ddict['xmax'])+1
if imax == 0:
selectedData = numpy.sum(numpy.sum(stack.data[:,ix1:ix2, iy1:iy2], 2),1)
else:
selectedData = numpy.sum(numpy.sum(stack.data[ix1:ix2,:, iy1:iy2], 2),0)
sel = {}
sel['SourceName'] = "Specfile Stack"
sel['Key'] = "Selection"
sel["selectiontype"] = "1D"
sel['legend'] = "EDF Stack Selection"
selDataObject = DataObject.DataObject()
selDataObject.info={'McaCalib': [100 , 2.0 ,0],
"selectiontype":"1D",
"SourceName":"EDF Stack Selection",
"Key":"Selection"}
selDataObject.x = [numpy.arange(len(mcaData0)).astype(numpy.float)]
selDataObject.y = [selectedData]
sel['dataobject'] = selDataObject
mca._addSelection([sel])
qt.QObject.connect(graph, qt.SIGNAL('QtBlissGraphSignal'),
graphSlot)
#w.replot()
if qt.qVersion() < '4.0.0':
app.exec_loop()
else:
app.exec_()
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