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#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2004-2015 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 os
import sys
import re
import struct
import numpy
import copy
from PyMca5 import DataObject
if sys.version < '2.6':
def bytes(x):
return str(x)
DEBUG = 0
SOURCE_TYPE = "EdfFileStack"
class MRCMap(DataObject.DataObject):
'''
Class to read MRC files
It reads the spectra into a DataObject instance.
This class info member contains all the parsed information.
This class data member contains the map itself as a 3D array.
'''
def __init__(self, filename):
'''
Parameters:
-----------
filename : str
Name of the input file.
It is expected to work with files generated at BESSY with raw2mrc
'''
DataObject.DataObject.__init__(self)
try:
fid = open(filename, 'rb')
header = fid.read(1024)
fid.close()
except:
fid.close()
raise
if not _isMRCHeader(header):
raise IOError("File does not seem to be an MRC file")
self.sourceName = filename
# check endianness
flag = struct.unpack("4B", header[212:216])[0]
if flag in [17, 18]:
# high endian (Motorola)
endianness = ">"
else:
# little endian (Intel)
endianness = "<"
fmt = endianness + "10i"
tenIntegers = struct.unpack(fmt, header[0:40])
nColumns, nRows, nImages, mode = tenIntegers[0:4]
fmt = endianness + "6f"
sixFloats = struct.unpack(fmt, header[40:64])
fmt = endianness + "3i"
threeIntegers = struct.unpack(fmt, header[64:76])
fmt = endianness + "3f"
threeFloats = struct.unpack(fmt, header[76:88])
# number of bytes in extended header
fmt = endianness + "i"
offset = struct.unpack(fmt, header[92:96])[0]
fmt = endianness + "ii"
imodStamp, imodFlags = struct.unpack(fmt, header[152:160])
if mode == 0:
# bytes
dataFormat = endianness + "%dB" % (nRows * nColumns)
elif mode == 1:
# signed short integers (16 bit)
dataFormat = endianness + "%dh" % (nRows * nColumns)
elif mode == 2:
# float
dataFormat = endianness + "%df" % (nRows * nColumns)
elif mode == 3:
# two shorts, complex data
dataFormat = endianness + "%dh" % (2 * nRows * nColumns)
elif mode == 4:
# two floats, complex data
dataFormat = endianness + "%df" % (2 * nRows * nColumns)
elif mode == 6:
# unsigned 16 bit integers (non-standard)
dataFormat = endianness + "%dH" % (nRows * nColumns)
elif mode == 16:
# unsigned char * 3(rgb data, non-standard)
dataFormat = endianness + "%dB" % (3 * nRows * nColumns)
else:
raise IOError("Data format not undestood")
if imodFlags == 1:
# bytes stored as signed
dataFormat = dataFormat.lower()
data = numpy.zeros((nImages, nRows * nColumns), numpy.float)
fid = open(filename, 'rb')
fileOffset = 1024 + offset
fid.seek(fileOffset)
dataSize= struct.calcsize(dataFormat)
try:
for i in range(nImages):
tmpData = fid.read(dataSize)
data[i] = struct.unpack(dataFormat, tmpData)
fid.close()
except:
fid.close()
raise
data.shape = nImages, nRows, nColumns
self.data = data
self.info = {}
self.info["SourceType"] = SOURCE_TYPE
self.info["SourceName"] = self.sourceName
shape = self.data.shape
for i in range(len(shape)):
key = 'Dim_%d' % (i + 1,)
self.info[key] = shape[i]
self.info["NumberOfFiles"] = 1
self.info["McaIndex"] = 0
self.info["McaCalib"] = [0.0, 1.0, 0.0]
self.info["Channel0"] = 0.0
def _isMRCHeader(header):
try:
if sys.version < '3.0':
test = "MAP "
else:
test = bytes("MAP ", "utf-8")
if struct.unpack("4s", header[208:212])[0] == test:
return True
except:
pass
return False
def isMRCFile(filename):
try:
fid = open(filename, 'rb')
header = fid.read(1024)
fid.close()
except:
fid.close()
return False
nColumns, nRows, nImages = struct.unpack("iii", header[0:12])
imodStamp, imodFlags = struct.unpack("ii", header[152:160])
#print(imodStamp, imodFlags)
# system byte order
#print("system ",sys.byteorder)
return _isMRCHeader(header)
if __name__ == "__main__":
filename = None
if len(sys.argv) > 1:
filename = sys.argv[1]
print("is MRC File?", isMRCFile(filename))
instance = MRCMap(filename)
print(instance.info)
print(instance.data)
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