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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__ = "S. Petitdemange & V.A. Sole - ESRF Software Group"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import sys
import struct
import numpy
class MarCCD(object):
def __init__(self, filename):
if isinstance(filename, file):
fd = filename
else:
#the b is needed for windows
fd = open(filename, 'rb')
order = fd.read(2)
if order == "II":
#intel, little endian
fileOrder = "little"
elif order == "MM":
#motorola, high endian
fileOrder = "low"
else:
raise IOError("File is not a Mar CCD file, nor a TIFF file")
if sys.byteorder != fileOrder:
swap = True
else:
swap = False
self.__header = MccdHeader(fd)
info = {}
info.update(self.__header.getFormat())
info.update(self.__header.getGonio())
info.update(self.__header.getDetector())
info.update(self.__header.getFile())
nbytes = info["nfast"]* info["nslow"] * info["depth"]
depth = info["depth"]
fd.seek(4096)
if depth == 1:
data = numpy.fromstring(fd.read(nbytes), numpy.uint8)
elif depth == 2:
data = numpy.fromstring(fd.read(nbytes), numpy.uint16)
elif depth == 4:
data = numpy.fromstring(fd.read(nbytes), numpy.uint32)
if swap:
data = data.byteswap()
data.shape = info["nfast"], info["nslow"]
self.__data = data
self.__info = info
if not isinstance(filename, file):
fd.close()
def getData(self, *var, **kw):
return self.__data
def getInfo(self, *var, **kw):
return self.__info
class MccdHeader(object):
formatHead = ["nfast",
"nslow",
"depth"]
gonioHead= [ "xtal_to_detector",
"beam_x",
"beam_y",
"integration_time",
"exposure_time",
"readout_time",
"nreads",
"start_twotheta",
"start_omega",
"start_chi",
"start_kappa",
"start_phi",
"start_delta",
"start_gamma",
"start_xtal_to_detector",
"end_twotheta",
"end_omega",
"end_chi",
"end_kappa",
"end_phi",
"end_delta",
"end_gamma",
"end_xtal_to_detector",
"rotation_axis",
"rotation_range",
"detector_rotx",
"detector_roty",
"detector_rotz"
]
detectorHead= [ "detector_type",
"pixelsize_x", #nanometers
"pixelsize_y" #nanometers
]
fileHead= [ ("filetitle", 128),
("filepath", 128),
("filename", 64),
("acquire_timestamp", 32),
("header_timestamp", 32),
("save_timestamp", 32),
("file_comments", 512)
]
def __init__(self, fd):
self.gonioValue= []
self.detectorValue= []
self.fileValue= []
self.datasetValue= None
self.__read(fd)
self.__unpack()
def __read(self, fp):
fp.seek(1024) #standard TIFF header
self.raw= fp.read(3072) #Mar CCD Header
def __unpack(self):
self.__unpack_format() #256 unsigned int
self.__unpack_gonio()
self.__unpack_detector()
self.__unpack_file()
self.__unpack_dataset()
def __unpack_format(self):
if 0:
self.__format = struct.unpack("256I", self.raw[0:256*4])
else:
self.__format = numpy.fromstring(self.raw[0:256*4], numpy.uint32)
def __unpack_gonio(self):
idx= 640
size= struct.calcsize("i")
for nb in range(len(self.gonioHead)):
self.gonioValue.append(struct.unpack("i", self.raw[idx+nb*size:idx+(nb+1)*size])[0])
def __unpack_detector(self):
idx= 768
size= struct.calcsize("i")
for nb in range(len(self.detectorHead)):
self.detectorValue.append(struct.unpack("i", self.raw[idx+nb*size:idx+(nb+1)*size])[0])
def __unpack_file(self):
idx= 1024
for (name, size) in self.fileHead:
self.fileValue.append(self.raw[idx:idx+size].replace("\x00",""))
idx= idx+size
def __unpack_dataset(self):
idx= 2048
txt = self.raw[idx:idx+512].replace("\x00", "")
if len(txt):
self.datasetValue= txt
else: self.datasetValue= None
def getFormat(self):
fformat = {}
#for i in range(19, 30):
# print i, "VALUE =", self.__format[i]
fformat['nfast'] = self.__format[20] #n pixels in one line
fformat['nslow'] = self.__format[21] #n lines in image
fformat['depth'] = self.__format[22] #n bytes per pixel
return fformat
def getGonio(self):
gonio= {}
for (name, value) in zip(self.gonioHead, self.gonioValue):
gonio[name]= value
return gonio
def getDetector(self):
det= {}
for (name, value) in zip(self.detectorHead, self.detectorValue):
det[name]= value
return det
def getFile(self):
ffile= {}
for (head, value) in zip(self.fileHead, self.fileValue):
ffile[head[0]]= value
return ffile
def getDataset(self):
return self.datasetValue
if __name__ == "__main__":
import os
from PyMca5 import EdfFile
#fd = open('Cu_ZnO_20289.mccd', 'rb')
filename = sys.argv[1]
mccd = MarCCD(filename)
edfFile = filename+".edf"
if os.path.exists(edfFile):
os.remove(edfFile)
edf = EdfFile.EdfFile(edfFile)
edf.WriteImage(mccd.getInfo(),mccd.getData())
edf = None
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