Source code for PyMca5.PyMcaIO.MarCCD

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# The PyMca X-Ray Fluorescence Toolkit
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__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

[docs]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()
[docs] def getData(self, *var, **kw): return self.__data
[docs] def getInfo(self, *var, **kw): return self.__info
[docs]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
[docs] 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
[docs] def getGonio(self): gonio= {} for (name, value) in zip(self.gonioHead, self.gonioValue): gonio[name]= value return gonio
[docs] def getDetector(self): det= {} for (name, value) in zip(self.detectorHead, self.detectorValue): det[name]= value return det
[docs] def getFile(self): ffile= {} for (head, value) in zip(self.fileHead, self.fileValue): ffile[head[0]]= value return ffile
[docs] 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