# coding: utf-8 # # Project: X-ray image reader # https://github.com/silx-kit/fabio # # # Copyright (C) European Synchrotron Radiation Facility, Grenoble, France # # Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu) # # 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 """ Authors: ........ * Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk * Jon Wright: European Synchrotron Radiation Facility; Grenoble (France) marccdimage can read MarCCD and MarMosaic images including header info. JPW : Use a parser in case of typos (sorry?) """ # Base this on the tifimage (as marccd seems to be tiff with a # special header import logging import struct from .tifimage import TifImage logger = logging.getLogger(__name__) # Now for the c definition (found on mar webpage) # The following string is therefore copyrighted by Mar I guess CDEFINITION = """ typedef struct frame_header_type { /* File/header format parameters (256 bytes) */ UINT32 header_type; /* flag for header type (can be used as magic number) */ char header_name[16]; /* header name (MMX) */ UINT32 header_major_version; /* header_major_version (n.) */ UINT32 header_minor_version; /* header_minor_version (.n) */ UINT32 header_byte_order;/* BIG_ENDIAN (Motorola,MIPS); LITTLE_ENDIAN (DEC, Intel) */ UINT32 data_byte_order; /* BIG_ENDIAN (Motorola,MIPS); LITTLE_ENDIAN (DEC, Intel) */ UINT32 header_size; /* in bytes */ UINT32 frame_type; /* flag for frame type */ UINT32 magic_number; /* to be used as a flag - usually to indicate new file */ UINT32 compression_type; /* type of image compression */ UINT32 compression1; /* compression parameter 1 */ UINT32 compression2; /* compression parameter 2 */ UINT32 compression3; /* compression parameter 3 */ UINT32 compression4; /* compression parameter 4 */ UINT32 compression5; /* compression parameter 4 */ UINT32 compression6; /* compression parameter 4 */ UINT32 nheaders; /* total number of headers */ UINT32 nfast; /* number of pixels in one line */ UINT32 nslow; /* number of lines in image */ UINT32 depth; /* number of bytes per pixel */ UINT32 record_length; /* number of pixels between succesive rows */ UINT32 signif_bits; /* true depth of data, in bits */ UINT32 data_type; /* (signed,unsigned,float...) */ UINT32 saturated_value; /* value marks pixel as saturated */ UINT32 sequence; /* TRUE or FALSE */ UINT32 nimages; /* total number of images - size of each is nfast*(nslow/nimages) */ UINT32 origin; /* corner of origin */ UINT32 orientation; /* direction of fast axis */ UINT32 view_direction; /* direction to view frame */ UINT32 overflow_location;/* FOLLOWING_HEADER, FOLLOWING_DATA */ UINT32 over_8_bits; /* # of pixels with counts 255 */ UINT32 over_16_bits; /* # of pixels with count 65535 */ UINT32 multiplexed; /* multiplex flag */ UINT32 nfastimages; /* # of images in fast direction */ UINT32 nslowimages; /* # of images in slow direction */ UINT32 background_applied;/* flags correction has been applied hold magic number ? */ UINT32 bias_applied; /* flags correction has been applied hold magic number ? */ UINT32 flatfield_applied;/* flags correction has been applied - hold magic number ? */ UINT32 distortion_applied;/*flags correction has been applied - hold magic number ? */ UINT32 original_header_type; /* Header/frame type from file that frame is read from */ UINT32 file_saved; /* Flag that file has been saved, should be zeroed if modified */ char reserve1[(64-40)*sizeof(INT32)-16]; /* Data statistics (128) */ UINT32 total_counts[2]; /* 64 bit integer range = 1.85E19*/ UINT32 special_counts1[2]; UINT32 special_counts2[2]; UINT32 min; UINT32 max; UINT32 mean; UINT32 rms; UINT32 p10; UINT32 p90; UINT32 stats_uptodate; UINT32 pixel_noise[MAXIMAGES]; /*1000*base noise value (ADUs) */ char reserve2[(32-13-MAXIMAGES)*sizeof(INT32)]; /* More statistics (256) */ UINT16 percentile[128]; /* Goniostat parameters (128 bytes) */ INT32 xtal_to_detector; /* 1000*distance in millimeters */ INT32 beam_x; /* 1000*x beam position (pixels) */ INT32 beam_y; /* 1000*y beam position (pixels) */ INT32 integration_time; /* integration time in milliseconds */ INT32 exposure_time; /* exposure time in milliseconds */ INT32 readout_time; /* readout time in milliseconds */ INT32 nreads; /* number of readouts to get this image */ INT32 start_twotheta; /* 1000*two_theta angle */ INT32 start_omega; /* 1000*omega angle */ INT32 start_chi; /* 1000*chi angle */ INT32 start_kappa; /* 1000*kappa angle */ INT32 start_phi; /* 1000*phi angle */ INT32 start_delta; /* 1000*delta angle */ INT32 start_gamma; /* 1000*gamma angle */ INT32 start_xtal_to_detector; /* 1000*distance in mm (dist in um)*/ INT32 end_twotheta; /* 1000*two_theta angle */ INT32 end_omega; /* 1000*omega angle */ INT32 end_chi; /* 1000*chi angle */ INT32 end_kappa; /* 1000*kappa angle */ INT32 end_phi; /* 1000*phi angle */ INT32 end_delta; /* 1000*delta angle */ INT32 end_gamma; /* 1000*gamma angle */ INT32 end_xtal_to_detector; /* 1000*distance in mm (dist in um)*/ INT32 rotation_axis; /* active rotation axis */ INT32 rotation_range; /* 1000*rotation angle */ INT32 detector_rotx; /* 1000*rotation of detector around X */ INT32 detector_roty; /* 1000*rotation of detector around Y */ INT32 detector_rotz; /* 1000*rotation of detector around Z */ char reserve3[(32-28)*sizeof(INT32)]; /* Detector parameters (128 bytes) */ INT32 detector_type; /* detector type */ INT32 pixelsize_x; /* pixel size (nanometers) */ INT32 pixelsize_y; /* pixel size (nanometers) */ INT32 mean_bias; /* 1000*mean bias value */ INT32 photons_per_100adu; /* photons / 100 ADUs */ INT32 measured_bias[MAXIMAGES];/* 1000*mean bias value for each image*/ INT32 measured_temperature[MAXIMAGES]; /* Temperature of each detector in milliKelvins */ INT32 measured_pressure[MAXIMAGES]; /* Pressure of each chamber in microTorr */ /* Retired reserve4 when MAXIMAGES set to 9 from 16 and two fields removed, and temp and pressure added char reserve4[(32-(5+3*MAXIMAGES))*sizeof(INT32)] */ /* X-ray source and optics parameters (128 bytes) */ /* X-ray source parameters (8*4 bytes) */ INT32 source_type; /* (code) - target, synch. etc */ INT32 source_dx; /* Optics param. - (size microns) */ INT32 source_dy; /* Optics param. - (size microns) */ INT32 source_wavelength; /* wavelength (femtoMeters) */ INT32 source_power; /* (Watts) */ INT32 source_voltage; /* (Volts) */ INT32 source_current; /* (microAmps) */ INT32 source_bias; /* (Volts) */ INT32 source_polarization_x; /* () */ INT32 source_polarization_y; /* () */ char reserve_source[4*sizeof(INT32)]; /* X-ray optics_parameters (8*4 bytes) */ INT32 optics_type; /* Optics type (code)*/ INT32 optics_dx; /* Optics param. - (size microns) */ INT32 optics_dy; /* Optics param. - (size microns) */ INT32 optics_wavelength; /* Optics param. - (size microns) */ INT32 optics_dispersion; /* Optics param. - (*10E6) */ INT32 optics_crossfire_x; /* Optics param. - (microRadians) */ INT32 optics_crossfire_y; /* Optics param. - (microRadians) */ INT32 optics_angle; /* Optics param. - (monoch. 2theta - microradians) */ INT32 optics_polarization_x; /* () */ INT32 optics_polarization_y; /* () */ char reserve_optics[4*sizeof(INT32)]; char reserve5[((32-28)*sizeof(INT32))]; /* File parameters (1024 bytes) */ char filetitle[128]; /* Title */ char filepath[128]; /* path name for data file */ char filename[64]; /* name of data file */ char acquire_timestamp[32]; /* date and time of acquisition */ char header_timestamp[32]; /* date and time of header update */ char save_timestamp[32]; /* date and time file saved */ char file_comments[512]; /* comments, use as desired */ char reserve6[1024-(128+128+64+(3*32)+512)]; /* Dataset parameters (512 bytes) */ char dataset_comments[512]; /* comments, used as desired */ /* pad out to 3072 bytes */ char pad[3072-(256+128+256+(3*128)+1024+512)]; } frame_header; """ # Convert mar c header file types to python struct module types C_TO_STRUCT = { "INT32": "i", "UINT32": "I", "char": "c", "UINT16": "H"} # Sizes (bytes) of mar c header objects C_SIZES = { "INT32": 4, "UINT32": 4, "char": 1, "UINT16": 2} # This was worked out by trial and error from a trial image I think MAXIMAGES = 9 def make_format(c_def_string): """ Reads the header definition in c and makes the format string to pass to struct.unpack """ lines = c_def_string.split("\n") fmt = "" names = [] expected = 0 for line in lines: if line.find(";") == -1: continue decl = line.split(";")[0].lstrip().rstrip() try: [typ, name] = decl.split() except ValueError: logger.debug("skipping: %s", line) continue if name.find("[") > -1: # repeated ... times try: num = name.split("[")[1].split("]")[0] num = num.replace("MAXIMAGES", str(MAXIMAGES)) num = num.replace("sizeof(INT32)", "4") times = eval(num) except Exception as error: logger.error("%s Please decode %s", error, decl) raise error else: times = 1 try: fmt += C_TO_STRUCT[typ] * times names += [name] * times expected += C_SIZES[typ] * times except KeyError: continue return names, fmt # Make these be compiled on loading module HEADER_NAMES, HEADER_FORMAT = make_format(CDEFINITION) def interpret_header(header, fmt, names): """ given a format and header interpret it """ values = struct.unpack(fmt, header) hdr = {} i = 0 for name in names: if name in hdr: if isinstance(values[i], str): hdr[name] = hdr[name] + values[i] else: try: hdr[name].append(values[i]) except AttributeError: hdr[name] = [hdr[name], values[i]] else: hdr[name] = values[i] i = i + 1 return hdr class MarccdImage(TifImage): """ Read in data in mar ccd format, also MarMosaic images, including header info """ DESCRIPTION = "File format from MarCCD and MarMosaic images" DEFAULT_EXTENSIONS = ["mccd"] def _readheader(self, infile): """ Parser based approach Gets all entries """ infile.seek(1024) hstr = infile.read(3072) self.header = interpret_header(hstr, HEADER_FORMAT, HEADER_NAMES) def _read(self, fname): """ inherited from tifimage ... a marccd image *is a* tif image just with a header """ return TifImage.read(self, fname) marccdimage = MarccdImage