Source code for fabio.marccdimage
#!/usr/bin/env python
"""
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
from tifimage import tifimage
import logging
logger = logging.getLogger("marccdimage")
# 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;
"""
import struct
# 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
HEADER_NAMES, HEADER_FORMAT = make_format(CDEFINITION)
[docs]class marccdimage(tifimage):
""" Read in data in mar ccd format, also
MarMosaic images, including header info """
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)