#!/usr/bin/env python ''' *ReadMarCCDFrame: Read Mar Files* --------------------------------- ''' """ from /opt/marccd/documentation/header.txt MarCCD Header Documentataion from C code in frame.h and types.h Documentation updated by R. Doyle Mon Mar 22 15:04:00 CDT 2010 Documentation updated by M. Blum Tue Oct 11 11:49:20 CDT 2005 Description documents marccd v0.20.0 Summary of file structure: |-- 1024 bytes TIFF HEADER -------------| |-- 3072 byte frame_header structure ---| |-- nfast*nslow*depth byte image -------| The full header, as written to the file, is a TIFF header. The initial 1024 bytes are a minimal TIFF header with a standard TIFF TAG pointing to the image data and a private TIFF TAG pointing to this header structure. As written by mmx/marccd, the frame_header structure always begins at byte 1024 and is 3072 bytes long making the full header 4096 bytes. immediately following the header is the image - it is of arbitrary size defined by the header fields nfast, nslow and depth. The total size is nfast * nslow * depth bytes. The meanings of the data types should be self evident: (example: UINT32 is an unsigned 32 bit integer) The exact C language definition is machine dependent but these are the most common definitions on a 32bit architecture cpu. #define UINT16 unsigned short #define INT16 short #define UINT32 unsigned int #define INT32 int Currently frames are always written as defined below: origin=UPPER_LEFT orientation=HFAST view_direction=FROM_SOURCE /* This number is written into the byte_order fields in the native byte order of the machine writing the file */ #define LITTLE_ENDIAN 1234 #define BIG_ENDIAN 4321 /* possible orientations of frame data (stored in orienation field) */ #define HFAST 0 /* Horizontal axis is fast */ #define VFAST 1 /* Vertical axis is fast */ /* possible origins of frame data (stored in origin field) */ #define UPPER_LEFT 0 #define LOWER_LEFT 1 #define UPPER_RIGHT 2 #define LOWER_RIGHT 3 /* possible view directions of frame data for the given orientation and origin (stored in view_direction field) */ #define FROM_SOURCE 0 #define TOWARD_SOURCE 1 /* possible types of data (in data_type field) */ #define DATA_UNSIGNED_INTEGER 0 #define DATA_SIGNED_INTEGER 1 #define DATA_FLOAT 2 #define MAXIMAGES 9 #define MAXSUBIMAGES 4096 #define MAXFRAMEDIMENSION 8192 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 (MARCCD) */ 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 darkcurrent_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 */ UINT32 n_valid_pixels; /* Number of pixels holding valid data - first N pixels */ UINT32 defectmap_applied; /* flags correction has been applied - hold magic number ? */ UINT32 subimage_nfast; /* when divided into subimages (eg. frameshifted) */ UINT32 subimage_nslow; /* when divided into subimages (eg. frameshifted) */ UINT32 subimage_origin_fast; /* when divided into subimages (eg. frameshifted) */ UINT32 subimage_origin_slow; /* when divided into subimages (eg. frameshifted) */ UINT32 readout_pattern; /* BIT Code - 1 = A, 2 = B, 4 = C, 8 = D */ UINT32 saturation_level; /* at this value and above, data are not reliable */ UINT32 orientation_code; /* Describes how this frame needs to be rotated to make it "right" */ UINT32 frameshift_multiplexed; /* frameshift multiplex flag */ UINT32 prescan_nfast; /* Number of non-image pixels preceeding imaging pixels - fast direction */ UINT32 prescan_nslow; /* Number of non-image pixels preceeding imaging pixels - slow direction */ UINT32 postscan_nfast; /* Number of non-image pixels followng imaging pixels - fast direction */ UINT32 postscan_nslow; /* Number of non-image pixels followng imaging pixels - slow direction */ UINT32 prepost_trimmed; /* trimmed==1 means pre and post scan pixels have been removed */ char reserve1[(64-55)*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; INT32 mean; /* mean * 1000 */ UINT32 rms; /* rms * 1000 */ UINT32 n_zeros; /* number of pixels with 0 value - not included in stats in unsigned data */ UINT32 n_saturated; /* number of pixels with saturated value - not included in stats */ UINT32 stats_uptodate; /* Flag that stats OK - ie data not changed since last calculation */ UINT32 pixel_noise[MAXIMAGES]; /* 1000*base noise value (ADUs) */ char reserve2[(32-13-MAXIMAGES)*sizeof(INT32)]; /* Sample Changer info */ char barcode[16]; UINT32 barcode_angle; UINT32 barcode_status; /* Pad to 256 bytes */ char reserve2a[(64-6)*sizeof(INT32)]; /* 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 (index into above ie. 0=twotheta,1=omega...) */ 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 */ INT32 total_dose; /* Hz-sec (counts) integrated over full exposure */ char reserve3[(32-29)*sizeof(INT32)]; /* Pad Gonisotat parameters to 128 bytes */ /* 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 (14*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; /* () */ INT32 source_intensity_0; /* (arbitrary units) */ INT32 source_intensity_1; /* (arbitrary units) */ char reserve_source[2*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))]; /* Pad X-ray parameters to 128 bytes */ /* 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_comment[512]; /* comments - can be used as desired */ char reserve6[1024-(128+128+64+(3*32)+512)]; /* Pad File parameters to 1024 bytes */ /* Dataset parameters (512 bytes) */ char dataset_comment[512]; /* comments - can be used as desired */ /* Reserved for user definable data - will not be used by Mar! */ char user_data[512]; /* char pad[----] USED UP! */ /* pad out to 3072 bytes */ } frame_header; """ import struct as st import array as ar import string, re MAXIMAGES=9 class marFrame(): '''A class to extract correct mar header and image info from a MarCCD file :param str File: file object [from open()] :param byteOrd: '<' (default) or '>' :param dict IFD: ? ''' def __init__(self,File,byteOrd='<',IFD={}): # simple TIFF header info self.TIFFsizeX = IFD[256][2][0] self.TIFFsizeY = IFD[257][2][0] self.TIFFbitDepth = IFD[258][2][0] self.TIFFcompression = IFD[259][2][0] # 1 = no compression self.TIFFphotometricInterpretation = IFD[262][2][0] # 1 = bilevel or grayscale where 0 is imaged as black self.TIFFstripOffsets = IFD[273][2][0] # seems to be 4096 for marCCD self.TIFForientation = IFD[274][2][0] # 1 = 0th row it top, 0th column is left self.TIFFrowsPerStrip = IFD[278][2][0] # varies based on image size self.TIFFstripByteCounts = IFD[279][2][0] # number of bytes in a strip also varies based on size self.TIFFxResolution = IFD[282][2][0] # pixels per resolutionUnit in X direction (ImageWidth direction) self.TIFFyResolution = IFD[283][2][0] # pixels per resolutionUnit in Y direction (ImageLength direction self.TIFFresolutionUnit = IFD[296][2][0] # 3 = centimeter self.byteDepth = self.TIFFbitDepth/8 self.arrayTypeCode = ['','B','H','L'][self.byteDepth] # MarCCD specific header info File.seek(IFD[34710][2][0]) self.headerType = st.unpack(byteOrd+'I',File.read(4))[0] #/* flag for header type (can be used as magic number) */ self.headerName = re.sub(r'\x00','',string.join(st.unpack(byteOrd+16*'c',File.read(16)),'')) self.headerMajorVersion = st.unpack(byteOrd+'I',File.read(4))[0] #/* header_major_version (n.) */ self.headerMinorVersion = st.unpack(byteOrd+'I',File.read(4))[0] #/* header_minor_version (.n) */ self.headerByteOrder = st.unpack(byteOrd+'I',File.read(4))[0] #/* BIG_ENDIAN (Motorola,MIPS); LITTLE_ENDIAN (DEC, Intel) */ self.dataByteOrder = st.unpack(byteOrd+'I',File.read(4))[0] #/* BIG_ENDIAN (Motorola,MIPS); LITTLE_ENDIAN (DEC, Intel) */ self.headerSize = st.unpack(byteOrd+'I',File.read(4))[0] #/* in bytes */ self.frameType = st.unpack(byteOrd+'I',File.read(4))[0] #/* flag for frame type */ self.magicNumber = st.unpack(byteOrd+'I',File.read(4))[0] #/* to be used as a flag - usually to indicate new file */ self.compressionType = st.unpack(byteOrd+'I',File.read(4))[0] #/* type of image compression */ self.compression1 = st.unpack(byteOrd+'I',File.read(4))[0] #/* compression parameter 1 */ self.compression2 = st.unpack(byteOrd+'I',File.read(4))[0] #/* compression parameter 2 */ self.compression3 = st.unpack(byteOrd+'I',File.read(4))[0] #/* compression parameter 3 */ self.compression4 = st.unpack(byteOrd+'I',File.read(4))[0] #/* compression parameter 4 */ self.compression5 = st.unpack(byteOrd+'I',File.read(4))[0] #/* compression parameter 4 */ self.compression6 = st.unpack(byteOrd+'I',File.read(4))[0] #/* compression parameter 4 */ self.nheaders = st.unpack(byteOrd+'I',File.read(4))[0] #/* total number of headers */ self.nfast = st.unpack(byteOrd+'I',File.read(4))[0] #/* number of pixels in one line */ self.nslow = st.unpack(byteOrd+'I',File.read(4))[0] #/* number of lines in image */ self.depth = st.unpack(byteOrd+'I',File.read(4))[0] #/* number of bytes per pixel */ self.recordLength = st.unpack(byteOrd+'I',File.read(4))[0] #/* number of pixels between succesive rows */ self.signifBits = st.unpack(byteOrd+'I',File.read(4))[0] #/* true depth of data, in bits */ self.dataType = st.unpack(byteOrd+'I',File.read(4))[0] #/* (signed,unsigned,float...) */ self.saturatedValue = st.unpack(byteOrd+'I',File.read(4))[0] #/* value marks pixel as saturated */ self.sequence = st.unpack(byteOrd+'I',File.read(4))[0] #/* TRUE or FALSE */ self.nimages = st.unpack(byteOrd+'I',File.read(4))[0] #/* total number of images - size of each is nfast*(nslow/nimages) */ self.origin = st.unpack(byteOrd+'I',File.read(4))[0] #/* corner of origin */ self.orientation = st.unpack(byteOrd+'I',File.read(4))[0] #/* direction of fast axis */ self.viewDirection = st.unpack(byteOrd+'I',File.read(4))[0] #/* direction to view frame */ self.overflowLocation = st.unpack(byteOrd+'I',File.read(4))[0] #/* FOLLOWING_HEADER, FOLLOWING_DATA */ self.over8Bits = st.unpack(byteOrd+'I',File.read(4))[0] #/* # of pixels with counts > 255 */ self.over16Bits = st.unpack(byteOrd+'I',File.read(4))[0] #/* # of pixels with count > 65535 */ self.multiplexed = st.unpack(byteOrd+'I',File.read(4))[0] #/* multiplex flag */ self.nfastimages = st.unpack(byteOrd+'I',File.read(4))[0] #/* # of images in fast direction */ self.nslowimages = st.unpack(byteOrd+'I',File.read(4))[0] #/* # of images in slow direction */ self.darkcurrentApplied = st.unpack(byteOrd+'I',File.read(4))[0] #/* flags correction has been applied - hold magic number ? */ self.biasApplied = st.unpack(byteOrd+'I',File.read(4))[0] #/* flags correction has been applied - hold magic number ? */ self.flatfieldApplied = st.unpack(byteOrd+'I',File.read(4))[0] #/* flags correction has been applied - hold magic number ? */ self.distortionApplied = st.unpack(byteOrd+'I',File.read(4))[0] #/* flags correction has been applied - hold magic number ? */ self.originalHeaderType = st.unpack(byteOrd+'I',File.read(4))[0] #/* Header/frame type from file that frame is read from */ self.fileSaved = st.unpack(byteOrd+'I',File.read(4))[0] #/* Flag that file has been saved, should be zeroed if modified */ self.nValidPixels = st.unpack(byteOrd+'I',File.read(4))[0] #/* Number of pixels holding valid data - first N pixels */ self.defectmapApplied = st.unpack(byteOrd+'I',File.read(4))[0] #/* flags correction has been applied - hold magic number ? */ self.subimageNfast = st.unpack(byteOrd+'I',File.read(4))[0] #/* when divided into subimages (eg. frameshifted) */ self.subimageNslow = st.unpack(byteOrd+'I',File.read(4))[0] #/* when divided into subimages (eg. frameshifted) */ self.subimageOriginFast = st.unpack(byteOrd+'I',File.read(4))[0] #/* when divided into subimages (eg. frameshifted) */ self.subimageOriginSlow = st.unpack(byteOrd+'I',File.read(4))[0] #/* when divided into subimages (eg. frameshifted) */ self.readoutPattern = st.unpack(byteOrd+'I',File.read(4))[0] #/* BIT Code - 1 = A, 2 = B, 4 = C, 8 = D */ self.saturationLevel = st.unpack(byteOrd+'I',File.read(4))[0] #/* at this value and above, data are not reliable */ self.orientationCode = st.unpack(byteOrd+'I',File.read(4))[0] #/* Describes how this frame needs to be rotated to make it "right" */ self.frameshiftMultiplexed = st.unpack(byteOrd+'I',File.read(4))[0] #/* frameshift multiplex flag */ self.prescanNfast = st.unpack(byteOrd+'I',File.read(4))[0] #/* Number of non-image pixels preceeding imaging pixels - fast direction */ self.prescanNslow = st.unpack(byteOrd+'I',File.read(4))[0] #/* Number of non-image pixels preceeding imaging pixels - slow direction */ self.postscanNfast = st.unpack(byteOrd+'I',File.read(4))[0] #/* Number of non-image pixels followng imaging pixels - fast direction */ self.postscanNslow = st.unpack(byteOrd+'I',File.read(4))[0] #/* Number of non-image pixels followng imaging pixels - slow direction */ self.prepostTrimmed = st.unpack(byteOrd+'I',File.read(4))[0] #/* trimmed==1 means pre and post scan pixels have been removed */ File.seek(IFD[34710][2][0]+256) #self.totalCounts = st.unpack(byteOrd+'Q',File.read(8))[0] # /* 64 bit integer range = 1.85E19*/ #self.specialCounts1 = st.unpack(byteOrd+'Q',File.read(8))[0] #self.specialCounts2 = st.unpack(byteOrd+'Q',File.read(8))[0] self.totalCounts = st.unpack(byteOrd+'II',File.read(8)) self.specialCounts1 = st.unpack(byteOrd+'II',File.read(8)) self.specialCounts2 = st.unpack(byteOrd+'II',File.read(8)) self.min = st.unpack(byteOrd+'I',File.read(4))[0] self.max = st.unpack(byteOrd+'I',File.read(4))[0] self.mean = st.unpack(byteOrd+'i',File.read(4))[0] # /* mean * 1000 */ self.rms = st.unpack(byteOrd+'I',File.read(4))[0] #/* rms * 1000 */ self.nZeros = st.unpack(byteOrd+'I',File.read(4))[0] #/* number of pixels with 0 value - not included in stats in unsigned data */ self.nSaturated = st.unpack(byteOrd+'I',File.read(4))[0] #/* number of pixels with saturated value - not included in stats */ self.statsUptodate = st.unpack(byteOrd+'I',File.read(4))[0] #/* Flag that stats OK - ie data not changed since last calculation */ self.pixelNoise = st.unpack(byteOrd+'I'*MAXIMAGES,File.read(4*MAXIMAGES)) # /* 1000*base noise value (ADUs) */ File.seek(IFD[34710][2][0]+256+128) self.barcode = re.sub(r'\x00','',string.join(st.unpack(byteOrd+16*'c',File.read(16)),'')) self.barcodeAngle = st.unpack(byteOrd+'I',File.read(4))[0] self.barcodeStatus = st.unpack(byteOrd+'I',File.read(4))[0] File.seek(IFD[34710][2][0]+256+128+256) self.xtalToDetector = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*distance in millimeters */ self.beamX = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*x beam position (pixels) */ self.beamY = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*y beam position (pixels) */ self.integrationTime = st.unpack(byteOrd+'i',File.read(4))[0] #/* integration time in milliseconds */ self.exposureTime = st.unpack(byteOrd+'i',File.read(4))[0] #/* exposure time in milliseconds */ self.readoutTime = st.unpack(byteOrd+'i',File.read(4))[0] #/* readout time in milliseconds */ self.nreads = st.unpack(byteOrd+'i',File.read(4))[0] #/* number of readouts to get this image */ self.startTwotheta = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*two_theta angle */ self.startOmega = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*omega angle */ self.startChi = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*chi angle */ self.startKappa = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*kappa angle */ self.startPhi = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*phi angle */ self.startDelta = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*delta angle */ self.startGamma = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*gamma angle */ self.startXtalToDetector = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*distance in mm (dist in um)*/ self.endTwotheta = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*two_theta angle */ self.endOmega = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*omega angle */ self.endChi = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*chi angle */ self.endKappa = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*kappa angle */ self.endPhi = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*phi angle */ self.endDelta = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*delta angle */ self.endGamma = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*gamma angle */ self.endXtalToDetector = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*distance in mm (dist in um)*/ self.rotationAxis = st.unpack(byteOrd+'i',File.read(4))[0] #/* active rotation axis (index into above ie. 0=twotheta,1=omega...) */ self.rotationRange = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*rotation angle */ self.detectorRotx = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*rotation of detector around X */ self.detectorRoty = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*rotation of detector around Y */ self.detectorRotz = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*rotation of detector around Z */ self.totalDose = st.unpack(byteOrd+'i',File.read(4))[0] #/* Hz-sec (counts) integrated over full exposure */ File.seek(IFD[34710][2][0]+256+128+256+128) self.detectorType = st.unpack(byteOrd+'i',File.read(4))[0] #/* detector type */ self.pixelsizeX = st.unpack(byteOrd+'i',File.read(4))[0] #/* pixel size (nanometers) */ self.pixelsizeY = st.unpack(byteOrd+'i',File.read(4))[0] #/* pixel size (nanometers) */ self.meanBias = st.unpack(byteOrd+'i',File.read(4))[0] #/* 1000*mean bias value */ self.photonsPer100adu = st.unpack(byteOrd+'i',File.read(4))[0] #/* photons / 100 ADUs */ self.measuredBias = st.unpack(byteOrd+'i'*MAXIMAGES,File.read(4*MAXIMAGES)) # /* 1000*mean bias value for each image*/ self.measuredTemperature = st.unpack(byteOrd+'i'*MAXIMAGES,File.read(4*MAXIMAGES)) # /* Temperature of each detector in milliKelvins */ self.measuredPressure = st.unpack(byteOrd+'i'*MAXIMAGES,File.read(4*MAXIMAGES)) # /* Pressure of each chamber in microTorr */ File.seek(IFD[34710][2][0]+256+128+256+128+128) self.sourceType = st.unpack(byteOrd+'i',File.read(4))[0] #/* (code) - target, synch. etc */ self.sourceDx = st.unpack(byteOrd+'i',File.read(4))[0] #/* Optics param. - (size microns) */ self.sourceDy = st.unpack(byteOrd+'i',File.read(4))[0] #/* Optics param. - (size microns) */ self.sourceWavelength = st.unpack(byteOrd+'i',File.read(4))[0] #/* wavelength (femtoMeters) */ self.sourcePower = st.unpack(byteOrd+'i',File.read(4))[0] #/* (Watts) */ self.sourceVoltage = st.unpack(byteOrd+'i',File.read(4))[0] #/* (Volts) */ self.sourceCurrent = st.unpack(byteOrd+'i',File.read(4))[0] #/* (microAmps) */ self.sourceBias = st.unpack(byteOrd+'i',File.read(4))[0] #/* (Volts) */ self.sourcePolarizationX = st.unpack(byteOrd+'i',File.read(4))[0] #/* () */ self.sourcePolarizationY = st.unpack(byteOrd+'i',File.read(4))[0] #/* () */ self.sourceIntensity0 = st.unpack(byteOrd+'i',File.read(4))[0] #/* (arbitrary units) */ self.sourceIntensity1 = st.unpack(byteOrd+'i',File.read(4))[0] #/* (arbitrary units) */ File.seek(IFD[34710][2][0]+256+128+256+128+128+14*4) self.opticsType = st.unpack(byteOrd+'i',File.read(4))[0] #/* Optics type (code)*/ self.opticsDx = st.unpack(byteOrd+'i',File.read(4))[0] #/* Optics param. - (size microns) */ self.opticsDy = st.unpack(byteOrd+'i',File.read(4))[0] #/* Optics param. - (size microns) */ self.opticsWavelength = st.unpack(byteOrd+'i',File.read(4))[0] #/* Optics param. - (size microns) */ self.opticsDispersion = st.unpack(byteOrd+'i',File.read(4))[0] #/* Optics param. - (*10E6) */ self.opticsCrossfireX = st.unpack(byteOrd+'i',File.read(4))[0] #/* Optics param. - (microRadians) */ self.opticsCrossfireY = st.unpack(byteOrd+'i',File.read(4))[0] #/* Optics param. - (microRadians) */ self.opticsAngle = st.unpack(byteOrd+'i',File.read(4))[0] #/* Optics param. - (monoch. 2theta - microradians) */ self.opticsPolarizationX = st.unpack(byteOrd+'i',File.read(4))[0] #/* () */ self.opticsPolarizationY = st.unpack(byteOrd+'i',File.read(4))[0] #/* () */ File.seek(IFD[34710][2][0]+256+128+256+128+128+128) self.filetitle = re.sub(r'\x00','',string.join(st.unpack(byteOrd+128*'c',File.read(128)),'')) self.filepath = re.sub(r'\x00','',string.join(st.unpack(byteOrd+'c'*128,File.read(128)),'')) #/* path name for data file*/ self.filename = re.sub(r'\x00','',string.join(st.unpack(byteOrd+'c'*64,File.read(64)),'')) #/* name of data file*/ self.acquireTimestamp = re.sub(r'\x00','',string.join(st.unpack(byteOrd+'c'*32,File.read(32)),'')) #/* date and time of acquisition*/ self.headerTimestamp = re.sub(r'\x00','',string.join(st.unpack(byteOrd+'c'*32,File.read(32)),'')) #/* date and time of header update*/ self.saveTimestamp = re.sub(r'\x00','',string.join(st.unpack(byteOrd+'c'*32,File.read(32)),'')) #/* date and time file saved */ self.fileComment = re.sub(r'\x00','',string.join(st.unpack(byteOrd+'c'*512,File.read(512)),'')) #/* comments - can be used as desired */ self.datasetComment = re.sub(r'\x00','',string.join(st.unpack(byteOrd+'c'*512,File.read(512)),'')) #/* comments - can be used as desired */ self.userData = re.sub(r'\x00','',string.join(st.unpack(byteOrd+'c'*512,File.read(512)),'')) File.seek(4096) self.image = ar.array(self.arrayTypeCode,File.read(self.byteDepth*self.TIFFsizeX*self.TIFFsizeY)) # reverse the array so if can have the same view as is read in marccd # also switch the view direction self.image.reverse() self.viewDirection = abs(self.viewDirection - 1) def outputHead(self): myHead = [] for curAttr in dir(self): if ( curAttr != '__doc__' and \ curAttr != '__init__' and \ curAttr != '__module__' and \ curAttr != 'outputHead' and \ curAttr != 'image' ): myHead.append(" %s = %s" % (curAttr,getattr(self,curAttr))) return myHead