1
2 """
3
4 Authors: Henning O. Sorensen & Erik Knudsen
5 Center for Fundamental Research: Metal Structures in Four Dimensions
6 Risoe National Laboratory
7 Frederiksborgvej 399
8 DK-4000 Roskilde
9 email:henning.sorensen@risoe.dk
10
11 + (mods for fabio) Jon Wright, ESRF
12 marccdimage can read MarCCD and MarMosaic images including header info.
13
14 JPW : Use a parser in case of typos (sorry?)
15
16 """
17
18
19
20
21
22 from tifimage import tifimage
23
24
25
26
27
28 CDEFINITION = """
29 typedef struct frame_header_type {
30 /* File/header format parameters (256 bytes) */
31 UINT32 header_type; /* flag for header type
32 (can be used as magic number) */
33 char header_name[16]; /* header name (MMX) */
34 UINT32 header_major_version; /* header_major_version (n.) */
35 UINT32 header_minor_version; /* header_minor_version (.n) */
36 UINT32 header_byte_order;/* BIG_ENDIAN (Motorola,MIPS);
37 LITTLE_ENDIAN (DEC, Intel) */
38 UINT32 data_byte_order; /* BIG_ENDIAN (Motorola,MIPS);
39 LITTLE_ENDIAN (DEC, Intel) */
40 UINT32 header_size; /* in bytes */
41 UINT32 frame_type; /* flag for frame type */
42 UINT32 magic_number; /* to be used as a flag -
43 usually to indicate new file */
44 UINT32 compression_type; /* type of image compression */
45 UINT32 compression1; /* compression parameter 1 */
46 UINT32 compression2; /* compression parameter 2 */
47 UINT32 compression3; /* compression parameter 3 */
48 UINT32 compression4; /* compression parameter 4 */
49 UINT32 compression5; /* compression parameter 4 */
50 UINT32 compression6; /* compression parameter 4 */
51 UINT32 nheaders; /* total number of headers */
52 UINT32 nfast; /* number of pixels in one line */
53 UINT32 nslow; /* number of lines in image */
54 UINT32 depth; /* number of bytes per pixel */
55 UINT32 record_length; /* number of pixels between
56 succesive rows */
57 UINT32 signif_bits; /* true depth of data, in bits */
58 UINT32 data_type; /* (signed,unsigned,float...) */
59 UINT32 saturated_value; /* value marks pixel as saturated */
60 UINT32 sequence; /* TRUE or FALSE */
61 UINT32 nimages; /* total number of images - size of
62 each is nfast*(nslow/nimages) */
63 UINT32 origin; /* corner of origin */
64 UINT32 orientation; /* direction of fast axis */
65 UINT32 view_direction; /* direction to view frame */
66 UINT32 overflow_location;/* FOLLOWING_HEADER, FOLLOWING_DATA */
67 UINT32 over_8_bits; /* # of pixels with counts 255 */
68 UINT32 over_16_bits; /* # of pixels with count 65535 */
69 UINT32 multiplexed; /* multiplex flag */
70 UINT32 nfastimages; /* # of images in fast direction */
71 UINT32 nslowimages; /* # of images in slow direction */
72 UINT32 background_applied;/* flags correction has been applied
73 hold magic number ? */
74 UINT32 bias_applied; /* flags correction has been applied
75 hold magic number ? */
76 UINT32 flatfield_applied;/* flags correction has been applied -
77 hold magic number ? */
78 UINT32 distortion_applied;/*flags correction has been applied -
79 hold magic number ? */
80 UINT32 original_header_type; /* Header/frame type from file
81 that frame is read from */
82 UINT32 file_saved; /* Flag that file has been saved,
83 should be zeroed if modified */
84 char reserve1[(64-40)*sizeof(INT32)-16];
85
86 /* Data statistics (128) */
87 UINT32 total_counts[2]; /* 64 bit integer range = 1.85E19*/
88 UINT32 special_counts1[2];
89 UINT32 special_counts2[2];
90 UINT32 min;
91 UINT32 max;
92 UINT32 mean;
93 UINT32 rms;
94 UINT32 p10;
95 UINT32 p90;
96 UINT32 stats_uptodate;
97 UINT32 pixel_noise[MAXIMAGES]; /*1000*base noise value (ADUs) */
98 char reserve2[(32-13-MAXIMAGES)*sizeof(INT32)];
99
100 /* More statistics (256) */
101 UINT16 percentile[128];
102
103
104 /* Goniostat parameters (128 bytes) */
105 INT32 xtal_to_detector; /* 1000*distance in millimeters */
106 INT32 beam_x; /* 1000*x beam position (pixels) */
107 INT32 beam_y; /* 1000*y beam position (pixels) */
108 INT32 integration_time; /* integration time in milliseconds */
109 INT32 exposure_time; /* exposure time in milliseconds */
110 INT32 readout_time; /* readout time in milliseconds */
111 INT32 nreads; /* number of readouts to get this image */
112 INT32 start_twotheta; /* 1000*two_theta angle */
113 INT32 start_omega; /* 1000*omega angle */
114 INT32 start_chi; /* 1000*chi angle */
115 INT32 start_kappa; /* 1000*kappa angle */
116 INT32 start_phi; /* 1000*phi angle */
117 INT32 start_delta; /* 1000*delta angle */
118 INT32 start_gamma; /* 1000*gamma angle */
119 INT32 start_xtal_to_detector; /* 1000*distance in mm (dist in um)*/
120 INT32 end_twotheta; /* 1000*two_theta angle */
121 INT32 end_omega; /* 1000*omega angle */
122 INT32 end_chi; /* 1000*chi angle */
123 INT32 end_kappa; /* 1000*kappa angle */
124 INT32 end_phi; /* 1000*phi angle */
125 INT32 end_delta; /* 1000*delta angle */
126 INT32 end_gamma; /* 1000*gamma angle */
127 INT32 end_xtal_to_detector; /* 1000*distance in mm (dist in um)*/
128 INT32 rotation_axis; /* active rotation axis */
129 INT32 rotation_range; /* 1000*rotation angle */
130 INT32 detector_rotx; /* 1000*rotation of detector around X */
131 INT32 detector_roty; /* 1000*rotation of detector around Y */
132 INT32 detector_rotz; /* 1000*rotation of detector around Z */
133 char reserve3[(32-28)*sizeof(INT32)];
134
135 /* Detector parameters (128 bytes) */
136 INT32 detector_type; /* detector type */
137 INT32 pixelsize_x; /* pixel size (nanometers) */
138 INT32 pixelsize_y; /* pixel size (nanometers) */
139 INT32 mean_bias; /* 1000*mean bias value */
140 INT32 photons_per_100adu; /* photons / 100 ADUs */
141 INT32 measured_bias[MAXIMAGES];/* 1000*mean bias value for each image*/
142 INT32 measured_temperature[MAXIMAGES]; /* Temperature of each
143 detector in milliKelvins */
144 INT32 measured_pressure[MAXIMAGES]; /* Pressure of each chamber
145 in microTorr */
146 /* Retired reserve4 when MAXIMAGES set to 9 from 16 and
147 two fields removed, and temp and pressure added
148 char reserve4[(32-(5+3*MAXIMAGES))*sizeof(INT32)]
149 */
150
151 /* X-ray source and optics parameters (128 bytes) */
152 /* X-ray source parameters (8*4 bytes) */
153 INT32 source_type; /* (code) - target, synch. etc */
154 INT32 source_dx; /* Optics param. - (size microns) */
155 INT32 source_dy; /* Optics param. - (size microns) */
156 INT32 source_wavelength; /* wavelength (femtoMeters) */
157 INT32 source_power; /* (Watts) */
158 INT32 source_voltage; /* (Volts) */
159 INT32 source_current; /* (microAmps) */
160 INT32 source_bias; /* (Volts) */
161 INT32 source_polarization_x; /* () */
162 INT32 source_polarization_y; /* () */
163 char reserve_source[4*sizeof(INT32)];
164
165 /* X-ray optics_parameters (8*4 bytes) */
166 INT32 optics_type; /* Optics type (code)*/
167 INT32 optics_dx; /* Optics param. - (size microns) */
168 INT32 optics_dy; /* Optics param. - (size microns) */
169 INT32 optics_wavelength; /* Optics param. - (size microns) */
170 INT32 optics_dispersion; /* Optics param. - (*10E6) */
171 INT32 optics_crossfire_x; /* Optics param. - (microRadians) */
172 INT32 optics_crossfire_y; /* Optics param. - (microRadians) */
173 INT32 optics_angle; /* Optics param. - (monoch.
174 2theta - microradians) */
175 INT32 optics_polarization_x; /* () */
176 INT32 optics_polarization_y; /* () */
177 char reserve_optics[4*sizeof(INT32)];
178
179 char reserve5[((32-28)*sizeof(INT32))];
180
181 /* File parameters (1024 bytes) */
182 char filetitle[128]; /* Title */
183 char filepath[128]; /* path name for data file */
184 char filename[64]; /* name of data file */
185 char acquire_timestamp[32]; /* date and time of acquisition */
186 char header_timestamp[32]; /* date and time of header update */
187 char save_timestamp[32]; /* date and time file saved */
188 char file_comments[512]; /* comments, use as desired */
189 char reserve6[1024-(128+128+64+(3*32)+512)];
190
191 /* Dataset parameters (512 bytes) */
192 char dataset_comments[512]; /* comments, used as desired */
193 /* pad out to 3072 bytes */
194 char pad[3072-(256+128+256+(3*128)+1024+512)];
195
196 } frame_header;
197 """
198
199 import struct
200
201
202 C_TO_STRUCT = {
203 "INT32" : "i",
204 "UINT32" : "I",
205 "char" : "c",
206 "UINT16" : "H"
207 }
208
209
210 C_SIZES = {
211 "INT32" : 4,
212 "UINT32" : 4,
213 "char" : 1,
214 "UINT16" : 2
215 }
216
217
218 MAXIMAGES = 9
219
220
260
261
262 HEADER_NAMES, HEADER_FORMAT = make_format(CDEFINITION)
263
265 """
266 given a format and header interpret it
267 """
268 values = struct.unpack(fmt, header)
269 hdr = {}
270 i = 0
271 for name in names:
272 if hdr.has_key(name):
273 if type(values[i]) == type("string"):
274 hdr[name] = hdr[name] + values[i]
275 else:
276 try:
277 hdr[name].append(values[i])
278 except AttributeError:
279 hdr[name] = [hdr[name], values[i]]
280 else:
281 hdr[name] = values[i]
282 i = i + 1
283
284 return hdr
285
286
288 """ Read in data in mar ccd format, also
289 MarMosaic images, including header info """
290
291
300
301
302
304 """
305 inherited from tifimage
306 ... a marccd image *is a* tif image
307 just with a header
308 """
309 return tifimage.read(self, fname)
310