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libraries/FabIO-0.0.7
Package fabio :: Module fabian_mar_header
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Source Code for Module fabio.fabian_mar_header

  1   
  2  """ 
  3  This is the mar header interpreter from Fabian by HOS and EK.  
  4  JPW replaced it with a parser based approach because: 
  5     this might be hard to maintain, in the even of a single incorrect number somewhere 
  6     theoretically all header items are picked up by the parser, automatically 
  7     the pylint score for this was rather low 
  8  """ 
  9   
 10   

 11 -class obselete: 

 12 -    def _readheader_fabian(self, infile): 

 13          """ 
 14          Read in the header from an already opened file 
 15          """ 
 16          self.header = {} 
 17          clip = '\x00' 
 18          l = infile.seek(1024) 
 19          l = infile.read(3072) 
 20          # Header information in MarCCD and MarMosaic images are obtained  
 21          # from http://www.mar-usa.com/support/data.htm 
 22          #/* File/header format parameters (256 bytes) */ 
 23          self.header['header_type'] = \ 
 24              N.fromstring(l[0:4], N.uint32)[0]   
 25          # UINT32 ; /* flag for header type (can be used as magic number) */ 
 26          self.header['header_name'] = l[4:4+l[4:20].find(clip)] # char[16] ; /* header name (MMX) */ 
 27          self.header['header_major_version'] = N.fromstring(l[20:24],N.uint32)[0]  # UINT32 ; /* header_major_version (n.) */ 
 28          self.header['header_minor_version'] = N.fromstring(l[24:28],N.uint32)[0]  # UINT32 ; /* header_minor_version (.n) */ 
 29          self.header['header_byte_orde'] = N.fromstring(l[28:32],N.uint32)[0]  # UINT32 r;/* BIG_ENDIAN (Motorola,MIPS); LITTLE_ENDIAN (DEC, Intel) */ 
 30          self.header['data_byte_order'] = N.fromstring(l[32:36],N.uint32)[0]  # UINT32 ; /* BIG_ENDIAN (Motorola,MIPS); LITTLE_ENDIAN (DEC, Intel) */ 
 31          self.header['header_size'] = N.fromstring(l[36:40],N.uint32)[0]  # UINT32 ; /* in bytes */ 
 32          self.header['frame_type'] = N.fromstring(l[40:44],N.uint32)[0]  # UINT32 ; /* flag for frame type */ 
 33          #self.header['magic_number'] = N.fromstring(l[44:48],N.uint32)[0]  # UINT32 ; /* to be used as a flag - usually to indicate new file */ 
 34          #self.header['compression_type'] = N.fromstring(l[48:52],N.uint32)[0]  # UINT32 ; /* type of image compression */ 
 35          #self.header['compression1'] = N.fromstring(l[52:56],N.uint32)[0]  # UINT32 ; /* compression parameter 1 */ 
 36          #self.header['compression2'] = N.fromstring(l[56:60],N.uint32)[0]  # UINT32 ; /* compression parameter 2 */ 
 37          #self.header['compression3'] = N.fromstring(l[60:64],N.uint32)[0]  # UINT32 ; /* compression parameter 3 */ 
 38          #self.header['compression4'] = N.fromstring(l[64:68],N.uint32)[0]  # UINT32 ; /* compression parameter 4 */ 
 39          #self.header['compression5'] = N.fromstring(l[68:72],N.uint32)[0]  # UINT32 ; /* compression parameter 4 */ 
 40          #self.header['compression6'] = N.fromstring(l[72:76],N.uint32)[0]  # UINT32 ; /* compression parameter 4 */ 
 41          #self.header['nheaders'] = N.fromstring(l[76:80],N.uint32)[0]  # UINT32 ; /* total number of headers */ 
 42          self.header['nfast'] = N.fromstring(l[80:84],N.uint32)[0]  # UINT32 ; /* number of pixels in one line */ 
 43          self.header['nslow'] = N.fromstring(l[84:88],N.uint32)[0]  # UINT32 ; /* number of lines in image */ 
 44          self.header['depth'] = N.fromstring(l[88:92],N.uint32)[0]  # UINT32 ; /* number of bytes per pixel */ 
 45          #self.header['record_length'] = N.fromstring(l[92:96],N.uint32)[0]  # UINT32 ; /* number of pixels between succesive rows */ 
 46          self.header['signif_bits'] = N.fromstring(l[96:100],N.uint32)[0]  # UINT32 ; /* true depth of data, in bits */ 
 47          #self.header['data_type'] = N.fromstring(l[100:104],N.uint32)[0]  # UINT32 ; /* (signed,unsigned,float...) */ 
 48          #self.header['saturated_value'] = N.fromstring(l[104:108],N.uint32)[0]  # UINT32 ; /* value marks pixel as saturated */ 
 49          self.header['sequence'] = N.fromstring(l[108:112],N.uint32)[0]  # UINT32 ; /* TRUE or FALSE */ 
 50          self.header['nimages'] = N.fromstring(l[112:116],N.uint32)[0]  # UINT32 ; /* total number of images - size of each is nfast*(nslow/nimages) */ 
 51          self.header['origin'] = N.fromstring(l[116:120],N.uint32)[0]  # UINT32 ; /* corner of origin */ 
 52          self.header['orientation'] = N.fromstring(l[120:124],N.uint32)[0]  # UINT32 ; /* direction of fast axis */ 
 53          self.header['view_direction'] = N.fromstring(l[124:128],N.uint32)[0]  # UINT32 ; /* direction to view frame */ 
 54          self.header['overflow_locatio'] = N.fromstring(l[128:132],N.uint32)[0]  # UINT32 n;/* FOLLOWING_HEADER, FOLLOWING_DATA */ 
 55          self.header['over_8_bits'] = N.fromstring(l[132:136],N.uint32)[0]  # UINT32 ; /* # of pixels with counts > 255 */ 
 56          self.header['over_16_bits'] = N.fromstring(l[136:140],N.uint32)[0]  # UINT32 ; /* # of pixels with count > 65535 */ 
 57          self.header['multiplexed'] = N.fromstring(l[140:144],N.uint32)[0]  # UINT32 ; /* multiplex flag */ 
 58          self.header['nfastimages'] = N.fromstring(l[144:148],N.uint32)[0]  # UINT32 ; /* # of images in fast direction */ 
 59          self.header['nslowimages'] = N.fromstring(l[148:152],N.uint32)[0]  # UINT32 ; /* # of images in slow direction */ 
 60          self.header['background_applied'] = N.fromstring(l[152:156],N.uint32)[0]  # UINT32 ; /* flags correction has been applied hold magic number ? */ 
 61          self.header['bias_applied'] = N.fromstring(l[156:160],N.uint32)[0]  # UINT32 ; /* flags correction has been applied - hold magic number ? */ 
 62          self.header['flatfield_applied'] = N.fromstring(l[160:164],N.uint32)[0]  # UINT32 ; /* flags correction has been applied hold magic number ? */ 
 63          self.header['distortion_applied'] = N.fromstring(l[164:168],N.uint32)[0]  # UINT32 ; /* flags correction has been applied hold magic number ? */ 
 64          #self.header['original_header_type'] = N.fromstring(l[168:172],N.uint32)[0]  # UINT32 ; /* Header/frame type from file that frame is read from */ 
 65          #self.header['file_saved'] = N.fromstring(l[172:176],N.uint32)[0]  # UINT32 ; /* Flag that file has been saved, should be zeroed if modified */ 
 66          #/* Goniostat parameters (128 bytes) */ 
 67          self.header['xtal_to_detector'] = N.fromstring(l[640:644],N.int32)[0]*1000  #INT32 ; /* 1000*distance in millimeters */ 
 68          self.header['beam_x'] = N.fromstring(l[644:648],N.int32)[0]*1000  #INT32 ; /* 1000*x beam position (pixels) */ 
 69          self.header['beam_y'] = N.fromstring(l[648:652],N.int32)[0]*1000  #INT32 ; /* 1000*y beam position (pixels) */ 
 70          self.header['integration_time'] = N.fromstring(l[652:656],N.int32)[0]  #INT32 ; /* integration time in milliseconds */ 
 71          self.header['exposure_time'] = N.fromstring(l[656:660],N.int32)[0]  #INT32 ; /* exposure time in milliseconds */ 
 72          self.header['readout_time'] = N.fromstring(l[660:664],N.int32)[0]  #INT32 ; /* readout time in milliseconds */ 
 73          self.header['nreads'] = N.fromstring(l[664:668],N.int32)[0]  #INT32 ; /* number of readouts to get this image */ 
 74          self.header['start_twotheta'] = N.fromstring(l[668:672],N.int32)[0]*1000  #INT32 ; /* 1000*two_theta angle */ 
 75          self.header['start_omega'] = N.fromstring(l[676:680],N.int32)[0]*1000  #INT32 ; /* 1000*omega angle */ 
 76          self.header['start_chi'] = N.fromstring(l[680:684],N.int32)[0]*1000  #INT32 ; /* 1000*chi angle */ 
 77          self.header['start_kappa'] = N.fromstring(l[684:688],N.int32)[0]*1000  #INT32 ; /* 1000*kappa angle */ 
 78          self.header['start_phi'] = N.fromstring(l[688:692],N.int32)[0]*1000  #INT32 ; /* 1000*phi angle */ 
 79          self.header['start_delta'] = N.fromstring(l[692:696],N.int32)[0]*1000  #INT32 ; /* 1000*delta angle */ 
 80          self.header['start_gamma'] = N.fromstring(l[696:700],N.int32)[0]*1000  #INT32 ; /* 1000*gamma angle */ 
 81          self.header['start_xtal_to_detector'] = N.fromstring(l[700:704],N.int32)[0]*1000  #INT32 ; /* 1000*distance in mm (dist in um)*/ 
 82          self.header['end_twotheta'] = N.fromstring(l[704:708],N.int32)[0]*1000  #INT32 ; /* 1000*two_theta angle */ 
 83          self.header['end_omega'] = N.fromstring(l[708:712],N.int32)[0]*1000  #INT32 ; /* 1000*omega angle */ 
 84          self.header['end_chi'] = N.fromstring(l[712:716],N.int32)[0]*1000  #INT32 ; /* 1000*chi angle */ 
 85          self.header['end_kappa'] = N.fromstring(l[716:720],N.int32)[0]*1000  #INT32 ; /* 1000*kappa angle */ 
 86          self.header['end_phi'] = N.fromstring(l[720:724],N.int32)[0]*1000  #INT32 ; /* 1000*phi angle */ 
 87          self.header['end_delta'] = N.fromstring(l[724:728],N.int32)[0]*1000  #INT32 ; /* 1000*delta angle */ 
 88          self.header['end_gamma'] = N.fromstring(l[728:732],N.int32)[0]*1000  #INT32 ; /* 1000*gamma angle */ 
 89          self.header['end_xtal_to_detector'] = N.fromstring(l[732:736],N.int32)[0]*1000  #INT32 ; /* 1000*distance in mm (dist in um)*/ 
 90          self.header['rotation_axis'] = N.fromstring(l[736:740],N.int32)[0]  #INT32 ; /* active rotation axis */ 
 91          self.header['rotation_range'] = N.fromstring(l[740:744],N.int32)[0]*1000  #INT32 ; /* 1000*rotation angle */ 
 92          self.header['detector_rotx'] = N.fromstring(l[744:748],N.int32)[0]*1000  #INT32 ; /* 1000*rotation of detector around X */ 
 93          self.header['detector_roty'] = N.fromstring(l[748:752],N.int32)[0]*1000  #INT32 ; /* 1000*rotation of detector around Y */ 
 94          self.header['detector_rotz'] = N.fromstring(l[752:756],N.int32)[0]*1000  #INT32 ; /* 1000*rotation of detector around Z */ 
 95          #/* Detector parameters (128 bytes) */ 
 96          self.header['detector_type'] = N.fromstring(l[768:772],N.int32)[0]  #INT32 ; /* detector type */ 
 97          self.header['pixelsize_x'] = N.fromstring(l[772:776],N.int32)[0]  #INT32 ; /* pixel size (nanometers) */ 
 98          self.header['pixelsize_y'] = N.fromstring(l[776:780],N.int32)[0]  #INT32 ; /* pixel size (nanometers) */ 
 99          self.header['mean_bias'] = N.fromstring(l[780:784],N.int32)[0]*1000  #INT32 ; /* 1000*mean bias value */ 
100          self.header['photons_per_100adu'] = N.fromstring(l[784:788],N.int32)[0]  #INT32 ; /* photons / 100 ADUs */ 
101          self.header['measured_bias'] = N.fromstring(l[788:792],N.int32)[0]*1000  #INT32 [MAXIMAGES]; /* 1000*mean bias value for each image*/ 
102          self.header['measured_temperature'] = N.fromstring(l[792:796],N.int32)[0] #INT32  [MAXIMAGES]; /* Temperature of each detector in milliKelvins */ 
103          self.header['measured_pressure'] = N.fromstring(l[796:800],N.int32)[0] #INT32 [MAXIMAGES] ; /* Pressure of each chamber in microTorr */ 
104          #/* X-ray source parameters (8*4 bytes) */ 
105          #self.header['source_type'] = N.fromstring(l[896:900],N.int32)[0]  #INT32 ; /* (code) - target, synch. etc */ 
106          #self.header['source_dx'] = N.fromstring(l[900:904],N.int32)[0]  #INT32 ; /* Optics param. - (size microns) */ 
107          #self.header['source_dy'] = N.fromstring(l[904:908],N.int32)[0]  #INT32 ; /* Optics param. - (size microns) */ 
108          self.header['source_wavelength'] = N.fromstring(l[908:912],N.int32)[0]  #INT32 ; /* wavelength (femtoMeters) */ 
109          #self.header['source_power'] = N.fromstring(l[912:916],N.int32)[0]  #INT32 ; /* (Watts) */ 
110          #self.header['source_voltage'] = N.fromstring(l[916:920],N.int32)[0]  #INT32 ; /* (Volts) */ 
111          #self.header['source_current'] = N.fromstring(l[920:924],N.int32)[0]  #INT32 ; /* (microAmps) */ 
112          #self.header['source_bias'] = N.fromstring(l[924:928],N.int32)[0]  #INT32 ; /* (Volts) */ 
113          #self.header['source_polarization_x'] = N.fromstring(l[928:932],N.int32)[0]  #INT32 ; /* () */ 
114          #self.header['source_polarization_y'] = N.fromstring(l[932:936],N.int32)[0]  #INT32 ; /* () */ 
115          #/* X-ray optics_parameters (8*4 bytes) */ 
116          #self.header['optics_type'] = N.fromstring(l[960:964],N.int32)[0]  #INT32 ; /* Optics type (code)*/ 
117          #self.header['optics_dx'] = N.fromstring(l[964:968],N.int32)[0]  #INT32 ; /* Optics param. - (size microns) */ 
118          #self.header['optics_dy'] = N.fromstring(l[968:972],N.int32)[0]  #INT32 ; /* Optics param. - (size microns) */ 
119          #self.header['optics_wavelength'] = N.fromstring(l[972:976],N.int32)[0]  #INT32 ; /* Optics param. - (size microns) */ 
120          #self.header['optics_dispersion'] = N.fromstring(l[976:980],N.int32)[0]  #INT32 ; /* Optics param. - (*10E6) */ 
121          #self.header['optics_crossfire_x'] = N.fromstring(l[980:984],N.int32)[0]  #INT32 ; /* Optics param. - (microRadians) */ 
122          #self.header['optics_crossfire_y'] = N.fromstring(l[984:988],N.int32)[0]  #INT32 ; /* Optics param. - (microRadians) */ 
123          #self.header['optics_angle'] = N.fromstring(l[988:992],N.int32)[0]  #INT32 ; /* Optics param. - (monoch. 2theta microradians) */ 
124          #self.header['optics_polarization_x'] = N.fromstring(l[992:996],N.int32)[0]  #INT32 ; /* () */ 
125          #self.header['optics_polarization_y'] = N.fromstring(l[996:1000],N.int32)[0]  #INT32 ; /* () */ 
126          #/* File parameters (1024 bytes) */ 
127          self.header['filetitle'] = l[1024:1024+l[1024:1152].find(clip)]#char[128]; /* Title */ 
128          self.header['filepath'] = l[1152:1152+l[1152:1280].find(clip)] #char[128]; /* path name for data file */ 
129          self.header['filename'] = l[1280:1280+l[1280:1344].find(clip)] #char[64]; /* name of data file */ 
130          #self.header['acquire_timestamp'] = l[1344:1344+l[1344:1376].find(clip)] #char[32]; /* date and time of acquisition */ 
131          #self.header['header_timestamp'] = l[1376:1376+l[1376:1408].find(clip)] #char[32]; /* date and time of header update */ 
132          #self.header['save_timestamp'] = l[1408:1408+l[1408:1440].find(clip)] #char[32]; /* date and time file saved */ 
133          self.header['file_comments'] = l[1440:1440+l[1440:1952].find(clip)] #char[512]; /* comments - can be used as desired */ 
134          #/* Dataset parameters (512 bytes) */ 
135          self.header['dataset_comments'] = l[2048:2048+l[2048:512].find(clip)] #char[512] ; /* comments - can be used as desired */ 

136

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libraries/FabIO-0.0.7
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