VIAS Source Code: pic.h Source File

00001 #ifndef __PIC_H__
00002 #define __PIC_H__
00003 /*=============================================================================   
00004      Module  : pic.h 1.0
00005      Purpose : Define routines to read and write Bio-Rad .pic files.
00006      Author  : Doug Ehlenberger, CNIC Mt. Sinai School of Medicine
00007                
00008 ==============================================================================*/
00009 #include <stdlib.h>
00010 #include <stdio.h>
00011 #include <string.h>
00012 #include <limits.h>
00013 #include <assert.h>
00014 
00015 #ifdef __cplusplus
00016 extern "C"{
00017 #endif
00018 
00019 /* NOTE: Undefine the following to eliminate stdout messages. */
00020 
00021 // #define PIC_VERBOSE
00022 
00023 
00024 typedef char            PicChar;
00025 typedef short           PicInt;
00026 typedef unsigned short  PicUint;
00027 typedef float           PicFloat;
00028 typedef void*           PicPointer;
00029 
00030 
00031 extern char _pic_compile_time_size_check[ ( 1 == sizeof( PicChar ) )    ? 1 : -1 ];
00032 extern char _pic_compile_time_size_check[ ( 2 == sizeof( PicInt ) )     ? 1 : -1 ];
00033 extern char _pic_compile_time_size_check[ ( 2 == sizeof( PicUint ) )    ? 1 : -1 ];
00034 extern char _pic_compile_time_size_check[ ( 4 == sizeof( PicFloat ) )   ? 1 : -1 ];
00035 extern char _pic_compile_time_size_check[ ( 4 == sizeof( PicPointer ) ) ? 1 : -1 ];
00036 
00037 
00038 typedef struct tagPICFILEHEADER
00039    {
00040    PicInt      imageWidth;      /* Width in pixels. */
00041    PicInt      imageHeight;     /* Height in pixels */
00042    PicInt      numImages;       /* Length in pixels */
00043    PicInt      ramp1min;        /* Gamma conversion ramp minimum. Set to 0.*/
00044    PicInt      ramp1max;        /* Gamma conversion ramp maximum. Set to 255. */
00045    PicPointer  notes;           /* Pointer to link list of notes. IGNORE!!! */
00046                                 /* Use the PICFILE pointer instead! */
00047    PicInt      byteFormat;      /* If 0 means 16 bits per channel, else 8. */
00048    PicInt      currentImage;    /* Not used, make 0. */
00049    PicChar     fileName[32];    /* Filename, Set to "untitled.pic" */
00050    PicInt      merged;          /* Currently not supported, make 0. */
00051    PicUint     color1;          /* Flags for RGB lookup table */
00052    PicUint     fileID;          /* Must be set to PIC_FILE_ID */
00053    PicInt      ramp2min;        /* Same as #1 */
00054    PicInt      ramp2max;        /* Same as #1 */
00055    PicUint     color2;          /* Same as #1 */
00056    PicInt      edited;          /* Ignore, make 0. */
00057    PicInt      lens;            /* Currently not used, set to 60 */
00058    PicFloat    magFactor;       /* Currently not used, set to 1.0 */
00059    PicChar     pad[6];          /* Not used */
00060    }
00061    PICFILEHEADER;
00062 
00063 
00064 #define PIC_FILE_ID  12345
00065 
00066 
00067 /* Values for 'color1' and 'color2' */
00068 
00069 #define PIC_RED_LUT    0x01
00070 #define PIC_GREEN_LUT  0x02
00071 #define PIC_BLUE_LUT   0x04
00072 
00073 
00074 
00075 #define PIC_HEADER_SIZE  76
00076 
00077 extern char _pic_compile_time_size_check
00078    [ 
00079    ( PIC_HEADER_SIZE == 
00080            sizeof( PicInt )     +
00081            sizeof( PicInt )     +
00082            sizeof( PicInt )     +
00083            sizeof( PicInt )     +
00084            sizeof( PicInt )     +
00085            sizeof( PicPointer ) +
00086            sizeof( PicInt )     +
00087            sizeof( PicInt )     +
00088            sizeof( PicChar )*32 +
00089            sizeof( PicInt )     +
00090            sizeof( PicUint )    +
00091            sizeof( PicUint )    +
00092            sizeof( PicInt )     +
00093            sizeof( PicInt )     +
00094            sizeof( PicUint )    +
00095            sizeof( PicInt )     +
00096            sizeof( PicInt )     +
00097            sizeof( PicFloat )   +
00098            sizeof( PicChar )*6
00099    )
00100    ? 1 : -1
00101    ];
00102 
00103 
00104 typedef struct tagPICFILENOTE
00105    {
00106    PicInt      level;
00107    PicPointer  next;
00108    PicInt      number;
00109    PicInt      status;
00110    PicUint     type;
00111    PicInt      x;
00112    PicInt      y;
00113    PicChar     text[80];
00114    }
00115    PICFILENOTE;
00116 
00117 
00118 #define PIC_NOTE_SIZE  96
00119 
00120 extern char _pic_compile_time_size_check
00121    [
00122    ( PIC_NOTE_SIZE ==
00123            sizeof( PicInt )     +
00124            sizeof( PicPointer ) +
00125            sizeof( PicInt )     +
00126            sizeof( PicInt )     +
00127            sizeof( PicUint )    +
00128            sizeof( PicInt )     +
00129            sizeof( PicInt )     +
00130            sizeof( PicChar )*80
00131    )
00132    ? 1 : -1
00133    ];
00134 
00135 
00136 typedef enum
00137    {
00138    PIC_MERGE_OFF       = 0,            /* Image is not merged                        */
00139    PIC_MERGE_16        = 1,            /* All pixels merged, 16 color (4-bit)        */
00140    PIC_MERGE_ALTERNATE = 2,            /* Alternate pixels merged, 128 color (7-bit) */
00141    PIC_MERGE_COLUMN    = 3,            /* Alternate columns merged                   */
00142    PIC_MERGE_ROW       = 4,            /* Alternate rows merged                      */
00143    PIC_MERGE_MAXIMUM   = 5,            /* Maximum pixels merged                      */
00144    PIC_MERGE_OPT12     = 6,            /* 64-color (12-bit) optimized 2-image merge  */
00145    PIC_MERGE_OPT12_V2  = 7             /* As above except convert look up table      */
00146                                        /* saved after the notes in file, as oppossed */
00147                                        /* to at the end of each image data           */
00148    }
00149    PIC_MERGE_TYPE;
00150 
00151 
00152 typedef enum
00153    { 
00154    PIC_NOTE_TYPE_LIVE      = 1,        /* # Information about live collection        */
00155    PIC_NOTE_TYPE_FILE1     = 2,        /*   Note from image #1                       */
00156    PIC_NOTE_TYPE_NUMBER    = 3,        /*   Number in multiple image file            */
00157    PIC_NOTE_TYPE_USER      = 4,        /*   User notes generated notes               */
00158    PIC_NOTE_TYPE_LINE      = 5,        /*   Line mode info                           */
00159    PIC_NOTE_TYPE_COLLECT   = 6,        /*   Collect mode info                        */
00160    PIC_NOTE_TYPE_FILE2     = 7,        /*   Note from image #2                       */
00161    PIC_NOTE_TYPE_SCALEBAR  = 8,        /*   Scale bar info                           */
00162    PIC_NOTE_TYPE_MERGE     = 9,        /* # Merge info                               */
00163    PIC_NOTE_TYPE_THRUVIEW  = 10,       /* # Thruview info                            */
00164    PIC_NOTE_TYPE_ARROW     = 11,       /*   Arrow info                               */
00165    PIC_NOTE_TYPE_VARIABLE  = 20,       /*   Internal variable                        */
00166    PIC_NOTE_TYPE_STRUCTURE = 21        /*   Again internal variable, except held as  */
00167                                        /*   a structure                              */
00168    }
00169    PIC_NOTE_TYPE;
00170 
00171 
00172 typedef enum
00173    { 
00174    PIC_NOTE_STATUS_ALL      = 0x0100,  /* Whether note is displayed on all images    */
00175    PIC_NOTE_STATUS_DISPLAY  = 0x0200,  /* Note is currently displayed                */
00176    PIC_NOTE_STATUS_POSITION = 0x0400   /* Note has been positioned by the user       */
00177    }
00178    PIC_NOTE_STATUS;
00179 
00180 
00181 #define PIC_AXIS_TYPE_D        1             /*   distance im microns                      */
00182 #define PIC_AXIS_TYPE_T        2             /*   time in sec                              */
00183 #define PIC_AXIS_TYPE_A        3             /*   angle in degrees                         */
00184 #define PIC_AXIS_TYPE_I        4             /*   intensity in grey levels                 */
00185 #define PIC_AXIS_TYPE_M4       5             /*   4-bit merged image                       */
00186 #define PIC_AXIS_TYPE_R        6             /*   Ratio                                    */
00187 #define PIC_AXIS_TYPE_LR       7             /*   Log Ratio                                */
00188 #define PIC_AXIS_TYPE_P        8             /*   Product                                  */
00189 #define PIC_AXIS_TYPE_C        9             /*   Calibrated concentration/pH       */
00190 #define PIC_AXIS_TYPE_PHOTON  10             /*   intensity in photons/sec                 */
00191 #define PIC_AXIS_TYPE_RGB     11             /*   RGB type (mixer/channel/colour)          */
00192 #define PIC_AXIS_TYPE_SEQ     12             /*   SEQ type (eg "experiments" of a "method" */
00193 #define PIC_AXIS_TYPE_6D      13             /*   6th level of axis "nesting", on top of   */
00194                                              /*   RGB & SEQ                                */
00195 #define PIC_AXIS_TYPE_TC      14             /*   Time Course axis                         */
00196 #define PIC_AXIS_TYPE_S       15             /*   Intensity sigmoid calibrated             */
00197                                              /*   concentration/pH                         */
00198 #define PIC_AXIS_TYPE_LS      16             /*   Intensity log sigmoid calibrated         */
00199                                              /*   concentration/pH                         */
00200 #define PIC_AXIS_TYPE_MASK    0xFF           /*   mask for axis TYPE                       */
00201 #define PIC_AXIS_TYPE_XY      0x100          /*   axis is XY, needs updating by LENS etc   */
00202 #define PIC_AXIS_TYPE_WORD    0x200          /*   axis is word, only corresponds to axis[0]*/
00203 
00204 
00205 
00206 typedef enum
00207    {
00208    PIC_NO_ERROR,
00209    PIC_ERROR_OUT_OF_MEMORY,
00210    PIC_ERROR_FILE_OPEN,
00211    PIC_ERROR_FILE_READ,
00212    PIC_ERROR_FILE_WRITE,
00213    PIC_ERROR_MAX_SIZE,
00214    PIC_ERROR_UNSUPPORTED,
00215    PIC_ERROR_FILE_INVALID
00216    }
00217    PIC_ERROR_CODE;
00218 
00219 
00220 
00221 typedef struct tagPICLUT
00222    {
00223    unsigned char rgb[256][3];
00224    }
00225    PICLUT;
00226 
00227 
00228 #define PIC_LUT_SIZE  768
00229 
00230 extern char _pic_compile_time_size_check[ ( PIC_LUT_SIZE == sizeof( PICLUT ) ) ? 1 : -1 ];
00231 
00232 
00233 typedef struct tagPICFILE
00234    {
00235    PICFILEHEADER   header;
00236    unsigned        bitsPerChannel;  /* 8 or 16 only. */
00237    unsigned        numChannels;     /* 1 if grayscale. */
00238    PICFILENOTE    *notes;           /* Should be NULL if no notes. */
00239    unsigned        numNotes;        /* Should be 0 if no notes. */
00240    void           *pixels;
00241    PICLUT         *luts;            /* Should be NULL if no lookup tables. */
00242    unsigned        numLuts;         /* Should be 0 if no lookup tables. */
00243    }
00244    PICFILE;
00245 
00246 
00247 void ConstructPicFile( PICFILE *const pic );
00248 
00249 void DestructPicFile( PICFILE *const pic );
00250 
00251 
00252 PIC_ERROR_CODE ReadPicFile( PICFILE *const pic, const char *const fileName );
00253 
00254 PIC_ERROR_CODE WritePicFile( const PICFILE *const pic, const char *const fileName );
00255 
00256 
00257 /* Retrieves all information except the actual pixels. */
00258 PIC_ERROR_CODE GetPicFileInfo( PICFILE *const pic, const char *const fileName );
00259 
00260 /* Gets the pixels at the Z level indicated. Call GetPicFileInfo() first. */
00261 PIC_ERROR_CODE ReadPicFileAt( PICFILE *const pic, const char *const fileName, unsigned z );
00262 
00263 #ifdef __cplusplus
00264 }
00265 #endif
00266 
00267 #endif/* __PIC_H__ */
00268