/*   b3dutil.h   - utility functions for getting version and copyright, 
 *                      trimming program name
 *
 *   Copyright (C) 1995-2007 by Boulder Laboratory for 3-Dimensional Electron
 *   Microscopy of Cells ("BL3DEMC") and the Regents of the University of 
 *   Colorado.
 *
 *   $Id$
 */                                                                           

#ifndef B3DUTIL_H
#define B3DUTIL_H

#include <stdio.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>

#ifdef _WIN32
#define snprintf _snprintf
#define vsnprintf _vsnprintf
#endif

/* Include this since this include file was split off from here */
#include "cfsemshare.h"

#define MAX_IMOD_ERROR_STRING  512

#define B3DMIN(a,b) ((a) < (b) ? (a) : (b))
#define B3DMAX(a,b) ((a) > (b) ? (a) : (b))
#define B3DSIGN(a,b) ((b) < 0 ? -(a) : (a))
#define B3DCLAMP(val,minv,maxv) val = B3DMAX((minv), B3DMIN((maxv), (val)))
#define B3DNINT(a) (int)floor((a) + 0.5)
#define B3DABS(a) ((a) >= 0 ? (a) : -(a))
#define B3DFREE(a) {free(a); a = NULL;}
#define B3DMALLOC(type,num) (type *)malloc((num) * sizeof(type))
#define B3DREALLOC(var,type,num) var = (type *)realloc(var, (num) * sizeof(type))
#define B3DSWAP(a,b,tmp) {tmp = (a); a = (b); b = tmp;}
#define B3DCHOICE(test,ifT,ifF) ((test) ? (ifT) : (ifF))
#define ACCUM_MAX(maxv, val) maxv = ((maxv) > (val) ? (maxv) : (val))
#define ACCUM_MIN(minv, val) minv = ((minv) < (val) ? (minv) : (val))

#define IMOD_MRC_STAMP 1146047817
#define WRITE_SBYTES_DEFAULT 1
#define WRITE_SBYTES_ENV_VAR "WRITE_MODE0_SIGNED"
#define READ_SBYTES_ENV_VAR "READ_MODE0_SIGNED"
#define MRC_FLAGS_SBYTES          1
#define MRC_FLAGS_PIXEL_FROM_EXT  2
#define MRC_FLAGS_INV_ORIGIN      4
#define MRC_FLAGS_BAD_RMS_NEG     8
#define MRC_FLAGS_4BIT_BYTES     16
#define MRC_FLAGS_CTF_CORRECTED  32
#define INVERT_MRC_ORIGIN_DEFAULT 1
#define INVERT_MRC_ORIGIN_ENV_VAR "INVERT_MRC_ORIGIN"
#define WRITE_FLOATS_16BIT "IMOD_WRITE_FLOATS_16BIT"

/* Duplicate definitions of output-capable IITYPE values to avoid including iimage.h */
#define OUTPUT_TYPE_TIFF    1
#define OUTPUT_TYPE_MRC     2
#define OUTPUT_TYPE_HDF     5
#define OUTPUT_TYPE_JPEG    6
#define OUTPUT_TYPE_DEFAULT OUTPUT_TYPE_MRC
#define OUTPUT_TYPE_ENV_VAR "IMOD_OUTPUT_FORMAT"

#define ALL_BIGTIFF_DEFAULT 0
#define ALL_BIGTIFF_ENV_VAR "IMOD_ALL_BIG_TIFF"

#define RADIANS_PER_DEGREE 0.01745329252

/* Defined types for calling getExtHeaderValue */
#define EXT_HEAD_VAL_BYTE   0
#define EXT_HEAD_VAL_SHORT  1
#define EXT_HEAD_VAL_FLOAT  2
#define EXT_HEAD_VAL_INT    3
#define EXT_HEAD_VAL_DOUBLE 4

/* Flags for call findautocorrpeaks */
#define FIND_ACPK_NO_WAFFLE   0x1
#define FIND_ACPK_BOTH_GEOMS  0x2
#define FIND_ACPK_HEX_GRID    0x4
#define FIND_ACPK_TILT_IN_VEC 0x8

/* Determinant of 3x3 matrix */
#define determ3(a1,a2,a3,b1,b2,b3,c1,c2,c3) ((a1)*(b2)*(c3) - (a1)*(b3)*(c2) +\
  (a2)*(b3)*(c1) - (a2)*(b1)*(c3) + (a3)*(b1)*(c2) - (a3)*(b2)*(c1))

#ifdef __cplusplus
extern "C" {
#endif

  int imodVersion(const char *pname);
  void imodCopyright(void);
  void imodUsageHeader(const char *pname);
  char *IMOD_DIR_or_default(int *assumed);
  char *imodProgName(const char *fullname);
  int imodBackupFile(const char *filename);
  FILE *b3dOpenFile(const char *name, const char *mode);
  int imodGetpid();
  void pidToStderr();
  char *f2cString(const char *str, int strSize);
  int c2fString(const char *cStr, char *fStr, int fSize);
  void b3dSetStoreError(int ival);
  int b3dGetStoreError();
  void b3dError(FILE *stream, const char *format, ...);
  char *b3dGetError(void);

  int b3dFseek(FILE *fp, int offset, int flag);
  size_t b3dFread(void *buf, size_t size, size_t count, FILE *fp);
  size_t b3dFwrite(void *buf, size_t size, size_t count, FILE *fp);
  void b3dRewind(FILE *fp);
  int mrc_big_seek(FILE *fp, int base, int size1, int size2, int flag);
  int mrcHugeSeek(FILE *fp, int base, int x, int y, int z, int nx, int ny, 
                  int dsize, int flag);
  int fgetline(FILE *fp, char s[],int limit);
  /*int readLinesForValues(FILE *fp, float *values1, float *values2, int *numToGet,
    int valSize, char *line, int maxLine);*/

  void b3dHeaderItemBytes(int *nflags, int *nbytes);
  int extraIsNbytesAndFlags(int nint, int nreal);
  void setOrClearFlags(b3dUInt32 *flags, b3dUInt32 mask, int state);
  int numberInList(int num, int *list, int nlist, int noListValue);
  void balancedGroupLimits(int numTotal, int numGroups, int groupInd, int *start, 
                           int *end);
  void groupLimitsRemainderAtEnd(int numTotal, int numGroups, int groupInd, int *start, 
                                 int *end);
  unsigned char **makeLinePointers(void *array, int xsize, int ysize, int dsize);

  int b3dIMin(int narg, ...);
  int b3dIMax(int narg, ...);
  double wallTime(void);
  int b3dMilliSleep(int msecs);
  int numOMPthreads(int optimalThreads);
  int b3dOMPthreadNum();
  void overrideWriteBytes(int value);
  int writeBytesSigned();
  int readBytesSigned(int stamp, int flags, int mode, float dmin, float dmax);
  int invertMrcOriginOnOutput();
  void overrideInvertMrcOrigin(int value);
  void b3dShiftBytes(unsigned char *usbuf, char *sbuf, int nx, int ny, int direction,
                     int bytesSigned);
  void overrideOutputType(int type);
  int b3dOutputFileType();
  int setOutputTypeFromString(const char *typeStr);
  void overrideAllBigTiff(int value);
  int makeAllBigTiff();
  void setNextOutputSize(int nx, int ny, int nz, int mode);
  int setTiffCompressionType(int typeIndex, int overrideEnv);
  void set4BitOutputMode(int inVal);
  int write4BitModeForBytes();
  void setFloat16outputMode(int inVal, int testForMRC);
  int setFloatOutputForEnteredMode(int mode);
  int write16BitModeForFloats();
  int dataSizeForMode(int mode, int *bytes, int *channels);
  int numCoresAndLogicalProcs(int *physical, int *logical);
  int totalCudaCores(int major, int minor, int multiprocCount);
  double b3dPhysicalMemory();
  double b3dAddressableMemory();
  char **expandArgList(const char **argVec, int numArg, int *newNum, int *ifAlloc,
                       int *noMatchInd);
  int replaceFileArgVec(const char ***argv, int *argc, int *firstInd, int *ifAlloc);
  double angleWithinLimits(float angle, float lowerLim, float upperLim);
  void b3dSetLockTimeout(float timeout);
  int b3dOpenLockFile(const char *filename);
  int b3dLockFile(int index);
  int b3dUnlockFile(int index);
  int b3dCloseLockFile(int index);

#ifdef __cplusplus
}
#endif


#endif