/* * clip.h -- Header file for command line image proccessing. * * Copyright (C) 1995-2015 by the Regents of the University of * Colorado. See dist/COPYRIGHT for full copyright notice. * * $Id$ */ #ifndef CLIP_H #define CLIP_H #include #include "mrcfiles.h" #include "mrcslice.h" #include "b3dutil.h" #include "CorrectDefects.h" /* processes */ enum {IP_NONE = 0, IP_ADD, IP_AVERAGE, IP_VARIANCE, IP_STANDEV, IP_BRIGHTNESS, IP_COLOR, IP_CONTRAST, IP_CORRELATE, IP_DIFFUSION, IP_FFT, IP_FILTER, IP_FLIP, IP_GRADIENT, IP_SUBTRACT, IP_MULTIPLY, IP_DIVIDE, IP_LOGARITHM, IP_SQROOT, IP_GRAHAM, IP_INFO, IP_JOINRGB, IP_LAPLACIAN, IP_MEDIAN, IP_PEAK, IP_PREWITT, IP_UNWRAP, IP_QUADRANT, IP_UNPACK, IP_HISTOGRAM, IP_NORMALIZE, IP_PROJECT, IP_RESIZE, IP_ROTATE, IP_SHADOW, IP_SHARPEN, IP_SMOOTH, IP_SPECTRUM, IP_SOBEL, IP_SPLITRGB, IP_STAT, IP_TRANSLATE, IP_ZOOM, IP_TRUNCATE, IP_THRESHOLD, IP_FILLEDGE, IP_DEFECTMAP}; #define IP_DEFAULT -99999 #define IP_APPEND_FALSE 0 #define IP_APPEND_OVERWRITE 1 #define IP_APPEND_ADD 2 typedef struct Grap_options { char *pname; /* Program name */ char *command; /* process command */ MrcHeader *hin; MrcHeader *hin2; MrcHeader *hout; int process; /* The process */ int x, y, z; int x2, y2, z2; int ix, iy, iz, iz2; int ox, oy, oz; int chunkX, chunkY, chunkZ; float cx, cy, cz; float high, low; float red, green, blue; float thresh; float weight; float pctlFrac; float falloffFrac; int minSize; float pad; int mode; int dim; int infiles; char **fnames; int sano; int add2file; int isec; float val; int nofsecs; /* Number of sections in section list. */ int *secs; /* Section list for 2-D */ int outBefore; /* Number of blank sections to output before and after */ int outAfter; int ocanresize; /* output size can be changed. */ int ocanchmode; /* output mode can be changed. */ int fromOne; /* Number Z from 1 not 0 */ char *ofname; char *plname; int newXoverlap, newYoverlap; int rotationFlip; // Rotation/flip to apply to gain reference or -1 to use r/f int readDefects; // Flag that defects were read from file CameraDefects defects; // The defect table itself int camSizeX, camSizeY; // Camera size in X and Y represented in table float binning; // Entered binning number int scaleDefects; // Flag to scale defects up if they aren't } ClipOptions; /* clip.cpp */ void usage(void); void show_error(const char *format, ...); void show_warning(char *reason); void show_status(char *info); void default_options(ClipOptions *opt); int *clipMakeSecList(char *clst, int *nofsecs); /* processing.cpp */ int clip_scaling(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); int clipEdge(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); int clip_flip(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); int clip_color(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); int clip_quadrant(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); int clipSpectrum(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); int clip2d_color(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); int clip_average(MrcHeader *h1, MrcHeader *h2, MrcHeader *hout, ClipOptions *opt); int clip_multdiv(MrcHeader *h1, MrcHeader *h2, MrcHeader *hout, ClipOptions *opt); int clipUnpack(MrcHeader *h1, MrcHeader *h2, MrcHeader *hout, ClipOptions *opt); int clipDefectMap(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); int clip_joinrgb(MrcHeader *h1, MrcHeader *h2, MrcHeader *hout, ClipOptions *opt); int clip_splitrgb(MrcHeader *h1, ClipOptions *opt); int clip2d_average(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); int clip_parxyz(Istack *v, int xmax, int ymax, int zmax, float *rx, float *ry, float *rz); int clip_stat3d(Istack *v); int clip_get_stat3d(Istack *v, float *rmin, float *rmax, float *rmean, int *rx, int *ry, int *rz); int clip_stat(MrcHeader *hin, ClipOptions *opt); int clipHistogram(MrcHeader *hin, ClipOptions *opt); int histogramPeaksAndDip(MrcHeader *hin, ClipOptions *opt); int clip_convolve(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); int clipMedian(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt, float *kernel, int size, int z); int clipDiffusion(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); int write_vol(Islice **vol, MrcHeader *hout); int free_vol(Islice **vol, int z); int correctDefects(Islice *slice, int nxFull, int nyFull, ClipOptions *opt); int fillDriftCorrectedEdges(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); /* file_io.cpp */ void set_input_options(ClipOptions *opt, MrcHeader *hin); int set_output_options(ClipOptions *opt, MrcHeader *hout); int set_options(ClipOptions *opt, MrcHeader *hin, MrcHeader *hout); int setChunkOutput(ClipOptions *opt, MrcHeader *hout, int *limits, int *numTiles, int *tileSizes); int clipWriteSlice(Islice *slice, MrcHeader *hout, ClipOptions *opt, int kSec, int *zWrite, int freeSlice); Istack *grap_volume_read(MrcHeader *hin, ClipOptions *opt); int grap_volume_write(Istack *v, MrcHeader *hout, ClipOptions *opt); int grap_volume_free(Istack *v); int mrc_head_print(MrcHeader *data); int set_mrc_coords(ClipOptions *opt); /* fft.cpp */ int slice_fft(Islice *slice); int clip_fftvol3(Istack *v, int idir); int clip_fftvol(Istack *v); int clip_3dfft(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); int clip_fft(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); int clip_nicesize(int size); void mrcToDFFT(float buf[], int nx, int ny, int idir); /* filter.cpp */ int clip_3dfilter(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); int clip_bandpass_filter(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt); /* correlation.cpp */ void corr_getmax(Islice *is, int sa, int xm, int ym, float *x, float *y); Islice *clip_slice_corr(Islice *s1, Islice *s2); int clip_corr3d(MrcHeader *hin1, MrcHeader *hin2, MrcHeader *hout, ClipOptions *opt); int grap_3dcorr(MrcHeader *hin1, MrcHeader *hin2, MrcHeader *hout, ClipOptions *opt); int grap_corr(MrcHeader *hin1, MrcHeader *hin2, MrcHeader *hout, ClipOptions *opt); int padfloat_volume(Istack *v, float pad); int clip_cor_scalevol(Istack *v); double parabolic_fit(double *outX, double *outY, double i[3][3]); int thresholdWithMinSize(MrcHeader *hin, MrcHeader *hout, ClipOptions *opt, float threshLo, float threshHi, int zWrite); #endif /* clip.h */