/* * clip -- Command Line Image Processing * * Original author: James Kremer * Revised by: David Mastronarde email: mast@colorado.edu * * Copyright (C) 1995-2015 by the Regents of the University of * Colorado. See dist/COPYRIGHT for full copyright notice. * * $Id$ */ #include #include #include "iimage.h" #include "clip.h" #include "imodconfig.h" #include "parse_params.h" void usage(void) { char *name = "clip"; printf( "%s: Command Line Image Processing. %s, %s %s\n", name, VERSION_NAME, __DATE__, __TIME__); imodCopyright(); printf( "----------------------------------------------------\n"); printf( "%s usage:\n", name); printf( "%s [process] [options] [input files...] [output file]\n", name); printf( "\nprocess:\n"); printf( "\tadd - Add images together.\n"); printf( "\taverage - Average files together.\n"); printf( "\tbrightness - Increase or decrease brightness.\n"); printf( "\tcolor - Add false color.\n"); printf( "\tcontrast - Increase or decrease contrast.\n"); printf( "\tcorrelation - Do a auto/cross correlation.\n"); printf( "\tdefectmap - Output map of all pixels in defects entered with -B.\n" ); printf( "\tdiffusion - Do 2-D anisotropic diffusion on slices.\n"); printf( "\tdivide - Divide one image volume by another.\n"); printf( "\tgradient - Compute gradient as in 3dmod.\n"); printf( "\tgraham - Apply Graham filter as in 3dmod.\n"); printf( "\thistogram - Print histogram of values.\n"); printf( "\tinfo - Print information to stdout.\n"); printf( "\tfft - Do a fft or inverse fft transform.\n"); printf( "\tfilter - Do a bandpass filter.\n"); printf( "\tflip.. - Flip image about various axes.\n"); /* printf( "\tpeak - Find peaks in image.\n"); */ printf( "\tjoinrgb - Join 3 byte files into an RGB file.\n"); printf( "\tlaplacian - Apply Laplacian filter as in 3dmod.\n"); printf( "\tmedian - Do median filtering.\n"); printf( "\tmultiply - Multiple one image volume by another.\n"); printf( "\tnormalize - Multiply by gain ref., scale, remove big values.\n"); printf( "\tprewitt - Apply Prewitt filter as in 3dmod.\n"); printf( "\tquadrant - Correct quadrant disparities from 4-port camera.\n"); printf( "\tresize - Cut out and/or pad image data.\n"); printf( "\trotx - Rotate volume by -90 about X axis.\n"); /* printf( "\trotation - Rotate image\n"); */ printf( "\tshadow - Increase or decrease image shadows.\n"); printf( "\tsharpen - Sharpen image as in 3dmod.\n"); printf( "\tsmooth - Smooth image as in 3dmod.\n"); printf( "\tsobel - Apply Sobel filter as in 3dmod.\n"); printf( "\tspectrum - Compute scaled, reduced power spectrum.\n"); printf( "\tsplitrgb - Split RGB image file into 3 byte files.\n"); printf( "\tstandev - Compute standard deviation for averaged images.\n"); printf( "\tstats - Print some stats on image file.\n"); printf( "\tsubtract - Subtract one image volume from another.\n"); printf( "\tthreshold - Apply threshold to make binary image.\n"); printf( "\ttruncate - Limit image values at low or high end.\n"); printf( "\tunwrap - Undo a wraparound of integer intensity values.\n"); printf( "\tunpack - Unpack 4-bit data into bytes - same as normalize.\n"); printf( "\tvariance - Compute variance for averaged images.\n"); /* printf( "\ttranslate - translate image.\n"); printf( "\tzoom - magnify image.\n"); */ printf( "\noptions:\n"); printf( "\t[-v] view output data.\n"); printf( "\t[-3d] or [-2d] treat image as 3d (default) or 2d.\n"); printf( "\t[-s] Switch, [-n #] Amount; Depends on function.\n"); printf( "\t[-n #] [-l #] Iterations and Gaussian sigma for smoothing.\n"); printf( "\t[-h #] [-l #] Values for filter, threshold, or truncate.\n"); printf( "\t[-cc #] [-l #] [-k #] values for anisotropic diffusion.\n"); printf( "\t[-r #] [-g #] [-b #] red, green, blue values.\n"); printf( "\t[-x #,#] [-y #,#] starting and ending input coords.\n"); printf( "\t[-cx #] [-cy #] [-cz #] center coords.\n"); printf( "\t[-ix #] [-iy #] [-iz #] input sizes.\n"); printf( "\t[-ox #] [-oy #] [-oz #] output sizes.\n"); printf( "\t[-CX #] [-CY #] [-CZ #] chunk sizes for tiled HDF output.\n"); printf( "\t[-a] Append output to file.\n"); printf( "\t[-ov #] Overwrite output starting at section #\n"); printf( "\t[-m (mode#)] Output data mode.\n"); printf( "\t[-f format] Output file format (MRC, TIFF, HDF, JPEG).\n"); printf( "\t[-p (pad#)] Pad empty data value.\n"); printf( "\t[-1] Number Z values from 1 instead of 0.\n"); printf( "\t[-P file] Name of piece list file for stats on a montage.\n"); printf( "\t[-O #,#] Overlaps in X and Y in displayed montage.\n"); printf( "\t[-D file] Apply defect correction using defect list in given " "file.\n"); printf( "\t[-B #] Binning value to use in defect correction.\n"); printf( "\t[-S] Scale defect list up by 2 if it is not already scaled.\n"); printf( "\t[-R #] Rotation/flip to apply to gain reference, or -1 for r/f.\n"); printf( "\t[-E #,#] Analyze histogram for extra counts on one side.\n"); printf( "\t[-F #,#] Analyze histogram for fastest falloff point.\n"); printf( "\t[-M #,#] Set minimum size of connected regions when " "thresholding.\n"); printf( "\t[-es #] Set super-resolution factor when reading from EER files.\n"); printf( "\t[-ez #] Set summing of frames when reading from EER files.\n"); printf( "\t[-et] Read thumbnail, not frames, from EER file.\n"); printf( "\t[-ep #] Set padding of defects from gain reference for EER file.\n"); printf( "\t[-ed file] Write defects from EER gain reference to file.\n"); printf( "\n"); } /* 11/4/04: switch to standard out and standard format to some extent */ void show_error(const char *format, ...) { char errorMess[512]; va_list args; va_start(args, format); vsprintf(errorMess, format, args); printf("ERROR: %s\n", errorMess); } void show_warning(char *reason) { printf("WARNING: %s\n", reason); } void show_status(char *info) { printf("%s", info); fflush(stdout); } void default_options(ClipOptions *opt) { opt->hin = opt->hin2 = opt->hout = NULL; opt->x = IP_DEFAULT; opt->x2 = IP_DEFAULT; opt->y = IP_DEFAULT; opt->y2 = IP_DEFAULT; opt->z = IP_DEFAULT; opt->z2 = IP_DEFAULT; opt->ix = IP_DEFAULT; opt->iy = IP_DEFAULT; opt->iz = IP_DEFAULT; opt->iz2 = IP_DEFAULT; opt->ox = IP_DEFAULT; opt->oy = IP_DEFAULT; opt->oz = IP_DEFAULT; opt->cx = IP_DEFAULT; opt->cy = IP_DEFAULT; opt->cz = IP_DEFAULT; opt->chunkX = IP_DEFAULT; opt->chunkY = IP_DEFAULT; opt->chunkZ = IP_DEFAULT; opt->outBefore = opt->outAfter = IP_DEFAULT; opt->red = IP_DEFAULT; opt->green = IP_DEFAULT; opt->blue = IP_DEFAULT; opt->high = IP_DEFAULT; opt->low = IP_DEFAULT; opt->thresh = IP_DEFAULT; opt->pctlFrac = IP_DEFAULT; opt->falloffFrac = IP_DEFAULT; opt->weight = IP_DEFAULT; opt->pad = IP_DEFAULT; opt->minSize = IP_DEFAULT; opt->process = IP_NONE; opt->dim = 3; opt->add2file = IP_APPEND_FALSE; opt->sano = FALSE; opt->val = IP_DEFAULT; opt->mode = IP_DEFAULT; opt->nofsecs = IP_DEFAULT; opt->secs = NULL; opt->ocanresize = TRUE; opt->ocanchmode = TRUE; opt->fromOne = FALSE; opt->ofname = NULL; opt->plname = NULL; opt->newXoverlap = IP_DEFAULT; opt->newYoverlap = IP_DEFAULT; opt->readDefects = FALSE; opt->rotationFlip = 0; opt->binning = IP_DEFAULT; opt->scaleDefects = FALSE; } int main( int argc, char *argv[] ) { MrcHeader hin, hin2, hout; ClipOptions opt; int process = IP_NONE; /* command to run. */ int view = FALSE; /* view file at end? */ int procout = TRUE; /* will process write output?. */ int needtwo = FALSE; /* Does process need two input files? */ int iarg, j, itemp, superFac; int retval = 0; int formatSet = -2; int feiDefPad = 0; int eerGroup = 1, eerSuper = 2, eerFlags = 0; char *dumpDefectName = NULL; ImodImageFile *iiFile; char *strng, *strCopy; b3dUInt16 count; std::string sstr; FILE *defFP; char viewcmd[1024]; char *progname = imodProgName(argv[0]); sprintf(viewcmd, "ERROR: %s - ", progname); setExitPrefix(viewcmd); if (argc < 3){ usage(); exit(3); } opt.command = argv[1]; /* Find which process to run */ if (!strncmp( argv[1], "add", 3)) { process = IP_ADD; needtwo = TRUE; } if ((!strncmp( argv[1], "avg", 3)) || (!strncmp( argv[1], "average", 3)) ) process = IP_AVERAGE; if (!strncmp( argv[1], "standev", 4)) process = IP_STANDEV; if (!strncmp( argv[1], "variance", 3)) process = IP_VARIANCE; if (!strncmp( argv[1], "multiply", 3)) { process = IP_MULTIPLY; needtwo = TRUE; } if (!strncmp( argv[1], "subtract", 3)) { process = IP_SUBTRACT; needtwo = TRUE; } if (!strncmp( argv[1], "divide", 3)) { process = IP_DIVIDE; needtwo = TRUE; } if (!strncmp( argv[1], "brightness", 3)) process = IP_BRIGHTNESS; if (!strncmp( argv[1], "color", 3)) process = IP_COLOR; if (!strncmp( argv[1], "contrast", 3)) process = IP_CONTRAST; if (!strncmp( argv[1], "correlation", 3)) process = IP_CORRELATE; if (!strncmp( argv[1], "diffusion", 3)) process = IP_DIFFUSION; if (!strncmp( argv[1], "info", 3)){ process = IP_INFO; procout = FALSE; } if (!strncmp( argv[1], "fft", 3)) process = IP_FFT; if (!strncmp( argv[1], "filter", 3)) process = IP_FILTER; if (!strncmp( argv[1], "flip", 4)) process = IP_FLIP; if (!strncmp( argv[1], "rotx", 4)) process = IP_FLIP; if (!strncmp( argv[1], "gradient", 4)) process = IP_GRADIENT; if (!strncmp( argv[1], "graham", 4)) process = IP_GRAHAM; if (!strncmp( argv[1], "histogram", 2)) { process = IP_HISTOGRAM; procout = FALSE; } if (!strncmp( argv[1], "laplacian", 2)) process = IP_LAPLACIAN; if (!strncmp( argv[1], "median", 2)) process = IP_MEDIAN; /* if (!strncmp( argv[1], "peak", 3)){ process = IP_PEAK; procout = FALSE; } */ if (!strncmp( argv[1], "prewitt", 2)) process = IP_PREWITT; if (!strncmp( argv[1], "resize", 3)) process = IP_RESIZE; /* if (!strncmp( argv[1], "rotate", 3)) process = IP_ROTATE; */ if (!strncmp( argv[1], "shadow", 4)) process = IP_SHADOW; if (!strncmp( argv[1], "sharpen", 4)) process = IP_SHARPEN; if (!strncmp( argv[1], "smooth", 2)) process = IP_SMOOTH; if (!strncmp( argv[1], "sobel", 2)) process = IP_SOBEL; if (!strncmp( argv[1], "spectrum", 2)) process = IP_SPECTRUM; if (!strncmp( argv[1], "stat", 4)){ process = IP_STAT; procout = FALSE; } /* if (!strncmp( argv[1], "translate", 2)) process = IP_TRANSLATE; if (!strncmp( argv[1], "zoom", 3)) process = IP_ZOOM; if (!strncmp( argv[1], "project", 3)){ process = IP_PROJECT; } */ if (!strncmp( argv[1], "threshold", 3)) process = IP_THRESHOLD; if (!strncmp( argv[1], "truncate", 3)) process = IP_TRUNCATE; if (!strncmp( argv[1], "unwrap", 3)) process = IP_UNWRAP; if (!strncmp( argv[1], "sqroot", 3)) process = IP_SQROOT; if (!strncmp( argv[1], "logarithm", 3)) process = IP_LOGARITHM; if (!strncmp( argv[1], "quadrant", 2)) { process = IP_QUADRANT; opt.dim = 2; } if (!strncmp( argv[1], "edgefill", 2)) { process = IP_FILLEDGE; opt.dim = 2; } if (!strncmp( argv[1], "unpack", 3)) process = IP_UNPACK; if (!strncmp( argv[1], "normalize", 3)) process = IP_NORMALIZE; if (!strncmp( argv[1], "defectmap", 3)) process = IP_DEFECTMAP; if (!strncmp( argv[1], "splitrgb", 3)){ process = IP_SPLITRGB; } if (!strncmp( argv[1], "joinrgb", 3)){ process = IP_JOINRGB; } if (process == IP_NONE){ usage(); exit(1); } default_options(&opt); opt.process = process; opt.pname = progname; /* get options */ for (iarg = 2; iarg < argc; iarg++) { if (argv[iarg][0] == '-') { switch (argv[iarg][1]){ case 'a': opt.add2file = IP_APPEND_ADD; break; case '3': if (process != IP_QUADRANT) opt.dim = 3; break; case '2': opt.dim = 2; break; case '1': opt.fromOne = TRUE; break; case 's': opt.sano = TRUE; break; case 'n': sscanf(argv[++iarg], "%f", &(opt.val)); break; case 'm': if (strcmp(argv[iarg + 1], "4-bit") == 0 || strcmp(argv[iarg + 1], "101") == 0) { set4BitOutputMode(1); opt.mode = MRC_MODE_BYTE; iarg++; } else { opt.mode = sliceMode(argv[++iarg]); } if (opt.mode == SLICE_MODE_UNDEFINED) exitError("Invalid mode entry %s.", argv[iarg]); if (opt.mode == SLICE_MODE_SBYTE || opt.mode == SLICE_MODE_UBYTE) { overrideWriteBytes(opt.mode == SLICE_MODE_SBYTE ? 1 : 0); opt.mode = 0; } break; case 'f': iarg++; formatSet = setOutputTypeFromString(argv[iarg]); if (formatSet < 0) exitError("Output file format entry %s is not %s.", argv[iarg], formatSet == -1 ? "recognized" : "available in this copy of IMOD"); break; case 'v': view = TRUE; break; case 'p': /* Pad option */ opt.pad = (float)atof(argv[++iarg]); break; case 't': sscanf(argv[++iarg], "%f", &(opt.thresh)); break; case 'E': sscanf(argv[++iarg], "%f%*c%d", &(opt.pctlFrac), &itemp); if (itemp < 0) opt.pctlFrac = -opt.pctlFrac; break; case 'F': sscanf(argv[++iarg], "%f%*c%d", &(opt.falloffFrac), &itemp); if (itemp < 0) opt.falloffFrac = -opt.falloffFrac; break; case 'M': sscanf(argv[++iarg], "%d%*c%d", &(opt.minSize), &itemp); if (itemp < 0) opt.minSize = -opt.minSize; break; case 'k': case 'w': sscanf(argv[++iarg], "%f", &(opt.weight)); break; case 'r': sscanf(argv[++iarg], "%f", &(opt.red)); break; case 'g': sscanf(argv[++iarg], "%f", &(opt.green)); break; case 'b': sscanf(argv[++iarg], "%f", &(opt.blue)); break; case 'l': sscanf(argv[++iarg], "%f", &(opt.low)); break; case 'h': sscanf(argv[++iarg], "%f", &(opt.high)); break; case 'x': case 'X': sscanf(argv[++iarg], "%d%*c%d", &(opt.x), &(opt.x2)); break; case 'y': case 'Y': sscanf(argv[++iarg], "%d%*c%d", &(opt.y), &(opt.y2)); break; /*case 'z': case 'Z': sscanf(argv[++iarg], "%f%*c%f", &(opt.z), &(opt.z2)); break; */ case 'o': switch (argv[iarg][2]){ case 0x00: case ' ': case 'v': opt.add2file = IP_APPEND_OVERWRITE; sscanf(argv[++iarg], "%d", &(opt.isec)); break; case 'x': case 'X': sscanf(argv[++iarg], "%d", &(opt.ox)); break; case 'y': case 'Y': sscanf(argv[++iarg], "%d", &(opt.oy)); break; case 'z': case 'Z': sscanf(argv[++iarg], "%d", &(opt.oz)); break; default: exitError("Invalid option %s.", argv[iarg]); } break; case 'i': case 'I': switch (argv[iarg][2]){ case 'x': case 'X': sscanf(argv[++iarg], "%d", &(opt.ix)); break; case 'y': case 'Y': sscanf(argv[++iarg], "%d", &(opt.iy)); break; case 'z': case 'Z': sscanf(argv[++iarg], "%d%*c%d", &(opt.iz),&opt.iz2); opt.secs = clipMakeSecList(argv[iarg], &opt.nofsecs); break; default: exitError("Invalid option %s.", argv[iarg]); } break; case 'c': switch (argv[iarg][2]){ case 'x': sscanf(argv[++iarg], "%g", &(opt.cx)); break; case 'y': sscanf(argv[++iarg], "%g", &(opt.cy)); break; case 'z': sscanf(argv[++iarg], "%g", &(opt.cz)); break; case 'c': sscanf(argv[++iarg], "%f", &(opt.thresh)); break; default: exitError("Invalid option %s.", argv[iarg]); } break; case 'C': switch (argv[iarg][2]){ case 'X': sscanf(argv[++iarg], "%d", &(opt.chunkX)); break; case 'Y': sscanf(argv[++iarg], "%d", &(opt.chunkY)); break; case 'Z': sscanf(argv[++iarg], "%d", &(opt.chunkZ)); break; default: exitError("Invalid option %s.", argv[iarg]); } break; case 'P': opt.plname = strdup(argv[++iarg]); break; case 'O': sscanf(argv[++iarg], "%d%*c%d", &opt.newXoverlap, &opt.newYoverlap); break; case 'D': j = CorDefParseDefects(argv[++iarg], 0, opt.defects, opt.camSizeX, opt.camSizeY); if (j) exitError("Error %s", (j == 1) ? "opening" : "reading or parsing lines in", argv[iarg]); opt.readDefects = TRUE; break; case 'B': opt.binning = atof(argv[++iarg]); if (opt.binning <= 0.49) exitError("Binning must be at least 0.5"); break; case 'S': opt.scaleDefects = TRUE; break; case 'R': opt.rotationFlip = atoi(argv[++iarg]); break; case 'e': if (argv[iarg][2] == 's') { eerSuper = atoi(argv[++iarg]); B3DCLAMP(eerSuper, 0, tiffGetMaxEERsuperRes()); } else if (argv[iarg][2] == 'z') { eerGroup = atoi(argv[++iarg]); eerGroup = B3DMAX(eerGroup, 0); } else if (argv[iarg][2] == 't') { eerFlags = IIFLAG_SKIP_EER_DIRS; } else if (argv[iarg][2] == 'p') { feiDefPad = atoi(argv[++iarg]); feiDefPad = B3DMAX(feiDefPad, 0); } else if (argv[iarg][2] == 'd') { dumpDefectName = strdup(argv[++iarg]);; } else exitError("Invalid option %s.", argv[iarg]); break; default: exitError("Invalid option %s.", argv[iarg]); } } else { break; } } if (iarg < argc && replaceFileArgVec((const char ***)&argv, &argc, &iarg, &j)) exit(1); tiffSetEERreadProperties(eerSuper, eerGroup, eerFlags); opt.fnames = &(argv[iarg]); if (!procout) { /* check for at least one input file */ if ((argc - 1) < iarg) { usage(); exit(3); } opt.infiles = argc - iarg; } else { /* check for at least one input and one output file name. */ if ((argc - 2) < iarg){ usage(); exit(3); } opt.infiles = argc - iarg - 1; } if (opt.chunkX != IP_DEFAULT || opt.chunkY != IP_DEFAULT || opt.chunkZ != IP_DEFAULT) { if (formatSet >= 0 && formatSet != OUTPUT_TYPE_HDF) exitError("You cannot specify chunk sizes and an output format other than HDF"); overrideOutputType(OUTPUT_TYPE_HDF); } // Check defect entries, flip in Y and find touching pixels if (opt.readDefects) { if (!opt.camSizeX || !opt.camSizeY) exitError("Problem with defect correction - Defect list file must" " have CameraSizeX and CameraSizeY entries"); CorDefFlipDefectsInY(&opt.defects, opt.camSizeX, opt.camSizeY, 0); CorDefFindTouchingPixels(opt.defects, opt.camSizeX, opt.camSizeY, 0); } if (process == IP_DEFECTMAP && b3dOutputFileType() == IIFILE_TIFF) setTiffCompressionType(3, 0); if (opt.x != IP_DEFAULT) { if (opt.cx != IP_DEFAULT || opt.ix != IP_DEFAULT) exitError("You cannot use -x together with -cx or -ix"); } if (opt.y != IP_DEFAULT) if (opt.cy != IP_DEFAULT || opt.iy != IP_DEFAULT) { exitError("You cannot use -y together with -cy or -iy"); } /* check and load files: * Always at least one input file. */ hin.fp = iiFOpen(argv[iarg], "rb"); hin.pathname = argv[iarg]; if (!hin.fp) exitError("Error opening %s", argv[iarg]); if (mrc_head_read(hin.fp, &hin)) exitError("Error reading %s", argv[iarg]); /* Set output header default same as first input file. */ hout = hin; // Do parallel read from a TIFF unless appending/overwriting if (opt.add2file == IP_APPEND_FALSE) iiUseTiffThreadsForFP(hin.fp, 0); /* 7/20/11: Consolidate all changes for output header into this call; eliminate * setting swapped to 0 below; this header is replaced if appending * There is also a new header made in lots of places, not sure how much this is used */ mrcInitOutputHeader(&hout); /* Load additional input files. */ iarg++; if (opt.infiles > 1){ hin2.fp = iiFOpen(argv[iarg], "rb"); hin2.pathname = argv[iarg]; if (!hin2.fp) exitError("Error opening %s", argv[iarg]); if (mrc_head_read(hin2.fp, &hin2)){ if (process == IP_INFO){ mrc_head_print(&hin); printf("**********************************************\n"); printf("WARNING: This file is not a readable MRC file.\n"); printf("**********************************************\n"); } exitError("Error reading %s", argv[iarg]); } iarg++; } // Check for norm or unpack with a tiff file and as second of two inputs if ((process == IP_NORMALIZE || process == IP_UNPACK || process == IP_DEFECTMAP) && opt.infiles == 2 && !opt.readDefects) { iiFile = iiLookupFileFromFP(hin2.fp); if (iiFile && iiFile->file == IIFILE_TIFF && tiffGetArray(iiFile, FEI_TIFF_DEFECT_TAG, &count, &strng) > 0) { strCopy = B3DMALLOC(char, count + 1); if (!strCopy) exitError("Memory error copying defect string from TIFF file"); strncpy(strCopy, strng, count); strCopy[count] = 0x00; retval = CorDefParseFeiXml(strCopy, opt.defects, feiDefPad); if (retval) exitError("Parsing defect string from TIFF file (error %d)", retval); free(strCopy); opt.readDefects = TRUE; if (dumpDefectName) { imodBackupFile(dumpDefectName); defFP = fopen(dumpDefectName, "w"); if (!defFP) exitError("Opening file to write defects to, %s", dumpDefectName); CorDefDefectsToString(opt.defects, sstr, hin2.nx, hin2.ny); fprintf(defFP, "%s", sstr.c_str()); fclose(defFP); B3DFREE(dumpDefectName); } superFac = hin.nx / hin2.nx; j = hin.ny / hin2.ny; if (j != superFac || superFac * hin2.nx != hin.nx || superFac * hin2.ny != hin.ny || (superFac != 1 && superFac != 2 && superFac != 4)) exitError("Image file size (%d x %d) must be exactly the same, twice, or 4 " "times the gain reference size (%d x %d)", hin.nx, hin.ny, hin2.nx, hin2.ny); CorDefFlipDefectsInY(&opt.defects, hin2.nx, hin2.ny, 0); CorDefFindTouchingPixels(opt.defects, hin2.nx, hin2.ny, 0); if (superFac > 1) CorDefScaleDefectsForFalcon(&opt.defects, superFac); opt.camSizeX = hin.nx; opt.camSizeY = hin.ny; } } /* Setup output file if needed and there are enough - otherwise let the process give the error message . */ if (procout && (!needtwo || opt.infiles > 1)){ opt.ofname = argv[argc - 1]; if (opt.add2file){ hout.fp = iiFOpen(argv[argc - 1], "rb+"); if (!hout.fp) exitError("Error finding %s", argv[argc - 1]); if (mrc_head_read(hout.fp, &hout)) exitError("Error reading %s", argv[iarg]); } else if (process != IP_SPLITRGB) { /* DNm 10/20/03: switch to calling routine for backup file */ if (!getenv("IMOD_NO_IMAGE_BACKUP")) imodBackupFile(argv[argc - 1]); if (process == IP_FFT && hin.mode != MRC_MODE_COMPLEX_FLOAT && (b3dOutputFileType() == IIFILE_TIFF || b3dOutputFileType() == IIFILE_JPEG)) { printf("WARNING: clip - Writing an MRC file; TIFF or JPEG files cannot contain " "FFTs\n"); overrideOutputType(IIFILE_MRC); } hout.fp = iiFOpen(argv[argc - 1], "wb+"); if (!hout.fp){ exitError("Error opening %s", argv[argc - 1]); } } } opt.hin = &hin; opt.hout = &hout; /* Massage the Z values if numbered from one */ if (opt.fromOne) { if (opt.add2file == IP_APPEND_OVERWRITE) opt.isec--; if (opt.nofsecs != IP_DEFAULT) for (j = 0; j < opt.nofsecs; j++) opt.secs[j]--; if (opt.cz != IP_DEFAULT) opt.cz--; if (opt.dim == 2) { if (opt.iz != IP_DEFAULT) opt.iz--; if (opt.iz2 != IP_DEFAULT) opt.iz2--; } } // Set the mode to float automatically for log if (process == IP_LOGARITHM && opt.mode == IP_DEFAULT) opt.mode = MRC_MODE_FLOAT; /* run the selected process */ switch(process){ case IP_AVERAGE: case IP_STANDEV: case IP_VARIANCE: case IP_ADD: case IP_SUBTRACT: retval = clip_average(&hin, &hin2, &hout, &opt); break; case IP_MULTIPLY: case IP_DIVIDE: retval = clip_multdiv(&hin, &hin2, &hout, &opt); break; case IP_UNPACK: case IP_NORMALIZE: retval = clipUnpack(&hin, &hin2, &hout, &opt); break; case IP_DEFECTMAP: retval = clipDefectMap(&hin, &hout, &opt); break; case IP_BRIGHTNESS: case IP_CONTRAST: case IP_SHADOW: case IP_RESIZE: case IP_THRESHOLD: case IP_TRUNCATE: case IP_UNWRAP: case IP_LOGARITHM: case IP_SQROOT: retval = clip_scaling(&hin, &hout, &opt); break; case IP_COLOR: retval = clip_color(&hin, &hout, &opt); break; case IP_QUADRANT: retval = clip_quadrant(&hin, &hout, &opt); break; case IP_SPECTRUM: retval = clipSpectrum(&hin, &hout, &opt); break; case IP_FILLEDGE: retval = fillDriftCorrectedEdges(&hin, &hout, &opt); break; case IP_CORRELATE: retval = grap_corr(&hin, &hin2, &hout, &opt); break; case IP_DIFFUSION: retval = clipDiffusion(&hin, &hout, &opt); break; case IP_GRADIENT: case IP_GRAHAM: case IP_PREWITT: case IP_SOBEL: retval = clipEdge(&hin, &hout, &opt); break; case IP_INFO: retval = mrc_head_print(&hin); break; case IP_FFT: retval = clip_fft(&hin, &hout, &opt); break; case IP_FILTER: /* opt.dim = 2; */ retval = clip_bandpass_filter(&hin, &hout, &opt); break; case IP_FLIP: retval = clip_flip(&hin, &hout, &opt); break; case IP_HISTOGRAM: retval = clipHistogram(&hin, &opt); break; case IP_JOINRGB: retval = clip_joinrgb(&hin, &hin2, &hout, &opt); break; case IP_LAPLACIAN: case IP_SMOOTH: case IP_SHARPEN: retval = clip_convolve(&hin, &hout, &opt); break; case IP_MEDIAN: retval = clipMedian(&hin, &hout, &opt, NULL, 0, 0); break; /*case IP_PEAK: retval = puts("peak: future function\n"); break; case IP_ROTATE: retval = grap_rotate(&hin, &hout, &opt); break; */ case IP_SPLITRGB: retval = clip_splitrgb(&hin, &opt); break; case IP_STAT: retval = clip_stat(&hin, &opt); break; /*case IP_TRANSLATE: retval = grap_trans(&hin, &hout, &opt); break; case IP_ZOOM: if (grap_zoom(&hin, &hout, &opt)) { fprintf(stderr, "%s: error doing zoom.\n", progname); retval = 1; } break; */ default: exitError("No process selected."); } if (retval) exit(retval); iiCloseTiffCopiesForFP(hin.fp); iiFClose (hin.fp); if (procout && process != IP_SPLITRGB) iiFClose (hout.fp); if (view){ sprintf(viewcmd, "3dmod %s", argv[argc - 1]); system(viewcmd); } // Had to switch from return(0) after converting to C++. It gave status 127 on Windows exit(0); } /* * Make a list of sections for use with the * -2d and -z option. commands can be like * -z 0,4-10 or -z 2,3,4-8,12,19 */ int *clipMakeSecList(char *clst, int *nofsecs) { int len; int i; int *secs; int *tsecs; int range, top, r; secs = (int *)malloc(sizeof(int)); len = strlen(clst); secs[0] = atoi(clst); *nofsecs = 1; for(i = 0; i < len; i++){ switch(clst[i]){ case ',': (*nofsecs)++; tsecs = (int *)realloc(secs, sizeof(int) * (*nofsecs)); secs = tsecs; secs[*nofsecs - 1] = atoi(&(clst[++i])); break; case '-': top = atoi(&(clst[++i])); if (top < secs[*nofsecs - 1]){ range = top; top = secs[*nofsecs - 1]; secs[*nofsecs - 1] = range; } if (top == secs[*nofsecs - 1]) continue; range = top - secs[*nofsecs - 1]; tsecs = (int *)realloc(secs, sizeof(int) * (*nofsecs + range)); secs = tsecs; for (r = 0; r < range; r++) secs[*nofsecs + r] = secs[*nofsecs - 1] + r + 1; *nofsecs += range; break; default: break; } } return(secs); }