wndchrm-1.50rc0.tar.gz_classification c_visual c

/* Translated from ImageJ Java Pluging into MATLAB MEX c code by Tom Macura <tmacura@nih.gov> July 21st, 2006 Modded by Chris Coletta and Ilya Goldberg to deal with 16-bit/chanel RGB, and make it independent of MATLAB */ /* G.Landini at bham ac uk 30/Mar/2004 released 03/Apr/2004 resolved ROI exiting 07/Apr/2004 added Methyl Green DAB vectors 08/Jul/2004 shortened the code 01/Aug/2005 added fast red/blue/DAB vectors 02/Nov/2005 changed code to work with image stacks (DLC - dchao at fhcrc org) 02/Nov/2005 changed field names so user-defined colours can be set within macros (DLC - dchao at fhcrc org) This plugin implements stain separation using the colour deconvolution method described in: Ruifrok AC, Johnston DA. Quantification of histological staining by color deconvolution. Analytical & Quantitative Cytology & Histology 2001; 23: 291-299. The code is based on "Color separation-30", a macro for NIH Image kindly provided by A.C. Ruifrok. Thanks Arnout! The plugin assumes images generated by color subtraction (i.e. light-absorbing dyes such as those used in bright field histology or ink on printed paper) but the dyes should not be neutral grey. I strongly suggest to read the paper reference above to understand how to determine new vectors and how the whole procedure works. The plugin works correctly when the background is neutral (white to light grey), so background subtraction and colour correction must be applied to the images before processing. The plugin provides a number of "bulit in" stain vectors some of which were determined experimentally in our lab (marked GL), but you may have to determine your own vectors to provide a more accurate stain separation, depending on the stains and methods you use. Ideally, vector determination should be done on slides stained with only one colour at a time (using the "From ROI" interactive option). The plugin takes an RGB image and returns three 8-bit images. If the specimen is stained with a 2 colour scheme (such as H & E) the 3rd image represents the complimentary of the first two colours (i.e. green). Please be *very* careful about how to interpret the results of colour deconvolution when analysing histological images. Most staining methods are not stochiometric and so intensity of the chromogen may not correlate well with the quantity of the reactants. This means that intensity of the colour may not be a good indicator of the amount of material stained. Read the paper! */ #include <errno.h> #include <math.h> #include <float.h> // for DBL_MAX #include <stdint.h> #include <string.h> #include <stdio.h> #include <stdlib.h> #include <tiffio.h> #include "readTIFF.h" #define XSTR(s) STR(s) #define STR(s) #s #define DEF_ITER 5 typedef struct { char *argP; // a non-specified stain has this NULL char label[256]; char isRGB; double MODx,MODy,MODz; double max,min; } stain_t; void usage (const char *argv0, const char *message); void prepare_conversion_vectors(char **stain, double *q); void getStainVecs (stain_t *stains, int nstains); void getNormStainMODs (stain_t *stains, double *RGBwht, double *cosx, double *cosy, double *cosz); void getStainMat(stain_t *stains, double *RGBwht, double *q); double color_decon (float *inBuf,float *outBuf,size_t imagesize,double max_pix_val,double *RGBwht,stain_t *stains); void getStainMODs (stain_t *stains,int nstains,double *MODx,double *MODy,double *MODz); void setStainMODs (stain_t *stains,int nstains,double *MODx,double *MODy,double *MODz); void getNewMOD (float *inBuf,float *outBuf,size_t imagesize,double *RGBwht,stain_t *stains, int nstains, double *MODx1,double *MODy1,double *MODz1); char pure_integer (const char *p, long *num); int main (int argc, char **argv) { int arg,ret, filename_arg; TIFF* tif; float *inBuf,*outBuf; void *img_stain; uint16_t bits; uint32_t width,height; char outfile[256],basename[256],ext[256],error[256],*cp; int nstains=0, stain_idx; stain_t stains[3]; size_t i,j; size_t imagesize; uint8_t *img_stain8; uint16_t *img_stain16; uint32_t *img_stain32; int minbits; // The minimum number of bits to express the maximum RGB value in the TIFF // Calculated by ReadRGBTIFFDataFlt char whtLvl=0; double MODx1[3],MODy1[3],MODz1[3]; double max_pix_val; // maximum possible value for scaling (2^bits type of number) double RGBwht[3]; double Rin,Gin,Bin; int iter_idx, n_iter = 1, best_iter; long iter_in; double total_stain; // the total stain accounted for in each iteration double bestMODx[3],bestMODy[3],bestMODz[3]; double best_total_stain; // the best total stain accounted for in each iteration if (argc < 3) { usage (argv[0],"Insufficient arguments"); } /* String [] stain={"From ROI", "H&E", "H DAB","FastRed FastBlue DAB","Methyl Green DAB", "H&E DAB", "H AEC","Azan-Mallory","Alcian blue & H","H PAS","RGB","CMY", "User values"}; IGG: stain is specified per-channel, so -s0 H -s1 E will put the default Haem matrix in MOD*[0], and the Eosin matrix in MOD*[1]. Viable stain strings are: "H", "E", "DAB", "FastRed", "FastBlue", "MethylGreen", "AEC", "Azan-Mallory", "AlcianBlue", "PAS", "R", "G", "B", "C", "M", "Y" To use specific user values, use -s0 '123.3 456.7 234.3', -s1 '1.23 4.56 7.89' corresponding to the RGB values. The parameter following s0, s1 or s2 is checked against all the stain strings, and finally we try to sscanf 3 floats. If we don't get 3 floats, then the parameter is malformed. */ memset (stains, 0, sizeof (stains)); // Get the CLI params for (arg = 1; arg < argc-1; arg++) { // Stain specification (will be parsed/checked later) if ( !strcmp (argv[arg],"-s") || !strcmp (argv[arg],"-sOD")) { filename_arg = arg + 2; // -s requires a following arg nstains++; if (nstains < 4) { stains[nstains-1].argP = argv[arg+1]; // Determine if an RGB triplet is an OD representation of stains if ( sscanf (argv[arg+1],"%lf,%lf,%lf",&Rin,&Gin,&Bin) == 3 && !strcmp (argv[arg],"-s")) stains[nstains-1].isRGB = 1; else stains[nstains-1].isRGB = 0; } else { usage (argv[0],"A maximum of 3 stains are supported"); } // Get the white-level } else if ( !strcmp (argv[arg],"-w") ) { filename_arg = arg + 2; // -w requires a following arg if ( sscanf (argv[arg+1],"%lf,%lf,%lf",&Rin,&Gin,&Bin) != 3 ) { usage (argv[0],"-w parameter is malformed. Three white levels expected (R,G,B)"); } else { whtLvl = 1; RGBwht[0] = Rin; RGBwht[1] = Gin; RGBwht[2] = Bin; fprintf (stdout,"white-level = (%lf, %lf, %lf)\n",RGBwht[0],RGBwht[1],RGBwht[2]); } } else if ( !strcmp (argv[arg],"-i") ) { filename_arg = arg + 1; if ( pure_integer (argv[arg+1],&iter_in) ) { filename_arg++; // -i has an optional following arg if (iter_in > 0) { n_iter = iter_in; } else { usage (argv[0],"-i parameter is malformed. Must greater than 0"); } } else { n_iter = DEF_ITER; } } } if (nstains < 1) usage (argv[0],"A minimum of 1 stain must be specified"); if (filename_arg >= argc) usage (argv[0],"At least one tiff file must be specified"); // suppress warnings TIFFSetWarningHandler (NULL); for (arg = filename_arg; arg < argc; arg++) { fprintf (stdout,"File: %s\n",argv[arg]); tif = TIFFOpen(argv[arg],"r"); if (!tif) { fprintf (stderr,"Could not open %s: %s\n",argv[arg], strerror (errno)); exit (-1); } // Check if its proper RGB if ( (ret = isRGB (tif)) < 0) { GetReadTIFFError (ret,error); fprintf