void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
{
OID ID;
/* OMEIS data structures */
omeis* is;
pixHeader* head;
/* MATLAB data structueres */
mxArray *m_url, *m_sessionkey;
mxArray *permute_inputs[2];
mxArray *copy_input_array; /* we need a local copy so we can transpose it */
char* url, *sessionkey;
if (nrhs != 3)
mexErrMsgTxt("\n [pix] = setPixels (is, ID, pixels)");
if (!mxIsStruct(prhs[0]))
mexErrMsgTxt("setPixels requires the first input to be the struct outputed"
" from openConnectionOMEIS\n");
if (!(m_url = mxGetField(prhs[0], 0, "url")))
mexErrMsgTxt("setPixels requires the first input, OMEIS struct, to have field: url");
if (!(m_sessionkey = mxGetField(prhs[0], 0, "sessionkey")))
mexErrMsgTxt("setPixels requires the first input, OMEIS struct, to have field: sessionkey");
if (!mxIsChar(m_url) || !mxIsChar(m_sessionkey))
mexErrMsgTxt("OMEIS field aren't character array.\n");
if (!mxIsNumeric(prhs[1]))
mexErrMsgTxt("setPixels requires the second input to be the PixelsID\n") ;
ID = (OID) mxGetScalar(prhs[1]) ;
url = mxArrayToString(m_url);
sessionkey = mxArrayToString(m_sessionkey);
is = openConnectionOMEIS (url, sessionkey);
if (!(head = pixelsInfo (is, ID))){
char err_str[128];
sprintf(err_str, "PixelsID %llu or OMEIS URL '%s' is probably wrong\n", ID, is->url);
/* clean up */
mxFree(url);
mxFree(sessionkey);
mxFree(is);
mexErrMsgTxt(err_str);
}
/*
In OMEIS Size_X corresponds to columns and Size_Y corresponds to rows.
This is diametrically opposite to MATLAB's assumptions.
hence we do
"$matlab_var_name = permute($matlab_var_name, [2 1 3 4 5]);"
the hard way (groan)
*/
permute_inputs[0] = prhs[2]; /* permute_input isn't being modified so
discarding the const qualifier is okay */
permute_inputs[1] = mxCreateDoubleMatrix(1, 5, mxREAL);
mxGetPr(permute_inputs[1])[0] = 2;
mxGetPr(permute_inputs[1])[1] = 1;
mxGetPr(permute_inputs[1])[2] = 3;
mxGetPr(permute_inputs[1])[3] = 4;
mxGetPr(permute_inputs[1])[4] = 5;
/* mexCallMATLAB allocates memory for copy_input_array */
if (mexCallMATLAB(1, ©_input_array, 2, permute_inputs, "permute")) {
/* clean up */
mxFree(url);
mxFree(sessionkey);
mxFree(head);
mxFree(is);
char err_str[128];
sprintf(err_str, "Couldn't permute the pixels to get them in MATLAB orientation");
mexErrMsgTxt(err_str);
}
/* check dimension and class check */
const mwSize* dims = mxGetDimensions (copy_input_array);
switch (mxGetNumberOfDimensions (copy_input_array)) {
char err_str[128];
case 5:
if (head->dt != dims[4]) {
sprintf (err_str, "5th Dimension (%d) of input array doesn't match OMEIS Pixels (%d).\n", dims[4], head->dt);
mexErrMsgTxt(err_str);
}
case 4:
if (head->dc != dims[3]) {
sprintf (err_str, "4th Dimension (%d) of input array doesn't match OMEIS Pixels (%d).\n", dims[3], head->dc);
mexErrMsgTxt(err_str);
}
case 3:
if (head->dz != dims[2]){
sprintf (err_str, "3th Dimension (%d) of input array doesn't match OMEIS Pixels (%d).\n", dims[2], head->dz);
mexErrMsgTxt(err_str);
}
case 2:
if (head->dy != dims[1]){
sprintf (err_str, "Height (%d) of input array doesn't match OMEIS Pixels (%d).\n", dims[1], head->dy);
mexErrMsgTxt(err_str);
}
case 1:
if (head->dx != dims[0]){
sprintf (err_str, "Width (%d) of input array doesn't match OMEIS Pixels (%d).\n", dims[0], head->dx);
mexErrMsgTxt(err_str);
}
break;
default:
/* clean up */
mxFree(url);
mxFree(sessionkey);
mxFree(head);
mxFree(is);
mxDestroyArray(copy_input_array);
mexErrMsgTxt("Input Array must be 5D or less");
break;
}
pixHeader tmp_head;
CtoOMEISDatatype ((char*) mxGetClassName(copy_input_array), &tmp_head);
if ( !samePixelType(&tmp_head, head)) {
/* clean up */
mxFree(url);
mxFree(sessionkey);
mxFree(head);
mxFree(is);
mxDestroyArray(copy_input_array);
mexErrMsgTxt("Types of input array and Pixels don't match\n");
}
/* set the pixels */
int pix = setPixels (is, ID, mxGetPr(copy_input_array));
/* record number of pixels written */
plhs[0] = mxCreateScalarDouble((double) pix);
/* clean up */
mxFree(url);
mxFree(sessionkey);
mxFree(head);
mxFree(is);
mxDestroyArray(copy_input_array);
}
void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
{
OID ID;
/* OMEIS data structures */
omeis* is;
pixHeader* head = (pixHeader*) mxMalloc(sizeof(pixHeader));
/* MATLAB data structueres */
mxArray *m_dx, *m_dy, *m_dz, *m_dc, *m_dt, *m_bp, *m_isSigned, *m_isFloat;
mxArray *m_url, *m_sessionkey;
char* url, *sessionkey;
if (nrhs != 2)
mexErrMsgTxt("\n [ID] = newPixels (is, ph)");
if (!mxIsStruct(prhs[0]))
mexErrMsgTxt("newPixels requires the first input to be the struct outputed"
" from openConnectionOMEIS\n");
if (!(m_url = mxGetField(prhs[0], 0, "url")))
mexErrMsgTxt("newPixels requires the first input, OMEIS struct, to have field: url");
if (!(m_sessionkey = mxGetField(prhs[0], 0, "sessionkey")))
mexErrMsgTxt("newPixels requires the first input, OMEIS struct, to have field: sessionkey");
if (!mxIsChar(m_url) || !mxIsChar(m_sessionkey))
mexErrMsgTxt("OMEIS field aren't character array.\n");
if (!mxIsStruct(prhs[0]))
mexErrMsgTxt("newPixels requires the first input to be the struct outputed"
" from openConnectionOMEIS\n");
if (!mxIsStruct(prhs[1]))
mexErrMsgTxt("newPixels requires the second input to be a pixHeader struct.");
if (!(m_dx = mxGetField(prhs[1], 0, "dx")))
mexErrMsgTxt("newPixels requires the second input, pixHeader struct, to have field: dx");
if (!(m_dy = mxGetField(prhs[1], 0, "dy")))
mexErrMsgTxt("newPixels requires the second input, pixHeader struct, to have field: dy");
if (!(m_dz = mxGetField(prhs[1], 0, "dz")))
mexErrMsgTxt("newPixels requires the second input, pixHeader struct, to have field: dz");
if (!(m_dc = mxGetField(prhs[1], 0, "dc")))
mexErrMsgTxt("newPixels requires the second input, pixHeader struct, to have field: dc");
if (!(m_dt = mxGetField(prhs[1], 0, "dt")))
mexErrMsgTxt("newPixels requires the second input, pixHeader struct, to have field: dt");
if (!(m_bp = mxGetField(prhs[1], 0, "bp")))
mexErrMsgTxt("newPixels requires the second input, pixHeader struct, to have field: bp");
if (!(m_isSigned = mxGetField(prhs[1], 0, "isSigned")))
mexErrMsgTxt("newPixels requires the second input, pixHeader struct, to have field: isSigned");
if (!(m_isFloat = mxGetField(prhs[1], 0, "isFloat")))
mexErrMsgTxt("newPixels requires the second input, pixHeader struct, to have field: isFloat");
head->dx = (ome_dim) mxGetScalar(m_dx);
head->dy = (ome_dim) mxGetScalar(m_dy);
head->dz = (ome_dim) mxGetScalar(m_dz);
head->dc = (ome_dim) mxGetScalar(m_dc);
head->dt = (ome_dim) mxGetScalar(m_dt);
head->bp = (u_int8_t) mxGetScalar(m_bp);
head->isSigned = (u_int8_t) mxGetScalar(m_isSigned);
head->isFloat = (u_int8_t) mxGetScalar(m_isFloat);
url = mxArrayToString(m_url);
sessionkey = mxArrayToString(m_sessionkey);
is = openConnectionOMEIS (url, sessionkey);
if ( !(ID = newPixels (is, head)) ) {
/* clean up */
mxFree(url);
mxFree(sessionkey);
mxFree(head);
mxFree(is);
mexErrMsgTxt("newPixels OMEIS method failed.\n");
}
plhs[0] = mxCreateScalarDouble((double) ID);
/* clean up */
mxFree(url);
mxFree(sessionkey);
mxFree(head);
mxFree(is);
}
void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
{
OID ID;
/* OMEIS data structures */
omeis* is;
pixHeader* head;
void* pixels;
/* MATLAB data structueres */
mxArray *m_url, *m_sessionkey;
mxArray *permute_inputs[2];
int result;
char* url, *sessionkey;
if (nrhs != 12)
mexErrMsgTxt("\n [pixels] = getROI (is, ID, row0 (OME:y0), column0 (OME:x0), z0, c0, t0, row1 (OME:y1), column1 (OME:x1), z1, c1, t1)");
if (!mxIsStruct(prhs[0]))
mexErrMsgTxt("getROI requires the first input to be the struct outputed"
" from openConnectionOMEIS\n");
if (!(m_url = mxGetField(prhs[0], 0, "url")))
mexErrMsgTxt("getROI requires the first input, OMEIS struct, to have field: url");
if (!(m_sessionkey = mxGetField(prhs[0], 0, "sessionkey")))
mexErrMsgTxt("getROI requires the first input, OMEIS struct, to have field: sessionkey");
if (!mxIsChar(m_url) || !mxIsChar(m_sessionkey))
mexErrMsgTxt("OMEIS field aren't character array.\n");
if (!mxIsNumeric(prhs[1]))
mexErrMsgTxt("getROI requires the second input to be the PixelsID\n") ;
ID = (OID) mxGetScalar(prhs[1]) ;
/* get ROI */
/* NB x0/y0 and x1/y1 are switched on purpose because of the different orientations
used in MATLAB and OME. See note below */
int y0 = (int) mxGetScalar(prhs[2]); /* switched */
int x0 = (int) mxGetScalar(prhs[3]); /* switched */
int z0 = (int) mxGetScalar(prhs[4]);
int c0 = (int) mxGetScalar(prhs[5]);
int t0 = (int) mxGetScalar(prhs[6]);
int y1 = (int) mxGetScalar(prhs[7]); /* switched */
int x1 = (int) mxGetScalar(prhs[8]); /* switched */
int z1 = (int) mxGetScalar(prhs[9]);
int c1 = (int) mxGetScalar(prhs[10]);
int t1 = (int) mxGetScalar(prhs[11]);
url = mxArrayToString(m_url);
sessionkey = mxArrayToString(m_sessionkey);
is = openConnectionOMEIS (url, sessionkey);
if (!(head = pixelsInfo (is, ID))) {
char err_str[128];
sprintf(err_str, "PixelsID %llu or OMEIS URL '%s' is probably wrong\n", ID, is->url);
/* clean up */
mxFree(url);
mxFree(sessionkey);
mxFree(is);
mexErrMsgTxt(err_str);
}
if (!(pixels = getROI (is, ID, x0, y0, z0, c0, t0, x1, y1, z1, c1, t1))) {
/* clean up */
mxFree(url);
mxFree(sessionkey);
mxFree(head);
mxFree(is);
char err_str[128];
sprintf(err_str, "Couldn't load ROI from pixelsID %llu. ROI dims are probably wrong.\n", ID);
mexErrMsgTxt(err_str);
}
/* convert ROI to dims */
mwSize dims[5];
dims[0] = (mwSize) (x1-x0+1);
dims[1] = (mwSize) (y1-y0+1);
dims[2] = (mwSize) (z1-z0+1);
dims[3] = (mwSize) (c1-c0+1);
dims[4] = (mwSize) (t1-t0+1);
/* attach pixels from OMEIS to MATLAB array */
mwSize tmp_dims[2] = {1,1};
plhs[0] = mxCreateNumericArray (2, tmp_dims, OMEIStoMATLABDatatype(head), mxREAL);
mxSetData (plhs[0], pixels);
mxSetDimensions (plhs[0], dims, 5);
/*
In OMEIS Size_X corresponds to columns and Size_Y corresponds to rows.
This is diametrically opposite to MATLAB's assumptions.
hence we do
"$matlab_var_name = permute($matlab_var_name, [2 1 3 4 5]);"
the hard way (groan)
*/
permute_inputs[0] = plhs[0];
permute_inputs[1] = mxCreateDoubleMatrix(1, 5, mxREAL);
mxGetPr(permute_inputs[1])[0] = 2;
mxGetPr(permute_inputs[1])[1] = 1;
mxGetPr(permute_inputs[1])[2] = 3;
mxGetPr(permute_inputs[1])[3] = 4;
mxGetPr(permute_inputs[1])[4] = 5;
/* returns 0 if successful */
result = mexCallMATLAB(1, plhs, 2, permute_inputs, "permute");
/* clean up */
mxFree(url);
mxFree(sessionkey);
mxFree(head);
mxFree(is);
mxDestroyArray(permute_inputs[1]);
if (result) {
char err_str[128];
sprintf(err_str, "Couldn't permute the pixels to get them in MATLAB orientation");
mexErrMsgTxt(err_str);
}
}
void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
{
OID ID;
/* OMEIS data structures */
omeis* is;
pixHeader* head;
void* pixels;
/* MATLAB data structueres */
mxArray *m_url, *m_sessionkey;
mxArray *permute_inputs[2];
int result;
char* url, *sessionkey;
if (nrhs != 2)
mexErrMsgTxt("\n [pixels] = getPixels (is, ID)");
if (!mxIsStruct(prhs[0]))
mexErrMsgTxt("getPixels requires the first input to be the struct outputed"
" from openConnectionOMEIS\n");
if (!(m_url = mxGetField(prhs[0], 0, "url")))
mexErrMsgTxt("getPixels requires the first input, OMEIS struct, to have field: url");
if (!(m_sessionkey = mxGetField(prhs[0], 0, "sessionkey")))
mexErrMsgTxt("getPixels requires the first input, OMEIS struct, to have field: sessionkey");
if (!mxIsChar(m_url) || !mxIsChar(m_sessionkey))
mexErrMsgTxt("OMEIS field aren't character array.\n");
if (!mxIsNumeric(prhs[1]))
mexErrMsgTxt("getPixels requires the second input to be the PixelsID\n") ;
ID = (OID) mxGetScalar(prhs[1]) ;
url = mxArrayToString(m_url);
sessionkey = mxArrayToString(m_sessionkey);
is = openConnectionOMEIS (url, sessionkey);
if (!(head = pixelsInfo (is, ID))) {
char err_str[128];
sprintf(err_str, "PixelsID %llu or OMEIS URL '%s' is probably wrong\n", ID, is->url);
/* clean up */
mxFree(url);
mxFree(sessionkey);
mxFree(is);
mexErrMsgTxt(err_str);
}
/* figure out dimensions */
mwSize dims[5]; dims[0] = (mwSize) head->dx; dims[1] = (mwSize) head->dy;
dims[2] = (mwSize) head->dz; dims[3] = (mwSize) head->dc; dims[4] = (mwSize) head->dt;
if (!(pixels = getPixels (is, ID))) {
/* clean up */
mxFree(url);
mxFree(sessionkey);
mxFree(head);
mxFree(is);
char err_str[128];
sprintf(err_str, "Couldn't load pixelsID %llu\n", ID);
mexErrMsgTxt(err_str);
}
/* attach pixels from OMEIS to MATLAB array */
mwSize tmp_dims[2] = {1,1};
plhs[0] = mxCreateNumericArray (2, tmp_dims, OMEIStoMATLABDatatype(head), mxREAL);
mxSetData (plhs[0], pixels);
mxSetDimensions (plhs[0], dims, 5);
/*
In OMEIS Size_X corresponds to columns and Size_Y corresponds to rows.
This is diametrically opposite to MATLAB's assumptions.
hence we do
"$matlab_var_name = permute($matlab_var_name, [2 1 3 4 5]);"
the hard way (groan)
*/
permute_inputs[0] = plhs[0];
permute_inputs[1] = mxCreateDoubleMatrix(1, 5, mxREAL);
mxGetPr(permute_inputs[1])[0] = 2;
mxGetPr(permute_inputs[1])[1] = 1;
mxGetPr(permute_inputs[1])[2] = 3;
mxGetPr(permute_inputs[1])[3] = 4;
mxGetPr(permute_inputs[1])[4] = 5;
/* returns 0 if successful */
result = mexCallMATLAB(1, plhs, 2, permute_inputs, "permute");
/* clean up */
mxFree(url);
mxFree(sessionkey);
mxFree(head);
mxFree(is);
mxDestroyArray(permute_inputs[1]);
/* If the flip failed write a message, we are doing it after cleanup */
if (result) {
char err_str[128];
sprintf(err_str, "Couldn't permute the pixels to get them in MATLAB orientation");
mexErrMsgTxt(err_str);
}
}
int main (int argc, char* argv[])
{
OID ID;
int distance, angle;
u_int8_t** p_gray; /*Image converted for texture calcs*/
TEXTURE* features ; /*Returned struct of features*/
/* OMEIS data structures */
omeis* is;
pixHeader* head;
void* pixels;
if (argc != 4) {
fprintf(stderr, "\n mb_texture (im, distance, angle),\n\n"
"This function returns the 14 image texture statistics described by R. Haralick.\n"
"The statistics are calculated from the image's co-occurence matrix specified\n"
"for a particular distance and angle. Distance is measured in pixels and\n"
"the angle is measured in degrees.\n");
return EXIT_FAILURE;
}
sscanf(argv[1], "%llu", &ID);
sscanf(argv[2], "%d", &distance);
sscanf(argv[3], "%d", &angle);
is = openConnectionOMEIS ("http://localhost/cgi-bin/omeis","0000");
if (!(head = pixelsInfo (is, ID))){
fprintf (stderr, "PixelsID %llu or OMEIS URL '%s' is probably wrong\n", ID, is->url);
return EXIT_FAILURE;
}
if (!(pixels = getPixels (is, ID))) {
fprintf (stderr, "Couldn't get Pixels with ID %llu\n", ID);
return 0;
}
p_gray = (u_int8_t**) OMEIStoCArray (pixels, head, "unsigned char");
if (! (features=Extract_Texture_Features(distance, angle, p_gray, head->dy, head->dx, 255))) {
fprintf(stderr, "ERROR: Could not compute Haralick Features.\n");
return EXIT_FAILURE;
}
printf("%f\n",features->ASM);
printf("%f\n",features->contrast);
printf("%f\n",features->correlation);
printf("%f\n",features->variance);
printf("%f\n",features->IDM);
printf("%f\n",features->sum_avg);
printf("%f\n",features->sum_var);
printf("%f\n",features->sum_entropy);
printf("%f\n",features->entropy);
printf("%f\n",features->diff_var);
printf("%f\n",features->diff_entropy);
printf("%f\n",features->meas_corr1);
printf("%f\n",features->meas_corr2);
printf("%f\n",features->max_corr_coef);
free(p_gray);
free(pixels);
free(features);
return(EXIT_SUCCESS);
}
