Added a function to apply the noise cut
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e43899cca8
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@ -61,11 +61,72 @@ static PyObject *ClusterFileReader_read(ClusterFileReader *self, PyObject *args)
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const int ndim = 1;
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Py_ssize_t size = 0;
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if (!PyArg_ParseTuple(args, "|n", &size))
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PyObject *noise_obj;
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if (!PyArg_ParseTuple(args, "nO", &size,&noise_obj)) {
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PyErr_SetString(
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PyExc_TypeError,
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"Could not parse args.");
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return NULL;
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}
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npy_intp dims[] = {size};
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// Create two numpy arrays from the passed objects, if possible numpy will
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// use the underlying buffer, otherwise it will create a copy, for example
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// if data type is different or we pass in a list. The
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// NPY_ARRAY_C_CONTIGUOUS flag ensures that we have contiguous memory.
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PyObject *noise_array = PyArray_FROM_OTF(noise_obj, NPY_DOUBLE, NPY_ARRAY_C_CONTIGUOUS);
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int nx=0,ny=0;
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double *noise_map=NULL;
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// If parsing of a or b fails we throw an exception in Python
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if (noise_array ) {
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int ndim_noise = PyArray_NDIM((PyArrayObject *)(noise_array));
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npy_intp *noise_shape = PyArray_SHAPE((PyArrayObject *)(noise_array));
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// For the C++ function call we need pointers (or another C++ type/data
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// structure)
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noise_map = (double *)(PyArray_DATA((PyArrayObject *)(noise_array)));
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/* for (int i=0; i< ndim_noise; i++) { */
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/* printf("Dimension %d size %d pointer \n",i,noise_shape[i], noise_map); */
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/* } */
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if (ndim_noise==2) {
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nx=noise_shape[0];
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ny=noise_shape[1];
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// printf("Noise map found size %d %d %d\n",nx,ny,noise_map);
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} else {
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nx=0;
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if (ndim_noise==1)
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nx=noise_shape[0];
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ny=0;
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noise_map = NULL;
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// printf("NO Noise map found %d %d %d %d\n",ndim_noise,nx,ny,noise_map);
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}
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}
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// Create an uninitialized numpy array
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PyObject *clusters = PyArray_SimpleNewFromDescr(ndim, dims, cluster_dt());
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@ -77,7 +138,11 @@ static PyObject *ClusterFileReader_read(ClusterFileReader *self, PyObject *args)
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// Call the standalone C code to read clusters from file
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// Here goes the looping, removing frame numbers etc.
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int n_read = read_clusters(self->fp, size, buf, &self->n_left);
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int n_read = 0;
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if (noise_map)
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read_clusters_with_cut(self->fp, size, buf, &self->n_left,noise_map, nx, ny);
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else
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read_clusters(self->fp, size, buf, &self->n_left);
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if (n_read != size) {
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// resize the array to match the number of read photons
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@ -25,6 +25,8 @@ int read_clusters(FILE *fp, int64_t n_clusters, Cluster *buf, int *n_left) {
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if (nph_read < n_clusters) {
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// keep on reading frames and photons until reaching n_clusters
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while (fread(&iframe, sizeof(iframe), 1, fp)) {
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if (fread(&nph, sizeof(nph), 1, fp)) {
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if (nph > n_clusters - nph_read)
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nn = n_clusters - nph_read;
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@ -37,25 +39,145 @@ int read_clusters(FILE *fp, int64_t n_clusters, Cluster *buf, int *n_left) {
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}
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if (nph_read >= n_clusters)
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break;
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}
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}
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assert(nph_read <= n_clusters); // sanity check in debug mode
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return nph_read;
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}
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int read_clusters_with_cut(FILE *fp, int64_t n_clusters, Cluster *buf, int *n_left, double *noise_map, int nx, int ny) {
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int iframe = 0;
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int nph = *n_left;
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size_t nph_read = 0;
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int32_t tot2[4], t2max, tot1;
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int32_t val, tot3;
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Cluster *ptr=buf;
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int good=1;
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double noise;
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// read photons left from previous frame
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if (nph) {
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for (int iph=0; iph<nph; iph++) {
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// read photons 1 by 1
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fread((void *)(ptr), sizeof(Cluster), 1, fp);
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good=1;
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if (noise_map) {
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if (ptr->x>=0 && ptr->x<nx && ptr->y>=0 && ptr->y<ny) {
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tot1=ptr->data[4];
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analyze_cluster(*ptr, &t2max, &tot3, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL);
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noise=noise_map[ptr->y*nx+ptr->x];
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if (tot1>noise && t2max>2*noise && tot3>3*noise) {
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;
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} else
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good=0;
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} else {
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printf("Bad pixel number %d %d\n",ptr->x,ptr->y);
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good=0;
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}
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}
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if (good) {
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ptr++;
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nph_read++;
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*n_left--;
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}
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if (nph_read >= n_clusters)
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break;
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}
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}
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if (nph_read < n_clusters) {
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// keep on reading frames and photons until reaching n_clusters
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while (fread(&iframe, sizeof(iframe), 1, fp)) {
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if (fread(&nph, sizeof(nph), 1, fp)) {
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*n_left = nph;
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for (int iph=0; iph<nph; iph++) {
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// read photons 1 by 1
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fread((void *)(ptr), sizeof(Cluster), 1, fp);
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good=1;
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if (noise_map) {
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if (ptr->x>=0 && ptr->x<nx && ptr->y>=0 && ptr->y<ny) {
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tot1=ptr->data[4];
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analyze_cluster(*ptr, &t2max, &tot3, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL);
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noise=noise_map[ptr->y*nx+ptr->x];
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if (tot1>noise && t2max>2*noise && tot3>3*noise) {
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;
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} else
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good=0;
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} else{
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printf("Bad pixel number %d %d\n",ptr->x,ptr->y);
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good=0;
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}
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}
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if (good) {
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ptr++;
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nph_read++;
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*n_left--;
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}
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if (nph_read >= n_clusters)
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break;
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}
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}
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if (nph_read >= n_clusters)
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break;
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}
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}
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assert(nph_read <= n_clusters); // sanity check in debug mode
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return nph_read;
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}
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int analyze_clusters(int64_t n_clusters, Cluster *cin, ClusterAnalysis *cout) {
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int32_t tot2[4], t2max;
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char quad;
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int32_t val, tot3;
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for (int ic = 0; ic < n_clusters; ic++) {
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analyze_cluster(*(cin+ic), &t2max, &tot3, &quad, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL);
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(cout + ic)->c = quad;
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(cout + ic)->tot2 = t2max;
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(cout + ic)->tot3 = tot3;
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// printf("%d %d %d %d %d %d\n",ic,(cin+ic)->x, (cin+ic)->y,
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// (cout+ic)->c, (cout+ic)->tot2, (cout+ic)->tot3);
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}
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return n_clusters;
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}
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int analyze_cluster(Cluster cin, int32_t *t2, int32_t *t3, char *quad, double *eta2x, double *eta2y, double *eta3x, double *eta3y, double *eta2Lx, double *eta2Ly, double *eta3Xx, double *eta3Xy) {
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int ok=1;
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int32_t tot2[4], t2max;
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char c;
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int32_t val, tot3;
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for (int ic = 0; ic < n_clusters; ic++) {
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tot3 = 0;
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for (int i = 0; i < 4; i++)
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tot2[i] = 0;
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// t2max=0;
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for (int ix = 0; ix < 3; ix++) {
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for (int iy = 0; iy < 3; iy++) {
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val = (cin + ic)->data[iy * 3 + ix];
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val = cin.data[iy * 3 + ix];
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tot3 += val;
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if (ix <= 1 && iy <= 1)
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tot2[0] += val;
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@ -67,6 +189,10 @@ int analyze_clusters(int64_t n_clusters, Cluster *cin, ClusterAnalysis *cout) {
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tot2[3] += val;
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}
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}
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if (t2 || quad) {
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t2max = tot2[0];
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c = cBottomLeft;
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for (int i = 1; i < 4; i++) {
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@ -75,11 +201,19 @@ int analyze_clusters(int64_t n_clusters, Cluster *cin, ClusterAnalysis *cout) {
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c = i;
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}
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}
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(cout + ic)->c = c;
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(cout + ic)->tot2 = t2max;
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(cout + ic)->tot3 = tot3;
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// printf("%d %d %d %d %d %d\n",ic,(cin+ic)->x, (cin+ic)->y,
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// (cout+ic)->c, (cout+ic)->tot2, (cout+ic)->tot3);
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}
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return n_clusters;
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if (quad)
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*quad = c;
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if (t2)
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*t2 = t2max;
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if (t3)
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*t3 = tot3;
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return ok;
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}
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@ -6,4 +6,10 @@
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//Pure C implementation to read a cluster file
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int read_clusters(FILE* fp, int64_t n_clusters, Cluster* buf, int *n_left);
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int read_clusters_with_cut(FILE* fp, int64_t n_clusters, Cluster* buf, int *n_left, double *noise_map, int nx, int ny);
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int analyze_clusters(int64_t n_clusters, Cluster* cin, ClusterAnalysis *cout);
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int analyze_cluster(Cluster cin, int32_t *t2, int32_t *t3, char *quad, double *eta2x, double *eta2y, double *eta3x, double *eta3y, double *eta2Lx, double *eta2Ly, double *eta3Xx, double *eta3Xy);
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4
test.py
4
test.py
@ -7,9 +7,11 @@ maxph=100
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from pathlib import Path
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fpath = Path("/mnt/sls_det_storage/moench_data/Moench_LGAD_SIM_Nov22/moenchLGAD202211/clustW17new/beam_En800eV_-40deg_300V_10us_d0_f5_0.clust")
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# r = ClusterFileReader()
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a=np.zeros([400,400])
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#a=None #np.array([])
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r = ClusterFileReader(fpath.as_posix())
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a=r.read(maxph)
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a=r.read(maxph,a)
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# b=clusterize(a)
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# #v=int(maxph/100)
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