detectors/python_cluster_reader
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This commit is contained in:
froejdh_e 2023-10-27 11:34:50 +02:00
parent 03043e0bc3
commit 706b341783
6 changed files with 251 additions and 288 deletions
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49
src/ClusterReader.c
View File

@ -27,7 +27,6 @@ static int ClusterFileReader_init(ClusterFileReader *self, PyObject *args,
static char *kwlist[] = {"fname", "chunk", NULL};
if (!PyArg_ParseTupleAndKeywords(args, kwds, "O|n", kwlist, &fname_obj,
&self->chunk)) {
return -1;
@ -44,7 +43,6 @@ static int ClusterFileReader_init(ClusterFileReader *self, PyObject *args,
self->fp = fopen((const char *)fname, "rb");
// Keep the return code to not return before releasing buffer
int rc = 0;
@ -116,14 +114,12 @@ static PyObject *ClusterFileReader_read(ClusterFileReader *self,
noise_map = (double *)(PyArray_DATA((PyArrayObject *)(noise_array)));
/* for (int i=0; i< ndim_noise; i++) { */
/* printf("Dimension %d size %d pointer \n",i,noise_shape[i],
* noise_map); */
/* } */
if (ndim_noise == 2) {
nx = noise_shape[0];
@ -180,7 +176,8 @@ static PyObject *ClusterFileReader_read(ClusterFileReader *self,
}
/* // clusterize method */
/* static PyObject *ClusterFileReader_clusterize(ClusterFileReader *self, PyObject *args) { */
/* static PyObject *ClusterFileReader_clusterize(ClusterFileReader *self,
* PyObject *args) { */
/* const int ndim = 1; */
@ -195,31 +192,32 @@ static PyObject *ClusterFileReader_read(ClusterFileReader *self,
/* // */
/* // Create two numpy arrays from the passed objects, if possible numpy will */
/* // use the underlying buffer, otherwise it will create a copy, for example */
/* // Create two numpy arrays from the passed objects, if possible numpy
* will */
/* // use the underlying buffer, otherwise it will create a copy, for
* example */
/* // if data type is different or we pass in a list. The */
/* // NPY_ARRAY_C_CONTIGUOUS flag ensures that we have contiguous memory. */
/* PyObject *data_array = PyArray_FROM_OTF(data_obj, NPY_INT32, NPY_ARRAY_C_CONTIGUOUS); */
/* PyObject *data_array = PyArray_FROM_OTF(data_obj, NPY_INT32,
* NPY_ARRAY_C_CONTIGUOUS); */
/* int nx=0,ny=0; */
/* int32_t *data=NULL; */
/* // If parsing of a or b fails we throw an exception in Python */
/* if (data_array ) { */
/* int ndim_data = PyArray_NDIM((PyArrayObject *)(data_array)); */
/* npy_intp *data_shape = PyArray_SHAPE((PyArrayObject *)(data_array)); */
/* // For the C++ function call we need pointers (or another C++ type/data */
/* // For the C++ function call we need pointers (or another C++ type/data
*/
/* // structure) */
/* data = (int32_t *)(PyArray_DATA((PyArrayObject *)(data_array))); */
/* /\* for (int i=0; i< ndim_noise; i++) { *\/ */
/* /\* printf("Dimension %d size %d pointer \n",i,noise_shape[i], noise_map); *\/ */
/* /\* printf("Dimension %d size %d pointer \n",i,noise_shape[i],
* noise_map); *\/ */
/* /\* } *\/ */
@ -247,7 +245,8 @@ static PyObject *ClusterFileReader_read(ClusterFileReader *self,
/* //npy_intp dims[] = {nx}; */
/* // printf("%d %d\n",ndim,nx); */
/* npy_intp dims[] = {nx}; */
/* PyObject *ca = PyArray_SimpleNewFromDescr(ndim, dims, cluster_analysis_dt()); */
/* PyObject *ca = PyArray_SimpleNewFromDescr(ndim, dims,
* cluster_analysis_dt()); */
/* // printf("1\n"); */
@ -283,28 +282,12 @@ static PyObject *ClusterFileReader_read(ClusterFileReader *self,
/* } */
// List all methods in our ClusterFileReader class
static PyMethodDef ClusterFileReader_methods[] = {
{"read", (PyCFunction)ClusterFileReader_read, METH_VARARGS,
"Read clusters"},
/* {"clusterize", (PyCFunction)ClusterFileReader_clusterize, METH_VARARGS, */
/* {"clusterize", (PyCFunction)ClusterFileReader_clusterize, METH_VARARGS,
*/
/* "Analyze clusters"}, */
{NULL, NULL, 0, NULL} /* Sentinel */
};

13
src/RawFileReader.c
View File

@ -110,12 +110,13 @@ static PyObject *RawFileReader_read(RawFileReader *self, PyObject *args) {
switch (self->detector) {
case DT_MOENCH_03:
n_read = read_raw_m03(self->fp, n_frames, out_buf, (Header*)header_out);
n_read =
read_raw_m03(self->fp, n_frames, out_buf, (Header *)header_out);
break;
case DT_MOENCH_04_A:
case DT_MOENCH_04_AD:
n_read =
read_raw_m04(self->fp, n_frames, out_buf, digital_out, (Header*)header_out);
n_read = read_raw_m04(self->fp, n_frames, out_buf, digital_out,
(Header *)header_out);
break;
default:
break;
@ -137,7 +138,8 @@ static PyObject *RawFileReader_read(RawFileReader *self, PyObject *args) {
PyArray_Resize((PyArrayObject *)frames, &new_shape, 1, NPY_ANYORDER);
if (digital_frames) {
PyArray_Resize((PyArrayObject *)digital_frames, &new_shape, 1, NPY_ANYORDER);
PyArray_Resize((PyArrayObject *)digital_frames, &new_shape, 1,
NPY_ANYORDER);
}
// if we also read header we need to reshape the header
@ -146,8 +148,6 @@ static PyObject *RawFileReader_read(RawFileReader *self, PyObject *args) {
PyArray_Resize((PyArrayObject *)header, &new_shape, 1,
NPY_ANYORDER);
}
}
// Build up a tuple with the return values
@ -171,7 +171,6 @@ static PyObject *RawFileReader_read(RawFileReader *self, PyObject *args) {
Py_DECREF(frames);
return ret;
}
}
// List all methods in our ClusterFileReader class

60
src/cluster_reader.c
View File

@ -1,14 +1,14 @@
#include "cluster_reader.h"
#include <assert.h>
size_t read_clusters(FILE *fp, size_t n_clusters, Cluster *buf, uint32_t *n_left) {
size_t read_clusters(FILE *fp, size_t n_clusters, Cluster *buf,
uint32_t *n_left) {
int32_t iframe = 0; // frame number needs to be 4 bytes!
uint32_t nph = *n_left; // number of clusters in frame needs to be 4 bytes!
size_t nph_read = 0;
uint32_t nn = *n_left;
// if there are photons left from previous frame read them first
if (nph) {
if (nph > n_clusters) {
@ -31,7 +31,8 @@ size_t read_clusters(FILE *fp, size_t n_clusters, Cluster *buf, uint32_t *n_left
else
nn = nph;
nph_read += fread((void *)(buf + nph_read), sizeof(Cluster), nn, fp);
nph_read +=
fread((void *)(buf + nph_read), sizeof(Cluster), nn, fp);
*n_left = nph - nn;
}
if (nph_read >= n_clusters)
@ -43,7 +44,8 @@ size_t read_clusters(FILE *fp, size_t n_clusters, Cluster *buf, uint32_t *n_left
}
size_t read_clusters_with_cut(FILE *fp, size_t n_clusters, Cluster *buf,
uint32_t *n_left, double *noise_map, int nx, int ny) {
uint32_t *n_left, double *noise_map, int nx,
int ny) {
int iframe = 0;
uint32_t nph = *n_left;
@ -99,17 +101,21 @@ size_t read_clusters_with_cut(FILE *fp, size_t n_clusters, Cluster *buf,
*n_left = nph;
for (size_t iph = 0; iph < nph; iph++) {
// read photons 1 by 1
size_t n_read = fread((void *)(ptr), sizeof(Cluster), 1, fp);
size_t n_read =
fread((void *)(ptr), sizeof(Cluster), 1, fp);
if (n_read != 1) {
return nph_read;
}
good = 1;
if (noise_map) {
if (ptr->x>=0 && ptr->x<nx && ptr->y>=0 && ptr->y<ny) {
if (ptr->x >= 0 && ptr->x < nx && ptr->y >= 0 &&
ptr->y < ny) {
tot1 = ptr->data[4];
analyze_cluster(*ptr, &t2max, &tot3, NULL, NULL, NULL, NULL,NULL);
analyze_cluster(*ptr, &t2max, &tot3, NULL, NULL,
NULL, NULL, NULL);
noise = noise_map[ptr->y * nx + ptr->x];
if (tot1>noise && t2max>2*noise && tot3>3*noise) {
if (tot1 > noise && t2max > 2 * noise &&
tot3 > 3 * noise) {
;
} else
good = 0;
@ -125,7 +131,6 @@ size_t read_clusters_with_cut(FILE *fp, size_t n_clusters, Cluster *buf,
}
if (nph_read >= n_clusters)
break;
}
}
@ -138,13 +143,8 @@ size_t read_clusters_with_cut(FILE *fp, size_t n_clusters, Cluster *buf,
return nph_read;
}
int analyze_clusters(int64_t n_clusters, int32_t *cin, ClusterAnalysis *co, int csize) {
int analyze_clusters(int64_t n_clusters, int32_t *cin, ClusterAnalysis *co,
int csize) {
char quad;
int32_t tot;
double etax, etay;
@ -154,14 +154,15 @@ int analyze_clusters(int64_t n_clusters, int32_t *cin, ClusterAnalysis *co, int
for (int ic = 0; ic < n_clusters; ic++) {
switch (csize) {
case 2:
ret=analyze_data((cin+9*ic), &tot, NULL, &quad, &etax,&etay, NULL, NULL);
ret = analyze_data((cin + 9 * ic), &tot, NULL, &quad, &etax, &etay,
NULL, NULL);
break;
default:
ret=analyze_data((cin+9*ic), NULL, &tot, &quad, NULL, NULL, &etax,&etay);
ret = analyze_data((cin + 9 * ic), NULL, &tot, &quad, NULL, NULL,
&etax, &etay);
}
if (ret == 0) {
printf("%d %d %d %f %f\n", ic, tot, quad, etax, etay);
}
nc += ret;
// printf("%d %d %d %d\n", ic , quad , t2max , tot3);
@ -173,19 +174,19 @@ int analyze_clusters(int64_t n_clusters, int32_t *cin, ClusterAnalysis *co, int
/* if (tot<=0) */
/* printf("%d %d %d %d %d %d\n",ic,(cin+ic)->x, (cin+ic)->y, */
/* (cout+ic)->c, (cout+ic)->tot2, (cout+ic)->tot3); */
}
return nc;
}
int analyze_cluster(Cluster cl, int32_t *t2, int32_t *t3, char *quad, double *eta2x, double *eta2y, double *eta3x, double *eta3y) {
int analyze_cluster(Cluster cl, int32_t *t2, int32_t *t3, char *quad,
double *eta2x, double *eta2y, double *eta3x,
double *eta3y) {
return analyze_data(cl.data, t2, t3, quad, eta2x, eta2y, eta3x, eta3y);
}
int analyze_data(int32_t *data, int32_t *t2, int32_t *t3, char *quad, double *eta2x, double *eta2y, double *eta3x, double *eta3y) {
int analyze_data(int32_t *data, int32_t *t2, int32_t *t3, char *quad,
double *eta2x, double *eta2y, double *eta3x, double *eta3y) {
int ok = 1;
@ -213,7 +214,6 @@ int analyze_data(int32_t *data, int32_t *t2, int32_t *t3, char *quad, double *et
tot2[cTopRight] += val;
}
// printf ("\n");
}
// printf ("\n");
@ -266,18 +266,18 @@ int analyze_data(int32_t *data, int32_t *t2, int32_t *t3, char *quad, double *et
if (eta2y && t2max != 0)
*eta2y = (double)(data[7]) / (data[7] + data[4]);
break;
default:
;
default:;
}
}
if (eta3x || eta3y) {
if (eta3x && (data[3] + data[4] + data[5]) != 0)
*eta3x=(double)(-data[3]+data[3+2])/(data[3]+data[4]+data[5]);
*eta3x = (double)(-data[3] + data[3 + 2]) /
(data[3] + data[4] + data[5]);
if (eta3y && (data[1] + data[4] + data[7]) != 0)
*eta3y=(double)(-data[1]+data[2*3+1])/(data[1]+data[4]+data[7]);
*eta3y = (double)(-data[1] + data[2 * 3 + 1]) /
(data[1] + data[4] + data[7]);
}
return ok;
}

19
src/cluster_reader.h
View File

@ -5,15 +5,18 @@
#include "data_types.h"
// Pure C implementation to read a cluster file
size_t read_clusters(FILE* fp, size_t n_clusters, Cluster* buf, uint32_t *n_left);
size_t read_clusters(FILE *fp, size_t n_clusters, Cluster *buf,
uint32_t *n_left);
size_t read_clusters_with_cut(FILE* fp, size_t n_clusters, Cluster* buf, uint32_t *n_left, double *noise_map, int nx, int ny);
size_t read_clusters_with_cut(FILE *fp, size_t n_clusters, Cluster *buf,
uint32_t *n_left, double *noise_map, int nx,
int ny);
int analyze_clusters(int64_t n_clusters, int32_t* cin, ClusterAnalysis *cout, int csize);
int analyze_clusters(int64_t n_clusters, int32_t *cin, ClusterAnalysis *cout,
int csize);
int analyze_data(int32_t *data, int32_t *t2, int32_t *t3, char *quad,
double *eta2x, double *eta2y, double *eta3x, double *eta3y);
int analyze_data(int32_t *data, int32_t *t2, int32_t *t3, char *quad, double *eta2x, double *eta2y, double *eta3x, double *eta3y);
int analyze_cluster(Cluster data, int32_t *t2, int32_t *t3, char *quad, double *eta2x, double *eta2y, double *eta3x, double *eta3y);
int analyze_cluster(Cluster data, int32_t *t2, int32_t *t3, char *quad,
double *eta2x, double *eta2y, double *eta3x, double *eta3y);

37
src/creader_module.c
View File

@ -30,7 +30,8 @@
/\* (PyArrayObject *)cl_obj, cluster_dt(), NPY_ARRAY_C_CONTIGUOUS); *\/
/\* if (cl_array == NULL) { *\/
/\* PyErr_SetString(PyExc_TypeError, *\/
/\* "Could not convert first argument to numpy array."); *\/
/\* "Could not convert first argument to numpy array.");
*\/
/\* return NULL; *\/
/\* } *\/
@ -56,18 +57,16 @@
*/
// clusterize method
//static PyObject *ClusterFileReader_clusterize(ClusterFileReader *self, PyObject *args) {
// static PyObject *ClusterFileReader_clusterize(ClusterFileReader *self,
// PyObject *args) {
static PyObject *clusterize(PyObject *Py_UNUSED(self), PyObject *args) {
const int ndim = 1;
Py_ssize_t size = 0;
PyObject *data_obj;
if (!PyArg_ParseTuple(args, "nO", &size, &data_obj)) {
PyErr_SetString(
PyExc_TypeError,
"Could not parse args.");
PyErr_SetString(PyExc_TypeError, "Could not parse args.");
return NULL;
}
@ -77,27 +76,25 @@ static PyObject *clusterize(PyObject *Py_UNUSED(self), PyObject *args) {
// use the underlying buffer, otherwise it will create a copy, for example
// if data type is different or we pass in a list. The
// NPY_ARRAY_C_CONTIGUOUS flag ensures that we have contiguous memory.
PyObject *data_array = PyArray_FROM_OTF(data_obj, NPY_INT32, NPY_ARRAY_C_CONTIGUOUS);
PyObject *data_array =
PyArray_FROM_OTF(data_obj, NPY_INT32, NPY_ARRAY_C_CONTIGUOUS);
int nx = 0, ny = 0;
int32_t *data = NULL;
// If parsing of a or b fails we throw an exception in Python
if (data_array) {
int ndim_data = PyArray_NDIM((PyArrayObject *)(data_array));
npy_intp *data_shape = PyArray_SHAPE((PyArrayObject *)(data_array));
// For the C++ function call we need pointers (or another C++ type/data
// structure)
data = (int32_t *)(PyArray_DATA((PyArrayObject *)(data_array)));
/* for (int i=0; i< ndim_noise; i++) { */
/* printf("Dimension %d size %d pointer \n",i,noise_shape[i], noise_map); */
/* printf("Dimension %d size %d pointer \n",i,noise_shape[i],
* noise_map); */
/* } */
@ -106,26 +103,21 @@ static PyObject *clusterize(PyObject *Py_UNUSED(self), PyObject *args) {
nx = data_shape[0];
ny = data_shape[1];
if (ny != 9) {
PyErr_SetString(
PyExc_TypeError,
"Wrong data type.");
PyErr_SetString(PyExc_TypeError, "Wrong data type.");
// printf("Data found size %d %d %d\n",nx,ny,ndim);
}
} else {
PyErr_SetString(
PyExc_TypeError,
"Wrong data type.");
PyErr_SetString(PyExc_TypeError, "Wrong data type.");
}
}
// Create an uninitialized numpy array
// npy_intp dims[] = {nx};
// printf("%d %d\n",ndim,nx);
npy_intp dims[] = {nx};
PyObject *ca = PyArray_SimpleNewFromDescr(ndim, dims, cluster_analysis_dt());
PyObject *ca =
PyArray_SimpleNewFromDescr(ndim, dims, cluster_analysis_dt());
// printf("1\n");
@ -164,11 +156,8 @@ static PyObject *clusterize(PyObject *Py_UNUSED(self), PyObject *args) {
}
Py_DECREF(data_array);
return ca;
}
static PyObject *get_cluster_dt(PyObject *Py_UNUSED(self), PyObject *args) {
if (!PyArg_ParseTuple(args, ""))
return NULL;

25
src/raw_reader.h
View File

@ -1,27 +1,16 @@
#pragma once
#include "data_types.h"
#include <stdbool.h>
#include <stdint.h>
#include <stdio.h>
#include "data_types.h"
int64_t read_raw_m03(
FILE *fp,
int64_t n_frames,
char* frame_out,
Header* header_out
);
int64_t read_raw_m03(FILE *fp, int64_t n_frames, char *frame_out,
Header *header_out);
int64_t read_raw_m04(
FILE *fp,
int64_t n_frames,
char* frame_out,
char* digital_out,
Header* header_out
);
int64_t read_raw_m04(FILE *fp, int64_t n_frames, char *frame_out,
char *digital_out, Header *header_out);
void decode_moench03(const uint16_t *buf, uint16_t *out_buf);
void decode_moench04(const uint16_t *analog_data,
const uint64_t *digital_data,
uint16_t *analog_frame,
uint8_t *digital_frame);
void decode_moench04(const uint16_t *analog_data, const uint64_t *digital_data,
uint16_t *analog_frame, uint8_t *digital_frame);