From 0846799f28ef4d9c47326846df53bdd622253c33 Mon Sep 17 00:00:00 2001
From: Anna Bergamaschi <anna.bergamaschi@psi.ch>
Date: Wed, 24 May 2023 10:26:00 +0200
Subject: [PATCH] creader_module added
---
src/creader_module.c | 180 +++++++++++++++++++++++++++++++++++++++++++
1 file changed, 180 insertions(+)
create mode 100644 src/creader_module.c
diff --git a/src/creader_module.c b/src/creader_module.c
new file mode 100644
index 0000000..31a75ab
--- /dev/null
+++ b/src/creader_module.c
@@ -0,0 +1,180 @@
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+#define PY_SSIZE_T_CLEAN
+#include <Python.h>
+#include <numpy/arrayobject.h>
+
+#include "data_types.h"
+#include "cluster_reader.h"
+
+
+
+PyDoc_STRVAR(read_doc, "Read clusters from open file.\n\n"
+ "Parameters\n"
+ "----------\n"
+ "n: max number of clusters\n"
+
+ "Returns\n"
+ "----------\n"
+ "Array of clusters read\n\n");
+
+
+
+// Create a custom numpy data type that should reflect
+// our cluster data type.
+// TODO! Update with the actual cluster data type
+static PyArray_Descr *cluster_dt() {
+ PyObject *dtype_dict;
+ PyArray_Descr *dtype;
+ dtype_dict = Py_BuildValue(
+ "[(s, s),(s, s),(s, s, (i))]",
+ "x", "u2", "y", "u2","data","i4",9 );
+ PyArray_DescrConverter(dtype_dict, &dtype);
+ Py_DECREF(dtype_dict);
+ return dtype;
+}
+
+
+// Structure holding our cluster reader class
+typedef struct {
+ PyObject_HEAD FILE *fp;
+ int n_left;
+ int n_read;
+} ClusterFileReader;
+
+
+// Constructor: sets the fp to NULL then tries to open the file
+// raises python exception if something goes wrong
+// returned object should mean file is open and ready to read
+static int ClusterFileReader_init(ClusterFileReader *self, PyObject *args,
+ PyObject *kwds) {
+ self->fp = NULL;
+
+ // Parse file name
+ const char *fname = NULL;
+ if (!PyArg_ParseTuple(args, "s", &fname))
+ return -1;
+
+ self->fp = fopen(fname, "rb");
+ self->n_left=0;
+
+ // Raise python exception using information from errno
+ if (self->fp == NULL) {
+ PyErr_SetFromErrnoWithFilename(PyExc_OSError, fname);
+ return -1;
+ }
+
+ //Success
+ return 0;
+}
+
+// Close file on clearing the object
+static int
+ClusterFileReader_clear(ClusterFileReader *self)
+{
+ if(self->fp){
+ printf("Closing file\n");
+ fclose(self->fp);
+ self->fp = NULL;
+ self->n_left=0;
+ }
+ return 0;
+}
+
+// Custom destructor, not sure this is needed
+// might be an easier way to access the fclose on clear
+static void
+ClusterFileReader_dealloc(ClusterFileReader *self)
+{
+ PyObject_GC_UnTrack(self);
+ ClusterFileReader_clear(self);
+ Py_TYPE(self)->tp_free((PyObject *) self);
+}
+
+
+// read method
+static PyObject *
+ClusterFileReader_read(ClusterFileReader *self, PyObject *args,
+ PyObject *kwds)
+{
+
+ const int ndim = 1;
+ Py_ssize_t size = 0;
+ if (!PyArg_ParseTuple(args, "|n", &size))
+ return NULL;
+
+ npy_intp dims[] = {size};
+
+ //Create an uninitialized numpy array
+ PyArray_Descr *dtype = cluster_dt();
+ PyObject *clusters = PyArray_SimpleNewFromDescr(ndim, dims, dtype);
+ PyArray_FILLWBYTE((PyArrayObject *)clusters, 0); //zero initialization can be removed later
+
+
+ //Get a pointer to the array memory
+ void* buf = PyArray_DATA((PyArrayObject *)clusters);
+
+ // Call the standalone C code to read clusters from file
+ // Here goes the looping, removing frame numbers etc.
+ self->n_read = read_clusters(self->fp, size, buf, &self->n_left);
+
+ //TODO! All kinds of error checking here!!! Resize array etc.
+
+ return clusters;
+}
+
+// List all methods in our ClusterFileReader class
+static PyMethodDef ClusterFileReader_methods[] = {
+ {"read", (PyCFunction) ClusterFileReader_read, METH_VARARGS,
+ "Read clusters"
+ },
+ {NULL} /* Sentinel */
+};
+
+
+// Class defenition
+static PyTypeObject ClusterFileReaderType = {
+ PyVarObject_HEAD_INIT(NULL, 0).tp_name = "creader.ClusterFileReader",
+ .tp_doc = PyDoc_STR("ClusterFileReader implemented in C"),
+ .tp_basicsize = sizeof(ClusterFileReader),
+ .tp_itemsize = 0,
+ .tp_flags = Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE | Py_TPFLAGS_HAVE_GC,
+ .tp_new = PyType_GenericNew,
+ .tp_clear = (inquiry) ClusterFileReader_clear,
+ .tp_dealloc = (destructor) ClusterFileReader_dealloc,
+ .tp_init = (initproc)ClusterFileReader_init,
+ .tp_methods = ClusterFileReader_methods,
+};
+
+//------------------------------------------- Module stuff from here
+
+// Docstring
+static char module_docstring[] =
+ "C functions to read cluster files";
+
+// This is the module itself
+static PyMethodDef module_methods[] = {
+ {NULL, NULL, 0, NULL}};
+
+static struct PyModuleDef creader_def = {PyModuleDef_HEAD_INIT, "creader",
+ module_docstring, -1, module_methods};
+
+PyMODINIT_FUNC PyInit_creader(void) {
+ PyObject *m;
+ if (PyType_Ready(&ClusterFileReaderType) < 0)
+ return NULL;
+ m = PyModule_Create(&creader_def);
+ if (m == NULL)
+ return NULL;
+
+ import_array();
+
+ Py_INCREF(&ClusterFileReaderType);
+ if (PyModule_AddObject(m, "ClusterFileReader",
+ (PyObject *)&ClusterFileReaderType) < 0) {
+ Py_DECREF(&ClusterFileReaderType);
+ Py_DECREF(m);
+ return NULL;
+ }
+ return m;
+}
+