creader_module added

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;
+}
+