cleanup
This commit is contained in:
Erik Frojdh
parent
b996ce5fe6
commit
06b5e97111
@ -1,203 +1,13 @@
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#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
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#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
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#define PY_SSIZE_T_CLEAN
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#define PY_SSIZE_T_CLEAN
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#include "cluster_reader.h"
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#include "data_types.h"
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#include "ClusterReader.h"
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#include "ClusterReader.h"
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#include <Python.h>
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#include <Python.h>
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#include <numpy/arrayobject.h>
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#include <stdbool.h>
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//Module docstring, shown as a part of help(creader)
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// static PyArray_Descr *cluster_analysis_dt() {
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// PyObject *dtype_dict;
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// PyArray_Descr *dtype;
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// dtype_dict = Py_BuildValue("[(s, s),(s, s),(s, s)]", "tot3", "i4", "tot2",
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// "i4", "corner", "u4");
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// PyArray_DescrConverter(dtype_dict, &dtype);
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// Py_DECREF(dtype_dict);
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// return dtype;
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// }
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// // Constructor: sets the fp to NULL then tries to open the file
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// // raises python exception if something goes wrong
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// // returned object should mean file is open and ready to read
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// static int ClusterFileReader_init(ClusterFileReader *self, PyObject *args,
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// PyObject *Py_UNUSED(kwds)) {
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// // Parse file name
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// const char *fname = NULL;
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// if (!PyArg_ParseTuple(args, "s", &fname))
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// return -1;
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// self->fp = fopen(fname, "rb");
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// self->n_left = 0;
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// // Raise python exception using information from errno
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// if (self->fp == NULL) {
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// PyErr_SetFromErrnoWithFilename(PyExc_OSError, fname);
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// return -1;
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// }
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// // Success
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// return 0;
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// }
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// // Custom destructor to make sure we close the file
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// static void ClusterFileReader_dealloc(ClusterFileReader *self) {
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// if (self->fp) {
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// #ifdef CR_VERBOSE
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// printf("Closing file\n");
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// #endif
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// fclose(self->fp);
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// self->fp = NULL;
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// }
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// Py_TYPE(self)->tp_free((PyObject *)self);
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// }
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// // read method
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// static PyObject *ClusterFileReader_read(ClusterFileReader *self, PyObject *args,
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// PyObject *Py_UNUSED(kwds)) {
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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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// return NULL;
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// npy_intp dims[] = {size};
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// // Create an uninitialized numpy array
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// PyArray_Descr *dtype = cluster_dt();
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// // PyObject *PyArray_SimpleNewFromDescr(int nd, npy_int const *dims,
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// // PyArray_Descr *descr)
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// PyObject *clusters = PyArray_SimpleNewFromDescr(ndim, dims, dtype);
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// PyArray_FILLWBYTE((PyArrayObject *)clusters,
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// 0); // zero initialization can be removed later
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// // Get a pointer to the array memory
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// void *buf = PyArray_DATA((PyArrayObject *)clusters);
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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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// if (n_read != size) {
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// // resize the array to match the number of read photons
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// // this will reallocate memory
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// // create a new_shape struct on the stack
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// PyArray_Dims new_shape;
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// // reuse dims for the shape
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// dims[0] = n_read;
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// new_shape.ptr = dims;
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// new_shape.len = 1;
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// // resize the array to match the number of clusters read
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// PyArray_Resize((PyArrayObject *)clusters, &new_shape, 1, NPY_ANYORDER);
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// }
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// return clusters;
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// }
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// // read method
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// static PyObject *ClusterFileReader_clusterize(ClusterFileReader *self,
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// PyObject *args,
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// PyObject *Py_UNUSED(kwds)) {
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// // Create an uninitialized numpy array
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// PyArray_Descr *dtypeIn = cluster_dt();
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// PyArray_Descr *dtypeOut = cluster_analysis_dt();
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// PyObject *c_obj;
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// if (!PyArg_ParseTuple(args, "O", &c_obj))
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// return NULL;
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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 *c_array = PyArray_FromArray((PyArrayObject *)c_obj, dtypeIn,
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// NPY_ARRAY_C_CONTIGUOUS);
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// // If parsing of a or b fails we throw an exception in Python
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// if (c_array == NULL) {
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// PyErr_SetString(
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// PyExc_TypeError,
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// "Could not convert one of the arguments to a numpy array.");
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// return NULL;
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// }
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// const int ndim = PyArray_NDIM((PyArrayObject *)c_array);
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// npy_intp *dims = PyArray_SHAPE((PyArrayObject *)c_array);
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// Py_ssize_t size = dims[0];
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// // printf("%d size %d %d\n",ndim,size,sizeof(ClusterAnalysis));
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// // dims[0]=size;
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// // Cluster *clusters = reinterpret_cast<Cluster *>(
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// // PyArray_DATA(reinterpret_cast<PyArrayObject *>(c_array)));
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// Cluster *clusters = (Cluster *)(PyArray_DATA((PyArrayObject *)(c_array)));
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// // PyObject *PyArray_SimpleNewFromDescr(int nd, npy_int const *dims,
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// // PyArray_Descr *descr)
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// PyObject *clustersA = PyArray_SimpleNewFromDescr(ndim, dims, dtypeOut);
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// // PyArray_FILLWBYTE((PyArrayObject *)clustersA, 0); //zero initialization
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// // can be removed later
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// npy_intp *strides = PyArray_STRIDES(((PyArrayObject *)(clustersA)));
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// // printf("strides %d %d\n", strides[0],sizeof(ClusterAnalysis));
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// // Get a pointer to the array memory
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// ClusterAnalysis *buf = PyArray_DATA((PyArrayObject *)clustersA);
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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 nc = analyze_clusters(size, clusters, buf);
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// // printf("%d %d\n",nc,size);
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// if (nc != size) {
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// PyErr_SetString(PyExc_TypeError, "Parsed wrong size array!");
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// }
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// return clustersA;
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// }
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// // List all methods in our ClusterFileReader class
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// static PyMethodDef ClusterFileReader_methods[] = {
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// {"read", (PyCFunction)ClusterFileReader_read, METH_VARARGS,
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// "Read clusters"},
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// {"clusterize", (PyCFunction)ClusterFileReader_clusterize, METH_VARARGS,
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// "Analyze clusters"},
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// {NULL, NULL, 0, NULL} /* Sentinel */
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// };
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// // Class defenition
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// static PyTypeObject ClusterFileReaderType = {
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// PyVarObject_HEAD_INIT(NULL, 0).tp_name = "creader.ClusterFileReader",
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// .tp_doc = PyDoc_STR("ClusterFileReader implemented in C"),
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// .tp_basicsize = sizeof(ClusterFileReader),
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// .tp_itemsize = 0,
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// .tp_flags = Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE,
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// .tp_new = PyType_GenericNew,
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// .tp_dealloc = (destructor)ClusterFileReader_dealloc,
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// .tp_init = (initproc)ClusterFileReader_init,
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// .tp_methods = ClusterFileReader_methods,
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// };
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//------------------------------------------- Module stuff from here
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// Docstring
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static char module_docstring[] = "C functions to read cluster files";
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static char module_docstring[] = "C functions to read cluster files";
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//Module defenition
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static struct PyModuleDef creader_def = {
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static struct PyModuleDef creader_def = {
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PyModuleDef_HEAD_INIT,
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PyModuleDef_HEAD_INIT,
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"creader",
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"creader",
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@ -210,12 +20,12 @@ static struct PyModuleDef creader_def = {
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NULL // m_free
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NULL // m_free
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};
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};
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//Initialize module and add classes
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PyMODINIT_FUNC PyInit_creader(void) {
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PyMODINIT_FUNC PyInit_creader(void) {
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PyObject *m = PyModule_Create(&creader_def);
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PyObject *m = PyModule_Create(&creader_def);
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if (m == NULL)
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if (m == NULL)
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return NULL;
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return NULL;
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init_ClusterFileReader(m);
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init_ClusterFileReader(m);
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return m;
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return m;
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}
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}
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