fix segfault, cleanup and resize

setup.py

@@ -8,10 +8,10 @@ c_ext = setuptools.Extension("creader",
                     include_dirs=[
                             np.get_include(),"src/"
                             ],
-                    extra_compile_args=['-std=c++11', '-Wall', '-Wextra'] )
+                    extra_compile_args=['-std=c99', '-Wall', '-Wextra'] )
                     
 
-c_ext.language = 'c++'
+c_ext.language = 'c'
 setuptools.setup(
     name= 'creader',
     version = '0.1',

src/cluster_reader.c

@@ -1,7 +1,7 @@
 #include "cluster_reader.h"
 
 int read_clusters(FILE* fp, int64_t n_clusters, Cluster* buf, int *n_left){
-  printf("Item size: %d n_clusters: %d, n_left: %d\n", sizeof(Cluster), n_clusters,*n_left);
+  printf("Item size: %lu n_clusters: %lld, n_left: %d\n", sizeof(Cluster), n_clusters,*n_left);
     int iframe=0, nph=*n_left;
     size_t n_read=0, nph_read=0, nn=*n_left, nr=0;
     //n_left=n_clusters;
@@ -39,7 +39,7 @@ int read_clusters(FILE* fp, int64_t n_clusters, Cluster* buf, int *n_left){
     }
     }
     // size_t n_read = fread(buf, sizeof(Cluster), n_clusters, fp);
-    printf("Read: %d items %d left %d\n", nph_read, n_read,*n_left);
+    printf("Read: %zu items %zu left %d\n", nph_read, n_read,*n_left);
     return nph_read;
 }
   

src/creader_module.c

@@ -67,26 +67,15 @@ static int ClusterFileReader_init(ClusterFileReader *self, PyObject *args,
     return 0;
 }
 
-// Close file on clearing the object
-static int
-ClusterFileReader_clear(ClusterFileReader *self)
+// Custom destructor to make sure we close the file
+static void
+ClusterFileReader_dealloc(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);
 }
 
@@ -106,6 +95,7 @@ ClusterFileReader_read(ClusterFileReader *self, PyObject *args,
 
     //Create an uninitialized numpy array
     PyArray_Descr *dtype = cluster_dt();
+    // PyObject *PyArray_SimpleNewFromDescr(int nd, npy_int const *dims, PyArray_Descr *descr)
     PyObject *clusters = PyArray_SimpleNewFromDescr(ndim, dims, dtype);
     PyArray_FILLWBYTE((PyArrayObject *)clusters, 0); //zero initialization can be removed later
     
@@ -117,7 +107,22 @@ ClusterFileReader_read(ClusterFileReader *self, PyObject *args,
     // 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.
+
+    if(self->n_read != size){
+        //resize the array to match the number of read photons
+        //this will reallocate memory
+        
+        //create a new_shape struct on the stack
+        PyArray_Dims new_shape;
+
+        //reuse dims for the shape
+        dims[0] = self->n_read;
+        new_shape.ptr = dims;
+        new_shape.len = 1;
+        
+        // resize the array to match the number of clusters read
+        PyArray_Resize((PyArrayObject *)clusters, &new_shape, 1, NPY_ANYORDER);
+    }
 
     return clusters;
 }
@@ -137,9 +142,8 @@ static PyTypeObject ClusterFileReaderType = {
     .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_flags = Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE,
     .tp_new = PyType_GenericNew,
-    .tp_clear = (inquiry) ClusterFileReader_clear,
     .tp_dealloc = (destructor) ClusterFileReader_dealloc,
     .tp_init = (initproc)ClusterFileReader_init,
     .tp_methods = ClusterFileReader_methods,

test.py

@@ -2,7 +2,13 @@ from creader import ClusterFileReader
 import numpy as np
 
 maxph=100000000
+maxph=100
+
+from pathlib import Path
+fpath = Path('/Users/erik/data/clusters/beam_En700eV_-40deg_300V_10us_d0_f0_100.clust')
+# r = ClusterFileReader("/mnt/moench_data/Moench_LGAD_SIM_Nov22/moenchLGAD202211/clustW17new/beam_En800eV_-40deg_300V_10us_d0_f5_0.clust")
+
+r = ClusterFileReader(fpath.as_posix())
 
-r = ClusterFileReader("/mnt/moench_data/Moench_LGAD_SIM_Nov22/moenchLGAD202211/clustW17new/beam_En800eV_-40deg_300V_10us_d0_f5_0.clust")
 a=r.read(maxph)
-print(a[::100000])
+# print(a[::100000])