From 916ec20a1c9bddafe7a23cda64aa0c01401046ca Mon Sep 17 00:00:00 2001
From: Erik Frojdh <erik.frojdh@gmail.com>
Date: Fri, 27 Oct 2023 09:24:52 +0200
Subject: [PATCH] fixing warnings

---
 src/ClusterReader.c  |  9 +++------
 src/RawFileReader.c  |  8 ++++----
 src/cluster_reader.c | 39 ++++++++++++++++++++++-----------------
 src/cluster_reader.h |  4 ++--
 src/raw_reader.c     |  6 +++---
 5 files changed, 34 insertions(+), 32 deletions(-)

diff --git a/src/ClusterReader.c b/src/ClusterReader.c
index 5f8ad11..85d479d 100644
--- a/src/ClusterReader.c
+++ b/src/ClusterReader.c
@@ -6,7 +6,7 @@
 //clang-format off
 typedef struct {
     PyObject_HEAD FILE *fp;
-    int n_left;
+    size_t n_left;
     Py_ssize_t chunk;
 } ClusterFileReader;
 //clang-format on
@@ -18,7 +18,7 @@ static int ClusterFileReader_init(ClusterFileReader *self, PyObject *args,
                                   PyObject *kwds) {
 
     // Parse file name, accepts string or pathlike objects
-    const char *fname = NULL;
+    char *fname = NULL;
     self->n_left = 0;
     self->chunk = 0;
     PyObject *fname_obj = NULL;
@@ -27,9 +27,6 @@ static int ClusterFileReader_init(ClusterFileReader *self, PyObject *args,
 
     static char *kwlist[] = {"fname", "chunk", NULL};
 
-    // if (!PyArg_ParseTuple(args, "O&", PyUnicode_FSConverter, &buf))
-    //     return -1;
-    // PyBytes_AsStringAndSize(buf, &fname, &len);
 
     if (!PyArg_ParseTupleAndKeywords(args, kwds, "O|n", kwlist, &fname_obj,
                                      &self->chunk)) {
@@ -45,7 +42,7 @@ static int ClusterFileReader_init(ClusterFileReader *self, PyObject *args,
     printf("Opening: %s\n chunk: %lu\n", fname, self->chunk);
 #endif
 
-    self->fp = fopen(fname, "rb");
+    self->fp = fopen((const char*)fname, "rb");
     
 
     // Keep the return code to not return before releasing buffer
diff --git a/src/RawFileReader.c b/src/RawFileReader.c
index 0b3084e..beaed49 100644
--- a/src/RawFileReader.c
+++ b/src/RawFileReader.c
@@ -22,7 +22,7 @@ static int RawFileReader_init(RawFileReader *self, PyObject *args,
                               PyObject *kwds) {
 
     // Parse file name, accepts string or pathlike objects
-    const char *fname = NULL;
+    char *fname = NULL;
     PyObject *fname_obj = NULL;
     PyObject *fname_bytes = NULL;
     Py_ssize_t len;
@@ -48,7 +48,7 @@ static int RawFileReader_init(RawFileReader *self, PyObject *args,
     printf("fname: %s\n read_header: %d detector type: %d\n", fname,
            self->read_header, self->detector);
 #endif
-    self->fp = fopen(fname, "rb");
+    self->fp = fopen((const char*)fname, "rb");
 
     // Keep the return code to not return before releasing buffer
     int rc = 0;
@@ -110,12 +110,12 @@ 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_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_out);
+            read_raw_m04(self->fp, n_frames, out_buf, digital_out, (Header*)header_out);
         break;
     default:
         break;
diff --git a/src/cluster_reader.c b/src/cluster_reader.c
index 7837482..6622e4e 100644
--- a/src/cluster_reader.c
+++ b/src/cluster_reader.c
@@ -1,9 +1,9 @@
 #include "cluster_reader.h"
 #include <assert.h>
 
-int read_clusters(FILE *fp, int64_t n_clusters, Cluster *buf, int *n_left) {
+size_t read_clusters(FILE *fp, size_t n_clusters, Cluster *buf, size_t *n_left) {
     int iframe = 0;
-    int nph = *n_left;
+    size_t nph = *n_left;
 
     size_t nph_read = 0;
     size_t nn = *n_left;
@@ -44,23 +44,27 @@ int read_clusters(FILE *fp, int64_t n_clusters, Cluster *buf, int *n_left) {
     return nph_read;
 }
 
-int read_clusters_with_cut(FILE *fp, int64_t n_clusters, Cluster *buf,
-                           int *n_left, double *noise_map, int nx, int ny) {
+size_t read_clusters_with_cut(FILE *fp, size_t n_clusters, Cluster *buf,
+                           size_t *n_left, double *noise_map, int nx, int ny) {
     int iframe = 0;
-    int nph = *n_left;
+    size_t nph = *n_left;
 
     size_t nph_read = 0;
 
-    int32_t tot2[4], t2max, tot1;
-    int32_t val, tot3;
+    int32_t t2max, tot1;
+    int32_t tot3;
     Cluster *ptr = buf;
     int good = 1;
     double noise;
     // read photons left from previous frame
     if (nph) {
-        for (int iph = 0; iph < nph; iph++) {
+        for (size_t iph = 0; iph < nph; iph++) {
             // read photons 1 by 1
-            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;
+            }
+            //TODO! error handling on read
             good = 1;
             if (noise_map) {
                 if (ptr->x >= 0 && ptr->x < nx && ptr->y >= 0 && ptr->y < ny) {
@@ -95,9 +99,12 @@ int read_clusters_with_cut(FILE *fp, int64_t n_clusters, Cluster *buf,
 	  if (fread(&nph, sizeof(nph), 1, fp)) {
 	    //printf("** %d\n",nph);
 	    *n_left = nph;
-	    for (int iph=0; iph<nph; iph++) {
+	    for (size_t iph=0; iph<nph; iph++) {
 	      // read photons 1 by 1
-	      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) {
@@ -140,10 +147,8 @@ int read_clusters_with_cut(FILE *fp, int64_t n_clusters, Cluster *buf,
 
 
 int analyze_clusters(int64_t n_clusters, int32_t *cin, ClusterAnalysis *co, int csize) {
-
-    int32_t tot2[4], t2max;
     char quad;
-    int32_t val, tot;
+    int32_t tot;
     double etax, etay;
     int nc=0;
     //printf("csize is %d\n",csize);
@@ -186,16 +191,16 @@ int analyze_data(int32_t *data, int32_t *t2, int32_t *t3, char *quad, double *et
 
   int ok=1;
 
-    int32_t tot2[4], t2max;
+    int32_t tot2[4];
+    int32_t t2max=0;
     char c;
     int32_t val, tot3;
 
     tot3 = 0;
     for (int i = 0; i < 4; i++)
         tot2[i] = 0;
-    // t2max=0;
-    for (int ix = 0; ix < 3; ix++) {
 
+    for (int ix = 0; ix < 3; ix++) {
       for (int iy = 0; iy < 3; iy++) {
 	val = data[iy * 3 + ix];
 	//	printf ("%d ",data[iy * 3 + ix]);
diff --git a/src/cluster_reader.h b/src/cluster_reader.h
index 4ec464c..64a226b 100644
--- a/src/cluster_reader.h
+++ b/src/cluster_reader.h
@@ -5,9 +5,9 @@
 #include "data_types.h"
 //Pure C implementation to read a cluster file
 
-int read_clusters(FILE* fp, int64_t n_clusters, Cluster* buf, int *n_left);
+size_t read_clusters(FILE* fp, size_t n_clusters, Cluster* buf, size_t *n_left);
 
-int read_clusters_with_cut(FILE* fp, int64_t n_clusters, Cluster* buf, int *n_left, double *noise_map, int nx, int ny);
+size_t read_clusters_with_cut(FILE* fp, size_t n_clusters, Cluster* buf, size_t *n_left, double *noise_map, int nx, int ny);
 
 int analyze_clusters(int64_t n_clusters, int32_t* cin, ClusterAnalysis *cout, int csize);
 
diff --git a/src/raw_reader.c b/src/raw_reader.c
index 7fa52c3..4f0ef89 100644
--- a/src/raw_reader.c
+++ b/src/raw_reader.c
@@ -44,8 +44,8 @@ int64_t read_raw_m04(FILE *fp, int64_t n_frames, char *frame_out,
 
     const size_t frame_size = 400 * 400 * 2;
     const size_t digital_frame_size = 5000 * 8;
-    char *tmp = malloc(frame_size);
-    char *digital_tmp = malloc(digital_frame_size);
+    void *tmp = malloc(frame_size);
+    void *digital_tmp = malloc(digital_frame_size);
     Header h;
 
     int64_t frames_read = 0;
@@ -75,7 +75,7 @@ int64_t read_raw_m04(FILE *fp, int64_t n_frames, char *frame_out,
 
         // Decode frame and write to numpy output array
         // decode_moench03((uint16_t *)tmp, (uint16_t *)frame_out);
-        decode_moench04(tmp, digital_tmp, frame_out, digital_out);
+        decode_moench04(tmp, digital_tmp, (uint16_t*)frame_out, (uint8_t*)digital_out);
 
         frame_out += frame_size;
         if (digital_out)