From de2ba7f4301502c9ef046a39806ee314fc46bbd7 Mon Sep 17 00:00:00 2001
From: Christian Gaser <christian.gaser@uni-jena.de>
Date: Sun, 7 Jan 2024 21:39:54 +0100
Subject: [PATCH] Corrected some smaller installation issues

---
 3rdparty/volume_io/Prog_utils/time.c | 26 --------------------------
 Include/CAT_Kmeans.h                 |  4 ++++
 Lib/CAT_Sanlm.c                      |  2 --
 Lib/CAT_Vol.c                        | 10 +++++-----
 Makefile.am                          |  9 +++++++--
 5 files changed, 16 insertions(+), 35 deletions(-)

diff --git a/3rdparty/volume_io/Prog_utils/time.c b/3rdparty/volume_io/Prog_utils/time.c
index a7bd045..2468306 100644
--- a/3rdparty/volume_io/Prog_utils/time.c
+++ b/3rdparty/volume_io/Prog_utils/time.c
@@ -248,32 +248,6 @@ VIOAPI  STRING  get_clock_time( void )
     return( create_string( str ) );
 }
 
-/* ----------------------------- MNI Header -----------------------------------
-@NAME       : sleep_program
-@INPUT      : seconds
-@OUTPUT     : 
-@RETURNS    : 
-@DESCRIPTION: Make the program sleep for the specified number of seconds.
-@METHOD     : 
-@GLOBALS    : 
-@CALLS      : 
-@CREATED    : 1993            David MacDonald
-@MODIFIED   : 
----------------------------------------------------------------------------- */
-
-VIOAPI  void  sleep_program( Real seconds )
-{
-#if HAVE_SELECT
-    struct  timeval  timeout;
-
-    timeout.tv_sec = (long) seconds;
-    timeout.tv_usec = (long) (1.0e6 * (seconds - (Real) timeout.tv_sec) + 0.5);
-
-    (void) select( 0, NULL, NULL, NULL, &timeout );
-#else
-    sleep((unsigned int) seconds);
-#endif
-}
 
 /* ----------------------------- MNI Header -----------------------------------
 @NAME       : get_date
diff --git a/Include/CAT_Kmeans.h b/Include/CAT_Kmeans.h
index 11718c1..687c93a 100644
--- a/Include/CAT_Kmeans.h
+++ b/Include/CAT_Kmeans.h
@@ -12,6 +12,10 @@
 
 #include "CAT_Vol.h"
 
+#ifndef HUGE
+#define HUGE 1e15 
+#endif
+
 double Kmeans(float *src, unsigned char *label, unsigned char *mask, int NI, int n_clusters, double *mean, double *voxelsize, int *dims, int thresh_mask, int thresh_kmeans);
 
 #endif
\ No newline at end of file
diff --git a/Lib/CAT_Sanlm.c b/Lib/CAT_Sanlm.c
index f30c3fc..120ebf8 100644
--- a/Lib/CAT_Sanlm.c
+++ b/Lib/CAT_Sanlm.c
@@ -609,8 +609,6 @@ void anlm(float* ima, int v, int f, int use_rician, const int* dims)
 
 #if defined(_WIN32)
 
-        /* printf("Windows system detected\n");fflush(stdout); */
-
         /* Reserve room for handles of threads in ThreadList*/
         ThreadList = (HANDLE*) malloc(Nthreads*sizeof( HANDLE ));
         ThreadArgs = (myargument*) malloc( Nthreads*sizeof(myargument));
diff --git a/Lib/CAT_Vol.c b/Lib/CAT_Vol.c
index 1c80789..5d61afd 100644
--- a/Lib/CAT_Vol.c
+++ b/Lib/CAT_Vol.c
@@ -384,10 +384,10 @@ double
 get_masked_mean_array_float(float arr[], int size, unsigned char mask[])
 {
     double sum = 0.0;
-    int n = 0;
+    int i, n = 0;
     
     /* Calculate mean */
-    for(int i = 0; i < size; i++) {
+    for (i = 0; i < size; i++) {
         if (!isnan(arr[i]) && ((mask && mask[i] > 0) || !mask)) {
             sum += arr[i];
             n++;
@@ -429,10 +429,10 @@ double
 get_masked_std_array_float(float arr[], int size, unsigned char mask[])
 {
     double mean = 0.0, variance = 0.0;
-    int n = 0;
+    int i, n = 0;
 
     /* Calculate mean */
-    for(int i = 0; i < size; i++) {
+    for (i = 0; i < size; i++) {
         if (!isnan(arr[i]) && ((mask && mask[i] > 0) || !mask)) {
             mean += arr[i];
             n++;
@@ -441,7 +441,7 @@ get_masked_std_array_float(float arr[], int size, unsigned char mask[])
     mean = mean / (double)n;
 
     /* Calculate variance */
-    for(int i = 0; i < size; i++)
+    for (i = 0; i < size; i++)
         if (!isnan(arr[i]) && ((mask && mask[i] > 0) || !mask))
             variance += pow(arr[i] - mean, 2);
     variance /= (double)n;
diff --git a/Makefile.am b/Makefile.am
index d631755..a8b1fad 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -3,8 +3,13 @@ SUBDIRS = . Progs
 AUTOMAKE_OPTIONS = subdir-objects
 ACLOCAL_AMFLAGS = -I m4
 
-AM_CFLAGS = -pthread -DHAVE_ZLIB -I$(top_srcdir)/Include -I$(top_srcdir)/3rdparty/MarchingCubes -I$(top_srcdir)/3rdparty/nifti -I$(top_srcdir)/3rdparty/zlib -I$(top_srcdir)/3rdparty/volume_io/Include -I$(top_srcdir)/3rdparty/bicpl-surface/Include -I$(top_srcdir)/3rdparty/bicpl-surface/Include/bicpl
-#AM_CPPFLAGS = -pthread -DHAVE_ZLIB -I$(top_srcdir)/Include -I$(top_srcdir)/3rdparty/MarchingCubes -I$(top_srcdir)/3rdparty/nifti -I$(top_srcdir)/3rdparty/zlib -I$(top_srcdir)/3rdparty/bicpl-surface/Include/bicpl
+CFLAGS0 = -DHAVE_ZLIB -I$(top_srcdir)/Include -I$(top_srcdir)/3rdparty/MarchingCubes -I$(top_srcdir)/3rdparty/nifti -I$(top_srcdir)/3rdparty/zlib -I$(top_srcdir)/3rdparty/volume_io/Include -I$(top_srcdir)/3rdparty/bicpl-surface/Include -I$(top_srcdir)/3rdparty/bicpl-surface/Include/bicpl
+
+if WINDOWS
+  AM_CFLAGS = ${CFLAGS0}
+else
+  AM_CFLAGS = -pthread ${CFLAGS0}
+endif
 
 lib_LTLIBRARIES = libCAT.la