Merge pull request #603 from dkazanc/stripes

Stripes detector and a mask generator

include/libtomo/stripe.h

@@ -51,5 +51,17 @@
 #    define DLL
 #endif
 
+#include <stdbool.h>
+
 DLL void
 remove_stripe_sf(float* data, int dx, int dy, int dz, int size, int istart, int iend);
+
+DLL int
+stripesdetect3d_main_float(float* Input, float* Output, int window_halflength_vertical,
+                           int ratio_radius, int ncores, int dimX, int dimY, int dimZ);
+
+DLL int
+stripesmask3d_main_float(float* Input, bool* Output, float threshold_val,
+                         int stripe_length_min, int stripe_depth_min,
+                         int stripe_width_min, float sensitivity, int ncores, int dimX,
+                         int dimY, int dimZ);

source/libtomo/misc/CMakeLists.txt

@@ -9,8 +9,6 @@ tomopy_add_library(
   morph.c
   remove_ring.c
   median_filt3d.c
-  utils.c
-  utils.h
   ${HEADERS})
 
 find_package(OpenMP REQUIRED COMPONENTS C)

source/libtomo/misc/median_filt3d.c

@@ -47,9 +47,22 @@
 #include <math.h>
 #include <omp.h>
 #include <stdlib.h>
+#include <string.h>
 
 #include "libtomo/median_filt3d.h"
-#include "utils.h"
+
+int floatcomp(const void* elem1, const void* elem2)
+{
+    if(*(const float*)elem1 < *(const float*)elem2)
+        return -1;
+    return *(const float*)elem1 > *(const float*)elem2;
+}
+int uint16comp(const void* elem1, const void* elem2)
+{
+    if(*(const unsigned short*)elem1 < *(const unsigned short*)elem2)
+        return -1;
+    return *(const unsigned short*)elem1 > *(const unsigned short*)elem2;
+}
 
 void
 medfilt3D_float(float* Input, float* Output, int radius, int sizefilter_total,
@@ -90,7 +103,8 @@ medfilt3D_float(float* Input, float* Output, int radius, int sizefilter_total,
             }
         }
     }
-    quicksort_float(ValVec, 0, sizefilter_total - 1); /* perform sorting */
+
+    qsort(ValVec, sizefilter_total, sizeof(float), floatcomp);
 
     if(mu_threshold == 0.0F)
     {
@@ -136,7 +150,7 @@ medfilt2D_float(float* Input, float* Output, int radius, int sizefilter_total,
             counter++;
         }
     }
-    quicksort_float(ValVec, 0, sizefilter_total - 1); /* perform sorting */
+    qsort(ValVec, sizefilter_total, sizeof(float), floatcomp);
 
     if(mu_threshold == 0.0F)
     {
@@ -191,7 +205,8 @@ medfilt3D_uint16(unsigned short* Input, unsigned short* Output, int radius,
             }
         }
     }
-    quicksort_uint16(ValVec, 0, sizefilter_total - 1); /* perform sorting */
+
+    qsort(ValVec, sizefilter_total, sizeof(unsigned short), uint16comp);
 
     if(mu_threshold == 0.0F)
     {
@@ -238,7 +253,8 @@ medfilt2D_uint16(unsigned short* Input, unsigned short* Output, int radius,
             counter++;
         }
     }
-    quicksort_uint16(ValVec, 0, sizefilter_total - 1); /* perform sorting */
+
+    qsort(ValVec, sizefilter_total, sizeof(unsigned short), uint16comp);
 
     if(mu_threshold == 0.0F)
     {
@@ -268,7 +284,7 @@ medianfilter_main_float(float* Input, float* Output, int radius, float mu_thresh
     diameter = (2 * radius + 1); /* diameter of the filter's kernel */
     if(mu_threshold != 0.0)
     {
-        copyIm(Input, Output, (long) (dimX), (long) (dimY), (long) (dimZ));
+        memcpy(Output, Input, dimX * dimY * dimZ * sizeof(float));
     } /* copy input into output */
 
     /* dealing here with a custom given number of cpu threads */
@@ -331,7 +347,7 @@ medianfilter_main_uint16(unsigned short* Input, unsigned short* Output, int radi
     diameter = (2 * radius + 1); /* diameter of the filter's kernel */
     if(mu_threshold != 0.0)
     {
-        copyIm_unshort(Input, Output, (long) (dimX), (long) (dimY), (long) (dimZ));
+        memcpy(Output, Input, dimX * dimY * dimZ * sizeof(unsigned short));
     } /* copy input into output */
 
     /* dealing here with a custom given number of cpu threads */