[gnuastro-commits] master e55594d: New Arithmetic operator to fill holes in a binary dataset

[Mohammad Akhlaghi]

branch: master
commit e55594de238dcc88df4c054a9a9e66754922e77a
Author: Mohammad Akhlaghi <address@hidden>
Commit: Mohammad Akhlaghi <address@hidden>

    New Arithmetic operator to fill holes in a binary dataset
    
    The necessary library function was already there, so it wasn't too hard to
    add this operator to Arithmetic. Currently the `maxsize' argument to the
    library function in Arithmetic is `-1' (no maximum!). Maybe later we can
    add a max hole size operand to fill-holes is well.
---
 NEWS                        |  1 +
 bin/arithmetic/arithmetic.c | 55 +++++++++++++++++++++++++++++++--------------
 bin/arithmetic/arithmetic.h |  1 +
 doc/gnuastro.texi           | 17 +++++++++-----
 4 files changed, 52 insertions(+), 22 deletions(-)

diff --git a/NEWS b/NEWS
index d4edc7f..388ec6d 100644
--- a/NEWS
+++ b/NEWS
@@ -12,6 +12,7 @@ GNU Astronomy Utilities NEWS                          -*- 
outline -*-
     - `set-A': Set a name (`A' in this case) for the popped dataset. This
                allows only reading the dataset it into memory once and
                possibly using it many times.
+    - `fill-holes': Flip background (0) pixels surrounded by foreground (1).
     - `collapse-sum': collapse/remove a dimension by summing over it.
     - `collapse-mean': collapse/remove a dimension by averaging over it.
     - `collapse-number': Number of elements included in the collapse.
diff --git a/bin/arithmetic/arithmetic.c b/bin/arithmetic/arithmetic.c
index ba8ef38..c2a2bb1 100644
--- a/bin/arithmetic/arithmetic.c
+++ b/bin/arithmetic/arithmetic.c
@@ -503,8 +503,8 @@ wrapper_for_filter(struct arithmeticparams *p, char *token, 
int operator)
 /*************            Other functions          *************/
 /***************************************************************/
 static int
-arithmetic_binary_conn_sanity_checks(gal_data_t *in, gal_data_t *conn,
-                                     char *operator)
+arithmetic_binary_sanity_checks(gal_data_t *in, gal_data_t *conn,
+                                char *operator)
 {
   int conn_int;
 
@@ -552,19 +552,14 @@ arithmetic_erode_dilate(struct arithmeticparams *p, char 
*token, int op)
   gal_data_t *conn = operands_pop(p, token);
   gal_data_t *in   = operands_pop(p, token);
 
-  /* Do the sanity checks and  */
+  /* Do the sanity checks. */
+  conn_int=arithmetic_binary_sanity_checks(in, conn, token);
+
+  /* Do the operation. */
   switch(op)
     {
-    case ARITHMETIC_OP_ERODE:
-      conn_int=arithmetic_binary_conn_sanity_checks(in, conn, "erode");
-      gal_binary_erode(in, 1, conn_int, 1);
-      break;
-
-    case ARITHMETIC_OP_DILATE:
-      conn_int=arithmetic_binary_conn_sanity_checks(in, conn, "dilate");
-      gal_binary_dilate(in, 1, conn_int, 1);
-      break;
-
+    case ARITHMETIC_OP_ERODE:  gal_binary_erode(in,  1, conn_int, 1); break;
+    case ARITHMETIC_OP_DILATE: gal_binary_dilate(in, 1, conn_int, 1); break;
     default:
       error(EXIT_FAILURE, 0, "%s: a bug! Please contact us at %s to fix the "
             "problem. The operator code %d not recognized", __func__,
@@ -573,8 +568,6 @@ arithmetic_erode_dilate(struct arithmeticparams *p, char 
*token, int op)
 
   /* Push the result onto the stack. */
   operands_add(p, NULL, in);
-
-  /* Recall that`conn' was freed in the sanity check. */
 }
 
 
@@ -592,8 +585,7 @@ arithmetic_connected_components(struct arithmeticparams *p, 
char *token)
   gal_data_t *in   = operands_pop(p, token);
 
   /* Basic sanity checks. */
-  conn_int=arithmetic_binary_conn_sanity_checks(in, conn,
-                                                "connected-components");
+  conn_int=arithmetic_binary_sanity_checks(in, conn, token);
 
   /* Do the connected components labeling. */
   gal_binary_connected_components(in, &out, conn_int);
@@ -610,6 +602,29 @@ arithmetic_connected_components(struct arithmeticparams 
*p, char *token)
 
 
 static void
+arithmetic_fill_holes(struct arithmeticparams *p, char *token)
+{
+  int conn_int;
+
+  /* Pop the two necessary operands. */
+  gal_data_t *conn = operands_pop(p, token);
+  gal_data_t *in   = operands_pop(p, token);
+
+  /* Basic sanity checks. */
+  conn_int=arithmetic_binary_sanity_checks(in, conn, token);
+
+  /* Fill the holes */
+  gal_binary_holes_fill(in, conn_int, -1);
+
+  /* Push the result onto the stack. */
+  operands_add(p, NULL, in);
+}
+
+
+
+
+
+static void
 arithmetic_invert(struct arithmeticparams *p, char *token)
 {
   gal_data_t *in = operands_pop(p, token);
@@ -958,6 +973,8 @@ reversepolish(struct arithmeticparams *p)
             { op=ARITHMETIC_OP_DILATE;                nop=0;  }
           else if (!strcmp(token->v, "connected-components"))
             { op=ARITHMETIC_OP_CONNECTED_COMPONENTS;  nop=0;  }
+          else if (!strcmp(token->v, "fill-holes"))
+            { op=ARITHMETIC_OP_FILL_HOLES;            nop=0;  }
           else if (!strcmp(token->v, "invert"))
             { op=ARITHMETIC_OP_INVERT;                nop=0;  }
           else if (!strcmp(token->v, "interpolate-medianngb"))
@@ -1051,6 +1068,10 @@ reversepolish(struct arithmeticparams *p)
                   arithmetic_connected_components(p, token->v);
                   break;
 
+                case ARITHMETIC_OP_FILL_HOLES:
+                  arithmetic_fill_holes(p, token->v);
+                  break;
+
                 case ARITHMETIC_OP_INVERT:
                   arithmetic_invert(p, token->v);
                   break;
diff --git a/bin/arithmetic/arithmetic.h b/bin/arithmetic/arithmetic.h
index 4144006..67bff24 100644
--- a/bin/arithmetic/arithmetic.h
+++ b/bin/arithmetic/arithmetic.h
@@ -38,6 +38,7 @@ enum arithmetic_prog_operators
   ARITHMETIC_OP_ERODE,
   ARITHMETIC_OP_DILATE,
   ARITHMETIC_OP_CONNECTED_COMPONENTS,
+  ARITHMETIC_OP_FILL_HOLES,
   ARITHMETIC_OP_INVERT,
   ARITHMETIC_OP_INTERPOLATE_MEDIANNGB,
   ARITHMETIC_OP_COLLAPSE_SUM,
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index c3ab4fe..537ddb2 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -11599,6 +11599,13 @@ If your input dataset doesn't have a binary type, but 
you know all its
 values are 0 or 1, you can use the @code{uint8} operator (below) to convert
 it to binary.
 
address@hidden fill-holes
+Flip background (0) pixels surrounded by foreground (1) in a binary
+dataset. This operator takes two operands (similar to
address@hidden): the first popped operand is the connectivity
+(to define a hole) and the second is the binary (0 or 1 valued) dataset to
+fill holes in.
+
 @item invert
 Invert an unsigned integer dataset. This is the only operator that ignores
 blank values (which are set to be the maximum values in the unsigned
@@ -27204,11 +27211,11 @@ pixels will have a value of @code{-1}. The total 
number of holes will be
 written where @code{numholes} points to.
 @end deftypefun
 
address@hidden void gal_binary_holes_fill (gal_data_t @code{*input}, int 
@code{connectivity})
-Fill all the holes (0 valued pixels surrounded by 1 valued pixels) within a
-region of the binary @code{input} dataset. The connectivity of the holes
-can be set with @code{connectivity}. This function currently only works on
-a 2D dataset.
address@hidden void gal_binary_holes_fill (gal_data_t @code{*input}, int 
@code{connectivity}, size_t @code{maxsize})
+Fill all the holes (0 valued pixels surrounded by 1 valued pixels) of the
+binary @code{input} dataset. The connectivity of the holes can be set with
address@hidden Holes larger than @code{maxsize} are not filled. This
+function currently only works on a 2D dataset.
 @end deftypefun
 
 @node Labeled datasets, Convolution functions, Binary datasets, Gnuastro 
library