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[gnuastro-commits] master e90b490 116/125: Internal headers moved to spe
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From: |
Mohammad Akhlaghi |
|
Subject: |
[gnuastro-commits] master e90b490 116/125: Internal headers moved to special directory |
|
Date: |
Sun, 23 Apr 2017 22:36:51 -0400 (EDT) |
branch: master
commit e90b490d2bd89270235b8706828e607952a656a0
Author: Mohammad Akhlaghi <address@hidden>
Commit: Mohammad Akhlaghi <address@hidden>
Internal headers moved to special directory
Until now, Gnuastro's internal headers were simply in the `lib/'
directory. So when you wanted to include `options.h', the include directive
would be `#include <options.h>'. Since Gnuastro's installed libraries are
in a `gnuastro' directory, the fact that the internal library headers are
simply mixed with the `.c' files of all the libraries can be confusing for
a new inquirer into the code.
To fix this issue and also to allow further symmetricity and clarity of the
source code, a new `lib/gnuastro-internal/' directory was created and all
internal headers are now put into there. So the include directive is now
`#include <gnuastro-internal/options.h>', it is longer, but it provides a
better level of documentation and clarity.
Work is also ongoing on the re-write of NoiseChisel, it has currently
reached the stage of filling holes that is necessary to define
pseudo-detections.
---
bin/arithmetic/arithmetic.c | 2 +-
bin/arithmetic/main.c | 2 +-
bin/arithmetic/main.h | 2 +-
bin/arithmetic/ui.c | 10 +-
bin/convertt/convertt.c | 2 +-
bin/convertt/eps.c | 4 +-
bin/convertt/main.c | 2 +-
bin/convertt/main.h | 2 +-
bin/convertt/ui.c | 10 +-
bin/convolve/convolve.c | 2 +-
bin/convolve/main.c | 2 +-
bin/convolve/main.h | 2 +-
bin/convolve/ui.c | 10 +-
bin/cosmiccal/main.c | 2 +-
bin/cosmiccal/main.h | 2 +-
bin/cosmiccal/ui.c | 10 +-
bin/crop/crop.c | 4 +-
bin/crop/main.c | 2 +-
bin/crop/main.h | 2 +-
bin/crop/onecrop.c | 4 +-
bin/crop/ui.c | 10 +-
bin/fits/fits.c | 4 +-
bin/fits/keywords.c | 2 +-
bin/fits/main.c | 2 +-
bin/fits/main.h | 2 +-
bin/fits/ui.c | 8 +-
bin/mknoise/main.c | 2 +-
bin/mknoise/main.h | 2 +-
bin/mknoise/mknoise.c | 2 +-
bin/mknoise/ui.c | 10 +-
bin/mkprof/main.c | 2 +-
bin/mkprof/main.h | 2 +-
bin/mkprof/mkprof.c | 4 +-
bin/mkprof/oneprofile.c | 2 +-
bin/mkprof/ui.c | 10 +-
bin/noisechisel/detection.c | 127 ++++++-
bin/noisechisel/detection.h | 3 +
bin/noisechisel/main.c | 2 +-
bin/noisechisel/main.h | 4 +-
bin/noisechisel/noisechisel.c | 5 +-
bin/noisechisel/threshold.c | 445 +++++++++++++++++------
bin/noisechisel/threshold.h | 18 +
bin/noisechisel/ui.c | 10 +-
bin/statistics/main.c | 2 +-
bin/statistics/main.h | 2 +-
bin/statistics/sky.c | 4 +-
bin/statistics/statistics.c | 4 +-
bin/statistics/ui.c | 10 +-
bin/table/main.c | 2 +-
bin/table/main.h | 2 +-
bin/table/ui.c | 10 +-
bin/warp/main.c | 2 +-
bin/warp/main.h | 2 +-
bin/warp/ui.c | 10 +-
doc/Makefile.am | 2 +-
lib/Makefile.am | 13 +-
lib/arithmetic-onlyint.c | 2 +-
lib/arithmetic.c | 4 +-
lib/binary.c | 32 ++
lib/blank.c | 2 +-
lib/checkset.c | 2 +-
lib/config.h.in | 78 ----
lib/convolve.c | 2 +-
lib/data.c | 2 +-
lib/fits.c | 4 +-
lib/gnuastro-internal/README | 9 +
lib/{ => gnuastro-internal}/arithmetic-binary.h | 0
lib/{ => gnuastro-internal}/arithmetic-onlyint.h | 0
lib/{ => gnuastro-internal}/checkset.h | 2 +-
lib/{ => gnuastro-internal}/commonopts.h | 0
lib/{ => gnuastro-internal}/fixedstringmacros.h | 0
lib/{ => gnuastro-internal}/options.h | 0
lib/{ => gnuastro-internal}/timing.h | 0
lib/gnuastro/binary.h | 6 +
lib/gnuastro/tile.h | 49 +++
lib/interpolate.c | 2 +-
lib/linkedlist.c | 2 +-
lib/options.c | 6 +-
lib/statistics.c | 2 +-
lib/table.c | 4 +-
lib/tile.c | 2 +-
lib/timing.c | 2 +-
lib/txt.c | 2 +-
tmpfs-config-make | 3 +-
84 files changed, 717 insertions(+), 323 deletions(-)
diff --git a/bin/arithmetic/arithmetic.c b/bin/arithmetic/arithmetic.c
index 182e039..44677fe 100644
--- a/bin/arithmetic/arithmetic.c
+++ b/bin/arithmetic/arithmetic.c
@@ -33,7 +33,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/array.h>
#include <gnuastro/arithmetic.h>
-#include <checkset.h>
+#include <gnuastro-internal/checkset.h>
#include "main.h"
diff --git a/bin/arithmetic/main.c b/bin/arithmetic/main.c
index b0eea01..5756181 100644
--- a/bin/arithmetic/main.c
+++ b/bin/arithmetic/main.c
@@ -25,7 +25,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <stdio.h>
#include <stdlib.h>
-#include <timing.h> /* Includes time.h and sys/time.h */
+#include <gnuastro-internal/timing.h>
#include "main.h"
diff --git a/bin/arithmetic/main.h b/bin/arithmetic/main.h
index 660ea80..df69d0c 100644
--- a/bin/arithmetic/main.h
+++ b/bin/arithmetic/main.h
@@ -26,7 +26,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/fits.h>
#include <gnuastro/linkedlist.h>
-#include <options.h>
+#include <gnuastro-internal/options.h>
/* Progarm name macros: */
diff --git a/bin/arithmetic/ui.c b/bin/arithmetic/ui.c
index 66711fa..f44ee51 100644
--- a/bin/arithmetic/ui.c
+++ b/bin/arithmetic/ui.c
@@ -31,10 +31,10 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/table.h>
#include <gnuastro/linkedlist.h>
-#include <timing.h>
-#include <options.h>
-#include <checkset.h>
-#include <fixedstringmacros.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/options.h>
+#include <gnuastro-internal/checkset.h>
+#include <gnuastro-internal/fixedstringmacros.h>
#include "main.h"
@@ -317,7 +317,7 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct
imgarithparams *p)
those headers which make them hard to read and modify. This also helps
in having a clean environment: everything in those headers is only
available within the scope of this function. */
-#include <commonopts.h>
+#include <gnuastro-internal/commonopts.h>
#include "args.h"
diff --git a/bin/convertt/convertt.c b/bin/convertt/convertt.c
index 285fe4e..f96a410 100644
--- a/bin/convertt/convertt.c
+++ b/bin/convertt/convertt.c
@@ -34,7 +34,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/txtarray.h>
#include <gnuastro/arithmetic.h>
-#include <timing.h>
+#include <gnuastro-internal/timing.h>
#include "main.h"
diff --git a/bin/convertt/eps.c b/bin/convertt/eps.c
index a4b2f61..6e75ea7 100644
--- a/bin/convertt/eps.c
+++ b/bin/convertt/eps.c
@@ -28,8 +28,8 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <stdlib.h>
#include <string.h>
-#include <timing.h>
-#include <checkset.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/checkset.h>
#include "main.h"
diff --git a/bin/convertt/main.c b/bin/convertt/main.c
index 443680b..2d1f9b8 100644
--- a/bin/convertt/main.c
+++ b/bin/convertt/main.c
@@ -25,7 +25,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <stdio.h>
#include <stdlib.h>
-#include <timing.h> /* Includes time.h and sys/time.h */
+#include <gnuastro-internal/timing.h>
#include "main.h"
diff --git a/bin/convertt/main.h b/bin/convertt/main.h
index 37d0c78..ea48dc7 100644
--- a/bin/convertt/main.h
+++ b/bin/convertt/main.h
@@ -26,7 +26,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
/* Include necessary headers */
#include <gnuastro/data.h>
-#include <options.h>
+#include <gnuastro-internal/options.h>
/* Progarm names. */
#define PROGRAM_NAME "ConvertType" /* Program full name. */
diff --git a/bin/convertt/ui.c b/bin/convertt/ui.c
index d6977aa..f32372b 100644
--- a/bin/convertt/ui.c
+++ b/bin/convertt/ui.c
@@ -34,10 +34,10 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/table.h>
#include <gnuastro/arithmetic.h>
-#include <timing.h>
-#include <options.h>
-#include <checkset.h>
-#include <fixedstringmacros.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/options.h>
+#include <gnuastro-internal/checkset.h>
+#include <gnuastro-internal/fixedstringmacros.h>
#include "main.h"
@@ -780,7 +780,7 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct
converttparams *p)
those headers which make them hard to read and modify. This also helps
in having a clean environment: everything in those headers is only
available within the scope of this function. */
-#include <commonopts.h>
+#include <gnuastro-internal/commonopts.h>
#include "args.h"
diff --git a/bin/convolve/convolve.c b/bin/convolve/convolve.c
index 7327598..4e993f4 100644
--- a/bin/convolve/convolve.c
+++ b/bin/convolve/convolve.c
@@ -36,7 +36,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/convolve.h>
#include <gnuastro/spatialconvolve.h>
-#include <timing.h>
+#include <gnuastro-internal/timing.h>
#include "main.h"
#include "convolve.h"
diff --git a/bin/convolve/main.c b/bin/convolve/main.c
index bdf018b..760746c 100644
--- a/bin/convolve/main.c
+++ b/bin/convolve/main.c
@@ -25,7 +25,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <stdio.h>
#include <stdlib.h>
-#include <timing.h> /* Includes time.h and sys/time.h */
+#include <gnuastro-internal/timing.h>
#include "main.h"
diff --git a/bin/convolve/main.h b/bin/convolve/main.h
index 03edab5..0e9d924 100644
--- a/bin/convolve/main.h
+++ b/bin/convolve/main.h
@@ -26,7 +26,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
/* Include necessary headers */
#include <gnuastro/data.h>
-#include <options.h>
+#include <gnuastro-internal/options.h>
/* Program names. */
#define PROGRAM_NAME "Convolve" /* Program full name. */
diff --git a/bin/convolve/ui.c b/bin/convolve/ui.c
index 052a0ee..582e33d 100644
--- a/bin/convolve/ui.c
+++ b/bin/convolve/ui.c
@@ -38,10 +38,10 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/statistics.h>
#include <gnuastro/linkedlist.h>
-#include <timing.h>
-#include <options.h>
-#include <checkset.h>
-#include <fixedstringmacros.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/options.h>
+#include <gnuastro-internal/checkset.h>
+#include <gnuastro-internal/fixedstringmacros.h>
#include "main.h"
@@ -495,7 +495,7 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct
convolveparams *p)
those headers which make them hard to read and modify. This also helps
in having a clean environment: everything in those headers is only
available within the scope of this function. */
-#include <commonopts.h>
+#include <gnuastro-internal/commonopts.h>
#include "args.h"
diff --git a/bin/cosmiccal/main.c b/bin/cosmiccal/main.c
index d4906ad..cc38b55 100644
--- a/bin/cosmiccal/main.c
+++ b/bin/cosmiccal/main.c
@@ -25,7 +25,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <stdio.h>
#include <stdlib.h>
-#include <timing.h> /* Includes time.h and sys/time.h */
+#include <gnuastro-internal/timing.h>
#include "main.h"
diff --git a/bin/cosmiccal/main.h b/bin/cosmiccal/main.h
index acdae15..248b348 100644
--- a/bin/cosmiccal/main.h
+++ b/bin/cosmiccal/main.h
@@ -26,7 +26,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
/* Include necessary headers */
#include <gnuastro/data.h>
-#include <options.h>
+#include <gnuastro-internal/options.h>
/* Progarm names. */
#define PROGRAM_NAME "CosmicCalculator" /* Program full name. */
diff --git a/bin/cosmiccal/ui.c b/bin/cosmiccal/ui.c
index 9521537..a212914 100644
--- a/bin/cosmiccal/ui.c
+++ b/bin/cosmiccal/ui.c
@@ -33,10 +33,10 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/table.h>
#include <gnuastro/linkedlist.h>
-#include <timing.h>
-#include <options.h>
-#include <checkset.h>
-#include <fixedstringmacros.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/options.h>
+#include <gnuastro-internal/checkset.h>
+#include <gnuastro-internal/fixedstringmacros.h>
#include "main.h"
@@ -247,7 +247,7 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct
cosmiccalparams *p)
those headers which make them hard to read and modify. This also helps
in having a clean environment: everything in those headers is only
available within the scope of this function. */
-#include <commonopts.h>
+#include <gnuastro-internal/commonopts.h>
#include "args.h"
diff --git a/bin/crop/crop.c b/bin/crop/crop.c
index 2de990d..433c119 100644
--- a/bin/crop/crop.c
+++ b/bin/crop/crop.c
@@ -32,8 +32,8 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/fits.h>
#include <gnuastro/threads.h>
-#include <timing.h>
-#include <checkset.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/checkset.h>
#include "main.h"
diff --git a/bin/crop/main.c b/bin/crop/main.c
index bf2a589..c929774 100644
--- a/bin/crop/main.c
+++ b/bin/crop/main.c
@@ -25,7 +25,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <stdio.h>
#include <stdlib.h>
-#include <timing.h> /* Includes time.h and sys/time.h */
+#include <gnuastro-internal/timing.h>
#include "main.h"
diff --git a/bin/crop/main.h b/bin/crop/main.h
index 77828b5..c53b3ec 100644
--- a/bin/crop/main.h
+++ b/bin/crop/main.h
@@ -26,7 +26,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
/* Include necessary headers */
#include <gnuastro/data.h>
-#include <options.h>
+#include <gnuastro-internal/options.h>
/* Progarm names. */
#define PROGRAM_NAME "Crop" /* Program full name. */
diff --git a/bin/crop/onecrop.c b/bin/crop/onecrop.c
index a09b52e..cd97e7b 100644
--- a/bin/crop/onecrop.c
+++ b/bin/crop/onecrop.c
@@ -36,8 +36,8 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/blank.h>
#include <gnuastro/polygon.h>
-#include <timing.h>
-#include <checkset.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/checkset.h>
#include "main.h"
diff --git a/bin/crop/ui.c b/bin/crop/ui.c
index f988f7a..85c17c6 100644
--- a/bin/crop/ui.c
+++ b/bin/crop/ui.c
@@ -34,10 +34,10 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/table.h>
#include <gnuastro/linkedlist.h>
-#include <timing.h>
-#include <options.h>
-#include <checkset.h>
-#include <fixedstringmacros.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/options.h>
+#include <gnuastro-internal/checkset.h>
+#include <gnuastro-internal/fixedstringmacros.h>
#include "main.h"
@@ -771,7 +771,7 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct
cropparams *p)
those headers which make them hard to read and modify. This also helps
in having a clean environment: everything in those headers is only
available within the scope of this function. */
-#include <commonopts.h>
+#include <gnuastro-internal/commonopts.h>
#include "args.h"
diff --git a/bin/fits/fits.c b/bin/fits/fits.c
index 2a70ed6..773c467 100644
--- a/bin/fits/fits.c
+++ b/bin/fits/fits.c
@@ -29,8 +29,8 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/fits.h>
#include <gnuastro/blank.h>
-#include "timing.h"
-#include "checkset.h"
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/checkset.h>
#include "main.h"
diff --git a/bin/fits/keywords.c b/bin/fits/keywords.c
index bfdaffe..d97c985 100644
--- a/bin/fits/keywords.c
+++ b/bin/fits/keywords.c
@@ -31,7 +31,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/fits.h>
#include <gnuastro/linkedlist.h>
-#include "checkset.h"
+#include <gnuastro-internal/checkset.h>
#include "main.h"
diff --git a/bin/fits/main.c b/bin/fits/main.c
index 4f3eefb..d19b6da 100644
--- a/bin/fits/main.c
+++ b/bin/fits/main.c
@@ -25,7 +25,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <stdio.h>
#include <stdlib.h>
-#include <timing.h> /* Includes time.h and sys/time.h */
+#include <gnuastro-internal/timing.h>
#include "main.h"
diff --git a/bin/fits/main.h b/bin/fits/main.h
index 142ab00..13f1405 100644
--- a/bin/fits/main.h
+++ b/bin/fits/main.h
@@ -25,7 +25,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/fits.h>
-#include <options.h>
+#include <gnuastro-internal/options.h>
/* Progarm name macros: */
#define PROGRAM_NAME "Fits" /* Program full name. */
diff --git a/bin/fits/ui.c b/bin/fits/ui.c
index f83c8f9..4359455 100644
--- a/bin/fits/ui.c
+++ b/bin/fits/ui.c
@@ -31,9 +31,9 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/fits.h>
#include <gnuastro/linkedlist.h>
-#include <options.h>
-#include <checkset.h>
-#include <fixedstringmacros.h>
+#include <gnuastro-internal/options.h>
+#include <gnuastro-internal/checkset.h>
+#include <gnuastro-internal/fixedstringmacros.h>
#include "main.h"
@@ -471,7 +471,7 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct
fitsparams *p)
those headers which make them hard to read and modify. This also helps
in having a clean environment: everything in those headers is only
available within the scope of this function. */
-#include <commonopts.h>
+#include <gnuastro-internal/commonopts.h>
#include "args.h"
diff --git a/bin/mknoise/main.c b/bin/mknoise/main.c
index 12e9c73..dd2c311 100644
--- a/bin/mknoise/main.c
+++ b/bin/mknoise/main.c
@@ -25,7 +25,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <stdio.h>
#include <stdlib.h>
-#include <timing.h> /* Includes time.h and sys/time.h */
+#include <gnuastro-internal/timing.h>
#include "main.h"
diff --git a/bin/mknoise/main.h b/bin/mknoise/main.h
index a09c350..d143cdd 100644
--- a/bin/mknoise/main.h
+++ b/bin/mknoise/main.h
@@ -27,7 +27,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/data.h>
#include <gsl/gsl_rng.h>
-#include <options.h>
+#include <gnuastro-internal/options.h>
/* Progarm names. */
#define PROGRAM_NAME "MakeNoise" /* Program full name. */
diff --git a/bin/mknoise/mknoise.c b/bin/mknoise/mknoise.c
index 873cca6..78d9bb5 100644
--- a/bin/mknoise/mknoise.c
+++ b/bin/mknoise/mknoise.c
@@ -34,7 +34,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/fits.h>
#include <gsl/gsl_randist.h> /* To make noise. */
-#include <timing.h>
+#include <gnuastro-internal/timing.h>
#include "main.h"
diff --git a/bin/mknoise/ui.c b/bin/mknoise/ui.c
index c9b283a..f2a6134 100644
--- a/bin/mknoise/ui.c
+++ b/bin/mknoise/ui.c
@@ -32,10 +32,10 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/table.h>
#include <gnuastro/linkedlist.h>
-#include <timing.h>
-#include <options.h>
-#include <checkset.h>
-#include <fixedstringmacros.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/options.h>
+#include <gnuastro-internal/checkset.h>
+#include <gnuastro-internal/fixedstringmacros.h>
#include "main.h"
@@ -334,7 +334,7 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct
mknoiseparams *p)
those headers which make them hard to read and modify. This also helps
in having a clean environment: everything in those headers is only
available within the scope of this function. */
-#include <commonopts.h>
+#include <gnuastro-internal/commonopts.h>
#include "args.h"
diff --git a/bin/mkprof/main.c b/bin/mkprof/main.c
index e47f538..9927864 100644
--- a/bin/mkprof/main.c
+++ b/bin/mkprof/main.c
@@ -25,7 +25,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <stdio.h>
#include <stdlib.h>
-#include <timing.h> /* Includes time.h and sys/time.h */
+#include <gnuastro-internal/timing.h>
#include "main.h"
#include "mkprof.h"
diff --git a/bin/mkprof/main.h b/bin/mkprof/main.h
index eac8c1d..74f62cf 100644
--- a/bin/mkprof/main.h
+++ b/bin/mkprof/main.h
@@ -28,7 +28,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/fits.h>
-#include <options.h>
+#include <gnuastro-internal/options.h>
/* Progarm name macros: */
diff --git a/bin/mkprof/mkprof.c b/bin/mkprof/mkprof.c
index fe4e961..2bebb33 100644
--- a/bin/mkprof/mkprof.c
+++ b/bin/mkprof/mkprof.c
@@ -37,8 +37,8 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/txtarray.h>
#include <gnuastro/statistics.h>
-#include <timing.h>
-#include <checkset.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/checkset.h>
#include "main.h"
diff --git a/bin/mkprof/oneprofile.c b/bin/mkprof/oneprofile.c
index aa2101c..9941f92 100644
--- a/bin/mkprof/oneprofile.c
+++ b/bin/mkprof/oneprofile.c
@@ -39,7 +39,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/statistics.h>
#include <gnuastro/linkedlist.h>
-#include <timing.h>
+#include <gnuastro-internal/timing.h>
#include "main.h"
diff --git a/bin/mkprof/ui.c b/bin/mkprof/ui.c
index 57bc439..0b352d7 100644
--- a/bin/mkprof/ui.c
+++ b/bin/mkprof/ui.c
@@ -35,10 +35,10 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/table.h>
#include <gnuastro/linkedlist.h>
-#include <timing.h>
-#include <options.h>
-#include <checkset.h>
-#include <fixedstringmacros.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/options.h>
+#include <gnuastro-internal/checkset.h>
+#include <gnuastro-internal/fixedstringmacros.h>
#include "main.h"
@@ -941,7 +941,7 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct
mkprofparams *p)
those headers which make them hard to read and modify. This also helps
in having a clean environment: everything in those headers is only
available within the scope of this function. */
-#include <commonopts.h>
+#include <gnuastro-internal/commonopts.h>
#include "args.h"
diff --git a/bin/noisechisel/detection.c b/bin/noisechisel/detection.c
index 404cd3b..827d30e 100644
--- a/bin/noisechisel/detection.c
+++ b/bin/noisechisel/detection.c
@@ -28,7 +28,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/fits.h>
#include <gnuastro/binary.h>
-#include <timing.h>
+#include <gnuastro-internal/timing.h>
#include "main.h"
@@ -50,7 +50,6 @@ detection_initial(struct noisechiselparams *p)
struct timeval t0, t1;
-
/* Get the starting time. */
if(!p->cp.quiet)
{
@@ -59,7 +58,6 @@ detection_initial(struct noisechiselparams *p)
}
-
/* Find and apply the threshold on the input. */
threshold_quantile_find_apply(p);
if(p->detectionname)
@@ -70,7 +68,6 @@ detection_initial(struct noisechiselparams *p)
}
-
/* Erode the image. */
if(!p->cp.quiet) gettimeofday(&t1, NULL);
gal_binary_erode(p->binary, p->erode, p->erodengb, 1);
@@ -88,12 +85,10 @@ detection_initial(struct noisechiselparams *p)
}
-
/* Correct the no-erode values. */
bf=(b=p->binary->array)+p->binary->size; do *b = *b>0; while(++b<bf);
-
/* Do the opening. */
if(!p->cp.quiet) gettimeofday(&t1, NULL);
gal_binary_open(p->binary, p->opening, p->openingngb, 1);
@@ -111,7 +106,6 @@ detection_initial(struct noisechiselparams *p)
}
-
/* Label the connected components. */
p->numobjects=gal_binary_connected_components(p->binary, &p->olabel, 1);
if(p->detectionname)
@@ -122,7 +116,6 @@ detection_initial(struct noisechiselparams *p)
}
-
/* Report the ending of initial detection. */
if(!p->cp.quiet)
{
@@ -130,7 +123,125 @@ detection_initial(struct noisechiselparams *p)
gal_timing_report(&t0, msg, 1);
free(msg);
}
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+/****************************************************************
+ ************ Pseudo detection S/N threshold ************
+ ****************************************************************/
+/* We have the thresholded image (with blank values for regions that should
+ not be used). Find the pseudo-detections in those regions. */
+void
+detection_find_pseudos(struct noisechiselparams *p, gal_data_t workbin)
+{
+
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+/****************************************************************
+ ************ Removing false detections ************
+ ****************************************************************/
+/* */
+static void
+detection_keep_sky_or_det(struct noisechiselparams *p, uint8_t *w, int s0d1)
+{
+ uint32_t *l=p->olabel->array;
+ uint8_t *b=p->binary->array, *bf=b+p->binary->size;
+
+ if(s0d1)
+ /* Set all sky regions (label equal to zero) to blank. */
+ do *w++ = *l++ ? *b : GAL_BLANK_UINT8; while(++b<bf);
+ else
+ /* Set all detected pixels (label larger than zero) to blank. */
+ do *w++ = *l++ ? GAL_BLANK_UINT8 : *b; while(++b<bf);
+}
+
+
+
+
+
+/* The initial detection has been done, now we want to remove false
+ detections. */
+void
+detection_remove_false(struct noisechiselparams *p)
+{
+ char *msg;
+ struct timeval t1;
+ gal_data_t *workbin;
+
+ /* Find the Sky and its Standard Deviation from the initial detectios. */
+ if(!p->cp.quiet) gettimeofday(&t1, NULL);
+ threshold_sky_and_std(p);
+ if(!p->cp.quiet)
+ gal_timing_report(&t1, "Initial (crude) Sky and its STD found.", 2);
+
+
+ /* Apply the sky threshold. */
+ if(!p->cp.quiet) gettimeofday(&t1, NULL);
+ threshold_apply(p, p->sky->array, p->std->array, THRESHOLD_SKY_STD);
+ if(!p->cp.quiet)
+ {
+ asprintf(&msg, "Pseudo-detection thresh (%.3f sigma) applied.",
+ p->dthresh);
+ gal_timing_report(&t1, msg, 2);
+ free(msg);
+ }
+
+
+ /* Allocate the space for the pseudo-detection threshold. */
+ workbin=gal_data_alloc(NULL, GAL_TYPE_UINT8, p->input->ndim,
+ p->input->dsize, p->input->wcs, 0, p->cp.minmapsize,
+ NULL, NULL, NULL);
+
+
+ /* Set all the initial detected pixels to blank values. */
+ detection_keep_sky_or_det(p, workbin->array, 0);
+ if(p->detectionname)
+ {
+ workbin->name="DTHRESH-ON-SKY";
+ gal_fits_img_write(workbin, p->detectionname, NULL, PROGRAM_STRING);
+ workbin->name=NULL;
+ }
+
+ /* Clean up. */
+ gal_data_free(workbin);
/* If the user wanted to check the threshold and hasn't called
diff --git a/bin/noisechisel/detection.h b/bin/noisechisel/detection.h
index 1923622..b785f9f 100644
--- a/bin/noisechisel/detection.h
+++ b/bin/noisechisel/detection.h
@@ -26,4 +26,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
void
detection_initial(struct noisechiselparams *p);
+void
+detection_remove_false(struct noisechiselparams *p);
+
#endif
diff --git a/bin/noisechisel/main.c b/bin/noisechisel/main.c
index d7eb2d5..53565a4 100644
--- a/bin/noisechisel/main.c
+++ b/bin/noisechisel/main.c
@@ -25,7 +25,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <stdio.h>
#include <stdlib.h>
-#include <timing.h> /* Includes time.h and sys/time.h */
+#include <gnuastro-internal/timing.h>
#include "main.h"
diff --git a/bin/noisechisel/main.h b/bin/noisechisel/main.h
index aa9c388..5bf608c 100644
--- a/bin/noisechisel/main.h
+++ b/bin/noisechisel/main.h
@@ -26,7 +26,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
/* Include necessary headers */
#include <gnuastro/data.h>
-#include <options.h>
+#include <gnuastro-internal/options.h>
/* Progarm names. */
#define PROGRAM_NAME "NoiseChisel" /* Program full name. */
@@ -97,6 +97,8 @@ struct noisechiselparams
gal_data_t *conv; /* Convolved input. */
gal_data_t *binary; /* For binary operations. */
gal_data_t *olabel; /* Labels of objects in the detection. */
+ gal_data_t *sky; /* Mean of undetected pixels, per tile. */
+ gal_data_t *std; /* STD of undetected pixels, per tile. */
time_t rawtime; /* Starting time of the program. */
size_t numobjects; /* Number of objects detected. */
diff --git a/bin/noisechisel/noisechisel.c b/bin/noisechisel/noisechisel.c
index d25fab8..39ec6ec 100644
--- a/bin/noisechisel/noisechisel.c
+++ b/bin/noisechisel/noisechisel.c
@@ -28,7 +28,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/fits.h>
#include <gnuastro/convolve.h>
-#include <timing.h>
+#include <gnuastro-internal/timing.h>
#include "main.h"
@@ -67,4 +67,7 @@ noisechisel(struct noisechiselparams *p)
/* Do the initial detection: */
detection_initial(p);
+
+ /* Remove false detections */
+ detection_remove_false(p);
}
diff --git a/bin/noisechisel/threshold.c b/bin/noisechisel/threshold.c
index 2a58e08..8b97bfa 100644
--- a/bin/noisechisel/threshold.c
+++ b/bin/noisechisel/threshold.c
@@ -34,7 +34,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/statistics.h>
#include <gnuastro/interpolate.h>
-#include <timing.h>
+#include <gnuastro-internal/timing.h>
#include "main.h"
@@ -44,6 +44,184 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
+
+
+
+
+
+
+/**********************************************************************/
+/*************** Apply a given threshold. *****************/
+/**********************************************************************/
+void
+threshold_apply(struct noisechiselparams *p, float *value1, float *value2,
+ int type)
+{
+ size_t tid;
+ void *tarray=NULL;
+ gal_data_t *tile, *tblock=NULL;
+
+ /* Clear the binary array (this is mainly because the input may contain
+ blank values and we won't be doing the thresholding no those
+ pixels. */
+ memset(p->binary->array, 0, p->binary->size);
+
+ /* Go over all the tiles. */
+ for(tid=0; tid<p->cp.tl.tottiles; ++tid)
+ {
+ /* For easy reading. */
+ tile=&p->cp.tl.tiles[tid];
+
+ switch(type)
+ {
+
+ /* This is a quantile threshold. */
+ case THRESHOLD_QUANTILES:
+ /* Correct the tile's pointers to apply the threshold on the
+ convolved image. */
+ if(p->conv)
+ {
+ tarray=tile->array; tblock=tile->block;
+ tile->array=gal_tile_block_relative_to_other(tile, p->conv);
+ tile->block=p->conv;
+ }
+
+ /* Apply the threshold. */
+ GAL_TILE_PARSE_OPERATE({
+ *o = ( *i > value1[tid]
+ ? ( *i > value2[tid] ? THRESHOLD_NO_ERODE_VALUE : 1 )
+ : 0 );
+ }, tile, p->binary, 1, 1);
+
+ /* Revert the tile's pointers back to what they were. */
+ if(p->conv) { tile->array=tarray; tile->block=tblock; }
+ break;
+
+
+ /* This is a Sky and Sky STD threshold. */
+ case THRESHOLD_SKY_STD:
+
+ /* The threshold is always low. So for the majority of non-NaN
+ pixels in the image, the condition above will be true. If we
+ come over a NaN pixel, then by definition of NaN, all
+ conditionals will fail.
+
+ If an image doesn't have any NaN pixels, only the pixels below
+ the threshold have to be checked for a NaN which are by
+ definition a very small fraction of the total pixels. And if
+ there are NaN pixels in the image. */
+ GAL_TILE_PARSE_OPERATE({
+ *o = ( ( *i - value1[tid] > p->dthresh * value2[tid] )
+ ? 1 : *i==*i ? 0 : GAL_BLANK_UINT8 );
+ }, tile, p->binary, 1, 1);
+ break;
+
+
+ default:
+ error(EXIT_FAILURE, 0, "a bug! please contact us at %s so we can "
+ "address the problem. For some reason a value of %d had "
+ "been given to `type' in `threshold_apply'",
+ PACKAGE_BUGREPORT, type);
+ }
+ }
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+/**********************************************************************/
+/*************** Interpolation and smoothing *****************/
+/**********************************************************************/
+/* Interpolate and smooth the values for each tile over the whole image. */
+static void
+threshold_interp_smooth(struct noisechiselparams *p, gal_data_t **first,
+ gal_data_t **second, char *filename)
+{
+ gal_data_t *tmp;
+ struct gal_options_common_params *cp=&p->cp;
+ struct gal_tile_two_layer_params *tl=&cp->tl;
+
+ /* A small sanity check. */
+ if( (*first)->next )
+ error(EXIT_FAILURE, 0, "the `first' argument to "
+ "`threshold_interp_smooth' must not have any `next' pointer.");
+
+
+ /* Do the interpolation of both arrays. */
+ (*first)->next = *second;
+ tmp=gal_interpolate_close_neighbors(*first, tl, cp->interpnumngb,
+ cp->numthreads, cp->interponlyblank, 1);
+ gal_data_free(*first);
+ gal_data_free(*second);
+ *first=tmp;
+ *second=tmp->next;
+ (*first)->next=(*second)->next=NULL;
+ if(filename)
+ {
+ gal_tile_full_values_write(*first, tl, filename, PROGRAM_STRING);
+ gal_tile_full_values_write(*second, tl, filename, PROGRAM_STRING);
+ }
+
+
+ /* Smooth the threshold if requested. */
+ if(p->smoothwidth>1)
+ {
+ /* Smooth the first. */
+ tmp=gal_tile_full_values_smooth(*first, tl, p->smoothwidth,
+ p->cp.numthreads);
+ gal_data_free(*first);
+ *first=tmp;
+
+ /* Smooth the second */
+ tmp=gal_tile_full_values_smooth(*second, tl, p->smoothwidth,
+ p->cp.numthreads);
+ gal_data_free(*second);
+ *second=tmp;
+
+ /* Add them to the check image. */
+ if(filename)
+ {
+ gal_tile_full_values_write(*first, tl, filename, PROGRAM_STRING);
+ gal_tile_full_values_write(*second, tl, filename, PROGRAM_STRING);
+ }
+ }
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
/****************************************************************
************ Quantile threshold ************
****************************************************************/
@@ -89,16 +267,14 @@ qthresh_on_tile(void *in_prm)
memcpy(usage->dsize, p->maxtsize, ndim*sizeof *p->maxtsize);
- /* Copy the tile's contents into the pre-allocated space. Note that
- we have to initialize the `dsize' and `size' elements of
- `contents', since they can be changed and the size is
- important. Recall that this is a 1D array. */
+ /* For easy reading. */
tind = tprm->indexs[i];
tile = &p->cp.tl.tiles[tind];
/* If we have a convolved image, temporarily change the tile's
- pointers so we can do the work on the convolved image. */
+ pointers so we can do the work on the convolved image, then copy
+ the desired contents into the already allocated `usage' array. */
if(p->conv)
{
tarray=tile->array; tblock=tile->block;
@@ -130,7 +306,7 @@ qthresh_on_tile(void *in_prm)
gal_data_free(qvalue);
/* Do the same for the no-erode quantile. */
- qvalue=gal_statistics_quantile(tile, p->noerodequant, 1);
+ qvalue=gal_statistics_quantile(usage, p->noerodequant, 1);
memcpy(gal_data_ptr_increment(qprm->noerode_th->array, tind, type),
qvalue->array, twidth);
gal_data_free(qvalue);
@@ -158,61 +334,10 @@ qthresh_on_tile(void *in_prm)
-static void
-apply_quantile_threshold(struct qthreshparams *qprm)
-{
- size_t tid;
- void *tarray=NULL;
- gal_data_t *tile, *tblock=NULL;
- struct noisechiselparams *p=qprm->p;
- float *erode_th=qprm->erode_th->array, *noerode_th=qprm->noerode_th->array;
-
- /* A small sanity check. */
- if(qprm->erode_th->type!=GAL_TYPE_FLOAT32)
- error(EXIT_FAILURE, 0, "`apply_quantile_threshold' currently only "
- "supports float arrays.");
-
- /* Clear the binary array (this is mainly because the input may contain
- blank values and we won't be doing the thresholding no those
- pixels. */
- memset(p->binary->array, 0, p->binary->size);
-
- /* Go over all the tiles. */
- for(tid=0; tid<p->cp.tl.tottiles;++tid)
- {
- /* For easy reading. */
- tile=&p->cp.tl.tiles[tid];
-
- /* Correct the tile's pointers to apply the threshold on the
- convolved image. */
- if(p->conv)
- {
- tarray=tile->array; tblock=tile->block;
- tile->array=gal_tile_block_relative_to_other(tile, p->conv);
- tile->block=p->conv;
- }
-
- /* Apply the threshold. */
- GAL_TILE_PARSE_OPERATE({
- *o = ( *i > erode_th[tid]
- ? ( *i > noerode_th[tid] ? THRESHOLD_NO_ERODE_VALUE : 1 )
- : 0 );
- }, tile, p->binary, 1, 1);
-
- /* Revert the tile's pointers back to what they were. */
- if(p->conv) { tile->array=tarray; tile->block=tblock; }
- }
-}
-
-
-
-
-
void
threshold_quantile_find_apply(struct noisechiselparams *p)
{
char *msg;
- gal_data_t *tmp;
struct timeval t1;
struct qthreshparams qprm;
struct gal_options_common_params *cp=&p->cp;
@@ -258,53 +383,14 @@ threshold_quantile_find_apply(struct noisechiselparams *p)
free(qprm.usage);
- /* Interpolate over the blank tiles. */
- qprm.erode_th->next = qprm.noerode_th;
- tmp=gal_interpolate_close_neighbors(qprm.erode_th, tl, cp->interpnumngb,
- cp->numthreads, cp->interponlyblank, 1);
- gal_data_free(qprm.erode_th);
- gal_data_free(qprm.noerode_th);
- qprm.erode_th=tmp;
- qprm.noerode_th=tmp->next;
- qprm.erode_th->next=qprm.noerode_th->next=NULL;
- if(p->qthreshname)
- {
- gal_tile_full_values_write(qprm.erode_th, tl, p->qthreshname,
- PROGRAM_STRING);
- gal_tile_full_values_write(qprm.noerode_th, tl, p->qthreshname,
- PROGRAM_STRING);
- }
-
-
- /* Smooth the threshold if requested. */
- if(p->smoothwidth>1)
- {
- /* Do the smoothing on the erosion quantile. */
- if(!cp->quiet) gettimeofday(&t1, NULL);
- tmp=gal_tile_full_values_smooth(qprm.erode_th, tl, p->smoothwidth,
- p->cp.numthreads);
- gal_data_free(qprm.erode_th);
- qprm.erode_th=tmp;
-
- /* Same for the no-erosion quantile. */
- tmp=gal_tile_full_values_smooth(qprm.noerode_th, tl, p->smoothwidth,
- p->cp.numthreads);
- gal_data_free(qprm.noerode_th);
- qprm.noerode_th=tmp;
-
- /* Add them to the check image. */
- if(p->qthreshname)
- {
- gal_tile_full_values_write(qprm.erode_th, tl, p->qthreshname,
- PROGRAM_STRING);
- gal_tile_full_values_write(qprm.noerode_th, tl, p->qthreshname,
- PROGRAM_STRING);
- }
- }
+ /* Interpolate and smooth the derived values. */
+ threshold_interp_smooth(p, &qprm.erode_th, &qprm.noerode_th,
+ p->qthreshname);
- /* The quantile threshold is found, now apply it. */
- apply_quantile_threshold(&qprm);
+ /* We now have a threshold for all tiles, apply it. */
+ threshold_apply(p, qprm.erode_th->array, qprm.noerode_th->array,
+ THRESHOLD_QUANTILES);
/* Write the binary image if check is requested. */
@@ -317,8 +403,8 @@ threshold_quantile_find_apply(struct noisechiselparams *p)
gal_data_free(qprm.noerode_th);
if(!p->cp.quiet)
{
- asprintf(&msg, "%.2f quantile threshold found and applied.",
- p->qthresh);
+ asprintf(&msg, "%.2f & %0.2f quantile thresholds applied.",
+ p->qthresh, p->noerodequant);
gal_timing_report(&t1, msg, 2);
}
@@ -328,3 +414,152 @@ threshold_quantile_find_apply(struct noisechiselparams *p)
if(p->qthreshname && !p->continueaftercheck)
ui_abort_after_check(p, p->qthreshname, "quantile threshold check");
}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+/****************************************************************
+ ************ Mean and STD of undetected ************
+ ****************************************************************/
+static void *
+threshold_mean_std_undetected(void *in_prm)
+{
+ struct gal_threads_params *tprm=(struct gal_threads_params *)in_prm;
+ struct noisechiselparams *p=(struct noisechiselparams *)tprm->params;
+
+ double *darr, s, s2;
+ int type=p->sky->type;
+ size_t i, tind, numsky, dsize=2;
+ gal_data_t *tile, *meanstd_d, *meanstd, *bintile;
+
+
+ /* A dataset to keep the mean and STD in double type. */
+ meanstd_d=gal_data_alloc(NULL, GAL_TYPE_FLOAT64, 1, &dsize,
+ NULL, 0, -1, NULL, NULL, NULL);
+ darr=meanstd_d->array;
+
+
+ /* An empty dataset to replicate a tile on the binary array. */
+ bintile=gal_data_alloc(NULL, GAL_TYPE_UINT8, 1, &dsize,
+ NULL, 0, -1, NULL, NULL, NULL);
+ free(bintile->array);
+ free(bintile->dsize);
+ bintile->block=p->binary;
+ bintile->ndim=p->binary->ndim;
+
+
+ /* Go over all the tiles given to this thread. */
+ for(i=0; tprm->indexs[i] != GAL_THREADS_NON_THRD_INDEX; ++i)
+ {
+ /* Basic definitions */
+ numsky=0;
+ tind = tprm->indexs[i];
+ tile = &p->cp.tl.tiles[tind];
+
+ /* Correct the fake binary tile's properties to be the same as this
+ one, then count the number of zero valued elements in it. */
+ bintile->size=tile->size;
+ bintile->dsize=tile->dsize;
+ bintile->array=gal_tile_block_relative_to_other(tile, p->binary);
+ GAL_TILE_PARSE_OPERATE({if(!*i) numsky++;}, bintile, NULL, 0, 0);
+
+ /* Only continue, if the fraction of Sky values are less than the
+ requested fraction. */
+ if( (float)(numsky)/(float)(tile->size) > p->minbfrac)
+ {
+ /* Calculate the mean and STD over this tile. */
+ s=s2=0.0f;
+ GAL_TILE_PARSE_OPERATE({ if(!*o) {s += *i; s2 += *i * *i;} },
+ tile, bintile, 1, 1);
+ darr[0]=s/numsky;
+ darr[1]=sqrt( (s2-s*s/numsky)/numsky );
+
+ /* Convert the mean and std into the same type as the sky and std
+ arrays. */
+ meanstd=gal_data_copy_to_new_type(meanstd_d, type);
+
+ /* Copy the mean and STD to their respective places in the tile
+ arrays. */
+ memcpy(gal_data_ptr_increment(p->sky->array, tind, type),
+ meanstd->array, gal_type_sizeof(type));
+ memcpy(gal_data_ptr_increment(p->std->array, tind, type),
+ gal_data_ptr_increment(meanstd->array, 1, type),
+ gal_type_sizeof(type));
+ }
+ else
+ {
+ gal_blank_write(gal_data_ptr_increment(p->sky->array, tind, type),
+ type);
+ gal_blank_write(gal_data_ptr_increment(p->std->array, tind, type),
+ type);
+ }
+ }
+
+ /* Clean up and wait for other threads to finish and abort. */
+ bintile->array=NULL;
+ bintile->dsize=NULL;
+ gal_data_free(bintile);
+ gal_data_free(meanstd_d);
+ if(tprm->b) pthread_barrier_wait(tprm->b);
+ return NULL;
+}
+
+
+
+
+
+void
+threshold_sky_and_std(struct noisechiselparams *p)
+{
+ struct gal_options_common_params *cp=&p->cp;
+ struct gal_tile_two_layer_params *tl=&cp->tl;
+
+
+ /* When the check image has the same resolution as the input, write the
+ binary array as a reference to help in the comparison. */
+ if(p->detskyname && !tl->oneelempertile)
+ gal_fits_img_write(p->binary, p->detskyname, NULL, PROGRAM_STRING);
+
+
+ /* Allocate space for the mean and standard deviation. */
+ p->sky=gal_data_alloc(NULL, p->input->type, p->input->ndim, tl->numtiles,
+ NULL, 0, cp->minmapsize, "SKY", p->input->unit, NULL);
+ p->std=gal_data_alloc(NULL, p->input->type, p->input->ndim, tl->numtiles,
+ NULL, 0, cp->minmapsize, "STD", p->input->unit, NULL);
+
+
+ /* Find the Sky and its STD on proper tiles. */
+ gal_threads_spin_off(threshold_mean_std_undetected, p, tl->tottiles,
+ cp->numthreads);
+ if(p->detskyname)
+ {
+ gal_tile_full_values_write(p->sky, tl, p->detskyname, PROGRAM_STRING);
+ gal_tile_full_values_write(p->std, tl, p->detskyname, PROGRAM_STRING);
+ }
+
+
+ /* Interpolate and smooth the derived values. */
+ threshold_interp_smooth(p, &p->sky, &p->std, p->detskyname);
+
+
+ /* If a check was requested, abort NoiseChisel. */
+ if(p->detskyname && !p->continueaftercheck)
+ ui_abort_after_check(p, p->detskyname, "showing derivation of Sky value"
+ "and its standard deviation, or STD");
+}
diff --git a/bin/noisechisel/threshold.h b/bin/noisechisel/threshold.h
index 2ffaceb..9c9a1fb 100644
--- a/bin/noisechisel/threshold.h
+++ b/bin/noisechisel/threshold.h
@@ -25,7 +25,25 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#define THRESHOLD_NO_ERODE_VALUE 2
+
+enum threshold_type
+ {
+ THRESHOLD_QUANTILES,
+ THRESHOLD_SKY_STD,
+ };
+
+
void
threshold_quantile_find_apply(struct noisechiselparams *p);
+
+void
+threshold_sky_and_std(struct noisechiselparams *p);
+
+
+void
+threshold_apply(struct noisechiselparams *p, float *value1, float *value2,
+ int type);
+
+
#endif
diff --git a/bin/noisechisel/ui.c b/bin/noisechisel/ui.c
index 9f59689..7d8f413 100644
--- a/bin/noisechisel/ui.c
+++ b/bin/noisechisel/ui.c
@@ -33,10 +33,10 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/threads.h>
#include <gnuastro/dimension.h>
-#include <timing.h>
-#include <options.h>
-#include <checkset.h>
-#include <fixedstringmacros.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/options.h>
+#include <gnuastro-internal/checkset.h>
+#include <gnuastro-internal/fixedstringmacros.h>
#include "main.h"
@@ -523,7 +523,7 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct
noisechiselparams *p)
those headers which make them hard to read and modify. This also helps
in having a clean environment: everything in those headers is only
available within the scope of this function. */
-#include <commonopts.h>
+#include <gnuastro-internal/commonopts.h>
#include "args.h"
diff --git a/bin/statistics/main.c b/bin/statistics/main.c
index eb3df66..1bf4f9a 100644
--- a/bin/statistics/main.c
+++ b/bin/statistics/main.c
@@ -25,7 +25,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <stdio.h>
#include <stdlib.h>
-#include <timing.h>
+#include <gnuastro-internal/timing.h>
#include "main.h"
diff --git a/bin/statistics/main.h b/bin/statistics/main.h
index 057541b..8761a9b 100644
--- a/bin/statistics/main.h
+++ b/bin/statistics/main.h
@@ -26,7 +26,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
/* Include necessary headers */
#include <gnuastro/data.h>
-#include <options.h>
+#include <gnuastro-internal/options.h>
/* Progarm names. */
#define PROGRAM_NAME "Statistics" /* Program full name. */
diff --git a/bin/statistics/sky.c b/bin/statistics/sky.c
index 0eb54c8..f4baed7 100644
--- a/bin/statistics/sky.c
+++ b/bin/statistics/sky.c
@@ -37,8 +37,8 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/statistics.h>
#include <gnuastro/interpolate.h>
-#include <timing.h>
-#include <checkset.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/checkset.h>
#include "main.h"
diff --git a/bin/statistics/statistics.c b/bin/statistics/statistics.c
index f1d0d48..8022a44 100644
--- a/bin/statistics/statistics.c
+++ b/bin/statistics/statistics.c
@@ -39,8 +39,8 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/interpolate.h>
#include <gnuastro/permutation.h>
-#include <timing.h>
-#include <checkset.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/checkset.h>
#include "main.h"
diff --git a/bin/statistics/ui.c b/bin/statistics/ui.c
index 7813f23..ca8a6f0 100644
--- a/bin/statistics/ui.c
+++ b/bin/statistics/ui.c
@@ -38,10 +38,10 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/linkedlist.h>
#include <gnuastro/statistics.h>
-#include <timing.h>
-#include <options.h>
-#include <checkset.h>
-#include <fixedstringmacros.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/options.h>
+#include <gnuastro-internal/checkset.h>
+#include <gnuastro-internal/fixedstringmacros.h>
#include "main.h"
@@ -892,7 +892,7 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct
statisticsparams *p)
those headers which make them hard to read and modify. This also helps
in having a clean environment: everything in those headers is only
available within the scope of this function. */
-#include <commonopts.h>
+#include <gnuastro-internal/commonopts.h>
#include "args.h"
diff --git a/bin/table/main.c b/bin/table/main.c
index d896bbb..5c374ca 100644
--- a/bin/table/main.c
+++ b/bin/table/main.c
@@ -25,7 +25,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <stdio.h>
#include <stdlib.h>
-#include <timing.h> /* Includes time.h and sys/time.h */
+#include <gnuastro-internal/timing.h>
#include "main.h"
diff --git a/bin/table/main.h b/bin/table/main.h
index b46c09d..9bbbf42 100644
--- a/bin/table/main.h
+++ b/bin/table/main.h
@@ -26,7 +26,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
/* Include necessary headers */
#include <gnuastro/data.h>
-#include <options.h>
+#include <gnuastro-internal/options.h>
/* Progarm names. */
#define PROGRAM_NAME "Table" /* Program full name. */
diff --git a/bin/table/ui.c b/bin/table/ui.c
index e859934..00c2167 100644
--- a/bin/table/ui.c
+++ b/bin/table/ui.c
@@ -31,10 +31,10 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/table.h>
#include <gnuastro/linkedlist.h>
-#include <timing.h>
-#include <options.h>
-#include <checkset.h>
-#include <fixedstringmacros.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/options.h>
+#include <gnuastro-internal/checkset.h>
+#include <gnuastro-internal/fixedstringmacros.h>
#include "main.h"
@@ -375,7 +375,7 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct
tableparams *p)
those headers which make them hard to read and modify. This also helps
in having a clean environment: everything in those headers is only
available within the scope of this function. */
-#include <commonopts.h>
+#include <gnuastro-internal/commonopts.h>
#include "args.h"
diff --git a/bin/warp/main.c b/bin/warp/main.c
index c999657..ef9f260 100644
--- a/bin/warp/main.c
+++ b/bin/warp/main.c
@@ -25,7 +25,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <stdio.h>
#include <stdlib.h>
-#include <timing.h>
+#include <gnuastro-internal/timing.h>
#include "main.h"
diff --git a/bin/warp/main.h b/bin/warp/main.h
index ca224fd..2d8c75e 100644
--- a/bin/warp/main.h
+++ b/bin/warp/main.h
@@ -26,7 +26,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
/* Include necessary headers */
#include <gnuastro/data.h>
-#include <options.h>
+#include <gnuastro-internal/options.h>
/* Progarm names. */
#define PROGRAM_NAME "Warp" /* Program full name. */
diff --git a/bin/warp/ui.c b/bin/warp/ui.c
index eadef37..7904a88 100644
--- a/bin/warp/ui.c
+++ b/bin/warp/ui.c
@@ -34,10 +34,10 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/threads.h>
#include <gnuastro/linkedlist.h>
-#include <timing.h>
-#include <options.h>
-#include <checkset.h>
-#include <fixedstringmacros.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/options.h>
+#include <gnuastro-internal/checkset.h>
+#include <gnuastro-internal/fixedstringmacros.h>
#include "main.h"
@@ -906,7 +906,7 @@ ui_read_check_inputs_setup(int argc, char *argv[], struct
warpparams *p)
those headers which make them hard to read and modify. This also helps
in having a clean environment: everything in those headers is only
available within the scope of this function. */
-#include <commonopts.h>
+#include <gnuastro-internal/commonopts.h>
#include "args.h"
diff --git a/doc/Makefile.am b/doc/Makefile.am
index f764c77..90f54fb 100644
--- a/doc/Makefile.am
+++ b/doc/Makefile.am
@@ -144,7 +144,7 @@ endif
# it. Unfortunately as far as I know, pattern rules are not portable in all
# implementations of Make, so we have to list all the utilities manually.
toputildir=$(top_builddir)/bin
-ALLMANSDEP = $(top_srcdir)/lib/commonopts.h
+ALLMANSDEP = $(top_srcdir)/lib/gnuastro-internal/options.h
man/astarithmetic.1: $(top_srcdir)/bin/arithmetic/args.h $(ALLMANSDEP)
$(MAYBE_HELP2MAN) -n "arithmetic operations on images and numbers" \
--libtool $(toputildir)/arithmetic/astarithmetic
diff --git a/lib/Makefile.am b/lib/Makefile.am
index 222d6c6..93c5d0b 100644
--- a/lib/Makefile.am
+++ b/lib/Makefile.am
@@ -85,9 +85,12 @@ pkginclude_HEADERS = gnuastro/config.h
$(headersdir)/arithmetic.h \
# and if they are not explicitly mentioned somewhere in the Makefile, they
# will not distributed, so we need to explicitly tell Automake to
# distribute them here.
-EXTRA_DIST = $(headersdir)/README gnuastro.pc.in arithmetic-binary.h \
- arithmetic-onlyint.h arithmetic-other.h config.h.in checkset.h \
- fixedstringmacros.h options.h timing.h
+internaldir=$(top_srcdir)/lib/gnuastro-internal
+EXTRA_DIST = gnuastro.pc.in $(headersdir)/README \
+ $(internaldir)/arithmetic-binary.h $(internaldir)/arithmetic-onlyint.h \
+ $(internaldir)/arithmetic-other.h $(internaldir)/config.h.in \
+ $(internaldir)/checkset.h $(internaldir)/fixedstringmacros.h \
+ $(internaldir)/options.h $(internaldir)/timing.h
@@ -105,7 +108,7 @@ CLEANFILES = gnuastro.pc gnuastro/config.h
# Build `gnuastro/config.h' based on the information in the Makefile after
# the Makefile has been built.
-gnuastro/config.h: Makefile config.h.in
+gnuastro/config.h: Makefile $(internaldir)/config.h.in
rm -f $@ address@hidden
$(MKDIR_P) gnuastro
$(SED) -e 's|@address@hidden|$(VERSION)|g' \
@@ -123,7 +126,7 @@ gnuastro/config.h: Makefile config.h.in
-e 's|@address@hidden|$(HAVE_BIN_OP_FLOAT32)|g' \
-e 's|@address@hidden|$(HAVE_BIN_OP_FLOAT64)|g' \
-e 's|@address@hidden|$(SIZEOF_SIZE_T)|g' \
- $(srcdir)/config.h.in >> address@hidden
+ $(internaldir)/config.h.in >> address@hidden
chmod a-w address@hidden
mv address@hidden $@
diff --git a/lib/arithmetic-onlyint.c b/lib/arithmetic-onlyint.c
index 0437866..028385f 100644
--- a/lib/arithmetic-onlyint.c
+++ b/lib/arithmetic-onlyint.c
@@ -29,7 +29,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/arithmetic.h>
-#include <arithmetic-onlyint.h>
+#include <gnuastro-internal/arithmetic-onlyint.h>
diff --git a/lib/arithmetic.c b/lib/arithmetic.c
index 112076b..f1b92c6 100644
--- a/lib/arithmetic.c
+++ b/lib/arithmetic.c
@@ -33,8 +33,8 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/statistics.h>
#include <gnuastro/arithmetic.h>
-#include <arithmetic-binary.h>
-#include <arithmetic-onlyint.h>
+#include <gnuastro-internal/arithmetic-binary.h>
+#include <gnuastro-internal/arithmetic-onlyint.h>
diff --git a/lib/binary.c b/lib/binary.c
index 263e2ec..faac02f 100644
--- a/lib/binary.c
+++ b/lib/binary.c
@@ -439,3 +439,35 @@ gal_binary_connected_components(gal_data_t *binary,
gal_data_t **out,
free(dinc);
return curlab-1;
}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+/*********************************************************************/
+/***************** Fill holes ********************/
+/*********************************************************************/
+void
+gal_binary_fill_holes(gal_data_t *input)
+{
+ /* A small sanity check. */
+ if( input->type != GAL_TYPE_UINT8 )
+ error(EXIT_FAILURE, 0, "input to `gal_binary_fill_holes' must have "
+ "`uint8' type, but its input dataset has `%s' type",
+ gal_type_to_string(input->type, 1));
+}
diff --git a/lib/blank.c b/lib/blank.c
index b675ac9..ee6351a 100644
--- a/lib/blank.c
+++ b/lib/blank.c
@@ -32,7 +32,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/tile.h>
#include <gnuastro/blank.h>
-#include <checkset.h>
+#include <gnuastro-internal/checkset.h>
diff --git a/lib/checkset.c b/lib/checkset.c
index 8ceec6b..24de5aa 100644
--- a/lib/checkset.c
+++ b/lib/checkset.c
@@ -34,7 +34,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/data.h>
-#include "checkset.h"
+#include <gnuastro-internal/checkset.h>
diff --git a/lib/config.h.in b/lib/config.h.in
deleted file mode 100644
index 0a094c9..0000000
--- a/lib/config.h.in
+++ /dev/null
@@ -1,78 +0,0 @@
-/*********************************************************************
-Functions dealing with general aspects of all Gnuastro.
-
-Original author:
- Mohammad Akhlaghi <address@hidden>
-Contributing author(s):
-Copyright (C) 2016, Free Software Foundation, Inc.
-
-Gnuastro is free software: you can redistribute it and/or modify it
-under the terms of the GNU General Public License as published by the
-Free Software Foundation, either version 3 of the License, or (at your
-option) any later version.
-
-Gnuastro is distributed in the hope that it will be useful, but
-WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with Gnuastro. If not, see <http://www.gnu.org/licenses/>.
-**********************************************************************/
-#ifndef __GAL_CONFIG_H__
-#define __GAL_CONFIG_H__
-
-/* Include other headers if necessary here. Note that other header files
- must be included before the C++ preparations below */
-
-
-
-/* Configuration macros: */
-
-#define GAL_CONFIG_VERSION "@VERSION@"
-
-#define GAL_CONFIG_HAVE_LIBGIT2 @HAVE_LIBGIT2@
-
-#define GAL_CONFIG_HAVE_WCSLIB_VERSION @HAVE_WCSLIB_VERSION@
-
-#define GAL_CONFIG_HAVE_PTHREAD_BARRIER @HAVE_PTHREAD_BARRIER@
-
-#define GAL_CONFIG_BIN_OP_UINT8 @HAVE_BIN_OP_UINT8@
-#define GAL_CONFIG_BIN_OP_INT8 @HAVE_BIN_OP_INT8@
-#define GAL_CONFIG_BIN_OP_UINT16 @HAVE_BIN_OP_UINT16@
-#define GAL_CONFIG_BIN_OP_INT16 @HAVE_BIN_OP_INT16@
-#define GAL_CONFIG_BIN_OP_UINT32 @HAVE_BIN_OP_UINT32@
-#define GAL_CONFIG_BIN_OP_INT32 @HAVE_BIN_OP_INT32@
-#define GAL_CONFIG_BIN_OP_UINT64 @HAVE_BIN_OP_UINT64@
-#define GAL_CONFIG_BIN_OP_INT64 @HAVE_BIN_OP_INT64@
-#define GAL_CONFIG_BIN_OP_FLOAT32 @HAVE_BIN_OP_FLOAT32@
-#define GAL_CONFIG_BIN_OP_FLOAT64 @HAVE_BIN_OP_FLOAT64@
-
-#define GAL_CONFIG_SIZEOF_SIZE_T @SIZEOF_SIZE_T@
-
-
-/* C++ Preparations */
-#undef __BEGIN_C_DECLS
-#undef __END_C_DECLS
-#ifdef __cplusplus
-# define __BEGIN_C_DECLS extern "C" {
-# define __END_C_DECLS }
-#else
-# define __BEGIN_C_DECLS /* empty */
-# define __END_C_DECLS /* empty */
-#endif
-/* End of C++ preparations */
-
-
-
-/* Actual header contants (the above were for the Pre-processor). */
-__BEGIN_C_DECLS /* From C++ preparations */
-
-
-
-
-
-
-__END_C_DECLS /* From C++ preparations */
-
-#endif /* __GAL_CONFIG_H__ */
diff --git a/lib/convolve.c b/lib/convolve.c
index 8d53fc0..87e00f9 100644
--- a/lib/convolve.c
+++ b/lib/convolve.c
@@ -33,7 +33,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/convolve.h>
#include <gnuastro/dimension.h>
-#include <checkset.h>
+#include <gnuastro-internal/checkset.h>
diff --git a/lib/data.c b/lib/data.c
index 4553f9a..59831bf 100644
--- a/lib/data.c
+++ b/lib/data.c
@@ -40,7 +40,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/table.h>
#include <gnuastro/linkedlist.h>
-#include <checkset.h>
+#include <gnuastro-internal/checkset.h>
diff --git a/lib/fits.c b/lib/fits.c
index 3869a5b..a456b3f 100644
--- a/lib/fits.c
+++ b/lib/fits.c
@@ -39,8 +39,8 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/tile.h>
#include <gnuastro/blank.h>
-#include "checkset.h"
-#include "fixedstringmacros.h"
+#include <gnuastro-internal/checkset.h>
+#include <gnuastro-internal/fixedstringmacros.h>
diff --git a/lib/gnuastro-internal/README b/lib/gnuastro-internal/README
new file mode 100644
index 0000000..d9c87b9
--- /dev/null
+++ b/lib/gnuastro-internal/README
@@ -0,0 +1,9 @@
+GNU Astronomy Utilities internal header files
+---------------------------------------------
+
+The `.h' files in this directory are headers to Gnuastro's internal
+libraries: libraries that are only available to Gnuastro's programs. These
+are functions that are mainly to do with running a program, for example the
+common options to all the programs, functions to manage options and
+configuration files, timing and etc (the names are hopefully descriptive
+enough).
\ No newline at end of file
diff --git a/lib/arithmetic-binary.h b/lib/gnuastro-internal/arithmetic-binary.h
similarity index 100%
rename from lib/arithmetic-binary.h
rename to lib/gnuastro-internal/arithmetic-binary.h
diff --git a/lib/arithmetic-onlyint.h
b/lib/gnuastro-internal/arithmetic-onlyint.h
similarity index 100%
rename from lib/arithmetic-onlyint.h
rename to lib/gnuastro-internal/arithmetic-onlyint.h
diff --git a/lib/checkset.h b/lib/gnuastro-internal/checkset.h
similarity index 98%
rename from lib/checkset.h
rename to lib/gnuastro-internal/checkset.h
index ec45dfd..43a6ed6 100644
--- a/lib/checkset.h
+++ b/lib/gnuastro-internal/checkset.h
@@ -27,7 +27,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
must be included before the C++ preparations below */
#include <math.h>
#include <fitsio.h>
-#include <options.h>
+#include <gnuastro-internal/options.h>
/* C++ Preparations */
#undef __BEGIN_C_DECLS
diff --git a/lib/commonopts.h b/lib/gnuastro-internal/commonopts.h
similarity index 100%
rename from lib/commonopts.h
rename to lib/gnuastro-internal/commonopts.h
diff --git a/lib/fixedstringmacros.h b/lib/gnuastro-internal/fixedstringmacros.h
similarity index 100%
rename from lib/fixedstringmacros.h
rename to lib/gnuastro-internal/fixedstringmacros.h
diff --git a/lib/options.h b/lib/gnuastro-internal/options.h
similarity index 100%
rename from lib/options.h
rename to lib/gnuastro-internal/options.h
diff --git a/lib/timing.h b/lib/gnuastro-internal/timing.h
similarity index 100%
rename from lib/timing.h
rename to lib/gnuastro-internal/timing.h
diff --git a/lib/gnuastro/binary.h b/lib/gnuastro/binary.h
index f5e24d8..b06cb5e 100644
--- a/lib/gnuastro/binary.h
+++ b/lib/gnuastro/binary.h
@@ -93,6 +93,12 @@ gal_binary_connected_components(gal_data_t *binary,
gal_data_t **out,
+/*********************************************************************/
+/***************** Fill holes ********************/
+/*********************************************************************/
+void
+gal_binary_fill_holes(gal_data_t *input);
+
__END_C_DECLS /* From C++ preparations */
diff --git a/lib/gnuastro/tile.h b/lib/gnuastro/tile.h
index 1db7e26..9b5c829 100644
--- a/lib/gnuastro/tile.h
+++ b/lib/gnuastro/tile.h
@@ -300,6 +300,55 @@ gal_tile_full_free_contents(struct
gal_tile_two_layer_params *tl);
`b': blank value in input't type.
See `lib/statistics.c' for some example applications of this function.
+
+ -----------
+ TIPS/TRICKS
+ -----------
+
+ You can use a given tile on a dataset that it was not initialized with
+ (but has the same size). You can do that like this:
+
+ void *tarray;
+ gal_data_t *tblock;
+
+ tarray=tile->array;
+ tblock=tile->block;
+ tile->array=gal_tile_block_relative_to_other(tile, THE_OTHER_DATASET);
+ tile->block=THE_OTHER_DATASET; <<-- `tile->block' must corrected
+ AFTER `tile->array'.
+ GAL_TILE_PARSE_OPERATE(...)
+
+ tile->array=tarray;
+ tile->block=tblock;
+
+ You can work on one other array while working on the one that tile
+ actually points to. To do that, you can make a fake tile and pass that as
+ the `OUT' argument to this macro. While the name is `OUT' it can be used
+ in any manner you like. To do this, you can take the following steps. In
+ this example, `tile' is the actual tile that you have.
+
+ gal_data_t *faketile;
+
+ // These can be done outside a loop.
+ faketile=gal_data_alloc(NULL, OTHER_DATASET->type, 1, &dsize,
+ NULL, 0, -1, NULL, NULL, NULL);
+ free(faketile->array);
+ free(faketile->dsize);
+ faketile->block=OTHER_DATASET;
+ faketile->ndim=OTHER_DATASET->ndim;
+
+ // These can be done in the loop over tiles.
+ faketile->size=tile->size;
+ faketile->dsize=tile->dsize;
+ faketile->array=gal_tile_block_relative_to_other(tile, OTHER_DATASET);
+
+ // Do your processing....
+ GAL_TILE_PARSE_OPERATE(PROCESSING, tile, faketile, 1, 1);
+
+ // Clean up.
+ bintile->array=NULL;
+ bintile->dsize=NULL;
+ gal_data_free(bintile);
*/
#define GAL_TILE_PARSE_OPERATE(OP, IN, OUT, PARSE_OUT, CHECK_BLANK) { \
int parse_out=(OUT && PARSE_OUT); \
diff --git a/lib/interpolate.c b/lib/interpolate.c
index 8323ff9..eba3fbd 100644
--- a/lib/interpolate.c
+++ b/lib/interpolate.c
@@ -37,7 +37,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/interpolate.h>
#include <gnuastro/permutation.h>
-#include <checkset.h>
+#include <gnuastro-internal/checkset.h>
diff --git a/lib/linkedlist.c b/lib/linkedlist.c
index 30193fe..cdba40a 100644
--- a/lib/linkedlist.c
+++ b/lib/linkedlist.c
@@ -30,7 +30,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/linkedlist.h>
-#include <checkset.h>
+#include <gnuastro-internal/checkset.h>
diff --git a/lib/options.c b/lib/options.c
index 8e634ec..84db9d8 100644
--- a/lib/options.c
+++ b/lib/options.c
@@ -35,9 +35,9 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/arithmetic.h>
#include <gnuastro/linkedlist.h>
-#include <timing.h>
-#include <options.h>
-#include <checkset.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/options.h>
+#include <gnuastro-internal/checkset.h>
diff --git a/lib/statistics.c b/lib/statistics.c
index a7f1acf..33f6996 100644
--- a/lib/statistics.c
+++ b/lib/statistics.c
@@ -38,7 +38,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/arithmetic.h>
#include <gnuastro/statistics.h>
-#include <checkset.h>
+#include <gnuastro-internal/checkset.h>
diff --git a/lib/table.c b/lib/table.c
index 6ca7f29..a862a1a 100644
--- a/lib/table.c
+++ b/lib/table.c
@@ -34,8 +34,8 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/blank.h>
#include <gnuastro/table.h>
-#include <timing.h>
-#include <checkset.h>
+#include <gnuastro-internal/timing.h>
+#include <gnuastro-internal/checkset.h>
diff --git a/lib/tile.c b/lib/tile.c
index d4671a9..4fe885d 100644
--- a/lib/tile.c
+++ b/lib/tile.c
@@ -37,7 +37,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/interpolate.h>
#include <gnuastro/permutation.h>
-#include "checkset.h"
+#include <gnuastro-internal/checkset.h>
diff --git a/lib/timing.c b/lib/timing.c
index 970461e..98f1228 100644
--- a/lib/timing.c
+++ b/lib/timing.c
@@ -25,7 +25,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <stdio.h>
#include <stdint.h>
-#include "timing.h"
+#include <gnuastro-internal/timing.h>
diff --git a/lib/txt.c b/lib/txt.c
index 3d50116..8d4df11 100644
--- a/lib/txt.c
+++ b/lib/txt.c
@@ -34,7 +34,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/blank.h>
#include <gnuastro/table.h>
-#include <checkset.h>
+#include <gnuastro-internal/checkset.h>
diff --git a/tmpfs-config-make b/tmpfs-config-make
index 09ab2df..0eacca9 100755
--- a/tmpfs-config-make
+++ b/tmpfs-config-make
@@ -134,7 +134,8 @@ if [ ! -f Makefile ]; then
--enable-arithmetic --enable-convertt --enable-convolve \
--enable-cosmiccal --enable-crop --enable-fits \
--enable-mknoise --enable-mkprof --enable-noisechisel \
- --enable-statistics --enable-table --enable-warp
+ --enable-statistics --enable-table --enable-warp \
+ CFLAGS="-g -O0" --disable-shared
fi
- [gnuastro-commits] master 5fa37eb 096/125: HDU modification now fully implemented in Fits program, (continued)
- [gnuastro-commits] master 5fa37eb 096/125: HDU modification now fully implemented in Fits program, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master 38f401b 121/125: Clump S/N threshold is now calculated on Sky clumps, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master 1e961f5 067/125: Starting to use gal_data_t in MakeProfiles, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master e58ed29 108/125: One value per tile in multi-channel tessellation, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master 0e344fe 086/125: Warp now uses gal_data_t and all its fruits, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master 8348f1e 119/125: NoiseChisel pseudo-detections identified on threads, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master fca5e80 117/125: First re-implementation of NoiseChisel's complete detection, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master a1ff97b 111/125: Permutations and neighbor finding algorithms, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master 0bc96c9 122/125: Clumps and their S/N tables over detections, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master 80cdd4f 118/125: Correction of convolution over channel borders, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master e90b490 116/125: Internal headers moved to special directory,
Mohammad Akhlaghi <=
- [gnuastro-commits] master 29d7e46 091/125: Statistics now successfully uses gal_data_t, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master 60c126f 120/125: New implementation of over-segmentation to find clumps, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master c250a6d 123/125: NoiseChisel's clumps grown and objects defined, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master ffaa059 101/125: Tessellation options now common to all programs, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master dec2b22 078/125: ImageCrop works with gal_data_t features, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master f8b1820 061/125: Other configuration files read immediately when seen, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master 46b4651 085/125: Image prefix removed from some program names, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master df716bc 097/125: Tesselation with the new data structure: work started, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master db39cee 088/125: Statistics returns basic results, no array lib, new blank lib, Mohammad Akhlaghi, 2017/04/23
- [gnuastro-commits] master 60cd76e 090/125: Statistics mostly complete, Mohammad Akhlaghi, 2017/04/23