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[gnuastro-commits] master 6086579 031/113: Merged recent work in master
|
From: |
Mohammad Akhlaghi |
|
Subject: |
[gnuastro-commits] master 6086579 031/113: Merged recent work in master (corrected conflicts) |
|
Date: |
Fri, 16 Apr 2021 10:33:37 -0400 (EDT) |
branch: master
commit 6086579f77e1bf1a50c4a254653862d2673ac691
Merge: 6bdc5d6 da0249e
Author: Mohammad Akhlaghi <akhlaghi@gnu.org>
Commit: Mohammad Akhlaghi <akhlaghi@gnu.org>
Merged recent work in master (corrected conflicts)
Some conflicts needed to be corrected, but generally the merge was smooth
and this branch now fits with the 0.4 release of Gnuastro.
In particular the `detgrowquant' value needed to be changed for 3D datasets
due to the much larger connectivity.
---
NEWS | 47 ++-
THANKS | 1 +
bin/convertt/convertt.c | 1 -
bin/crop/ui.c | 2 +-
bin/noisechisel/args.h | 62 ++--
bin/noisechisel/astnoisechisel-3d.conf | 3 +-
bin/noisechisel/astnoisechisel.conf | 45 +--
bin/noisechisel/clumps.c | 49 +++-
bin/noisechisel/clumps.h | 2 +-
bin/noisechisel/detection.c | 216 ++++++++++----
bin/noisechisel/main.h | 15 +-
bin/noisechisel/noisechisel.c | 30 +-
bin/noisechisel/segmentation.c | 5 +-
bin/noisechisel/sky.c | 8 +-
bin/noisechisel/threshold.c | 148 ++++++++--
bin/noisechisel/threshold.h | 3 +-
bin/noisechisel/ui.c | 76 +++--
bin/noisechisel/ui.h | 10 +-
bin/statistics/sky.c | 16 +-
bin/statistics/statistics.c | 2 +-
configure.ac | 2 +-
doc/announce-acknowledge.txt | 15 +-
doc/gnuastro-top.html | 8 +-
doc/gnuastro.texi | 520 +++++++++++++++++++++------------
doc/release-checklist.txt | 28 +-
lib/arithmetic-binary.c | 50 +++-
lib/binary.c | 31 +-
lib/blank.c | 8 +-
lib/fits.c | 59 +++-
lib/gnuastro/binary.h | 2 +-
lib/gnuastro/fits.h | 3 +
lib/gnuastro/tile.h | 6 +-
lib/statistics.c | 2 +-
lib/tile.c | 18 +-
tests/during-dev.sh | 2 +-
tests/noisechisel/noisechisel.sh | 4 +-
36 files changed, 1041 insertions(+), 458 deletions(-)
diff --git a/NEWS b/NEWS
index c3380cb..ec75d66 100644
--- a/NEWS
+++ b/NEWS
@@ -1,6 +1,51 @@
GNU Astronomy Utilities NEWS -*- outline -*-
-* Noteworthy changes in release 0.3.XXX (library 2.0.0) (YYYY-MM-DD) [stable]
+
+* Noteworthy changes in release 0.4.XXX (library 3.0.0) (YYYY-MM-DD) [stable]
+
+** New features
+
+ NoiseChisel: with the new `--widekernel' option it is now possible to use
+ a wider kernel to identify which tiles contain signal. The rest of the
+ steps (identifying the quantile threshold on the selected tiles and etc)
+ are done on the dataset convolved with `--kernel' as they were
+ before. Since it is time consuming, this is an optional feature.
+
+ NoiseChisel: the finally selected true detections are now grown based on
+ signal contiguity, not by blind dilation. The growth process is the same
+ as the growing of clumps to define objects. Only for true detections, the
+ growth occurs in the noise. You can configure this growth with the
+ `--detgrowquant' and `--detgrowmaxholesize'. With this new feature it is
+ now possible to detect signal out to much lower surface brightness limits
+ and the detections don't look boxy any more.
+
+ `gal_fits_key_img_blank': returns the value that must be used in the
+ BLANK keyword for the given type as defined by the FITS standard.
+
+** Removed features
+
+** Changed features
+
+ `gal_binary_fill_holes' now accepts a `connectivity' and `maxsize'
+ argument to specify the connectivity of the holes and the maximum size of
+ acceptable holes to fill.
+
+ `gal_tile_block_write_const_value' and `gal_tile_full_values_write' now
+ accept a new `withblank' option to set all pixels that are blank in the
+ tile's block to be blank in the check image.
+
+** Bug fixes
+
+ ConvertType crash when changing values (bug #52010).
+
+ Arithmetic not accounting for integer blank pixels in binary operators
+ (bug #52014).
+
+
+
+
+
+* Noteworthy changes in release 0.4 (library 2.0.0) (2017-09-13) [stable]
** New features
diff --git a/THANKS b/THANKS
index 0b5e215..5f34189 100644
--- a/THANKS
+++ b/THANKS
@@ -27,6 +27,7 @@ support in Gnuastro. The list is ordered alphabetically (by
family name).
Takashi Ichikawa ichikawa@astr.tohoku.ac.jp
Raúl Infante Sainz infantesainz@gmail.com
Brandon Invergo brandon@gnu.org
+ Aurélien Jarno aurelien.jarno@univ-lyon1.fr
Lee Kelvin l.s.kelvin@ljmu.ac.uk
Mohammad-Reza Khellat moha.khe@gmail.com
Alan Lefor alefor@astr.tohoku.ac.jp
diff --git a/bin/convertt/convertt.c b/bin/convertt/convertt.c
index 729811a..88df4d0 100644
--- a/bin/convertt/convertt.c
+++ b/bin/convertt/convertt.c
@@ -79,7 +79,6 @@ convertt_change(struct converttparams *p)
/* Clean up, since we set the free flag, all extra arrays have been
freed.*/
- gal_data_free(cond);
gal_data_free(change->from);
}
diff --git a/bin/crop/ui.c b/bin/crop/ui.c
index 3a516de..cf7d043 100644
--- a/bin/crop/ui.c
+++ b/bin/crop/ui.c
@@ -879,7 +879,7 @@ ui_preparations(struct cropparams *p)
/* Set the basic information. */
firsttype = p->type;
firstndim = img->ndim;
- p->bitnul = gal_blank_alloc_write(p->type);
+ p->bitnul = gal_fits_key_img_blank(p->type);
/* Make sure the number of dimensions is supported. */
if(firstndim>MAXDIM)
diff --git a/bin/noisechisel/args.h b/bin/noisechisel/args.h
index 772b09a..80de2ce 100644
--- a/bin/noisechisel/args.h
+++ b/bin/noisechisel/args.h
@@ -38,7 +38,7 @@ struct argp_option program_options[] =
UI_KEY_KERNEL,
"STR",
0,
- "Filename of Kernel to convolve with input",
+ "Filename of kernel to convolve with input",
GAL_OPTIONS_GROUP_INPUT,
&p->kernelname,
GAL_TYPE_STRING,
@@ -51,7 +51,7 @@ struct argp_option program_options[] =
UI_KEY_KHDU,
"STR",
0,
- "HDU containing Kernel image.",
+ "HDU containing kernel image.",
GAL_OPTIONS_GROUP_INPUT,
&p->khdu,
GAL_TYPE_STRING,
@@ -60,6 +60,32 @@ struct argp_option program_options[] =
GAL_OPTIONS_NOT_SET
},
{
+ "widekernel",
+ UI_KEY_WIDEKERNEL,
+ "STR",
+ 0,
+ "Filename of wider kernel for better qthresh",
+ GAL_OPTIONS_GROUP_INPUT,
+ &p->widekernelname,
+ GAL_TYPE_STRING,
+ GAL_OPTIONS_RANGE_ANY,
+ GAL_OPTIONS_NOT_MANDATORY,
+ GAL_OPTIONS_NOT_SET
+ },
+ {
+ "wkhdu",
+ UI_KEY_WKHDU,
+ "STR",
+ 0,
+ "HDU containing wide kernel image.",
+ GAL_OPTIONS_GROUP_INPUT,
+ &p->wkhdu,
+ GAL_TYPE_STRING,
+ GAL_OPTIONS_RANGE_ANY,
+ GAL_OPTIONS_NOT_MANDATORY,
+ GAL_OPTIONS_NOT_SET
+ },
+ {
"skysubtracted",
UI_KEY_SKYSUBTRACTED,
0,
@@ -365,39 +391,39 @@ struct argp_option program_options[] =
GAL_OPTIONS_NOT_SET
},
{
- "dilate",
- UI_KEY_DILATE,
- "INT",
+ "detgrowquant",
+ UI_KEY_DETGROWQUANT,
+ "FLT",
0,
- "Number of times to dilate true detections.",
+ "Minimum quant. to expand true detections.",
ARGS_GROUP_DETECTION,
- &p->dilate,
- GAL_TYPE_SIZE_T,
- GAL_OPTIONS_RANGE_ANY,
+ &p->detgrowquant,
+ GAL_TYPE_FLOAT32,
+ GAL_OPTIONS_RANGE_GE_0_LE_1,
GAL_OPTIONS_MANDATORY,
GAL_OPTIONS_NOT_SET
},
{
- "dilatengb",
- UI_KEY_DILATENGB,
+ "detgrowmaxholesize",
+ UI_KEY_DETGROWMAXHOLESIZE,
"INT",
0,
- "4 or 8 connectivity in final dilation.",
+ "Max. area of holes after growth to fill.",
ARGS_GROUP_DETECTION,
- &p->dilatengb,
+ &p->detgrowmaxholesize,
GAL_TYPE_SIZE_T,
- GAL_OPTIONS_RANGE_ANY,
+ GAL_OPTIONS_RANGE_GE_0,
GAL_OPTIONS_MANDATORY,
GAL_OPTIONS_NOT_SET
},
{
- "cleandilated",
- UI_KEY_CLEANDILATED,
+ "cleangrowndet",
+ UI_KEY_CLEANGROWNDET,
0,
0,
- "Remove small S/N dilated objects.",
+ "Remove small S/N grown detections.",
ARGS_GROUP_DETECTION,
- &p->cleandilated,
+ &p->cleangrowndet,
GAL_OPTIONS_NO_ARG_TYPE,
GAL_OPTIONS_RANGE_ANY,
GAL_OPTIONS_NOT_MANDATORY,
diff --git a/bin/noisechisel/astnoisechisel-3d.conf
b/bin/noisechisel/astnoisechisel-3d.conf
index 73fe65d..ee8007b 100644
--- a/bin/noisechisel/astnoisechisel-3d.conf
+++ b/bin/noisechisel/astnoisechisel-3d.conf
@@ -25,4 +25,5 @@
# Detection
erodengb 6
openingngb 18
- dilatengb 18
\ No newline at end of file
+ detgrowquant 0.85
+ detgrowmaxholesize 300
\ No newline at end of file
diff --git a/bin/noisechisel/astnoisechisel.conf
b/bin/noisechisel/astnoisechisel.conf
index 6217e43..a037355 100644
--- a/bin/noisechisel/astnoisechisel.conf
+++ b/bin/noisechisel/astnoisechisel.conf
@@ -19,6 +19,7 @@
# Input:
khdu 1
+ wkhdu 1
minskyfrac 0.7
minnumfalse 100
@@ -26,29 +27,29 @@
largetilesize 200,200
# Detection:
- mirrordist 1.5
- modmedqdiff 0.01
- qthresh 0.3
- smoothwidth 3
- erode 2
- erodengb 4
- noerodequant 0.9331
- opening 1
- openingngb 8
- sigmaclip 3,0.2
- dthresh 0.0
- detsnminarea 10
- detquant 0.95
- dilate 3
- dilatengb 8
+ mirrordist 1.5
+ modmedqdiff 0.01
+ qthresh 0.3
+ smoothwidth 3
+ erode 2
+ erodengb 4
+ noerodequant 0.9331
+ opening 1
+ openingngb 8
+ sigmaclip 3,0.2
+ dthresh 0.0
+ detsnminarea 10
+ detquant 0.95
+ detgrowquant 0.65
+ detgrowmaxholesize 100
# Segmentation
- segsnminarea 15
- keepmaxnearriver 0
- segquant 0.95
- gthresh 0.5
- minriverlength 15
- objbordersn 1
+ segsnminarea 15
+ keepmaxnearriver 0
+ segquant 0.95
+ gthresh 0.5
+ minriverlength 15
+ objbordersn 1
# Operating mode
- continueaftercheck 0
+ continueaftercheck 0
diff --git a/bin/noisechisel/clumps.c b/bin/noisechisel/clumps.c
index 03df913..481d44f 100644
--- a/bin/noisechisel/clumps.c
+++ b/bin/noisechisel/clumps.c
@@ -534,19 +534,34 @@ clumps_grow_prepare_final(struct clumps_thread_params
*cltprm)
This function is going to be used before identifying objects and also
after it (to completely fill in the diffuse area). The distinguishing
point between these two steps is the presence of rivers, so you can use
- the `withrivers' argument. */
+ the `withrivers' argument.
+
+
+ Input:
+
+ labels: The labels array that must be operated on. The pixels that
+ must be "grown" must have the value `CLUMPS_INIT' (negative).
+
+ diffuseindexs: The indexs of the pixels that must be grown.
+
+ withrivers: as described abvoe.
+*/
void
-clumps_grow(struct clumps_thread_params *cltprm, int withrivers)
+clumps_grow(gal_data_t *labels, gal_data_t *diffuseindexs, int withrivers)
{
- struct noisechiselparams *p=cltprm->clprm->p;
- gal_data_t *diffuseindexs=cltprm->diffuseindexs;
- size_t ndim=p->input->ndim, *dsize=p->input->dsize;
-
int searchngb;
- size_t *diarray=cltprm->diffuseindexs->array;
- int32_t n1, nlab, *olabel=p->olabel->array;
- size_t *dinc=gal_dimension_increment(ndim, dsize);
+ size_t *diarray=diffuseindexs->array;
+ int32_t n1, nlab, *olabel=labels->array;
size_t *s, *sf, thisround, ndiffuse=diffuseindexs->size;
+ size_t *dinc=gal_dimension_increment(labels->ndim, labels->dsize);
+
+ /* A small sanity check: */
+ if(labels->type!=GAL_TYPE_INT32)
+ error(EXIT_FAILURE, 0, "%s: `labels' has to have type of int32_t",
+ __func__);
+ if(diffuseindexs->type!=GAL_TYPE_SIZE_T)
+ error(EXIT_FAILURE, 0, "%s: `diffuseindexs' has to have type of size_t",
+ __func__);
/* The basic idea is this: after growing, not all the blank pixels are
necessarily filled, for example the pixels might belong to two regions
@@ -582,7 +597,7 @@ clumps_grow(struct clumps_thread_params *cltprm, int
withrivers)
in a 2D image). Note that since this macro has multiple loops
within it, we can't use break. We'll use a variable instead. */
searchngb=1;
- GAL_DIMENSION_NEIGHBOR_OP(*s, ndim, dsize, 1, dinc,
+ GAL_DIMENSION_NEIGHBOR_OP(*s, labels->ndim, labels->dsize, 1, dinc,
{
if(searchngb)
{
@@ -938,6 +953,11 @@ clumps_correct_sky_labels_for_check(struct
clumps_thread_params *cltprm,
size_t len=cltprm->numinitclumps+1;
struct noisechiselparams *p=cltprm->clprm->p;
+ /* If there are no clumps in this tile, then this function can be
+ ignored. */
+ if(cltprm->snind->size==0) return;
+
+
/* A small sanity check. */
if(gal_tile_block(tile)!=p->clabel)
error(EXIT_FAILURE, 0, "%s: a bug! Please contact us at %s to address "
@@ -976,7 +996,6 @@ clumps_correct_sky_labels_for_check(struct
clumps_thread_params *cltprm,
do { ninds[*l]=curlab++; *l=ninds[*l]; } while(++l<lf);
-
/* Go over this tile and correct the values. */
GAL_TILE_PARSE_OPERATE( tile, NULL, 0, 1,
{if(*i>0) *i=ninds[ *(int32_t *)i ];} );
@@ -1043,7 +1062,11 @@ clumps_find_make_sn_table(void *in_prm)
/* Find the number of detected pixels over this tile. Since this is
- the binary image, this is just the sum of all the pixels. */
+ the binary image, this is just the sum of all the pixels.
+
+ Note that `numdet' can be `nan' when the whole tile is blank and
+ so there was no values to sum. Recall that in summing, when there
+ is not input, the output is `nan'. */
tmp=gal_statistics_sum(tile);
numdet=*((double *)(tmp->array));
gal_data_free(tmp);
@@ -1062,6 +1085,7 @@ clumps_find_make_sn_table(void *in_prm)
NULL, 0, p->cp.minmapsize, NULL, NULL,
NULL);
+
/* Change the tile's block to the clump labels dataset (because
we'll need to set the labels of the rivers on the edge of the
tile here). */
@@ -1300,7 +1324,6 @@ clumps_true_find_sn_thresh(struct noisechiselparams *p)
p->ltl.tottiles, p->cp.numthreads);
}
-
/* Destroy the mutex if it was initialized. */
if( p->cp.numthreads>1 && (p->checksegmentation || p->checkclumpsn) )
pthread_mutex_destroy(&clprm.labmutex);
diff --git a/bin/noisechisel/clumps.h b/bin/noisechisel/clumps.h
index 85e5d57..1557955 100644
--- a/bin/noisechisel/clumps.h
+++ b/bin/noisechisel/clumps.h
@@ -79,7 +79,7 @@ void
clumps_grow_prepare_final(struct clumps_thread_params *cltprm);
void
-clumps_grow(struct clumps_thread_params *cltprm, int withrivers);
+clumps_grow(gal_data_t *labels, gal_data_t *diffuseindexs, int withrivers);
void
clumps_true_find_sn_thresh(struct noisechiselparams *p);
diff --git a/bin/noisechisel/detection.c b/bin/noisechisel/detection.c
index 3c82a74..b9858f0 100644
--- a/bin/noisechisel/detection.c
+++ b/bin/noisechisel/detection.c
@@ -40,6 +40,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include "ui.h"
#include "sky.h"
+#include "clumps.h"
#include "threshold.h"
@@ -271,8 +272,9 @@ detection_fill_holes_open(void *in_prm)
copy->size=p->maxltcontig;
gal_data_copy_to_allocated(tile, copy);
- /* Fill the holes in this tile. */
- gal_binary_fill_holes(copy);
+ /* Fill the holes in this tile: holes with maximal connectivity means
+ that they are most strongly bounded. */
+ gal_binary_fill_holes(copy, copy->ndim, -1);
if(fho_prm->step==1)
{
detection_write_in_large(tile, copy);
@@ -435,7 +437,7 @@ detection_sn_write_to_file(struct noisechiselparams *p,
gal_data_t *sn,
/* Description comment. */
str = ( s0d1D2
? ( s0d1D2==2
- ? "S/N of dilated detections."
+ ? "S/N of grown detections."
: "Pseudo-detection S/N over initial detections." )
: "Pseudo-detection S/N over initial undetections.");
gal_list_str_add(&comments, str, 1);
@@ -452,8 +454,8 @@ detection_sn_write_to_file(struct noisechiselparams *p,
gal_data_t *sn,
/* Abort NoiseChisel if the user asked for it. */
if(s0d1D2==2 && !p->continueaftercheck)
ui_abort_after_check(p, p->detsn_s_name, p->detsn_d_name,
- "pseudo-detection and dilated S/N values in "
- "a table");
+ "pseudo-detection and grown/final detection S/N "
+ "values in a table");
}
@@ -783,9 +785,10 @@ detection_pseudo_real(struct noisechiselparams *p)
-/* This is for the final detections (dilated) detections. */
+/* This is for the final detections (grown) detections. */
static size_t
-detection_final_remove_small_sn(struct noisechiselparams *p, size_t num)
+detection_final_remove_small_sn(struct noisechiselparams *p,
+ gal_data_t *workbin, size_t num)
{
size_t i;
int8_t *b;
@@ -796,7 +799,6 @@ detection_final_remove_small_sn(struct noisechiselparams
*p, size_t num)
int32_t *newlabs=gal_data_calloc_array(GAL_TYPE_INT32, num+1, __func__,
"newlabs");
-
/* Get the Signal to noise ratio of all detections. */
sn=detection_sn(p, p->olabel, num, 2, "DILATED");
@@ -808,7 +810,7 @@ detection_final_remove_small_sn(struct noisechiselparams
*p, size_t num)
/* Go over the labeled image and correct the labels. */
- b=p->binary->array;
+ b=workbin->array;
lf=(l=p->olabel->array)+p->olabel->size;
if( p->input->flag & GAL_DATA_FLAG_HASBLANK )
{
@@ -840,8 +842,7 @@ detection_final_remove_small_sn(struct noisechiselparams
*p, size_t num)
/* Make the comments, then write the table. */
gal_list_str_add(&comments, "See also: `DILATED' "
"HDU of output with `--checkdetection'.", 1);
- gal_list_str_add(&comments, "S/N of finally dilated "
- "detections.", 1);
+ gal_list_str_add(&comments, "S/N of finally grown detections.", 1);
threshold_write_sn_table(p, sn, snind, p->detsn_D_name, comments);
@@ -850,15 +851,6 @@ detection_final_remove_small_sn(struct noisechiselparams
*p, size_t num)
}
- /* For a check image. */
- if(p->detectionname)
- {
- p->olabel->name="DETECTION-FINAL";
- gal_fits_img_write(p->olabel, p->detectionname, NULL,
- PROGRAM_NAME);
- p->olabel->name=NULL;
- }
-
/* Clean up and return. */
free(newlabs);
gal_data_free(sn);
@@ -928,13 +920,20 @@ detection_remove_false_initial(struct noisechiselparams
*p,
for(i=0;i<p->numinitialdets;++i) if(newlabels[i]) newlabels[i] = curlab++;
- /* Replace the byt and olab values with their proper values. If the
- user doesn't want to dilate, then change the labels in `lab'
- too. Otherwise, you don't have to worry about the label
- array. After dilation a new labeling will be done and the whole
- labeled array will be re-filled.*/
+ /* Replace the byt and olab values with their proper values. If the user
+ doesn't want to grow, then change the labels in `lab' too. Otherwise,
+ you don't have to worry about the label array. After dilation a new
+ labeling will be done and the whole labeled array will be re-filled.*/
b=workbin->array; l=p->olabel->array;
- if(p->dilate)
+ if(p->detgrowquant==1.0f) /* We need the binary array even when */
+ do /* there is no growth: the binary */
+ { /* array is used for estimating the */
+ if(*l!=GAL_BLANK_INT32) /* Sky and its STD. */
+ *b = ( *l = newlabels[ *l ] ) > 0;
+ ++b;
+ }
+ while(++l<lf);
+ else
do
{
if(*l!=GAL_BLANK_INT32)
@@ -942,14 +941,6 @@ detection_remove_false_initial(struct noisechiselparams *p,
++b;
}
while(++l<lf);
- else /* We need the binary array even when */
- do /* there is no dilation: the binary */
- { /* array is used for estimating the */
- if(*l!=GAL_BLANK_INT32) /* Sky and its STD. */
- *b = ( *l = newlabels[ *l ] ) > 0;
- ++b;
- }
- while(++l<lf);
/* Clean up and return. */
@@ -961,6 +952,108 @@ detection_remove_false_initial(struct noisechiselparams
*p,
+static size_t
+detection_quantile_expand(struct noisechiselparams *p, gal_data_t *workbin)
+{
+ int32_t *o, *of;
+ size_t *d, counter=0, numexpanded;
+ float *i, *e_th, *arr=p->conv->array;
+ gal_data_t *exp_thresh_full, *diffuseindexs;
+ uint8_t *b=workbin->array, *bf=b+workbin->size;
+
+ /* Expand the threshold values (from one value for each tile) to the
+ whole dataset. Since we know the tiles cover the whole image, we don't
+ neeed to initialize or check for blanks.*/
+ exp_thresh_full=gal_tile_block_write_const_value(p->expand_thresh,
+ p->cp.tl.tiles, 0, 0);
+
+ /* Count the pixels that must be expanded. */
+ e_th=exp_thresh_full->array;
+ do { if(*b++==0 && *arr>*e_th) ++counter; ++arr; ++e_th; } while(b<bf);
+
+ /* Allocate the space necessary to keep all the index of all the pixels
+ that must be expanded and re-initialize the necessary pointers. */
+ diffuseindexs=gal_data_alloc(NULL, GAL_TYPE_SIZE_T, 1, &counter, NULL, 0,
+ p->cp.minmapsize, NULL, NULL, NULL);
+
+ /* Fill in the diffuse indexs and initialize the objects dataset. */
+ b=workbin->array;
+ arr=p->conv->array;
+ d=diffuseindexs->array;
+ e_th=exp_thresh_full->array;
+ of=(o=p->olabel->array)+p->olabel->size;
+ do
+ {
+ /* If the binary value is 1, then we want an initial label of 1 (the
+ object is already detected). If it isn't, then we only want it if
+ it is above the threshold. */
+ *o = *b==1 ? 1 : ( *arr>*e_th ? CLUMPS_INIT : 0);
+ if(*b==0 && *arr>*e_th)
+ *d++ = o - (int32_t *)(p->olabel->array);
+
+ /* Increment the points and go onto the next pixel. */
+ ++b;
+ ++arr;
+ ++e_th;
+ }
+ while(++o<of);
+
+ /* Expand the detections. */
+ clumps_grow(p->olabel, diffuseindexs, 0);
+
+
+ /* Only keep the 1 valued pixels in the binary array. */
+ o=p->olabel->array;
+ bf=(b=workbin->array)+workbin->size;
+ do *b = (*o++ == 1); while(++b<bf);
+ workbin=gal_binary_dilate(workbin, 1, 1, 1);
+ if(p->detectionname)
+ {
+ workbin->name="TRUE-DETECTIONS-GROWN";
+ gal_fits_img_write(workbin, p->detectionname, NULL, PROGRAM_NAME);
+ workbin->name=NULL;
+ }
+
+ /* Fill the holes */
+ gal_binary_fill_holes(workbin, 1, p->detgrowmaxholesize);
+ if(p->detectionname)
+ {
+ workbin->name="TRUE-DETECTIONS-HOLES-FILLED";
+ gal_fits_img_write(workbin, p->detectionname, NULL, PROGRAM_NAME);
+ workbin->name=NULL;
+ }
+
+ /* Get the labeled image. */
+ numexpanded=gal_binary_connected_components(workbin, &p->olabel, 8);
+
+ /* Set all the input's blank pixels to blank in the labeled and binary
+ arrays. */
+ if( gal_blank_present(p->input, 1) )
+ {
+ b=workbin->array;
+ i=p->input->array;
+ of=(o=p->olabel->array)+p->olabel->size;
+ do
+ {
+ if(isnan(*i++))
+ {
+ *o=GAL_BLANK_INT32;
+ *b=GAL_BLANK_UINT8;
+ }
+ ++b;
+ }
+ while(++o<of);
+ }
+
+ /* Clean up and return */
+ gal_data_free(exp_thresh_full);
+ return numexpanded;
+}
+
+
+
+
+
/* The initial detection has been done, now we want to remove false
detections. */
void
@@ -999,11 +1092,13 @@ detection(struct noisechiselparams *p)
/* Find the real pseudo-detections. */
+ if(!p->cp.quiet) gettimeofday(&t1, NULL);
workbin=detection_pseudo_real(p);
/* Only keep the initial detections that overlap with the real
pseudo-detections. */
+ if(!p->cp.quiet) gettimeofday(&t1, NULL);
num_true_initial=detection_remove_false_initial(p, workbin);
if(!p->cp.quiet)
{
@@ -1014,51 +1109,46 @@ detection(struct noisechiselparams *p)
}
- /* If the user asked for dilation, then apply it. */
- if(p->dilate)
- {
- gal_binary_dilate(workbin, p->dilate,
- detection_ngb_to_connectivity(p->input->ndim,
- p->dilatengb),
- 1);
- num_true_initial = gal_binary_connected_components(workbin, &p->olabel,
- 8);
- }
+ /* If the user asked for dilation/expansion, then apply it and report the
+ final number of detections. */
+ if(!p->cp.quiet) gettimeofday(&t1, NULL);
+ if(p->detgrowquant!=1.0f)
+ num_true_initial=detection_quantile_expand(p, workbin);
if(!p->cp.quiet)
{
- asprintf(&msg, "%zu detections after %zu dilation%s (%zu-connected)",
- num_true_initial, p->dilate, p->dilate>1 ? "s." : ".",
- p->dilatengb);
- gal_timing_report(&t0, msg, 2);
+ if(p->detgrowquant==1.0f)
+ asprintf(&msg, "%zu detections with no growth.", num_true_initial);
+ else
+ asprintf(&msg, "%zu detections after growth to %.3f quantile.",
+ num_true_initial, p->detgrowquant);
+ gal_timing_report(&t1, msg, 2);
free(msg);
}
- /* When the final (dilated or over-all object) detection's S/N is less
- than the pseudo-detection's S/N limit, the object is false. For a real
+ /* When the final (grown or over-all object) detection's S/N is less than
+ the pseudo-detection's S/N limit, the object is false. For a real
detection, the actual object S/N should be higher than any of its
pseudo-detection because it has a much larger area (and possibly more
flux under it). So when the final S/N is smaller than the minimum
acceptable S/N threshold, we have a false pseudo-detection. */
- if(p->cleandilated)
- p->numdetections = detection_final_remove_small_sn(p, num_true_initial);
- else
- {
- p->numdetections = num_true_initial;
- if(p->detectionname)
- {
- p->olabel->name="DETECTION-FINAL";
- gal_fits_img_write(p->olabel, p->detectionname, NULL,
- PROGRAM_NAME);
- p->olabel->name=NULL;
- }
- }
+ p->numdetections = ( p->cleangrowndet
+ ? detection_final_remove_small_sn(p, workbin,
+ num_true_initial)
+ : num_true_initial );
if(!p->cp.quiet)
{
asprintf(&msg, "%zu final true detections.", p->numdetections);
gal_timing_report(&t0, msg, 1);
free(msg);
}
+ if(p->detectionname)
+ {
+ p->olabel->name="DETECTION-FINAL";
+ gal_fits_img_write(p->olabel, p->detectionname, NULL,
+ PROGRAM_NAME);
+ p->olabel->name=NULL;
+ }
/* p->binary was used to keep the initial pseudo-detection threshold. But
diff --git a/bin/noisechisel/main.h b/bin/noisechisel/main.h
index bdd7396..5d08e59 100644
--- a/bin/noisechisel/main.h
+++ b/bin/noisechisel/main.h
@@ -47,7 +47,9 @@ struct noisechiselparams
struct gal_tile_two_layer_params ltl;/* Large tessellation. */
char *inputname; /* Input filename. */
char *kernelname; /* Input kernel filename. */
+ char *widekernelname; /* Name of wider kernel to be used. */
char *khdu; /* Kernel HDU. */
+ char *wkhdu; /* Wide kernel HDU. */
uint8_t skysubtracted; /* Input has been Sky subtracted before. */
float minskyfrac; /* Undetected area min. frac. in tile. */
size_t minnumfalse; /* Min No. of det/seg for true quantile. */
@@ -72,9 +74,9 @@ struct noisechiselparams
size_t detsnminarea; /* Minimum pseudo-detection area for S/N. */
uint8_t checkdetsn; /* Save pseudo-detection S/N values. */
float detquant; /* True detection quantile. */
- size_t dilate; /* Number of times to dilate true dets. */
- size_t dilatengb; /* Connectivity for final dilation. */
- uint8_t cleandilated; /* Remove dilated objects with small S/N. */
+ float detgrowquant; /* Quantile to grow true detections. */
+ size_t detgrowmaxholesize; /* Max. size of holes to fill in growth. */
+ uint8_t cleangrowndet; /* Remove grown objects with small S/N. */
uint8_t checkdetection; /* Save all detection steps to a file. */
uint8_t checksky; /* Check the Sky value estimation. */
@@ -100,11 +102,14 @@ struct noisechiselparams
char *segmentationname; /* Name of segmentation steps file. */
gal_data_t *input; /* Input image. */
- gal_data_t *kernel; /* Input image. */
- gal_data_t *conv; /* Convolved input. */
+ gal_data_t *kernel; /* Sharper kernel. */
+ gal_data_t *widekernel; /* Wider kernel. */
+ gal_data_t *conv; /* Convolved wth sharper kernel. */
+ gal_data_t *wconv; /* Convolved with wider kernel. */
gal_data_t *binary; /* For binary operations. */
gal_data_t *olabel; /* Labels of objects in the detection. */
gal_data_t *clabel; /* Labels of clumps in the detection. */
+ gal_data_t *expand_thresh; /* Quantile threshold to expand per tile. */
gal_data_t *sky; /* Mean of undetected pixels, per tile. */
gal_data_t *std; /* STD of undetected pixels, per tile. */
size_t maxtcontig; /* Maximum contiguous space for a tile. */
diff --git a/bin/noisechisel/noisechisel.c b/bin/noisechisel/noisechisel.c
index f5d4fc8..58aae42 100644
--- a/bin/noisechisel/noisechisel.c
+++ b/bin/noisechisel/noisechisel.c
@@ -58,19 +58,39 @@ noisechisel_convolve(struct noisechiselparams *p)
struct timeval t1;
struct gal_tile_two_layer_params *tl=&p->cp.tl;
- /* Do the convolution. */
+ /* Convovle with sharper kernel. */
if(!p->cp.quiet) gettimeofday(&t1, NULL);
p->conv=gal_convolve_spatial(tl->tiles, p->kernel, p->cp.numthreads,
1, tl->workoverch);
- gal_checkset_allocate_copy("CONVOLVED", &p->conv->name);
+ gal_checkset_allocate_copy(p->widekernel?"CONVOLVED-SHARPER":"CONVOLVED",
+ &p->conv->name);
/* Report timing and write check image if necessary. */
- if(!p->cp.quiet) gal_timing_report(&t1, "Convolved with kernel.", 1);
+ if(!p->cp.quiet)
+ {
+ if(p->widekernel)
+ gal_timing_report(&t1, "Convolved with sharper kernel.", 1);
+ else
+ gal_timing_report(&t1, "Convolved with kernel.", 1);
+ }
if(p->detectionname)
{
gal_fits_img_write(p->input, p->detectionname, NULL, PROGRAM_NAME);
gal_fits_img_write(p->conv, p->detectionname, NULL, PROGRAM_NAME);
}
+
+ /* Convolve with wider kernel (if requested). */
+ if(p->widekernel)
+ {
+ if(!p->cp.quiet) gettimeofday(&t1, NULL);
+ p->wconv=gal_convolve_spatial(tl->tiles, p->widekernel,
+ p->cp.numthreads, 1, tl->workoverch);
+ gal_checkset_allocate_copy("CONVOLVED-WIDER", &p->wconv->name);
+
+ /* Report the status: */
+ if(!p->cp.quiet)
+ gal_timing_report(&t1, "Convolved with wider kernel.", 1);
+ }
}
@@ -232,7 +252,7 @@ noisechisel_output(struct noisechiselparams *p)
/* Write the Sky image into the output */
if(p->sky->name) free(p->sky->name);
p->sky->name="SKY";
- gal_tile_full_values_write(p->sky, &p->cp.tl, p->cp.output,
+ gal_tile_full_values_write(p->sky, &p->cp.tl, 1, p->cp.output,
NULL, PROGRAM_NAME);
p->sky->name=NULL;
@@ -248,7 +268,7 @@ noisechisel_output(struct noisechiselparams *p)
gal_fits_key_list_add(&keys, GAL_TYPE_FLOAT32, "MEDSTD", 0, &p->medstd, 0,
"Median raw tile standard deviation", 0,
p->input->unit);
- gal_tile_full_values_write(p->std, &p->cp.tl, p->cp.output, keys,
+ gal_tile_full_values_write(p->std, &p->cp.tl, 1, p->cp.output, keys,
PROGRAM_NAME);
p->std->name=NULL;
}
diff --git a/bin/noisechisel/segmentation.c b/bin/noisechisel/segmentation.c
index eb3e706..0b6bd65 100644
--- a/bin/noisechisel/segmentation.c
+++ b/bin/noisechisel/segmentation.c
@@ -469,7 +469,8 @@ segmentation_on_threads(void *in_prm)
{
/* Grow the true clumps over the detection. */
clumps_grow_prepare_initial(&cltprm);
- if(cltprm.diffuseindexs->size) clumps_grow(&cltprm, 1);
+ if(cltprm.diffuseindexs->size)
+ clumps_grow(p->olabel, cltprm.diffuseindexs, 1);
if(clprm->step==3)
{ gal_data_free(cltprm.diffuseindexs); continue; }
@@ -508,7 +509,7 @@ segmentation_on_threads(void *in_prm)
clumps_grow_prepare_final(&cltprm);
/* Cover the whole area. */
- clumps_grow(&cltprm, 0);
+ clumps_grow(p->olabel, cltprm.diffuseindexs, 0);
}
gal_data_free(cltprm.diffuseindexs);
if(clprm->step==5) { gal_data_free(cltprm.clumptoobj); continue; }
diff --git a/bin/noisechisel/sky.c b/bin/noisechisel/sky.c
index 5cc9340..23ac8da 100644
--- a/bin/noisechisel/sky.c
+++ b/bin/noisechisel/sky.c
@@ -174,8 +174,10 @@ sky_and_std(struct noisechiselparams *p, char *checkname)
cp->numthreads);
if(checkname)
{
- gal_tile_full_values_write(p->sky, tl, checkname, NULL, PROGRAM_NAME);
- gal_tile_full_values_write(p->std, tl, checkname, NULL, PROGRAM_NAME);
+ gal_tile_full_values_write(p->sky, tl, 1, checkname, NULL,
+ PROGRAM_NAME);
+ gal_tile_full_values_write(p->std, tl, 1, checkname, NULL,
+ PROGRAM_NAME);
}
/* Get the basic information about the standard deviation
@@ -202,7 +204,7 @@ sky_and_std(struct noisechiselparams *p, char *checkname)
p->cpscorr = p->minstd>1 ? 1.0f : p->minstd;
/* Interpolate and smooth the derived values. */
- threshold_interp_smooth(p, &p->sky, &p->std, checkname);
+ threshold_interp_smooth(p, &p->sky, &p->std, NULL, checkname);
/* If a check was requested, abort NoiseChisel. */
diff --git a/bin/noisechisel/threshold.c b/bin/noisechisel/threshold.c
index 6584d38..ad3cce0 100644
--- a/bin/noisechisel/threshold.c
+++ b/bin/noisechisel/threshold.c
@@ -248,7 +248,8 @@ threshold_write_sn_table(struct noisechiselparams *p,
gal_data_t *insn,
/* Interpolate and smooth the values for each tile over the whole image. */
void
threshold_interp_smooth(struct noisechiselparams *p, gal_data_t **first,
- gal_data_t **second, char *filename)
+ gal_data_t **second, gal_data_t **third,
+ char *filename)
{
gal_data_t *tmp;
struct gal_options_common_params *cp=&p->cp;
@@ -256,26 +257,45 @@ threshold_interp_smooth(struct noisechiselparams *p,
gal_data_t **first,
/* A small sanity check. */
if( (*first)->next )
- error(EXIT_FAILURE, 0, "%s: the `first' argument to must not have any "
- "`next' pointer.", __func__);
+ error(EXIT_FAILURE, 0, "%s: `first' must not have any `next' pointer.",
+ __func__);
+ if( (*second)->next )
+ error(EXIT_FAILURE, 0, "%s: `second' must not have any `next' pointer.",
+ __func__);
+ if( third && (*third)->next )
+ error(EXIT_FAILURE, 0, "%s: `third' must not have any `next' pointer.",
+ __func__);
/* Do the interpolation of both arrays. */
(*first)->next = *second;
+ if(third) (*second)->next = *third;
tmp=gal_interpolate_close_neighbors(*first, tl, cp->interpnumngb,
cp->numthreads, cp->interponlyblank, 1);
gal_data_free(*first);
gal_data_free(*second);
+ if(third) gal_data_free(*third);
*first=tmp;
- *second=tmp->next;
+ *second=(*first)->next;
+ if(third)
+ {
+ *third=(*second)->next;
+ (*third)->next=NULL;
+ }
(*first)->next=(*second)->next=NULL;
if(filename)
{
(*first)->name="THRESH1_INTERP";
(*second)->name="THRESH2_INTERP";
- gal_tile_full_values_write(*first, tl, filename, NULL, PROGRAM_NAME);
- gal_tile_full_values_write(*second, tl, filename, NULL, PROGRAM_NAME);
+ if(third) (*third)->name="THRESH3_INTERP";
+ gal_tile_full_values_write(*first, tl, 1, filename, NULL, PROGRAM_NAME);
+ gal_tile_full_values_write(*second, tl, 1, filename, NULL,
+ PROGRAM_NAME);
+ if(third)
+ gal_tile_full_values_write(*third, tl, 1, filename, NULL,
+ PROGRAM_NAME);
(*first)->name = (*second)->name = NULL;
+ if(third) (*third)->name=NULL;
}
/* Smooth the threshold if requested. */
@@ -293,16 +313,30 @@ threshold_interp_smooth(struct noisechiselparams *p,
gal_data_t **first,
gal_data_free(*second);
*second=tmp;
+ /* Smooth the third */
+ if(third)
+ {
+ tmp=gal_tile_full_values_smooth(*third, tl, p->smoothwidth,
+ p->cp.numthreads);
+ gal_data_free(*third);
+ *third=tmp;
+ }
+
/* Add them to the check image. */
if(filename)
{
(*first)->name="THRESH1_SMOOTH";
(*second)->name="THRESH2_SMOOTH";
- gal_tile_full_values_write(*first, tl, filename, NULL,
+ if(third) (*third)->name="THRESH3_SMOOTH";
+ gal_tile_full_values_write(*first, tl, 1, filename, NULL,
PROGRAM_NAME);
- gal_tile_full_values_write(*second, tl, filename, NULL,
+ gal_tile_full_values_write(*second, tl, 1, filename, NULL,
PROGRAM_NAME);
+ if(third)
+ gal_tile_full_values_write(*third, tl, 1, filename, NULL,
+ PROGRAM_NAME);
(*first)->name = (*second)->name = NULL;
+ if(third) (*third)->name=NULL;
}
}
}
@@ -333,6 +367,7 @@ struct qthreshparams
{
gal_data_t *erode_th;
gal_data_t *noerode_th;
+ gal_data_t *expand_th;
void *usage;
struct noisechiselparams *p;
};
@@ -351,6 +386,7 @@ qthresh_on_tile(void *in_prm)
double *darr;
void *tarray=NULL;
int type=qprm->erode_th->type;
+ gal_data_t *modeconv = p->wconv ? p->wconv : p->conv;
gal_data_t *tile, *mode, *qvalue, *usage, *tblock=NULL;
size_t i, tind, twidth=gal_type_sizeof(type), ndim=p->input->ndim;
@@ -376,23 +412,18 @@ qthresh_on_tile(void *in_prm)
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, then copy
- the desired contents into the already allocated `usage' array. */
- if(p->conv)
- {
- tarray=tile->array; tblock=tile->block;
- tile->array=gal_tile_block_relative_to_other(tile, p->conv);
- tile->block=p->conv;
- }
+ /* Temporarily change the tile's pointers so we can do the work on
+ the convolved image, then copy the desired contents into the
+ already allocated `usage' array. */
+ tarray=tile->array; tblock=tile->block;
+ tile->array=gal_tile_block_relative_to_other(tile, modeconv);
+ tile->block=modeconv;
gal_data_copy_to_allocated(tile, usage);
- if(p->conv) { tile->array=tarray; tile->block=tblock; }
+ tile->array=tarray; tile->block=tblock;
- /* Find the mode on this dataset, note that we have set the `inplace'
- flag to `1'. So as a byproduct of finding the mode, `usage' is not
- going to have any blank elements and will be sorted (thus ready to
- be used by the quantile functions). */
+ /* Find the mode on this tile, note that we have set the `inplace'
+ flag to `1' to avoid extra allocation. */
mode=gal_statistics_mode(usage, p->mirrordist, 1);
@@ -402,6 +433,24 @@ qthresh_on_tile(void *in_prm)
darr=mode->array;
if( fabs(darr[1]-0.5f) < p->modmedqdiff )
{
+ /* The mode was (possibly) found on the wider convolved image,
+ but the qthresh values have to be found on the sharper
+ convolved images. This is because the distribution becomes
+ more skewed with a wider kernel, helping us find tiles with no
+ data more easily. But for the quantile threshold, we want to
+ use the sharper convolved image to loose less of the spatial
+ information. */
+ if(modeconv!=p->conv)
+ {
+ tarray=tile->array; tblock=tile->block;
+ tile->array=gal_tile_block_relative_to_other(tile, p->conv);
+ tile->block=p->conv;
+ usage->ndim=ndim; /* Since usage was modified in */
+ usage->size=p->maxtcontig; /* place, it needs to be */
+ gal_data_copy_to_allocated(tile, usage); /* re-initialized. */
+ tile->array=tarray; tile->block=tblock;
+ }
+
/* Get the erosion quantile for this tile and save it. Note that
the type of `qvalue' is the same as the input dataset. */
qvalue=gal_statistics_quantile(usage, p->qthresh, 1);
@@ -409,11 +458,21 @@ qthresh_on_tile(void *in_prm)
qvalue->array, twidth);
gal_data_free(qvalue);
- /* Do the same for the no-erode quantile. */
+ /* Same for the no-erode quantile. */
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);
+
+ /* Same for the expansion quantile. */
+ if(p->detgrowquant!=1.0f)
+ {
+ qvalue=gal_statistics_quantile(usage, p->detgrowquant, 1);
+ memcpy(gal_data_ptr_increment(qprm->expand_th->array, tind,
+ type),
+ qvalue->array, twidth);
+ gal_data_free(qvalue);
+ }
}
else
{
@@ -421,6 +480,9 @@ qthresh_on_tile(void *in_prm)
tind, type), type);
gal_blank_write(gal_data_ptr_increment(qprm->noerode_th->array,
tind, type), type);
+ if(p->detgrowquant!=1.0f)
+ gal_blank_write(gal_data_ptr_increment(qprm->expand_th->array,
+ tind, type), type);
}
/* Clean up and fix the tile's pointers. */
@@ -457,8 +519,13 @@ threshold_quantile_find_apply(struct noisechiselparams *p)
as the input, making it hard to inspect visually. So we'll only put
the full input when `oneelempertile' isn't requested. */
if(p->qthreshname && !tl->oneelempertile)
- gal_fits_img_write(p->conv ? p->conv : p->input, p->qthreshname, NULL,
- PROGRAM_NAME);
+ {
+ gal_fits_img_write(p->conv ? p->conv : p->input, p->qthreshname, NULL,
+ PROGRAM_NAME);
+ if(p->wconv)
+ gal_fits_img_write(p->wconv ? p->wconv : p->input, p->qthreshname,
+ NULL, PROGRAM_NAME);
+ }
/* Allocate space for the quantile threshold values. */
@@ -468,6 +535,12 @@ threshold_quantile_find_apply(struct noisechiselparams *p)
qprm.noerode_th=gal_data_alloc(NULL, p->input->type, p->input->ndim,
tl->numtiles, NULL, 0, cp->minmapsize,
NULL, p->input->unit, NULL);
+ if(p->detgrowquant!=1.0f)
+ qprm.expand_th=gal_data_alloc(NULL, p->input->type, p->input->ndim,
+ tl->numtiles, NULL, 0, cp->minmapsize,
+ NULL, p->input->unit, NULL);
+ else
+ qprm.expand_th=NULL;
/* Allocate temporary space for processing in each tile. */
@@ -484,22 +557,35 @@ threshold_quantile_find_apply(struct noisechiselparams *p)
gal_threads_spin_off(qthresh_on_tile, &qprm, tl->tottiles, cp->numthreads);
free(qprm.usage);
if( gal_blank_present(qprm.erode_th, 1) )
- qprm.noerode_th->flag |= GAL_DATA_FLAG_HASBLANK;
+ {
+ qprm.noerode_th->flag |= GAL_DATA_FLAG_HASBLANK;
+ if(qprm.expand_th) qprm.expand_th->flag |= GAL_DATA_FLAG_HASBLANK;
+ }
qprm.noerode_th->flag |= GAL_DATA_FLAG_BLANK_CH;
+ if(p->detgrowquant!=1.0f) qprm.expand_th->flag |= GAL_DATA_FLAG_BLANK_CH;
if(p->qthreshname)
{
qprm.erode_th->name="QTHRESH_ERODE";
qprm.noerode_th->name="QTHRESH_NOERODE";
- gal_tile_full_values_write(qprm.erode_th, tl, p->qthreshname, NULL,
+ gal_tile_full_values_write(qprm.erode_th, tl, 1, p->qthreshname, NULL,
PROGRAM_NAME);
- gal_tile_full_values_write(qprm.noerode_th, tl, p->qthreshname, NULL,
+ gal_tile_full_values_write(qprm.noerode_th, tl, 1, p->qthreshname, NULL,
PROGRAM_NAME);
- qprm.erode_th->name = qprm.noerode_th->name = NULL;
+ qprm.erode_th->name=qprm.noerode_th->name=NULL;
+
+ if(qprm.expand_th)
+ {
+ qprm.expand_th->name="QTHRESH_EXPAND";
+ gal_tile_full_values_write(qprm.expand_th, tl, 1, p->qthreshname,
+ NULL, PROGRAM_NAME);
+ qprm.expand_th->name=NULL;
+ }
}
/* Interpolate and smooth the derived values. */
threshold_interp_smooth(p, &qprm.erode_th, &qprm.noerode_th,
+ qprm.expand_th ? & qprm.expand_th : NULL,
p->qthreshname);
@@ -513,6 +599,10 @@ threshold_quantile_find_apply(struct noisechiselparams *p)
gal_fits_img_write(p->binary, p->qthreshname, NULL, PROGRAM_NAME);
+ /* Set the expansion quantile if necessary. */
+ p->expand_thresh = qprm.expand_th ? qprm.expand_th : NULL;
+
+
/* Clean up and report duration if necessary. */
gal_data_free(qprm.erode_th);
gal_data_free(qprm.noerode_th);
diff --git a/bin/noisechisel/threshold.h b/bin/noisechisel/threshold.h
index 75f88c0..595fa11 100644
--- a/bin/noisechisel/threshold.h
+++ b/bin/noisechisel/threshold.h
@@ -44,7 +44,8 @@ threshold_write_sn_table(struct noisechiselparams *p,
gal_data_t *sntable,
void
threshold_interp_smooth(struct noisechiselparams *p, gal_data_t **first,
- gal_data_t **second, char *filename);
+ gal_data_t **second, gal_data_t **third,
+ char *filename);
void
threshold_quantile_find_apply(struct noisechiselparams *p);
diff --git a/bin/noisechisel/ui.c b/bin/noisechisel/ui.c
index 5f634c1..ab52ee2 100644
--- a/bin/noisechisel/ui.c
+++ b/bin/noisechisel/ui.c
@@ -119,7 +119,6 @@ ui_initialize_options(struct noisechiselparams *p,
cp->numthreads = gal_threads_number();
cp->coptions = gal_commonopts_options;
-
/* Modify common options. */
for(i=0; !gal_options_is_last(&cp->coptions[i]); ++i)
{
@@ -236,7 +235,6 @@ ui_read_check_only_options(struct noisechiselparams *p)
{
/* A general check on the neighbor connectivity values. */
ui_ngb_check(p->erodengb, "erodengb");
- ui_ngb_check(p->dilatengb, "dilatengb");
ui_ngb_check(p->openingngb, "openingngb");
/* Make sure that the no-erode-quantile is not smaller or equal to
@@ -256,6 +254,36 @@ ui_read_check_only_options(struct noisechiselparams *p)
"following command for more information (use `SPACE' to go down "
"the page and `q' to return to the command-line):\n\n"
" $ info gnuastro \"Input Output options\"");
+
+ /* Kernel checks. */
+ if(p->kernelname)
+ {
+ /* Check if it exists. */
+ gal_checkset_check_file(p->kernelname);
+
+ /* If its FITS, see if a HDU has been provided. */
+ if( gal_fits_name_is_fits(p->kernelname) && p->khdu==NULL )
+ error(EXIT_FAILURE, 0, "no HDU specified for kernel. When the "
+ "kernel is a FITS file, a HDU must also be specified. You "
+ "can use the `--khdu' option and give it the HDU number "
+ "(starting from zero), extension name, or anything "
+ "acceptable by CFITSIO");
+ }
+
+ /* Wide kernel checks. */
+ if(p->widekernelname)
+ {
+ /* Check if it exists. */
+ gal_checkset_check_file(p->widekernelname);
+
+ /* If its FITS, see if a HDU has been provided. */
+ if( gal_fits_name_is_fits(p->widekernelname) && p->wkhdu==NULL )
+ error(EXIT_FAILURE, 0, "no HDU specified for wide kernel. When the "
+ "wide kernel is a FITS file, a HDU must also be specified. You "
+ "can use the `--khdu' option and give it the HDU number "
+ "(starting from zero), extension name, or anything "
+ "acceptable by CFITSIO");
+ }
}
@@ -281,21 +309,6 @@ ui_check_options_and_arguments(struct noisechiselparams *p)
}
else
error(EXIT_FAILURE, 0, "no input file is specified");
-
- /* Basic Kernel file checks. */
- if(p->kernelname)
- {
- /* Check if it exists. */
- gal_checkset_check_file(p->kernelname);
-
- /* If its FITS, see if a HDU has been provided. */
- if( gal_fits_name_is_fits(p->kernelname) && p->khdu==NULL )
- error(EXIT_FAILURE, 0, "no HDU specified for kernel. When the "
- "kernel is a FITS file, a HDU must also be specified, you "
- "can use the `--khdu' option and give it the HDU number "
- "(starting from zero), extension name, or anything "
- "acceptable by CFITSIO");
- }
}
@@ -367,7 +380,7 @@ ui_set_output_names(struct noisechiselparams *p)
? "_detsn_det.txt" : "_detsn_det.fits") );
p->detsn_D_name=gal_checkset_automatic_output(&p->cp, basename,
( p->cp.tableformat==GAL_TABLE_FORMAT_TXT
- ? "_detsn_dilated.txt" : "_detsn_dilated.fits") );
+ ? "_detsn_grown.txt" : "_detsn_grown.fits") );
}
/* Detection steps. */
@@ -535,6 +548,13 @@ ui_prepare_kernel(struct noisechiselparams *p)
ff = (f=p->kernel->array) + p->kernel->size;
do *f=*k++; while(++f<ff);
}
+
+
+ /* If a wide kernel is given, then read it into memory. Otherwise, just
+ ignore it. */
+ if(p->widekernelname)
+ p->widekernel=gal_fits_img_read_kernel(p->widekernelname, p->wkhdu,
+ p->cp.minmapsize);
}
@@ -699,9 +719,7 @@ ui_preparations(struct noisechiselparams *p)
ui_preparations_read_input(p);
- /* Check for blank values to help later processing. AFTERWARDS, set the
- USE_ZERO flag, so the zero-bit (if the input doesn't have any blank
- value) will be meaningful. */
+ /* Check for blank values to help later processing. */
gal_blank_present(p->input, 1);
@@ -805,12 +823,18 @@ ui_read_check_inputs_setup(int argc, char *argv[],
p->cp.numthreads==1 ? "." : "s.");
printf(" - Input: %s (hdu: %s)\n", p->inputname, p->cp.hdu);
if(p->kernelname)
- printf(" - Kernel: %s (hdu: %s)\n", p->kernelname, p->khdu);
+ printf(" - %s: %s (hdu: %s)\n",
+ p->widekernelname ? "Sharp Kernel" : "Kernel",
+ p->kernelname, p->khdu);
else
printf(p->kernel->ndim==2
- ? " - Kernel: FWHM=2 pixel Gaussian.\n"
- : " - Kernel: FWHM=1.5 pixel Gaussian (half extent in "
- "3rd dimension).\n");
+ ? " - %s: FWHM=2 pixel Gaussian.\n"
+ : " - %s: FWHM=1.5 pixel Gaussian (half extent in "
+ "3rd dimension).\n",
+ p->widekernelname ? "Sharp Kernel" : "Kernel");
+ if(p->widekernelname)
+ printf(" - Wide Kernel: %s (hdu: %s)\n", p->widekernelname,
+ p->wkhdu);
}
}
@@ -890,11 +914,13 @@ ui_free_report(struct noisechiselparams *p, struct
timeval *t1)
gal_data_free(p->sky);
gal_data_free(p->std);
gal_data_free(p->conv);
+ gal_data_free(p->wconv);
gal_data_free(p->input);
gal_data_free(p->kernel);
gal_data_free(p->binary);
gal_data_free(p->olabel);
gal_data_free(p->clabel);
+ gal_data_free(p->widekernel);
/* Clean up the tile structure. */
p->ltl.numchannels=NULL;
diff --git a/bin/noisechisel/ui.h b/bin/noisechisel/ui.h
index 416cd76..bfe3b22 100644
--- a/bin/noisechisel/ui.h
+++ b/bin/noisechisel/ui.h
@@ -29,7 +29,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
/* Available letters for short options:
- a b f j l n u w x z
+ a b f j l n u x z
A H J W X Y
*/
enum option_keys_enum
@@ -37,6 +37,7 @@ enum option_keys_enum
/* With short-option version. */
UI_KEY_LARGETILESIZE = 'L',
UI_KEY_KERNEL = 'k',
+ UI_KEY_WIDEKERNEL = 'w',
UI_KEY_SKYSUBTRACTED = 'E',
UI_KEY_MINSKYFRAC = 'B',
UI_KEY_MIRRORDIST = 'r',
@@ -48,7 +49,7 @@ enum option_keys_enum
UI_KEY_DTHRESH = 'R',
UI_KEY_DETSNMINAREA = 'i',
UI_KEY_DETQUANT = 'c',
- UI_KEY_DILATE = 'd',
+ UI_KEY_DETGROWQUANT = 'd',
UI_KEY_SEGSNMINAREA = 'm',
UI_KEY_SEGQUANT = 'g',
UI_KEY_KEEPMAXNEARRIVER = 'v',
@@ -61,6 +62,7 @@ enum option_keys_enum
/* Only with long version (start with a value 1000, the rest will be set
automatically). */
UI_KEY_KHDU = 1000,
+ UI_KEY_WKHDU,
UI_KEY_MINNUMFALSE,
UI_KEY_ONLYDETECTION,
UI_KEY_GROWNCLUMPS,
@@ -71,8 +73,8 @@ enum option_keys_enum
UI_KEY_OPENINGNGB,
UI_KEY_CHECKDETSKY,
UI_KEY_CHECKDETSN,
- UI_KEY_DILATENGB,
- UI_KEY_CLEANDILATED,
+ UI_KEY_DETGROWMAXHOLESIZE,
+ UI_KEY_CLEANGROWNDET,
UI_KEY_CHECKDETECTION,
UI_KEY_CHECKSKY,
UI_KEY_CHECKCLUMPSN,
diff --git a/bin/statistics/sky.c b/bin/statistics/sky.c
index f68678c..098338f 100644
--- a/bin/statistics/sky.c
+++ b/bin/statistics/sky.c
@@ -192,9 +192,9 @@ sky(struct statisticsparams *p)
}
if(p->checksky)
{
- gal_tile_full_values_write(p->sky_t, tl, p->checkskyname, NULL,
+ gal_tile_full_values_write(p->sky_t, tl, 1, p->checkskyname, NULL,
PROGRAM_NAME);
- gal_tile_full_values_write(p->std_t, tl, p->checkskyname, NULL,
+ gal_tile_full_values_write(p->std_t, tl, 1, p->checkskyname, NULL,
PROGRAM_NAME);
}
@@ -213,9 +213,9 @@ sky(struct statisticsparams *p)
gal_timing_report(&t1, "All blank tiles filled (interplated).", 1);
if(p->checksky)
{
- gal_tile_full_values_write(p->sky_t, tl, p->checkskyname, NULL,
+ gal_tile_full_values_write(p->sky_t, tl, 1, p->checkskyname, NULL,
PROGRAM_NAME);
- gal_tile_full_values_write(p->std_t, tl, p->checkskyname, NULL,
+ gal_tile_full_values_write(p->std_t, tl, 1, p->checkskyname, NULL,
PROGRAM_NAME);
}
@@ -237,9 +237,9 @@ sky(struct statisticsparams *p)
1);
if(p->checksky)
{
- gal_tile_full_values_write(p->sky_t, tl, p->checkskyname, NULL,
+ gal_tile_full_values_write(p->sky_t, tl, 1, p->checkskyname, NULL,
PROGRAM_NAME);
- gal_tile_full_values_write(p->std_t, tl, p->checkskyname, NULL,
+ gal_tile_full_values_write(p->std_t, tl, 1, p->checkskyname, NULL,
PROGRAM_NAME);
}
}
@@ -250,8 +250,8 @@ sky(struct statisticsparams *p)
( p->cp.output
? p->cp.output
: p->inputname ), "_sky.fits");
- gal_tile_full_values_write(p->sky_t, tl, outname, NULL, PROGRAM_NAME);
- gal_tile_full_values_write(p->std_t, tl, outname, NULL, PROGRAM_NAME);
+ gal_tile_full_values_write(p->sky_t, tl, 1, outname, NULL, PROGRAM_NAME);
+ gal_tile_full_values_write(p->std_t, tl, 1, outname, NULL, PROGRAM_NAME);
if(!cp->quiet)
printf(" - Written to `%s'.\n", outname);
diff --git a/bin/statistics/statistics.c b/bin/statistics/statistics.c
index 7b27985..e4a2e2b 100644
--- a/bin/statistics/statistics.c
+++ b/bin/statistics/statistics.c
@@ -254,7 +254,7 @@ statistics_interpolate_and_write(struct statisticsparams *p,
}
/* Write the values. */
- gal_tile_full_values_write(values, &cp->tl, output, NULL, PROGRAM_NAME);
+ gal_tile_full_values_write(values, &cp->tl, 1, output, NULL, PROGRAM_NAME);
}
diff --git a/configure.ac b/configure.ac
index 4b9d39f..73d8679 100644
--- a/configure.ac
+++ b/configure.ac
@@ -50,7 +50,7 @@ AC_CONFIG_MACRO_DIRS([bootstrapped/m4])
# Library version, see the GNU Libtool manual ("Library interface versions"
# section for the exact definition of each) for
-GAL_CURRENT=2
+GAL_CURRENT=3
GAL_REVISION=0
GAL_AGE=0
GAL_LT_VERSION="${GAL_CURRENT}:${GAL_REVISION}:${GAL_AGE}"
diff --git a/doc/announce-acknowledge.txt b/doc/announce-acknowledge.txt
index 20169f3..b76e5bb 100644
--- a/doc/announce-acknowledge.txt
+++ b/doc/announce-acknowledge.txt
@@ -1,17 +1,4 @@
This file is meant to keep the names of the people who's help must be
acknowledged in the next release.
-Marjan Akbari
-Fernando Buitrago
-Adrian Bunk
-Antonio Diaz Diaz
-Mosè Giordano
-Stephen Hamer
-Raúl Infante Sainz
-Aurélien Jarno
-Alan Lefor
-Guillaume Mahler
-William Pence
-Ole Streicher
-Ignacio Trujillo
-David Valls-Gabaud
+Takashi Ichikawa
diff --git a/doc/gnuastro-top.html b/doc/gnuastro-top.html
index 73880ea..ad74e98 100644
--- a/doc/gnuastro-top.html
+++ b/doc/gnuastro-top.html
@@ -128,9 +128,9 @@ for entertaining and easy to read real world examples of
using
<p>
The current stable release
- is <a href="http://ftp.gnu.org/gnu/gnuastro/gnuastro-0.3.tar.gz";>Gnuastro
- 0.3</a> (June 1st, 2017).
- Use <a href="http://ftpmirror.gnu.org/gnuastro/gnuastro-0.3.tar.gz";>a
+ is <a href="http://ftp.gnu.org/gnu/gnuastro/gnuastro-0.4.tar.gz";>Gnuastro
+ 0.4</a> (September 13th, 2017).
+ Use <a href="http://ftpmirror.gnu.org/gnuastro/gnuastro-0.4.tar.gz";>a
mirror</a> if possible.
<!-- Comment the test release notice when the test release is not more
@@ -141,7 +141,7 @@ for entertaining and easy to read real world examples of
using
To stay up to date, please subscribe.</p>
<p>For details of the significant changes please see the
- <a
href="http://git.savannah.gnu.org/cgit/gnuastro.git/plain/NEWS?id=gnuastro_v0.3";>NEWS</a>
+ <a
href="http://git.savannah.gnu.org/cgit/gnuastro.git/plain/NEWS?id=gnuastro_v0.4";>NEWS</a>
file.</p>
<p>The
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index b6c95a1..474640a 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -1545,12 +1545,12 @@ management of its version controlled source server
there.
@c (alphabetical, except for the names in the paragraph above).
We would also like to gratefully thank (in alphabetical order by family
name) Marjan Akbari, Roland Bacon, Nicolas Bouch@'e, Fernando Buitrago,
-Adrian Bunk, Rosa Calvi, Antonio Diaz Diaz, Stephen Hamer, Raúl Infante
-Sainz, Lee Kelvin, Mohammad-Reza Khellat, Alan Lefor, Guillaume Mahler,
-Francesco Montanari, William Pence, Yahya Sefidbakht, Ole Streicher,
-Ignacio Trujillo, David Valls-Gabaud and Christopher Willmer for their
-useful and constructive comments and suggestions. Finally we should thank
-all the (sometimes anonymous) people in various online forums which
+Adrian Bunk, Rosa Calvi, Antonio Diaz Diaz, Stephen Hamer, Ra@'ul Infante
+Sainz, Aur@'elien Jarno, Lee Kelvin, Mohammad-Reza Khellat, Alan Lefor,
+Guillaume Mahler, Francesco Montanari, William Pence, Yahya Sefidbakht, Ole
+Streicher, Ignacio Trujillo, David Valls-Gabaud and Christopher Willmer for
+their useful and constructive comments and suggestions. Finally we should
+thank all the (sometimes anonymous) people in various online forums which
patiently answered all our small (but important) technical questions.
All work on Gnuastro has been voluntary, but the authors are most grateful
@@ -1699,8 +1699,8 @@ column it has each object's Right Ascension (the first
column is a label he
has given to each object) and in the third the object's declination.
@example
-$ astcrop --racol=2 --deccol=3 /mnt/data/images/*.fits \
- /mnt/data/catalogs/extragalactic.txt
+$ astcrop --coordcol=2 --coordcol=3 /mnt/data/images/*.fits \
+ --mode=wcs /mnt/data/catalogs/extragalactic.txt
Crop started on Tue Jun 14 10:18:11 1932
---- ./4_crop.fits 1 1
---- ./2_crop.fits 1 1
@@ -3380,29 +3380,34 @@ but not run the tests and directly install after
building.
@cindex Root access, not possible
@cindex No access to super-user install
@cindex Install with no super-user access
-One of the most commonly used options to configure is the directory that
-will host all the files which require installing (for example the actual
-executable files for the program and/or the documentation and configuration
-files). This is done through the @option{--prefix} option. To demonstrate
-its applicability, let's assume you don't have administrator or root access
-but you want to be able to access the installed files from anywhere while
-you are logged in (one of the most common uses of @option{--prefix}).
-
-The most basic way to run an executable is to explicitly type the full file
-name (including all the directory information) and run it. One example is
-running the configuration script with the @command{$ ./configure} command
-(see @ref{Quick start}). By giving a specific directory (the current
-directory or @file{./}), we are explicitly telling the shell to look in the
-current directory for an executable file named `@file{configure}'. Directly
-specifying the directory is thus useful for simple shell scripts in the
-current (or nearby) directories. However, when the program (an executable)
-is to be used a lot, specifying all those directories will become a
-significant burden. For example, the @file{ls} executable lists the
-contents in a given directory and it is (usually) installed in the
-@file{/usr/bin/} directory by the operating system maintainers. So each
-time you you want to use it you would have to run the following command
-(which is very inconvenient, both in typing and in remembering the various
-directories).
+One of the most commonly used options to @file{./configure} is
+@option{--prefix}, it is used to define the directory that will host all
+the installed files (or the ``prefix'' in their final absolute file
+name). For example, when you are using a server and you don't have
+administrator or root access. In this example scenario, if you don't use
+the @option{--prefix} option, you won't be able to install the built files
+and thus access them from anywhere without having to worry about where they
+are installed. However, once you prepare your startup file to look into the
+proper place (as discussed thoroughly below), you will be able to easily
+use this option and benefit from any software you want to install without
+having to ask the system administrators or install and use a different
+version of a software that is already installed on the server.
+
+The most basic way to run an executable is to explicitly write its full
+file name (including all the directory information) and run it. One example
+is running the configuration script with the @command{$ ./configure}
+command (see @ref{Quick start}). By giving a specific directory (the
+current directory or @file{./}), we are explicitly telling the shell to
+look in the current directory for an executable file named
+`@file{configure}'. Directly specifying the directory is thus useful for
+executables in the current (or nearby) directories. However, when the
+program (an executable file) is to be used a lot, specifying all those
+directories will become a significant burden. For example, the @file{ls}
+executable lists the contents in a given directory and it is (usually)
+installed in the @file{/usr/bin/} directory by the operating system
+maintainers. So each time you want to use it you would have to run the
+following command (which is very inconvenient, both in writing and in
+remembering the various directories).
@example
$ /usr/bin/ls
@@ -3413,31 +3418,37 @@ $ /usr/bin/ls
To address this problem, we have the @file{PATH} environment variable. To
understand it better, we will start with a short introduction to the shell
variables. Shell variable values are basically treated as strings of
-characters. You can define a variable and a value for it by running
+characters. For example, it doesn't matter if the value is a name (string
+of @emph{alphabetic} characters) or a number (string of @emph{numeric}
+characters). You can define a variable and a value for it by running
@example
-$ myvariable=a_test_value
+$ myvariable1=a_test_value
+$ myvariable2="a test value"
@end example
@noindent
-You can see the value it represents by running
+As you see above, if the value contains white space characters, you have to
+put the whole value (including white space characters) in double quotes
+(@key{"}). You can see the value it represents by running
@example
-$ echo $myvariable
+$ echo $myvariable1
+$ echo $myvariable2
@end example
@noindent
@cindex Environment
@cindex Environment variables
-If a variable has no value, the last command will only print an empty
-line. A variable defined like this will be known as long as this shell or
-terminal is running. Other terminals will have no idea it existed. The
-main advantage of shell variables is that if they are exported@footnote{By
-running @command{$ export myvariable=a_test_value} instead of the simpler
-case in the text}, subsequent programs that are run within that shell can
-access their value. So by giving them different values, you can change the
-``environment'' of a program which uses their values. The shell variables
-which are accessed by programs are therefore known as ``environment
-variables''@footnote{You can use shell variables for other actions too, for
-example to temporarily keep some names or run loops on some files.}. You
-can see the full list of the environment variables that your shell
-currently recognizes by running:
+If a variable has no value or it wasn't defined, the last command will only
+print an empty line. A variable defined like this will be known as long as
+this shell or terminal is running. Other terminals will have no idea it
+existed. The main advantage of shell variables is that if they are
+exported@footnote{By running @command{$ export myvariable=a_test_value}
+instead of the simpler case in the text}, subsequent programs that are run
+within that shell can access their value. So by changing their value, you
+can change the ``environment'' of a program which uses them. The shell
+variables which are accessed by programs are therefore known as
+``environment variables''@footnote{You can use shell variables for other
+actions too, for example to temporarily keep some names or run loops on
+some files.}. You can see the full list of exported variables that your
+shell recognizes by running:
@example
$ printenv
@@ -3447,11 +3458,11 @@ $ printenv
@cindex @file{HOME/.local/}
@cindex Environment variable, @code{HOME}
@file{HOME} is one commonly used environment variable, it is any user's
-(the one that is logged in) top directory. It is used so often that the
-shell has a special expansion (alternative) for it: `@file{~}'. Whenever
-you see file names starting with the tilde sign, it actually represents the
-value to the @file{HOME} environment variable, so @file{~/doc} is the same
-as @file{$HOME/doc}.
+(the one that is logged in) top directory. Try finding it in the command
+above. It is used so often that the shell has a special expansion
+(alternative) for it: `@file{~}'. Whenever you see file names starting with
+the tilde sign, it actually represents the value to the @file{HOME}
+environment variable, so @file{~/doc} is the same as @file{$HOME/doc}.
@vindex PATH
@pindex ./configure
@@ -3489,13 +3500,15 @@ components: programs (executables), libraries, include
(header) files,
shared data (like manuals), or configuration files (see @ref{Review of
library fundamentals} for a thorough introduction to headers and
linking). So it commonly has some of the following sub-directories for each
-class of components respectively: @file{bin/}, @file{lib/}, @file{include/}
-@file{man/}, @file{share/}, @file{etc/}. Since the @file{PATH} variable is
-only used for executables, you can add the @file{~/.local/bin} directory to
-@file{PATH} with the following command. As defined below, first the
-existing value of @file{PATH} is used, then your given directory is added
-to its end and the combined value is put back in @file{PATH} (run
-`@command{$ echo $PATH}' afterwards to check if it was added).
+class of installed components respectively: @file{bin/}, @file{lib/},
+@file{include/} @file{man/}, @file{share/}, @file{etc/}. Since the
+@file{PATH} variable is only used for executables, you can add the
+@file{~/.local/bin} directory (which keeps the executables/programs or more
+generally, ``binary'' files) to @file{PATH} with the following command. As
+defined below, first the existing value of @file{PATH} is used, then your
+given directory is added to its end and the combined value is put back in
+@file{PATH} (run `@command{$ echo $PATH}' afterwards to check if it was
+added).
@example
$ PATH=$PATH:~/.local/bin
@@ -3504,14 +3517,15 @@ $ PATH=$PATH:~/.local/bin
@cindex GNU Bash
@cindex Startup scripts
@cindex Scripts, startup
-Any executable that you installed in this directory will now be usable
-without having to remember and type its full address. However, as soon as
-you leave your current terminal session, this modified @file{PATH} variable
-will be forgotten. Adding your specified directory to the @file{PATH}
-environment variable each time you start a terminal is also very
-inconvenient and prone to errors. So there are standard `startup files'
-defined by your shell. There is a special startup file for every
-significant starting step:
+Any executable that you installed in @file{~/.local/bin} will now be usable
+without having to remember and write its full address. However, as soon as
+you leave/close your current terminal session, this modified @file{PATH}
+variable will be forgotten. Adding the directories which contain
+executables to the @file{PATH} environment variable each time you start a
+terminal is also very inconvenient and prone to errors. Fortunately, there
+are standard `startup files' defined by your shell precisely for this (and
+other) purposes. There is a special startup file for every significant
+starting step:
@table @asis
@@ -3535,17 +3549,13 @@ emulator in the graphic user interface).
For security reasons, it is highly recommended to directly type in your
@file{HOME} directory value by hand in startup files instead of using
variables. So in the following, let's assume your user name is
-`@file{name}'. To add @file{~/.local/bin} to your @file{PATH} automatically
-on any startup file, you have to ``export'' the new value of @command{PATH}
-in the startup file that is most relevant to you with the line
-`@command{export PATH=$PATH:/home/name/.local/bin}'. You can either do it
-manually using a text editor, or by running the following command which
-will add this line as the last line of the file. Let's assume you want to
-add it to @file{~/.bashrc} (afterwards, open your @file{~/.bashrc} with a
-text editor and check it out, to see the result for your self):
+`@file{name}' (so @file{~} may be replaced with @file{/home/name}). To add
+@file{~/.local/bin} to your @file{PATH} automatically on any startup file,
+you have to ``export'' the new value of @command{PATH} in the startup file
+that is most relevant to you by adding this line:
@example
-$ echo 'export PATH=$PATH:/home/name/.local/bin' >> ~/.bashrc
+export PATH=$PATH:/home/name/.local/bin
@end example
@cindex GNU build system
@@ -3554,17 +3564,17 @@ $ echo 'export PATH=$PATH:/home/name/.local/bin' >>
~/.bashrc
Now that you know your system will look into @file{~/.local/bin} for
executables, you can tell Gnuastro's configure script to install everything
in the top @file{~/.local} directory using the @option{--prefix}
-option. The configure script will then put the executables in
-@file{~/.local/bin}, the compiled library files in @file{~/.local/lib}, the
-library header files in @file{~/.local/include} and so on (see @ref{Review
-of library fundamentals} for a review of the compiled library files and the
-headers). When you subsequently run @command{$ make install}, all the
+option. When you subsequently run @command{$ make install}, all the
install-able files will be put in their respective directory under
-@file{~/.local/} (as discussed above). Note that tilde (`@key{~}')
-expansion will not happen if you put a `@key{=}' between @option{--prefix}
-and @file{~/.local}@footnote{If you insist on using `@key{=}', you can use
-@option{--prefix=$HOME/.local}.}, so we have avoided the @key{=} character
-here which is optional in GNU-style options, see @ref{Options}.
+@file{~/.local/} (the executables in @file{~/.local/bin}, the compiled
+library files in @file{~/.local/lib}, the library header files in
+@file{~/.local/include} and so on, to learn more about these different
+files, please see @ref{Review of library fundamentals}). Note that tilde
+(`@key{~}') expansion will not happen if you put a `@key{=}' between
+@option{--prefix} and @file{~/.local}@footnote{If you insist on using
+`@key{=}', you can use @option{--prefix=$HOME/.local}.}, so we have avoided
+the @key{=} character here which is optional in GNU-style options, see
+@ref{Options}.
@example
$ ./configure --prefix ~/.local
@@ -3576,14 +3586,16 @@ $ ./configure --prefix ~/.local
@cindex Library search directory
@cindex Default library search directory
You can install everything (including libraries like GSL, CFITSIO, or
-WCSLIB) locally by configuring them as above. However, recall that
-@command{PATH} is only for executable files, not libraries. Therefore, when
-building programs or libraries@footnote{For example WCSLIB which needs
-CFITSIO, or Gnuastro which needs both.} that depend on libraries you
-installed like this, you have to guide your compiler to the necessary
-directories. To do that, you have to define the @command{LDFLAGS} and
-@command{CPPFLAGS} environment variables respectively. This can be done
-while calling @file{./configure} as shown below:
+WCSLIB which are Gnuastro's mandatory dependencies, see @ref{Mandatory
+dependencies}) locally by configuring them as above. However, recall that
+@command{PATH} is only for executable files, not libraries and that
+libraries can also depend on other libraries. For example WCSLIB depends on
+CFITSIO and Gnuastro needs both. Therefore, when you installed a library in
+a non-recognized directory, you have to guide the program that depends on
+them to look into the necessary library and header file directories. To do
+that, you have to define the @command{LDFLAGS} and @command{CPPFLAGS}
+environment variables respectively. This can be done while calling
+@file{./configure} as shown below:
@example
$ ./configure LDFLAGS=-L/home/name/.local/lib \
@@ -3591,39 +3603,36 @@ $ ./configure LDFLAGS=-L/home/name/.local/lib
\
--prefix ~/.local
@end example
-If you do this for all your libraries, it can be annoying to do this when
-configuring every software that depends on them. Hence, you can define
-these two variables in the most relevant startup file (discussed
-above). The convention on using these variables doesn't include a colon to
-separate values (as @command{PATH}-like variables do), they use white space
-characters and each value is prefixed with a compiler option@footnote{These
-variables are ultimately used as options while building the programs, so
-every value has be an option name followed be a value as discussed in
-@ref{Options}.} (note the @option{-L} and @option{-I} above, see
-@ref{Options}, @ref{Headers} for @option{-I}, and @ref{Linking} for
-@option{-L}). Therefore we have to keep the value in double quotation signs
-to keep the white space characters. Run the following two commands to do
-that if you want them in your @file{~/.bashrc}.
+It can be annoying/buggy to do this when configuring every software that
+depends on such libraries. Hence, you can define these two variables in the
+most relevant startup file (discussed above). The convention on using these
+variables doesn't include a colon to separate values (as
+@command{PATH}-like variables do), they use white space characters and each
+value is prefixed with a compiler option@footnote{These variables are
+ultimately used as options while building the programs, so every value has
+be an option name followed be a value as discussed in @ref{Options}.}: note
+the @option{-L} and @option{-I} above (see @ref{Options}), for @option{-I}
+see @ref{Headers}, and for @option{-L}, see @ref{Linking}. Therefore we
+have to keep the value in double quotation signs to keep the white space
+characters and adding the following two lines to the startup file of
+choice:
@example
-echo 'export LDFLAGS="$LDFLAGS -L/home/name/.local/lib"' >> ~/.bashrc
-echo 'export CPPFLAGS="$CPPFLAGS -I/home/name/.local/include"' \
- >> ~/.bashrc
+export LDFLAGS="$LDFLAGS -L/home/name/.local/lib"
+export CPPFLAGS="$CPPFLAGS -I/home/name/.local/include"
@end example
+@cindex Dynamic libraries
Dynamic libraries are linked to the executable every time you run a program
that depends on them (see @ref{Linking} to fully understand this important
concept). Hence dynamic libraries also require a special path variable
-called @command{LD_LIBRARY_PATH}. To use programs that depend on these
-libraries, you will need to have @file{~/.local/lib} added to your
-@command{LD_LIBRARY_PATH} environment variable in the relevant start-up
-file (similar to @command{PATH}) as shown below (the @key{\} is only to fit
-this command within the page width, you can ignore it when typing on the
-terminal):
+called @command{LD_LIBRARY_PATH} (same formatting as @command{PATH}). To
+use programs that depend on these libraries, you need to add
+@file{~/.local/lib} to your @command{LD_LIBRARY_PATH} environment variable
+by adding the following line to the relevant start-up file:
@example
-echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/name/.local/lib' \
- >> ~/.bashrc
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/name/.local/lib
@end example
If you also want to access the Info (see @ref{Info}) and man pages (see
@@ -3659,20 +3668,46 @@ export
LD_LIBRARY_PATH=/home/name/.local/lib:$LD_LIBRARY_PATH
This is good when a library, for example CFITSIO, is already present on the
system, but the system-wide install wasn't configured with the correct
configuration flags (see @ref{CFITSIO}), or you want to use a newer version
-and you don't have administrator or root access to update it. If you update
-@file{LD_LIBRARY_PATH} with the @file{~/.local/lib} installation first, the
-linker will first find the CFITSIO you installed for yourself and link with
-it. It will never reach the system-wide installation. However there are
-important security problems with this order: all important system-wide
-programs and libraries can be replaced by non-secure versions with the same
-file names and put in the customized directory (@file{./.local/lib} in this
-example). So if you choose to search in your customized directory first, be
-sure to keep it clean from executables or libraries with the same names as
-important system programs or libraries.
-
+and you don't have administrator or root access to update it on the whole
+system/server. If you update @file{LD_LIBRARY_PATH} by placing
+@file{~/.local/lib} first (like above), the linker will first find the
+CFITSIO you installed for yourself and link with it. It thus will never
+reach the system-wide installation.
+
+There are important security problems with using local installations first:
+all important system-wide executables and libraries (important executables
+like @command{ls} and @command{cp}, or libraries like the C library) can be
+replaced by non-secure versions with the same file names and put in the
+customized directory (@file{~/.local} in this example). So if you choose to
+search in your customized directory first, please @emph{be sure} to keep it
+clean from executables or libraries with the same names as important system
+programs or libraries.
+@cartouche
+@noindent
+@strong{Summary:} When you are using a server which doesn't give you
+administrator/root access AND you would like to give priority to your own
+built programs and libraries, not the version that is (possibly already)
+present on the server, add these lines to your startup file. See above for
+which startup file is best for your case and for a detailed explanation on
+each. Don't forget to replace `@file{/YOUR-HOME-DIR}' with your home
+directory (for example `@file{/home/your-id}'):
+@example
+export PATH="/YOUR-HOME-DIR/.local/bin:$PATH"
+export LDFLAGS="-L/YOUR-HOME-DIR/.local/lib $LDFLAGS"
+export MANPATH="/YOUR-HOME-DIR/.local/share/man/:$MANPATH"
+export CPPFLAGS="-I/YOUR-HOME-DIR/.local/include $CPPFLAGS"
+export INFOPATH="/YOUR-HOME-DIR/.local/share/info/:$INFOPATH"
+export LD_LIBRARY_PATH="/YOUR-HOME-DIR/.local/lib:$LD_LIBRARY_PATH"
+@end example
+@noindent
+Afterwards, you just need to add an extra
+@option{--prefix=/YOUR-HOME-DIR/.local} to the @file{./configure} command
+of the software that you intend to install. Everything else will be the
+same as a standard build and install, see @ref{Quick start}.
+@end cartouche
@node Executable names, Configure and build in RAM, Installation directory,
Configuring
@subsubsection Executable names
@@ -4161,18 +4196,18 @@ tokens that are not preceded by any hyphens
(@command{-}, see
@ref{Arguments}). Here is one example:
@example
-$ astcrop --ra=53.162551 --dec=-27.789676 -w10 hubble-udf.fits
+$ astcrop --center=53.162551,-27.789676 -w10/3600 --mode=wcs udf.fits
@end example
-In this example, the argument is @file{hubble-udf.fits}. Arguments are most
+In this example, the argument is @file{udf.fits}. Arguments are most
commonly the input file names containing your data. Options start with one
or two hyphens, followed by an identifier for the option (the option's
name) and its value (see @ref{Options}). Through options you tell the
program how to interpret the data. In this example, we are running
-@ref{Crop} to crop a region of width 10 arc-seconds centered at the given RA
-and Dec from the input Hubble Ultra-Deep Field (UDF) FITS image. So options
-come with an identifier (the option name which is separate from their
-value).
+@ref{Crop} to crop a region of width 10 arc-seconds centered at the given
+RA and Dec from the input Hubble Ultra-Deep Field (UDF) FITS image. So
+options come with an identifier (the option name which is separate from
+their value).
@vindex --help
@vindex --usage
@@ -5402,7 +5437,7 @@ are inclusive.
@item i8
@itemx int8
8-bit signed integers, range:@*
-@mymath{[-2^7\rm{\ to\ }2^7-1]} or @mymath{[-127\rm{\ to\ }127]}.
+@mymath{[-2^7\rm{\ to\ }2^7-1]} or @mymath{[-128\rm{\ to\ }127]}.
@item u16
@itemx uint16
@@ -5412,7 +5447,7 @@ are inclusive.
@item i16
@itemx int16
16-bit signed integers, range:@* @mymath{[-2^{15}\rm{\ to\ }2^{15}-1]} or
-@mymath{[-32768\rm{\ to\ }32768]}.
+@mymath{[-32768\rm{\ to\ }32767]}.
@item u32
@itemx uint32
@@ -5825,14 +5860,16 @@ $ asttable --information table-file
@end example
Gnuastro's programs need the columns for different purposes, for example in
-Crop, you specify the column containing the Right Ascension of the crop
-centers with the @option{--racol} option and the column containing the
-Declination with @option{--deccol}. Thus, there is no unified common option
-name to select columns for all programs. However, when the program expects
-the column for a specific context (like the RA and Dec example above), the
-option names end in the @option{col} suffix (for example @option{--racol}
-and @option{--deccol}). These options accept values in integer (column
-number), or string (metadata match/search) format.
+Crop, you specify the columns containing the central coordinates of the
+crop centers with the @option{--coordcol} option (see @ref{Crop
+options}). On the other hand, in MakeProfiles, to specify the column
+containing the profile position angles, you must use the @option{--pcol}
+option (see @ref{MakeProfiles catalog}). Thus, there can be no unified
+common option name to select columns for all programs (different columns
+have different purposes). However, when the program expects a column for a
+specific context, the option names end in the @option{col} suffix like the
+examples above. These options accept values in integer (column number), or
+string (metadata match/search) format.
If the value can be parsed as a positive integer, it will be seen as the
low-level column number. Note that column counting starts from 1, so if you
@@ -5847,12 +5884,13 @@ convention:
@itemize
@item
-If the value is enclosed in two slashes (for example @command{-r/RA_/}, or
-@option{--racol=/RA_/}), then it is assumed to be a regular expression with
-the same convention as GNU AWK. GNU AWK has a very well written
+If the value is enclosed in two slashes (for example @command{-x/RA_/}, or
+@option{--coordcol=/RA_/}, see @ref{Crop options}), then it is assumed to
+be a regular expression with the same convention as GNU AWK. GNU AWK has a
+very well written
@url{https://www.gnu.org/software/gawk/manual/html_node/Regexp.html,
chapter} describing regular expressions, so we we will not continue
-discussing it here. Regular expressions are a very powerful tool in
+discussing them here. Regular expressions are a very powerful tool in
matching text and useful in many contexts. We thus strongly encourage
reviewing this chapter for greatly improving the quality of your work in
many cases, not just for searching column meta-data in Gnuastro.
@@ -12151,6 +12189,23 @@ major changes since that paper was published.
@itemize
@item
+@option{--widekernel}: NoiseChisel uses the difference between the mode and
+median to identify if a tile should be used for estimating the quantile
+thresholds (see @ref{Quantifying signal in a tile}). Until now, NoiseChisel
+would convolve an image once and estimate the proper tiles for quantile
+estimations on the convolved image. The same convolved image would later be
+used for quantile estimation. A larger kernel does increase the skewness
+(and thus difference between the mode and median), however, it disfigures
+the shapes/morphology of the objects.
+
+This new @option{--widekernel} option (and a corresponding @option{--wkhdu}
+option to specify its HDU) option are added to solve such cases. When its
+given, the input will be convolved with both the sharp (given through the
+@option{--kernel} option) and wide kernels. The mode and median are
+calculated on the dataset that is convolved with the wider kernel, then the
+quantiles are estimated on the image convolved with the sharper kernel.
+
+@item
@option{--noerodequant}: to specify a quantile threshold where erosion
will not apply. This is useful to detect sharper point-like sources that
will be missed due to too much erosion. To completely ignore this features
@@ -12158,29 +12213,23 @@ give this option a value of 1 (only the largest
valued pixel in the input
will not be eroded).
@item
-@option{--dilatengb}: to specify the final dilation connectivity. Prior to
-Gnuastro 0.4, it was assumed to be 8 (maximum connectivity in a 2D image
-where each pixel has 8 neighbors).
+@option{--detgrowquant}: is used to grow the final true detections until a
+given quantile in the same way that clumps are grown during segmentation
+(compare columns 2 and 3 in Figure 10 of the paper). It replaces the old
+@option{--dilate} option in the paper and older versions of
+Gnuastro. Dilation is a blind growth method which causes objects to be boxy
+or diamond shaped when too many layers are added. However, with the growth
+method that is defined now, we can follow the signal into the noise with
+any shape. The appropriate quantile depends on your dataset's correlated
+noise properties and how cleanly it was Sky subtracted. The new
+@option{--detgrowmaxholesize} can also be used to specify the maximum hole
+size to fill as part of this growth, see the description in @ref{Detection
+options} for more details.
@item
-@option{--cleandilated}: After dilation, if the signal-to-noise ratio of a
-detection is less than the derived pseudo-detection S/N limit, that
-detection will be discarded. In an ideal/clean noise, a true detection's
-S/N should be larger than its constituent pseudo-detections because its
-area is larger and it also covers more signal. However, on a false
-detections (especially at lower @option{--detquant} values), the increase
-in size can cause a decrease in S/N below that threshold.
-
-This will improve purity and not change completeness (a true detection will
-not be discarded). Because a true detection has flux in its vicinity and
-dilation will catch more of that flux and increase the S/N. So on a true
-detection, the final S/N cannot be less than pseudo-detections.
-
-However, in many real images bad processing creates artifacts that cannot
-be accurately removed by the Sky subtraction. In such cases, this option
-will decrease the completeness (will artificially discard true
-detections). So this feature is not default and should to be explicitly
-called when you know the noise is clean.
+@option{--cleangrowndet}: A process to further clean/remove the possibility
+of false detections, see the descriptions under this option in
+@ref{Detection options}.
@end itemize
@@ -12380,6 +12429,23 @@ a wider FWHM in the spatial directions, see
@ref{Sampling theorem}.
HDU containing the kernel in the file given to the @option{--kernel}
option.
+@item -w STR
+@itemx --widekernel=STR
+File name of a wider kernel to use in estimating the difference of the mode
+and median in a tile (this difference is used to identify the significance
+of signal in that tile, see @ref{Quantifying signal in a tile}). This
+convolved image is only used for this purpose. Once the mode is found to be
+sufficiently close to the median, the input convolved with the sharper
+kernel (@option{--kernel}) is used to identify the quantile threshold (see
+@option{--qthresh}).
+
+Since this convolution will significantly slow down the processing, it is
+optional. If no image is given, the mode and median will be found on the
+image that is convolved with the dataset in @option{--kernel}.
+
+@item --wkhdu=STR
+HDU containing the kernel file given to the @option{--widekernel} option.
+
@item -E
@itemx --skysubtracted
If this option is called, it is assumed that the image has already been sky
@@ -12688,18 +12754,68 @@ that this is only calculated for the large mesh grids
that satisfy the
minimum fraction of undetected pixels (value of @option{--minbfrac}) and
minimum number of psudo-detections (value of @option{--minnumfalse}).
-@item -d INT
-@itemx --dilate=INT
-Number of times to dilate the final true detections. See the explanations
-in @option{--opening} for more information on dilation. The structuring
-element for this final dilation is fixed to an 8-connected
-neighborhood. This is because astronomical objects, except cosmic rays,
-never have a clear cutoff, so all the 8-pixels connected to the border
-pixels of a detection might harbor data.
+@item -d FLT
+@itemx --detgrowquant=FLT
+Quantile limit to ``grow'' the final detections. As discussed in the
+previous options, after applying the initial quantile threshold, layers of
+pixels are carved off the objects to identify true signal. With this step
+you can return those low surface brightness layers that were carved off
+back to the detections. To disable growth, set the value of this option to
+@code{1}.
+
+The process is as follows: after the true detections are found, all the
+non-detected pixels above this quantile will be put in a list and used to
+``grow'' the true detections (seeds of the growth). Like all quantile
+thresholds, this threshold is defined and applied to the convolved
+dataset. Afterwards, the dataset is dilated once (with minimum
+connectivity) to connect very thin regions on the boundary: imagine
+building a dam at the point rivers spill into an open sea/ocean. Finally,
+all holes are filled. In the geography metaphor, holes can be seen as the
+closed (by the dams) rivers and lakes, so this process is like turning the
+water in all such rivers and lakes into soil. See
+@option{--detgrowmaxholesize} for configuring the hole filling.
+
+Note that since the growth occurs on all neighbors of a data element, the
+quantile for 3D detection must be must larger than that of 2D
+detection. Recall that in 2D each element has 8 neighbors while in 3D there
+are 27 neighbors.
+
+@item --detgrowmaxholesize=INT
+The maximum hole size to fill during the final expansion of the true
+detections as described in @option{--detgrowquant}. This is necessary when
+the input contains many smaller objects and can be used to avoid marking
+blank sky regions as detections. For example multiple galaxies can be
+positioned such that they surround an empty region of sky. If all the holes
+are filled, the Sky region in between them will be taken as a detection
+which is not desired. To avoid such cases, the integer given to this option
+must be smaller than the hole between the objects.
+
+On the other hand, if you have a very large (and extended) galaxy, the
+diffuse wings of the galaxy may create very large holes. In such cases, a
+larger value to this option will cause the whole region to be detected as
+part of the large galaxy and thus detect it to extremely low surface
+brightness limits.
+
+@item --cleangrowndet
+After dilation, if the signal-to-noise ratio of a detection is less than
+the derived pseudo-detection S/N limit, that detection will be
+discarded. In an ideal/clean noise, a true detection's S/N should be larger
+than its constituent pseudo-detections because its area is larger and it
+also covers more signal. However, on a false detections (especially at
+lower @option{--detquant} values), the increase in size can cause a
+decrease in S/N below that threshold.
+
+This will improve purity and not change completeness (a true detection will
+not be discarded). Because a true detection has flux in its vicinity and
+dilation will catch more of that flux and increase the S/N. So on a true
+detection, the final S/N cannot be less than pseudo-detections.
+
+However, in many real images bad processing creates artifacts that cannot
+be accurately removed by the Sky subtraction. In such cases, this option
+will decrease the completeness (will artificially discard true
+detections). So this feature is not default and should to be explicitly
+called when you know the noise is clean.
-@item --dilatengb=INT
-The connectivity used for the final dilation, see @option{--erodengb} for
-more information about connectivity or a structuring element.
@item --checkdetection
Every step of the detection process will be added as an extension to a file
@@ -18329,7 +18445,7 @@ to manually copy and paste the function name or worry
about it changing
later (@code{__func__} was standardized in C99).
@end deftypefun
-@deftypefun {void *} gal_data_calloc_array (uint8_t @code{type}, size_t
@code{size)}, const char @code{*funcname}, const char @code{*varname})
+@deftypefun {void *} gal_data_calloc_array (uint8_t @code{type}, size_t
@code{size}, const char @code{*funcname}, const char @code{*varname})
Similar to @code{gal_data_malloc_array}, but the space is cleared (set to
0) after allocation.
@end deftypefun
@@ -19629,6 +19745,20 @@ typedef struct gal_fits_list_key_t
@end example
@end deftp
+@deftypefun {void *} gal_fits_key_img_blank (uint8_t @code{type})
+Returns a pointer to an allocated space for the FITS @code{BLANK} header
+keyword when the input array has a type of @code{type}.
+
+According to the FITS standard: ``If the @code{BSCALE} and @code{BZERO}
+keywords do not have the default values of 1.0 and 0.0, respectively, then
+the value of the @code{BLANK} keyword must equal the actual value in the
+FITS data array that is used to represent an undefined pixel and not the
+corresponding physical value''. Therefore a special @code{BLANK} value is
+needed for datasets containing signed 8-bit integers and unsigned 16-bit,
+32-bit and 64-bit integers (types that are defined with @code{BSCALE} and
+@code{BZERO} in the FITS standard).
+@end deftypefun
+
@deftypefun void gal_fits_key_clean_str_value (char @code{*string})
Remove the single quotes and possible extra spaces around the keyword values
that CFITSIO returns when reading a string keyword. CFITSIO doesn't remove
@@ -20785,7 +20915,7 @@ function, it should be @code{1}. In subsequent calls
(while you are parsing
a tile), it should be increased by one.
@end deftypefun
-@deftypefun {gal_data_t *} gal_tile_block_write_const_value (gal_data_t
@code{*tilevalues}, gal_data_t @code{*tilesll}, int @code{initialize})
+@deftypefun {gal_data_t *} gal_tile_block_write_const_value (gal_data_t
@code{*tilevalues}, gal_data_t @code{*tilesll}, int @code{withblank}, int
@code{initialize})
Write a constant value for each tile over the area it covers in an
allocated dataset that is the size of @code{tile}'s allocated block of
memory (found through @code{gal_tile_block} described above). The arguments
@@ -20806,6 +20936,11 @@ doesn't care, it will parse the @code{next} elements
to go to the next
tile. This function will not pop-from or free the @code{tilesll}, it will
only parse it from start to end.
+@item withblank
+If the block containing the tiles has blank elements, those blank elements
+will be blank in the output of this function also, hence the array will be
+initialzied with blank values when this option is called (see below).
+
@item initialize
Initialize the allocated space with blank values before writing in the
constant values. This can be useful when the tiles don't cover the full
@@ -20821,7 +20956,7 @@ values. The output dataset will have a type of
@code{GAL_TYPE_INT32} (see
This function can be used when you want to check the coverage of each tile
over the allocated block of memory. It is just a wrapper over the
-@code{gal_tile_block_write_const_value}.
+@code{gal_tile_block_write_const_value} (with @code{withblank} set to zero).
@end deftypefun
@deftypefun {void *} gal_tile_block_relative_to_other (gal_data_t
@code{*tile}, gal_data_t @code{*other})
@@ -21192,13 +21327,17 @@ inverse: IN_ALL[ perm[i] ] = IN_MEMORY[ i
]
@end example
@end deftypefun
-@deftypefun void gal_tile_full_values_write (gal_data_t @code{*tilevalues},
struct gal_tile_two_layer_params @code{*tl}, char @code{*filename},
gal_fits_list_key_t @code{*keys}, char @code{*program_string})
+@deftypefun void gal_tile_full_values_write (gal_data_t @code{*tilevalues},
struct gal_tile_two_layer_params @code{*tl}, int @code{withblank}, char
@code{*filename}, gal_fits_list_key_t @code{*keys}, char @code{*program_string})
Write one value for each tile into a file. It is important to note that the
values in @code{tilevalues} must be ordered in the same manner as the
tiles, so @code{tilevalues->array[i]} is the value that should be given to
@code{tl->tiles[i]}. The @code{tl->permutation} array must have been
initialized before calling this function with
@code{gal_tile_full_permutation}.
+
+If @code{withblank} is non-zero, then block structure of the tiles will be
+checked and all blank pixels in the block will be blank in the final output
+file also.
@end deftypefun
@deftypefun {gal_data_t *} gal_tile_full_values_smooth (gal_data_t
@code{*tilevalues}, struct gal_tile_two_layer_params @code{*tl}, size_t
@code{width}, size_t @code{numthreads})
@@ -21978,10 +22117,11 @@ Although the adjacency matrix as used here is
symmetric, currently this
function assumes that it is filled on both sides of the diagonal.
@end deftypefun
-@deftypefun void gal_binary_fill_holes (gal_data_t @code{*input})
-Fill all the holes that are bounded within a 4-connected region of the
-binary @code{input} dataset. This function currently only works on a 2D
-dataset.
+@deftypefun void gal_binary_fill_holes (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.
@end deftypefun
@node Convolution functions, Interpolation, Binary datasets, Gnuastro library
diff --git a/doc/release-checklist.txt b/doc/release-checklist.txt
index 3b25ac0..483e22c 100644
--- a/doc/release-checklist.txt
+++ b/doc/release-checklist.txt
@@ -12,12 +12,10 @@ all the commits needed for this release have been completed.
of the GNU Libtool manual as a guide.
- - [ALPHA] Run a spell-check (in emacs with `M-x ispell') on the whole book.
+ - [STABLE] Run a spell-check (in emacs with `M-x ispell') on the whole book.
- - Update the NEWS file (use `git log --reverse gnuastro_vA.B..HEAD').
-
- - Also update the library version for this release in the NEWS file.
+ - Update the versions in the NEWS file.
- Check if README includes all the recent updates and important features.
@@ -61,6 +59,7 @@ all the commits needed for this release have been completed.
- [STABLE]: After the `make distcheck' is safely finished, tag the release:
+ $ cd ..
$ git tag -a gnuastro_vX.X
@@ -93,15 +92,27 @@ all the commits needed for this release have been completed.
- [STABLE] Build the manual in all the formats and upload everything. Note
- that you will need to configure Gnuastro in the main source directory to
- build the full webpage with this script.
+ that you will need to configure and build Gnuastro in the main source
+ directory to build the full webpage with this script.
$ ./configure
+ $ make -j8
$ cd doc
$ ./forwebpage /path/to/local/copy/of/webpage
+ If any of the files have a `?' infront of them, run these two commands
+ in the webpage directory:
+
+ $ cvs add filename1 filename2 filename3
+ $ cvs commit
+
+ Afterwards, clean up the source directory from all the built files:
- - Push all the changes and tag to the main repo:
+ $ cd ..
+ $ make distclean
+
+
+ - [STABLE] Push all the changes and tag to the main repo:
$ git push --follow-tags
@@ -112,7 +123,8 @@ all the commits needed for this release have been completed.
`stable' or `alpha' and in YYYY, put `ftp' for a stable, and `alpha' for
an alpha release.
- $ /path/to/gnulib/build-aux/announce-gen --release-type=XXXX \
+ $ cd build
+ $ /path/to/gnulib/build-aux/announce-gen --release-type=XXXX \
--package-name=gnuastro --previous-version=0.1 \
--current-version=0.2 --gpg-key-id=16A8A4B2AEC42AFF \
--url-directory=http://YYYY.gnu.org/gnu/gnuastro \
diff --git a/lib/arithmetic-binary.c b/lib/arithmetic-binary.c
index 02d7ce1..c5facc8 100644
--- a/lib/arithmetic-binary.c
+++ b/lib/arithmetic-binary.c
@@ -27,6 +27,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <error.h>
#include <stdlib.h>
+#include <gnuastro/blank.h>
#include <gnuastro/arithmetic.h>
#include <gnuastro-internal/arithmetic-internal.h>
@@ -196,20 +197,41 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
/************* High level macros *****************/
/************************************************************************/
/* Final step to be used by all operators and all types. */
-#define BINARY_OP_OT_RT_LT_SET(OP, OT, RT, LT) { \
- LT *la=l->array; \
- RT *ra=r->array; \
- OT *oa=o->array, *of=oa + o->size; \
- if(l->size==r->size) do *oa = *la++ OP *ra++; while(++oa<of); \
- else if(l->size==1) do *oa = *la OP *ra++; while(++oa<of); \
- else do *oa = *la++ OP *ra; while(++oa<of); \
+#define BINARY_OP_OT_RT_LT_SET(OP, OT, RT, LT) { \
+ LT lb, *la=l->array; \
+ RT rb, *ra=r->array; \
+ OT ob, *oa=o->array, *of=oa + o->size; \
+ if(checkblank) \
+ { \
+ gal_blank_write(&lb, l->type); \
+ gal_blank_write(&rb, r->type); \
+ gal_blank_write(&ob, o->type); \
+ do \
+ { \
+ if(lb==lb && rb==rb)/* Both are integers. */ \
+ *oa = (*la!=lb && *ra!=rb) ? *la OP *ra : ob ; \
+ else if(lb==lb) /* Only left operand is an integer. */ \
+ *oa = (*la!=lb && *ra==*ra) ? *la OP *ra : ob; \
+ else /* Only right operand is an integer. */ \
+ *oa = (*la==*la && *ra!=rb) ? *la OP *ra : ob; \
+ if(l->size>1) ++la; \
+ if(r->size>1) ++ra; \
+ } \
+ while(++oa<of); \
+ } \
+ else \
+ { \
+ if(l->size==r->size) do *oa = *la++ OP *ra++; while(++oa<of); \
+ else if(l->size==1) do *oa = *la OP *ra++; while(++oa<of); \
+ else do *oa = *la++ OP *ra; while(++oa<of); \
+ } \
}
/* This is for operators like `&&' and `||', where the right operator is
- not necessarily read (and thus incremented) incremented. */
+ not necessarily read (and thus incremented). */
#define BINARY_OP_INCR_OT_RT_LT_SET(OP, OT, RT, LT) { \
LT *la=l->array; \
RT *ra=r->array; \
@@ -332,6 +354,7 @@ arithmetic_binary(int operator, uint8_t flags, gal_data_t
*lo,
/* Read the variable arguments. `lo' and `ro' keep the original data, in
case their type isn't built (based on configure options are configure
time). */
+ int checkblank;
int32_t otype, final_otype;
size_t out_size, minmapsize;
gal_data_t *l, *r, *o=NULL, *tmp_o;
@@ -398,6 +421,17 @@ arithmetic_binary(int operator, uint8_t flags, gal_data_t
*lo,
0, minmapsize, NULL, NULL, NULL );
+ /* See if we should check for blanks. When both types are floats, blanks
+ don't need to be checked (the floating point standard will do the job
+ for us). It is also not necessary to check blanks in bitwise
+ operators, but bitwise operators have their own macro
+ (`BINARY_OP_INCR_OT_RT_LT_SET') which doesn' use `checkblanks'.*/
+ checkblank = ((((l->type!=GAL_TYPE_FLOAT32 && l->type!=GAL_TYPE_FLOAT64)
+ || (r->type!=GAL_TYPE_FLOAT32 && r->type!=GAL_TYPE_FLOAT64))
+ && (gal_blank_present(l, 1) || gal_blank_present(r, 1)))
+ ? 1 : 0 );
+
+
/* Start setting the operator and operands. */
switch(l->type)
{
diff --git a/lib/binary.c b/lib/binary.c
index 8d7fe21..077c1ab 100644
--- a/lib/binary.c
+++ b/lib/binary.c
@@ -411,8 +411,8 @@ gal_binary_connected_components(gal_data_t *binary,
gal_data_t **out,
/* Make sure the given dataset has the same size as the input. */
if( gal_data_dsize_is_different(binary, lab) )
- error(EXIT_FAILURE, 0, "%s: the `binary' and `out' datasets must have "
- "the same size", __func__);
+ error(EXIT_FAILURE, 0, "%s: the `binary' and `out' datasets must "
+ "have the same size", __func__);
/* Make sure it has a `int32' type. */
if( lab->type!=GAL_TYPE_INT32 )
@@ -661,8 +661,7 @@ binary_make_padded_inverse(gal_data_t *input, gal_data_t
**outtile)
-/* Fill all the holes in an input unsigned char array that are bounded
- within a 4-connected region.
+/* Fill all the holes in an input unsigned char array.
The basic method is this:
@@ -685,9 +684,11 @@ binary_make_padded_inverse(gal_data_t *input, gal_data_t
**outtile)
Any pixel with a label larger than 1, is therefore a bounded
hole that is not 8-connected to the rest of the holes. */
void
-gal_binary_fill_holes(gal_data_t *input)
+gal_binary_fill_holes(gal_data_t *input, int connectivity, size_t maxsize)
{
uint8_t *in;
+ uint32_t *i, *fi;
+ size_t numholes, *sizes;
gal_data_t *inv, *tile, *holelabs=NULL;
/* A small sanity check. */
@@ -701,8 +702,8 @@ gal_binary_fill_holes(gal_data_t *input)
inv=binary_make_padded_inverse(input, &tile);
- /* Label the 8-connected (connectivity==2) holes. */
- gal_binary_connected_components(inv, &holelabs, 2);
+ /* Label the holes */
+ numholes=gal_binary_connected_components(inv, &holelabs, connectivity);
/* Any pixel with a label larger than 1 is a hole in the input image and
@@ -712,6 +713,22 @@ gal_binary_fill_holes(gal_data_t *input)
tile->array=gal_tile_block_relative_to_other(tile, holelabs);
tile->block=holelabs; /* has to be after correcting `tile->array'. */
+ /* If the user wants to only fill holes to a certain size, then remove
+ those with a larger size. */
+ if(maxsize<-1)
+ {
+ /* Allocate space to keep the size of each hole: */
+ sizes=gal_data_calloc_array(GAL_TYPE_SIZE_T, numholes+1, __func__,
+ "sizes");
+ fi=(i=holelabs->array)+holelabs->size; do ++sizes[*i]; while(++i<fi);
+
+ /* Set those labels with a larger size to 1 (treat it as
+ background). */
+ fi=(i=holelabs->array)+holelabs->size;
+ do
+ if(*i!=GAL_BLANK_INT32) *i = sizes[*i]>maxsize ? 1 : *i;
+ while(++i<fi);
+ }
/* The type of the tile is already known (it is `int32_t') and we have no
output, so we'll just put `int' as a place-holder. In this way we can
diff --git a/lib/blank.c b/lib/blank.c
index 44dee32..b3550a9 100644
--- a/lib/blank.c
+++ b/lib/blank.c
@@ -168,10 +168,10 @@ gal_blank_present(gal_data_t *input, int updateflag)
blank is present. */
if(input->size==0) return 0;
- /* From the user's flags, it might not be necessary to go through the
- dataset any more. */
- if( ( input->flag & GAL_DATA_FLAG_HASBLANK )
- || ( input->flag & GAL_DATA_FLAG_BLANK_CH ) )
+ /* From the user's flags, you can tell if the dataset has already been
+ checked for blank values or not. If it has, then just return the
+ checked result. */
+ if( input->flag & GAL_DATA_FLAG_BLANK_CH )
return input->flag & GAL_DATA_FLAG_HASBLANK;
/* Go over the pixels and check: */
diff --git a/lib/fits.c b/lib/fits.c
index 9df4228..b0f901e 100644
--- a/lib/fits.c
+++ b/lib/fits.c
@@ -794,6 +794,63 @@ gal_fits_hdu_open_format(char *filename, char *hdu, int
img0_tab1)
/**************************************************************/
/********** Header keywords ************/
/**************************************************************/
+/* Return allocated pointer to the blank value to use in a FITS file header
+ keyword. */
+void *
+gal_fits_key_img_blank(uint8_t type)
+{
+ void *out=NULL, *tocopy=NULL;
+ uint8_t u8=0; /* Equivalent of minimum in signed with BZERO. */
+ int16_t s16=INT16_MAX; /* Equivalend of maximum in unsigned with BZERO. */
+ int32_t s32=INT32_MAX; /* Equivalend of maximum in unsigned with BZERO. */
+ int64_t s64=INT64_MAX; /* Equivalend of maximum in unsigned with BZERO. */
+
+ switch(type)
+ {
+ /* Types with no special treatment: */
+ case GAL_TYPE_BIT:
+ case GAL_TYPE_UINT8:
+ case GAL_TYPE_INT16:
+ case GAL_TYPE_INT32:
+ case GAL_TYPE_INT64:
+ case GAL_TYPE_FLOAT32:
+ case GAL_TYPE_FLOAT64:
+ case GAL_TYPE_COMPLEX32:
+ case GAL_TYPE_COMPLEX64:
+ case GAL_TYPE_STRING:
+ case GAL_TYPE_STRLL:
+ out = gal_blank_alloc_write(type);
+ break;
+
+ /* Types that need values from their opposite-signed types. */
+ case GAL_TYPE_INT8: tocopy=&u8; break;
+ case GAL_TYPE_UINT16: tocopy=&s16; break;
+ case GAL_TYPE_UINT32: tocopy=&s32; break;
+ case GAL_TYPE_UINT64: tocopy=&s64; break;
+
+ default:
+ error(EXIT_FAILURE, 0, "%s: type code %u not recognized as a Gnuastro "
+ "data type", __func__, type);
+ }
+
+ /* If `gal_blank_alloc_write' wasn't used (copy!=NULL), then allocate the
+ necessary space and fill it in. Note that the width of the signed and
+ unsigned values doesn't differ, so we can use the actual input
+ type. */
+ if(tocopy)
+ {
+ out = gal_data_malloc_array(type, 1, __func__, "out");
+ memcpy(out, tocopy, gal_type_sizeof(type));
+ }
+
+ /* Return. */
+ return out;
+}
+
+
+
+
+
/* CFITSIO doesn't remove the two single quotes around the string value, so
the strings it reads are like: 'value ', or 'some_very_long_value'. To
use the value, it is commonly necessary to remove the single quotes (and
@@ -1710,7 +1767,7 @@ gal_fits_img_write_to_ptr(gal_data_t *input, char
*filename)
break;
default:
- blank=gal_blank_alloc_write(towrite->type);
+ blank=gal_fits_key_img_blank(towrite->type);
if(fits_write_key(fptr, datatype, "BLANK", blank,
"Pixels with no data.", &status) )
gal_fits_io_error(status, "adding the BLANK keyword");
diff --git a/lib/gnuastro/binary.h b/lib/gnuastro/binary.h
index cb19650..1f25915 100644
--- a/lib/gnuastro/binary.h
+++ b/lib/gnuastro/binary.h
@@ -98,7 +98,7 @@ gal_binary_connected_adjacency_matrix(gal_data_t *adjacency,
/***************** Fill holes ********************/
/*********************************************************************/
void
-gal_binary_fill_holes(gal_data_t *input);
+gal_binary_fill_holes(gal_data_t *input, int connectivity, size_t maxsize);
diff --git a/lib/gnuastro/fits.h b/lib/gnuastro/fits.h
index a44a3d5..2744062 100644
--- a/lib/gnuastro/fits.h
+++ b/lib/gnuastro/fits.h
@@ -159,6 +159,9 @@ gal_fits_hdu_open_format(char *filename, char *hdu, int
img0_tab1);
/**************************************************************/
/********** Header keywords ************/
/**************************************************************/
+void *
+gal_fits_key_img_blank(uint8_t type);
+
void
gal_fits_key_clean_str_value(char *string);
diff --git a/lib/gnuastro/tile.h b/lib/gnuastro/tile.h
index e33f1d8..02ae328 100644
--- a/lib/gnuastro/tile.h
+++ b/lib/gnuastro/tile.h
@@ -85,7 +85,7 @@ gal_tile_block_increment(gal_data_t *block, size_t *tsize,
gal_data_t *
gal_tile_block_write_const_value(gal_data_t *tilevalues, gal_data_t *tilesll,
- int initialize);
+ int withblank, int initialize);
gal_data_t *
gal_tile_block_check_tiles(gal_data_t *tiles);
@@ -151,8 +151,8 @@ gal_tile_full_permutation(struct gal_tile_two_layer_params
*tl);
void
gal_tile_full_values_write(gal_data_t *tilevalues,
struct gal_tile_two_layer_params *tl,
- char *filename, gal_fits_list_key_t *keys,
- char *program_string);
+ int withblank, char *filename,
+ gal_fits_list_key_t *keys, char *program_string);
gal_data_t *
gal_tile_full_values_smooth(gal_data_t *tilevalues,
diff --git a/lib/statistics.c b/lib/statistics.c
index 7e77964..6d5e013 100644
--- a/lib/statistics.c
+++ b/lib/statistics.c
@@ -58,8 +58,8 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
gal_data_t *
gal_statistics_number(gal_data_t *input)
{
- uint64_t counter=0;
size_t dsize=1;
+ uint64_t counter=0;
gal_data_t *out=gal_data_alloc(NULL, GAL_TYPE_UINT64, 1, &dsize,
NULL, 1, -1, NULL, NULL, NULL);
diff --git a/lib/tile.c b/lib/tile.c
index cbff41e..05c8eac 100644
--- a/lib/tile.c
+++ b/lib/tile.c
@@ -423,7 +423,7 @@ gal_tile_block_increment(gal_data_t *block, size_t *tsize,
don't cover the full allocated block. */
gal_data_t *
gal_tile_block_write_const_value(gal_data_t *tilevalues, gal_data_t *tilesll,
- int initialize)
+ int withblank, int initialize)
{
void *in;
int type=tilevalues->type;
@@ -443,7 +443,7 @@ gal_tile_block_write_const_value(gal_data_t *tilevalues,
gal_data_t *tilesll,
/* If requested, initialize `tofill', otherwise it is assumed that the
full area of the output is covered by the tiles. */
- if(initialize) gal_blank_initialize(tofill);
+ if(withblank || initialize) gal_blank_initialize(tofill);
else
{
/* Copy the flags. */
@@ -465,9 +465,9 @@ gal_tile_block_write_const_value(gal_data_t *tilevalues,
gal_data_t *tilesll,
{
/* Set the pointer to use as input. The `if(o)' statement is set
because GCC 7.1.1 complained about the possiblity of the first
- argument of `memcpy' being NULL. */
+ argument of `memcpy' being NULL. Recall that `o' is a pointer. */
in=gal_data_ptr_increment(tilevalues->array, tile_ind++, type);;
- GAL_TILE_PARSE_OPERATE( tile, tofill, 1, 0, {
+ GAL_TILE_PARSE_OPERATE( tile, tofill, 1, withblank, {
if(o) memcpy(o, in, gal_type_sizeof(type));
} );
}
@@ -497,7 +497,7 @@ gal_tile_block_check_tiles(gal_data_t *tilesll)
arr=ids->array; for(i=0;i<dsize;++i) arr[i]=i;
/* Make the output. */
- out=gal_tile_block_write_const_value(ids, tilesll, 1);
+ out=gal_tile_block_write_const_value(ids, tilesll, 0, 1);
/* Clean up and return. */
gal_data_free(ids);
@@ -1088,8 +1088,8 @@ gal_tile_full_permutation(struct
gal_tile_two_layer_params *tl)
void
gal_tile_full_values_write(gal_data_t *tilevalues,
struct gal_tile_two_layer_params *tl,
- char *filename, gal_fits_list_key_t *keys,
- char *program_string)
+ int withblank, char *filename,
+ gal_fits_list_key_t *keys, char *program_string)
{
gal_data_t *disp;
@@ -1113,8 +1113,8 @@ gal_tile_full_values_write(gal_data_t *tilevalues,
else disp = tilevalues;
}
else
- disp=gal_tile_block_write_const_value(tilevalues, tl->tiles, 0);
-
+ disp=gal_tile_block_write_const_value(tilevalues, tl->tiles,
+ withblank, 0);
/* Write the array as a file and then clean up (if necessary). */
gal_fits_img_write(disp, filename, keys, program_string);
diff --git a/tests/during-dev.sh b/tests/during-dev.sh
index 36f6f26..18c9bf4 100755
--- a/tests/during-dev.sh
+++ b/tests/during-dev.sh
@@ -140,7 +140,7 @@ if make -j$numjobs -C "$builddir"; then
# the last line in the configuration file doesn't actualy end with a
# new line (in which case the appended string will be added to the end
# of the last line).
- cp "$srcdir/bin/gnuastro.conf" "$srcdir/bin/$utilname/ast$utilname.conf" \
+ cp "$srcdir/bin/gnuastro.conf" "$srcdir/bin/$utilname/"*.conf \
.gnuastro/
echo "" >> .gnuastro/gnuastro.conf
echo " lastconfig 1" >> .gnuastro/gnuastro.conf
diff --git a/tests/noisechisel/noisechisel.sh b/tests/noisechisel/noisechisel.sh
index 14578c4..c60aebf 100755
--- a/tests/noisechisel/noisechisel.sh
+++ b/tests/noisechisel/noisechisel.sh
@@ -49,5 +49,5 @@ if [ ! -f $img ]; then echo "$img does not exist.";
exit 77; fi
# Actual test script
# ==================
-$execname $img --cleandilated --checkdetection --checksegmentation \
- --continueaftercheck
+$execname $img --cleangrowndet --checkdetection --checksegmentation \
+ --continueaftercheck --tilesize=100,100
- [gnuastro-commits] master bdeaba9 012/113: Corrected name of 3D catalog for tarball inclusion, (continued)
- [gnuastro-commits] master bdeaba9 012/113: Corrected name of 3D catalog for tarball inclusion, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 6b53c5e 015/113: Bug fixes in master: commits 1ff1c25 and 540af65, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master adeb1c6 016/113: NoiseChisel's convolution step in 3D completed, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master ace4160 017/113: New --mcolisbrightness option for MakeProfiles, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master f06acc5 018/113: Merged recent work from master, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 61aec7b 019/113: Convolve name and dimensionality checks, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 4627ddf 021/113: NoiseChisel segmentation working in 3D, test added, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 1560a54 022/113: Default NoiseChisel kernel in 3D changed to 1.5 pixels, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 4d2508f 028/113: Fixed NoiseChisel opening and dilation and merged with master, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 4223e60 025/113: Suggestions on viewing/inspecting NoiseChisel's output, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 6086579 031/113: Merged recent work in master (corrected conflicts),
Mohammad Akhlaghi <=
- [gnuastro-commits] master b0d5fab 034/113: Merged recent work from master, no conflicts, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 06798a5 035/113: Crop's --checkcenter works on 3D dataset, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master fd51c80 050/113: Imported recent work from master, no conflicts, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master a4dbaba 055/113: Recent work in master imported, minor conflict fixed, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 0597cea 058/113: Imported work in master, no conflicts, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master e11098d 053/113: Recent work in master imported, minor conflicts fixed, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 0a8324f 059/113: MakeProfiles kernel option can be elongated in 3rd-dimension, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master ec3c102 056/113: Single to conditionally open ds9 for multi-HDU 2D or 3D, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 2491c91 064/113: Imported work in master, minor conflict in book fixed, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 9dda05c 040/113: Merged recent work from the master branch with corrections, Mohammad Akhlaghi, 2021/04/16