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[gnuastro-commits] master ac2a821 103/113: Imported recent work in maste
|
From: |
Mohammad Akhlaghi |
|
Subject: |
[gnuastro-commits] master ac2a821 103/113: Imported recent work in master, conflicts fixed |
|
Date: |
Fri, 16 Apr 2021 10:34:00 -0400 (EDT) |
branch: master
commit ac2a8218dad0ff94fbc43a00d4c44f2e79672e3a
Merge: b3416de 95d7fc5
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Imported recent work in master, conflicts fixed
Several conflicts came up during the merging of Match and they were fixed.
---
NEWS | 24 ++-
THANKS | 1 +
bin/arithmetic/arithmetic.c | 18 +-
bin/cosmiccal/ui.c | 1 -
bin/crop/main.h | 3 +-
bin/crop/onecrop.c | 11 +-
bin/crop/ui.c | 5 +-
bin/gnuastro.conf | 1 +
bin/match/args.h | 14 ++
bin/match/astmatch.conf | 4 +-
bin/match/main.h | 3 +-
bin/match/match.c | 99 ++++++++--
bin/match/ui.c | 361 +++++++++++++++++++++++++------------
bin/match/ui.h | 3 +-
bin/mkprof/ui.c | 19 ++
bin/noisechisel/threshold.c | 5 +-
bin/noisechisel/ui.c | 1 +
bin/statistics/sky.c | 5 +-
bin/statistics/statistics.c | 1 +
bin/statistics/ui.c | 8 +-
doc/announce-acknowledge.txt | 1 +
doc/gnuastro.texi | 121 ++++++++++---
lib/arithmetic.c | 91 ++++++++--
lib/dimension.c | 14 +-
lib/gnuastro-internal/commonopts.h | 16 +-
lib/gnuastro-internal/options.h | 6 +
lib/gnuastro/dimension.h | 5 +-
lib/gnuastro/interpolate.h | 17 +-
lib/gnuastro/type.h | 3 +
lib/interpolate.c | 32 +++-
lib/options.c | 50 +++++
lib/type.c | 24 ++-
tests/match/merged-cols.sh | 4 +-
tests/match/positions.sh | 4 +-
34 files changed, 758 insertions(+), 217 deletions(-)
diff --git a/NEWS b/NEWS
index ab729be..29a09bc 100644
--- a/NEWS
+++ b/NEWS
@@ -26,6 +26,9 @@ GNU Astronomy Utilities NEWS -*-
outline -*-
different file for reading the WCS of the output. This is useful when
the default (theh WCS of the first dataset that is read) is not the
required one.
+ --interpmetric: new option that is necessary with the
+ `interpolate-medianngb' operator. For more, see the description of
+ this option in NoiseChisel.
Fits:
- Add "title" to group FITS keywords with `--write=/,"title name". This
@@ -49,9 +52,21 @@ GNU Astronomy Utilities NEWS -*-
outline -*-
contain all the columns from the first input and the 5th column of the
second input. This greatly simplifies the mergining of different table
columns into one.
+ --coord: manually specify coordinates to match on the
+ command-line. Until now, if you only wanted to make check a specific
+ coordinate's matching with a catalog. It was necessary to make a
+ single-row catalog as a file and feed that into Match. With this
+ option, you can now specify the coordinates to match against another
+ catalog with the command-line.
NoiseChisel:
-
+ --interpmetric: Set the metric to use to identify the nearest neighbors
+ for tile interpolation (quantile threshold, initial Sky, and final
+ Sky). Until now only the manhattan/taxicab metric was available, which
+ is fast, but could cause 45-degree lines in the interpolation. From
+ this version, with this option, its also possible to use the radial
+ distance (which is now the default). Just note that if there are many
+ tiles over the image, the radial distance will be slower.
--snthresh: Manually set the signal-to-noise ratio of true
pseudo-detections. With this option, NoiseChisel will not attempt to
find pseudo-detections over the noisy regions of the dataset, but will
@@ -67,12 +82,17 @@ GNU Astronomy Utilities NEWS -*-
outline -*-
--dopening: The number of openings to do after applying `--dthresh'.
--dopeningngb: The connectivity (4 or 8) to use for `--dopening'.
+ Statistics:
+ --interpmetric: Similar to NoiseChisel.
+
Library:
GAL_BLANK_LONG: new macro for the `long' type blank value.
GAL_BLANK_ULONG: new macro for the `unsigned long' type blank value.
gal_blank_number: Return the number of blank elements in a dataset.
+ gal_dimension_dist_radial: Radial distance between two coordinates.
gal_statistics_outlier_cumulative: Uses flatness of the cumulative
distribution to find outliers.
+ gal_type_is_int: to see if we have an integer (any width, any sign).
** Removed features
@@ -117,6 +137,8 @@ GNU Astronomy Utilities NEWS -*-
outline -*-
bug #55478: Memory mapping crashes when .gnuastro is not writable.
bug #55491: NoiseChisel crash when no tiles good for quantile thresholding.
bug #55544: Arithmetic's output WCS with where operator is not as expected.
+ bug #55740: Diamond shapes in nearst-ngb interpolation affecting NoiseChisel.
+ bug #55763: Crop not keeping Blank pixels on unsigned types.
diff --git a/THANKS b/THANKS
index 6f34d21..c803745 100644
--- a/THANKS
+++ b/THANKS
@@ -18,6 +18,7 @@ support in Gnuastro. The list is ordered alphabetically (by
family name).
Valentina Abril-melgarejo valentina.abril@lam.fr
Marjan Akbari mrjakbari@gmail.com
Roland Bacon roland.bacon@univ-lyon1.fr
+ Roberto Baena Gallé rbaena@iac.es
Karl Berry karl@gnu.org
Leindert Boogaard boogaard@strw.leidenuniv.nl
Nicolas Bouché nicolas.bouche@irap.omp.eu
diff --git a/bin/arithmetic/arithmetic.c b/bin/arithmetic/arithmetic.c
index 68e3912..b221ce9 100644
--- a/bin/arithmetic/arithmetic.c
+++ b/bin/arithmetic/arithmetic.c
@@ -728,8 +728,9 @@ arithmetic_interpolate(struct arithmeticparams *p, char
*token)
num_int = *((int32_t *)(num->array));
/* Call the interpolation function. */
- interpolated=gal_interpolate_close_neighbors(in, NULL, num_int,
- p->cp.numthreads, 1, 0);
+ interpolated=gal_interpolate_close_neighbors(in, NULL, p->cp.interpmetric,
+ num_int, p->cp.numthreads,
+ 1, 0);
/* Clean up and push the interpolated array onto the stack. */
gal_data_free(in);
@@ -904,9 +905,9 @@ void
reversepolish(struct arithmeticparams *p)
{
int op=0, nop=0;
- char *filename, *hdu;
unsigned int numop, i;
gal_list_str_t *token;
+ char *hdu, *filename, *printnum;
gal_data_t *d1=NULL, *d2=NULL, *d3=NULL;
int flags = ( GAL_ARITHMETIC_INPLACE | GAL_ARITHMETIC_FREE
| GAL_ARITHMETIC_NUMOK );
@@ -1255,11 +1256,12 @@ reversepolish(struct arithmeticparams *p)
d1=p->operands->data;
if(d1->size==1)
{
- /* To simplify the printing process, we will first change it to
- double, then use printf's `%g' to print it, so integers will be
- printed as an integer. */
- d2=gal_data_copy_to_new_type(d1, GAL_TYPE_FLOAT64);
- printf("%g\n", *(double *)d2->array);
+ /* Make the string to print the number. */
+ printnum=gal_type_to_string(d1->array, d1->type, 0);
+ printf("%s\n", printnum);
+
+ /* Clean up. */
+ free(printnum);
if(d2!=d1) gal_data_free(d2);
}
else
diff --git a/bin/cosmiccal/ui.c b/bin/cosmiccal/ui.c
index 4b6263f..e52842b 100644
--- a/bin/cosmiccal/ui.c
+++ b/bin/cosmiccal/ui.c
@@ -135,7 +135,6 @@ ui_initialize_options(struct cosmiccalparams *p,
case GAL_OPTIONS_KEY_QUIET:
case GAL_OPTIONS_KEY_SEARCHIN:
case GAL_OPTIONS_KEY_NUMTHREADS:
- case GAL_OPTIONS_KEY_MINMAPSIZE:
case GAL_OPTIONS_KEY_IGNORECASE:
case GAL_OPTIONS_KEY_TABLEFORMAT:
case GAL_OPTIONS_KEY_STDINTIMEOUT:
diff --git a/bin/crop/main.h b/bin/crop/main.h
index e60d1cc..528645e 100644
--- a/bin/crop/main.h
+++ b/bin/crop/main.h
@@ -112,7 +112,8 @@ struct cropparams
time_t rawtime; /* Starting time of the program. */
int outnameisfile; /* Output filename is a directory. */
int type; /* Type of output(s). */
- void *bitnul; /* Null value for this data-type. */
+ void *blankptrread; /* Null value for reading of output type.*/
+ void *blankptrwrite; /* Null value for writing of output type.*/
struct inputimgs *imgs; /* WCS and size information for inputs. */
gal_data_t *log; /* Log file contents. */
};
diff --git a/bin/crop/onecrop.c b/bin/crop/onecrop.c
index 4e14bc8..55c85cd 100644
--- a/bin/crop/onecrop.c
+++ b/bin/crop/onecrop.c
@@ -642,7 +642,7 @@ onecrop_make_array(struct onecropparams *crp, long
*fpixel_i,
/* When CFITSIO creates a FITS extension it adds two comments linking to
the FITS paper. Since we are mentioning the version of CFITSIO and
- only use its ruitines to read/write from/to FITS files, this is
+ only use its routines to read/write from/to FITS files, this is
redundant. If `status!=0', then `gal_fits_io_error' will abort, but in
case CFITSIO doesn't write the comments, status will become
non-zero. So we are resetting it to zero after these (because not
@@ -671,7 +671,8 @@ onecrop_make_array(struct onecropparams *crp, long
*fpixel_i,
/* Write the blank value as a FITS keyword if necessary. */
if( type!=GAL_TYPE_FLOAT32 && type!=GAL_TYPE_FLOAT64 )
if(fits_write_key(ofp, gal_fits_type_to_datatype(crp->p->type), "BLANK",
- crp->p->bitnul, "pixels with no data", &status) )
+ crp->p->blankptrwrite, "Pixels with no data.",
+ &status) )
gal_fits_io_error(status, "adding Blank");
totsize = naxes[0]*naxes[1] * (ndim==3?naxes[2]:1);
if(fits_write_null_img(ofp, 1, totsize, &status))
@@ -774,7 +775,7 @@ onecrop(struct onecropparams *crp)
for(i=0;i<ndim;++i) cropsize *= ( lpixel_i[i] - fpixel_i[i] + 1 );
array=gal_pointer_allocate(p->type, cropsize, 0, __func__, "array");
if(fits_read_subset(ifp, gal_fits_type_to_datatype(p->type),
- fpixel_i, lpixel_i, inc, p->bitnul, array,
+ fpixel_i, lpixel_i, inc, p->blankptrread, array,
&anynul, &status))
gal_fits_io_error(status, NULL);
@@ -928,8 +929,8 @@ onecrop_center_filled(struct onecropparams *crp)
/* Allocate the array and read in the pixels. */
array=gal_pointer_allocate(type, size, 0, __func__, "array");
if( fits_read_subset(ofp, gal_fits_type_to_datatype(type), fpixel, lpixel,
- inc, p->bitnul, array, &anynul, &status) )
- gal_fits_io_error(status, NULL);
+ inc, p->blankptrread, array, &anynul, &status) )
+ gal_fits_io_error(status, NULL);
free(array);
/* CFITSIO already checks if there are any blank pixels. If there are,
diff --git a/bin/crop/ui.c b/bin/crop/ui.c
index d0c9555..2a00410 100644
--- a/bin/crop/ui.c
+++ b/bin/crop/ui.c
@@ -895,7 +895,8 @@ ui_preparations(struct cropparams *p)
/* Set the basic information. */
firsttype = p->type;
firstndim = img->ndim;
- p->bitnul = gal_fits_key_img_blank(p->type);
+ p->blankptrread = gal_blank_alloc_write(p->type);
+ p->blankptrwrite = gal_fits_key_img_blank(p->type);
/* Make sure the number of dimensions is supported. */
if(firstndim>MAXDIM)
@@ -1090,6 +1091,8 @@ ui_free_report(struct cropparams *p, struct timeval *t1)
size_t i;
/* Free the simple arrays (if they were set). */
+ free(p->blankptrread);
+ free(p->blankptrwrite);
gal_data_free(p->center);
if(p->cp.hdu) free(p->cp.hdu);
if(p->cathdu) free(p->cathdu);
diff --git a/bin/gnuastro.conf b/bin/gnuastro.conf
index 3652e6a..a901b99 100644
--- a/bin/gnuastro.conf
+++ b/bin/gnuastro.conf
@@ -28,6 +28,7 @@
numchannels 1,1
remainderfrac 0.1
workoverch 0
+ interpmetric radial
interpnumngb 9
interponlyblank 0
diff --git a/bin/match/args.h b/bin/match/args.h
index 512d7aa..5dd2424 100644
--- a/bin/match/args.h
+++ b/bin/match/args.h
@@ -129,6 +129,20 @@ struct argp_option program_options[] =
gal_options_parse_csv_strings
},
{
+ "coord",
+ UI_KEY_COORD,
+ "FLT[,FLT]",
+ 0,
+ "Manually input coordiantes.",
+ UI_GROUP_CATALOGMATCH,
+ &p->coord,
+ GAL_TYPE_STRING,
+ GAL_OPTIONS_RANGE_ANY,
+ GAL_OPTIONS_NOT_MANDATORY,
+ GAL_OPTIONS_NOT_SET,
+ gal_options_parse_csv_float64
+ },
+ {
"aperture",
UI_KEY_APERTURE,
"FLT[,...]",
diff --git a/bin/match/astmatch.conf b/bin/match/astmatch.conf
index 6506993..85a90ec 100644
--- a/bin/match/astmatch.conf
+++ b/bin/match/astmatch.conf
@@ -20,6 +20,4 @@
# Input
hdu2 1
-# Catalog matching
- ccol1 2,3
- ccol2 2,3
\ No newline at end of file
+# Catalog matching
\ No newline at end of file
diff --git a/bin/match/main.h b/bin/match/main.h
index f9a5a85..1e776a6 100644
--- a/bin/match/main.h
+++ b/bin/match/main.h
@@ -53,8 +53,9 @@ struct matchparams
char *input1name; /* First input filename. */
char *input2name; /* Second input filename. */
char *hdu2; /* Second input's HDU. */
- gal_data_t *ccol1; /* Array of firs input column names. */
+ gal_data_t *ccol1; /* Array of first input column names. */
gal_data_t *ccol2; /* Array of second input column names. */
+ gal_data_t *coord; /* Array of manual coordinate values. */
gal_data_t *outcols; /* Array of second input column names. */
gal_data_t *aperture; /* Acceptable matching aperture. */
uint8_t logasoutput; /* Don't rearrange inputs, out is log. */
diff --git a/bin/match/match.c b/bin/match/match.c
index 94132a1..e32a74b 100644
--- a/bin/match/match.c
+++ b/bin/match/match.c
@@ -97,6 +97,57 @@ match_add_all_cols(char *filename, char *extname,
gal_list_str_t *stdinlines,
+static gal_data_t *
+match_cat_from_coord(struct matchparams *p, gal_list_str_t *cols,
+ size_t *numcolmatch)
+{
+ void *rptr;
+ gal_list_str_t *col;
+ uint8_t read, readtype;
+ size_t colcounter, counter;
+ gal_data_t *tmp, *ttmp, *out=NULL;
+
+ /* Go over the desired columns and only return the good ones. */
+ colcounter=0;
+ for(col=cols;col!=NULL;col=col->next)
+ {
+ /* In `ui_preparations_out_cols', we have done the necessary sanity
+ checks, so we can safely use the values. */
+ rptr=gal_type_string_to_number(col->v, &readtype);
+ if(readtype!=GAL_TYPE_UINT8)
+ error(EXIT_FAILURE, 0, "%s: a bug! Please contact us at %s to fix "
+ "the problem. The given string didn't have a `uint8' type",
+ __func__, PACKAGE_BUGREPORT);
+ read=*((uint8_t *)rptr);
+
+ /* Find the proper column in the second input's columns. Just note
+ that column counting starts from 1.*/
+ counter=1;
+ for(tmp=p->cols2;tmp!=NULL;tmp=tmp->next)
+ if(counter++ == read)
+ {
+ ttmp=gal_data_copy(tmp);
+ ttmp->next=NULL;
+ gal_list_data_add(&out, ttmp);
+ ++numcolmatch[colcounter];
+ break;
+ }
+
+ /* Increment the column counter. */
+ ++colcounter;
+ }
+
+ /* Reverse the list. */
+ gal_list_data_reverse(&out);
+
+ /* Return the output columns. */
+ return out;
+}
+
+
+
+
+
/* Read the catalog in the given file and use the given permutation to keep
the proper columns. */
static gal_data_t *
@@ -143,18 +194,21 @@ match_catalog_read_write_all(struct matchparams *p,
size_t *permutation,
/* When the output contains columns from both inputs, we need to keep
the number of columns matched against each column identifier. */
*numcolmatch=gal_pointer_allocate(GAL_TYPE_SIZE_T,
- gal_list_str_number(cols), 0,
+ gal_list_str_number(cols), 1,
__func__, "numcolmatch");
}
else cols=incols;
- /* Read the full table and free the `cols' array if it was allocated
- here. */
- cat=gal_table_read(filename, hdu, filename ? NULL : p->stdinlines, cols,
- p->cp.searchin, p->cp.ignorecase, p->cp.minmapsize,
- *numcolmatch);
- origsize=cat->size;
+ /* Read the full table. NOTE that with `--coord', for the second input,
+ both `filename' and `p->stdinlines' will be NULL. */
+ if(filename || p->stdinlines)
+ cat=gal_table_read(filename, hdu, filename ? NULL : p->stdinlines, cols,
+ p->cp.searchin, p->cp.ignorecase, p->cp.minmapsize,
+ *numcolmatch);
+ else
+ cat=match_cat_from_coord(p, cols, *numcolmatch);
+ origsize = cat ? cat->size : 0;
/* Go over each column and permute its contents. */
@@ -198,10 +252,11 @@ match_catalog_read_write_all(struct matchparams *p,
size_t *permutation,
}
}
+
/* Write the catalog to the output. */
if(p->outcols)
return cat;
- else
+ else if(cat)
{
/* Write the catalog to a file. */
gal_table_write(cat, NULL, p->cp.tableformat, outname, extname, 0);
@@ -227,8 +282,9 @@ match_catalog_read_write_all(struct matchparams *p, size_t
*permutation,
/* Clean up. */
gal_list_data_free(cat);
- return NULL;
}
+
+ return NULL;
}
@@ -380,7 +436,14 @@ match_catalog(struct matchparams *p)
/* Print the number of matches if not in quiet mode. */
if(!p->cp.quiet)
- fprintf(stdout, "%zu\n", nummatched);
+ {
+ fprintf(stdout, "Number of maching rows in both catalogs: %zu\n",
+ nummatched);
+ if(p->out2name && strcmp(p->out1name, p->out2name))
+ fprintf(stdout, "Output:\n %s\n %s", p->out1name, p->out2name);
+ else
+ fprintf(stdout, "Output: %s\n", p->out1name);
+ }
}
@@ -409,8 +472,16 @@ void
match(struct matchparams *p)
{
/* Do the correct type of matching. */
- if(p->mode==MATCH_MODE_CATALOG)
- match_catalog(p);
+ switch(p->mode)
+ {
+ case MATCH_MODE_CATALOG: match_catalog(p); break;
+ case MATCH_MODE_WCS:
+ error(EXIT_FAILURE, 0, "matching by WCS is not yet supported");
+ default:
+ error(EXIT_FAILURE, 0, "%s: a bug! please contact us at %s to fix "
+ "the problem: %d is not a recognized mode",
+ __func__, PACKAGE_BUGREPORT, p->mode);
+ }
/* Write Match's configuration as keywords into the first extension of
the output. */
@@ -420,7 +491,9 @@ match(struct matchparams *p)
? p->input1name
: "Standard input" ),
&p->cp.okeys, 1);
- gal_fits_key_write_filename("input2", p->input2name, &p->cp.okeys, 1);
+ gal_fits_key_write_filename("input2",
+ p->input2name?p->input2name:"--coord",
+ &p->cp.okeys, 1);
gal_fits_key_write_config(&p->cp.okeys, "Match configuration",
"MATCH-CONFIG", p->out1name, "0");
}
diff --git a/bin/match/ui.c b/bin/match/ui.c
index df1fb9b..af1206e 100644
--- a/bin/match/ui.c
+++ b/bin/match/ui.c
@@ -224,24 +224,45 @@ ui_read_check_only_options(struct matchparams *p)
-
+/* Two necessary catalogs: First: Standard input, or a file.
+ Second: `--coord', or a file.
+ */
static void
ui_check_options_and_arguments(struct matchparams *p)
{
- /* The first input might come from the standard input, in that case, the
- second input's name is stored in `input1name' and `input2name' will be
- left to NULL. So we'll first correct for this. */
- if(p->input1name)
+ /* When `--coord' is given, there should be no second catalog
+ (argument). */
+ if(p->coord)
+ {
+ /* Make sure no second argument is given. */
+ if(p->input2name)
+ error(EXIT_FAILURE, 0, "only one argument can be given with the "
+ "`--coord' option");
+
+ /* No need for `p->input2name' or `p->ccol2'. */
+ gal_data_free(p->ccol2);
+ p->ccol2=NULL;
+ }
+
+ /* `--coord' is not given. */
+ else
{
+ /* Without `coord' atleast one input is necessary. */
+ if(p->input1name==NULL)
+ error(EXIT_FAILURE, 0, "no inputs!\n\n"
+ "Two inputs are necessary. The first can be a file, or from "
+ "the standard input (e.g., a pipe). The second can be a "
+ "file, or its coordinates can be directly specified on the "
+ "command-line with `--coord'");
+
+ /* If the first input should be read from the standard input, the
+ contents of `input1name' actually belong to `input2name'. */
if(p->input2name==NULL)
{
p->input2name=p->input1name;
p->input1name=NULL;
}
}
- else
- error(EXIT_FAILURE, 0, "no inputs! two inputs are necessary. The first "
- "can be from the standard input (e.g., a pipe)");
/* If the first input is a FITS file, make sure its HDU is also given. */
@@ -253,20 +274,13 @@ ui_check_options_and_arguments(struct matchparams *p)
"`--hdu' (`-h') option and give it the HDU number (starting "
"from zero), extension name, or anything acceptable by "
"CFITSIO");
-
- /* If the second input is a FITS file, make sure its HDU is also
- given. */
- if(p->input2name)
- {
- if( gal_fits_name_is_fits(p->input2name) && p->hdu2==NULL )
- error(EXIT_FAILURE, 0, "no HDU for second input. Please use the "
- "`--hdu2' (`-H') option and give it the HDU number (starting "
- "from zero), extension name, or anything acceptable by "
- "CFITSIO");
- }
- else
- error(EXIT_FAILURE, 0, "second input file not specified: two inputs are "
- "necessary");
+ if( p->input2name
+ && gal_fits_name_is_fits(p->input2name)
+ && p->hdu2==NULL )
+ error(EXIT_FAILURE, 0, "no HDU for second input. Please use "
+ "the `--hdu2' (`-H') option and give it the HDU number "
+ "(starting from zero), extension name, or anything "
+ "acceptable by CFITSIO");
}
@@ -294,41 +308,67 @@ ui_check_options_and_arguments(struct matchparams *p)
static void
ui_set_mode(struct matchparams *p)
{
- /* Check if we are in image or catalog mode. We will base the mode on the
- first input, then check with the second. */
+ int tin1, tin2;
+ char *t1=NULL, *t2=NULL;
+
+ /* We will base the mode on the first input, then check with the
+ second. Note that when the first is from standard input (it is
+ `NULL'), then we go into catalog mode because currently we assume
+ standard input is only for plain text and WCS matching is not defined
+ on plain text. */
if( p->input1name && gal_fits_name_is_fits(p->input1name) )
- p->mode = ( (gal_fits_hdu_format(p->input1name, p->cp.hdu) == IMAGE_HDU)
- ? MATCH_MODE_WCS
- : MATCH_MODE_CATALOG );
+ {
+ tin1=gal_fits_hdu_format(p->input1name, p->cp.hdu);
+ p->mode = (tin1 == IMAGE_HDU) ? MATCH_MODE_WCS : MATCH_MODE_CATALOG;
+ }
else
p->mode=MATCH_MODE_CATALOG;
- /* Now that the mode is set, check the second input's type. */
- if( gal_fits_name_is_fits(p->input2name) )
+
+ /* Necessary sanity checks. */
+ if(p->mode==MATCH_MODE_CATALOG && p->cp.searchin==0)
+ error(EXIT_FAILURE, 0, "no `--searchin' option specified. Please run "
+ "the following command for more information:\n\n"
+ " $ info gnuastro \"selecting table columns\"\n");
+
+
+ /* Now that the mode is set, do some sanity checks on the second
+ catalog. Recall that when `--coord' is given, there is no second input
+ file.*/
+ if(p->input2name)
{
- if(gal_fits_hdu_format(p->input2name, p->hdu2) == IMAGE_HDU)
+ if(gal_fits_name_is_fits(p->input2name))
{
- if( p->mode==MATCH_MODE_CATALOG)
- error(EXIT_FAILURE, 0, "%s is a catalog, while %s is an image. "
- "Both inputs have to be images or catalogs",
- gal_checkset_dataset_name(p->input1name, p->cp.hdu),
- gal_checkset_dataset_name(p->input2name, p->hdu2) );
+ tin2=gal_fits_hdu_format(p->input2name, p->hdu2);
+ if(tin1==IMAGE_HDU && tin2!=IMAGE_HDU)
+ {
+ t1 = (tin1==IMAGE_HDU) ? "image" : "catalog";
+ t2 = (tin2==IMAGE_HDU) ? "image" : "catalog";
+ }
+ if(t1)
+ error(EXIT_FAILURE, 0, "%s is a %s, while %s is an "
+ "%s. Both inputs have to be images or catalogs",
+ gal_checkset_dataset_name(p->input1name, p->cp.hdu), t1,
+ gal_checkset_dataset_name(p->input2name, p->hdu2), t2 );
}
else
{
- if( p->mode==MATCH_MODE_WCS)
- error(EXIT_FAILURE, 0, "%s is an image, while %s is a catalog. "
+ if(p->mode==MATCH_MODE_WCS)
+ error(EXIT_FAILURE, 0, "%s is an image, while %s is a catalog! "
"Both inputs have to be images or catalogs",
gal_checkset_dataset_name(p->input1name, p->cp.hdu),
- gal_checkset_dataset_name(p->input2name, p->hdu2));
+ gal_checkset_dataset_name(p->input2name, p->hdu2) );
}
}
else
- if(p->mode==MATCH_MODE_WCS)
- error(EXIT_FAILURE, 0, "%s is an image, while %s is a catalog! Both "
- "inputs have to be images or catalogs",
- gal_checkset_dataset_name(p->input1name, p->cp.hdu),
- gal_checkset_dataset_name(p->input2name, p->hdu2));
+ {
+ /* When there is no second-input file name (`--coord' is given), we
+ cannot be in WCS mode (requiring a FITS file). */
+ if(p->mode==MATCH_MODE_WCS)
+ error(EXIT_FAILURE, 0, "%s is an image, while `--coord' is only "
+ "meaningful for catalogs",
+ gal_checkset_dataset_name(p->input1name, p->cp.hdu));
+ }
}
@@ -534,6 +574,98 @@ ui_read_columns_aperture_3d(struct matchparams *p)
+static size_t
+ui_set_columns_sanity_check_read_aperture(struct matchparams *p)
+{
+ size_t ccol1n, ccol2n;
+
+ /* Make sure the columns to read are given. */
+ if(p->coord)
+ {
+ if(p->ccol1==NULL)
+ error(EXIT_FAILURE, 0, "no value given to `--ccol1' (necessary with "
+ "`--coord')");
+ }
+ else
+ {
+ if(p->ccol1==NULL || p->ccol2==NULL)
+ error(EXIT_FAILURE, 0, "both `--ccol1' and `--ccol2' must be given. "
+ "They specify the columns containing the coordinates to match");
+ }
+
+ /* Make sure the same number of columns is given to both. */
+ ccol1n = p->ccol1->size;
+ ccol2n = p->coord ? p->coord->size : p->ccol2->size;
+ if(ccol1n!=ccol2n)
+ error(EXIT_FAILURE, 0, "number of coordinates given to `--ccol1' "
+ "(%zu) and `--%s' (%zu) must be equal.\n\n"
+ "If you didn't call these options, run with `--checkconfig' to "
+ "see which configuration file is responsible. You can always "
+ "override the configuration file values by calling the option "
+ "manually on the command-line",
+ ccol1n, p->coord ? "coord" : "ccol2", ccol2n);
+
+ /* Read/check the aperture values. */
+ if(p->aperture)
+ switch(ccol1n)
+ {
+ case 1:
+ if(p->aperture->size>1)
+ error(EXIT_FAILURE, 0, "%zu values given to `--aperture'. In a 1D "
+ "match, this option can only take one value",
+ p->aperture->size);
+ break;
+
+ case 2: ui_read_columns_aperture_2d(p); break;
+ case 3: ui_read_columns_aperture_3d(p); break;
+ default:
+ error(EXIT_FAILURE, 0, "%zu dimensional matches are not currently "
+ "supported (maximum is 2 dimensions). The number of "
+ "dimensions is deduced from the number of values given to "
+ "`--ccol1' (or `--coord') and `--ccol2'", ccol1n);
+ }
+ else
+ error(EXIT_FAILURE, 0, "no matching aperture specified. Please use "
+ "the `--aperture' option to define the acceptable aperture for "
+ "matching the coordinates (in the same units as each "
+ "dimension). Please run the following command for more "
+ "information.\n\n $ info %s\n", PROGRAM_EXEC);
+
+ /* Return the number of dimensions. */
+ return ccol1n;
+}
+
+
+
+
+
+/* Save the manually given coordinates (with `--coord') in column format (a
+ list of datasets). */
+static gal_data_t *
+ui_set_columns_from_coord(struct matchparams *p)
+{
+ size_t i, one=1;
+ gal_data_t *out=NULL;
+ double *coord=p->coord->array;
+
+ /* Write each given value as a one-row table column (single element
+ datasets that are linked) */
+ for(i=0;i<p->coord->size;++i)
+ {
+ gal_list_data_add_alloc(&out, NULL, GAL_TYPE_FLOAT64, 1, &one, NULL,
+ 0, -1, NULL, NULL, NULL);
+ *((double *)(out->array))=coord[i];
+ }
+ gal_list_data_reverse(&out);
+
+ /* Return the list. */
+ return out;
+}
+
+
+
+
+
/* We want to keep the columns as double type. So what-ever their original
type is, convert it. */
static gal_data_t *
@@ -599,69 +731,32 @@ ui_read_columns_to_double(struct matchparams *p, char
*filename, char *hdu,
static void
ui_read_columns(struct matchparams *p)
{
- size_t i;
- size_t ccol1n=p->ccol1->size;
- size_t ccol2n=p->ccol2->size;
+ size_t i, ndim;
+ char **strarr1, **strarr2;
gal_list_str_t *cols1=NULL, *cols2=NULL;
- char **strarr1=p->ccol1->array, **strarr2=p->ccol2->array;
-
- /* Make sure the same number of columns is given to both. */
- if(ccol1n!=ccol2n)
- error(EXIT_FAILURE, 0, "the number of values given to `--ccol1' and "
- "`--ccol2' (%zu and %zu) are not equal", ccol1n, ccol2n);
-
-
- /* Read/check the aperture values. */
- if(p->aperture)
- switch(ccol1n)
- {
- case 1:
- if(p->aperture->size>1)
- error(EXIT_FAILURE, 0, "%zu values given to `--aperture'. In a 1D "
- "match, this option can only take one value",
- p->aperture->size);
- break;
-
- case 2: ui_read_columns_aperture_2d(p); break;
- case 3: ui_read_columns_aperture_3d(p); break;
- default:
- error(EXIT_FAILURE, 0, "%zu dimensional matches are not currently "
- "supported (maximum is 2 dimensions). The number of "
- "dimensions is deduced from the number of values given to "
- "`--ccol1' and `--ccol2'", ccol1n);
- }
- else
- error(EXIT_FAILURE, 0, "no matching aperture specified. Please use "
- "the `--aperture' option to define the acceptable aperture for "
- "matching the coordinates (in the same units as each "
- "dimension). Please run the following command for more "
- "information.\n\n $ info %s\n", PROGRAM_EXEC);
+ /* Basic sanity checks and reading of aperture values. */
+ ndim=ui_set_columns_sanity_check_read_aperture(p);
/* Convert the array of strings to a list of strings for the column
names. */
- for(i=0;i<ccol1n;++i)
+ strarr1=p->ccol1->array;
+ strarr2=p->coord?NULL:p->ccol2->array;
+ for(i=0;i<ndim;++i)
{
gal_list_str_add(&cols1, strarr1[i], 1);
- gal_list_str_add(&cols2, strarr2[i], 1);
+ if(strarr2) gal_list_str_add(&cols2, strarr2[i], 1);
}
gal_list_str_reverse(&cols1);
- gal_list_str_reverse(&cols2);
+ if(cols2) gal_list_str_reverse(&cols2);
-
- /* Read the columns. */
- if(p->cp.searchin)
- {
- /* Read the first dataset. */
- p->cols1=ui_read_columns_to_double(p, p->input1name, p->cp.hdu,
- cols1, ccol1n);
- p->cols2=ui_read_columns_to_double(p, p->input2name, p->hdu2,
- cols2, ccol2n);
- }
- else
- error(EXIT_FAILURE, 0, "no `--searchin' option specified. Please run "
- "the following command for more information:\n\n"
- " $ info gnuastro \"selecting table columns\"\n");
+ /* Read-in the columns. */
+ p->cols1=ui_read_columns_to_double(p, p->input1name, p->cp.hdu,
+ cols1, ndim);
+ p->cols2=( p->coord
+ ? ui_set_columns_from_coord(p)
+ : ui_read_columns_to_double(p, p->input2name, p->hdu2,
+ cols2, ndim) );
/* Free the extra spaces. */
gal_list_str_free(cols1, 1);
@@ -675,27 +770,65 @@ ui_read_columns(struct matchparams *p)
static void
ui_preparations_out_cols(struct matchparams *p)
{
- size_t i;
- char **strarr=p->outcols->array;
+ void *rptr;
+ int goodvalue;
+ gal_data_t *read;
+ uint8_t readtype;
+ char *col, **strarr=p->outcols->array;
+ size_t i, one=1, ndim=p->coord?p->coord->size:0;
/* Go over all the values and put the respective column identifier in the
proper list. */
for(i=0;i<p->outcols->size;++i)
- switch(strarr[i][0])
- {
- case 'a': gal_list_str_add(&p->acols, strarr[i]+1, 0); break;
- case 'b': gal_list_str_add(&p->bcols, strarr[i]+1, 0); break;
- default:
- error(EXIT_FAILURE, 0, "`%s' is not a valid value for `--outcols'. "
- "The first character of each value to this option must be "
- "either `a' or `b'. The former specifies a column from the "
- "first input and the latter a column from the second. The "
- "characters after them can be any column identifier (number, "
- "name, or regular expression). For more on column selection, "
- "please run this command:\n\n"
- " $ info gnuastro \"Selecting table columns\"\n",
- strarr[i]);
- }
+ {
+ col=strarr[i];
+ switch(col[0])
+ {
+ case 'a': gal_list_str_add(&p->acols, col+1, 0); break;
+ case 'b':
+ /* With `--coord', only numbers that are smaller than the number
+ of the dimensions are acceptable. */
+ if(p->coord)
+ {
+ goodvalue=0;
+ rptr=gal_type_string_to_number(col+1, &readtype);
+ if(rptr)
+ {
+ read=gal_data_alloc(rptr, readtype, 1, &one, NULL, 0, -1,
+ NULL, NULL, NULL);
+ if(gal_type_is_int(readtype))
+ {
+ read=gal_data_copy_to_new_type_free(read,GAL_TYPE_LONG);
+ if( *((long *)(read->array)) <= ndim )
+ goodvalue=1;
+ }
+ gal_data_free(read);
+ }
+ if(goodvalue==0)
+ error(EXIT_FAILURE, 0, "bad value to second catalog "
+ "column (%s) of `--outcols'.\n\n"
+ "With the `--coord' option, the second catalog is "
+ "assumed to have a single row and the given number "
+ "of columns. Therefore when using `--outcols', only "
+ "integers that are less than the number of "
+ "dimensions (%zu in this case) are acceptable", col+1,
+ ndim);
+ }
+ gal_list_str_add(&p->bcols, col+1, 0);
+ break;
+ default:
+ error(EXIT_FAILURE, 0, "`%s' is not a valid value for "
+ "`--outcols'.\n\n"
+ "The first character of each value to this option must be "
+ "either `a' or `b'. The former specifies a column from the "
+ "first input and the latter a column from the second. The "
+ "characters after them can be any column identifier (number, "
+ "name, or regular expression). For more on column selection, "
+ "please run this command:\n\n"
+ " $ info gnuastro \"Selecting table columns\"\n",
+ col);
+ }
+ }
/* Revere the lists so they correspond to the input order. */
gal_list_str_reverse(&p->acols);
@@ -738,7 +871,7 @@ ui_preparations_out_name(struct matchparams *p)
}
else
{
- if(p->outcols)
+ if(p->outcols || p->coord)
{
if(p->cp.output)
gal_checkset_allocate_copy(p->cp.output, &p->out1name);
diff --git a/bin/match/ui.h b/bin/match/ui.h
index e949fb4..6d66082 100644
--- a/bin/match/ui.h
+++ b/bin/match/ui.h
@@ -40,7 +40,7 @@ enum program_args_groups
/* Available letters for short options:
- b d e f g i j k m n p r s t u v w x y z
+ b e f g i j k m n p r s t u v w x y z
A B E G J L O Q R W X Y
*/
enum option_keys_enum
@@ -51,6 +51,7 @@ enum option_keys_enum
UI_KEY_LOGASOUTPUT = 'l',
UI_KEY_CCOL1 = 'c',
UI_KEY_CCOL2 = 'C',
+ UI_KEY_COORD = 'd',
/* Only with long version (start with a value 1000, the rest will be set
automatically). */
diff --git a/bin/mkprof/ui.c b/bin/mkprof/ui.c
index 207389e..f3408b3 100644
--- a/bin/mkprof/ui.c
+++ b/bin/mkprof/ui.c
@@ -825,6 +825,25 @@ ui_read_cols_2d(struct mkprofparams *p)
gal_data_free(corrtype);
}
}
+
+ /* Multi-column sanity checks. */
+ counter=0;
+ if( !p->cp.quiet && (p->mforflatpix || p->mcolisbrightness) )
+ for(i=0;i<p->num;++i)
+ if( p->m[i]==0.0 && ( p->f[i]==PROFILE_POINT
+ || p->f[i]==PROFILE_FLAT
+ || p->f[i]==PROFILE_CIRCUMFERENCE ) )
+ {
+ error(0, 0, "WARNING: atleast one single-valued profile (point, "
+ "flat, or circumference profiles) has a magnitude column "
+ "value of 0.0 while `--mforflatpix' or "
+ "`--mcolforbrightness' have also been given. In such cases "
+ "the profile's pixels will have a value of zero and thus "
+ "they will not be identifiable from the zero-valued "
+ "background. If this behavior is intended, this warning "
+ "can be supressed with the `--quiet' (or `-q') option.\n");
+ break;
+ }
}
diff --git a/bin/noisechisel/threshold.c b/bin/noisechisel/threshold.c
index 47dcd19..4fe408a 100644
--- a/bin/noisechisel/threshold.c
+++ b/bin/noisechisel/threshold.c
@@ -282,8 +282,9 @@ threshold_interp_smooth(struct noisechiselparams *p,
gal_data_t **first,
/* 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);
+ tmp=gal_interpolate_close_neighbors(*first, tl, cp->interpmetric,
+ cp->interpnumngb, cp->numthreads,
+ cp->interponlyblank, 1);
gal_data_free(*first);
gal_data_free(*second);
if(third) gal_data_free(*third);
diff --git a/bin/noisechisel/ui.c b/bin/noisechisel/ui.c
index 7a6a438..66df6e6 100644
--- a/bin/noisechisel/ui.c
+++ b/bin/noisechisel/ui.c
@@ -135,6 +135,7 @@ ui_initialize_options(struct noisechiselparams *p,
case GAL_OPTIONS_KEY_TILESIZE:
case GAL_OPTIONS_KEY_MINMAPSIZE:
case GAL_OPTIONS_KEY_NUMCHANNELS:
+ case GAL_OPTIONS_KEY_INTERPMETRIC:
case GAL_OPTIONS_KEY_INTERPNUMNGB:
case GAL_OPTIONS_KEY_REMAINDERFRAC:
cp->coptions[i].mandatory=GAL_OPTIONS_MANDATORY;
diff --git a/bin/statistics/sky.c b/bin/statistics/sky.c
index 6d6a3fe..865cfc4 100644
--- a/bin/statistics/sky.c
+++ b/bin/statistics/sky.c
@@ -220,8 +220,9 @@ sky(struct statisticsparams *p)
/* Interpolate the Sky and its standard deviation. */
if(!cp->quiet) gettimeofday(&t1, NULL);
p->sky_t->next=p->std_t;
- tmp=gal_interpolate_close_neighbors(p->sky_t, tl, cp->interpnumngb,
- cp->numthreads, cp->interponlyblank, 1);
+ tmp=gal_interpolate_close_neighbors(p->sky_t, tl, cp->interpmetric,
+ cp->interpnumngb, cp->numthreads,
+ cp->interponlyblank, 1);
gal_data_free(p->sky_t);
gal_data_free(p->std_t);
p->sky_t=tmp;
diff --git a/bin/statistics/statistics.c b/bin/statistics/statistics.c
index c92ca8b..333b432 100644
--- a/bin/statistics/statistics.c
+++ b/bin/statistics/statistics.c
@@ -251,6 +251,7 @@ statistics_interpolate_and_write(struct statisticsparams *p,
&& !(p->cp.interponlyblank && gal_blank_present(values, 1)==0) )
{
interpd=gal_interpolate_close_neighbors(values, &cp->tl,
+ cp->interpmetric,
cp->interpnumngb,
cp->numthreads,
cp->interponlyblank, 0);
diff --git a/bin/statistics/ui.c b/bin/statistics/ui.c
index dfa3c21..4e1c7d4 100644
--- a/bin/statistics/ui.c
+++ b/bin/statistics/ui.c
@@ -418,10 +418,10 @@ ui_read_check_only_options(struct statisticsparams *p)
{
/* Mandatory options. */
if( isnan(p->meanmedqdiff) || isnan(p->sclipparams[0])
- || p->cp.interpnumngb==0 )
- error(EXIT_FAILURE, 0, "`--meanmedqdiff', `--sclipparams' and "
- "`--interpnumngb' are mandatory when requesting Sky "
- "measurement (`--sky')");
+ || p->cp.interpmetric==0 || p->cp.interpnumngb==0 )
+ error(EXIT_FAILURE, 0, "`--meanmedqdiff', `--sclipparams', "
+ "`--interpmetric' and `--interpnumngb' are mandatory when "
+ "requesting Sky measurement (`--sky')");
/* If mode and median distance is a reasonable value. */
if(p->meanmedqdiff>0.5)
diff --git a/doc/announce-acknowledge.txt b/doc/announce-acknowledge.txt
index 8e5463a..02c7b76 100644
--- a/doc/announce-acknowledge.txt
+++ b/doc/announce-acknowledge.txt
@@ -1,5 +1,6 @@
Alphabetically ordered list to acknowledge in the next release.
+Roberto Baena Gallé
Leindert Boogaard
Raúl Infante Sainz
David Valls-Gabaud
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index b7b6537..c01fa0e 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -7816,6 +7816,22 @@ is desirable).
When values are to be interpolated, only change the values of the blank
elements, keep the non-blank elements untouched.
+@item --interpmetric=STR
+@cindex Radial metric
+@cindex Taxicab metric
+@cindex Manhattan metric
+@cindex Metric: Manhattan, Taxicab, Radial
+The metric to use for finding nearest neighbors. Currently it only accepts
+the Manhattan (or taxicab) metric with @code{manhattan}, or the radial
+metric with @code{radial}.
+
+The Manhattan distance between two points is defined with
+@mymath{|\Delta{x}|+|\Delta{y}|}. Thus the Manhattan metric has the
+advantage of being fast, but at the expense of being less accurate. The
+radial distance is the standard definition of distance in a Euclidean
+space: @mymath{\sqrt{\Delta{x}^2+\Delta{y}^2}}. It is accurate, but the
+multiplication and square root can slow down the processing.
+
@item --interpnumngb=INT
The number of nearby non-blank neighbors to use for interpolation.
@end table
@@ -12146,18 +12162,17 @@ non-zero decimals) put an @code{f} after it.
@item sqrt
The square root of the first operand, so ``@command{5 sqrt}'' is equivalent
-to @mymath{\sqrt{5}}. The output type is determined from the input, so the
-output of this example will be @command{2} (since @command{5} doesn't have
-any non-zero decimal digits). If you want @command{2.23607}, run
-@command{5f sqrt} instead, the @command{f} will ensure that a number will
-be read as a floating point number, even if it doesn't have decimal
-digits. If the input image has an integer type, you should explicitly
-convert the image to floating point, for example @command{a.fits float
-sqrt}, see the type conversion operators below.
+to @mymath{\sqrt{5}}. The output will have a floating point type, but its
+precision is determined from the input: if the input is a 64-bit floating
+point, the output will also be 64-bit. Otherwise, the output will be 32-bit
+floating point (see @ref{Numeric data types} for the respective
+precision). Therefore if you require 64-bit precision in estimating the
+square root, convert the input to 64-bit floating point first, for example
+with @code{5 float64 sqrt}.
@item log
Natural logarithm of first operand, so ``@command{4 log}'' is equivalent to
-@mymath{\ln(4)}. The output type is determined from the input, see the
+@mymath{ln(4)}. The output type is determined from the input, see the
explanation under @command{sqrt} for more.
@item log10
@@ -19926,10 +19941,14 @@ $ astmatch --ccol1=2,3,4 --ccol2=2,3,4
-a0.5/3600,0.5/3600,5e-10 \
in1.fits in2.txt
@end example
-Two inputs are necessary for Match to start processing. The inputs can be
-plain text tables or FITS tables, see @ref{Tables}. If only one argument is
-provided, Match will assume look for the first input in Standard input (see
-@ref{Standard input}).
+Match will find the rows that are nearest to each other in two catalogs
+(given some coordinate columns). Therefore two catalogs are necessary for
+input. However, they don't necessarily have to be files: 1) the first
+catalog can also come from the standard input (for example a pipe, see
+@ref{Standard input}); 2) when only one point is needed, you can use the
+@option{--coord} option to avoid creating a file for the second
+catalog. When the inputs are files, they can be plain text tables or FITS
+tables, for more see @ref{Tables}.
Match follows the same basic behavior of all Gnuastro programs as fully
described in @ref{Common program behavior}. If the first input is a FITS
@@ -20022,6 +20041,15 @@ re-arrange the necessary columns and it will write a
single output
table. Combined with regular expressions in large tables, this can be a
very powerful and convenient way to merge various tables into one.
+When @option{--coord} is given, no second catalog will be read. The second
+catalog will be created internally based on the values given to
+@option{--coord}. So column names aren't defined and you can only request
+integer column numbers that are less than the number of coordinates given
+to @option{--coord}. For example if you want to find the row matching RA of
+1.2345 and Dec of 6.7890, then you should use
+@option{--coord=1.2345,6.7890}. But when using @option{--outcols}, you
+can't give @code{bRA}, or @code{b25}.
+
@item -l
@itemx --logasoutput
The output file will have the contents of the log file: indexes in the two
@@ -20051,8 +20079,27 @@ columns}. See the one-line examples above for some
usages of this option.
The coordinate columns of the second input. See the example in
@option{--ccol1} for more.
-@item -a FLT[,...]
-@itemx --aperture=FLT[,...]
+@item -d FLT[,FLT]
+@itemx --coord=FLT[,FLT]
+Manually specify the coordinates to match against the given catalog. With
+this option, Match will not look for a second input file/table and will
+directly use the coordinates given to this option.
+
+When this option is called, the output changes in the following ways: 1)
+when @option{--outcols} is specified, for the second input, it can only
+accept integer numbers that are less than the number of values given to
+this option, see description of that option for more. 2) By default (when
+@option{--outcols} isn't used), only the matching row of the first table
+will be output (a single file), not two separate files (one for each
+table).
+
+This option is good when you have a (large) catalog and only want to match
+a single coordinate to it (for example to find the nearest catalog entry to
+your desired point). With this option, you can write the coordinates on the
+command-line and thus avoid the need to make a single-row file.
+
+@item -a FLT[,FLT[,FLT]]
+@itemx --aperture=FLT[,FLT[,FLT]]
Parameters of the aperture for matching. The values given to this option
can be fractions, for example when the position columns are in units of
degrees, @option{1/3600} can be used to ask for one arcsecond. The
@@ -23944,6 +23991,10 @@ Note: Do not use the maximum value for a blank value
of a general
@ref{Library blank values} for the definition and usage of blank values.
@end deftypefun
+@deftypefun int gal_type_is_int (uint8_t @code{type})
+Return 1 if the type is an integer (any width and any sign).
+@end deftypefun
+
@deftypefun int gal_type_is_list (uint8_t @code{type})
Return 1 if the type is a linked list and zero otherwise.
@end deftypefun
@@ -24861,6 +24912,11 @@ the two coordinates @code{a} and @code{b} (each an
array of @code{ndim}
elements).
@end deftypefun
+@deftypefun float gal_dimension_dist_radial (size_t @code{*a}, size_t
@code{*b}, size_t @code{ndim})
+Return the radial distance between the two coordinates @code{a} and
+@code{b} (each an array of @code{ndim} elements).
+@end deftypefun
+
@deftypefun {gal_data_t *} gal_dimension_collapse_sum (gal_data_t @code{*in},
size_t @code{c_dim}, gal_data_t @code{*weight})
Collapse the input dataset (@code{in}) along the given dimension
(@code{c_dim}, in C definition: starting from zero, from the slowest
@@ -26265,17 +26321,29 @@ typedef struct gal_fits_list_key_t
@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}.
+Returns a pointer to an allocated space containing the value to the FITS
+@code{BLANK} header keyword, when the input array has a type of
+@code{type}. This is useful when you want to write the @code{BLANK} keyword
+using CFITSIO's @code{fits_write_key} function.
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).
+needed for datasets containing signed 8-bit, unsigned 16-bit, unsigned
+32-bit, and unsigned 64-bit integers (types that are defined with
+@code{BSCALE} and @code{BZERO} in the FITS standard).
+
+@cartouche
+@noindent
+@strong{Not usable when reading a dataset:} As quoted from the FITS
+standard above, the value returned by this function can only be generically
+used for the writing of the @code{BLANK} keyword header. It @emph{must not}
+be used as the blank pointer when when reading a FITS array using
+CFITSIO. When reading an array with CFITSIO, you can use
+@code{gal_blank_alloc_write} to generate the necessary pointer.
+@end cartouche
@end deftypefun
@deftypefun void gal_fits_key_clean_str_value (char @code{*string})
@@ -27336,11 +27404,14 @@ polish notation}).
@deffnx Macro GAL_ARITHMETIC_OP_LOG10
Unary operator functions for calculating the square root
(@mymath{\sqrt{i}}), @mymath{ln(i)} and @mymath{log(i)} mathematic
-operators on each element of the input dataset. The output will have the
-same type as the input, so if your inputs are integer types be careful.
-
-If you want your output to be floating point but your input is an integer
-type, you can convert the input to a floating point type with
+operators on each element of the input dataset. The returned dataset will
+have a floating point type, but its precision is determined from the input:
+if the input is a 64-bit floating point, the output will also be
+64-bit. Otherwise, the returned dataset will be 32-bit floating point. See
+@ref{Numeric data types} for the respective precision.
+
+If you want your output to be 64-bit floating point but your input is a
+different type, you can convert the input to a floating point type with
@code{gal_data_copy_to_new_type} or
@code{gal_data_copy_to_new_type_free}(see @ref{Copying datasets}).
@end deffn
diff --git a/lib/arithmetic.c b/lib/arithmetic.c
index d24e960..aba3df2 100644
--- a/lib/arithmetic.c
+++ b/lib/arithmetic.c
@@ -350,43 +350,82 @@ arithmetic_abs(int flags, gal_data_t *in)
-#define UNIFUNC_RUN_FUNCTION_ON_ELEMENT(IT, OP){ \
- IT *ia=in->array, *oa=o->array, *iaf=ia + in->size; \
+#define UNIFUNC_RUN_FUNCTION_ON_ELEMENT(OT, IT, OP){ \
+ OT *oa=o->array; \
+ IT *ia=in->array, *iaf=ia + in->size; \
do *oa++ = OP(*ia++); while(ia<iaf); \
}
+#define UNIFUNC_RUN_FUNCTION_ON_ELEMENT_INSET(IT, OP) \
+ switch(o->type) \
+ { \
+ case GAL_TYPE_UINT8: \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT(uint8_t, IT, OP) \
+ break; \
+ case GAL_TYPE_INT8: \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT(int8_t, IT, OP) \
+ break; \
+ case GAL_TYPE_UINT16: \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT(uint16_t, IT, OP) \
+ break; \
+ case GAL_TYPE_INT16: \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT(int16_t, IT, OP) \
+ break; \
+ case GAL_TYPE_UINT32: \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT(uint32_t, IT, OP) \
+ break; \
+ case GAL_TYPE_INT32: \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT(int32_t, IT, OP) \
+ break; \
+ case GAL_TYPE_UINT64: \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT(uint64_t, IT, OP) \
+ break; \
+ case GAL_TYPE_INT64: \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT(int64_t, IT, OP) \
+ break; \
+ case GAL_TYPE_FLOAT32: \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT(float, IT, OP) \
+ break; \
+ case GAL_TYPE_FLOAT64: \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT(double, IT, OP) \
+ break; \
+ default: \
+ error(EXIT_FAILURE, 0, "%s: type code %d not recognized", \
+ "UNIARY_FUNCTION_ON_ELEMENT", in->type); \
+ }
+
#define UNIARY_FUNCTION_ON_ELEMENT(OP) \
switch(in->type) \
{ \
case GAL_TYPE_UINT8: \
- UNIFUNC_RUN_FUNCTION_ON_ELEMENT(uint8_t, OP) \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT_INSET(uint8_t, OP) \
break; \
case GAL_TYPE_INT8: \
- UNIFUNC_RUN_FUNCTION_ON_ELEMENT(int8_t, OP) \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT_INSET(int8_t, OP) \
break; \
case GAL_TYPE_UINT16: \
- UNIFUNC_RUN_FUNCTION_ON_ELEMENT(uint16_t, OP) \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT_INSET(uint16_t, OP) \
break; \
case GAL_TYPE_INT16: \
- UNIFUNC_RUN_FUNCTION_ON_ELEMENT(int16_t, OP) \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT_INSET(int16_t, OP) \
break; \
case GAL_TYPE_UINT32: \
- UNIFUNC_RUN_FUNCTION_ON_ELEMENT(uint32_t, OP) \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT_INSET(uint32_t, OP) \
break; \
case GAL_TYPE_INT32: \
- UNIFUNC_RUN_FUNCTION_ON_ELEMENT(int32_t, OP) \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT_INSET(int32_t, OP) \
break; \
case GAL_TYPE_UINT64: \
- UNIFUNC_RUN_FUNCTION_ON_ELEMENT(uint64_t, OP) \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT_INSET(uint64_t, OP) \
break; \
case GAL_TYPE_INT64: \
- UNIFUNC_RUN_FUNCTION_ON_ELEMENT(int64_t, OP) \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT_INSET(int64_t, OP) \
break; \
case GAL_TYPE_FLOAT32: \
- UNIFUNC_RUN_FUNCTION_ON_ELEMENT(float, OP) \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT_INSET(float, OP) \
break; \
case GAL_TYPE_FLOAT64: \
- UNIFUNC_RUN_FUNCTION_ON_ELEMENT(double, OP) \
+ UNIFUNC_RUN_FUNCTION_ON_ELEMENT_INSET(double, OP) \
break; \
default: \
error(EXIT_FAILURE, 0, "%s: type code %d not recognized", \
@@ -396,15 +435,31 @@ arithmetic_abs(int flags, gal_data_t *in)
static gal_data_t *
arithmetic_unary_function(int operator, int flags, gal_data_t *in)
{
+ uint8_t otype;
+ int inplace=0;
gal_data_t *o;
- /* If we want inplace output, set the output pointer to the input
- pointer, for every pixel, the operation will be independent. */
- if(flags & GAL_ARITHMETIC_INPLACE)
- o = in;
+ /* See if the operation should be done in place. Note that so far, the
+ output of these operators is defined in the real space (floating
+ point). So even if the user requested inplace opereation, if its not a
+ floating point type, its not useful.*/
+ if( (flags & GAL_ARITHMETIC_INPLACE)
+ && (in->type==GAL_TYPE_FLOAT32 || in->type==GAL_TYPE_FLOAT64) )
+ inplace=1;
+
+ if(inplace)
+ {
+ o = in;
+ otype=in->type;
+ }
else
- o = gal_data_alloc(NULL, in->type, in->ndim, in->dsize, in->wcs,
- 0, in->minmapsize, NULL, NULL, NULL);
+ {
+ otype = ( in->type==GAL_TYPE_FLOAT64
+ ? GAL_TYPE_FLOAT64
+ : GAL_TYPE_FLOAT32 );
+ o = gal_data_alloc(NULL, otype, in->ndim, in->dsize, in->wcs,
+ 0, in->minmapsize, NULL, NULL, NULL);
+ }
/* Start setting the operator and operands. */
switch(operator)
diff --git a/lib/dimension.c b/lib/dimension.c
index 070265e..310b5cb 100644
--- a/lib/dimension.c
+++ b/lib/dimension.c
@@ -263,7 +263,7 @@ gal_dimension_index_to_coord(size_t index, size_t ndim,
size_t *dsize,
/************************************************************************/
/******************** Distances **********************/
/************************************************************************/
-size_t
+float
gal_dimension_dist_manhattan(size_t *a, size_t *b, size_t ndim)
{
size_t i, out=0;
@@ -275,6 +275,18 @@ gal_dimension_dist_manhattan(size_t *a, size_t *b, size_t
ndim)
+float
+gal_dimension_dist_radial(size_t *a, size_t *b, size_t ndim)
+{
+ size_t i, out=0;
+ for(i=0;i<ndim;++i) out += (a[i]-b[i])*(a[i]-b[i]);
+ return sqrt(out);
+}
+
+
+
+
+
diff --git a/lib/gnuastro-internal/commonopts.h
b/lib/gnuastro-internal/commonopts.h
index 4420947..cadd541 100644
--- a/lib/gnuastro-internal/commonopts.h
+++ b/lib/gnuastro-internal/commonopts.h
@@ -199,6 +199,20 @@ struct argp_option gal_commonopts_options[] =
GAL_OPTIONS_NOT_SET
},
{
+ "interpmetric",
+ GAL_OPTIONS_KEY_INTERPMETRIC,
+ "INT",
+ 0,
+ "Interpolation metric (radial, manhattan).",
+ GAL_OPTIONS_GROUP_TESSELLATION,
+ &cp->interpmetric,
+ GAL_TYPE_STRING,
+ GAL_OPTIONS_RANGE_ANY,
+ GAL_OPTIONS_NOT_MANDATORY,
+ GAL_OPTIONS_NOT_SET,
+ gal_options_read_interpmetric
+ },
+ {
"interpnumngb",
GAL_OPTIONS_KEY_INTERPNUMNGB,
"INT",
@@ -252,7 +266,7 @@ struct argp_option gal_commonopts_options[] =
GAL_OPTIONS_KEY_TABLEFORMAT,
"STR",
0,
- "Table format: `fits-ascii', `fits-binary'.",
+ "Table fmt: `fits-ascii', `fits-binary', `txt'.",
GAL_OPTIONS_GROUP_OUTPUT,
&cp->tableformat,
GAL_TYPE_STRING,
diff --git a/lib/gnuastro-internal/options.h b/lib/gnuastro-internal/options.h
index 294e96f..3ba3da8 100644
--- a/lib/gnuastro-internal/options.h
+++ b/lib/gnuastro-internal/options.h
@@ -122,6 +122,7 @@ enum options_common_keys
GAL_OPTIONS_KEY_CHECKTILES,
GAL_OPTIONS_KEY_ONEELEMPERTILE,
GAL_OPTIONS_KEY_INTERPONLYBLANK,
+ GAL_OPTIONS_KEY_INTERPMETRIC,
GAL_OPTIONS_KEY_INTERPNUMNGB,
};
@@ -180,6 +181,7 @@ struct gal_options_common_params
/* Tessellation. */
struct gal_tile_two_layer_params tl; /* Two layer tessellation params. */
uint8_t interponlyblank; /* Only interpolate over blank values. */
+ uint8_t interpmetric; /* Metric to use for nearest-ngb interp. */
size_t interpnumngb; /* Number of neighbors for interpolation. */
/* Input. */
@@ -275,6 +277,10 @@ void *
gal_options_read_tableformat(struct argp_option *option, char *arg,
char *filename, size_t lineno, void *junk);
+void *
+gal_options_read_interpmetric(struct argp_option *option, char *arg,
+ char *filename, size_t lineno, void *junk);
+
gal_data_t *
gal_options_parse_list_of_numbers(char *string, char *filename,
size_t lineno);
diff --git a/lib/gnuastro/dimension.h b/lib/gnuastro/dimension.h
index 205820a..2bdc9c4 100644
--- a/lib/gnuastro/dimension.h
+++ b/lib/gnuastro/dimension.h
@@ -89,10 +89,11 @@ gal_dimension_index_to_coord(size_t index, size_t ndim,
size_t *dsize,
/************************************************************************/
/******************** Distances **********************/
/************************************************************************/
-size_t
+float
gal_dimension_dist_manhattan(size_t *a, size_t *b, size_t ndim);
-
+float
+gal_dimension_dist_radial(size_t *a, size_t *b, size_t ndim);
diff --git a/lib/gnuastro/interpolate.h b/lib/gnuastro/interpolate.h
index 1c72730..5f1ec26 100644
--- a/lib/gnuastro/interpolate.h
+++ b/lib/gnuastro/interpolate.h
@@ -46,6 +46,18 @@ __BEGIN_C_DECLS /* From C++ preparations */
+
+/* Metrics to use for nearest-neighbor */
+enum gal_interpolate_close_metric
+{
+ GAL_INTERPOLATE_CLOSE_METRIC_INVALID,
+
+ GAL_INTERPOLATE_CLOSE_METRIC_RADIAL,
+ GAL_INTERPOLATE_CLOSE_METRIC_MANHATTAN,
+};
+
+
+
/* Types of interpolation. */
enum gal_interpolate_1D_types
{
@@ -65,8 +77,9 @@ enum gal_interpolate_1D_types
gal_data_t *
gal_interpolate_close_neighbors(gal_data_t *input,
struct gal_tile_two_layer_params *tl,
- size_t numneighbors, size_t numthreads,
- int onlyblank, int aslinkedlist);
+ uint8_t metric, size_t numneighbors,
+ size_t numthreads, int onlyblank,
+ int aslinkedlist);
gsl_spline *
gal_interpolate_1d_make_gsl_spline(gal_data_t *X, gal_data_t *Y, int type_1d);
diff --git a/lib/gnuastro/type.h b/lib/gnuastro/type.h
index a57214e..195cfce 100644
--- a/lib/gnuastro/type.h
+++ b/lib/gnuastro/type.h
@@ -138,6 +138,9 @@ void
gal_type_max(uint8_t type, void *in);
int
+gal_type_is_int(uint8_t type);
+
+int
gal_type_is_list(uint8_t type);
int
diff --git a/lib/interpolate.c b/lib/interpolate.c
index 8cd99c5..bdc4f50 100644
--- a/lib/interpolate.c
+++ b/lib/interpolate.c
@@ -67,6 +67,8 @@ struct interpolate_params
uint8_t *thread_flags;
int onlyblank;
gal_list_void_t *ngb_vals;
+ float (*metric)(size_t *, size_t *, size_t );
+
struct gal_tile_two_layer_params *tl;
};
@@ -87,11 +89,11 @@ interpolate_close_neighbors_on_thread(void *in_prm)
/* Rest of variables. */
void *nv;
- float pdist;
+ float dist, pdist;
uint8_t *b, *bf, *bb;
gal_list_void_t *tvll;
gal_list_dosizet_t *lQ, *sQ;
- size_t ngb_counter, dist, pind, *dinc;
+ size_t ngb_counter, pind, *dinc;
size_t i, index, fullind, chstart=0, ndim=input->ndim;
gal_data_t *median, *tin, *tout, *tnear, *nearest=NULL;
size_t size = (correct_index ? tl->tottilesinch : input->size);
@@ -233,7 +235,7 @@ interpolate_close_neighbors_on_thread(void *in_prm)
gal_dimension_index_to_coord(nind, ndim, dsize, ncoord);
/* Distance of this neighbor to the one to be filled. */
- dist=gal_dimension_dist_manhattan(icoord, ncoord, ndim);
+ dist=prm->metric(icoord, ncoord, ndim);
/* Add this neighbor to the list. */
gal_list_dosizet_add(&lQ, &sQ, nind, dist);
@@ -257,7 +259,9 @@ interpolate_close_neighbors_on_thread(void *in_prm)
tout=prm->out;
for(tnear=nearest; tnear!=NULL; tnear=tnear->next)
{
- /* Find the median and copy it. */
+ /* Find the median and copy it, but first, reset the flags (which
+ remain from the last time). */
+ tnear->flag &= ~(GAL_DATA_FLAG_SORT_CH | GAL_DATA_FLAG_BLANK_CH);
median=gal_statistics_median(tnear, 1);
memcpy(gal_pointer_increment(tout->array, fullind, tout->type),
median->array, gal_type_sizeof(tout->type));
@@ -326,8 +330,9 @@ interpolate_copy_input(gal_data_t *input, int aslinkedlist)
gal_data_t *
gal_interpolate_close_neighbors(gal_data_t *input,
struct gal_tile_two_layer_params *tl,
- size_t numneighbors, size_t numthreads,
- int onlyblank, int aslinkedlist)
+ uint8_t metric, size_t numneighbors,
+ size_t numthreads, int onlyblank,
+ int aslinkedlist)
{
gal_data_t *tin, *tout;
struct interpolate_params prm;
@@ -352,6 +357,21 @@ gal_interpolate_close_neighbors(gal_data_t *input,
prm.num = aslinkedlist ? gal_list_data_number(input) : 1;
+ /* Set the metric. */
+ switch(metric)
+ {
+ case GAL_INTERPOLATE_CLOSE_METRIC_RADIAL:
+ prm.metric=gal_dimension_dist_radial;
+ break;
+ case GAL_INTERPOLATE_CLOSE_METRIC_MANHATTAN:
+ prm.metric=gal_dimension_dist_manhattan;
+ break;
+ default:
+ error(EXIT_FAILURE, 0, "%s: %d is not a valid metric identifier",
+ __func__, metric);
+ }
+
+
/* Flag the blank values. */
prm.blanks=gal_blank_flag(input);
diff --git a/lib/options.c b/lib/options.c
index 5e286e9..d962789 100644
--- a/lib/options.c
+++ b/lib/options.c
@@ -38,6 +38,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/threads.h>
#include <gnuastro/pointer.h>
#include <gnuastro/arithmetic.h>
+#include <gnuastro/interpolate.h>
#include <gnuastro-internal/timing.h>
#include <gnuastro-internal/options.h>
@@ -511,6 +512,55 @@ gal_options_read_tableformat(struct argp_option *option,
char *arg,
+void *
+gal_options_read_interpmetric(struct argp_option *option, char *arg,
+ char *filename, size_t lineno, void *junk)
+{
+ char *str;
+ if(lineno==-1)
+ {
+ switch(*(uint8_t *)(option->value))
+ {
+ case GAL_INTERPOLATE_CLOSE_METRIC_RADIAL:
+ gal_checkset_allocate_copy("radial", &str);
+ break;
+ case GAL_INTERPOLATE_CLOSE_METRIC_MANHATTAN:
+ gal_checkset_allocate_copy("manhattan", &str);
+ break;
+ default:
+ error(EXIT_FAILURE, 0, "%s: a bug! Please contact us at %s to "
+ "fix the problem. The code %u is not recognized as a "
+ "nearest-neighbor interpolation metric", __func__,
+ PACKAGE_BUGREPORT, *(uint8_t *)(option->value));
+ }
+ return str;
+ }
+ else
+ {
+ /* If the option is already set, just return. */
+ if(option->set) return NULL;
+
+ /* Set the value. */
+ if( !strcmp(arg, "radial") )
+ *(uint8_t *)(option->value) = GAL_INTERPOLATE_CLOSE_METRIC_RADIAL;
+ else if ( !strcmp(arg, "manhattan") )
+ *(uint8_t *)(option->value) = GAL_INTERPOLATE_CLOSE_METRIC_MANHATTAN;
+ else
+ error_at_line(EXIT_FAILURE, 0, filename, lineno, "`%s' (value to "
+ "`%s' option) isn't valid. Currently only `radial' "
+ "and `manhattan' metrics are recognized for nearest "
+ "neighbor interpolation", arg, option->name);
+
+ /* For no un-used variable warning. This function doesn't need the
+ pointer. */
+ return junk=NULL;
+ }
+}
+
+
+
+
+
/* The input to this function is a string of any number of numbers
separated by a comma (`,') and possibly containing fractions, for
example: `1,2/3, 4.95'. The output `gal_data_t' contains the array of
diff --git a/lib/type.c b/lib/type.c
index 560a305..af21dec 100644
--- a/lib/type.c
+++ b/lib/type.c
@@ -280,7 +280,29 @@ gal_type_max(uint8_t type, void *in)
case GAL_TYPE_FLOAT32: *(float *) in = FLT_MAX; break;
case GAL_TYPE_FLOAT64: *(double *) in = DBL_MAX; break;
default:
- error(EXIT_FAILURE, 0, "%s: type code %d not recognized", __func__,
type);
+ error(EXIT_FAILURE, 0, "%s: type code %d not recognized", __func__,
+ type);
+ }
+}
+
+
+
+
+
+int
+gal_type_is_int(uint8_t type)
+{
+ switch(type)
+ {
+ case GAL_TYPE_UINT8: return 1;
+ case GAL_TYPE_INT8: return 1;
+ case GAL_TYPE_UINT16: return 1;
+ case GAL_TYPE_INT16: return 1;
+ case GAL_TYPE_UINT32: return 1;
+ case GAL_TYPE_INT32: return 1;
+ case GAL_TYPE_UINT64: return 1;
+ case GAL_TYPE_INT64: return 1;
+ default: return 0;
}
}
diff --git a/tests/match/merged-cols.sh b/tests/match/merged-cols.sh
index 3e4ac2a..9a21aa3 100755
--- a/tests/match/merged-cols.sh
+++ b/tests/match/merged-cols.sh
@@ -53,6 +53,6 @@ if [ ! -f $execname ]; then echo "$execname not created.";
exit 77; fi
# `check_with_program' can be something like `Valgrind' or an empty
# string. Such programs will execute the command if present and help in
# debugging when the developer doesn't have access to the user's system.
-$check_with_program $execname $cat1 $cat2 --aperture=0.5 \
- -omatch-merged-cols.txt \
+$check_with_program $execname $cat1 $cat2 --aperture=0.5 --ccol1=2,3 \
+ --ccol2=2,3 -omatch-merged-cols.txt \
--outcols=a1,aEFGH,bACCU1,aIJKL,bACCU2
diff --git a/tests/match/positions.sh b/tests/match/positions.sh
index 2622750..e9b51c9 100755
--- a/tests/match/positions.sh
+++ b/tests/match/positions.sh
@@ -53,5 +53,5 @@ if [ ! -f $execname ]; then echo "$execname not created.";
exit 77; fi
# `check_with_program' can be something like `Valgrind' or an empty
# string. Such programs will execute the command if present and help in
# debugging when the developer doesn't have access to the user's system.
-$check_with_program $execname $cat1 $cat2 --aperture=0.5 --log \
- --output=match-positions.fits
+$check_with_program $execname $cat1 $cat2 --aperture=0.5 --log --ccol1=2,3 \
+ --ccol2=2,3 --output=match-positions.fits
- [gnuastro-commits] master 486f915 067/113: Imported recent work in master, conflicts fixed, (continued)
- [gnuastro-commits] master 486f915 067/113: Imported recent work in master, conflicts fixed, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master d6051a1 074/113: Upperlimit magnitude in 3D, corrected creation of check table, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 5dac3c3 075/113: Recent work in master imported, small conflict in book fixed, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 3882956 077/113: Narrow-band areas from MakeCatalog in 3D datasets, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master abe82cb 086/113: Imported recent work in master, no conflicts, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 924787b 098/113: Updated copyright year in files specific to this branch, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master fbbc2fc 100/113: Imported recent work in master, minor conflict fixed, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 22d0fba 089/113: Imported recent work in master, no conflicts, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 8edc804 092/113: Imported recent work in master, minor conflic fixed, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master b5385f7 093/113: Projected spectra given NaN when no measurement on slice, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master ac2a821 103/113: Imported recent work in master, conflicts fixed,
Mohammad Akhlaghi <=
- [gnuastro-commits] master 3f51e31 108/113: Imported work in master, conflicts fixed, corrections made, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 45bd003 049/113: Imported recent work in master, conflicts fixed, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 6f85919 060/113: Connectivity of 2, for filling pseudo-detection holes in 3D, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 442d052 061/113: Imported work in master, no conflicts, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 9285abe 057/113: Imported recent work from master with corrections, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master c91d988 063/113: Recent work in master merged, conflicts corrected, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 05cc693 080/113: Added 3rd dimension to MakeCatalog's minimum-maximum columns, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 0eaf0dc 091/113: Imported recent work in master, conflicts fixed, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 9e2397a 094/113: Imported recent work in master, no conflicts, Mohammad Akhlaghi, 2021/04/16
- [gnuastro-commits] master 9258f68 096/113: Imported recent work in master, minor conflict fixed, Mohammad Akhlaghi, 2021/04/16