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[gnuastro-commits] master 4b0fccc 6/7: Merged MakeCatalog not making a c
|
From: |
Mohammad Akhlaghi |
|
Subject: |
[gnuastro-commits] master 4b0fccc 6/7: Merged MakeCatalog not making a clump catalog branch |
|
Date: |
Tue, 16 Aug 2016 14:30:38 +0000 (UTC) |
branch: master
commit 4b0fccced200209dbca136ceca0002f81a6024fc
Merge: ce19153 e74f2b6
Author: Mohammad Akhlaghi <address@hidden>
Commit: Mohammad Akhlaghi <address@hidden>
Merged MakeCatalog not making a clump catalog branch
The branch (ending with e74f2b6) is now merged into master. Some minor
issues were also fixed after the merge.
---
bootstrap.conf | 1 +
lib/fits.c | 69 +++++++++++-----
lib/gnuastro/fits.h | 23 +++---
lib/gnuastro/statistics.h | 8 ++
lib/statistics.c | 41 ++++++++++
src/mkcatalog/Makefile.am | 8 +-
src/mkcatalog/mkcatalog.c | 43 ++++++----
src/mkcatalog/ui.c | 175 ++++++++++++++++++++++++++++++-----------
src/mkprof/ui.c | 22 +++++-
src/noisechisel/noisechisel.c | 23 +++---
10 files changed, 306 insertions(+), 107 deletions(-)
diff --git a/bootstrap.conf b/bootstrap.conf
index 5908d99..88ca654 100644
--- a/bootstrap.conf
+++ b/bootstrap.conf
@@ -163,6 +163,7 @@ gnulib_modules="
argp
error
nproc
+ strcase
gendocs
progname
git-version-gen
diff --git a/lib/fits.c b/lib/fits.c
index a48cfb7..1168bd3 100644
--- a/lib/fits.c
+++ b/lib/fits.c
@@ -361,7 +361,7 @@ blanktovalue(void *array, int bitpix, size_t size, void
*value)
void
gal_fits_change_type(void *in, int inbitpix, size_t size, int anyblank,
- void **out, int outbitpix)
+ void **out, int outbitpix)
{
size_t i=0;
unsigned char *b, *bf, *ib=in, *iib=in;
@@ -773,11 +773,19 @@ gal_fits_read_hdu(char *filename, char *hdu, int
desiredtype,
/* Read keywords from a FITS file. The gal_fits_read_header_keys pointer is
an array of gal_fits_read_header_keys structures, which keep the basic
information for each keyword that is to be read and also stores the
- value in the appropriate type.*/
+ value in the appropriate type.
+
+ ABOUT THE STRING VALUES:
+
+ The space for a string value is statically allocated within the
+ `gal_fits_read_header_keys' structure (to be `FLEN_VALUE' characters,
+ `FLEN_VALUE' is defined by CFITSIO). So if the value is necessary where
+ `gal_fits_read_header_keys' is no longer available, then you have to
+ allocate space dynamically and copy the string there.
+*/
void
gal_fits_read_keywords(char *filename, char *hdu,
- struct gal_fits_read_header_keys *keys,
- size_t num)
+ struct gal_fits_read_header_keys *keys, size_t num)
{
int status=0;
char *ffname;
@@ -800,10 +808,14 @@ gal_fits_read_keywords(char *filename, char *hdu,
/* Get the desired keywords. */
for(i=0;i<num;++i)
{
+ /* Initialize the status: */
+ keys[i].status=0;
+
+ /* Set the value-pointer based on the required type. */
switch(keys[i].datatype)
{
case TSTRING:
- valueptr=&keys[i].c;
+ valueptr=keys[i].str;
break;
case TBYTE:
valueptr=&keys[i].u;
@@ -827,9 +839,26 @@ gal_fits_read_keywords(char *filename, char *hdu,
error(EXIT_FAILURE, 0, "the value of keys[%lu].datatype (=%d) "
"is not recognized", i, keys[i].datatype);
}
- if( fits_read_key(fptr, keys[i].datatype, keys[i].keyname,
- valueptr, NULL, &status) )
- gal_fits_io_error(status, "reading the keyword");
+
+ /* Read the keyword and place its value in the poitner. */
+ fits_read_key(fptr, keys[i].datatype, keys[i].keyname,
+ valueptr, NULL, &keys[i].status);
+
+
+ /* In some cases, the caller might be fine with some kinds of errors,
+ so we will only report an error here is the situation is not
+ expected. For example, the caller might have alternatives for a
+ keyword if it doesn't exist, or the non-existence of a keyword
+ might itself be meaningful. So when the key doesn't exist, this
+ function will not abort, it will just keep the status.
+
+ The reason only non-existance is acceptable is this: if the
+ keyword does exist, but CFITSIO cannot read it due to some
+ technical difficulty, then the user probably wanted to give the
+ value. But is not aware of the technical problem.
+ */
+ if(keys[i].status!=0 && keys[i].status!=KEY_NO_EXIST)
+ gal_fits_io_error(keys[i].status, "reading the keyword");
}
/* Close the FITS file. */
@@ -1049,7 +1078,7 @@ gal_fits_add_wcs_to_header(fitsfile *fptr, char
*wcsheader, int nkeyrec)
the pointer to the linked list (to correct it after we finish). */
void
gal_fits_update_keys(fitsfile *fptr,
- struct gal_fits_header_ll **keylist)
+ struct gal_fits_header_ll **keylist)
{
int status=0;
struct gal_fits_header_ll *tmp, *ttmp;
@@ -1094,8 +1123,8 @@ gal_fits_update_keys(fitsfile *fptr,
void
gal_fits_copyright_end(fitsfile *fptr,
- struct gal_fits_header_ll *headers,
- char *spack_string)
+ struct gal_fits_header_ll *headers,
+ char *spack_string)
{
size_t i;
int status=0;
@@ -1496,8 +1525,8 @@ gal_fits_atof_correct_wcs(char *filename, char *hdu, int
bitpix,
to the appropriate value. */
void
gal_fits_file_or_ext_name(char *inputname, char *inhdu, int othernameset,
- char **othername, char *ohdu, int ohduset,
- char *type)
+ char **othername, char *ohdu, int ohduset,
+ char *type)
{
if(othernameset)
{
@@ -1540,8 +1569,8 @@ gal_fits_file_or_ext_name(char *inputname, char *inhdu,
int othernameset,
return it back to the input type if you please. */
void
gal_fits_file_to_float(char *inputname, char *maskname, char *inhdu,
- char *mhdu, float **img, int *inbitpix,
- int *anyblank, size_t *ins0, size_t *ins1)
+ char *mhdu, float **img, int *inbitpix,
+ int *anyblank, size_t *ins0, size_t *ins1)
{
void *array;
int maskbitpix;
@@ -1605,8 +1634,8 @@ gal_fits_file_to_float(char *inputname, char *maskname,
char *inhdu,
/* Similar to filetofloat, but for double type */
void
gal_fits_file_to_double(char *inputname, char *maskname, char *inhdu,
- char *mhdu, double **img, int *inbitpix,
- int *anyblank, size_t *ins0, size_t *ins1)
+ char *mhdu, double **img, int *inbitpix,
+ int *anyblank, size_t *ins0, size_t *ins1)
{
void *array;
int maskbitpix;
@@ -1671,8 +1700,8 @@ gal_fits_file_to_double(char *inputname, char *maskname,
char *inhdu,
void
gal_fits_file_to_long(char *inputname, char *inhdu, long **img,
- int *inbitpix, int *anyblank, size_t *ins0,
- size_t *ins1)
+ int *inbitpix, int *anyblank, size_t *ins0,
+ size_t *ins1)
{
void *array;
@@ -1695,7 +1724,7 @@ gal_fits_file_to_long(char *inputname, char *inhdu, long
**img,
void
gal_fits_prep_float_kernel(char *inputname, char *inhdu, float **outkernel,
- size_t *ins0, size_t *ins1)
+ size_t *ins0, size_t *ins1)
{
size_t i, size;
double sum=0.0f;
diff --git a/lib/gnuastro/fits.h b/lib/gnuastro/fits.h
index cca2c14..a0456a4 100644
--- a/lib/gnuastro/fits.h
+++ b/lib/gnuastro/fits.h
@@ -103,15 +103,16 @@ struct gal_fits_header_ll
struct gal_fits_read_header_keys
{
- char *keyname;
- int datatype;
- char *c;
- unsigned char u;
- short s;
- long l;
- LONGLONG L;
- float f;
- double d;
+ int status;
+ char *keyname;
+ int datatype;
+ char str[FLEN_VALUE];
+ unsigned char u;
+ short s;
+ long l;
+ LONGLONG L;
+ float f;
+ double d;
};
@@ -137,7 +138,7 @@ gal_fits_add_to_fits_header_ll_end(struct
gal_fits_header_ll **list,
void
gal_fits_file_name_in_keywords(char *keynamebase, char *filename,
- struct gal_fits_header_ll **list);
+ struct gal_fits_header_ll **list);
void
gal_fits_add_wcs_to_header(fitsfile *fptr, char *wcsheader, int nkeyrec);
@@ -179,7 +180,7 @@ gal_fits_bitpix_alloc(size_t size, int bitpix);
void
gal_fits_change_type(void *in, int inbitpix, size_t size, int anyblank,
- void **out, int outbitpix);
+ void **out, int outbitpix);
void
gal_fits_read_wcs_from_pointer(fitsfile *fptr, int *nwcs,
diff --git a/lib/gnuastro/statistics.h b/lib/gnuastro/statistics.h
index ad910e1..d4df04b 100644
--- a/lib/gnuastro/statistics.h
+++ b/lib/gnuastro/statistics.h
@@ -31,6 +31,14 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
***************** Mininum and Maximum ********************
****************************************************************/
void
+gal_statistics_long_non_blank_min(long *in, size_t size, long *min,
+ long blank);
+
+void
+gal_statistics_long_non_blank_max(long *in, size_t size, long *max,
+ long blank);
+
+void
gal_statistics_float_min(float *in, size_t size, float *min);
void
diff --git a/lib/statistics.c b/lib/statistics.c
index 9d25b69..b6a0b81 100644
--- a/lib/statistics.c
+++ b/lib/statistics.c
@@ -27,6 +27,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <errno.h>
#include <error.h>
#include <float.h>
+#include <stdint.h>
#include <stdlib.h>
#include <gnuastro/qsort.h>
@@ -44,6 +45,46 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
/****************************************************************
***************** Mininum and Maximum ********************
****************************************************************/
+/* Find the the minimum (non-blank) value in an array of type long. Note
+ that the long type doesn't have a NaN value like the floats above. So as
+ blank pixels, a value in the range of acceptable values is given. so we
+ have to explicitly ignore those values.*/
+void
+gal_statistics_long_non_blank_min(long *in, size_t size, long *min,
+ long blank)
+{
+ long tmin=INT32_MAX, *lpt;
+ lpt=in+size;
+ do
+ if(*in!=blank && *in<tmin)
+ tmin=*in;
+ while(++in<lpt);
+ *min=tmin;
+}
+
+
+
+
+
+/* Find the the minimum (non-blank) value in an array of type long. See the
+ explanation above `gal_statistics_long_min'. */
+void
+gal_statistics_long_non_blank_max(long *in, size_t size, long *max,
+ long blank)
+{
+ long tmax=INT32_MIN, *lpt;
+ lpt=in+size;
+ do
+ if(*in!=blank && *in>tmax)
+ tmax=*in;
+ while(++in<lpt);
+ *max=tmax;
+}
+
+
+
+
+
void
gal_statistics_float_min(float *in, size_t size, float *min)
{
diff --git a/src/mkcatalog/Makefile.am b/src/mkcatalog/Makefile.am
index 2f96074..2077c3c 100644
--- a/src/mkcatalog/Makefile.am
+++ b/src/mkcatalog/Makefile.am
@@ -25,12 +25,12 @@
## Utility and its sources
bin_PROGRAMS = astmkcatalog
-astmkcatalog_SOURCES = main.c main.h cite.h ui.c ui.h args.h \
+astmkcatalog_SOURCES = main.c main.h cite.h ui.c ui.h args.h \
mkcatalog.c mkcatalog.h columns.c columns.h
-astmkcatalog_LDADD = $(top_builddir)/bootstrapped/lib/libgnu.la \
--lgalconfigfiles -lgalfits -lgalwcs -lgalcheckset -lgaltiming \
--lgallinkedlist -lgaltxtarray
+astmkcatalog_LDADD = $(top_builddir)/bootstrapped/lib/libgnu.la \
+-lgalconfigfiles -lgalstatistics -lgalarraymanip -lgalqsort -lgalfits \
+-lgalwcs -lgalcheckset -lgaltiming -lgallinkedlist -lgaltxtarray
diff --git a/src/mkcatalog/mkcatalog.c b/src/mkcatalog/mkcatalog.c
index af178c3..80352d9 100644
--- a/src/mkcatalog/mkcatalog.c
+++ b/src/mkcatalog/mkcatalog.c
@@ -154,7 +154,7 @@ firstpass(struct mkcatalogparams *p)
}
}
- if(clumps[i]>0)
+ if(clumps && clumps[i]>0)
{
/* The largest clump ID over each object is the number of
clumps that object has. */
@@ -191,11 +191,10 @@ firstpass(struct mkcatalogparams *p)
-/* In the second pass, we have the number of clumps so we can find
- store the total values for the clumps. In this second round we can
- also find second order moments of the objects if we want to. */
+/* In the second pass, we have the number of clumps so we can find the
+ total values for the clumps. */
void
-secondpass(struct mkcatalogparams *p)
+clumppass(struct mkcatalogparams *p)
{
float imgss;
double x, y, sx, sy;
@@ -412,6 +411,11 @@ makeoutput(struct mkcatalogparams *p)
for(p->obj0clump1=0;p->obj0clump1<2;++p->obj0clump1)
{
+ /* If no clumps image was provided, then ignore the clumps
+ catalog. */
+ if(p->obj0clump1==1 && p->clumps==NULL)
+ continue;
+
/* Do the preparations for this round: */
p->intcounter=p->accucounter=p->curcol=0;
@@ -483,13 +487,16 @@ makeoutput(struct mkcatalogparams *p)
strcat(comment, p->line);
sn = p->obj0clump1 ? p->clumpsn : p->detsn;
- sprintf(tline, "%s limiting Signal to noise ratio: ",
- p->obj0clump1 ? "Clump" : "Detection");
- sprintf(p->line, "# "CATDESCRIPTLENGTH"%.3f\n", tline, sn);
- strcat(comment, p->line);
- if(p->obj0clump1==0)
- strcat(comment, "# (NOTE: limits above are for detections, not "
- "objects)\n");
+ if(!isnan(sn))
+ {
+ sprintf(tline, "%s limiting Signal to noise ratio: ",
+ p->obj0clump1 ? "Clump" : "Detection");
+ sprintf(p->line, "# "CATDESCRIPTLENGTH"%.3f\n", tline, sn);
+ strcat(comment, p->line);
+ if(p->obj0clump1==0)
+ strcat(comment, "# (NOTE: limits above are for detections, not "
+ "objects)\n");
+ }
/* If cpscorr was used, report it: */
@@ -518,8 +525,9 @@ makeoutput(struct mkcatalogparams *p)
strcat(comment, "#\n# Columns:\n# --------\n");
- /* Fill the catalog array, in the end set the last elements in intcols
and
- accucols to -1, so gal_txtarray_array_to_txt knows when to stop. */
+ /* Fill the catalog array, in the end set the last elements in
+ intcols and accucols to -1, so gal_txtarray_array_to_txt knows
+ when to stop. */
for(p->curcol=0;p->curcol<p->numcols;++p->curcol)
{
col=cols[p->curcol];
@@ -687,8 +695,9 @@ makeoutput(struct mkcatalogparams *p)
/* Write the catalog to file: */
- gal_txtarray_array_to_txt(p->cat, p->num, p->numcols, comment,
p->intcols,
- p->accucols, space, prec, 'f', p->filename);
+ gal_txtarray_array_to_txt(p->cat, p->num, p->numcols, comment,
+ p->intcols, p->accucols, space, prec,
+ 'f', p->filename);
/* Clean up: */
free(p->intcols);
@@ -723,7 +732,7 @@ mkcatalog(struct mkcatalogparams *p)
{
/* Run through the data for the first time: */
firstpass(p);
- secondpass(p);
+ if(p->clumps) clumppass(p);
/* Write the output: */
makeoutput(p);
diff --git a/src/mkcatalog/ui.c b/src/mkcatalog/ui.c
index f982081..8035f7d 100644
--- a/src/mkcatalog/ui.c
+++ b/src/mkcatalog/ui.c
@@ -36,6 +36,7 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#include <gnuastro/timing.h> /* Includes time.h and sys/time.h */
#include <gnuastro/checkset.h>
#include <gnuastro/txtarray.h>
+#include <gnuastro/statistics.h>
#include <gnuastro/commonargs.h>
#include <gnuastro/configfiles.h>
@@ -836,51 +837,43 @@ checkifset(struct mkcatalogparams *p)
void
sanitycheck(struct mkcatalogparams *p)
{
- struct gal_fits_read_header_keys keys[2];
+ struct uiparams *up=&p->up;
+ struct gal_fits_read_header_keys keys[1];
/* Make sure the input file exists. */
- gal_checkset_check_file(p->up.inputname);
+ gal_checkset_check_file(up->inputname);
/* Set the names of the files. */
- gal_fits_file_or_ext_name(p->up.inputname, p->cp.hdu, p->up.masknameset,
- &p->up.maskname, p->up.mhdu, p->up.mhduset,
+ gal_fits_file_or_ext_name(up->inputname, p->cp.hdu, up->masknameset,
+ &up->maskname, up->mhdu, up->mhduset,
"mask");
- gal_fits_file_or_ext_name(p->up.inputname, p->cp.hdu,
- p->up.objlabsnameset, &p->up.objlabsname,
- p->up.objhdu, p->up.objhduset,
+ gal_fits_file_or_ext_name(up->inputname, p->cp.hdu,
+ up->objlabsnameset, &up->objlabsname,
+ up->objhdu, up->objhduset,
"object labels");
- gal_fits_file_or_ext_name(p->up.inputname, p->cp.hdu,
- p->up.clumplabsnameset, &p->up.clumplabsname,
- p->up.clumphdu, p->up.clumphduset,
- "clump labels");
- gal_fits_file_or_ext_name(p->up.inputname, p->cp.hdu, p->up.skynameset,
- &p->up.skyname, p->up.skyhdu, p->up.skyhduset,
+ gal_fits_file_or_ext_name(up->inputname, p->cp.hdu, up->skynameset,
+ &up->skyname, up->skyhdu, up->skyhduset,
"sky value image");
- gal_fits_file_or_ext_name(p->up.inputname, p->cp.hdu, p->up.stdnameset,
- &p->up.stdname, p->up.stdhdu, p->up.stdhduset,
+ gal_fits_file_or_ext_name(up->inputname, p->cp.hdu, up->stdnameset,
+ &up->stdname, up->stdhdu, up->stdhduset,
"sky standard deviation");
- /* Read the number of labels for the objects: */
- keys[0].keyname="DETSN"; keys[0].datatype=TDOUBLE;
- keys[1].keyname="NOBJS"; keys[1].datatype=TLONG;
- gal_fits_read_keywords(p->up.objlabsname, p->up.objhdu, keys, 2);
- p->detsn=keys[0].d;
- p->numobjects=keys[1].l;
-
- /* Read the clumps information. Note that the datatypes don't change. */
- keys[0].keyname="CLUMPSN";
- keys[1].keyname="NCLUMPS";
- gal_fits_read_keywords(p->up.clumplabsname, p->up.clumphdu, keys, 2);
- p->clumpsn=keys[0].d;
- p->numclumps=keys[1].l;
-
- /* Read the minimum and maximum standard deviation values. */
- keys[0].keyname="MINSTD"; keys[0].datatype=TFLOAT;
- keys[1].keyname="MEDSTD"; keys[1].datatype=TFLOAT;
- gal_fits_read_keywords(p->up.stdname, p->up.stdhdu, keys, 2);
- p->minstd=keys[0].f;
- p->medstd=keys[1].f;
- p->cpscorr = p->minstd>1 ? 1.0f : p->minstd;
+ /* The WCLUMPS (with-clumps) keyword in the object HDU says that there is
+ also a clumps image accompaning the object image. If it exists and its
+ value is `yes' (not case sensitive), then set the image name to the
+ proper string. Otherwise, set the image name to NULL, so future
+ functions can check. */
+ keys[0].str[0]='\0';
+ keys[0].datatype=TSTRING;
+ keys[0].keyname="WCLUMPS";
+ gal_fits_read_keywords(up->objlabsname, up->objhdu, keys, 1);
+ if(strcasecmp(keys[0].str, "yes"))
+ up->clumplabsname=NULL;
+ else
+ gal_fits_file_or_ext_name(up->inputname, p->cp.hdu,
+ up->clumplabsnameset, &up->clumplabsname,
+ up->clumphdu, up->clumphduset,
+ "clump labels");
/* When the RA and Dec are needed, make sure that the X and Y
columns and the RA and Dec columns in the information array are
@@ -891,7 +884,7 @@ sanitycheck(struct mkcatalogparams *p)
NOTE: the information array is separate from the output array
*/
- if(p->up.raset || p->up.decset)
+ if(up->raset || up->decset)
{
if( OFlxWhtX!=OFlxWhtY-1 || OFlxWhtRA!=OFlxWhtDec-1 )
error(EXIT_FAILURE, 0, "a bug! Please contact us at %s so we can "
@@ -909,10 +902,10 @@ sanitycheck(struct mkcatalogparams *p)
}
else
{
- gal_checkset_automatic_output(p->up.inputname, "_o.txt",
+ gal_checkset_automatic_output(up->inputname, "_o.txt",
p->cp.removedirinfo, p->cp.dontdelete,
&p->ocatname);
- gal_checkset_automatic_output(p->up.inputname, "_c.txt",
+ gal_checkset_automatic_output(up->inputname, "_c.txt",
p->cp.removedirinfo, p->cp.dontdelete,
&p->ccatname);
}
@@ -998,6 +991,92 @@ checksetfloat(struct mkcatalogparams *p, char *filename,
char *hdu,
+/* Read the necessary keywords and if they aren't present do the
+ appropriate action. */
+void
+readkeywords(struct mkcatalogparams *p)
+{
+ long numobjects;
+ size_t size=p->s0*p->s1;
+ struct uiparams *up=&p->up;
+ struct gal_fits_read_header_keys keys[2];
+
+ /* Read keywords from the standard deviation image: */
+ keys[0].keyname="MINSTD"; keys[0].datatype=TFLOAT;
+ keys[1].keyname="MEDSTD"; keys[1].datatype=TFLOAT;
+ gal_fits_read_keywords(up->stdname, up->stdhdu, keys, 2);
+
+ /* The minimum standard deviation value. */
+ if(keys[0].status)
+ gal_statistics_float_min(p->std, size, &p->minstd);
+ else
+ p->minstd=keys[0].f;
+ p->cpscorr = p->minstd>1 ? 1.0f : p->minstd;
+
+ /* Median standard deviation value (only necessary in catalog
+ comments). */
+ if(keys[1].status)
+ {
+ p->medstd=gal_statistics_median(p->std, size);
+ fprintf(stderr, "Warning: Could not find the MEDSTD keyword in %s "
+ "(hdu: %s). The median standard deviation is thus found on"
+ "the (interpolated) standard deviation image. NoiseChisel "
+ "finds the median before interpolation, so the reported value "
+ "in the final catalog will not be accurate (will depend on "
+ "how many meshs were blank and their spatial position "
+ "relative to the non-blank ones.", up->stdname, up->stdhdu);
+ }
+ else
+ p->medstd=keys[1].f;
+
+ /* Read the keywords from the objects image: */
+ keys[0].keyname="DETSN"; keys[0].datatype=TDOUBLE;
+ keys[1].keyname="NOBJS"; keys[1].datatype=TLONG;
+ gal_fits_read_keywords(up->objlabsname, up->objhdu, keys, 2);
+
+ /* If DETSN is not given, there is no way we can calculate it here, so we
+ will just set it to NaN to check and not report in the end. */
+ p->detsn = keys[0].status ? NAN : keys[0].d;
+
+ /* Read the total number of objects. */
+ if(keys[1].status)
+ {
+ gal_statistics_long_non_blank_max(p->objects, size, &numobjects,
+ GAL_FITS_LONG_BLANK);
+ p->numobjects=numobjects;
+ }
+ else
+ p->numobjects=keys[1].l;
+
+ /* Read the clumps information if it is necessary.
+
+ Note that unlike finding the number of objects, finding the number of
+ clumps is not an easy process, since the clumps of each object start
+ with a label of one. So if the number of clumps is not given, we have
+ to abort. For now, is up to the program that built the clumps to give
+ the total number, later we can take a procedure to find them (for
+ example first only taking the positive labels (that are clumps) and
+ making a binary image, then running the connected component algorithm
+ to find the number of clumps in the image.*/
+ if(up->clumplabsname)
+ {
+ keys[0].keyname="CLUMPSN";
+ keys[1].keyname="NCLUMPS";
+ gal_fits_read_keywords(up->clumplabsname, up->clumphdu, keys, 2);
+ p->clumpsn = keys[0].status ? NAN : keys[0].d;
+ if(keys[1].status)
+ error(EXIT_FAILURE, 0, "couldn't find NCLUMPS in the header of "
+ "%s (hdu: %s).", up->clumplabsname, up->clumphdu);
+ else
+ p->numclumps=keys[1].l;
+ }
+
+}
+
+
+
+
+
void
preparearrays(struct mkcatalogparams *p)
@@ -1185,12 +1264,19 @@ preparearrays(struct mkcatalogparams *p)
&p->wcs);
- /* Read and check the other arrays: */
- checksetlong(p, p->up.objlabsname, p->up.objhdu, &p->objects);
- checksetlong(p, p->up.clumplabsname, p->up.clumphdu, &p->clumps);
+ /* Read and check the object, sky and skystd HDUs. Note that the
+ clumps image is only used when the objects image says a clumps
+ image exists. */
checksetfloat(p, p->up.skyname, p->up.skyhdu, &p->sky);
checksetfloat(p, p->up.stdname, p->up.stdhdu, &p->std);
+ checksetlong(p, p->up.objlabsname, p->up.objhdu, &p->objects);
+ if(p->up.clumplabsname)
+ checksetlong(p, p->up.clumplabsname, p->up.clumphdu, &p->clumps);
+ else
+ p->clumps=NULL;
+ /* Read the necessary keywords. */
+ readkeywords(p);
/* Allocate the catalog arrays: */
if(p->objncols>0 && p->numobjects>0)
@@ -1312,8 +1398,9 @@ setparams(int argc, char *argv[], struct mkcatalogparams
*p)
printf(" - Mask %s (hdu: %s)\n", p->up.maskname, p->up.mhdu);
printf(" - Objects %s (hdu: %s)\n", p->up.objlabsname,
p->up.objhdu);
- printf(" - Clumps %s (hdu: %s)\n", p->up.clumplabsname,
- p->up.clumphdu);
+ if(p->up.clumplabsname)
+ printf(" - Clumps %s (hdu: %s)\n", p->up.clumplabsname,
+ p->up.clumphdu);
printf(" - Sky %s (hdu: %s)\n", p->up.skyname, p->up.skyhdu);
printf(" - Sky STD %s (hdu: %s)\n", p->up.stdname, p->up.stdhdu);
}
diff --git a/src/mkprof/ui.c b/src/mkprof/ui.c
index 2508923..daafda0 100644
--- a/src/mkprof/ui.c
+++ b/src/mkprof/ui.c
@@ -415,7 +415,27 @@ printvalues(FILE *fp, struct mkprofparams *p)
if(up->replaceset)
fprintf(fp, CONF_SHOWFMT"%d\n", "replace", p->replace);
if(up->typeset)
- fprintf(fp, CONF_SHOWFMT"%s\n", "type", up->type);
+ {
+ switch(up->type)
+ {
+ case BYTE_IMG:
+ fprintf(fp, CONF_SHOWFMT"%s\n", "type", "byte");
+ case SHORT_IMG:
+ fprintf(fp, CONF_SHOWFMT"%s\n", "type", "short");
+ case LONG_IMG:
+ fprintf(fp, CONF_SHOWFMT"%s\n", "type", "long");
+ case LONGLONG_IMG:
+ fprintf(fp, CONF_SHOWFMT"%s\n", "type", "longlong");
+ case FLOAT_IMG:
+ fprintf(fp, CONF_SHOWFMT"%s\n", "type", "float");
+ case DOUBLE_IMG:
+ fprintf(fp, CONF_SHOWFMT"%s\n", "type", "double");
+ default:
+ error(EXIT_FAILURE, 0, "a bug! the value of up->type is not "
+ "recognized in `ui.c'. Please contact us at %s so we can "
+ "address the problem.", PACKAGE_BUGREPORT);
+ }
+ }
fprintf(fp, "\n# Profiles:\n");
if(up->tunitinpset)
diff --git a/src/noisechisel/noisechisel.c b/src/noisechisel/noisechisel.c
index cd65b3e..6a57abf 100644
--- a/src/noisechisel/noisechisel.c
+++ b/src/noisechisel/noisechisel.c
@@ -70,16 +70,19 @@ makeoutput(struct noisechiselparams *p)
s0, s1, 0, p->wcs, NULL, SPACK_STRING);
- /* The object labels image with a keyword mentioning the number of
- objects. */
+ /* Add the necessary FITS keywords for MakeCatalog when reading the
+ objects image. */
+ gal_fits_add_to_fits_header_ll(&keys, TSTRING, "WCLUMPS", 0, "yes", 0,
+ "Is there a clumps image companion?",
+ 0, NULL);
num[0]=p->numobjects-1;
gal_fits_add_to_fits_header_ll(&keys, TLONG, "NOBJS", 0, num, 0,
- "Number of objects in the image.", 0,
- NULL);
+ "Number of objects in the image.", 0,
+ NULL);
dpt=&p->detsn;
gal_fits_add_to_fits_header_ll(&keys, TDOUBLE, "DETSN", 0, dpt, 0,
- "Signal to noise of true "
- "pseudo-detections.", 0, NULL);
+ "Signal to noise of true "
+ "pseudo-detections.", 0, NULL);
gal_fits_array_to_file(p->cp.output, "Objects", LONG_IMG, p->olab,
s0, s1, p->anyblank, p->wcs, keys,
SPACK_STRING);
@@ -92,12 +95,12 @@ makeoutput(struct noisechiselparams *p)
on the 3rd and 4th extensions. */
num[0] = p->detectonly ? 0 : p->numclumps-1;
gal_fits_add_to_fits_header_ll(&keys, TLONG, "NCLUMPS", 0, num, 0,
- "Number of clumps in the image.", 0,
- NULL);
+ "Number of clumps in the image.", 0,
+ NULL);
dpt=&p->clumpsn;
gal_fits_add_to_fits_header_ll(&keys, TDOUBLE, "CLUMPSN", 0, dpt, 0,
- "Signal to noise of true clumps.", 0,
- NULL);
+ "Signal to noise of true clumps.", 0,
+ NULL);
gal_fits_array_to_file(p->cp.output, "Clumps", LONG_IMG, p->clab, s0,
s1, p->anyblank, p->wcs, keys, SPACK_STRING);
keys=NULL;
- [gnuastro-commits] master updated (e182991 -> 0c30450), Mohammad Akhlaghi, 2016/08/16
- [gnuastro-commits] master d48638d 1/7: Key in NoiseChisel objects HDU, for clumps extension, Mohammad Akhlaghi, 2016/08/16
- [gnuastro-commits] master b4b0ab2 3/7: Strings and non-existing keys in gal_fits_read_keywords, Mohammad Akhlaghi, 2016/08/16
- [gnuastro-commits] master ce19153 5/7: Type of output can be specified in MakeProfiles, Mohammad Akhlaghi, 2016/08/16
- [gnuastro-commits] master 8481efc 2/7: Non-blank minimum and maximum for long in statistics, Mohammad Akhlaghi, 2016/08/16
- [gnuastro-commits] master 0c30450 7/7: Aperture photometry test added for MakeCatalog, Mohammad Akhlaghi, 2016/08/16
- [gnuastro-commits] master 4b0fccc 6/7: Merged MakeCatalog not making a clump catalog branch,
Mohammad Akhlaghi <=
- [gnuastro-commits] master e74f2b6 4/7: MakeCatalog makes clump catalog only when asked, Mohammad Akhlaghi, 2016/08/16