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[gnuastro-commits] master cd5b5cf 13/16: Table prints contents of a FITS
|
From: |
Mohammad Akhlaghi |
|
Subject: |
[gnuastro-commits] master cd5b5cf 13/16: Table prints contents of a FITS table |
|
Date: |
Wed, 24 Aug 2016 22:27:44 +0000 (UTC) |
branch: master
commit cd5b5cfbacefc602bc1704ec29d7351f28b5fc9b
Author: Mohammad Akhlaghi <address@hidden>
Commit: Mohammad Akhlaghi <address@hidden>
Table prints contents of a FITS table
Table can now print the contents of a FITS table to the standard
output. There are several options to determine the formatting of the output
when it is printed. Currently for each column on each row a separate printf
statement is issued, the speed is not bad, but there might be more
efficient ways that we will have to work on.
---
src/table/args.h | 118 +++++++++++++++++++-
src/table/asttable.conf | 12 +-
src/table/main.h | 50 +++++++--
src/table/table.c | 278 ++++++++++++++++++++++++++++++++++++++++++++++-
src/table/table.h | 2 +
src/table/ui.c | 241 ++++++++++++++++++++++++++++++++--------
src/table/ui.h | 3 +
7 files changed, 640 insertions(+), 64 deletions(-)
diff --git a/src/table/args.h b/src/table/args.h
index 9adb9ce..8708878 100644
--- a/src/table/args.h
+++ b/src/table/args.h
@@ -58,7 +58,10 @@ static char args_doc[] = "ASTRdata";
const char doc[] =
/* Before the list of options: */
GAL_STRINGS_TOP_HELP_INFO
- SPACK_NAME" print a FITS table or its information. \n"
+ SPACK_NAME" prints (in a human readable format) a FITS table or its "
+ "information. The output columns can either be selected by number, name "
+ "or using regular expressions. The format of their printing can also "
+ "be set (based on the type of data in the column).\n"
GAL_STRINGS_MORE_HELP_INFO
/* After the list of options: */
"\v"
@@ -73,7 +76,7 @@ const char doc[] =
a b d e f g j k l m n p r s t u v w x y z
A B C E F G H J L M O Q R T U W X Y Z
- Number keys used: Nothing!
+ Number keys used: 1008
Options with keys (second structure element) larger than 500 do not
have a short version.
@@ -110,6 +113,71 @@ static struct argp_option options[] =
"Output:",
2
},
+ {
+ "feg",
+ 1001,
+ "STR",
+ 0,
+ "`f': only decimals, `e': scientific, `g': either.",
+ 2
+ },
+ {
+ "sintwidth",
+ 1002,
+ "INT",
+ 0,
+ "Shorter integer column(s) width (num charachers).",
+ 2
+ },
+ {
+ "lintwidth",
+ 1003,
+ "INT",
+ 0,
+ "Longer integer column(s) width (num charachers).",
+ 2
+ },
+ {
+ "floatwidth",
+ 1004,
+ "INT",
+ 0,
+ "`float' column(s) width (num charachers).",
+ 2
+ },
+ {
+ "doublewidth",
+ 1005,
+ "INT",
+ 0,
+ "`double' column(s) width (num charachers).",
+ 2
+ },
+ {
+ "strwidth",
+ 1006,
+ "INT",
+ 0,
+ "String column(s) width (num charachers).",
+ 2
+ },
+ {
+ "floatprecision",
+ 1007,
+ "INT",
+ 0,
+ "`float' column(s) precision.",
+ 2
+ },
+ {
+ "doubleprecision",
+ 1008,
+ "INT",
+ 0,
+ "`double' column(s) precision.",
+ 2
+ },
+
@@ -176,6 +244,52 @@ parse_opt(int key, char *arg, struct argp_state *state)
/* Output: */
+ case 1001:
+ checkfge(arg, &p->up.feg);
+ p->up.fegset=1;
+ break;
+
+ case 1002:
+ gal_checkset_sizet_el_zero(arg, &p->up.sintwidth, "sintwidth", key,
+ SPACK, NULL, 0);
+ p->up.sintwidthset=1;
+ break;
+
+ case 1003:
+ gal_checkset_sizet_el_zero(arg, &p->up.lintwidth, "lintwidth", key,
+ SPACK, NULL, 0);
+ p->up.lintwidthset=1;
+ break;
+
+ case 1004:
+ gal_checkset_sizet_el_zero(arg, &p->up.floatwidth, "floatwidth", key,
+ SPACK, NULL, 0);
+ p->up.floatwidthset=1;
+ break;
+
+ case 1005:
+ gal_checkset_sizet_el_zero(arg, &p->up.doublewidth, "doublewidth", key,
+ SPACK, NULL, 0);
+ p->up.doublewidthset=1;
+ break;
+
+ case 1006:
+ gal_checkset_sizet_el_zero(arg, &p->up.strwidth, "strwidth", key,
+ SPACK, NULL, 0);
+ p->up.strwidthset=1;
+ break;
+
+ case 1007:
+ gal_checkset_sizet_el_zero(arg, &p->up.floatprecision,
+ "floatprecision", key, SPACK, NULL, 0);
+ p->up.floatprecisionset=1;
+ break;
+
+ case 1008:
+ gal_checkset_sizet_el_zero(arg, &p->up.doubleprecision,
+ "doubleprecision", key, SPACK, NULL, 0);
+ p->up.doubleprecisionset=1;
+ break;
/* Operating modes: */
diff --git a/src/table/asttable.conf b/src/table/asttable.conf
index f5d6183..77973eb 100644
--- a/src/table/asttable.conf
+++ b/src/table/asttable.conf
@@ -18,6 +18,14 @@
# without any warranty.
# Input:
- hdu 0
+ hdu 0
-# Output:
\ No newline at end of file
+# Output:
+ feg f
+ sintwidth 5
+ lintwidth 15
+ floatwidth 10
+ doublewidth 15
+ strwidth 20
+ floatprecision 3
+ doubleprecision 8
diff --git a/src/table/main.h b/src/table/main.h
index eea7b56..2e7bfd1 100644
--- a/src/table/main.h
+++ b/src/table/main.h
@@ -31,9 +31,19 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#define SPACK_NAME "Table" /* Subpackage full name. */
#define SPACK_STRING SPACK_NAME" ("PACKAGE_NAME") "PACKAGE_VERSION
+#define MAX_COL_FORMAT_LENGTH 20
+/* Structure to keep the information for each output column */
+struct outcolumn
+{
+ size_t inindex; /* Row index (from 0) in input array. */
+ int datatype; /* Type of data (from CFITSIO macros). */
+ int anynul; /* If there is any blank characters. */
+ void *data; /* Array keeping the column data. */
+ char fmt[MAX_COL_FORMAT_LENGTH]; /* format to use in printf. */
+};
@@ -47,9 +57,36 @@ struct uiparams
char *txtname; /* Name of input text file. */
int ignorecase; /* Ignore case matching column names. */
+ /* Input table parameters. */
+ size_t ncols; /* Number of columns in table. */
+ int *datatype; /* Type of data in column. */
+ char **tform; /* TFORM (another format for type). */
+ char **ttype; /* Column name (one word). */
+ char **tunit; /* Unit of values in column. */
+
+ /* Print parameters: */
+ int feg; /* format of floating points. */
+ size_t sintwidth; /* Full width for short integers. */
+ size_t lintwidth; /* Full width for short integers. */
+ size_t floatwidth; /* Full width for all floats. */
+ size_t doublewidth; /* Full width for all doubles. */
+ size_t strwidth; /* Full width for all floats. */
+ size_t floatprecision; /* Number of decimals for floats. */
+ size_t doubleprecision; /* Number of decimals for doubles. */
+
+ /* If values are set: */
int inputset;
int informationset;
int ignorecaseset;
+ int fegset;
+ int sintwidthset;
+ int lintwidthset;
+ int floatwidthset;
+ int doublewidthset;
+ int strwidthset;
+ int floatprecisionset;
+ int doubleprecisionset;
+
struct gal_linkedlist_stll *columns;
};
@@ -69,20 +106,13 @@ struct tableparams
fitsfile *fitsptr; /* FITS pointer (input or output). */
/* Output: */
- size_t nocols; /* Number of output columns. */
- size_t *ocols; /* Output column indexs in input table. */
-
- /* FITS table */
size_t nrows; /* Number of rows in table. */
- size_t ncols; /* Number of columns in table. */
- int *typecode; /* Type of data in column. */
- char **tform; /* TFORM (another format for type). */
- char **ttype; /* Column name (one word). */
- char **tunit; /* Unit of values in column. */
+ size_t nocols; /* Number of output columns. */
+ struct outcolumn *ocols; /* Array of output column informatio. */
/* Internal: */
int onlyview;
- time_t rawtime; /* Starting time of the program. */
+ time_t rawtime; /* Starting time of the program. */
};
#endif
diff --git a/src/table/table.c b/src/table/table.c
index 079800a..588aa42 100644
--- a/src/table/table.c
+++ b/src/table/table.c
@@ -34,16 +34,290 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
+/**************************************************************/
+/*************** Input table *******************/
+/**************************************************************/
+/* Set the format string for each column: */
+void
+setformatstring(struct tableparams *p, size_t outcolid)
+{
+ struct uiparams *up=&p->up;
+ char width[10], accu[10], *type=NULL;
+ struct outcolumn *ocol=&p->ocols[outcolid];
+
+
+ switch(ocol->datatype)
+ {
+ case TBIT:
+ error(EXIT_FAILURE, 0, "Table doesn't print TBIT data type "
+ "currently, please contact us at %s so we can implement "
+ "it.", PACKAGE_BUGREPORT);
+
+ case TBYTE:
+ type="u";
+ sprintf(width, "%lu", up->sintwidth);
+ accu[0]='\0';
+ break;
+
+ case TLOGICAL: case TSBYTE:
+ type="d";
+ sprintf(width, "%lu", up->sintwidth);
+ accu[0]='\0';
+ break;
+
+ case TSTRING:
+ type="s";
+ if(up->sintwidth) sprintf(width, "%lu", up->sintwidth);
+ else width[0]='\0';
+ accu[0]='\0';
+ break;
+
+ case TSHORT:
+ type="d";
+ sprintf(width, "%lu", up->sintwidth);
+ accu[0]='\0';
+ break;
+
+ case TLONG:
+ type="ld";
+ sprintf(width, "%lu", up->lintwidth);
+ accu[0]='\0';
+ break;
+
+ case TLONGLONG:
+ type="ld";
+ sprintf(width, "%lu", up->lintwidth);
+ accu[0]='\0';
+ break;
+
+ case TFLOAT:
+ type = up->feg=='f' ? "f" : ( up->feg=='e' ? "e" : "g");
+ sprintf(width, "%lu", up->floatwidth);
+ sprintf(accu, ".%lu", up->floatprecision);
+ break;
+
+ case TDOUBLE:
+ type = up->feg=='f' ? "f" : ( up->feg=='e' ? "e" : "g");
+ sprintf(width, "%lu", up->doublewidth);
+ sprintf(accu, ".%lu", up->doubleprecision);
+ break;
+
+ case TCOMPLEX:
+ error(EXIT_FAILURE, 0, "Table doesn't print TCOMPLEX data type "
+ "currently, please contact us at %s so we can implement "
+ "it.", PACKAGE_BUGREPORT);
+ break;
+
+ case TDBLCOMPLEX:
+ error(EXIT_FAILURE, 0, "Table doesn't print TDBLCOMPLEX data type "
+ "currently, please contact us at %s so we can implement "
+ "it.", PACKAGE_BUGREPORT);
+ break;
+
+ case TINT:
+ type="d";
+ sprintf(width, "%lu", up->sintwidth);
+ accu[0]='\0';
+ break;
+
+ case TUINT:
+ type="u";
+ sprintf(width, "%lu", up->sintwidth);
+ accu[0]='\0';
+ break;
+
+ case TUSHORT:
+ type="u";
+ sprintf(width, "%lu", up->sintwidth);
+ accu[0]='\0';
+ break;
+
+ case TULONG:
+ type="lu";
+ sprintf(width, "%lu", up->lintwidth);
+ accu[0]='\0';
+ break;
+
+ default:
+ error(EXIT_FAILURE, 0, "datatype value of %d not recognized in "
+ "gal_fits_datatype_alloc", ocol->datatype);
+ }
+
+ /* Put the type, width and accu into the format string for this
+ column: */
+ sprintf(ocol->fmt, "%%-%s%s%s", width, accu, type);
+}
+
+
+
+
+
+/* Read all the input columns */
+void
+readinputcols(struct tableparams *p)
+{
+ size_t i;
+ void *nulval;
+ struct outcolumn *col;
+ int datatype, status=0;
+
+ /* Get the contents of each table column: */
+ for(i=0;i<p->nocols;++i)
+ {
+ /* Variables for simple reading */
+ col=&p->ocols[i];
+ datatype=col->datatype;
+
+ /* Allocate the blank value and array to keep the actual of this
+ column. */
+ nulval=gal_fits_datatype_blank(datatype);
+ col->data=gal_fits_datatype_alloc(p->nrows, datatype);
+
+ /* Call CFITSIO to read the column information. */
+ fits_read_col(p->fitsptr, datatype, col->inindex+1, 1, 1,
+ p->nrows, nulval, col->data, &col->anynul,
+ &status);
+
+ /* Free the space allocated for the blank value, we don't need it any
+ more: it is an internal macro to Gnuastro (see `fits.h'), */
+ free(nulval);
+
+ /* Set the format string to print the column values. */
+ setformatstring(p, i);
+ }
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+/**************************************************************/
+/*************** Output table *******************/
+/**************************************************************/
+void
+printoutput(struct tableparams *p)
+{
+ size_t i, row;
+ struct outcolumn *ocols=p->ocols;
+
+ for(row=0;row<p->nrows;++row)
+ {
+ for(i=0;i<p->nocols;++i)
+ switch(ocols[i].datatype)
+ {
+ case TBIT:
+ error(EXIT_FAILURE, 0, "Table doesn't print TBIT data type "
+ "currently, please contact us at %s so we can implement "
+ "it.", PACKAGE_BUGREPORT);
+
+ case TBYTE:
+ printf(ocols[i].fmt, ((unsigned char *)ocols[i].data)[row]);
+ break;
+
+ case TLOGICAL: case TSBYTE:
+ printf(ocols[i].fmt, ((char *)ocols[i].data)[row]);
+ break;
+
+ case TSTRING:
+ printf(ocols[i].fmt, ((char **)ocols[i].data)[row]);
+ break;
+
+ case TSHORT:
+ printf(ocols[i].fmt, ((short *)ocols[i].data)[row]);
+ break;
+
+ case TLONG:
+ printf(ocols[i].fmt, ((long *)ocols[i].data)[row]);
+ break;
+
+ case TLONGLONG:
+ printf(ocols[i].fmt, ((LONGLONG *)ocols[i].data)[row]);
+ break;
+
+ case TFLOAT:
+ printf(ocols[i].fmt, ((float *)ocols[i].data)[row]);
+ break;
+
+ case TDOUBLE:
+ printf(ocols[i].fmt, ((double *)ocols[i].data)[row]);
+ break;
+
+ case TCOMPLEX:
+ error(EXIT_FAILURE, 0, "Table doesn't print TCOMPLEX data type "
+ "currently, please contact us at %s so we can implement "
+ "it.", PACKAGE_BUGREPORT);
+ break;
+
+ case TDBLCOMPLEX:
+ error(EXIT_FAILURE, 0, "Table doesn't print TDBLCOMPLEX data "
+ "type currently, please contact us at %s so we can "
+ "implement it.", PACKAGE_BUGREPORT);
+ break;
+
+ case TINT:
+ printf(ocols[i].fmt, ((char *)ocols[i].data)[row]);
+ break;
+
+ case TUINT:
+ printf(ocols[i].fmt, ((unsigned int *)ocols[i].data)[row]);
+ break;
+
+ case TUSHORT:
+ printf(ocols[i].fmt, ((unsigned short *)ocols[i].data)[row]);
+ break;
+
+ case TULONG:
+ printf(ocols[i].fmt, ((unsigned long *)ocols[i].data)[row]);
+ break;
+
+ default:
+ error(EXIT_FAILURE, 0, "datatype value of %d not recognized in "
+ "printoutput", ocols[i].datatype);
+ }
+ printf("\n");
+ }
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
-/* Print all the column information: */
-/* Top level function */
+/**************************************************************/
+/*************** Top function *******************/
+/**************************************************************/
void
table(struct tableparams *p)
{
+ readinputcols(p);
+ printoutput(p);
}
diff --git a/src/table/table.h b/src/table/table.h
index e28f32e..8c164ec 100644
--- a/src/table/table.h
+++ b/src/table/table.h
@@ -23,6 +23,8 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#ifndef TABLE_H
#define TABLE_H
+
+
void
table(struct tableparams *p);
diff --git a/src/table/ui.c b/src/table/ui.c
index c9fd8e5..f65a344 100644
--- a/src/table/ui.c
+++ b/src/table/ui.c
@@ -65,6 +65,21 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
/**************************************************************/
/************** Options and parameters ***************/
/**************************************************************/
+/* Check the value given for the fge option. */
+void
+checkfge(char *optarg, int *fge)
+{
+ *fge=optarg[0];
+ if( *fge!='f' && *fge!='g' && *fge!='g' )
+ error(EXIT_FAILURE, 0, "the value of `--fge' (`-f') must only be "
+ "one of the three `f', `g', or `e' characters. You have "
+ "given `%s'.", optarg);
+}
+
+
+
+
+
void
readconfig(char *filename, struct tableparams *p)
{
@@ -125,6 +140,69 @@ readconfig(char *filename, struct tableparams *p)
else if(strcmp(name, "output")==0)
gal_checkset_allocate_copy_set(value, &cp->output, &cp->outputset);
+ else if (strcmp(name, "feg")==0)
+ {
+ if(p->up.fegset) continue;
+ checkfge(value, &p->up.feg);
+ p->up.fegset=1;
+ }
+
+ else if (strcmp(name, "sintwidth")==0)
+ {
+ if(p->up.sintwidthset) continue;
+ gal_checkset_sizet_el_zero(value, &p->up.sintwidth, name,
+ key, SPACK, filename, lineno);
+ p->up.sintwidthset=1;
+ }
+
+ else if (strcmp(name, "lintwidth")==0)
+ {
+ if(p->up.lintwidthset) continue;
+ gal_checkset_sizet_el_zero(value, &p->up.lintwidth, name,
+ key, SPACK, filename, lineno);
+ p->up.lintwidthset=1;
+ }
+
+ else if (strcmp(name, "floatwidth")==0)
+ {
+ if(p->up.floatwidthset) continue;
+ gal_checkset_sizet_el_zero(value, &p->up.floatwidth, name,
+ key, SPACK, filename, lineno);
+ p->up.floatwidthset=1;
+ }
+
+ else if (strcmp(name, "doublewidth")==0)
+ {
+ if(p->up.doublewidthset) continue;
+ gal_checkset_sizet_el_zero(value, &p->up.doublewidth, name,
+ key, SPACK, filename, lineno);
+ p->up.doublewidthset=1;
+ }
+
+ else if (strcmp(name, "strwidth")==0)
+ {
+ if(p->up.strwidthset) continue;
+ gal_checkset_sizet_el_zero(value, &p->up.strwidth, name,
+ key, SPACK, filename, lineno);
+ p->up.strwidthset=1;
+ }
+
+ else if (strcmp(name, "floatprecision")==0)
+ {
+ if(p->up.floatprecisionset) continue;
+ gal_checkset_sizet_el_zero(value, &p->up.floatprecision,
+ name, key, SPACK, filename, lineno);
+ p->up.floatprecisionset=1;
+ }
+
+ else if (strcmp(name, "doubleprecision")==0)
+ {
+ if(p->up.doubleprecisionset) continue;
+ gal_checkset_sizet_el_zero(value, &p->up.doubleprecision,
+ name, key, SPACK, filename, lineno);
+ p->up.doubleprecisionset=1;
+ }
+
/* Operating modes: */
@@ -164,7 +242,7 @@ printvalues(FILE *fp, struct tableparams *p)
/* Print all the options that are set. Separate each group with a
commented line explaining the options in that group. */
- fprintf(fp, "\n# Input image:\n");
+ fprintf(fp, "\n# Input:\n");
if(cp->hduset)
GAL_CHECKSET_PRINT_STRING_MAYBE_WITH_SPACE("hdu", cp->hdu);
if(up->columns)
@@ -174,6 +252,25 @@ printvalues(FILE *fp, struct tableparams *p)
fprintf(fp, CONF_SHOWFMT"%d\n", "ignorecase", up->ignorecase);
+ fprintf(fp, "\n# Output:\n");
+ if(up->fegset)
+ fprintf(fp, CONF_SHOWFMT"%c\n", "feg", up->feg);
+ if(up->sintwidthset)
+ fprintf(fp, CONF_SHOWFMT"%lu\n", "sintwidth", up->sintwidth);
+ if(up->lintwidthset)
+ fprintf(fp, CONF_SHOWFMT"%lu\n", "lintwidth", up->lintwidth);
+ if(up->floatwidthset)
+ fprintf(fp, CONF_SHOWFMT"%lu\n", "floatwidth", up->floatwidth);
+ if(up->doublewidthset)
+ fprintf(fp, CONF_SHOWFMT"%lu\n", "doublewidth", up->doublewidth);
+ if(up->strwidthset)
+ fprintf(fp, CONF_SHOWFMT"%lu\n", "strwidth", up->strwidth);
+ if(up->floatprecisionset)
+ fprintf(fp, CONF_SHOWFMT"%lu\n", "floatprecision", up->floatprecision);
+ if(up->doubleprecisionset)
+ fprintf(fp, CONF_SHOWFMT"%lu\n", "doubleprecision", up->doubleprecision);
+
+
/* For the operating mode, first put the macro to print the common
options, then the (possible options particular to this
program). */
@@ -195,12 +292,29 @@ void
checkifset(struct tableparams *p)
{
/*struct uiparams *up=&p->up;*/
+ struct uiparams *up=&p->up;
struct gal_commonparams *cp=&p->cp;
int intro=0;
if(cp->hduset==0)
GAL_CONFIGFILES_REPORT_NOTSET("hdu");
+ if(up->fegset==0)
+ GAL_CONFIGFILES_REPORT_NOTSET("feg");
+ if(up->sintwidthset==0)
+ GAL_CONFIGFILES_REPORT_NOTSET("sintwidth");
+ if(up->lintwidthset==0)
+ GAL_CONFIGFILES_REPORT_NOTSET("lintwidth");
+ if(up->floatwidthset==0)
+ GAL_CONFIGFILES_REPORT_NOTSET("floatwidth");
+ if(up->doublewidthset==0)
+ GAL_CONFIGFILES_REPORT_NOTSET("doublewidth");
+ if(up->strwidthset==0)
+ GAL_CONFIGFILES_REPORT_NOTSET("strwidth");
+ if(up->floatprecisionset==0)
+ GAL_CONFIGFILES_REPORT_NOTSET("floatprecision");
+ if(up->doubleprecisionset==0)
+ GAL_CONFIGFILES_REPORT_NOTSET("doubleprecision");
GAL_CONFIGFILES_END_OF_NOTSET_REPORT;
}
@@ -344,16 +458,16 @@ printinfo(struct tableparams *p)
{
size_t i;
char *typestring=NULL;
+ struct uiparams *up=&p->up;
printf("%s (hdu: %s)\n", p->up.fitsname, p->cp.hdu);
- printf("Column information\n");
printf("---------------------------------------------------------\n");
- printf("%-5s%-25s%-20s%s\n", "No.", "Column name", "Data type",
- "Units");
+ printf("%-5s%-25s%-15s%s\n", "No.", "Column name", "Units",
+ "Data type");
printf("---------------------------------------------------------\n");
- for(i=0;i<p->ncols;++i)
+ for(i=0;i<up->ncols;++i)
{
- switch(p->typecode[i])
+ switch(up->datatype[i])
{
case TBIT:
typestring="bit";
@@ -399,11 +513,11 @@ printinfo(struct tableparams *p)
break;
default:
error(EXIT_FAILURE, 0, "%d (from TFORM%lu='%c') is not a "
- "recognized CFITSIO datatype.",
- p->typecode[i], i, p->tform[i][0]);
+ "recognized CFITSIO datatype.", up->datatype[i],
+ i, up->tform[i][0]);
}
- printf("%-5lu%-25s%-20s%s\n", i+1, p->ttype[i] ? p->ttype[i] : "---",
- typestring, p->tunit[i] ? p->tunit[i] : "---");
+ printf("%-5lu%-25s%-15s%s\n", i+1, up->ttype[i] ? up->ttype[i] : "---",
+ up->tunit[i] ? up->tunit[i] : "---", typestring);
}
@@ -437,12 +551,15 @@ printinfo(struct tableparams *p)
void
sanitycheck(struct tableparams *p)
{
+ struct uiparams *up=&p->up;
/* Set the FITS pointer and check the type of the fits file. */
if(p->up.fitsname)
{
gal_fits_read_hdu(p->up.fitsname, p->cp.hdu, 1, &p->fitsptr);
- gal_fits_table_size(p->fitsptr, &p->nrows, &p->ncols);
+ gal_fits_table_size(p->fitsptr, &p->nrows, &up->ncols);
+ readallcolinfo(p->fitsptr, up->ncols, &up->datatype,
+ &up->tform, &up->ttype, &up->tunit);
}
else
error(EXIT_FAILURE, 0, "Table is a new addition to Gnuastro and "
@@ -456,8 +573,6 @@ sanitycheck(struct tableparams *p)
{
if(p->up.fitsname)
{
- readallcolinfo(p->fitsptr, p->ncols, &p->typecode,
- &p->tform, &p->ttype, &p->tunit);
printinfo(p);
freeandreport(p);
exit(EXIT_SUCCESS);
@@ -493,6 +608,7 @@ sanitycheck(struct tableparams *p)
/**************************************************************/
/*************** Preparations *******************/
/**************************************************************/
+
/* FUnction to print regular expression error. This is taken from the GNU C
library manual, with small modifications to fit out style, */
void
@@ -523,11 +639,12 @@ regexerrorexit(int errcode, regex_t *compiled, char
*input)
void
outputcolumns(struct tableparams *p)
{
- size_t i;
long tlong;
regex_t *regex;
int regreturn=0;
+ size_t i, inindex;
char *tailptr, *colstring;
+ struct uiparams *up=&p->up;
struct gal_linkedlist_sll *colsll=NULL;
/* Go through each given column string and take the appropriate step. */
@@ -553,10 +670,10 @@ outputcolumns(struct tableparams *p)
/* Check if the given value is not larger than the number of
columns in the input catalog. */
- if(tlong>p->ncols)
+ if(tlong>up->ncols)
error(EXIT_FAILURE, 0, "%s (hdu: %s) has %lu columns, but "
"you have asked for column number %lu", p->up.fitsname,
- p->cp.hdu, p->ncols, tlong);
+ p->cp.hdu, up->ncols, tlong);
/* Everything seems to be fine, put this column number in the
output column numbers linked list. Note that internally, the
@@ -565,15 +682,6 @@ outputcolumns(struct tableparams *p)
}
else
{
- /* First we need to make sure that the full column information is
- ready (so we can parse the values of the column names in
- p->ttype). Note that the parsing function to read all column
- information is not set by default. Note that this is only done
- once (for the first string value to the `--column' option).*/
- if(p->ttype==NULL)
- readallcolinfo(p->fitsptr, p->ncols, &p->typecode,
- &p->tform, &p->ttype, &p->tunit);
-
/* Allocate the regex_t structure: */
errno=0; regex=malloc(sizeof *regex);
if(regex==NULL)
@@ -604,9 +712,9 @@ outputcolumns(struct tableparams *p)
column names. Just note that column names are not mandatory in
the FITS standard, so some (or all) columns might not have
names, if so `p->ttype[i]' will be NULL. */
- for(i=0;i<p->ncols;++i)
- if(p->ttype[i] && regexec(regex, p->ttype[i], 0, 0, 0)==0)
- gal_linkedlist_add_to_sll(&colsll, i);
+ for(i=0;i<up->ncols;++i)
+ if(up->ttype[i] && regexec(regex, up->ttype[i], 0, 0, 0)==0)
+ gal_linkedlist_add_to_sll(&colsll, i);
/* Free the regex_t structure: */
regfree(regex);
@@ -616,12 +724,28 @@ outputcolumns(struct tableparams *p)
free(colstring);
}
- /* Put the desired columns (in reverse order due to the nature of a
- linked list) into an array to read from later, then pop everything to
- the un-used `i' variable from the list (which will automatically free
- any allocate space). */
- gal_linkedlist_sll_to_array(colsll, &p->ocols, &p->nocols, 1);
- while(colsll) gal_linkedlist_pop_from_sll(&colsll, &i);
+ /* Based on the number of columns found above, allocate an array of
+ `outcolumn' structures to keep the information for each column. */
+ p->nocols=gal_linkedlist_num_in_sll(colsll);
+ errno=0;
+ p->ocols=malloc(p->nocols*sizeof *p->ocols);
+ if(p->ocols==NULL)
+ error(EXIT_FAILURE, errno, "%lu bytes for p->ocols",
+ p->nocols*sizeof *p->ocols);
+
+ /* Fill in the output column with the needed input table
+ information. Note that a simple linked list is first-in-last-out, so
+ we have to fill in the output columns in reverse order. Also, note
+ that we are popping from the linked list keeping the indexs of the
+ output columns and thus also freeing their allocated space. */
+ i=p->nocols-1;
+ while(colsll)
+ {
+ gal_linkedlist_pop_from_sll(&colsll, &inindex);
+ p->ocols[i].datatype=up->datatype[inindex];
+ p->ocols[i].inindex=inindex;
+ --i;
+ }
}
@@ -632,6 +756,7 @@ void
preparearrays(struct tableparams *p)
{
size_t i;
+ struct uiparams *up=&p->up;
/* Set the columns that should be included in the output. If up->columns
is set, then use it, otherwise, set all the columns for printing. */
@@ -639,13 +764,17 @@ preparearrays(struct tableparams *p)
outputcolumns(p);
else
{
- p->nocols=p->ncols;
+ p->nocols=up->ncols;
errno=0;
p->ocols=malloc(p->nocols * sizeof *p->ocols);
if(p->ocols==NULL)
error(EXIT_FAILURE, errno, "%lu bytes for p->ocols",
p->nocols * sizeof *p->ocols);
- for(i=0;i<p->nocols;++i) p->ocols[i]=i;
+ for(i=0;i<p->nocols;++i)
+ {
+ p->ocols[i].datatype=up->datatype[i];
+ p->ocols[i].inindex=i;
+ }
}
}
@@ -684,9 +813,10 @@ setparams(int argc, char *argv[], struct tableparams *p)
cp->removedirinfo = 1;
/* Initialize this utility's pointers to NULL. */
+ p->ocols=NULL;
up->columns=NULL;
up->txtname=up->fitsname=NULL;
- p->tform=p->ttype=p->tunit=NULL;
+ up->tform=up->ttype=up->tunit=NULL;
/* Read the arguments. */
errno=0;
@@ -739,25 +869,40 @@ setparams(int argc, char *argv[], struct tableparams *p)
void
freeandreport(struct tableparams *p)
{
- size_t i;
+ size_t i, j;
int status=0;
+ char **rowofstrings;
+ struct uiparams *up=&p->up;
/* Free the allocated arrays: */
- free(p->ocols);
free(p->cp.hdu);
- free(p->typecode);
+ free(up->datatype);
free(p->cp.output);
- /* Free the internal pointers first, then the actual arrays: */
- for(i=0;i<p->ncols;++i)
+ /* Free the input column information: */
+ for(i=0;i<up->ncols;++i)
{
- if(p->tform) free(p->tform[i]);
- if(p->ttype) free(p->ttype[i]);
- if(p->tunit) free(p->tunit[i]);
+ if(up->tform) free(up->tform[i]);
+ if(up->ttype) free(up->ttype[i]);
+ if(up->tunit) free(up->tunit[i]);
}
- free(p->tform);
- free(p->ttype);
- free(p->tunit);
+ free(up->tform);
+ free(up->ttype);
+ free(up->tunit);
+
+ /* Free the output column information: */
+ for(i=0;i<p->nocols;++i)
+ {
+ if(p->ocols[i].datatype==TSTRING)
+ {
+ rowofstrings=(char **)(p->ocols[i].data);
+ for(j=0;j<p->nrows;++j)
+ free(rowofstrings[j]);
+ }
+ else
+ free(p->ocols[i].data);
+ }
+ free(p->ocols);
/* Close the FITS file: */
if(p->up.fitsname && fits_close_file(p->fitsptr, &status))
diff --git a/src/table/ui.h b/src/table/ui.h
index c200304..76c304e 100644
--- a/src/table/ui.h
+++ b/src/table/ui.h
@@ -24,6 +24,9 @@ along with Gnuastro. If not, see
<http://www.gnu.org/licenses/>.
#define UI_H
void
+checkfge(char *optarg, int *fge);
+
+void
setparams(int argc, char *argv[], struct tableparams *p);
void
- [gnuastro-commits] master c113fc3 09/16: Allocation for FITS types by datatype, not bitpix, (continued)
- [gnuastro-commits] master c113fc3 09/16: Allocation for FITS types by datatype, not bitpix, Mohammad Akhlaghi, 2016/08/24
- [gnuastro-commits] master 9c7d9a0 10/16: Blank replacement function now accepts datatype, Mohammad Akhlaghi, 2016/08/24
- [gnuastro-commits] master 2071999 08/16: Blank CFITSIO pointers set by datatype, not bitpix, Mohammad Akhlaghi, 2016/08/24
- [gnuastro-commits] master 01dfb1b 05/16: Some code management in Table, Mohammad Akhlaghi, 2016/08/24
- [gnuastro-commits] master d09e850 04/16: FITS table column information printed by Table, Mohammad Akhlaghi, 2016/08/24
- [gnuastro-commits] master 5606978 11/16: Configuration file in tests/during-dev.sh, Mohammad Akhlaghi, 2016/08/24
- [gnuastro-commits] master c719806 06/16: Table accepts specified column number, name and regex, Mohammad Akhlaghi, 2016/08/24
- [gnuastro-commits] master 647406f 02/16: Table utility bare minimum structure in place, Mohammad Akhlaghi, 2016/08/24
- [gnuastro-commits] master ad16c2a 12/16: Cosmetic changes in fits and txtarray libraries, Mohammad Akhlaghi, 2016/08/24
- [gnuastro-commits] master b16c7a4 15/16: New Section added to the book for Table, Mohammad Akhlaghi, 2016/08/24
- [gnuastro-commits] master cd5b5cf 13/16: Table prints contents of a FITS table,
Mohammad Akhlaghi <=
- [gnuastro-commits] master b553085 01/16: Template for creating a new utility added, Mohammad Akhlaghi, 2016/08/24
- [gnuastro-commits] master ce08c34 14/16: FITS (binary) tables <--> plain text in Table, Mohammad Akhlaghi, 2016/08/24
- [gnuastro-commits] master b78b0c7 16/16: New Table utility merged, Mohammad Akhlaghi, 2016/08/24