Added ASCII format support to gennoise and genmap

Author: cschreib

doc/EGG.pdf

@@ -1,6 +1,6 @@
 \subsubsection{Basic usage}
 
-These two tools can be used to create the images corresponding to a given mock catalog created by \bashinline{egg-gencat}. They provide a simple alternative to \skymaker, with the added limitation that galaxies are all considered as point sources. This is usually fine for long wavelength images (\spitzer MIPS and \herschel, typically) in cosmological deep fields. In addition, more control is given relative to the noise properties.
+These two tools can be used to create the images corresponding to a given mock catalog created by \bashinline{egg-gencat} (custom catalogs are also supported, see below). They provide a simple alternative to \skymaker, with the added limitation that galaxies are all considered as point sources. This is usually fine for long wavelength images (\spitzer MIPS and \herschel, typically) in cosmological deep fields. In addition, more control is given relative to the noise properties.
 
 The typical call sequence consists of two steps: creating the noise map with \bashinline{egg-gennoise}, then painting the galaxies on top of it with \bashinline{egg-genmap}. The standard way to use \bashinline{egg-gennoise} is the following:
 \begin{bashcode}
@@ -31,7 +31,7 @@ \subsubsection{Basic usage}
 
 \subsubsection{Using a custom astrometry and image dimensions}
 
-The tool \bashinline{egg-gennoise} can compute automatically a suitable astrometry and image dimensions according the input catalog. However, you also have the possibility to copy the astrometry and image properties of an existing file. To do so, just use the \bashinline{astro} command line argument and make it point to the FITS image you want to copy the data from:
+The tool \bashinline{egg-gennoise} can compute automatically a suitable astrometry and image dimensions according to the input catalog. However, you also have the possibility to copy the astrometry and image dimensions of an existing file. To do so, just use the \bashinline{astro} command line argument and make it point to the FITS image you want to copy the data from:
 \begin{bashcode}
 egg-gennoise cat=egg-20151201.fits out=pacs160-noise.fits \
     psf=herschel-pacs160.fits rms=1.68e-5 verbose \
@@ -70,14 +70,16 @@ \subsubsection{Generate error and coverage maps}
 
 \subsubsection{Using a custom noise map}
 
-The whole point of separating the map-making process into two steps is that one can be used without the other. Indeed, \bashinline{egg-genmap} can work with noise map, provided that it contains valid WCS astrometry. The tool can handle sources outside of the map, so it is fine if the provided noise map does not overlap perfectly with the input catalog. Just make sure that the PSF you provide is tabulated on the same pixel scale as your noise map. If you use the \bashinline{beam_smoothed} option, note that the noise map must be provided \emph{unfiltered} (i.e., before beam convolution).
+The whole point of separating the map-making process into two steps is that one can be used without the other. Indeed, \bashinline{egg-genmap} can work with any noise map, provided that it contains valid WCS astrometry. The tool can handle sources outside of the map, so it is fine if the provided noise map does not overlap perfectly with the input catalog. Just make sure that the PSF you provide is tabulated on the same pixel scale as your noise map. If you use the \bashinline{beam_smoothed} option, note that the noise map must be provided \emph{unfiltered} (i.e., before beam convolution).
 
 For example, realistic \herschel noise maps can be obtained by jackknifing the observed data, and provide noise statistics (correlation, amplitude, etc.) that match very well the real images. Such kind of map can be fed naturally to \bashinline{egg-genmap} through the \bashinline{noise_map} argument.
 
 
 \subsubsection{Using a custom flux catalog}
 
-Similarly, both tools can work with input catalogs that were not produced by \bashinline{egg-gencat}. They only need a limited set of columns: \cppinline{"ra"} and \cppinline{"dec"} to know the position of each galaxy on the sky, and \cppinline{"flux"} and \cppinline{"bands"} to know their flux. The format of these columns must be the same as that created by \bashinline{egg-gencat}, but this can be easily achieved in any language. Alternatively, the program can also work with a \cppinline{"flux"} column containing a single band (i.e., a 1D vector column), in which case the \cppinline{"bands"} column and the \bashinline{band} command line argument are useless and can be omitted.
+Similarly, both tools can work with input catalogs that were not produced by \bashinline{egg-gencat}. They only need a limited set of columns: \cppinline{"ra"} and \cppinline{"dec"} to know the position of each galaxy on the sky, and \cppinline{"flux"} must contain the flux of each galaxy in $\uJy$.
+
+Catalogs produced by \bashinline{egg-gencat} contain multiple fluxes per galaxy, so in this case you also need the \cppinline{"bands"} column and the \bashinline{band} command line argument to identify the correct flux. Alternatively, the program can also work with a \cppinline{"flux"} column containing a single band (i.e., a 1D vector column), in which case the \cppinline{"bands"} column and the \bashinline{band} command line argument can be omitted. If you prefer to use ASCII format, the order of the columns must be \cppinline{"ra"}, \cppinline{"dec"} and \cppinline{"flux"} (1D only).
 
 
 \subsubsection{Adjusting accuracy and speed}

doc/doc-egg-gennoise.tex

@@ -86,33 +86,40 @@ int main(int argc, char* argv[]) {
         vec1s bands;
     } cat;
 
-    fits::input_table table(cat_file);
-    table.read_columns(ftable(cat.ra, cat.dec));
-    table.read_column(fits::dim_promote, "flux", cat.flux);
+    uint_t idb;
+    if (end_with(cat_file, ".fits")) {
+        fits::input_table table(cat_file);
+        table.read_columns(ftable(cat.ra, cat.dec));
+        table.read_column(fits::dim_promote, "flux", cat.flux);
 
-    if (cat.flux.dims[1] > 1) {
-        table.read_column("bands", cat.bands);
-    } else {
-        table.read_column(fits::missing, "bands", cat.bands);
-    }
+        if (cat.flux.dims[1] > 1) {
+            table.read_column("bands", cat.bands);
+        } else {
+            table.read_column(fits::missing, "bands", cat.bands);
+        }
 
-    table.close();
+        table.close();
 
-    // Find the band we are looking for
-    uint_t idb;
-    if (cat.bands.empty() || (cat.bands.size() == 1 && band.empty())) {
-        idb = 0;
-    } else {
-        vec1u ids = where(cat.bands == band);
-        if (ids.empty()) {
-            warning("no band named '", band, "' in this catalog");
-            return 1;
-        } else if (ids.size() > 1) {
-            warning("multiple bands matching '", band, "'");
-            return 1;
+        // Find the band we are looking for
+        if (cat.bands.empty() || (cat.bands.size() == 1 && band.empty())) {
+            idb = 0;
+        } else {
+            vec1u ids = where(cat.bands == band);
+            if (ids.empty()) {
+                warning("no band named '", band, "' in this catalog");
+                return 1;
+            } else if (ids.size() > 1) {
+                warning("multiple bands matching '", band, "'");
+                return 1;
+            }
+
+            idb = ids[0];
         }
+    } else {
+        file::read_table(cat_file, file::find_skip(cat_file),
+            cat.ra, cat.dec, file::columns(1,cat.flux));
 
-        idb = ids[0];
+        idb = 0;
     }
 
     // Read the PSF

src/egg-genmap.cpp

@@ -92,7 +92,11 @@ int main(int argc, char* argv[]) {
         vec1d ra, dec;
     } cat;
 
-    fits::read_table(cat_file, ftable(cat.ra, cat.dec));
+    if (end_with(cat_file, ".fits")) {
+        fits::read_table(cat_file, ftable(cat.ra, cat.dec));
+    } else {
+        file::read_table(cat_file, file::find_skip(cat_file), cat.ra, cat.dec);
+    }
 
     // Read the PSF
     if (verbose) note("reading and normalizing PSF...");