[gnuastro-commits] master bda6945e: Book: explained how to derive SKY_STD in MakeCatalog's --sum-error

[Mohammad Akhlaghi]

branch: master
commit bda6945e0f3c49097d3e18bf26a850a9eba2703c
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    Book: explained how to derive SKY_STD in MakeCatalog's --sum-error
    
    Until now, the description of the '--sum-error' column of MakeCatalog did
    not mention how the users can create the sky standard deviation image.
    
    With this commit, the description now has a link to NoiseChisel to clarify
    this point. Two other minor issues in the radial profile script have been
    implemented in this commit:
      1. The '--instd' and '--stdhdu' options were listed under the "Output"
         group of options. They have been brought to the "Input" group.
      2. The error message for the number of values given to the '--azimuth'
         option did not contain a new-line character in the end. As a result,
         the prompt of the user would be printed after it in interactive mode
         (which is inconvenient).
    
    This was suggested by Rahna Payyasseri Thanduparackal.
---
 bin/script/radial-profile.sh | 8 ++++----
 doc/announce-acknowledge.txt | 1 +
 doc/gnuastro.texi            | 7 +++++--
 3 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/bin/script/radial-profile.sh b/bin/script/radial-profile.sh
index 8a274be4..83a684a7 100755
--- a/bin/script/radial-profile.sh
+++ b/bin/script/radial-profile.sh
@@ -118,6 +118,9 @@ $scriptname options:
   -s, --sigmaclip=FLT,FLT  Sigma-clip multiple and tolerance.
   -z, --zeropoint=FLT      Zeropoint magnitude of input dataset.
   -Z, --zeroisnotblank     0.0 in float or double images are not blank.
+  -i, --instd=FLT/STR      Sky standard deviation per pixel, as a single
+                           number or as the filename (given to MakeCatalog).
+  -d, --stdhdu=STR         HDU/extension of the sky standard deviation image.
 
  Output:
   -o, --output             Output table with the radial profile.
@@ -127,9 +130,6 @@ $scriptname options:
   -P, --precision=INT      Number of digits after decimal point for radius.
   -v, --oversample=INT     Oversample for higher resolution radial profile.
   -u, --undersample=INT    Undersample for lower resolution radial profile.
-  -i, --instd=FLT/STR      Sky standard deviation per pixel, as a single
-                           number or as the filename.
-  -d, --stdhdu=STR         HDU/extension of the sky standard deviation image.
 
  Operating mode:
   -?, --help               Print this help list.
@@ -407,7 +407,7 @@ do
         if [ x$naz != x2 ]; then
             printf "$scriptname: '--azimuth' (or '-a') only takes "
             printf "two numbers, but $naz number(s) were given "
-            printf "in '$aztmp'"; exit 1
+            printf "in '$aztmp'\n"; exit 1
         fi
 
         # Add the give values to any potentially pre-existing values.
diff --git a/doc/announce-acknowledge.txt b/doc/announce-acknowledge.txt
index 41dff5b6..3423ea44 100644
--- a/doc/announce-acknowledge.txt
+++ b/doc/announce-acknowledge.txt
@@ -3,6 +3,7 @@ Alphabetically ordered list to acknowledge in the next release.
 Antonio Diaz Diaz
 Hok Kan (Ronald) Tsang
 Phil Wyett
+Rahna Payyasseri Thanduparackal
 
 
 
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index 28f893f5..48aa914b 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -30404,10 +30404,13 @@ So the sum of all the clump-sums in the clump catalog 
of one object will be smal
 If no usable pixels are present over the clump or object (for example, they 
are all blank), the returned value will be NaN (note that zero is meaningful).
 
 @item --sum-error
-The (@mymath{1\sigma}) error in measuring the sum of values of a label 
(objects or clumps).
+The error in measuring the sum of values of a label (objects or clumps).
+The value is calculated by using the values image (for signal above the sky 
level) and the sky standard deviation image (extension @option{--stdhdu} of 
file given to @option{--instd}); which you can derive for any image using 
@ref{NoiseChisel}.
 
 The returned value will be NaN when the label covers only NaN pixels in the 
values image, or a pixel is NaN in the @option{--instd} image, but non-NaN in 
the values image.
-The latter situation usually happens when there is a bug in the previous steps 
of your analysis, and is important because those pixels with a NaN in the 
@option{--instd} image may contribute significantly to the final error.
+The latter situation usually happens when there is a bug in the previous steps 
of your analysis.
+This is because the sky standard deviation should have a value in all pixels.
+In such cases, it is important to find the cause and fix it because those 
pixels with a NaN in the @option{--instd} image may contribute significantly to 
the final error.
 If you want to ignore those pixels in the error measurement, set them to zero 
(which is a meaningful number in such scenarios).
 
 @item --clumps-sum