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[gnuastro-commits] master 4b38991f: Book: full edit of first tutorial, w
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From: |
Mohammad Akhlaghi |
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Subject: |
[gnuastro-commits] master 4b38991f: Book: full edit of first tutorial, with redirection to make catalog |
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Date: |
Mon, 16 May 2022 19:20:17 -0400 (EDT) |
branch: master
commit 4b38991fc2ab09f8db927ff65fb4143242ebe298
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Book: full edit of first tutorial, with redirection to make catalog
Until now, in the first tutorial, we were simply asking the user to
copy-paste the contents of the table (to produce the necessary mock image)
using a plain-text editor. However, the series of commands were
confusing. Also, there was only metadata for one column (which could again
confuse a reader!).
With this commit, we now describe metadata, add metadata for all the
columns and use shell re-direction to automatically create the table. In
the process, I also reviewed the whole tutorial and added some more modern
features like using 'astscript-fits-view'.
Also, until now, the "Getting involved" part of the main webpage had a
sub-section on the Google Summer of Code (GSoC) 2022. But GSoC 2022
application period has already finished, so there is no more need to have
that entry in the webpage for this year.
With this commit, that part of the webpage has been commented, so we can
use it again for next year if necessary.
The issues in the first tutorial were reported by Marjan Akbari.
---
doc/announce-acknowledge.txt | 1 +
doc/gnuastro.en.html | 2 +
doc/gnuastro.texi | 320 ++++++++++++++++++++++++++++++++++---------
3 files changed, 255 insertions(+), 68 deletions(-)
diff --git a/doc/announce-acknowledge.txt b/doc/announce-acknowledge.txt
index 9950067f..befb0246 100644
--- a/doc/announce-acknowledge.txt
+++ b/doc/announce-acknowledge.txt
@@ -1,5 +1,6 @@
Alphabetically ordered list to acknowledge in the next release.
+Marjan Akbari
Faezeh Bijarchian
Sepideh Eskandarlou
SÃlvia Farras
diff --git a/doc/gnuastro.en.html b/doc/gnuastro.en.html
index 8b760f33..7dd0b633 100644
--- a/doc/gnuastro.en.html
+++ b/doc/gnuastro.en.html
@@ -297,12 +297,14 @@ mailing list for advice.</p>
<dl>
+<!--
<dt>Google Summer of Code 2022</dt>
<dd>Gnuastro has some two suggested projects (one medium and one large) for
Google Summer of Code (GSoC) 2022 as part of <a
href="https://openastronomy.org/gsoc/gsoc2022/#/projects";>OpenAstronomy</a>.
The medium project is for estimating <a
href="https://openastronomy.org/gsoc/gsoc2022/#/projects?project=distortion_coefficients_in_astrometry";>Distortion
coefficients in astrometry</a>, and the larger one is for <a
href="https://openastronomy.org/gsoc/gsoc2022/#/projects?project=gnuastro_library_in_python";>Python
wrappers to Gnuastro's library</a>.
A checklist of steps to get you started in developing Gnuastro is <a
href="https://savannah.gnu.org/support/index.php?110613#comment0";>available
here</a>.
Generally, if you are interested in any of the Gnuastro <a
href="https://savannah.gnu.org/task/?group=gnuastro";>open tasks</a> for the
GSoC please get in touch.
We are also open to any new suggestion to contribute to Gnuastro through
GSoC 2022.</dd>
+-->
<dt>Test releases</dt>
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index 943ff4b3..d329be68 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -1800,9 +1800,10 @@ $ astmkprof -P
# Columns, by info (see `--searchin'), or number (starting from 1):
ccol 2 # Coord. columns (one call for each dim.).
ccol 3 # Coord. columns (one call for each dim.).
- fcol 4 # sersic (1), moffat (2), gaussian (3),
- # point (4), flat (5), circumference (6),
- # distance (7), radial-table (8).
+ fcol 4 # sersic (1), moffat (2), gaussian (3), point
+ # (4), flat (5), circumference (6), distance
+ # (7), custom-prof (8), azimuth (9),
+ # custom-img (10).
rcol 5 # Effective radius or FWHM in pixels.
ncol 6 # Sersic index or Moffat beta.
pcol 7 # Position angle.
@@ -1820,71 +1821,238 @@ It is also possible to use column names for the values
of these options and chan
Fortunately MakeProfiles has the capability to also make the PSF which is to
be used on the mock image and using the @option{--prepforconv} option, he can
also make the mock image to be larger by the correct amount and all the sources
to be shifted by the correct amount.
For his initial check he decides to simulate the nebula in the Andromeda
constellation.
-The night he was observing, the PSF had roughly a FWHM of about 5 pixels, so
as the first row (profile), he defines the PSF parameters and sets the radius
column (@code{rcol} above, fifth column) to @code{5.000}, he also chooses a
Moffat function for its functional form.
+The night he was observing, the PSF had roughly a FWHM of about 5 pixels, so
as the first row (profile) in the table below, he defines the PSF parameters.
+Sufi sets the radius column (@code{rcol} above, fifth column) to @code{5.000},
he also chooses a Moffat function for its functional form.
Remembering how diffuse the nebula in the Andromeda constellation was, he
decides to simulate it with a mock S@'{e}rsic index 1.0 profile.
-He wants the output to be 499 pixels by 499 pixels, so he can put the center
of the mock profile in the central pixel of the image (note that an even number
doesn't have a central element).
+He wants the output to be 499 pixels by 499 pixels, so he can put the center
of the mock profile in the central pixel of the image which is the 250th pixel
along both dimensions (note that an even number doesn't have a ``central''
pixel).
-Looking at his drawings of it, he decides a reasonable effective radius for it
would be 40 pixels on this image pixel scale, he sets the axis ratio and
position angle to approximately correct values too and finally he sets the
total magnitude of the profile to 3.44 which he had accurately measured.
+Looking at his drawings of it, he decides a reasonable effective radius for it
would be 40 pixels on this image pixel scale (second row, 5th column below).
+He also sets the axis ratio (0.4) and position angle (-25 degrees) to
approximately correct values too, and finally he sets the total magnitude of
the profile to 3.44 which he had measured.
Sufi also decides to truncate both the mock profile and PSF at 5 times the
respective radius parameters.
In the end he decides to put four stars on the four corners of the image at
very low magnitudes as a visual scale.
While he was preparing the catalog, one of his students approached him and was
also following the steps.
-Using all the information above, he creates the catalog of mock profiles he
wants in a file named @file{cat.txt} (short for catalog) using his favorite
text editor and stores it in a directory named @file{simulationtest} in his
home directory.
-[The @command{cat} command prints the contents of a file, short for
``concatenation''.
-So please copy-paste the lines after ``@command{cat cat.txt}'' into
@file{cat.txt} when the editor opens in the steps above it, note that there are
7 lines, first one starting with @key{#}.
-Also be careful when copying from the PDF format, the Info, web, or text
formats shouldn't have any problem]:
+@noindent
+As described above, the catalog of profiles to build will be a table (multiple
columns of numbers) like below:
+
+@example
+0 0.000 0.000 2 5 4.7 0.0 1.0 30.0 5.0
+1 250.0 250.0 1 40 1.0 -25 0.4 3.44 5.0
+2 50.00 50.00 4 0 0.0 0.0 0.0 6.00 0.0
+3 450.0 50.00 4 0 0.0 0.0 0.0 6.50 0.0
+4 50.00 450.0 4 0 0.0 0.0 0.0 7.00 0.0
+5 450.0 450.0 4 0 0.0 0.0 0.0 7.50 0.0
+@end example
+
+This contains all the ``data'' to build the profile, and you can easily pass
it to Gnuastro's MakeProfiles: since Sufi already knows the columns and
expeccted values very good, he has placed the information in the proper columns.
+However, when the student sees this, he just sees a mumble-jumple of numbers!
+Generally, Sufi explains to the student that even if you know the number
positions and values very nicely today, in a couple of months you will forget!
+It will then be very hard for you to interpret the numbers properly.
+So you should never use naked data (or data without any extra information).
+
+@cindex Metadata
+Data (or information) that describes other data is called ``metadata''!
+One common example is column names (the name of a column is itself a data
element, but data that describes the lower-level data within that column: how
to interpret the numbers within it).
+Sufi explains to his student that Gnuastro has a convention for adding
metadata within a plain-text file; and guides him to @ref{Gnuastro text table
format}.
+Because we don't want metadata to be confused with the actual data, in a
plain-text file, we start lines containing metadata with a `@code{#}'.
+For example, see the same data above, but this time with metadata for every
column:
+
+@example
+# Column 1: ID [counter, u8] Identifier
+# Column 2: X [pix, f32] Horizontal position
+# Column 3: Y [pix, f32] Vertical position
+# Column 4: PROFILE [name, u8] Radial profile function
+# Column 5: R [pix, f32] Effective radius
+# Column 6: N [n/a, f32] Sersic index
+# Column 7: PA [deg, f32] Position angle
+# Column 8: Q [n/a, f32] Axis ratio
+# Column 9: MAG [log, f32] Magnitude
+# Column 10: TRUNC [n/a, f32] Truncation (multiple of R)
+0 0.000 0.000 2 5 4.7 0.0 1.0 30.0 5.0
+1 250.0 250.0 1 40 1.0 -25 0.4 3.44 5.0
+2 50.00 50.00 4 0 0.0 0.0 0.0 6.00 0.0
+3 450.0 50.00 4 0 0.0 0.0 0.0 6.50 0.0
+4 50.00 450.0 4 0 0.0 0.0 0.0 7.00 0.0
+5 450.0 450.0 4 0 0.0 0.0 0.0 7.50 0.0
+@end example
+
+@noindent
+The numbers now make much more sense to for the student!
+Before continuing, Sufi reminded the student that even though metadata may not
be strictly/technically necessary (for the computer programs), metadata are
critical for human readers!
+Therefore, a good scientist should never forget to keep metadata with any data
that they create, use or archive.
+
+To start simulating the nebula, Sufi creates a directory named
@file{simulationtest} in his home directory.
+Note that the @command{pwd} command will print the ``parent working
directory'' of the current directory (its a good way to confirm/check your
current location in the full file system: it always starts from the root, or
`@code{/}').
@example
$ mkdir ~/simulationtest
$ cd ~/simulationtest
$ pwd
/home/rahman/simulationtest
-$ emacs cat.txt
+@end example
+
+@cindex Redirection
+@cindex Standard output
+It is possible to use a plain-text editor to manually put the catalog contents
above into a plain-text file.
+But to easily automate catalog production (in later trials), Sufi decides to
fill the input catalog with the redirection features of the command-line (or
shell).
+Sufi's student wasn't familiar with this feature of the shell!
+So Sufi decided to do a fast demo; giving the following explanations while
running the commands:
+
+Shell redirection allows you to ``re-direct'' the ``standard output'' of a
program (which is usually printed by the program on the command-line during its
execution; like the output of @command{pwd} above) into a file.
+For example, let's simply ``echo'' (or print to standard output) the line
``This is a test.'':
+
+@example
+$ echo "This is a test."
+This is a test.
+@end example
+
+@noindent
+As you see, our statement was simply ``echo''-ed to the standard output!
+To redirect this sentence into a file (instead of simply printing it on the
standard output), we can simply use the @code{>} character, followed by the
name of the file we want it to be dumped in.
+
+@example
+$ echo "This is a test." > test.txt
+@end example
+
+This time, the @command{echo} command didn't print anything in the terminal.
+Instead, the shell (command-line environment) took the output, and
``re-directed'' it into a file called @file{test.txt}.
+Let's confirm this with the @command{ls} command (@command{ls} is short for
``list'' and will list all the files in the current directory):
+
+@example
$ ls
-cat.txt
-$ cat cat.txt
-# Column 4: PROFILE_NAME [,str6] Radial profile's functional name
- 1 0.0000 0.0000 moffat 5.000 4.765 0.0000 1.000 30.000 5.000
- 2 250.00 250.00 sersic 40.00 1.000 -25.00 0.400 3.4400 5.000
- 3 50.000 50.000 point 0.000 0.000 0.0000 0.000 6.0000 0.000
- 4 450.00 50.000 point 0.000 0.000 0.0000 0.000 6.5000 0.000
- 5 50.000 450.00 point 0.000 0.000 0.0000 0.000 7.0000 0.000
- 6 450.00 450.00 point 0.000 0.000 0.0000 0.000 7.5000 0.000
+test.txt
@end example
@noindent
-The zero point magnitude for his observation was 18.
-Now he has all the necessary parameters and runs MakeProfiles with the
following command:
+Now that you confirm the existance of @file{test.txt}, you can see its
contents with the @command{cat} command (short for ``concatenation''; because
it can also merge multiple files together):
+
+@example
+$ cat test.txt
+This is a test.
+@end example
+
+@noindent
+Now that we have written our first line in @file{test.txt}, let's try adding a
second line (don't forget that our final catalog of objects to simulate will
have multiple lines):
+
+@example
+$ echo "This is my second line." > test.txt
+$ cat test.txt
+This is my second line.
+@end example
+
+As you see, the first line that you put in the file is no longer present!
+This happens because `@code{>}' always starts dumping content to a file from
the start of the file.
+In effect, this means that any possibly pre-existing content is over-written
by the new content!
+To append new lines (or dumping new content at the end of existing content),
you can use `@code{>>}'.
+For example with the commands below, first we'll write the first sentence
(using `@code{>}'), then use `@code{>>}' to add the second and third sentences.
+Finally, we'll print the contents of @file{test.txt} to confirm that all three
lines are preserved.
+
+@example
+$ echo "My first sentence." > test.txt
+$ echo "My second sentence." >> test.txt
+$ echo "My third sentence." >> test.txt
+$ cat test.txt
+My first sentence.
+My second sentence.
+My third sentence.
+@end example
+
+The student thanked Sufi for this explanation and now feels more comfortable
with redirection.
+Therefore Sufi continues with the main project.
+But before that, he deletes the temporary test file:
+
+@example
+$ rm test.txt
+@end example
+
+To put the catalog of profile data and their metadata (that was described
above) into a file, Sufi uses the commands below.
+While Sufi was writing these commands, the student complained that ``I could
have done in this in a text editor''.
+Sufi reminded the student that it is indeed possible; but it requires manual
intervention.
+The advantage of a solution like below is that it can be automated (for
example adding more rows; for more profiles in the final image).
@example
+$ echo "# Column 1: ID [counter, u8] Identifier" > cat.txt
+$ echo "# Column 2: X [pix, f32] Horizontal position" >> cat.txt
+$ echo "# Column 3: Y [pix, f32] Vertical position" >> cat.txt
+$ echo "# Column 4: PROF [name, u8] Radial profile function" \
+ >> cat.txt
+$ echo "# Column 5: R [pix, f32] Effective radius" >> cat.txt
+$ echo "# Column 6: N [n/a, f32] Sersic index" >> cat.txt
+$ echo "# Column 7: PA [deg, f32] Position angle" >> cat.txt
+$ echo "# Column 8: Q [n/a, f32] Axis ratio" >> cat.txt
+$ echo "# Column 9: MAG [log, f32] Magnitude" >> cat.txt
+$ echo "# Column 10: TRUNC [n/a, f32] Truncation (multiple of R)" \
+ >> cat.txt
+$ echo "0 0.000 0.000 2 5 4.7 0.0 1.0 30.0 5.0" >> cat.txt
+$ echo "1 250.0 250.0 1 40 1.0 -25 0.4 3.44 5.0" >> cat.txt
+$ echo "2 50.00 50.00 4 0 0.0 0.0 0.0 6.00 0.0" >> cat.txt
+$ echo "3 450.0 50.00 4 0 0.0 0.0 0.0 6.50 0.0" >> cat.txt
+$ echo "4 50.00 450.0 4 0 0.0 0.0 0.0 7.00 0.0" >> cat.txt
+$ echo "5 450.0 450.0 4 0 0.0 0.0 0.0 7.50 0.0" >> cat.txt
+@end example
+
+@noindent
+To make sure if the catalog's content is correct (and there was no typo for
example!), Sufi runs `@command{cat cat.txt}', and confirms that it is correct.
+@cindex Zero point
+Now that the catalog is created, Sufi is ready to call MakeProfiles to build
the image containing these objects.
+He looks into his records and finds that the zero point magnitude for that
night and that detector 18.
+The student was a little confused on the concept of zero point, so Sufi
pointed him to @ref{Brightness flux magnitude}, which the student can study in
detail later.
+Sufi therefore runs MakeProfiles with the command below:
+
+@example
$ astmkprof --prepforconv --mergedsize=499,499 --zeropoint=18.0 cat.txt
-MakeProfiles started on Sat Oct 6 16:26:56 953
+MakeProfiles @value{VERSION} started on Sat Oct 6 16:26:56 953
- 6 profiles read from cat.txt
- - Random number generator (RNG) type: mt19937
- - Using 8 threads.
- ---- row 2 complete, 5 left to go
- ---- row 3 complete, 4 left to go
- ---- row 4 complete, 3 left to go
+ - Random number generator (RNG) type: ranlxs1
+ - Basic RNG seed: 1652884540
+ - Using 12 threads.
+ ---- row 3 complete, 5 left to go
+ ---- row 4 complete, 4 left to go
+ ---- row 6 complete, 3 left to go
---- row 5 complete, 2 left to go
---- ./0_cat_profiles.fits created.
- ---- row 0 complete, 1 left to go
- ---- row 1 complete, 0 left to go
- - ./cat_profiles.fits created. 0.041651 seconds
+ ---- row 1 complete, 1 left to go
+ ---- row 2 complete, 0 left to go
+ - ./cat_profiles.fits created. 0.092573 seconds
-- Output: ./cat_profiles.fits
-MakeProfiles finished in 0.267234 seconds
+MakeProfiles finished in 0.293644 seconds
+@end example
+
+Sufi encourages the student to read through the printed output.
+As the statements say, two FITS files should have been created in the running
directory.
+So Sufi ran the command below to confirm:
-$ls
-0_cat_profiles.fits cat_profiles.fits cat.txt
+@example
+$ ls
+0_cat_profiles.fits cat_profiles.fits cat.txt
@end example
@cindex Oversample
@noindent
The file @file{0_cat_profiles.fits} is the PSF Sufi had asked for, and
@file{cat_profiles.fits} is the image containing the main objects in the
catalog.
-The size of @file{cat_profiles.fits} was surprising for the student, instead
of 499 by 499 (as we had requested), it was 2615 by 2615 pixels (from the
command below):
+Sufi opened the main image with the command below (using SAO DS9):
@example
-$ astfits cat_profiles.fits -h1 | grep NAXIS
+$ astscript-fits-view cat_profiles.fits --ds9scale=95
+@end example
+
+The student could clearly see the main elliptical structure in the center.
+However, the size of @file{cat_profiles.fits} was surprising for the student,
instead of 499 by 499 (as we had requested), it was 2615 by 2615 pixels (from
the command below):
+
+@example
+$ astfits cat_profiles.fits
+Fits (GNU Astronomy Utilities) @value{VERSION}
+Run on Sat Oct 6 16:26:58 953
+-----
+HDU (extension) information: 'cat_profiles.fits'.
+ Column 1: Index (counting from 0, usable with '--hdu').
+ Column 2: Name ('EXTNAME' in FITS standard, usable with '--hdu').
+ Column 3: Image data type or 'table' format (ASCII or binary).
+ Column 4: Size of data in HDU.
+-----
+0 MKPROF-CONFIG no-data 0
+1 Mock profiles float32 2615x2615
@end example
@noindent
@@ -1892,7 +2060,6 @@ So Sufi explained why oversampling is important in
modeling, especially for part
Recall that when you oversample the model (for example by 5 times), for every
desired pixel, you get 25 pixels (@mymath{5\times5}).
Sufi then explained that after convolving (next step below) we will
down-sample the image to get our originally desired size/resolution.
-Sufi then opened @code{cat_profiles.fits} [you can use any FITS viewer, for
example, @command{ds9}].
After seeing the image, the student complained that only the large elliptical
model for the Andromeda nebula can be seen in the center.
He couldn't see the four stars that we had also requested in the catalog.
So Sufi had to explain that the stars are there in the image, but the reason
that they aren't visible when looking at the whole image at once, is that they
only cover a single pixel!
@@ -1917,13 +2084,15 @@ Convolve started on Sat Oct 6 16:35:32 953
- Padded parts removed. 0.016767 seconds
- Output: cat_convolved.fits
Convolve finished in: 10.422161 seconds
-
-$ls
-0_cat_profiles.fits cat_convolved.fits cat_profiles.fits cat.txt
@end example
@noindent
-When convolution finished, Sufi opened @file{cat_convolved.fits} and the four
stars could be easily seen now.
+When convolution finished, Sufi opened @file{cat_convolved.fits} and the four
stars could be easily seen now:
+
+@example
+$ astscript-fits-view cat_convolved.fits --ds9scale=95
+@end example
+
It was interesting for the student that all the flux in that single pixel is
now distributed over so many pixels (the sum of all the pixels in each
convolved star is actually equal to the value of the single pixel before
convolution).
Sufi explained how a PSF with a larger FWHM would make the points even wider
than this (distributing their flux in a larger area).
With the convolved image ready, they were prepared to re-sample it to the
original pixel scale Sufi had planned [from the @command{$ astmkprof -P}
command above, recall that MakeProfiles had over-sampled the image by 5 times].
@@ -1939,31 +2108,26 @@ Warp started on Sat Oct 6 16:51:59 953
0.0000 0.2000 0.4000
0.0000 0.0000 1.0000
-$ ls
-0_cat_profiles.fits cat_convolved_scaled.fits cat.txt
-cat_convolved.fits cat_profiles.fits
-
-$ astfits -p cat_convolved_scaled.fits | grep NAXIS
-NAXIS = 2 / number of data axes
-NAXIS1 = 523 / length of data axis 1
-NAXIS2 = 523 / length of data axis 2
+$ astfits cat_convolved_scaled.fits --quiet
+0 WARP-CONFIG no-data 0
+1 Warped float32 523x523
@end example
@noindent
@file{cat_convolved_scaled.fits} now has the correct pixel scale.
-However, the image is still larger than what we had wanted, it is 523
(@mymath{499+12+12}) by 523 pixels.
+However, the image is still larger than what we had wanted, it is
@mymath{523\times523} pixels (not our desired @mymath{499\times499}).
The student is slightly confused, so Sufi also re-samples the PSF with the
same scale by running
@example
$ astwarp --scale=1/5 --centeroncorner 0_cat_profiles.fits
-$ astfits -p 0_cat_profiles_scaled.fits | grep NAXIS
-NAXIS = 2 / number of data axes
-NAXIS1 = 25 / length of data axis 1
-NAXIS2 = 25 / length of data axis 2
+$ astfits 0_cat_profiles_scaled.fits --quiet
+0 WARP-CONFIG no-data 0
+1 Warped float32 25x25
@end example
@noindent
-Sufi notes that @mymath{25=(2\times12)+1} and goes on to explain how frequency
space convolution will dim the edges and that is why he added the
@option{--prepforconv} option to MakeProfiles, see @ref{If convolving
afterwards}.
+Sufi notes that @mymath{25=12+12+1} and that @mymath{523=499+12+12}.
+He goes on to explain that frequency space convolution will dim the edges and
that is why he added the @option{--prepforconv} option to MakeProfiles above.
Now that convolution is done, Sufi can remove those extra pixels using Crop
with the command below.
Crop's @option{--section} option accepts coordinates inclusively and counting
from 1 (according to the FITS standard), so the crop region's first pixel has
to be 13, not 12.
@@ -1974,39 +2138,44 @@ Crop started on Sat Oct 6 17:03:24 953
- Read metadata of 1 image. 0.001304 seconds
---- ...nvolved_scaled_cropped.fits created: 1 input.
Crop finished in: 0.027204 seconds
+@end example
-$ls
-0_cat_profiles.fits cat_convolved_scaled_cropped.fits cat_profiles.fits
-cat_convolved.fits cat_convolved_scaled.fits cat.txt
+@noindent
+To fully convince the student, Sufi checks the size of the output of the crop
command above:
+
+@example
+$ astfits cat_convolved_scaled_cropped.fits --quiet
+0 n/a no-data 0
+1 n/a float32 499x499
@end example
@noindent
-Finally, @file{cat_convolved_scaled_cropped.fits} is @mymath{499\times499}
pixels and the mock Andromeda galaxy is centered on the central pixel (open the
image in a FITS viewer and confirm this by zooming into the center, note that
an even-width image wouldn't have a central pixel).
+Finally, @file{cat_convolved_scaled_cropped.fits} is @mymath{499\times499}
pixels and the mock Andromeda galaxy is centered on the central pixel.
This is the same dimensions as Sufi had desired in the beginning.
All this trouble was certainly worth it because now there is no dimming on the
edges of the image and the profile centers are more accurately sampled.
The final step to simulate a real observation would be to add noise to the
image.
Sufi set the zero point magnitude to the same value that he set when making
the mock profiles and looking again at his observation log, he had measured the
background flux near the nebula had a magnitude of 7 that night.
For more on how the background value determines the noise, see @ref{Noise
basics}.
-So using these values he ran MakeNoise:
+So using these values he ran MakeNoise, and with the second command, he
visually inspected the image.
@example
$ astmknoise --zeropoint=18 --background=7 --output=out.fits \
cat_convolved_scaled_cropped.fits
-MakeNoise started on Sat Oct 6 17:05:06 953
+MakeNoise @value{VERSION} started on Sat Oct 6 17:05:06 953
- Generator type: ranlxs1
- Generator seed: 1428318100
MakeNoise finished in: 0.033491 (seconds)
-$ls
-0_cat_profiles.fits cat_convolved_scaled_cropped.fits cat_profiles.fits
-cat_convolved.fits cat_convolved_scaled.fits cat.txt out.fits
+$ astscript-fits-view out.fits
@end example
@noindent
The @file{out.fits} file now contains the noised image of the mock catalog
Sufi had asked for.
+The student hadn't observed the nebula in the sky, so when he saw the mock
image in SAO DS9 (with the second command above), he understood why Sufi was
dubious: it was very diffuse!
+
Seeing how the @option{--output} option allows the user to specify the name of
the output file, the student was confused and wanted to know why Sufi hadn't
used it more regularly before?
-Sufi then explained to him that for intermediate steps, you can rely on the
automatic output of the programs, see @ref{Automatic output}.
+Sufi explained that for intermediate steps, you can rely on the automatic
output of the programs (see @ref{Automatic output}).
Doing so will give all the intermediate files a similar basic name structure,
so in the end you can simply remove them all with the Shell's capabilities, and
it will be familiar for other users.
So Sufi decided to show this to the student by making a shell script from the
commands he had used before.
@@ -2056,10 +2225,11 @@ rm 0*.fits "$base"*.fits
@end example
@cindex Comments
-He used this chance to remind the student of the importance of comments in
code or shell scripts: when writing the code, you have a good mental picture of
what you are doing, so writing comments might seem superfluous and excessive.
+He used this chance to remind the student of the importance of comments in
code or shell scripts!
+Just like metadata in a dataset, when writing the code, you have a good mental
picture of what you are doing, so writing comments might seem superfluous and
excessive.
However, in one month when you want to re-use the script, you have lost that
mental picture and remembering it can be time-consuming and frustrating.
The importance of comments is further amplified when you want to share the
script with a friend/colleague.
-So it is good to accompany any script/code with useful comments while you are
writing it (create a good mental picture of what/why you are doing something).
+So it is good to accompany any step of a script, or code, with useful comments
while you are writing it (create a good mental picture of why you are doing
something: don't just describe the command, but its purpose).
@cindex Gedit
@cindex GNU Emacs
@@ -2089,11 +2259,25 @@ The student was also happy to hear that he won't need
to make it executable agai
The student was really excited, since now, through simple shell scripting, he
could really speed up his work and run any command in any fashion he likes
allowing him to be much more creative in his works.
Until now he was using the graphical user interface which doesn't have such a
facility and doing repetitive things on it was really frustrating and some
times he would make mistakes.
So he left to go and try scripting on his own computer.
+He later reminded Sufi that the second tutorial in the Gnuastro book as more
complex commands in data analysis, and a more advanced introduction to
scripting (see @ref{General program usage tutorial}).
Sufi could now get back to his own work and see if the simulated nebula which
resembled the one in the Andromeda constellation could be detected or not.
Although it was extremely faint@footnote{The brightness of a diffuse object is
added over all its pixels to give its final magnitude, see @ref{Brightness flux
magnitude}.
So although the magnitude 3.44 (of the mock nebula) is orders of magnitude
brighter than 6 (of the stars), the central galaxy is much fainter.
-Put another way, the brightness is distributed over a large area in the case
of a nebula.}, fortunately it passed his detection tests and he wrote it in the
draft manuscript that would later become ``Book of fixed stars''.
+Put another way, the brightness is distributed over a large area in the case
of a nebula.}.
+Therefore, Sufi ran Gnuastro's detection software (@ref{NoiseChisel}) to see
if this object is detectable or not.
+NoiseChisel's output (@file{out_detected.fits}) is a multi-extension FITS
file, so he used Gnuastro's @command{astscript-fits-view} program in the second
command to see the output:
+
+@example
+$ astnoisechisel out.fits
+
+$ astscript-fits-view out_detected.fits
+@end example
+
+In the ``Cube'' window (that was opened with DS9), if Sufi clicked on the
``Next'' button to see the pixels that were detected to contain significant
signal.
+Fortuantely the nebula's shape was detectable and he cound finally confirm
that the nebula he kept in his notebook was actually observable.
+He wrote this result in the draft manuscript that would later become ``Book of
fixed stars''@footnote{@url{https://en.wikipedia.org/wiki/Book_of_Fixed_Stars}}.
+
He still had to check the other nebula he saw from Yemen and several other
such objects, but they could wait until tomorrow (thanks to the shell script,
he only has to define a new catalog).
It was nearly sunset and they had to begin preparing for the night's
measurements on the ecliptic.
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- [gnuastro-commits] master 4b38991f: Book: full edit of first tutorial, with redirection to make catalog,
Mohammad Akhlaghi <=