---- gnuastro-0.7/doc/gnuastro.texi.orig 2018-08-08 14:30:59.000000000 +0200
-+++ gnuastro-0.7/doc/gnuastro.texi 2018-12-19 21:30:37.749829833 +0100
+--- gnuastro-0.8/doc/gnuastro.texi.orig 2018-12-28 02:05:05.000000000 +0100
++++ gnuastro-0.8/doc/gnuastro.texi 2019-01-06 12:18:14.505783992 +0100
@@ -44,60 +44,60 @@
@c To include in the info directory.
@dircategory Astronomy
@end direntry
-@@ -353,7 +353,7 @@
+@@ -354,7 +354,7 @@
Fits
Invoking Fits
-@@ -364,11 +364,11 @@
+@@ -365,11 +365,11 @@
* Recognized file formats:: Recognized file formats
* Color:: Some explanations on color.
Data manipulation
-@@ -382,7 +382,7 @@
+@@ -383,7 +383,7 @@
* Crop modes:: Basic modes to define crop region.
* Crop section syntax:: How to define a section to crop.
* Blank pixels:: Pixels with no value.
Invoking Crop
-@@ -393,7 +393,7 @@
+@@ -394,7 +394,7 @@
* Reverse polish notation:: The current notation style for Arithmetic
* Arithmetic operators:: List of operators known to Arithmetic
Convolve
-@@ -401,7 +401,7 @@
+@@ -402,7 +402,7 @@
* Frequency domain and Fourier operations:: Using frequencies in input.
* Spatial vs. Frequency domain:: When to use which?
* Convolution kernel:: How to specify the convolution kernel.
Spatial domain convolution
-@@ -426,7 +426,7 @@
+@@ -427,7 +427,7 @@
* Warping basics:: Basics of coordinate transformation.
* Merging multiple warpings:: How to merge multiple matrices.
* Resampling:: Warping an image is re-sampling it.
Data analysis
-@@ -441,7 +441,7 @@
+@@ -442,7 +442,7 @@
* Histogram and Cumulative Frequency Plot:: Basic definitions.
* Sigma clipping:: Definition of @mymath{\sigma}-clipping.
* Sky value:: Definition and derivation of the Sky value.
Sky value
-@@ -452,7 +452,7 @@
+@@ -453,7 +453,7 @@
NoiseChisel
* NoiseChisel changes after publication:: NoiseChisel updates after paper's publication.
Invoking NoiseChisel
-@@ -463,7 +463,7 @@
+@@ -464,7 +464,7 @@
Segment
* Segment changes after publication:: Segment updates after paper's publication.
Invoking Segment
-@@ -477,7 +477,7 @@
+@@ -478,7 +478,7 @@
* Quantifying measurement limits:: For comparing different catalogs.
* Measuring elliptical parameters:: Estimating elliptical parameters.
* Adding new columns to MakeCatalog:: How to add new columns.
Invoking MakeCatalog
-@@ -488,7 +488,7 @@
+@@ -489,7 +489,7 @@
Match
Modeling and fitting
-@@ -501,7 +501,7 @@
+@@ -502,7 +502,7 @@
* If convolving afterwards:: Considerations for convolving later.
* Flux Brightness and magnitude:: About these measures of energy.
* Profile magnitude:: Definition of total profile magnitude.
Modeling basics
-@@ -522,7 +522,7 @@
+@@ -523,7 +523,7 @@
MakeNoise
* Noise basics:: Noise concepts and definitions.
Noise basics
-@@ -539,7 +539,7 @@
+@@ -540,7 +540,7 @@
* Distance on a 2D curved space:: Distances in 2D for simplicity
* Extending distance concepts to 3D:: Going to 3D (our real universe).
Invoking CosmicCalculator
-@@ -561,7 +561,7 @@
+@@ -562,7 +562,7 @@
BuildProgram
Gnuastro library
-@@ -803,7 +803,7 @@
+@@ -804,7 +804,7 @@
See @ref{Known issues} if you confront any complications. For each program
there is an `Invoke ProgramName' sub-section in this book which explains
how the programs should be run on the command-line (for example
by running @command{$ info astprogname} (for example @command{info
asttable}). The `Invoke ProgramName' sub-section starts with a few examples
of each program and goes on to explain the invocation details. See
-@@ -1835,7 +1835,7 @@
+@@ -1862,7 +1862,7 @@
@ref{Convolve}. If you only want practical information on running a
program, for example its options/configuration, input(s) and output(s),
please consult the subsection titled ``Invoking ProgramName'', for example
use in the example codes through the book, please see @ref{Conventions}.
@menu
-@@ -2392,7 +2392,7 @@
+@@ -2421,7 +2421,7 @@
@key{<ENTER>}.
You don't need to start from the top of the manual every time. For example,
general, all programs have such an ``Invoking ProgramName'' section in this
book. These sections are specifically for the description of inputs,
outputs and configuration options of each program. You can access them
-@@ -2976,7 +2976,7 @@
+@@ -3038,7 +3038,7 @@
that since this is done through matrix multiplication, order matters in the
separate operations. In fact through Warp's @option{--matrix} option, you
can directly request your desired final warp and don't have to break it up
Fortunately these datasets are already aligned to the same pixel grid, so
you don't actually need the files that were just generated. You can safely
-@@ -3467,8 +3467,8 @@
+@@ -3733,8 +3733,8 @@
below will print some basic information about the distribution (minimum,
maximum, median and etc), along with a cute little ASCII histogram to
visually help you understand the distribution on the command-line without
coarse and general information on the input dataset. It is also useful when
working on a server (where you may not have graphic user interface), and
finally, its fast.
-@@ -3539,7 +3539,7 @@
+@@ -3805,7 +3805,7 @@
@end example
We can now feed this catalog into MakeProfiles to build the apertures for
important for this particular job is @option{--mforflatpix}, it tells
MakeProfiles that the values in the magnitude column should be used for
each pixel of a flat profile. Without it, MakeProfiles would build the
-@@ -6851,7 +6851,7 @@
- The command-line text that you type is passed onto the shell (or program
- managing the command-line) as a string of characters. See the ``Invoking
- ProgramName'' sections in this manual for some examples of commands with
--each program, for example @ref{Invoking asttable}. That string is then
-+each program, for example @ref{asttable}. That string is then
- broken up into separate @emph{tokens} or @emph{words} by any
- @emph{metacharacters} (like space, tab, @command{|}, @command{>} or
- @command{;}) that might exist in the text. To learn more, please see the
-@@ -7104,7 +7104,7 @@
+@@ -7249,8 +7249,7 @@
+ generic name for the program that manages the command-line) as a string of
+ characters. As an example, see the ``Invoking ProgramName'' sections in
+ this manual for some examples of commands with each program, like
+-@ref{Invoking asttable}, @ref{Invoking astfits}, or @ref{Invoking
+-aststatistics}.
++@ref{asttable}, @ref{astfits}, or @ref{aststatistics}.
+
+ The shell then brakes up your string into separate @emph{tokens} or
+ @emph{words} using any @emph{metacharacters} (like white-space, tab,
+@@ -7489,7 +7488,7 @@
On the other hand, some options can be called multiple times in one run of
a program and can thus take multiple values (for example see the
order of stored values is the same order that you specified on the
command-line.
-@@ -7674,7 +7674,7 @@
+@@ -8186,7 +8185,7 @@
programs which don't rely on that value as an input@footnote{One example of
a program which uses the value given to @option{--output} as an input is
ConvertType, this value specifies the type of the output through the value
output}.
-@@ -8242,8 +8242,8 @@
+@@ -9068,8 +9067,8 @@
property. One such property can be the object's magnitude, which is the sum
of pixels with that label, or its center can be defined as the
light-weighted average value of those pixels. Many such properties can be
As a summary, for each labeled region (or, galaxy) we have one @emph{row}
and for each measured property we have one @emph{column}. This high-level
-@@ -9315,8 +9315,7 @@
- whole file (grouping of extensions). Subsequent extensions may contain data
- along with their own separate meta-data. All of Gnuastro's programs also
- follow this convention: the main dataset (image or table) is in the second
--extension. See the example list of extension properties in @ref{Invoking
--astfits}.
-+extension. See the example list of extension properties in @ref{astfits}.
-
- The meta-data contain information about the data, for example which region
- of the sky an image corresponds to, the units of the data, what telescope,
-@@ -9357,10 +9356,10 @@
+@@ -9921,10 +9920,10 @@
within one HDU.
@menu
@subsection Invoking Fits
Fits can print or manipulate the FITS file HDUs (extensions), meta-data
-@@ -9472,7 +9471,7 @@
+@@ -10036,7 +10035,7 @@
@subsubsection HDU manipulation
Each header data unit, or HDU (also known as an extension), in a FITS file
is an independent dataset (data + meta-data). Multiple HDUs can be stored
-@@ -9520,7 +9519,7 @@
+@@ -10070,7 +10069,7 @@
+
+ For a complete list of basic meta-data on the extensions in a FITS file,
+ don't use any of the options in this section or in @ref{Keyword
+-manipulation}. For more, see @ref{Invoking astfits}.
++manipulation}. For more, see @ref{astfits}.
+
+ @item -C STR
+ @itemx --copy=STR
+@@ -10095,7 +10094,7 @@
@end table
@subsubsection Keyword manipulation
The meta-data in each header data unit, or HDU (also known as extension,
see @ref{Fits}) is stored as ``keyword''s. Each keyword consists of a name,
-@@ -9777,7 +9776,7 @@
+@@ -10345,14 +10344,14 @@
+ image or text file into a FITS image. Basically, other than EPS/PDF, you
+ can use any of the recognized formats as different color channel inputs to
+ get any of the recognized outputs. So before explaining the options and
+-arguments (in @ref{Invoking astconvertt}), we'll start with a short
++arguments (in @ref{astconvertt}), we'll start with a short
+ description of the recognized files types in @ref{Recognized file formats},
+ followed a short introduction to digital color in @ref{Color}.
+
@menu
* Recognized file formats:: Recognized file formats
* Color:: Some explanations on color.
@end menu
@node Recognized file formats, Color, ConvertType, ConvertType
-@@ -9928,7 +9927,7 @@
+@@ -10504,7 +10503,7 @@
color channel.
In ConvertType, the recognized extensions for plain text files are
you just give these extensions, (and not a full filename) as output, then
automatic output will be preformed to determine the final output name (see
@ref{Automatic output}). Besides these, when the format of a file cannot be
-@@ -9965,7 +9964,7 @@
+@@ -10541,7 +10540,7 @@
@end table
@subsection Color
@cindex RGB
-@@ -10038,7 +10037,7 @@
- are approximately the same file size.
+@@ -10580,7 +10579,7 @@
+ single-channel dataset (for example in the FITS image format) as an
+ argument (in the proper order), then asking for the output in a format that
+ supports multi-channel datasets (for example JPEG or PDF, see the examples
+-in @ref{Invoking astconvertt}).
++in @ref{astconvertt}).
+
+ @cindex Grayscale
+ @cindex Visualization
+@@ -10599,7 +10598,7 @@
+ @url{https://en.wikipedia.org/wiki/HSL_and_HSV, Hue-Saturation-Value} (HSV)
+ color space (while fixing the ``Saturation'' and ``Value'' terms). In
+ ConvertType, you can use the @option{--colormap} option to choose between
+-different mappings of mono-channel inputs, see @ref{Invoking astconvertt}.
++different mappings of mono-channel inputs, see @ref{astconvertt}.
+
+ Since grayscale is a commonly used mapping of single-valued datasets, we'll
+ continue with a closer look at how it is stored. One way to represent a
+@@ -10640,7 +10639,7 @@
+ has only the K-channel filled are approximately the same file size.
-@node Invoking astconvertt, , Color, ConvertType
+@node astconvertt, , Color, ConvertType
@subsection Invoking ConvertType
- ConvertType will convert any recognized input file type to any
-@@ -10326,14 +10325,14 @@
+ ConvertType will convert any recognized input file type to any specified
+@@ -10996,14 +10995,14 @@
formats) is only one command away from AWK (or any other tool you want to
use). Just like a plain text file that you read with the @command{cat}
command. You can pipe the output of Table into any other tool for
@subsection Invoking Table
Table will read/write, select, convert, or show the information of the
-@@ -10509,7 +10508,7 @@
+@@ -11184,7 +11183,7 @@
Besides cropping postage stamps around certain coordinates, Crop can also
crop arbitrary polygons from an image (or a set of tiles by stitching the
relevant parts of different tiles within the polygon), see
out rectangular regions through the @option{--section} option from one
image, see @ref{Crop section syntax}.
-@@ -10517,7 +10516,7 @@
+@@ -11192,7 +11191,7 @@
* Crop modes:: Basic modes to define crop region.
* Crop section syntax:: How to define a section to crop.
* Blank pixels:: Pixels with no value.
@end menu
@node Crop modes, Crop section syntax, Crop, Crop
-@@ -10544,7 +10543,7 @@
+@@ -11219,7 +11218,7 @@
the @emph{mode} in Crop, you define the standard that the given coordinates
must be interpreted. Here, the different ways to specify the crop region
are discussed within each standard. For the full list options, please see
When the crop is defined by its center, the respective (integer) central
pixel position will be found internally according to the FITS standard. To
-@@ -10557,8 +10556,7 @@
+@@ -11232,8 +11231,7 @@
center (your primary target). This can be very convenient when your input
catalog/coordinates originated from another survey/filter which is not
fully covered by your input image, to learn more about this feature, please
@table @asis
@item Image coordinates
-@@ -10593,7 +10591,7 @@
+@@ -11268,7 +11266,7 @@
The latter option (@option{--polygon}) is a higher-level method to define
any convex polygon (with any number of vertices) with floating point
for its syntax.
@end table
-@@ -10639,7 +10637,7 @@
+@@ -11314,7 +11312,7 @@
@item Vertices of a single crop
The @option{--polygon} option is a high-level method to define any convex
polygon (with any number of vertices). Please see the description of this
@end table
@cartouche
-@@ -10716,7 +10714,7 @@
+@@ -11391,7 +11389,7 @@
the command-line works.
@subsection Blank pixels
@cindex Blank pixel
-@@ -10752,7 +10750,7 @@
+@@ -11427,7 +11425,7 @@
@option{--zeroisnotblank} option.
@subsection Invoking Crop
Crop will crop a region from an image. If in WCS mode, it will also
-@@ -10829,7 +10827,7 @@
+@@ -11504,7 +11502,7 @@
* Crop output:: The outputs of Crop.
@end menu
@subsubsection Crop options
The options can be classified into the following contexts: Input,
-@@ -11105,7 +11103,7 @@
+@@ -11780,7 +11778,7 @@
@subsubsection Crop output
The string given to @option{--output} option will be interpreted depending
-@@ -11159,7 +11157,7 @@
+@@ -11834,7 +11832,7 @@
A @code{0} if the central few pixels (value to the @option{--checkcenter}
option) are blank and @code{1} if they aren't. When the crop was not
defined by its center (see @ref{Crop modes}), or @option{--checkcenter} was
checked and this column will be given a value of @code{-1}.
@end enumerate
-@@ -11196,13 +11194,13 @@
+@@ -11871,13 +11869,13 @@
polish or post-fix notation, see @ref{Reverse polish notation} and will work
on the native data types of the input images/data to reduce CPU and RAM
resources, see @ref{Numeric data types}. For more information on how to run
@end menu
@node Reverse polish notation, Arithmetic operators, Arithmetic, Arithmetic
-@@ -11266,7 +11264,7 @@
+@@ -11941,7 +11939,7 @@
@subsection Arithmetic operators
The recognized operators in Arithmetic are listed below. See @ref{Reverse
-@@ -11922,7 +11920,7 @@
+@@ -12597,7 +12595,7 @@
@end cartouche
@subsection Invoking Arithmetic
Arithmetic will do pixel to pixel arithmetic operations on the individual
-@@ -12113,7 +12111,7 @@
+@@ -12802,7 +12800,7 @@
On an image, convolution can be thought of as a process to blur or remove
the contrast in an image. If you are already familiar with the concept and
just want to run Convolve, you can jump to @ref{Convolution kernel} and
definitions and concepts of convolution.
There are generally two methods to convolve an image. The first and
-@@ -12163,7 +12161,7 @@
+@@ -12852,7 +12850,7 @@
* Frequency domain and Fourier operations:: Using frequencies in input.
* Spatial vs. Frequency domain:: When to use which?
* Convolution kernel:: How to specify the convolution kernel.
@end menu
@node Spatial domain convolution, Frequency domain and Fourier operations, Convolve, Convolve
-@@ -13258,7 +13256,7 @@
+@@ -13947,7 +13945,7 @@
frequency domain convolution will significantly improve the processing
time, see @ref{Oversampling}.
@subsection Convolution kernel
All the programs that need convolution will need to be given a
-@@ -13285,7 +13283,7 @@
+@@ -13974,7 +13972,7 @@
process}. All the programs that do convolution will normalize the
kernel internally, so if you choose this option, you don't have to
worry about normalizing the kernel. Only within Convolve, there is an
@end itemize
-@@ -13330,7 +13328,7 @@
+@@ -14019,7 +14017,7 @@
@end table
+@node astconvolve, , Convolution kernel, Convolve
@subsection Invoking Convolve
- Convolve an input image with a known kernel or make the kernel necessary to
-@@ -13587,7 +13585,7 @@
+ Convolve an input dataset (2D image or 1D spectrum for example) with a
+@@ -14296,7 +14294,7 @@
* Warping basics:: Basics of coordinate transformation.
* Merging multiple warpings:: How to merge multiple matrices.
* Resampling:: Warping an image is re-sampling it.
@end menu
@node Warping basics, Merging multiple warpings, Warp, Warp
-@@ -13777,7 +13775,7 @@
+@@ -14486,7 +14484,7 @@
@subsection Resampling
@cindex Pixel
-@@ -13871,7 +13869,7 @@
+@@ -14580,7 +14578,7 @@
applications, see @ref{PSF}.
@subsection Invoking Warp
Warp an input dataset into a new grid. Any homographic warp (for example
-@@ -14063,11 +14061,11 @@
+@@ -14772,11 +14770,11 @@
@item --hstartwcs=INT
Specify the first header keyword number (line) that should be used to read
@item -k
@itemx --keepwcs
-@@ -14157,7 +14155,7 @@
+@@ -14866,7 +14864,7 @@
* Histogram and Cumulative Frequency Plot:: Basic definitions.
* Sigma clipping:: Definition of @mymath{\sigma}-clipping.
* Sky value:: Definition and derivation of the Sky value.
@end menu
-@@ -14180,7 +14178,7 @@
+@@ -14889,7 +14887,7 @@
directly within @TeX{} (the same tool that generates your document).}, or
it can be shown with ASCII characters on the command-line, which is very
crude, but good enough for a fast and on-the-go analysis, see the example
@cindex Intervals, histogram
@cindex Bin width, histogram
-@@ -14219,8 +14217,8 @@
+@@ -14928,8 +14926,8 @@
Statistics program), the number reported for each bin is the total number
of data points until the larger interval value for that bin. You can see an
example histogram and cumulative frequency plot of a single dataset under
So as a summary, both the histogram and cumulative frequency plot in
Statistics will work with bins. Within each bin/interval, the lower value
-@@ -14332,7 +14330,7 @@
+@@ -15041,7 +15039,7 @@
@subsection Sky value
@cindex Sky
-@@ -14611,7 +14609,7 @@
+@@ -15376,7 +15374,7 @@
@subsection Invoking Statistics
Statistics will print statistical measures of an input dataset (table
-@@ -15294,8 +15292,8 @@
+@@ -16082,8 +16080,8 @@
a more complete introduction to NoiseChisel in this book. However,
published papers cannot be updated any more, but the software has
evolved/changed. The changes since publication are documented in
discussed.
As discussed above, detection is one of the most important steps for your
-@@ -15304,7 +15302,7 @@
+@@ -16092,7 +16090,7 @@
@ref{MakeCatalog}). We thus strongly recommend that after reading the
papers above and the respective sections of Gnuastro's book, you play a
little with the settings (in the order presented in the paper and
inspect all the check images (options starting with @option{--check}) to
see the effect of each parameter.
-@@ -15331,10 +15329,10 @@
+@@ -16119,10 +16117,10 @@
@menu
* NoiseChisel changes after publication:: NoiseChisel updates after paper's publication.
@subsection NoiseChisel changes after publication
NoiseChisel was initially introduced in
-@@ -15448,7 +15446,7 @@
+@@ -16261,7 +16259,7 @@
@end itemize
@subsection Invoking NoiseChisel
NoiseChisel will detect signal in noise producing a multi-extension dataset
-@@ -15566,7 +15564,7 @@
+@@ -16379,7 +16377,7 @@
* NoiseChisel output:: NoiseChisel's output options and format.
@end menu
@subsubsection NoiseChisel input
The options here can be used to configure the inputs and output of
-@@ -15706,7 +15704,7 @@
+@@ -16519,7 +16517,7 @@
that is discussed in that section.
@end table
@subsubsection Detection options
Detection is the process of separating the pixels in the image into two
-@@ -16056,7 +16054,7 @@
+@@ -16884,7 +16882,7 @@
@subsubsection NoiseChisel output
NoiseChisel's output is a multi-extension FITS file. The main
-@@ -16314,16 +16312,16 @@
+@@ -17144,16 +17142,16 @@
those papers were published). Therefore this book is the definitive
reference. To help in the transition from those papers to the software you
are using, see @ref{Segment changes after publication}. Finally, in
@subsection Segment changes after publication
Segment's main algorithm and working strategy were initially defined and
-@@ -16418,7 +16416,7 @@
+@@ -17248,7 +17246,7 @@
@end itemize
@subsection Invoking Segment
Segment will identify substructure within the detected regions of an input
-@@ -16484,7 +16482,7 @@
+@@ -17314,7 +17312,7 @@
* Segment output:: Outputs of Segment
@end menu
@subsubsection Segment input
Besides the input dataset (for example astronomical image), Segment also
-@@ -16692,7 +16690,7 @@
+@@ -17522,7 +17520,7 @@
@end table
@subsubsection Segmentation options
The options below can be used to configure every step of the segmentation
-@@ -16852,7 +16850,7 @@
+@@ -17686,7 +17684,7 @@
@end table
@subsubsection Segment output
The main output of Segment are two label datasets (with integer types,
-@@ -17034,8 +17032,8 @@
- will be ignored by MakeCatalog. In other words, the number of rows in
- MakeCatalog's output is already known before running it.
+@@ -17891,8 +17889,8 @@
+ rows in MakeCatalog's output is already known before running it (the
+ maximum value of the labeled dataset).
-Before getting into the details of running MakeCatalog (in @ref{Invoking
-astmkcatalog}, we'll start with a discussion on the basics of its approach
to separating detection from measurements in @ref{Detection and catalog
production}. A very important factor in any measurement is understanding
its validity range, or limits. Therefore in @ref{Quantifying measurement
-@@ -17052,7 +17050,7 @@
+@@ -17909,7 +17907,7 @@
* Quantifying measurement limits:: For comparing different catalogs.
* Measuring elliptical parameters:: Estimating elliptical parameters.
* Adding new columns to MakeCatalog:: How to add new columns.
@end menu
@node Detection and catalog production, Quantifying measurement limits, MakeCatalog, MakeCatalog
-@@ -17549,7 +17547,7 @@
+@@ -18409,7 +18407,7 @@
@subsection Adding new columns to MakeCatalog
MakeCatalog is designed to allow easy addition of different measurements
-@@ -17577,7 +17575,7 @@
+@@ -18437,7 +18435,7 @@
in @file{main.h} (hopefully the comments in the code are clear enough).
In all these different places, the final columns are sorted in the same
column/option to be easily found in all steps. Therefore in adding your new
option, be sure to keep it in the same relative place in the list in all
the separate places (it doesn't necessarily have to be in the end), and
-@@ -17647,7 +17645,7 @@
+@@ -18507,7 +18505,7 @@
@subsection Invoking MakeCatalog
MakeCatalog will do measurements and produce a catalog from a labeled
-@@ -17709,7 +17707,7 @@
- * MakeCatalog output file:: File names of MakeCatalog's output table.
+@@ -18569,7 +18567,7 @@
+ * MakeCatalog output:: File names of MakeCatalog's output table.
@end menu
-@node MakeCatalog inputs and basic settings, Upper-limit settings, Invoking astmkcatalog, Invoking astmkcatalog
@subsubsection MakeCatalog inputs and basic settings
MakeCatalog works by using a localized/labeled dataset (see
-@@ -17785,7 +17783,7 @@
+@@ -18645,7 +18643,7 @@
To summarize: if the input file to MakeCatalog is the default/full output
of Segment (see @ref{Segment output}) you don't have to worry about any of
the @option{--*file} options below. You can just give Segment's output file
NoiseChisel's output into MakeCatalog, just change the labeled dataset's
header (with @option{--hdu=DETECTIONS}). The full list of input dataset
options and general setting options are described below.
-@@ -17878,7 +17876,7 @@
+@@ -18738,7 +18736,7 @@
@end table
--@node Upper-limit settings, MakeCatalog output columns, MakeCatalog inputs and basic settings, Invoking astmkcatalog
-+@node Upper-limit settings, MakeCatalog output columns, MakeCatalog inputs and basic settings, astmkcatalog
+-@node Upper-limit settings, MakeCatalog measurements, MakeCatalog inputs and basic settings, Invoking astmkcatalog
++@node Upper-limit settings, MakeCatalog measurements, MakeCatalog inputs and basic settings, astmkcatalog
@subsubsection Upper-limit settings
The upper-limit magnitude was discussed in @ref{Quantifying measurement
-@@ -18016,7 +18014,7 @@
+@@ -18878,7 +18876,7 @@
@end table
--@node MakeCatalog output columns, MakeCatalog output file, Upper-limit settings, Invoking astmkcatalog
-+@node MakeCatalog output columns, MakeCatalog output file, Upper-limit settings, astmkcatalog
- @subsubsection MakeCatalog output columns
+-@node MakeCatalog measurements, MakeCatalog output, Upper-limit settings, Invoking astmkcatalog
++@node MakeCatalog measurements, MakeCatalog output, Upper-limit settings, astmkcatalog
+ @subsubsection MakeCatalog measurements
The final group of options particular to MakeCatalog are those that specify
-@@ -18378,7 +18376,7 @@
+@@ -19251,7 +19249,7 @@
--@node MakeCatalog output file, , MakeCatalog output columns, Invoking astmkcatalog
-+@node MakeCatalog output file, , MakeCatalog output columns, astmkcatalog
- @subsubsection MakeCatalog output file
+-@node MakeCatalog output, , MakeCatalog measurements, Invoking astmkcatalog
++@node MakeCatalog output, , MakeCatalog measurements, astmkcatalog
+ @subsubsection MakeCatalog output
- When complete, MakeCatalog will store its measurements as a table. If an
-@@ -18481,10 +18479,10 @@
+ After it has completed all the requested measurements (see @ref{MakeCatalog
+@@ -19356,10 +19354,10 @@
orientation.
@menu
@subsection Invoking Match
When given two catalogs, Match finds the rows that are nearest to each
-@@ -18774,7 +18772,7 @@
+@@ -19652,7 +19650,7 @@
* If convolving afterwards:: Considerations for convolving later.
* Flux Brightness and magnitude:: About these measures of energy.
* Profile magnitude:: Definition of total profile magnitude.
@end menu
-@@ -19184,7 +19182,7 @@
+@@ -20064,7 +20062,7 @@
also remove all discrete Fourier transform artifacts (blurred sides) from
the final image. To facilitate this shift, MakeProfiles has the options
@option{--xshift}, @option{--yshift} and @option{--prepforconv}, see
-@@ -19266,7 +19264,7 @@
+@@ -20146,7 +20144,7 @@
magnitude.
@subsection Profile magnitude
@cindex Brightness
-@@ -19307,7 +19305,7 @@
+@@ -20187,7 +20185,7 @@
@subsection Invoking MakeProfiles
MakeProfiles will make any number of profiles specified in a catalog either
-@@ -19387,7 +19385,7 @@
+@@ -20268,7 +20266,7 @@
* MakeProfiles log file:: A description of the optional log file.
@end menu
+@node MakeProfiles catalog, MakeProfiles profile settings, astmkprof, astmkprof
@subsubsection MakeProfiles catalog
The catalog containing information about each profile can be in the FITS
- ASCII, FITS binary, or plain text formats (see @ref{Tables}). Its columns
-@@ -19521,7 +19519,7 @@
+ ASCII, FITS binary, or plain text formats (see @ref{Tables}). The latter
+@@ -20403,7 +20401,7 @@
@end table
@subsubsection MakeProfiles profile settings
The profile parameters that differ between each created profile are
-@@ -19700,7 +19698,7 @@
+@@ -20584,7 +20582,7 @@
@end table
@subsubsection MakeProfiles output dataset
MakeProfiles takes an input catalog uses basic properties that are defined
there to build a dataset, for example a 2D image containing the profiles in
-@@ -19914,7 +19912,7 @@
+@@ -20800,7 +20798,7 @@
@end table
@subsubsection MakeProfiles log file
Besides the final merged dataset of all the profiles, or the individual
-@@ -19969,16 +19967,16 @@
+@@ -20855,16 +20853,16 @@
with MakeProfiles, see @ref{MakeProfiles}. Below, the general
principles and concepts to help understand how noise is quantified is
discussed. MakeNoise options and argument are then discussed in
@subsection Noise basics
@cindex Noise
-@@ -20267,7 +20265,7 @@
+@@ -21158,7 +21156,7 @@
@end cartouche
@subsection Invoking MakeNoise
MakeNoise will add noise to an existing image. The executable name is
-@@ -20384,7 +20382,7 @@
+@@ -21277,7 +21275,7 @@
extra-galactic astronomy, cosmological calculations are necessary. In
Gnuastro, CosmicCalculator is in charge of such calculations. Before
discussing how CosmicCalculator is called and operates (in
mostly self sufficient review of the basics and the equations used in
the analysis. In @ref{Distance on a 2D curved space} the basic idea of
understanding distances in a curved and expanding 2D universe (which
-@@ -20401,7 +20399,7 @@
+@@ -21294,7 +21292,7 @@
@menu
* Distance on a 2D curved space:: Distances in 2D for simplicity
* Extending distance concepts to 3D:: Going to 3D (our real universe).
@end menu
@node Distance on a 2D curved space, Extending distance concepts to 3D, CosmicCalculator, CosmicCalculator
-@@ -20637,7 +20635,7 @@
+@@ -21530,7 +21528,7 @@
@dispmath{ds^2=c^2dt^2-a^2(t)ds_s^2 = c^2dt^2-a^2(t)(d\chi^2+r^2d\phi^2).}
@subsection Extending distance concepts to 3D
The concepts of @ref{Distance on a 2D curved space} are here extended to a
-@@ -20694,7 +20692,7 @@
+@@ -21587,7 +21585,7 @@
@subsection Invoking CosmicCalculator
CosmicCalculator will calculate cosmological variables based on the
-@@ -20746,7 +20744,7 @@
+@@ -21639,7 +21637,7 @@
* CosmicCalculator specific calculations:: Requesting specific outputs.
@end menu
@subsubsection CosmicCalculator input options
The inputs to CosmicCalculator can be specified with the following options:
-@@ -20778,11 +20776,11 @@
+@@ -21671,11 +21669,11 @@
calculations can be useful when you don't want any specific value, but just
a general view. In other contexts (for example in a batch script or during
a discussion), you know exactly what you want and don't want to be
-@@ -21586,10 +21584,10 @@
+@@ -22479,10 +22477,10 @@
@end cartouche
@menu
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