From 6fa839d4b80472c6aedb18aaa86450be7fcd7ea2 Mon Sep 17 00:00:00 2001 From: James Nightingale Date: Fri, 20 Sep 2024 10:31:39 +0100 Subject: [PATCH] docs --- README.rst | 2 +- docs/howtogalaxy/chapter_2_modeling.rst | 4 ++-- docs/index.rst | 6 ++---- docs/installation/overview.rst | 2 +- docs/overview/overview_1_start_here.rst | 26 ++++++++++++------------- docs/overview/overview_3_features.rst | 17 +++++++++++----- 6 files changed, 31 insertions(+), 26 deletions(-) diff --git a/README.rst b/README.rst index dc6fa8ac..c1bf2bd5 100644 --- a/README.rst +++ b/README.rst @@ -40,7 +40,7 @@ Getting Started The following links are useful for new starters: -- `The PyAutoGalaxy readthedocs `_, which includes `an overview of PyAutoGalaxy's core features `_, `a new user starting guide `_ and `an installation guide `_. +- `The PyAutoGalaxy readthedocs `_, which includes `an overview of PyAutoGalaxy's core features `_, `a new user starting guide `_ and `an installation guide `_. - `The introduction Jupyter Notebook on Binder `_, where you can try **PyAutoGalaxy** in a web browser (without installation). diff --git a/docs/howtogalaxy/chapter_2_modeling.rst b/docs/howtogalaxy/chapter_2_modeling.rst index b25118c5..d912944d 100644 --- a/docs/howtogalaxy/chapter_2_modeling.rst +++ b/docs/howtogalaxy/chapter_2_modeling.rst @@ -1,5 +1,5 @@ -Chapter 2: Lens Modeling -======================== +Chapter 2: Modeling +=================== In chapter 2, we'll take you through how to model galaxies using a non-linear search. diff --git a/docs/index.rst b/docs/index.rst index 263dc175..fa62d8d3 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,9 +1,7 @@ What is PyAutoGalaxy? ===================== -``PyAutoGalaxy`` is an open-source Python 3.9 - 3.12 package for analysing the morphologies and structures of large -multi-wavelength galaxy samples. **PyAutoGalaxy** makes it simple to model galaxies, for example this Hubble Space -Telescope imaging of a spiral galaxy: +**PyAutoGalaxy** is software for analysing the morphologies and structures of galaxies: |pic1| @@ -21,7 +19,7 @@ Getting Started The following links are useful for new starters: -- `The PyAutoGalaxy readthedocs `_, which includes `an overview of PyAutoGalaxy's core features `_, `a new user starting guide `_ and `an installation guide `_. +- `The PyAutoGalaxy readthedocs `_, which includes `an overview of PyAutoGalaxy's core features `_, `a new user starting guide `_ and `an installation guide `_. - `The introduction Jupyter Notebook on Binder `_, where you can try **PyAutoGalaxy** in a web browser (without installation). diff --git a/docs/installation/overview.rst b/docs/installation/overview.rst index 4b627287..87beb953 100644 --- a/docs/installation/overview.rst +++ b/docs/installation/overview.rst @@ -3,7 +3,7 @@ Overview ======== -**PyAutoGalaxy** requires Python 3.9 - 3.11 and support the Linux, MacOS and Windows operating systems. +**PyAutoGalaxy** requires Python 3.9 - 3.12 and support the Linux, MacOS and Windows operating systems. **PyAutoGalaxy** can be installed via the Python distribution `Anaconda `_ or using `PyPI `_ to ``pip install`` **PyAutoGalaxy** into your Python distribution. diff --git a/docs/overview/overview_1_start_here.rst b/docs/overview/overview_1_start_here.rst index 21fe6d6a..5d7a399d 100644 --- a/docs/overview/overview_1_start_here.rst +++ b/docs/overview/overview_1_start_here.rst @@ -5,7 +5,9 @@ Start Here **PyAutoGalaxy** is software for analysing the morphologies and structures of galaxies: -![HST Image](https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/paper/hstcombined.png) +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/paper/hstcombined.png + :width: 400 + :alt: Alternative text **PyAutoGalaxy** has three core aims: @@ -26,8 +28,6 @@ You'll see these imports in the majority of workspace examples. .. code:: python - # %matplotlib inline - import autogalaxy as ag import autogalaxy.plot as aplt @@ -57,7 +57,7 @@ We make and plot a uniform Cartesian grid: The ``Grid2D`` looks like this: .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/0_grid.png - :width: 400 + :width: 600 :alt: Alternative text Light Profiles @@ -112,7 +112,7 @@ for fits to large datasets. The light profile appears as follows: .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/1_image_2d.png - :width: 400 + :width: 600 :alt: Alternative text Galaxy @@ -146,7 +146,7 @@ The ``GalaxyPlotter`` object plots the image of the galaxy, which is the sum of The galaxy, with both a bulge and disk, appears as follows: .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/2_image_2d.png - :width: 400 + :width: 600 :alt: Alternative text One example of the plotter's customizability is the ability to plot the individual light profiles of the galaxy @@ -159,7 +159,7 @@ on a subplot. The light profiles appear as follows: .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/3_subplot_image.png - :width: 400 + :width: 600 :alt: Alternative text @@ -190,7 +190,7 @@ the galaxy is used below where the ``Sersic`` is passed directly to the ``Galaxy galaxies_plotter.figures_2d(image=True) .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/4_image_2d.png - :width: 400 + :width: 600 :alt: Alternative text Extensibility @@ -244,7 +244,7 @@ To further illustrate this, we create a merging galaxy system with 4 star formin The image of the merging galaxy system appears as follows: .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/5_image_2d.png - :width: 400 + :width: 600 :alt: Alternative text Simulating Data @@ -317,7 +317,7 @@ import dataset attributes like the noise-map and PSF. The observed dataset appears as follows: .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/6_data.png - :width: 400 + :width: 600 :alt: Alternative text If you have come to **PyAutoGalaxy** to perform interferometry, the API above is easily adapted to use @@ -363,7 +363,7 @@ and the plot axis automatically zooms in around the mask. Here is the masked dataset: .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/7_data.png - :width: 400 + :width: 600 :alt: Alternative text Fitting @@ -422,7 +422,7 @@ In this example, the galaxies used to simulate the data are used to fit it, thus as shown by the subplots below: .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/10_subplot_fit.png - :width: 400 + :width: 600 :alt: Alternative text The overall quality of the fit is quantified with the ``log_likelihood``. @@ -585,7 +585,7 @@ Here is an example corner plot of the model-fit, which shows the probability den model: .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/cornerplot.png - :width: 400 + :width: 600 :alt: Alternative text Wrap Up diff --git a/docs/overview/overview_3_features.rst b/docs/overview/overview_3_features.rst index 05b532c3..2f619211 100644 --- a/docs/overview/overview_3_features.rst +++ b/docs/overview/overview_3_features.rst @@ -9,12 +9,19 @@ Firstly, brief one sentence descriptions of each feature are given, with more de links to the relevant workspace examples. **Interferometry**: Modeling of interferometer data (e.g. ALMA, LOFAR) directly in the uv-plane. + **Multi-Wavelength**: Simultaneous analysis of imaging and / or interferometer datasets observed at different wavelengths. + **Ellipse Fitting**: Fitting ellipses to determine a galaxy's ellipticity, position angle and centre. + **Multi Gaussian Expansion (MGE)**: Decomposing a galaxy into hundreds of Gaussians, capturing more complex structures than simple light profiles. + **Shapelets**: Decomposing a galaxy into a set of shapelet orthogonal basis functions, capturing more complex structures than simple light profiles. + **Sky Background**: Including the background sky in the model to ensure robust fits to the outskirts of galaxies. + **Operated Light Profiles**: Assuming a light profile has already been convolved with the PSF, for when the PSF is a significant effect. + **Pixelizations**: Reconstructing a galaxy's on a mesh of pixels, to capture extremely irregular structures like spiral arms. Interferometry @@ -23,7 +30,7 @@ Interferometry Modeling interferometer data from submillimeter (e.g. ALMA) and radio (e.g. LOFAR) observatories: .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/paper/almacombined.png - :width: 400 + :width: 600 :alt: Alternative text Visibilities data is fitted directly in the uv-plane, circumventing issues that arise when fitting a dirty image @@ -60,7 +67,7 @@ Ellipse fitting is a technique which fits many ellipses to a galaxy's emission t angle and centre, without assuming a parametric form for its light (e.g. a Sersic profile): .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_3/ellipse.png - :width: 400 + :width: 600 :alt: Alternative text This provides complementary information to parametric light profile fitting, for example giving insights on whether @@ -79,7 +86,7 @@ Multi Gaussian Expansion (MGE) An MGE decomposes the light of a galaxy into tens or hundreds of two dimensional Gaussians: .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_3/mge.png - :width: 400 + :width: 600 :alt: Alternative text In the image above, 30 Gaussians are shown, where their sizes go from below the pixel scale (in order to resolve @@ -97,7 +104,7 @@ Shapelets Shapelets are a set of orthogonal basis functions that can be combined the represent galaxy structures: .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoLens/main/docs/overview/images/overview_3/shapelets.png - :width: 400 + :width: 600 :alt: Alternative text Scientific Applications include capturing symmetric structures in a galaxy which are more complex than a Sersic profile, @@ -142,7 +149,7 @@ fitted accurately using light profiles, whereas its asymmetric and irregular spi captured using a rectangular mesh: .. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/paper/hstcombined.png - :width: 400 + :width: 600 :alt: Alternative text Checkout ``autogalaxy_workspace/notebooks/features/pixelizations.ipynb`` to learn how to use a pixelization, however