Added CSV fill and outputfile option

MIT License

Copyright (c) <year> <copyright holders>

Copyright (c) 2024 <copyright holders>

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

We also provide help tools to:

- Download images from SDSS.

- Create a instructions pdf.

- Create an instructions pdf.

The main tool can be customized with the `config` file. See [Customizing the tool](#customizing-the-tool) for more information.

## Installation

### Creating a virtual environment

Using a virtual enviroment is recommended to execute this tool:

```bash

cd DIR_GALAssify

python -m venv .env

source .env/bin/activate

```

Now, you can choose installing `GALAssify` by using [PIP](#installing-from-pip) or by cloning this repository for [installing from source](#installing-from-source).

### Installing from PIP

Install and update using [pip](https://pip.pypa.io/en/stable/getting-started/):

- For install with [pyds9](https://github.com/ericmandel/pyds9) support:

```

$ pip install "galassify[ds9] @ git+https://gloton.ugr.es/gitlab/lss/galassify.git"

```

- For standard installation:

```

$ pip install git+https://gloton.ugr.es/gitlab/lss/galassify.git

```

Using a virtual enviroment is recommended to execute this tool:

### Installing from source

First, clone the repository:

```bash

cd DIR_GALAssify

python -m venv .env

source .env/bin/activate

git clone https://gloton.ugr.es/gitlab/lss/galassify.git

cd galassify

```

Install requirements:

Then, install `GALAssify` with [pyds9](https://github.com/ericmandel/pyds9) support:

```bash

pip install .[ds9]

```

or without it:

```bash

pip install -r requirements.txt

pip install .

```

 **NOTE:** The installation could fail with the next message if the package `libxt-dev` is not found in your OS:

### Installation troubleshooting

The installation could fail with the next message if the package `libxt-dev` is not found in your OS:

```bash

xtloop.c:9:10: fatal error: X11/Intrinsic.h: No such file or directory

    9 | #include <X11/Intrinsic.h>

- Debian / Ubuntu: `sudo apt-get install libxt-dev`

- Fedora: `sudo dnf install libXt-devel`

Then, run again: `pip install -r requirements.txt`

Then, try installing `GALAssify` again using you prefered method.

## Usage

To run the included example, execute the following command on the installation directory (with the activated enviroment):

```python

python galassify.py -i files/galaxies.csv -s files/output.csv -p img/ 

galassify -i files/galaxies.csv -s files/output.csv -p img/ 

```

For the main tool check:

```python

python galassify.py --help

galassify --help

```

For helper tools check:

```python

python get_images_sdss.py --help

get_images_sdss --help

```

## Input data

- filename: name of the image file to be displayed in the tool. Relative to the image path specified on execution.

- fits: name of the fits file to be displayed in the tool. Relative to the image path specified on execution.

Example: `galaxies.csv`

```csv

group,galaxy,ra,dec,filename

1,15,210.927048,-1.137346,img_1_15_.jpeg

1,254,211.020782,0.998166,img_1_254.jpeg

...

```

## Customizing the tool

[build-system]

requires = ["setuptools>=61.0"]

build-backend = "setuptools.build_meta"

[project]

name = "galassify"

version = "0.1.4"

authors = [

  { name="Manuel Alcázar-Laynez", email="manalclay@ugr.es"},

  { name="Andoni Jimenez", email="andonijimenez@ugr.es"},

  { name="Salvador Duarte Puertas", email="sduarte@ugr.es"},

  { name="Cristian Pozo González", email="cpozo@ugr.es"},

  { name="Jesús Domínguez-Gómez", email="jesusdg@ugr.es"},

  { name="Guillermo Blázquez", email="gblazquez@iaa.es"},

  { name="Maria del Carmen Argudo-Fernández", email="margudo@ugr.es"},

  { name="Simon Verley", email="simon@ugr.es"},

  { name="Daniel Espada", email="despada@ugr.es"},

  { name="Estrella Florido", email="estrella@ugr.es"},

  { name="Isabel Pérez", email="isa@ugr.es"},

  { name="Tomás Ruiz-Lara", email="tomasruizlara@gmail.com"},

  { name="Almudena Zurita", email="azurita@ugr.es"}

]

maintainers = [

  { name="Manuel Alcázar-Laynez", email="manalclay@ugr.es"},

  { name="Andoni Jimenez", email="andonijimenez@ugr.es"},

  { name="Salvador Duarte Puertas", email="sduarte@ugr.es"},

  { name="Cristian Pozo González", email="cpozo@ugr.es"},

  { name="Jesús Domínguez-Gómez", email="jesusdg@ugr.es"},

  { name="Guillermo Blázquez", email="gblazquez@iaa.es"},

  { name="Maria del Carmen Argudo-Fernández", email="margudo@ugr.es"},

  { name="Simon Verley", email="simon@ugr.es"}

]

description = "A tool to manually classify galaxies"

readme = {file = "README.md", content-type = "text/markdown"}

license = {file = "LICENSE"}

requires-python = ">=3.8"

keywords = ["astronomy", "astrophysics", "classification", "galaxies"]

classifiers = [

    "Programming Language :: Python :: 3",

    "License :: OSI Approved :: MIT License",

    "Operating System :: OS Independent",

    "Development Status :: 5 - Production/Stable",

    "Environment :: X11 Applications :: Qt",

    "Intended Audience :: Science/Research",

    "Topic :: Scientific/Engineering :: Astronomy",

    "Topic :: Scientific/Engineering :: Physics",

    "Topic :: Scientific/Engineering :: Visualization"

]

dependencies = [

  'pandas>=2.0',

  'PyQt5>=5.15',

  'matplotlib>=3.7',

  'astropy>=5.3',

  'requests>=2.31',

  'Pillow>=9.5'

]

[project.optional-dependencies]

ds9 = ['pyds9>=1.8.1']

[tools.setuptools]

include_package_data = true

[tool.setuptools.package-dir]

galassify = "src/galassify"

get_images_sdss = 'src/get_images_sdss'

[tool.setuptools.packages.find]

where = ["src"]

include = ["galassify*", "get_images_sdss*"]

[tool.setuptools.package-data]

galassify = [

  "img/*.jpeg",

  "img/fits/*.fits",

  "img/nog/*.jpeg",

  "files/*.csv",

  "res/*.png",

  "*.ui",

  "config"

]

[project.gui-scripts]

galassify = "galassify.galassify:main"

[project.scripts]

get_images_sdss = "get_images_sdss.get_images_sdss:main"

[project.urls]

Homepage = "https://gitlab.com/astrogal/GALAssify"

Issues = "https://gitlab.com/astrogal/GALAssify/-/issues"

 No newline at end of file

pandas==2.0.1

PyQt5==5.15.9

matplotlib==3.7.1

astropy==5.3

requests==2.31.0

Pillow==9.5.0

pyds9==1.8.1