Merge branch 'clickable-image' (5b3ab0c9) · Commits · LSS / GALAssify

LICENSE

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		MIT License

		Copyright (c) 2024, GALAssify contributors

		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:

		The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

		THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

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		GALAssify
		==========
		# GALAssify

		A tool to manually classify galaxies.
		A tool to manually classify galaxies

		We also provide a help tools to:
		<img src="instructions/GALAssify.png" alt="galassyfy_default" height="700px">

		We also provide help tools to:
		- Download images from SDSS.
		- Create a instructions pdf.
		- Create an instructions pdf.

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

		<!--
		<!-- toc -->
		<!--
		- [Requirements](#requirements)
		- [Installation](#installation)
		- [Usage](#usage)
		- [Customizing the tool](#customizing-the-tool)
		- [Tag groups](#tag-groups)
		- [Tag group elements](#tag-group-elements)
		-->
		<!-- /toc -->

		Installing
		----------
		## Requirements

		Install and update using [pip](https://pip.pypa.io/en/stable/getting-started/):
		GALAssify is written in Python. The following requirements are mandatory:

		```
		$ pip install git+https://gloton.ugr.es/gitlab/lss/GALAssify.git
		```
		* Python `>=3.9`
		* pandas
		* pyqt5
		* matplotlib
		* Pillow
		* astropy
		* pyds9 (to open fits files directly form the tool)
		* requests (used by the help tool to download sdss images)

		Should work with `python >= 3.9`. Feel free to try for lower versions.

		Usage
		-----
		## 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
		pip install -r requirements.txt
		```
		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
		```

		### Installing from source

		First, clone the repository:
		```bash
		git clone https://gloton.ugr.es/gitlab/lss/galassify.git
		cd galassify
		```
		Then, install `GALAssify` with [pyds9](https://github.com/ericmandel/pyds9) support:
		```bash
		pip install .[ds9]
		```
		or without it:
		```bash
		pip install .
		```

		### 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>
		\| ^~~~~~~~~~~~~~~~~
		```
		To solve that, you can install it with the following commands:

		- openSUSE: `sudo zypper install libXt-devel`
		- Debian / Ubuntu: `sudo apt-get install libxt-dev`
		- Fedora: `sudo dnf install libXt-devel`

		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
		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

		Minimum required columns:
		- galaxy: identifier or name of the galaxy

		Additional columns:
		- group: identifier or name of the group/person to which the galaxy was assigned. Used to filter the galaxies when executing the tool.
		- 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

		GALAssify tags can be customized to meet users needs. The default `config` file provides the configuration used to perform the galaxy sample selection in the [CAVITY](https://cavity.caha.es/) (Calar Alto Void Integral-field Treasury surveY) project.

		### Tag groups

		Tags are grouped depending on the needs, each of this groups correspond to one type. The available types are:

		- radiobutton: group of elements were only one element can be selected
		- checkbox: group of elements were each element can be checked independetly
		- text: a textbox to add comments

		### Tag group options

		Each group type mentioned above has options that can (or must) be changed.
		Options marked as `optional` are not required but provide a better customization and user experience.

		Common options for all group types:

		- id: group identifier. Must be unique as it will be used on the output csv file.
		- name (optional, default: id is used): Text to be used on the tool.
		- type: Type to be used to initalize the group (one of the above).

		Options that only apply for the `text` type group:
		- shortcut (optional, default: None) :Key press to be used to focus on the comment-box. Must be unique, and not used in other groups/group-elements.
		- save (unimplemented, [Enter] is used currently): Key press to be used to save the content, only used if focus is set on the group.
		- discard (unimplemented, [Esc] is used currently): Key press to be used to discard the content, only used if focus is set on the group.

		Options that only apply for the `radiobutton` type groups:
		- add_clear (optional, default: false): Boolean indicating to add a clear button to the group. Not added by default.
		- clear_shortcut (optional): Key press to be used to clear on the radiobutton group. Must be unique, and not used in other groups/group-elements.

		Options that apply for the `radiobutton` and `checkbox` type groups:
		- ncolumns (optional, default: 2): number of columns to be used to display the elements.
		- elements: list on elements to be included.

		### Tag element options

		Each element has the following options:

		- id: element identifier. Must be unique as it will be used on the output csv file.
		- name (optional, default: id is used): Text to be used on the tool.
		- shortcut (optional, default: None): Key press to be used to check on the element.
		- description (optional, default: None): Short text to be displayed when the mouse is over the element.
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pyproject.toml

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		[build-system]
		requires = ["setuptools>=61.0"]
		build-backend = "setuptools.build_meta"

		[project]
		name = "galassify"
		version = "0.1.5"
		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',
		'PyConsoleMenu>=1.0'
		]

		[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"
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src/galassify/init.py

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src/galassify/config

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		[{
		"id":"morphology",
		"name":"Morphology",
		"type":"radiobutton",
		"ncolumns":1,
		"add_clear":true,
		"clear_shortcut":"F9",
		"elements":[{
		"id":"elliptical",
		"name":"Elliptical",
		"shortcut":"F5",
		"description":"<b>Elliptical</b> or <b>lenticular</b> galaxies."
		},{
		"id":"spiral",
		"name":"Spiral",
		"shortcut":"F6",
		"description":"<b>Disc</b> galaxy."
		},{
		"id":"irregular",
		"name":"Irregular",
		"shortcut":"F7",
		"description":"<b>Irregular</b> galaxy."
		},{
		"id":"other",
		"name":"Other",
		"shortcut":"F8",
		"description":"<b>Star</b> or <b>HII region</b> for instance."
		}
		]
		},
		{
		"id":"tags",
		"name":"Tags",
		"type":"checkbox",
		"ncolumns":2,
		"elements":[{
		"id":"large",
		"name":"Large",
		"shortcut":"L",
		"description":"The galaxy is <b>too large</b> and does not entirely fit within the main hexagon."
		},{
		"id":"tiny",
		"name":"Tiny",
		"shortcut":"T",
		"description":"The galaxy is <b>too small</b>"
		},{
		"id":"faceon",
		"name":"Face-on",
		"shortcut":"F",
		"description":"The galaxy is <b>too face-on</b>\n(inclination near 0 degrees)."
		},{
		"id":"edgeon",
		"name":"Edge-on",
		"shortcut":"E",
		"description":"The galaxy is <b>too edge-on</b>\n(inclination near 90 degrees)."
		},{
		"id":"star",
		"name":"Star",
		"shortcut":"S",
		"description":"There is at least one relatively <b>bright star</b> in the main hexagon."
		},{
		"id":"calibration",
		"name":"Calibration",
		"shortcut":"C",
		"description":"There is at least <b>one bright star</b>, possibly saturated in PPak, <b>in at least one</b> of the six surrounding, small <b>calibration hexagons</b>."
		},{
		"id":"recentre",
		"name":"Recentre",
		"shortcut":"R",
		"description":"The galaxy is <b>not well centred</b> in the main hexagon <b>or</b> two or <b>more galaxies would fit</b> within the main hexagonal footprint if it is recentred."
		},{
		"id":"duplicated",
		"name":"Duplicated",
		"shortcut":"D",
		"description":"The galaxy <b>appears several times</b>.\nMark as \"duplicated\" the ones to remove."
		},{
		"id":"member",
		"name":"Member",
		"shortcut":"M",
		"description":"The galaxy is a <b>member of</b> a pair, triplet, group or <b>system of galaxies</b>."
		},{
		"id":"hiiregion",
		"name":"HII Region",
		"shortcut":"H",
		"description":"The main hexagon is <b>centred</b> on an <b>HII region</b>."
		},{
		"id":"yes",
		"name":"Yes",
		"shortcut":"Y",
		"description":"You <b>really want</b> this galaxy in the final sample."
		},{
		"id":"no",
		"name":"No",
		"shortcut":"N",
		"description":"You <b>really do not want</b> this galaxy in the final sample."
		}
		]
		},
		{
		"id":"comment",
		"name":"Comments",
		"type":"text",
		"shortcut":"F1",
		"save":"Enter",
		"discard":"Esc"
		}
		]
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