Commit 6a8855a6 authored by Manuel Luis Alcazar Laynez's avatar Manuel Luis Alcazar Laynez
Browse files

Merge branch 'clickable-image' into 9-get_images_sdss-update-the-csv-with-the-img-path

parents d35e5a90 70feffd3

LICENSE

+1 −1
Original line number Diff line number Diff line 
MIT License



Copyright (c) 2024 <copyright holders>

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:

pyproject.toml

+2 −1
Original line number Diff line number Diff line
@@ -52,7 +52,8 @@ dependencies = [ 
  'matplotlib>=3.7',

  'astropy>=5.3',

  'requests>=2.31',

  'Pillow>=9.5'

  'Pillow>=9.5',

  'PyConsoleMenu>=1.0'

]



[project.optional-dependencies]

src/galassify/galassify.py

+26 −3
Original line number Diff line number Diff line
@@ -5,6 +5,7 @@ 
#######################################################



import sys

import os

from PyQt5 import QtWidgets

from . import utils

from . import gui
@@ -13,12 +14,32 @@ VERSION = '0.1.4' 


def main():

    args = utils.getOptions(VERSION)

    selectedFiles, selectedGroups = utils.getFiles()

    if not len(sys.argv) > 1:

        if utils.exist_basic_files():

            run_gui(args)

        else:    

            selec = utils.load_menu()

            if selec == 0:

                utils.init_flag()            

            elif selec == 10:

                utils.example_flag('basic')

            elif selec == 11:

                utils.example_flag('fits')

    else:

        if args.init:

            utils.init_flag()

        elif args.example != '':

            print(f"INFO:\t Create the {args.example} example files")

            utils.example_flag(args.example)

        else:

            run_gui(args)





def run_gui(args):

    selectedFiles, selectedGroups = utils.getFiles()

    if len(selectedFiles) > 0:

        if args.list:

            print(selectedFiles.filename)



        else:

            print(f"INFO:\t {str(len(selectedFiles))} galaxies found in selected group(s).")

            df = selectedFiles # utils.expand_df(selectedFiles)
@@ -26,7 +47,9 @@ def main(): 
            window = gui.Ui(df, selectedGroups)

            app.exec_()

    else:

        print('ERROR: No files found with the arguments given.')

        print('ERROR:\tNo files found with the arguments given.')

        print('HINT:\tDid you populate your .csv file?')





if __name__ == '__main__':

    sys.exit(main())
 
 No newline at end of file

src/galassify/utils.py

+110 −6
Original line number Diff line number Diff line 
import os

import re

import sys

import glob

import argparse

from pathlib import Path

import pandas as pd

import pkg_resources

from PyConsoleMenu import SelectorMenu





import warnings

from typing import Union
@@ -21,28 +24,37 @@ def getOptions(version): 
    global VERSION



    parser = argparse.ArgumentParser(prog='GALAssify', description="GALAssify: Tool to manually classify galaxies.")



    parser.add_argument('--version', action='version', version='%(prog)s ' + version,

                        help="Prints software version and exit.\n")

    parser.add_argument('-p', '--path', type=dir_path, default='img',



    parser.add_argument('--init',action='store_true',help='Generate a basic config file, and the basic folder structure.')



    parser.add_argument('--example', type=example_type, default='', help='Run a galassify (basic or fits) example.')

    

    parser.add_argument('-p', '--path', type=dir_path, default='img/',

                        help="Path to image files.\n")

    

    parser.add_argument('-c', '--config', type=dir_file, default='config',

                        help="Config json file to load.\n")

    

    #parser.add_argument('-f', '--filename', nargs='+',

    #                    required=not('-p' in sys.argv

    #                    or '--path' in sys.argv

    #                    or '--version' in sys.argv), type=dir_file,

    #                    help="Image or list to classify. Not required if path or path + group are given.\n")



    parser.add_argument('-s', '--savefile',

                        #required=not('--version' in sys.argv),

                        default='output.csv',

                        help="CSV file to load and export changes. If does not exists, a new one is created.\n")

    parser.add_argument("-l", "--list", action="store_true",

                        help="List selected files only and exit.\n")

    parser.add_argument('-i', '--inputfile', default='galaxies.csv', type=dir_file,

    

    parser.add_argument('-i', '--inputfile', type=dir_file, default='files/galaxies.csv',

                        help="""Galaxy database file in *.csv format.

                        Minimum required columns: ['galaxy'].

                        Recomended columns: ['group', 'galaxy', 'ra', 'dec',  'filename' and/or 'fits']""")

    

    parser.add_argument('group', metavar='GROUP', nargs='*',

                        help="Group number. Selects images with name format: img_<group>_*.png\n")
@@ -50,6 +62,84 @@ def getOptions(version): 
    VERSION = version

    return args



def exist_basic_files():

    files = ['files/','img/','config']

    test_files = True

    for file in files:

        if not Path(file).exists():

            test_files = False

    if not Path('files/galaxies.csv').exists:

        test_files = False

    return test_files



def load_menu():    

    

    global select_option

    select_option = 3



    options = ["INIT (--init):\t Generate a basic config file, and the basic folder structure.", 

                "EXAMPLE (--example):\t Generate a files whit a galassify example", 

                "EXIT"]

    menu = SelectorMenu(options, title='GALAssify: A tool to manually classify galaxies.')

    ans = menu.input()

    if ans.index==0:

        select_option = 0

        #return(0)

    elif ans.index==1:

        options_2 = ["BASIC (--example basic):\t Load the images example", 

                    "FITS (--example fits):\t Load the images fits example", 

                    "BACK"]

        menu_2 = SelectorMenu(options_2, title='GALAssify Example: Generate a files whit a galassify example')

        ans_2 = menu_2.input()

        if (ans_2.index==0):

            select_option = 10

            #return(10)

        elif (ans_2.index==1):

            select_option = 11

            #return(11)

        else:

            load_menu()

    return select_option



def init_flag():

    print(f"INFO:\t Generating the necessary files...")

    try:

        os.system(f"cp '{getPackageResource('config')}' config")

        os.system("mkdir -p files img/fits")

        os.system('echo "group,galaxy,ra,dec,filename,fits" >> files/galaxies.csv')

        print(f"INFO:\t The necessary files were created. \nINFO:\t Now, complete de input files and open GALAssify with: galassify -i files/galaxies.csv -s files/output.csv -p img/ ")

    except:

        pass



def example_flag(type_example):

    print(f"INFO:\t Generating the necessary files...")

    try:

        # Copy common files

        os.system(f"cp '{getPackageResource('config')}' config")

        os.system("mkdir -p files img")



        # Copy and create example-specific files

        if type_example == 'basic':

            os.system(f"cp '{getPackageResource('files/galaxies.csv')}' files/galaxies.csv")

            content = glob.glob(f"{getPackageResource('img/')}")

            content = [f for f in os.listdir(f"{getPackageResource('img/')}") if re.match(r'.*\.jpeg', f)]

            for element in content:

                elemet_dir = getPackageResource('img/'+element)

                os.system(f"cp '{elemet_dir}' img/{element}")



        else:

            os.system(f"cp '{getPackageResource('files/galaxies_fits.csv')}' files/galaxies.csv")

            os.system("mkdir -p img/fits")

            content=glob.glob(f"{getPackageResource('img/fits/')}")

            content = [f for f in os.listdir(f"{getPackageResource('img/fits/')}") if re.match(r'.*\.fits', f)]

            for element in content:

                elemet_dir = getPackageResource('img/fits/'+element)

                os.system(f"cp '{elemet_dir}' img/fits/{element}")



        print(f"INFO:\t The necessary files were created. \nINFO:\t Now, open GALAssify with: galassify -i files/galaxies.csv -s files/output.csv -p img/ ")

        print(f"INFO:\t If needed, you can download catalogue images by executing: get_images_sdss -i files/galaxies.csv -p img/ ")

    except Exception as e:

        print(f"ERROR: Error while creating the necessary files: {e}")



def getVersion():

    global VERSION
@@ -74,7 +164,8 @@ def getFiles(): 
    

    if imgpath:

        fname = args.inputfile

        if Path(fname).is_file():

        file = Path(fname)

        if file.is_file():

            groups = readInputFile(fname)

        else:

            groups = createInputFile(imgpath, fname)
@@ -116,16 +207,29 @@ def getFiles(): 
    #    files = []

    return selectedFiles, selectedGroups



def example_type(type_text):

    if type_text == 'basic':

        return(type_text)

    elif type_text == 'fits':

        return(type_text)

    elif type_text == '':

        return(type_text)

    else:

        raise argparse.ArgumentTypeError(f"readable_example_type: {type_text} is not a valid example type.")



def dir_path(path):

    d = Path(path)

    if not d.is_dir():

    if path == 'img/':

        return path

    elif not d.is_dir():

        raise argparse.ArgumentTypeError(f"readable_dir: {path} is not a valid path.")

    return path



def dir_file(file):

    d = Path(file)

    if not d.is_file():

    if file == 'config' or file == 'files/galaxies.csv':

        return file

    elif not d.is_file():

        raise argparse.ArgumentTypeError(f"readable_file: {file} is not a valid file.")

    return file