Commit 70feffd3 authored by Manuel Luis Alcazar Laynez's avatar Manuel Luis Alcazar Laynez
Browse files

Merge branch '7-add-a-init-and-a-example-options-for-users' into clickable-image

parents c79b75cd 5abc9a5d

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