Commit 7ac08608 authored by Manuel Luis Alcazar Laynez's avatar Manuel Luis Alcazar Laynez
Browse files

Added Cristian modifications

parent cba089f2

src/galassify/utils.py

+31 −14
Original line number Diff line number Diff line 
import os

import re

import sys

import os.path as path

import glob

import argparse

from pathlib import Path
@@ -31,10 +32,10 @@ def getOptions(version): 


    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=getPackageResource('img'),

    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=getPackageResource('config'),

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

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

    

    #parser.add_argument('-f', '--filename', nargs='+',
@@ -50,7 +51,7 @@ def getOptions(version): 
    parser.add_argument("-l", "--list", action="store_true",

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

    

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

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

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

                        Minimum required columns: ['galaxy'].

                        Recomended columns: ['group', 'galaxy', 'ra', 'dec',  'filename' and/or 'fits']""")
@@ -62,6 +63,18 @@ def getOptions(version): 
    VERSION = version

    return args



def exist_basic_files():

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

    test_files = True;

    for file in files:

        print(path.exists(file))

        if not path.exists(file):

            test_files = False;

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

        if not path.exists('files/galaxies_fits.csv'):

            test_files = False;

    print(test_files)

    return test_files



def load_menu():
@@ -74,7 +87,6 @@ def load_menu(): 
    menu = SelectorMenu(options, title='GALAssify: A tool to manually classify galaxies.')

    ans = menu.input()

    if ans.index==0:

        print(f"INFO:\t Input example files was created")

        select_option = 0

        #return(0)

    elif ans.index==1:
@@ -94,24 +106,27 @@ def load_menu(): 
    return select_option



def init_flag():

    print(f"INFO:\t Input example files was created")

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

    try:

        os.system("mkdir files")

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

        os.system('cd files; echo "group,galaxy,ra,dec,filename,fits" >> galaxies_fits.csv')

        os.system('cd files; echo "group,galaxy,filename,morphology,large,tiny,faceon,edgeon,star,calibration,recentre,duplicated,member,hiiregion,yes,no,comment" >> output.csv')

        os.system('cd files; echo "group,galaxy,filename,fits,fits_coords,morphology,large,tiny,faceon,edgeon,star,calibration,recentre,duplicated,member,hiiregion,yes,no,comment" >> output_fits.csv')

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

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

        #os.system('cd files; echo "group,galaxy,ra,dec,filename,fits" >> galaxies_fits.csv')

        #os.system('cd files; echo "group,galaxy,filename,morphology,large,tiny,faceon,edgeon,star,calibration,recentre,duplicated,member,hiiregion,yes,no,comment" >> output.csv')

        #os.system('cd files; echo "group,galaxy,filename,fits,fits_coords,morphology,large,tiny,faceon,edgeon,star,calibration,recentre,duplicated,member,hiiregion,yes,no,comment" >> output_fits.csv')

        os.system("mkdir img")

        os.system("cd img; mkdir fits; mkdir nog")

        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

    print(f"RUN:\t 'galassify -i files/galaxies.csv -s files/output.csv -p img/' or 'galassify -i files/galaxies_fits.csv -s files/output_fits.csv -p img/'")



def example_flag(type_example):

    if type_example == 'basic':

        try:

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

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

            os.system("mkdir files")

            os.system('cd files; echo "group,galaxy,filename,morphology,large,tiny,faceon,edgeon,star,calibration,recentre,duplicated,member,hiiregion,yes,no,comment" >> output.csv')

            #os.system('cd files; echo "group,galaxy,filename,morphology,large,tiny,faceon,edgeon,star,calibration,recentre,duplicated,member,hiiregion,yes,no,comment" >> output.csv')

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

            os.system("mkdir img")

            content=glob.glob(f"{getPackageResource('img/')}")
@@ -119,13 +134,15 @@ def example_flag(type_example): 
            for element in content:

                elemet_dir = getPackageResource('img/'+element)

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

        except:

            pass

        print(f"RUN:\t galassify -i files/galaxies.csv -s files/output.csv -p img/ ")

    else:

        try:

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

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

            os.system("mkdir files")

            os.system('cd files; echo "group,galaxy,filename,fits,fits_coords,morphology,large,tiny,faceon,edgeon,star,calibration,recentre,duplicated,member,hiiregion,yes,no,comment" >> output_fits.csv')

            #os.system('cd files; echo "group,galaxy,filename,fits,fits_coords,morphology,large,tiny,faceon,edgeon,star,calibration,recentre,duplicated,member,hiiregion,yes,no,comment" >> output_fits.csv')

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

            os.system("mkdir img; cd img; mkdir fits")            

            content=glob.glob(f"{getPackageResource('img/fits/')}")
@@ -133,9 +150,9 @@ def example_flag(type_example): 
            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_fits.csv -s files/output.csv -p img/ ")

        except:

            pass

        print(f"RUN:\t galassify -i files/galaxies_fits.csv -s files/output_fits.csv -p img/fits/ ")



def getVersion():

    global VERSION