Add new arguments and menu (cba089f2) · Commits · LSS / GALAssify

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

+28 −12

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 +14,27 @@ VERSION = '0.1.4'

		def main():
		args = utils.getOptions(VERSION)
		selectedFiles, selectedGroups = utils.getFiles()
		if not len(sys.argv) > 1:
		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:
		print(args.init)
		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:
		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)

src/galassify/utils.py

+99 −4

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=getPackageResource('img'),
		help="Path to image files.\n")
		parser.add_argument('-c', '--config', type=dir_file, default='config',

		parser.add_argument('-c', '--config', type=dir_file, default=getPackageResource('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', default=getPackageResource('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']""")

		parser.add_argument('group', metavar='GROUP', nargs='*',
		help="Group number. Selects images with name format: img_<group>_*.png\n")

		@@ -51,6 +63,80 @@ def getOptions(version):
		return args


		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:
		print(f"INFO:\t Input example files was created")
		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 Input example files was created")
		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("mkdir img")
		os.system("cd img; mkdir fits; mkdir nog")
		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:
		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(f"cp '{getPackageResource('files/galaxies.csv')}' files/galaxies.csv")
		os.system("mkdir img")
		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}")
		except:
		pass
		print(f"RUN:\t galassify -i files/galaxies.csv -s files/output.csv -p img/ ")
		else:
		try:
		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(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/')}")
		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}")
		except:
		pass
		print(f"RUN:\t galassify -i files/galaxies_fits.csv -s files/output_fits.csv -p img/fits/ ")

		def getVersion():
		global VERSION
		return VERSION
		@@ -116,6 +202,15 @@ 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)