Merge branch 'rename-gui-texts' into 'main' (cd522c5a) · Commits · LSS / GALAssify

galassify.py

+3 −4

Original line number	Diff line number	Diff line
		@@ -13,18 +13,17 @@ VERSION = '0.1.2'

		if __name__ == '__main__':
		args = utils.getOptions(VERSION)
		selectedFiles, selectedVoids = utils.getFiles()
		selectedFiles, selectedGroups = utils.getFiles()

		if len(selectedFiles) > 0:
		if args.list:
		print(selectedFiles.filename)

		else:
		print('INFO:\t' + str(len(selectedFiles)) + ' galaxies found '+
		'in selected voids.')
		print(f"INFO:\t {str(len(selectedFiles))} galaxies found in selected groups.")
		df = utils.expand_df(selectedFiles)
		app = QtWidgets.QApplication(sys.argv)
		window = gui.Ui(df, selectedVoids)
		window = gui.Ui(df, selectedGroups)
		app.exec_()
		else:
		print('ERROR: No files found with the arguments given.')

src/gui.py

+13 −13

Original line number	Diff line number	Diff line
		@@ -8,16 +8,16 @@ import sys


		class Ui(QtWidgets.QMainWindow):
		def __init__(self, df, selectedVoids):
		def __init__(self, df, selectedGroups):
		super(Ui, self).__init__()
		uic.loadUi(str(Path('src')/Path('gui.ui')), self)

		self.title = 'CAVIssify ' + utils.getVersion()
		self.title = 'GALAssify ' + utils.getVersion()
		self.setWindowIcon(QIcon(str(Path('res/window_icon.png'))))

		# Load data frame and make it accessible along the class:
		self.df = df
		self.voids = selectedVoids
		self.galaxies = selectedGroups

		# Find buttons:
		self.pb_prev = self.findChild(QtWidgets.QPushButton, 'pb_prev')
		@@ -93,10 +93,10 @@ class Ui(QtWidgets.QMainWindow):
		def fillList(self, showAllSavedData=False):
		#self.fileList.setRowCount(len(self.df.index))
		self.fileList.setColumnCount(6)
		self.fileList.setHorizontalHeaderLabels(['Void',
		self.fileList.setHorizontalHeaderLabels(['Group',
		'Galaxy',
		'Processed',
		'RA',
		'Ra',
		'Dec',
		'Filename'])
		self.fileList.horizontalHeaderItem(2).setTextAlignment(Qt.AlignHCenter)
		@@ -119,7 +119,7 @@ class Ui(QtWidgets.QMainWindow):
		for i, row in self.df.iterrows():
		# Place void data in integer format:
		self.fileList.setItem(i, 0, QtWidgets.QTableWidgetItem())
		self.fileList.item(i, 0).setData(Qt.DisplayRole, int(row['void']))
		self.fileList.item(i, 0).setData(Qt.DisplayRole, int(row['group']))

		# Place galaxy data in integer format:
		self.fileList.setItem(i, 1, QtWidgets.QTableWidgetItem())
		@@ -137,7 +137,7 @@ class Ui(QtWidgets.QMainWindow):
		# Place filename in the row:
		self.fileList.setItem(i, 5, QtWidgets.QTableWidgetItem(str(row['filename'])))

		if (not showAllSavedData) and (int(row['void']) not in self.voids):
		if (not showAllSavedData) and (int(row['group']) not in self.galaxies):
		self.fileList.hideRow(i)

		# Order by RA coordinate:
		@@ -200,10 +200,10 @@ class Ui(QtWidgets.QMainWindow):
		item = self.df.loc[self.df['filename'] == fn]
		self.imgPath = item['fullpath'].item()

		v = str(item['void'].item())
		g = str(item['galaxy'].item())
		self.setWindowTitle('V: ' + v +
		' \| G: ' + g +
		grp = str(item['group'].item())
		gal = str(item['galaxy'].item())
		self.setWindowTitle('Grp: ' + grp +
		' \| Gal: ' + gal +
		' \| ' + self.title)

		self.fileList.setCellWidget(index, 2,
		@@ -259,8 +259,8 @@ class Ui(QtWidgets.QMainWindow):
		def toggleAIDVisibility(self):
		showAllSavedData = self.act_allSavedData.isChecked()
		for i in range(self.fileList.rowCount()):
		rowVoid = self.fileList.item(i, 0).text()
		if (not showAllSavedData) and (int(rowVoid) not in self.voids):
		row = self.fileList.item(i, 0).text()
		if (not showAllSavedData) and (int(row) not in self.galaxies):
		self.fileList.hideRow(i)
		else:
		self.fileList.showRow(i)

src/gui.ui

+1 −1

Original line number	Diff line number	Diff line
		@@ -583,7 +583,7 @@
		</widget>
		<action name="action_vn">
		<property name="text">
		<string>Void number...</string>
		<string>Group number...</string>
		</property>
		</action>
		<action name="action_folder">

src/utils.py

+72 −55

Original line number	Diff line number	Diff line
		@@ -13,13 +13,13 @@ from typing import Union
		args = None
		VERSION = ''
		importData = pd.DataFrame()
		voids = pd.DataFrame()
		groups = pd.DataFrame()

		def getOptions(version):
		global args
		global VERSION

		parser = argparse.ArgumentParser(prog='CAVYssify', description="CAVYssify: Tool to manually classify void galaxies.")
		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")
		@@ -29,17 +29,17 @@ def getOptions(version):
		# 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 + void are given.\n")
		# 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('-vf', '--voidsfile', default='voids.csv',
		help="Voids database file in *.csv format.\n")
		parser.add_argument('void', metavar='VOID', type=int, nargs='+',
		help="Void number. Selects images with name format: _<void>__*.png\n")
		parser.add_argument('-vf', '--inputfile', default='galaxies.csv',
		help="Galaxy database file in *.csv format.\n")
		parser.add_argument('group', metavar='GROUP', type=int, nargs='*',
		help="Group number. Selects images with name format: _<group>__*.png\n")

		args = parser.parse_args()
		VERSION = version
		@@ -53,28 +53,33 @@ def getVersion():

		def getFiles():
		global args
		global voids
		files = []
		selectedVoids = []
		selectedFiles = pd.DataFrame()
		global groups
		# files = []
		selectedGroups = []
		selectedFiles = pd.DataFrame(columns = groups.columns)

		if args.path:
		if Path(args.voidsfile).is_file():
		voids = readVoidsFile()
		if Path(args.inputfile).is_file():
		groups = readInputFile()
		else:
		voids = createVoidsFile()
		groups = createInputFile()

		availableGroups = groups.group.unique()
		print(f"INFO:\tAvailable groups: {str(availableGroups)}")

		availableVoids = voids.void.unique()
		print('INFO:\tAvailable voids: ' + str(availableVoids))

		if len(args.void) > 0:
		for void in args.void:
		if void in availableVoids:
		selectedFiles = pd_concat(selectedFiles, voids[voids.void == void])
		#selectedFiles = selectedFiles.append(voids[voids.void == void ])
		selectedVoids.append(int(void))
		if len(args.group) > 0:
		for group in args.group:
		if group in availableGroups:
		selectedFiles = pd_concat(selectedFiles, groups[groups.group == group])
		selectedGroups.append(int(group))
		else:
		print(f'WARNING:\tGroup {group} not available.')
		else:
		print('WARNING:\tVoid ', void, 'not available.')
		print(f'INFO:\tNo subgroup selected. Using all available by default.')
		selectedFiles = groups.copy()
		selectedGroups = availableGroups

		#else:
		# formats = ['*.png']

		@@ -88,8 +93,7 @@ def getFiles():

		#else:
		# files = []

		return selectedFiles, selectedVoids
		return selectedFiles, selectedGroups


		def dir_path(path):
		@@ -109,49 +113,51 @@ def dir_file(file):
		raise argparse.ArgumentTypeError("readable_file:" + file
		+ " is not a valid file.")

		VFCOLUMNS = ['void','galaxy','ra','dec','filename']
		VFCOLUMNS = ['group','galaxy','ra','dec','filename']

		def readVoidsFile():
		print('INFO:\tReading from voids.csv file... ', end='', flush=True)
		voids = pd.read_csv(args.voidsfile,
		def readInputFile():
		fname = args.inputfile
		print(f'INFO:\tReading from {fname} file... ', end='', flush=True)
		groups = pd.read_csv(fname,
		converters={
		'void': int,
		'group': int,
		'galaxy': int,
		'ra': float,
		'dec': float,
		}
		)
		voids = voids.sort_values(by=['void', 'ra', 'galaxy'])
		groups = groups.sort_values(by=['group', 'ra', 'galaxy'])
		print('Done!')
		return voids
		return groups

		def createVoidsFile():
		print('INFO:\tCreating voids.csv file... ', end='', flush=True)
		voids = pd.DataFrame(columns=VFCOLUMNS)
		def createInputFile():
		fname = args.inputfile
		print(f'INFO:\tCreating {fname} file... ', end='', flush=True)
		groups = pd.DataFrame(columns=VFCOLUMNS)
		if args.path:
		for file in Path(args.path).glob('pan___ppak.png'):
		entry = {
		'void': int(file.stem.split('_')[1]),
		'group': int(file.stem.split('_')[1]),
		'galaxy': int(file.stem.split('_')[2]),
		'ra':float(0),
		'dec':float(0),
		'filename': str(file.name),
		}
		voids = pd_concat(voids, entry)
		#voids = voids.append(entry, ignore_index=True)
		voids = voids.sort_values(by=['void','galaxy'])
		voids.to_csv(args.voidsfile, columns=VFCOLUMNS, index=False)
		groups = pd_concat(groups, entry)
		#groups = groups.append(entry, ignore_index=True)
		groups = groups.sort_values(by=['group','galaxy'])
		groups.to_csv(fname, columns=VFCOLUMNS, index=False)
		print('Done!')
		return voids
		return groups


		### PANDAS UTILS


		COLUMNS = ["filename", "void", "galaxy", "morphology", "large", "tiny", "faceon",
		COLUMNS = ["filename", "group", "galaxy", "morphology", "large", "tiny", "faceon",
		"edgeon", "star", "calibration", "recentre", "duplicated",
		"member", "hiiregion", "yes", "no", "comment", "processed",
		"fullpath"]
		"fullpath", "ra", "dec"]

		MORPHOLOGY = ['elliptical', 'spiral', 'irregular', 'other', '']

		@@ -169,11 +175,11 @@ def getRadioButtonsMorphology():


		def getCheckBoxesColumns():
		return COLUMNS[4:-3]
		return COLUMNS[4:-5]


		def getExportableColumns():
		return COLUMNS[:-2]
		return COLUMNS[:-4]


		def checkColumnsMismatch(importDataColumns):
		@@ -194,11 +200,11 @@ def checkColumnsMismatch(importDataColumns):
		def expand_df(selectedFiles):
		global args
		global importData
		global voids
		global groups
		if Path(args.savefile).is_file():
		importData = pd.read_csv(args.savefile,
		converters={
		'void': int,
		'group': int,
		'galaxy': int,
		}
		)
		@@ -227,8 +233,8 @@ def expand_df(selectedFiles):
		processedUnselectedData = importData[importData.fullpath == '']
		for i, row in processedUnselectedData.iterrows():
		file = Path(args.path) / Path(row['filename'])
		ra = voids.loc[voids.galaxy == row.galaxy].ra.item()
		dec = voids.loc[voids.galaxy == row.galaxy].dec.item()
		ra = groups.loc[groups.galaxy == row.galaxy].ra.item()
		dec = groups.loc[groups.galaxy == row.galaxy].dec.item()
		importData.loc[importData.galaxy == row.galaxy, 'fullpath'] = file.absolute()
		importData.loc[importData.galaxy == row.galaxy, 'ra'] = ra
		importData.loc[importData.galaxy == row.galaxy, 'dec'] = dec
		@@ -248,7 +254,7 @@ def newEntry(row):
		file = Path(args.path) / Path(row['filename'])
		entry = {
		'filename': file.name,
		'void': row.void,
		'group': row.group,
		'galaxy': row.galaxy,
		'morphology': MORPHOLOGY[-1],
		}
		@@ -279,14 +285,14 @@ def save_df(df):
		# df.loc[df['processed'] == True]])

		# Remove old values, keep last ones:
		exportData = processedItems.drop_duplicates(['void','galaxy'],keep='last').sort_values('void')
		exportData = processedItems.drop_duplicates(['group','galaxy'],keep='last').sort_values('group')

		# Export final dataframe:
		exportData.to_csv(args.savefile, columns=getExportableColumns(),
		index=False)

		def pd_concat(df: pd.DataFrame, data: Union[pd.DataFrame, list, dict]) -> pd.DataFrame:
		""" Concats data in an array to the given dataframe
		""" Concats data to the given dataframe

		Parameters
		----------
		@@ -296,7 +302,9 @@ def pd_concat(df: pd.DataFrame, data: Union[pd.DataFrame, list, dict]) -> pd.Dat
		data: list, dict or pandas.Dataframe
		Data to be concatenated to the input pandas Dataframe.
		- List of the values to be concatenated (order of input values and Dataframe columns must match).
		- Dict of the key:values, where keys match the Dataframe columns.
		- Dict of the 'key:values', where keys match the Dataframe columns (if not, values are put to NaN).
		- pandas.Dataframe where columns (should) match the input Dataframe
		(if not, new columns are created or values are put to NaN).

		Returns
		-------
		@@ -309,9 +317,18 @@ def pd_concat(df: pd.DataFrame, data: Union[pd.DataFrame, list, dict]) -> pd.Dat
		df_data = pd.DataFrame([data], columns=df.columns)
		elif type(data) == dict:
		if len(data) != len(df.columns):
		warnings.warn('Input data [dict] missing input dataframe keys. Missing values insterted as NaN')
		warnings.warn('Input data [dict] missing input dataframe keys. Missing values inserted as NaN')
		print(list(data.keys()))
		print(list(df.columns))
		df_data = pd.DataFrame([data])
		elif type(data) == pd.DataFrame:
		if not df.empty:
		cmp_df_data = list(df.keys()[~df.keys().isin(data.keys())])
		cmp_data_df = list(data.keys()[~data.keys().isin(df.keys())])
		if len(cmp_df_data) > 0:
		warnings.warn(f'Input data missing input dataframe column. {cmp_df_data}')
		if len(cmp_data_df) > 0:
		warnings.warn(f'Input data column(s) not in input dataframe. {cmp_data_df}')
		df_data = data

		df = pd.concat([df, df_data], ignore_index=True)