Add clickable fits image widget. Refactor static image widget. (5e38e8c1) · Commits · LSS / GALAssify

requirements.txt

+1 −0

Original line number	Diff line number	Diff line
		@@ -3,3 +3,4 @@ pyqt5
		pyqt5-tool
		requests
		Pillow
		pyds9

src/gui.py

+39 −23

Original line number	Diff line number	Diff line
		@@ -3,7 +3,7 @@ from PyQt5 import QtWidgets, uic
		from PyQt5.QtCore import Qt, QObject, QEvent, QSize, QCoreApplication
		from PyQt5.QtGui import QPixmap, QIcon
		import pandas as pd
		from src import utils
		from src import utils, widgets
		import sys

		import json
		@@ -61,16 +61,20 @@ class Ui(QtWidgets.QMainWindow):
		policy = QtWidgets.QSizePolicy.Policy
		gb_img:QtWidgets.QWidget = self.findChild(QtWidgets.QGroupBox, 'gb_img')

		# Add clickable image widget
		widget = widgets.ClickableImage()
		gb_img.layout().addWidget(widget, 0, 0, 1, wcols/2) # Full row width
		wcount += wcols/2
		# Save widget:
		self.widget_clickimg = widget

		# Add image container widget
		widget = QtWidgets.QLabel(None)
		widget.setObjectName("imageLabel")
		widget.setSizePolicy(QtWidgets.QSizePolicy(policy.Expanding, policy.Expanding))
		widget.setAlignment(Qt.AlignmentFlag.AlignHCenter \| Qt.AlignmentFlag.AlignVCenter)
		gb_img.layout().addWidget(widget, 0, 0, 1, wcols) # Full row width
		wcount += wcols
		# Save image widget:
		widget = widgets.StaticImage()
		gb_img.layout().addWidget(widget, wcount//wcols, wcount%wcols, 1, wcols/2) # Full row width
		wcount += wcols/2
		# Save widget:
		self.defaultImgPath = Path("res") / Path("image_not_found.png")
		self.imageLabel = widget
		self.widget_staticimg = widget

		# Instances to widget saves
		self.rbg = {} # buttongroups
		@@ -103,14 +107,14 @@ class Ui(QtWidgets.QMainWindow):
		elif wcols-(wcount%wcols) == 1: # last column
		wpol = QtWidgets.QSizePolicy(policy.Maximum, policy.Preferred)
		else:
		wpol = QtWidgets.QSizePolicy(policy.Minimum, policy.Maximum)
		wpol = QtWidgets.QSizePolicy(policy.Minimum, policy.Preferred)

		gb = newGroupBox(id, name, wpol)
		# COMMENTBOX
		if tconf['type'] == 'text':
		widget = QtWidgets.QPlainTextEdit(None)
		widget.setObjectName(f"tb_{id}")
		widget.setSizePolicy(QtWidgets.QSizePolicy(policy.Expanding, policy.Minimum))
		widget.setSizePolicy(QtWidgets.QSizePolicy(policy.Expanding, policy.Preferred))
		addTextBoxTexts(widget, tconf)
		widget.installEventFilter(self) # Set enter as save

		@@ -207,6 +211,8 @@ class Ui(QtWidgets.QMainWindow):

		# Dynamic COLUMNS
		utils.IDS['FILE'] = list(df.columns)
		utils.IDS['WIDGET'] = ['fits_coords']

		utils.IDS['TB'] = list(self.tb.keys())
		for _, cb in self.cb.items():
		utils.IDS['CB'].extend(list(cb.keys()))
		@@ -216,7 +222,7 @@ class Ui(QtWidgets.QMainWindow):
		utils.IDS['RB'].extend(list(rb.keys()))
		utils.IDS['RB'].extend([""])

		utils.COLUMNS = utils.IDS['FILE'] + utils.IDS['RBG'] + utils.IDS['CB'] + utils.IDS['TB']
		utils.COLUMNS = utils.IDS['FILE'] + utils.IDS['WIDGET'] + utils.IDS['RBG'] + utils.IDS['CB'] + utils.IDS['TB']
		for v in ['ra', 'dec']:
		try:
		utils.COLUMNS.remove(v)
		@@ -265,6 +271,7 @@ class Ui(QtWidgets.QMainWindow):
		self.show()

		# self.load_row() # not needed first row loaded on fillList
		self.showImage(self.imgPath) # img appears streched, so refresh img

		# List helpers:

		@@ -355,10 +362,10 @@ class Ui(QtWidgets.QMainWindow):
		if self.has_groups:
		grp = int(self.fileList.item(index, 0).text())
		gal = int(self.fileList.item(index, 1).text())
		item_index = (self.df['group']==grp) & (self.df['galaxy']==gal)
		item_index = self.df.index[(self.df['group']==grp) & (self.df['galaxy']==gal)]
		else:
		gal = int(self.fileList.item(index, 0).text())
		item_index = self.df['galaxy']==gal
		item_index = self.df.index[self.df['galaxy']==gal]

		self.df.loc[item_index, 'processed'] = True
		if self.has_groups:
		@@ -393,6 +400,9 @@ class Ui(QtWidgets.QMainWindow):
		self.df.loc[item_index, id] = tb.toPlainText().replace('\n', '')
		# self.df.loc[item_index, 'comment'] = self.commentBox.toPlainText().replace('\n', '')

		if hasattr(self, 'widget_clickimg'):
		self.df.at[item_index.item(), 'fits_coords'] = self.widget_clickimg.get_coords() # not working with .loc

		self.fileList.selectRow(index+1)

		utils.save_df(self.df)
		@@ -465,6 +475,11 @@ class Ui(QtWidgets.QMainWindow):
		# else:
		# self.commentBox.setPlainText('')

		if hasattr(self, 'widget_clickimg'):
		fname = item['fullpath'].item().parent / Path(item['fits'].item())
		coords = item['fits_coords'].item()
		self.widget_clickimg.new_file(fname, coords)

		except (AttributeError, KeyError) as e:
		print(f"WARNING:\tEmpty item. [{e}]")
		self.imgPath = self.defaultImgPath
		@@ -517,15 +532,16 @@ class Ui(QtWidgets.QMainWindow):
		# Image helpers:

		def showImage(self, imageFile:str) -> None:

		if hasattr(self, 'widget_staticimg'):
		if imageFile and Path.is_file(imageFile):
		pixmap = QPixmap(str(imageFile))
		fname = str(imageFile)
		else:
		pixmap = QPixmap(str(self.defaultImgPath))

		w = self.imageLabel.width()
		h = self.imageLabel.height()
		fname = str(self.defaultImgPath)
		self.widget_staticimg.set_pixmap(QPixmap(fname))

		self.imageLabel.setPixmap(pixmap.scaled(w, h, Qt.KeepAspectRatio, Qt.SmoothTransformation))
		# if hasattr(self, 'widget_clickimg'):
		# self.widget_clickimg.canvas.draw()

		def getIconCell(self, active:bool) -> QtWidgets.QWidget:
		iconLabel = QtWidgets.QLabel()

src/utils.py

+12 −3

Original line number	Diff line number	Diff line
		@@ -249,6 +249,10 @@ def expand_df(selectedFiles):
		'galaxy': int,
		}
		)

		if 'fits_coords' in importData.columns:
		importData['fits_coords'] = importData['fits_coords'].fillna("[]").apply(lambda x: eval(x))

		checkColumnsMismatch(importData.columns.values)
		importData['processed'] = True
		importData['fullpath'] = ''
		@@ -311,6 +315,10 @@ def newEntry(row:pd.Series) -> dict:
		for i, tbCol in enumerate(getTextBoxes()):
		entry.update({tbCol: ''})

		if 'fits' in row:
		entry.update({'fits': row.fits})
		entry.update({'fits_coords': []})

		entry.update(
		{
		'processed': False,
		@@ -333,10 +341,11 @@ def save_df(df:pd.DataFrame) -> None:
		# df.loc[df['processed'] == True]])

		# Remove old values, keep last ones:

		s_cols = ['galaxy']
		if 'group' in processedItems.columns:
		exportData = processedItems.drop_duplicates(['group','galaxy'], keep='last').sort_values('group')
		else:
		exportData = processedItems.drop_duplicates(['galaxy'], keep='last').sort_values('galaxy')
		s_cols.insert(0,'group')
		exportData = processedItems.drop_duplicates(s_cols, keep='last').sort_values(by=s_cols)

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

src/widgets.py

0 → 100644

+159 −0

Original line number	Diff line number	Diff line
		from PyQt5 import QtWidgets
		from PyQt5.QtCore import Qt
		import pandas as pd
		import numpy as np
		from src import utils

		from matplotlib.backends.backend_qt5agg import (
		FigureCanvasQTAgg as FigureCanvas,
		NavigationToolbar2QT as NavigationToolbar
		)

		from matplotlib.figure import Figure

		from astropy.io import fits
		from astropy.wcs import WCS
		from astropy.coordinates import SkyCoord
		from astropy import units as u
		from astropy.visualization import ImageNormalize, BaseInterval, MinMaxInterval, PercentileInterval, ZScaleInterval, AsinhStretch, SqrtStretch, HistEqStretch

		import pyds9 as ds9


		policy = QtWidgets.QSizePolicy.Policy


		class ClickableImage(QtWidgets.QWidget):

		def __init__(self, has_toolbar:bool = True, args, *kwargs):
		super(ClickableImage, self).__init__(args, *kwargs)

		self.setMinimumSize(150,170)
		self.setSizePolicy(QtWidgets.QSizePolicy(policy.Expanding, policy.Expanding))
		#self.setAlignment(Qt.AlignmentFlag.AlignHCenter \| Qt.AlignmentFlag.AlignVCenter)

		# Create internal canvas
		layout = QtWidgets.QGridLayout(self)

		self.figure = Figure()
		self.canvas = FigureCanvas(self.figure)
		self.button = QtWidgets.QPushButton(None)
		self.button.setSizePolicy(QtWidgets.QSizePolicy(policy.Maximum, policy.Fixed))
		self.button.setText("Open DS9")
		self.button.clicked.connect(self.callback_ds9)

		if has_toolbar:
		self.toolbar = NavigationToolbar(self.canvas, coordinates=False)
		layout.addWidget(self.toolbar, 0, 0, 1, 1)
		layout.addWidget(self.button, 0, 1, 1, 1)

		layout.addWidget(self.canvas, 1, 0, 1, 2)
		self.canvas.mpl_connect('button_press_event', self.callback_button_press)

		# funtionality
		def new_file(self, file:str, coords:list = None) -> None:
		self.add_image(file)

		if coords is None or len(coords)==0:
		return
		hdu = self.projection
		for coord in coords:
		ra, dec = coord
		point = SkyCoord(ra, dec, unit=(u.deg, u.deg)).to_pixel(self.projection)
		self.add_point(point)

		def add_image(self, path_img:str):
		# add image
		try:
		with fits.open(path_img) as hdul:
		self.projection = WCS(hdul[0].header)
		data = hdul[0].data
		self.isfits = True
		self.path_img = path_img
		except OSError as e:
		print(e)
		return

		# Add main axes
		if hasattr(self, 'ax'):
		self.ax.remove()
		self.ax = self.figure.add_axes([0,0,1,1], projection=self.projection)
		self.ax.set_axis_off()

		# Add normalized image
		normalize = ImageNormalize(data, interval=PercentileInterval(99.5), stretch=AsinhStretch())
		self.ax.imshow(data, origin='lower', norm=normalize, aspect='equal')

		# Create point arrays and scatter plot
		self.coords = np.empty([0,2], dtype=float)
		self.points = np.empty([0,2], dtype=int)
		self._scatter = self.ax.scatter(None, None, color='r', marker='2')

		# Update canvas
		self.canvas.draw_idle()

		def update_points(self) -> None:
		# print(self.coords, self.points)
		self._scatter.set_offsets(self.points)
		self.canvas.draw_idle()

		def add_point(self, point) -> None:
		if self.isfits:
		hdu = self.projection
		coords = hdu.pixel_to_world(point[0], point[1])
		point_deg = np.round([coords.ra.deg, coords.dec.deg], 6)

		self.coords = np.insert(self.coords, 0, point_deg, axis=0)
		self.points = np.insert(self.points, 0, point, axis=0)
		self.update_points()

		def delete_point(self, point) -> None:
		if self.points.size == 0:
		return
		# find nearest point by euclidean distance
		idx_min = np.sum((self.points-point)**2, axis=1, keepdims=True).argmin(axis=0)

		self.coords = np.delete(self.coords, idx_min, axis=0)
		self.points = np.delete(self.points, idx_min, axis=0)
		self.update_points()

		def get_coords(self):
		"""Convert coords list of lists to list of tuples and return"""
		return [tuple(c) for c in self.coords.tolist()]

		# button callbacks
		def callback_button_press(self, event) -> None:
		x, y = event.xdata, event.ydata
		if x is None or y is None: # out of bounds
		return
		point = [x, y]
		if event.dblclick and event.button == 1: # left doubleclick
		self.add_point(point)
		elif event.dblclick and event.button == 3: # right doubleclick
		self.delete_point(point)

		def callback_ds9(self):
		d = ds9.DS9() # Open ds9 (this assumes no ds9 instance is yet running)
		d.set(f"file '{self.path_img}'") # Load file
		d.set('zoom to fit') # Zoom to fit
		# Change the colormap and scaling
		d.set('cmap bb')
		d.set('scale log')
		# Add a label
		#d.set('regions command {text 30 20 #text="Texto Ejemplo" font="times 18 bold"}')


		class StaticImage(QtWidgets.QLabel):

		def __init__(self, args, *kwargs):
		super(StaticImage, self).__init__(args, *kwargs)

		self.setObjectName("imageLabel")
		self.setMinimumSize(100,100)
		self.setSizePolicy(QtWidgets.QSizePolicy(policy.Expanding, policy.Expanding))
		self.setAlignment(Qt.AlignmentFlag.AlignHCenter \| Qt.AlignmentFlag.AlignVCenter)

		def set_pixmap(self, pixmap) -> None:
		w = self.width()
		h = self.height()
		self.setPixmap(pixmap.scaled(w, h, Qt.KeepAspectRatio, Qt.SmoothTransformation))
		No newline at end of file