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cube_viewer.py
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cube_viewer.py
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import astropy.units as u
import numpy as np
import os
import pyqtgraph as pg
import sys
from astropy.io import fits
from mpdaf.obj import Cube, Spectrum
from mpdaf.tools import zscale
from pyqtgraph.Qt import QtCore, QtGui
from pyqtgraph.parametertree import Parameter, ParameterTree
SKYREF = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'sky-ref-spectra.fits')
PARAMS = [
{'name': 'Sky', 'type': 'group', 'children': [
{'name': 'Show', 'type': 'bool', 'value': False},
{'name': 'Line Color', 'type': 'str', 'value': 'aaaa'},
]},
{'name': 'Spectrum', 'type': 'group', 'children': [
{'name': 'Line color', 'type': 'str', 'value': 'fffa'},
{'name': 'Lambda Min', 'type': 'int', 'value': 0},
{'name': 'Lambda Max', 'type': 'int', 'value': 100},
{'name': 'Selection color', 'type': 'str', 'value': '3333'},
{'name': 'Show Zoom', 'type': 'bool', 'value': False},
]},
{'name': 'Median filter', 'type': 'group', 'children': [
{'name': 'Show', 'type': 'bool', 'value': False},
{'name': 'Kernel Size', 'type': 'int', 'value': 5},
{'name': 'Line Size', 'type': 'int', 'value': 2},
{'name': 'Line Color', 'type': 'str', 'value': 'r'},
]},
]
class MuseApp(object):
def __init__(self):
self.img = None
self.cube = None
self.spec = None
if os.path.exists(SKYREF):
self.sky = Spectrum(SKYREF)
self.sky.data /= self.sky.data.max()
else:
print('Sky file missing')
self.sky = None
pg.mkQApp()
self.win = win = QtGui.QWidget()
win.setWindowTitle('MUSE Cube Viewer')
# layout = QtGui.QGridLayout()
layout = QtGui.QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
win.setLayout(layout)
self.splitter = QtGui.QSplitter()
self.splitter.setOrientation(QtCore.Qt.Horizontal)
layout.addWidget(self.splitter)
self.tree = ParameterTree(showHeader=False)
self.splitter.addWidget(self.tree)
self.params = Parameter.create(name='params', type='group',
children=PARAMS)
self.tree.setParameters(self.params, showTop=False)
self.tree.setWindowTitle('pyqtgraph example: Parameter Tree')
self.connect(('Median filter', ), self.update_spec_plot)
self.connect(('Sky', ), self.update_spec_plot)
self.connect(('Spectrum', 'Lambda Max'), self.show_image)
self.connect(('Spectrum', 'Lambda Min'), self.show_image)
self.connect(('Spectrum', 'Line color'), self.update_spec_plot)
self.connect(('Spectrum', 'Selection color'), self.update_spec_plot)
self.connect(('Spectrum', 'Show Zoom'), self.add_zoom_window)
self.win_inner = win = pg.GraphicsLayoutWidget()
self.splitter2 = QtGui.QSplitter()
self.splitter2.setOrientation(QtCore.Qt.Vertical)
self.splitter.addWidget(self.win_inner)
# self.img_label = win.addLabel('Hello !', justify='right')
# A plot area (ViewBox + axes) for displaying the white-light image
win.nextRow()
self.white_plot = win.addPlot(title='White-light Image')
self.white_plot.setAspectLocked(lock=True, ratio=1)
self.white_item = pg.ImageItem()
self.white_plot.addItem(self.white_item)
# A plot area (ViewBox + axes) for displaying the image
win.nextColumn()
self.img_plot = win.addPlot(title='Band Image')
self.img_plot.setAspectLocked(lock=True, ratio=1)
self.img_item = pg.ImageItem()
self.img_plot.addItem(self.img_item)
# pg.SignalProxy(self.img_plot.scene().sigMouseMoved, rateLimit=60,
# slot=self.on_mouse_moved)
# Contrast/color control
self.hist = hist = pg.HistogramLUTItem()
hist.setImageItem(self.img_item)
win.addItem(hist)
# self.specplot = win.addPlot(row=2, col=0, colspan=2)
win.nextRow()
self.specplot = win.addPlot(title='Spectrum', colspan=3)
self.zoomplot = None
self.zoomplot_visible = False
# self.lbdareg = region = pg.LinearRegionItem(movable=False)
# self.specplot.addItem(region)
# region.setZValue(10)
self.zoomreg = region = pg.LinearRegionItem()
region.setZValue(10)
self.specplot.addItem(self.zoomreg, ignoreBounds=True)
region.sigRegionChanged.connect(self.update_zoom_spec_from_region)
p = self.params
lmin = p['Spectrum', 'Lambda Min']
lmax = p['Spectrum', 'Lambda Max']
region.setRegion([lmin, lmax])
self.win.resize(1000, 800)
self.win.show()
def connect(self, names, func):
self.params.param(*names).sigTreeStateChanged.connect(func)
def add_zoom_window(self):
if self.zoomplot_visible:
return
else:
self.zoomplot_visible = True
self.win_inner.nextRow()
self.zoomplot = self.win_inner.addPlot(title='Zoomed Spectrum',
colspan=3)
self.zoomplot.setAutoVisible(y=True)
def update_region_from_zoom():
self.zoomreg.setRegion(self.zoomplot.getViewBox().viewRange()[0])
self.zoomplot.sigRangeChanged.connect(update_region_from_zoom)
def update_zoom_spec_from_region(self):
lmin, lmax = self.zoomreg.getRegion()
print('update_zoom_spec_from_region', lmin, lmax)
p = self.params
p['Spectrum', 'Lambda Min'] = int(lmin)
p['Spectrum', 'Lambda Max'] = int(lmax)
if self.zoomplot:
self.zoomplot.plot(self.spec.data.data, clear=True,
pen=self.params['Spectrum', 'Line color'])
# Add the LinearRegionItem to the ViewBox, but tell the ViewBox to
# exclude this item when doing auto-range calculations.
self.specplot.addItem(self.zoomreg, ignoreBounds=True)
self.zoomreg.setZValue(10)
self.zoomplot.setXRange(lmin, lmax, padding=0)
def load_cube(self, filename):
print('Loading cube {} ... '.format(filename), end='')
self.cube = Cube(filename, dtype=None, copy=False)
print('OK')
with fits.open(filename) as hdul:
if 'WHITE' in hdul:
print('Loading white image ... ', end='')
img = hdul['WHITE'].data
print('OK')
else:
print('Creating white-light image ... ', end='')
img = self.cube.mean(axis=0).data.data
print('OK')
self.white_item.setImage(img.T)
# self.white_item.setLevels(zscale(img.data.filled(0)))
self.white_item.setLevels(zscale(img))
self.show_image()
self.add_roi(center=np.array(self.img.shape) / 2)
# zoom to fit image
self.white_plot.autoRange()
self.img_plot.autoRange()
self.update_spec_plot()
def show_image(self):
p = self.params
lmin = p['Spectrum', 'Lambda Min']
lmax = p['Spectrum', 'Lambda Max']
print(f'Creating image {lmin}-{lmax} ... ', end='')
self.img = self.cube[lmin:lmax, :, :].mean(axis=0)
print('OK')
self.img_item.setImage(self.img.data.data.T)
# self.hist.setLevels(self.img.data.min(), self.img.data.max())
self.hist.setLevels(*zscale(self.img.data.filled(0)))
# self.lbdareg.setBrush(self.params['Spectrum', 'Selection color'])
# self.lbdareg.setRegion([self.params['Spectrum', 'Lambda Min'],
# self.params['Spectrum', 'Lambda Max']])
def add_roi(self, center=(0, 0), size=(5, 5)):
# Custom ROI for selecting an image region
size = np.asarray(size) / self.cube.wcs.get_step(unit=u.arcsec)
position = np.asarray(center) - size / 2
self.roi = roi = pg.ROI(position, size, pen=dict(color='g', size=5))
roi.addScaleHandle([0.5, 1], [0.5, 0.5])
roi.addScaleHandle([0, 0.5], [0.5, 0.5])
# roi.addRotateHandle([1, 0], [0.5, 0.5])
self.img_plot.addItem(roi)
roi.setZValue(10) # make sure ROI is drawn above image
roi.sigRegionChangeFinished.connect(self.update_spec_plot)
# def on_mouse_moved(self, evt):
# # using signal proxy turns original arguments into a tuple
# pos = evt[0]
# if self.img_plot.sceneBoundingRect().contains(pos):
# mousePoint = self.img_plot.vb.mapSceneToView(pos)
# pos = list(mousePoint.pos())
# if pos[0] > 0 and pos[0] < self.img.shape[0] and \
# pos[1] > 0 and pos[1] < self.img.shape[1]:
# self.img_label.setText(
# "<span style='font-size: 12pt'>x=%0.1f, "
# "<span style='color: red'>y1=%0.1f</span>, "
# "<span style='color: green'>y2=%0.1f</span>" % (
# mousePoint.x(), mousePoint.y(), 0))
def update_spec_plot(self):
"""Callbacks for handling user interaction"""
if self.img is None:
return
p = self.params
pos = np.array(self.roi.pos(), dtype=int)
size = np.array(self.roi.size(), dtype=int)
imin = np.clip(pos, 0, self.cube.shape[1])
imax = np.clip(pos + size, 0, self.cube.shape[2])
print('Extract mean spectrum for {}'.format(list(zip(imin, imax))))
data = self.cube[:, imin[1]:imax[1], imin[0]:imax[0]]
self.spec = spec = data.mean(axis=(1, 2))
self.specplot.clearPlots()
if p['Sky', 'Show'] and self.sky is not None:
sp = self.sky.data.data * (2 * spec.data.max()) + spec.data.min()
self.specplot.plot(sp, pen=p['Sky', 'Line Color'])
self.specplot.plot(spec.data.data, pen=p['Spectrum', 'Line color'])
if p['Median filter', 'Show']:
sp = spec.median_filter(p['Median filter', 'Kernel Size'])
self.specplot.plot(sp.data.data, pen={
'color': p['Median filter', 'Line Color'],
'width': p['Median filter', 'Line Size']
})
# self.specplot.autoRange()
if self.zoomplot is not None:
self.update_zoom_spec_from_region()
def main():
# Start Qt event loop unless running in interactive mode or using pyside.
if sys.flags.interactive != 1 or not hasattr(QtCore, 'PYQT_VERSION'):
app = MuseApp()
# pg.dbg()
if len(sys.argv) != 2:
print('No cube filename provided ?')
app.load_cube(sys.argv[1])
QtGui.QApplication.instance().exec_()
if __name__ == '__main__':
main()