def test_navigate():
# Init
nav_dict = dict(nav=ltgu.navigate(0,0,init=True))
assert isinstance(nav_dict['nav'], list)
nav_dict['x_minmax'] = [0., 1]
nav_dict['y_minmax'] = [0., 1]
nav_dict['sv_xy_minmax'] = [[0,1], [0,1]]
nav_dict['tmp_xy'] = None
# Usage
o = type(str('Dummy'), (object,), {})
o.xdata = 22.
o.ydata = 1.
for key in nav_dict['nav']:
o.key = key
ltgu.navigate(nav_dict, o)
def test_navigate():
# Init
nav_dict = dict(nav=ltgu.navigate(0, 0, init=True))
assert isinstance(nav_dict["nav"], list)
nav_dict["x_minmax"] = [0.0, 1]
nav_dict["y_minmax"] = [0.0, 1]
nav_dict["sv_xy_minmax"] = [[0, 1], [0, 1]]
nav_dict["tmp_xy"] = None
# Usage
o = type(str("Dummy"), (object,), {})
o.xdata = 22.0
o.ydata = 1.0
for key in nav_dict["nav"]:
o.key = key
ltgu.navigate(nav_dict, o)
def on_key(self,event):
# Init
rescale = True
flg = 0
## NAVIGATING
if event.key in self.psdict['nav']:
flg = ltgu.navigate(self.psdict,event)
if event.key in ['b','t','W','Z','Y','l','r']:
rescale = False
self.on_draw(rescale=rescale)
def on_key(self, event):
# Init
rescale = True
flg = 0
## NAVIGATING
if event.key in self.psdict['nav']:
flg = ltgu.navigate(self.psdict, event)
if event.key in ['b', 't', 'W', 'Z', 'Y', 'l', 'r']:
rescale = False
self.on_draw(rescale=rescale)
def __init__(self,
spec,
z,
wrest,
parent=None,
vmnx=[-300., 300.] * u.km / u.s,
norm=True,
linelist=None):
'''
spec = Spectrum1D
'''
super(AODMWidget, self).__init__(parent)
# Initialize
self.spec = spec
self.norm = norm
self.z = z
self.vmnx = vmnx
self.wrest = wrest # Expecting (requires) units
self.lines = []
if linelist is None:
self.linelist = LineList('ISM')
for iwrest in self.wrest:
self.lines.append(AbsLine(iwrest, linelist=self.linelist))
self.psdict = {} # Dict for spectra plotting
self.psdict[
'x_minmax'] = self.vmnx.value # Too painful to use units here
self.psdict['y_minmax'] = [-0.1, 1.1]
self.psdict['nav'] = ltgu.navigate(0, 0, init=True)
# Create the mpl Figure and FigCanvas objects.
#
self.dpi = 150
self.fig = Figure((8.0, 4.0), dpi=self.dpi)
self.canvas = FigureCanvas(self.fig)
self.canvas.setParent(self)
self.canvas.setFocusPolicy(QtCore.Qt.ClickFocus)
self.canvas.setFocus()
self.canvas.mpl_connect('key_press_event', self.on_key)
self.canvas.mpl_connect('button_press_event', self.on_click)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.canvas)
self.setLayout(vbox)
# Draw on init
self.on_draw()
def init_spec(self):
""" Initialize parameters for plotting the spectrum
"""
#xy min/max
xmin = np.min(self.spec.dispersion.value)
xmax = np.max(self.spec.dispersion.value)
from linetools.spectra.plotting import get_flux_plotrange
ymin, ymax = get_flux_plotrange(self.spec.flux.value)
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
self.psdict['x_minmax'] = np.array([xmin, xmax])
self.psdict['y_minmax'] = [ymin, ymax]
self.psdict['sv_xy_minmax'] = [[xmin, xmax], [ymin, ymax]]
self.psdict['tmp_xy'] = None
self.psdict['nav'] = ltgu.navigate(0, 0, init=True)
# Analysis dict
self.adict['flg'] = 0 # Column density flag
def __init__(self, spec, z, wrest, parent=None, vmnx=[-300., 300.]*u.km/u.s,
norm=True, linelist=None):
'''
spec = Spectrum1D
'''
super(AODMWidget, self).__init__(parent)
# Initialize
self.spec = spec
self.norm = norm
self.z = z
self.vmnx = vmnx
self.wrest = wrest # Expecting (requires) units
self.lines = []
if linelist is None:
self.linelist = LineList('ISM')
for iwrest in self.wrest:
self.lines.append(AbsLine(iwrest,linelist=self.linelist))
self.psdict = {} # Dict for spectra plotting
self.psdict['xmnx'] = self.vmnx.value # Too painful to use units here
self.psdict['ymnx'] = [-0.1, 1.1]
self.psdict['nav'] = ltgu.navigate(0,0,init=True)
# Create the mpl Figure and FigCanvas objects.
#
self.dpi = 150
self.fig = Figure((8.0, 4.0), dpi=self.dpi)
self.canvas = FigureCanvas(self.fig)
self.canvas.setParent(self)
self.canvas.setFocusPolicy( QtCore.Qt.ClickFocus )
self.canvas.setFocus()
self.canvas.mpl_connect('key_press_event', self.on_key)
self.canvas.mpl_connect('button_press_event', self.on_click)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.canvas)
self.setLayout(vbox)
# Draw on init
self.on_draw()
def on_key(self, event):
""" Deals with key events
Parameters
----------
event : event object
"""
# Flag to control re-draw
flg = -1
# NAVIGATING
if event.key in self.psdict['nav']:
flg = ltgu.navigate(self.psdict, event)
# DOUBLETS
if event.key in ['C', 'M', 'X', '4', '8', 'B']:
wave = ltgu.set_doublet(self, event)
#print('wave = {:g},{:g}'.format(wave[0], wave[1]))
self.ax.plot([wave[0], wave[0]], self.psdict['y_minmax'], '--', color='red')
self.ax.plot([wave[1], wave[1]], self.psdict['y_minmax'], '--', color='red')
flg = 2 # Layer
## SMOOTH
if event.key == 'S':
self.spec = self.spec.box_smooth(2)
flg = 1
if event.key == 'U':
self.spec = self.orig_spec
flg = 1
## Lya Profiles
if event.key in ['D', 'R']:
# Set NHI
if event.key == 'D':
NHI = 10**20.3 * u.cm**-2
elif event.key == 'R':
NHI = 10**19.0 * u.cm**-2
zlya = event.xdata/1215.6701 - 1.
self.llist['z'] = zlya
# Generate Lya profile
lya_line = AbsLine(1215.6701*u.AA)
lya_line.attrib['z'] = zlya
lya_line.attrib['N'] = NHI
lya_line.attrib['b'] = 30. * u.km/u.s
self.lya_line = ltv.voigt_from_abslines(self.spec.dispersion,
lya_line, fwhm=3.)
self.adict['flg'] = 4
# QtCore.pyqtRemoveInputHook()
# import pdb; pdb.set_trace()
# QtCore.pyqtRestoreInputHook()
flg = 1
# ANALYSIS: AODM, EW, Stats, Gaussian
if event.key in ['N', 'E', '$', 'G']:
# If column check for line list
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
if (event.key in ['N', 'E']) & (self.llist['List'] == 'None'):
print('xspec: Choose a Line list first!')
try:
self.statusBar().showMessage('Choose a Line list first!')
except AttributeError:
pass
self.adict['flg'] = 0
return
flg = 1
if self.adict['flg'] == 0:
self.adict['wv_1'] = event.xdata # wavelength
self.adict['C_1'] = event.ydata # continuum
self.adict['flg'] = 1 # Plot dot
else:
self.adict['wv_2'] = event.xdata # wavelength
self.adict['C_2'] = event.ydata # continuum
self.adict['flg'] = 2 # Ready to plot + print
# Sort em + make arrays
iwv = np.array(sorted([self.adict['wv_1'],
self.adict['wv_2']])) * self.spec.wcs.unit
ic = np.array(sorted([self.adict['C_1'],
self.adict['C_2']]))
# Calculate the continuum (linear fit)
param = np.polyfit(iwv, ic, 1)
cfunc = np.poly1d(param)
self.spec.conti = cfunc(self.spec.dispersion)
if event.key == '$': # Simple stats
pix = self.spec.pix_minmax(iwv)[0]
mean = np.mean(self.spec.flux[pix])
median = np.median(self.spec.flux[pix])
stdv = np.std(self.spec.flux[pix]-self.spec.conti[pix])
S2N = median / stdv
mssg = 'Mean={:g}, Median={:g}, S/N={:g}'.format(
mean,median,S2N)
elif event.key == 'G': # Fit a Gaussian
# Good pixels
pix = self.spec.pix_minmax(iwv)[0]
# EW
EW = np.sum(self.spec.conti[pix]-self.spec.flux[pix])
if EW > 0.: # Absorption line
sign=-1
else: # Emission
sign=1
# Amplitude
Aguess = np.max(self.spec.flux[pix]-self.spec.conti[pix])
Cguess = np.mean(self.spec.dispersion[pix])
sguess = 0.1*np.abs(self.adict['wv_1']-self.adict['wv_2'])
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
#QtCore.pyqtRestoreInputHook()
g_init = models.Gaussian1D(amplitude=Aguess, mean=Cguess, stddev=sguess)
fitter = fitting.LevMarLSQFitter()
parm = fitter(g_init, self.spec.wavelength[pix].value,
sign*(self.spec.flux[pix]-self.spec.conti[pix]))
g_final = models.Gaussian1D(amplitude=parm.amplitude.value, mean=parm.mean.value, stddev=parm.stddev.value)
# Plot
model_Gauss = g_final(self.spec.dispersion.value)
self.model = XSpectrum1D.from_tuple((self.spec.wavelength, self.spec.conti + sign*model_Gauss))
# Message
mssg = 'Gaussian Fit: '
mssg = mssg+' :: Mean={:g}, Amplitude={:g}, sigma={:g}, flux={:g}'.format(
parm.mean.value, parm.amplitude.value, parm.stddev.value,
parm.stddev.value*(parm.amplitude.value-np.median(self.spec.conti[pix]))*np.sqrt(2*np.pi))
else:
# Find the spectral line (or request it!)
rng_wrest = iwv / (self.llist['z']+1)
gdl = np.where( (self.llist[self.llist['List']].wrest-rng_wrest[0]) *
(self.llist[self.llist['List']].wrest-rng_wrest[1]) < 0.)[0]
if len(gdl) == 1:
wrest = self.llist[self.llist['List']].wrest[gdl[0]]
else:
if len(gdl) == 0: # Search through them all
gdl = np.arange(len(self.llist[self.llist['List']]))
sel_widg = ltgl.SelectLineWidget(self.llist[self.llist['List']]._data[gdl])
sel_widg.exec_()
line = sel_widg.line
#wrest = float(line.split('::')[1].lstrip())
quant = line.split('::')[1].lstrip()
spltw = quant.split(' ')
wrest = Quantity(float(spltw[0]), unit=spltw[1])
# Units
if not hasattr(wrest,'unit'):
# Assume Ang
wrest = wrest * u.AA
# Generate the Spectral Line
aline = AbsLine(wrest,linelist=self.llist[self.llist['List']])
aline.attrib['z'] = self.llist['z']
aline.analy['spec'] = self.spec
# AODM
if event.key == 'N':
# Calculate the velocity limits and load-up
aline.analy['vlim'] = const.c.to('km/s') * (
( iwv/(1+self.llist['z']) - wrest) / wrest )
# AODM
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
aline.measure_aodm()
mssg = 'Using '+ aline.__repr__()
mssg = mssg + ' :: logN = {:g} +/- {:g}'.format(
aline.attrib['logN'], aline.attrib['sig_logN'])
elif event.key == 'E': #EW
aline.analy['wvlim'] = iwv
aline.measure_restew()
mssg = 'Using '+ aline.__repr__()
mssg = mssg + ' :: Rest EW = {:g} +/- {:g}'.format(
aline.attrib['EW'].to(mAA), aline.attrib['sig_EW'].to(mAA))
# Display values
try:
self.statusBar().showMessage(mssg)
except AttributeError:
pass
print(mssg)
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
"""
## Velocity plot
if event.key == 'v':
z=self.llist['z']
# Check for a match in existing list and use it if so
if len(self.abs_sys) > 0:
zabs = np.array([abs_sys.zabs for abs_sys in self.abs_sys])
mt = np.where( np.abs(zabs-z) < 1e-4)[0]
else:
mt = []
if len(mt) == 1:
ini_abs_sys = self.abs_sys[mt[0]]
outfil = ini_abs_sys.absid_file
self.vplt_flg = 0 # Old one
print('Using existing ID file {:s}'.format(outfil))
else:
ini_abs_sys = None
outfil = None
if self.llist['List'] == 'None':
print('Need to set a line list first!!')
self.vplt_flg = -1 # Nothing to do here
return
self.vplt_flg = 1 # New one
# Outfil
if outfil is None:
i0 = self.spec.filename.rfind('/')
i1 = self.spec.filename.rfind('.')
if i0 < 0:
path = './ID_LINES/'
else:
path = self.spec.filename[0:i0]+'/ID_LINES/'
outfil = path + self.spec.filename[i0+1:i1]+'_z'+'{:.4f}'.format(z)+'_id.fits'
d = os.path.dirname(outfil)
if not os.path.exists(d):
os.mkdir(d)
self.outfil = outfil
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
# Launch
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
gui = xsgui.XVelPltGui(self.spec, z=z, outfil=outfil, llist=self.llist,
abs_sys=ini_abs_sys, norm=self.norm,
sel_wv=self.xval*self.spec.wcs.unit)
gui.exec_()
if gui.flg_quit == 0: # Quit without saving (i.e. discarded)
self.vplt_flg = 0
else:
# Push to Abs_Sys
if len(mt) == 1:
self.abs_sys[mt[0]] = gui.abs_sys
else:
self.abs_sys.append(gui.abs_sys)
print('Adding new abs system')
# Redraw
flg=1
"""
# Dummy keys
if event.key in ['shift', 'control', 'shift+super', 'super+shift']:
flg = 0
# Draw
if flg==1: # Default is not to redraw
self.on_draw()
elif flg==2: # Layer (no clear)
self.on_draw(replot=False)
elif flg==-1: # Layer (no clear)
try:
self.statusBar().showMessage('Not a valid key! {:s}'.format(event.key))
except AttributeError:
pass
def on_key(self,event):
# Init
rescale = True
fig_clear = False
wrest = None
flg = 0
sv_idx = self.idx_line
## Change rows/columns
if event.key == 'k':
self.sub_xy[0] = max(0, self.sub_xy[0]-1)
if event.key == 'K':
self.sub_xy[0] = self.sub_xy[0]+1
if event.key == 'c':
self.sub_xy[1] = max(0, self.sub_xy[1]-1)
if event.key == 'C':
self.sub_xy[1] = max(0, self.sub_xy[1]+1)
## NAVIGATING
if event.key in self.psdict['nav']:
flg = ltgu.navigate(self.psdict,event)
if event.key == '-':
self.idx_line = max(0, self.idx_line-self.sub_xy[0]*self.sub_xy[1]) # Min=0
if self.idx_line == sv_idx:
print('Edge of list')
if event.key == '=':
self.idx_line = min(len(self.llist['show_line'])-self.sub_xy[0]*self.sub_xy[1],
self.idx_line + self.sub_xy[0]*self.sub_xy[1])
if self.idx_line == sv_idx:
print('Edge of list')
## Reset z
if event.key == 'z':
newz = ltu.z_from_v(self.z, event.xdata)
self.z = newz
# Drawing
self.psdict['x_minmax'] = self.vmnx.value
# Single line command
if event.key in ['1','2','B','U','L','N','V','A', 'x', 'X',
'^', '&']:
try:
wrest = event.inaxes.get_gid()
except AttributeError:
return
else:
absline = self.grab_line(wrest)
## Velocity limits
unit = u.km/u.s
if event.key == '1':
absline.limits.set((event.xdata, absline.limits.vlim[1].value)*unit)
if event.key == '2':
absline.limits.set((absline.limits.vlim[0].value, event.xdata)*unit)
if event.key == '!': # Set all lines to this value
for iline in self.abs_lines:
iline.limits.set((event.xdata, iline.limits.vlim[1].value)*unit)
if event.key == '@':
for iline in self.abs_lines:
iline.limits.set((iline.limits.vlim[0].value, event.xdata)*unit)
## Line type
if event.key == 'A': # Add to lines
self.generate_line((self.z,wrest))
if event.key == 'x': # Remove line
if self.remove_line(wrest):
print('VelPlot: Removed line {:g}'.format(wrest))
if event.key == 'X': # Remove all lines
# Double check
gui = simple_widgets.WarningWidg('About to remove all lines. \n Continue??')
gui.exec_()
if gui.ans is False:
return
#
self.abs_lines = [] # Flush??
# Kinematics
if event.key == '^': # Low-Ion
try:
fkin = absline.analy['flag_kin']
except KeyError:
fkin = 0
fkin += (-1)**(fkin % 2**1 >= 2**0) * 2**0
absline.analy['flag_kin'] = fkin
if event.key == '&': # High-Ion
try:
fkin = absline.analy['flag_kin']
except KeyError:
fkin = 0
fkin += (-1)**(fkin % 2**2 >= 2**1) * 2**1
absline.analy['flag_kin'] = fkin
# Toggle blend
if event.key == 'B':
try:
feye = absline.analy['flg_eye']
except KeyError:
feye = 0
feye = (feye + 1) % 2
absline.analy['flg_eye'] = feye
# Toggle NG
if event.key == 'N':
try:
fanly = absline.analy['do_analysis']
except KeyError:
fanly = 1
if fanly == 0:
fanly = 1
else:
fanly = 0
absline.analy['do_analysis'] = fanly
if event.key == 'V': # Normal
absline.analy['flg_limit'] = 1
if event.key == 'L': # Lower limit
absline.analy['flg_limit'] = 2
if event.key == 'U': # Upper limit
absline.analy['flg_limit'] = 3
'''
# AODM plot
if event.key == ':': #
# Grab good lines
from xastropy.xguis import spec_guis as xsgui
gdl = [iline.wrest for iline in self.abs_sys.lines
if iline.analy['do_analysis'] > 0]
# Launch AODM
if len(gdl) > 0:
gui = xsgui.XAODMGui(self.spec, self.z, gdl, vmnx=self.vmnx, norm=self.norm)
gui.exec_()
else:
print('VelPlot.AODM: No good lines to plot')
'''
if wrest is not None: # Single window
flg = 3
if event.key in ['c','C','k','K','W','!', '@', '=', '-', 'X', 'z','R']: # Redraw all
flg = 1
if event.key in ['Y']:
rescale = False
if event.key in ['k','c','C','K', 'R']:
fig_clear = True
# Print help message
if event.key == '?':
print(self.help_message)
if flg == 1: # Default is not to redraw
self.on_draw(rescale=rescale, fig_clear=fig_clear)
elif flg == 2: # Layer (no clear)
self.on_draw(replot=False, rescale=rescale)
elif flg == 3: # Layer (no clear)
self.on_draw(in_wrest=wrest, rescale=rescale)
def __init__(self, ispec, z, abs_lines=None, parent=None, llist=None, norm=True,
vmnx=[-300., 300.]*u.km/u.s):
'''
spec : XSpectrum1D
z : float
abs_lines: list, optional
List of AbsLines
llist : LineList, optional
Input line list. Defaults to 'Strong'
norm : bool, optional
Normalized spectrum?
vmnx : Quantity array, optional
Starting velocity range for the widget
'''
super(VelPlotWidget, self).__init__(parent)
self.help_message = """
Click on any white region within the velocity plots
for the following keystroke commands to work:
i,o : zoom in/out x limits
I,O : zoom in/out x limits (larger re-scale)
y : zoom out y limits
t,b : set y top/bottom limit
l,r : set left/right x limit
[,] : pan left/right
C,c : add/remove column
K,k : add/remove row
=,- : move to next/previous page
1,2 : Modify velocity region of the single line (left, right sides)
!,@ : Modify velocity region of all lines (left, right)
A,x : Add/remove select line from analysis list
X : Remove all lines from analysis list
^,& : Flag line to be analyzed for low/high-ion kinematics
B : Toggle as blend/no-blend (orange color = blend)
N : Toggle as do/do-not include for analysis (red color = exclude)
V : Indicate as a normal value
L : Indicate as a lower limit
U : Indicate as a upper limit
? : Print this
"""
# Initialize
spec, spec_fil = ltgu.read_spec(ispec)
self.spec = spec
self.spec_fil = spec_fil
self.z = z
self.vmnx = vmnx
self.norm = norm
# Abs Lines
if abs_lines is None:
self.abs_lines = []
else:
self.abs_lines = abs_lines
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
self.psdict = {} # Dict for spectra plotting
self.psdict['x_minmax'] = self.vmnx.value # Too much pain to use units with this
self.psdict['y_minmax'] = [-0.1, 1.1]
self.psdict['nav'] = ltgu.navigate(0,0,init=True)
# Line List
if llist is None:
self.llist = ltgu.set_llist('Strong')
else:
self.llist = llist
self.llist['z'] = self.z
# Indexing for line plotting
self.idx_line = 0
self.init_lines()
# Create the mpl Figure and FigCanvas objects.
self.dpi = 150
self.fig = Figure((8.0, 4.0), dpi=self.dpi)
self.canvas = FigureCanvas(self.fig)
self.canvas.setParent(self)
self.canvas.setFocusPolicy( QtCore.Qt.ClickFocus )
self.canvas.setFocus()
self.canvas.mpl_connect('key_press_event', self.on_key)
self.canvas.mpl_connect('button_press_event', self.on_click)
# Sub_plots (Initial)
self.sub_xy = [3,4]
self.fig.subplots_adjust(hspace=0.0, wspace=0.1)
# Layout
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.canvas)
self.setLayout(vbox)
# Print help message
print(self.help_message)
# Draw on init
self.on_draw()
def on_key(self, event):
""" Deals with key events
Parameters
----------
event : event object
"""
# Flag to control re-draw
flg = -1
# Quit
if event.key == 'q':
self.parent.quit()
return
# NAVIGATING
if event.key in self.psdict['nav']:
flg = ltgu.navigate(self.psdict, event,
flux=self.spec.flux.value,
wave=self.spec.wavelength.value)
# DOUBLETS
if event.key in ['C', 'M', 'X', '4', '8', 'B']:
wave, name = ltgu.set_doublet(self, event)
# Lines
self.ax.plot([wave[0]]*2, self.psdict['y_minmax'], '--', color='red')
self.ax.plot([wave[1]]*2, self.psdict['y_minmax'], '--', color='red')
# Name
for wv in wave:
self.ax.text(wv, self.psdict['y_minmax'][0]+0.8*(
self.psdict['y_minmax'][1]-self.psdict['y_minmax'][0]), name, color='red')
flg = 2 # Layer
## SMOOTH
if event.key == 'S':
self.spec = self.spec.box_smooth(2)
flg = 1
if event.key == 'U':
self.spec = self.orig_spec
flg = 1
## Lya Profiles
if event.key in ['D', 'R']:
# Set NHI
if event.key == 'D':
NHI = 10**20.3 * u.cm**-2
elif event.key == 'R':
NHI = 10**19.0 * u.cm**-2
zlya = event.xdata/1215.6701 - 1.
self.llist['z'] = zlya
# Generate Lya profile
lya_line = AbsLine(1215.6701*u.AA)
lya_line.attrib['z'] = zlya
lya_line.attrib['N'] = NHI
lya_line.attrib['b'] = 30. * u.km/u.s
lya_spec = ltv.voigt_from_abslines(self.spec.wavelength, lya_line, fwhm=3.)
lconti = event.ydata
self.lya_line = XSpectrum1D.from_tuple((lya_spec.wavelength, lya_spec.flux*lconti))
self.adict['flg'] = 4
# QtCore.pyqtRemoveInputHook()
# import pdb; pdb.set_trace()
# QtCore.pyqtRestoreInputHook()
flg = 1
# ANALYSIS: AODM, EW, Stats, Gaussian
if event.key in ['N', 'E', '$', 'G']:
# If column check for line list
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
if (event.key in ['N', 'E']) & (self.llist['List'] == 'None'):
print('xspec: Choose a Line list first!')
try:
self.statusBar().showMessage('Choose a Line list first!')
except AttributeError:
pass
self.adict['flg'] = 0
return
flg = 1
if (self.adict['flg'] == 0) or (self.adict['flg'] > 2):
self.adict['wv_1'] = event.xdata # wavelength
self.adict['C_1'] = event.ydata # local continuum
self.adict['flg'] = 1 # Plot dot
print("Dot at x={:g}, y={:g}".format(event.xdata, event.ydata))
else:
self.adict['wv_2'] = event.xdata # wavelength
self.adict['C_2'] = event.ydata # local continuum
self.adict['flg'] = 2 # Ready to plot + print
print("Dot at x={:g}, y={:g}".format(event.xdata, event.ydata))
# Sort em + make arrays
iwv = np.array(sorted([self.adict['wv_1'],
self.adict['wv_2']])) * self.spec.units['wave']
ic = np.array(sorted([self.adict['C_1'],
self.adict['C_2']]))
# Calculate the continuum (linear fit)
param = np.polyfit(iwv, ic, 1)
cfunc = np.poly1d(param)
lconti = cfunc(self.spec.wavelength.value) # Local continuum
if event.key == '$': # Simple stats
pix = self.spec.pix_minmax(iwv)[0]
mean = np.mean(self.spec.flux[pix])
median = np.median(self.spec.flux[pix])
stdv = np.std(self.spec.flux[pix]-lconti[pix])
S2N = median / stdv
mssg = 'Mean={:g}, Median={:g}, S/N={:g}'.format(
mean,median,S2N)
elif event.key == 'G': # Fit a Gaussian
# Good pixels
pix = self.spec.pix_minmax(iwv)[0]
# EW
EW = np.sum(lconti[pix]-self.spec.flux[pix])
if EW > 0.: # Absorption line
sign=-1
else: # Emission
sign=1
# Amplitude
Aguess = np.max(self.spec.flux[pix]-lconti[pix])
Cguess = np.mean(self.spec.wavelength[pix])
sguess = 0.1*np.abs(self.adict['wv_1']-self.adict['wv_2'])
# Fit
g_init = models.Gaussian1D(amplitude=Aguess, mean=Cguess, stddev=sguess)
fitter = fitting.LevMarLSQFitter()
parm = fitter(g_init, self.spec.wavelength[pix].value,
sign*(self.spec.flux[pix]-lconti[pix]))
# Error
var = [fitter.fit_info['param_cov'][ii,ii] for ii in range(3)]
sig = np.sqrt(var) # amplitude, mean, stddev
sig_dict = {g_init.param_names[0]:sig[0],
g_init.param_names[1]:sig[1],
g_init.param_names[2]:sig[2], }
# Plot
g_final = models.Gaussian1D(amplitude=parm.amplitude.value,
mean=parm.mean.value, stddev=parm.stddev.value)
model_Gauss = g_final(self.spec.wavelength.value)
self.model = XSpectrum1D.from_tuple((self.spec.wavelength, lconti + sign*model_Gauss))
# Flux
flux = parm.stddev.value*parm.amplitude.value*np.sqrt(2*np.pi)
#flux = parm.stddev.value*(parm.amplitude.value-np.median(lconti[pix]))*np.sqrt(2*np.pi)
sig_flux1 = np.sqrt( (sig_dict['stddev']*parm.amplitude.value*np.sqrt(2*np.pi))**2 + (parm.stddev.value*sig_dict['amplitude']*np.sqrt(2*np.pi))**2)
if self.spec.sig_is_set:
sig_flux2 = np.sqrt(np.sum(self.spec.sig[pix].value**2))
else:
sig_flux2 = 9e9
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
#QtCore.pyqtRestoreInputHook()
# Message
mssg = 'Gaussian Fit: '
mssg = mssg+' :: Mean={:g}, Amplitude={:g}, sigma={:g}, flux={:g}'.format(
parm.mean.value, parm.amplitude.value, parm.stddev.value, flux)
mssg = mssg+' :: sig(Mean)={:g}, sig(Amplitude)={:g}, sig(sigma)={:g}, sig(flux)={:g}'.format(
sig_dict['mean'], sig_dict['amplitude'], sig_dict['stddev'], min(sig_flux1,sig_flux2))
else:
# Find the spectral line (or request it!)
rng_wrest = iwv / (self.llist['z']+1)
gdl = np.where( (self.llist[self.llist['List']].wrest-rng_wrest[0]) *
(self.llist[self.llist['List']].wrest-rng_wrest[1]) < 0.)[0]
if len(gdl) == 1:
wrest = self.llist[self.llist['List']].wrest[gdl[0]]
closest = False
else:
if len(gdl) == 0: # Search through them all
gdl = np.arange(len(self.llist[self.llist['List']]))
sel_widg = ltgl.SelectLineWidget(self.llist[self.llist['List']]._data[gdl])
sel_widg.exec_()
line = sel_widg.line
#wrest = float(line.split('::')[1].lstrip())
quant = line.split('::')[1].lstrip()
spltw = quant.split(' ')
wrest = Quantity(float(spltw[0]), unit=spltw[1])
closest = True
# Units
if not hasattr(wrest,'unit'):
# Assume Ang
wrest = wrest * u.AA
# Generate the Spectral Line
aline = AbsLine(wrest,linelist=self.llist[self.llist['List']],
z=self.llist['z'], closest=closest)
# Generate a temporary spectrum for analysis and apply the local continuum
tspec = XSpectrum1D.from_tuple((self.spec.wavelength,
self.spec.flux, self.spec.sig))
tspec.normalize(lconti)
aline.analy['spec'] = tspec
# AODM
if event.key == 'N':
# Calculate the velocity limits and load-up
aline.limits.set(const.c.to('km/s') * (
(iwv/(1+self.llist['z']) - wrest) / wrest ))
# AODM
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
aline.measure_aodm()
mssg = 'Using '+ aline.__repr__()
mssg = mssg + ' :: logN = {:g} +/- {:g}'.format(
aline.attrib['logN'], aline.attrib['sig_logN'])
elif event.key == 'E': #EW
aline.limits.set(iwv)
aline.measure_restew()
mssg = 'Using '+ aline.__repr__()
mssg = mssg + ' :: Rest EW = {:g} +/- {:g}'.format(
aline.attrib['EW'].to(mAA), aline.attrib['sig_EW'].to(mAA))
# Display values
try:
self.statusBar().showMessage(mssg)
except AttributeError:
pass
print(mssg)
## Velocity plot
if event.key == 'v':
z=self.llist['z']
# Launch
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
abs_sys = GenericAbsSystem((0.,0.), z, (-300,300)*u.km/u.s)
gui = XAbsSysGui(self.spec, abs_sys, norm=self.norm, llist=self.llist)
gui.exec_()
# Redraw
flg=1
# Dummy keys
if event.key in ['shift', 'control', 'shift+super', 'super+shift']:
flg = 0
if event.key == '?': # open the XSpecGUI help page
import webbrowser
webbrowser.open("http://linetools.readthedocs.org/en/latest/xspecgui.html#navigating-these-key-strokes-help-you-explore-the-spectrum-be-sure-to-click-in-the-spectrum-panel-first")
# Draw
if flg==1: # Default is not to redraw
self.on_draw()
elif flg==2: # Layer (no clear)
self.on_draw(replot=False)
elif flg==-1: # Layer (no clear)
try:
self.statusBar().showMessage('Not a valid key! {:s}'.format(event.key))
except AttributeError:
pass
def test_navigate():
# Init
nav_dict = dict(nav=ltgu.navigate(0, 0, init=True))
assert isinstance(nav_dict['nav'], list)
nav_dict['x_minmax'] = [0., 1]
nav_dict['y_minmax'] = [0., 1]
nav_dict['sv_xy_minmax'] = [[0, 1], [0, 1]]
nav_dict['tmp_xy'] = None
# Usage
o = type(str('Dummy'), (object, ), {})
o.xdata = 22.
o.ydata = 1.
for key in nav_dict['nav']:
o.key = key
if key == 's':
# test two options
nav_dict['tmp_xy'] = [0, 0.5] # is not None
ltgu.navigate(nav_dict, o)
nav_dict['tmp_xy'] = None # is None again
ltgu.navigate(nav_dict, o)
elif key == 'y':
# test two options
ltgu.navigate(nav_dict,
o,
wave=np.linspace(0, 1, 100),
flux=np.ones(100))
ltgu.navigate(nav_dict, o)
else:
ltgu.navigate(nav_dict, o)
# test wrong key event
o.xdata = 'this_is_not_float'
out = ltgu.navigate(nav_dict, o)
assert out == 0
def __init__(self, ispec, z=None, parent=None, llist=None, norm=True,
vmnx=[-300., 300.]*u.km/u.s, abs_sys=None):
'''
spec = Spectrum1D
Norm: Bool (False)
Normalized spectrum?
abs_sys: AbsSystem
Absorption system class
'''
super(VelPlotWidget, self).__init__(parent)
# Initialize
spec, spec_fil = ltgu.read_spec(ispec)
self.spec = spec
self.spec_fil = spec_fil
self.z = z
self.vmnx = vmnx
self.norm = norm
# Abs_System
self.abs_sys = abs_sys
if self.abs_sys is None:
self.abs_sys = GenericAbsSystem((0.*u.deg,0.*u.deg), self.z, self.vmnx)
self.abs_lines = []
else:
self.z = self.abs_sys.zabs
# Line list
if llist is None:
self.abs_lines = self.abs_sys.list_of_abslines()
if len(self.abs_lines)>0:
lwrest = [iline.wrest for iline in self.abs_lines]
else:
lwrest = None
if lwrest is not None:
llist = ltgu.set_llist(lwrest) # Not sure this is working..
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
self.psdict = {} # Dict for spectra plotting
self.psdict['xmnx'] = self.vmnx.value # Too much pain to use units with this
self.psdict['ymnx'] = [-0.1, 1.1]
self.psdict['nav'] = ltgu.navigate(0,0,init=True)
# Status Bar?
#if not status is None:
# self.statusBar = status
# Line List
if llist is None:
self.llist = ltgu.set_llist('Strong')
else:
self.llist = llist
self.llist['z'] = self.z
# Indexing for line plotting
self.idx_line = 0
self.init_lines()
# Create the mpl Figure and FigCanvas objects.
#
self.dpi = 150
self.fig = Figure((8.0, 4.0), dpi=self.dpi)
self.canvas = FigureCanvas(self.fig)
self.canvas.setParent(self)
self.canvas.setFocusPolicy( QtCore.Qt.ClickFocus )
self.canvas.setFocus()
self.canvas.mpl_connect('key_press_event', self.on_key)
self.canvas.mpl_connect('button_press_event', self.on_click)
# Sub_plots
self.sub_xy = [3,4]
self.fig.subplots_adjust(hspace=0.0, wspace=0.1)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.canvas)
self.setLayout(vbox)
# Draw on init
self.on_draw()
def on_key(self, event):
# Init
rescale = True
fig_clear = False
wrest = None
flg = 0
sv_idx = self.idx_line
## Change rows/columns
if event.key == 'k':
self.sub_xy[0] = max(0, self.sub_xy[0] - 1)
if event.key == 'K':
self.sub_xy[0] = self.sub_xy[0] + 1
if event.key == 'c':
self.sub_xy[1] = max(0, self.sub_xy[1] - 1)
if event.key == 'C':
self.sub_xy[1] = max(0, self.sub_xy[1] + 1)
## NAVIGATING
if event.key in self.psdict['nav']:
flg = ltgu.navigate(self.psdict, event)
if event.key == '-':
self.idx_line = max(0, self.idx_line -
self.sub_xy[0] * self.sub_xy[1]) # Min=0
if self.idx_line == sv_idx:
print('Edge of list')
if event.key == '=':
self.idx_line = min(
len(self.llist['show_line']) - self.sub_xy[0] * self.sub_xy[1],
self.idx_line + self.sub_xy[0] * self.sub_xy[1])
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
if self.idx_line == sv_idx:
print('Edge of list')
## Reset z
if event.key == 'z':
newz = ltu.z_from_v(self.z, event.xdata)
self.z = newz
self.abs_sys.zabs = newz
# Drawing
self.psdict['xmnx'] = self.vmnx.value
# Single line command
if event.key in [
'1', '2', 'B', 'U', 'L', 'N', 'V', 'A', 'x', 'X', '^', '&'
]:
try:
wrest = event.inaxes.get_gid()
except AttributeError:
return
else:
absline = self.grab_line(wrest)
kwrest = wrest.value
## Velocity limits
unit = u.km / u.s
if event.key == '1':
absline.analy['vlim'][0] = event.xdata * unit
if event.key == '2':
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
absline.analy['vlim'][1] = event.xdata * unit
if event.key == '!':
for iline in self.abs_sys.lines:
iline.analy['vlim'][0] = event.xdata * unit
if event.key == '@':
for iline in self.abs_sys.lines:
iline.analy['vlim'][1] = event.xdata * unit
## Line type
if event.key == 'A': # Add to lines
self.generate_line((self.z, wrest))
if event.key == 'x': # Remove line
if self.remove_line(wrest):
print('VelPlot: Removed line {:g}'.format(wrest))
if event.key == 'X': # Remove all lines
# Double check
gui = xguiu.WarningWidg(
'About to remove all lines. \n Continue??')
gui.exec_()
if gui.ans is False:
return
#
self.abs_lines = [] # Flush??
# Kinematics
if event.key == '^': # Low-Ion
try:
fkin = absline.analy['flag_kin']
except KeyError:
fkin = 0
fkin += (-1)**(fkin % 2**1 >= 2**0) * 2**0
absline.analy['flag_kin'] = fkin
if event.key == '&': # High-Ion
try:
fkin = absline.analy['flag_kin']
except KeyError:
fkin = 0
fkin += (-1)**(fkin % 2**2 >= 2**1) * 2**1
absline.analy['flag_kin'] = fkin
# Toggle blend
if event.key == 'B':
try:
feye = absline.analy['flg_eye']
except KeyError:
feye = 0
feye = (feye + 1) % 2
absline.analy['flg_eye'] = feye
# Toggle NG
if event.key == 'N':
try:
fanly = absline.analy['do_analysis']
except KeyError:
fanly = 1
if fanly == 0:
fanly = 1
else:
fanly = 0
absline.analy['do_analysis'] = fanly
if event.key == 'V': # Normal
absline.analy['flg_limit'] = 1
if event.key == 'L': # Lower limit
absline.analy['flg_limit'] = 2
if event.key == 'U': # Upper limit
absline.analy['flg_limit'] = 3
# AODM plot
if event.key == ':': #
# Grab good lines
from xastropy.xguis import spec_guis as xsgui
gdl = [
iline.wrest for iline in self.abs_sys.lines
if iline.analy['do_analysis'] > 0
]
# Launch AODM
if len(gdl) > 0:
gui = xsgui.XAODMGui(self.spec,
self.z,
gdl,
vmnx=self.vmnx,
norm=self.norm)
gui.exec_()
else:
print('VelPlot.AODM: No good lines to plot')
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
if not wrest is None: # Single window
flg = 3
if event.key in [
'c', 'C', 'k', 'K', 'W', '!', '@', '=', '-', 'X', 'z', 'R'
]: # Redraw all
flg = 1
if event.key in ['Y']:
rescale = False
if event.key in ['k', 'c', 'C', 'K', 'R']:
fig_clear = True
if flg == 1: # Default is not to redraw
self.on_draw(rescale=rescale, fig_clear=fig_clear)
elif flg == 2: # Layer (no clear)
self.on_draw(replot=False, rescale=rescale)
elif flg == 3: # Layer (no clear)
self.on_draw(in_wrest=wrest, rescale=rescale)
def __init__(self,
ispec,
z=None,
parent=None,
llist=None,
norm=True,
vmnx=[-300., 300.] * u.km / u.s,
abs_sys=None):
'''
spec = Spectrum1D
Norm: Bool (False)
Normalized spectrum?
abs_sys: AbsSystem
Absorption system class
'''
super(VelPlotWidget, self).__init__(parent)
# Initialize
spec, spec_fil = ltgu.read_spec(ispec)
self.spec = spec
self.spec_fil = spec_fil
self.z = z
self.vmnx = vmnx
self.norm = norm
# Abs_System
self.abs_sys = abs_sys
if self.abs_sys is None:
self.abs_sys = GenericAbsSystem((0. * u.deg, 0. * u.deg), self.z,
self.vmnx)
self.abs_lines = []
else:
self.z = self.abs_sys.zabs
# Line list
if llist is None:
self.abs_lines = self.abs_sys.list_of_abslines()
if len(self.abs_lines) > 0:
lwrest = [iline.wrest for iline in self.abs_lines]
else:
lwrest = None
if lwrest is not None:
llist = ltgu.set_llist(
lwrest) # Not sure this is working..
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
self.psdict = {} # Dict for spectra plotting
self.psdict[
'xmnx'] = self.vmnx.value # Too much pain to use units with this
self.psdict['ymnx'] = [-0.1, 1.1]
self.psdict['nav'] = ltgu.navigate(0, 0, init=True)
# Status Bar?
#if not status is None:
# self.statusBar = status
# Line List
if llist is None:
self.llist = ltgu.set_llist('Strong')
else:
self.llist = llist
self.llist['z'] = self.z
# Indexing for line plotting
self.idx_line = 0
self.init_lines()
# Create the mpl Figure and FigCanvas objects.
#
self.dpi = 150
self.fig = Figure((8.0, 4.0), dpi=self.dpi)
self.canvas = FigureCanvas(self.fig)
self.canvas.setParent(self)
self.canvas.setFocusPolicy(QtCore.Qt.ClickFocus)
self.canvas.setFocus()
self.canvas.mpl_connect('key_press_event', self.on_key)
self.canvas.mpl_connect('button_press_event', self.on_click)
# Sub_plots
self.sub_xy = [3, 4]
self.fig.subplots_adjust(hspace=0.0, wspace=0.1)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.canvas)
self.setLayout(vbox)
# Draw on init
self.on_draw()
def test_navigate():
# Init
nav_dict = dict(nav=ltgu.navigate(0,0,init=True))
assert isinstance(nav_dict['nav'], list)
nav_dict['x_minmax'] = [0., 1]
nav_dict['y_minmax'] = [0., 1]
nav_dict['sv_xy_minmax'] = [[0,1], [0,1]]
nav_dict['tmp_xy'] = None
# Usage
o = type(str('Dummy'), (object,), {})
o.xdata = 22.
o.ydata = 1.
for key in nav_dict['nav']:
o.key = key
if key == 's':
# test two options
nav_dict['tmp_xy'] = [0, 0.5] # is not None
ltgu.navigate(nav_dict, o)
nav_dict['tmp_xy'] = None # is None again
ltgu.navigate(nav_dict, o)
elif key == 'y':
# test two options
ltgu.navigate(nav_dict, o, wave = np.linspace(0,1,100), flux = np.ones(100))
ltgu.navigate(nav_dict, o)
else:
ltgu.navigate(nav_dict, o)
# test wrong key event
o.xdata = 'this_is_not_float'
out = ltgu.navigate(nav_dict, o)
assert out == 0