Tools for Mapping 1D Spectra to 2D Detector Images

Sometimes we want to check the detector image corresponds to a point of the extracted spectrum.

Preparations

The first part is the same as the usual reduction process before assign wavelength to the extracted spectrum. See the tutorial of IRD_stream for more detail.

from pyird.utils import irdstream
import pathlib
from pyird.image.bias import bias_subtract_image
from pyird.image.hotpix import identify_hotpix_sigclip
import astropy.io.fits as pyf

#--------SETTINGS--------#
basedir = pathlib.Path('~/pyird/data/20210317/').expanduser()

band = 'h' #'h' or 'y'
mmf = 'mmf2' #'mmf1' (comb fiber) or 'mmf2' (star fiber)
readout_noise_mode = "real" #'real' or 'default'

datadir_flat = basedir/'flat/'
datadir_dark = basedir/'dark/'
datadir_thar = basedir/'thar'
datadir_target = basedir/'target/'
anadir = basedir/'reduc/'

fitsid_flat_comb = list(range(41704,41804,2))
fitsid_flat_star = (range(41804,41904,2))
fitsid_dark = [41504]
fitsid_thar = list(range(14632,14732))
fitsid_target = [41510]
#-------------------------#

#--------FOR CALIBRATION--------#
# aperture extraction
flat=irdstream.Stream2D("flat",datadir_flat,anadir)
flat.fitsid=fitsid_flat_comb ##FLAT_COMB

################################
### SELECT H band or YJ band ###
################################
flat.band=band
if flat.band=='h':
    flat.fitsid_increment() # when you use H-band
    trace_mmf=flat.aptrace(cutrow = 800,nap=42) #TraceAperture instance
elif flat.band=='y':
    trace_mmf=flat.aptrace(cutrow = 1000,nap=102) #TraceAperture instance

# hotpixel mask
dark = irdstream.Stream2D('dark', datadir_dark, anadir,fitsid=fitsid_dark)
if flat.band=='h':
    dark.fitsid_increment() # when you use H-band
for data in dark.rawpath:
    im = pyf.open(str(data))[0].data
im_subbias = bias_subtract_image(im)
hotpix_mask = identify_hotpix_sigclip(im_subbias)

if mmf=="mmf2":
    trace_mmf.choose_mmf2_aperture() #mmf2 (star fiber)
elif mmf=="mmf1":
    trace_mmf.choose_mmf1_aperture() #mmf1 (comb fiber)

# load ThAr raw image
if band=='h':
    rawtag='IRDAD000'
elif band=='y':
    rawtag='IRDBD000'

#wavelength calibration
thar=irdstream.Stream2D("thar",datadir_thar,anadir,rawtag=rawtag,fitsid=fitsid_thar)
thar.trace = trace_mmf
thar.clean_pattern(extin='', extout='_cp', hotpix_mask=hotpix_mask)
thar.calibrate_wavelength()

### TARGET ###
# Load data
target = irdstream.Stream2D('targets', datadir_target, anadir, fitsid=fitsid_target)
if flat.band=='h':
    target.fitsid_increment() # when you use H-band
target.info = True  # show detailed info
target.trace = trace_mmf
# clean pattern
target.clean_pattern(extin='', extout='_cp', hotpix_mask=hotpix_mask)

No fitsid yet.
median combine:

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default nap value
cross-section: row  1170

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fitsid: [41504]
hotpix mask = 0.58 percent
fitsid: [14632, 14633, 14634, 14635, 14636, 14637, 14638, 14639, 14640, 14641, 14642, 14643, 14644, 14645, 14646, 14647, 14648, 14649, 14650, 14651, 14652, 14653, 14654, 14655, 14656, 14657, 14658, 14659, 14660, 14661, 14662, 14663, 14664, 14665, 14666, 14667, 14668, 14669, 14670, 14671, 14672, 14673, 14674, 14675, 14676, 14677, 14678, 14679, 14680, 14681, 14682, 14683, 14684, 14685, 14686, 14687, 14688, 14689, 14690, 14691, 14692, 14693, 14694, 14695, 14696, 14697, 14698, 14699, 14700, 14701, 14702, 14703, 14704, 14705, 14706, 14707, 14708, 14709, 14710, 14711, 14712, 14713, 14714, 14715, 14716, 14717, 14718, 14719, 14720, 14721, 14722, 14723, 14724, 14725, 14726, 14727, 14728, 14729, 14730, 14731]
clean_pattern: output extension=_cp

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/Users/yuikasagi/miniforge3/envs/py39_pip/lib/python3.9/site-packages/numpy/lib/nanfunctions.py:1218: RuntimeWarning: All-NaN slice encountered
  r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,

fitsid: [41510]
clean_pattern: output extension=_cp

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Settings to display figures

You can set some parameters for plot(s). For example, you can get images for several orders.

import matplotlib
matplotlib.use('tkagg')
from pyird.utils.image_widget import image_1Dand2D
import tkinter as tk

### SET PARAMETERS ###
hotpix_mask = None # comment out this if you want to show hotpixels
target.imcomb = False # set 'True' if you want to median combine images.
wavcal_path = thar.anadir/('thar_%s_%s.fits'%(thar.band,thar.trace.mmf))

## additional parameters for plot
vmin = -10
vmax = 50
scale = 'linear' # 'linear' or 'log'
params = {'vmin':vmin,'vmax':vmax,'scale':scale}

orders=[10,12] # orders to be plotted
#######################

## Values needed for plotting
rsd,wav,mask,pixcoord,rotim,iys_plot,iye_plot = target.flatten(extin='_cp',check=True,master_path=wavcal_path)

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Case 1. Plot Absorption Lines

show_spec_to_image() will create two figures in one window for each order.

The upper figure is the spectrum of a order, and the lower figure is the detector image.
You can zoom up both image.
When you press any key on the spectrum, corresponding positions on the detector will be plotted as ‘x’.

Note:

If you run in jupyter notebook, add %matplolib notebook and comment out root.mainloop().

## show 1d spectrum and 2d image
%matplotlib notebook
for order in orders:
    print(order)
    ## draw window
    root = tk.Tk()
    window = image_1Dand2D(root,order=order,band=flat.band)
    window.show_spec_to_image(rsd,wav,mask,pixcoord,rotim,iys_plot,iye_plot,wavcal_path=wavcal_path,hotpix_mask=hotpix_mask,**params)
#root.mainloop()

<IPython.core.display.Javascript object>

<IPython.core.display.Javascript object>

Case 2. Plot Emission Lines

show_emission_position() will be useful for the emission spectrum (e.g. sky spectrum).

The upper figure is the detector image of one aperture, and the lower figure is the spectra of the order.
By fitting 2D gaussian to the emissions on the detector, the emission like signal and hotpixels are distinguished automatically.

Note:

If you run in jupyter notebook, add %matplolib notebook and comment out root.mainloop().

## show positions of emissions on a detector image
%matplotlib notebook
for order in orders:
    ## draw window
    root2 = tk.Tk()
    window2 = image_1Dand2D(root2,order=order,band=flat.band)
    window2.show_emission_position(target,rsd,wav,mask,pixcoord,rotim,iys_plot,iye_plot,wavcal_path=wavcal_path,hotpix_mask=hotpix_mask,**params)
#root2.mainloop()

<IPython.core.display.Javascript object>

WARNING: The fit may be unsuccessful; check fit_info['message'] for more information. [astropy.modeling.fitting]

<IPython.core.display.Javascript object>

WARNING: The fit may be unsuccessful; check fit_info['message'] for more information. [astropy.modeling.fitting]