NIRSpec Visibility Fix

env/environment-3.10.yml

@@ -35,7 +35,6 @@ dependencies:
     - docutils>=0.16
     - flask_wtf>=1.1.1
     - h5py>=3.9.0
-    - hotsoss>=0.1.9
     - gunicorn>=21.1.0
     - numpy>=1.25.1
     - platon>=5.4
@@ -47,6 +46,6 @@ dependencies:
     - scipy>=1.11.1
     - sphinx_astropy>=1.9.1
     - svo-filters>=0.4.4
-    - werkzeug==2.0.3
+    - werkzeug>=3.0.1
     - jwst_gtvt>=1.0.0
     - astroquery>=0.4.6

env/environment-3.11.yml

@@ -35,7 +35,6 @@ dependencies:
     - docutils>=0.16
     - flask_wtf>=1.1.1
     - h5py>=3.9.0
-    - hotsoss>=0.1.9
     - gunicorn>=21.1.0
     - numpy>=1.25.1
     - platon>=5.4
@@ -47,6 +46,6 @@ dependencies:
     - scipy>=1.11.1
     - sphinx_astropy>=1.9.1
     - svo-filters>=0.4.4
-    - werkzeug==2.0.3
+    - werkzeug>=3.0.1
     - jwst_gtvt>=1.0.0
     - astroquery>=0.4.6

env/environment-3.9.yml

@@ -35,7 +35,6 @@ dependencies:
     - docutils>=0.16
     - flask_wtf>=1.1.1
     - h5py>=3.9.0
-    - hotsoss>=0.1.9
     - gunicorn>=21.1.0
     - markupsafe==2.0.1
     - numpy>=1.25.1
@@ -48,6 +47,6 @@ dependencies:
     - scipy>=1.11.1
     - sphinx_astropy>=1.9.1
     - svo-filters>=0.4.4
-    - werkzeug==2.0.3
+    - werkzeug>=3.0.1
     - jwst_gtvt>=1.0.0
     - astroquery>=0.4.6

exoctk/contam_visibility/new_vis_plot.py

@@ -11,7 +11,8 @@ def get_exoplanet_positions(ra, dec, in_FOR=None):
     """Use the jwst_gtvt to obtain positions of exoplanet.
     """
 
-    eph = Ephemeris()
+    # Set ephemeris to go from Cycle 3 to Cycle 6:
+    eph = Ephemeris(start_date=Time('2024-07-30'), end_date=Time('2028-07-30'))
     exoplanet_data = eph.get_fixed_target_positions(ra, dec)
 
     if in_FOR is None:
@@ -68,4 +69,4 @@ def build_visibility_plot(target_name, instrument, ra, dec):
 
         p.add_tools(HoverTool(tooltips=TOOLTIPS, formatters={'@times': 'datetime'}))
 
-    return p
+    return p

exoctk/exoctk_app/app_exoctk.py

@@ -17,7 +17,6 @@
 
 from exoctk import log_exoctk
 from exoctk.contam_visibility.new_vis_plot import build_visibility_plot, get_exoplanet_positions
-#from exoctk.contam_visibility import visibilityPA as vpa
 from exoctk.contam_visibility import field_simulator as fs
 from exoctk.contam_visibility import contamination_figure as cf
 from exoctk.contam_visibility.miniTools import contamVerify
@@ -139,7 +138,7 @@ def fortney():
                                  plot_div=div,
                                  js_resources=js_resources,
                                  css_resources=css_resources,
-                                 temp=temp_out,
+                                 temp=sorted(temp_out, key=float),
                                  table_string=table_string
                                  )
 
@@ -453,10 +452,12 @@ def contam_visibility():
 
     if form.validate_on_submit() and (form.calculate_submit.data or form.calculate_contam_submit.data):
 
-        instrument = fs.APERTURES[form.inst.data]['inst']
+        if form.inst.data == "NIRSpec":
+            instrument = form.inst.data
+        else:
+            instrument = fs.APERTURES[form.inst.data]['inst']
 
         try:
-
             # Log the form inputs
             log_exoctk.log_form_input(request.form, 'contam_visibility', DB)
 
@@ -507,7 +508,7 @@ def contam_visibility():
                         companion = {'name': 'Companion', 'ra': ra_deg, 'dec': dec_deg, 'teff': comp_teff, 'delta_mag': comp_mag, 'dist': comp_dist, 'pa': comp_pa}
 
                     # Make field simulation
-                    targframe, starcube, results = fs.field_simulation(ra_deg, dec_deg, form.inst.data, binComp=companion, plot=False, multi=False)
+                    targframe, starcube, results = fs.field_simulation(ra_deg, dec_deg, form.inst.data, target_date=form.epoch.data, binComp=companion, plot=False, multi=False)
 
                     # Make the plot
                     # contam_plot = fs.contam_slider_plot(results)
@@ -520,20 +521,19 @@ def contam_visibility():
                     starCube[0, :, :] = (targframe[0]).T[::-1, ::-1]
                     starCube[1, :, :] = (targframe[1]).T[::-1, ::-1]
                     starCube[2:, :, :] = starcube.swapaxes(1, 2)[:, ::-1, ::-1]
-                    contam_plot = cf.contam(starCube, 'NIS_SUBSTRIP256', targetName=form.targname.data, badPAs=badPAs)
+                    contam_plot = cf.contam(starCube, form.inst.data, targetName=form.targname.data, badPAs=badPAs)
 
                 else:
 
                     # Get stars
-                    stars = fs.find_stars(ra_deg, dec_deg, verbose=False)
+                    stars = fs.find_sources(ra_deg, dec_deg, target_date=form.epoch.data, verbose=False)
 
                     # Add companion
-                    print(comp_teff, comp_mag, comp_dist, comp_pa)
                     if comp_teff is not None and comp_mag is not None and comp_dist is not None and comp_pa is not None:
-                        stars = fs.add_star(stars, 'Companion', ra_deg, dec_deg, comp_teff, delta_mag=comp_mag, dist=comp_dist, pa=comp_pa)
+                        stars = fs.add_source(stars, 'Companion', ra, dec, teff=comp_teff, delta_mag=comp_mag, dist=comp_dist, pa=comp_pa, type='STAR')
 
                     # Calculate contam
-                    result, contam_plot = fs.calc_v3pa(pa_val, stars, 'NIS_SUBSTRIP256', plot=True, verbose=False)
+                    result, contam_plot = fs.calc_v3pa(pa_val, stars, form.inst.data, plot=True, verbose=False)
 
                 # Get scripts
                 contam_js = INLINE.render_js()
@@ -551,7 +551,7 @@ def contam_visibility():
                                    vis_css=vis_css, contam_plot=contam_div,
                                    contam_script=contam_script,
                                    contam_js=contam_js,
-                                   contam_css=contam_css, pa_val=pa_val)
+                                   contam_css=contam_css, pa_val=pa_val, epoch=form.epoch.data)
 
         except Exception as e:
             err = 'The following error occurred: ' + str(e)

exoctk/exoctk_app/form_validation.py

@@ -1,6 +1,7 @@
 import os
 
 from flask_wtf import FlaskForm
+from astropy.time import Time
 import numpy as np
 from svo_filters import svo
 from wtforms import StringField, SubmitField, DecimalField, RadioField, SelectField, SelectMultipleField, IntegerField, FloatField
@@ -39,7 +40,8 @@ class ContamVisForm(BaseForm):
     ra = DecimalField('ra', validators=[NumberRange(min=0, max=360, message='RA must be between 0 and 360 degrees')])
     dec = DecimalField('dec', validators=[NumberRange(min=-90, max=90, message='Declinaton must be between -90 and 90 degrees')])
     v3pa = DecimalField('v3pa', default=-1, validators=[NumberRange(min=-1, max=360, message='PA must be between 0 and 360 degrees')])
-    inst = SelectField('inst', choices=[('NIS_SUBSTRIP256', 'NIRISS - SOSS - SUBSTRIP256'), ('NIS_SUBSTRIP96', 'NIRISS - SOSS - SUBSTRIP96'), ('NRCA5_GRISM256_F322W2', 'NIRCam - Grism Time Series - F322W2 (Visibility Only)'), ('NRCA5_GRISM256_F444W', 'NIRCam - Grism Time Series - F444W (Visibility Only)'), ('MIRI_SLITLESSPRISM', 'MIRI - LRS (Visibility Only)'), ('NIRSpec', 'NIRSpec (Visibility Only)')])
+    epoch = IntegerField('epoch', default=Time.now().value.year, validators=[NumberRange(min=2000, max=2050, message='Epoch must be between 2000 and 2050')])
+    inst = SelectField('inst', choices=[('NIS_SUBSTRIP256', 'NIRISS - SOSS - SUBSTRIP256'), ('NIS_SUBSTRIP96', 'NIRISS - SOSS - SUBSTRIP96'), ('NRCA5_GRISM256_F322W2', 'NIRCam - Grism Time Series - F322W2 (Visibility Only)'), ('NRCA5_GRISM256_F444W', 'NIRCam - Grism Time Series - F444W (Visibility Only)'), ('MIRIM_SLITLESSPRISM', 'MIRI - LRS (Visibility Only)'), ('NIRSpec', 'NIRSpec (Visibility Only)')])
     delta_mag = DecimalField('delta_mag', default=None, validators=[Optional()])
     dist = DecimalField('dist', default=None, validators=[Optional()])
     pa = DecimalField('pa', default=None, validators=[Optional(), NumberRange(min=0, max=360, message='PA must be between 0 and 360 degrees')])
@@ -54,9 +56,9 @@ class FortneyModelForm(BaseForm):
     planet_mass_unit = SelectField('planet_mass_unit', choices=[('M_jup', 'Jupiter Mass'), ('kilogram', 'kilogram'), ('g', 'gram'), ('M_earth', 'Earth Mass'), ('M_sun', 'Solar Mass')], validators=[InputRequired('A mass unit is required')])
     planet_radius = DecimalField('planet_radius', default=1.25, validators=[InputRequired('A planet radius is required!'), NumberRange(min=0, message='Planet radius must be positive')])
     planet_radius_unit = SelectField('planet_radius_unit', choices=[('R_jup', 'Jupiter Radius'), ('kilometer', 'kilometer'), ('m', 'meter'), ('R_earth', 'Earth Radius'), ('R_sun', 'Solar Radius')], validators=[InputRequired('A planet radius unit is required')])
-    stellar_radius = DecimalField('stellar_radius', default=1.0, validators=[InputRequired('A stellar radius is required!'), NumberRange(min=0, message='Stellar radius must be positive')])
+    stellar_radius = DecimalField('stellar_radius', validators=[InputRequired('A stellar radius is required!'), NumberRange(min=0, message='Stellar radius must be positive')])
     stellar_radius_unit = SelectField('stellar_radius_unit', choices=[('R_sun', 'Solar Radius'), ('R_jup', 'Jupiter Radius'), ('kilometer', 'kilometer'), ('m', 'meter'), ('R_earth', 'Earth Radius')], validators=[InputRequired('A stellar radius unit is required')])
-    chemistry = SelectField('chemistry', choices=[('noTiO', '500'), ('eqchem', '750'), (1000, '1000'), (1250, '1250'), (1500, '1500'), (1750, '1750'), (2000, '2000'), (2250, '2250'), (2500, '2500')], validators=[InputRequired('A chemistry type is required')])
+    chemistry = SelectField('chemistry', choices=[('noTiO', '500'), ('eqchem', '750')], validators=[InputRequired('A chemistry type is required')])
     clouds = SelectField('clouds', choices=[('0', 'Nothing'), ('ray10', 'Weak Rayleigh'), ('ray100', 'Medium Rayleigh'), ('ray1000', 'Strong Rayleigh'), ('flat10', 'Weak Cloud'), ('flat100', 'Medium Cloud'), ('flat1000', 'Strong Cloud')], validators=[InputRequired('A cloud model is required')])
 
     # Form submits

exoctk/exoctk_app/templates/base.html

@@ -110,7 +110,7 @@
                         </li>
 
                         <li class="dropdown">
-                            <a href="https://github.com/ExoCTK/exoctk#obtain-the-exoctk-data">ExoCTK Data Downlaod</span></a></li>
+                            <a href="https://github.com/ExoCTK/exoctk#obtain-the-exoctk-data">ExoCTK Data Download</span></a></li>
                 </div>
             </div>
         </nav>
@@ -146,7 +146,7 @@
                         <div style="float:right; width:120px;text-align:center;">
                             <p>
                                 Running<br>
-                                <a href='https://github.com/ExoCTK/exoctk/releases/tag/v1.2.5'>exoctk v1.2.5</a>{{version|safe}}
+                                <a href='https://github.com/ExoCTK/exoctk/releases/tag/v1.2.6'>exoctk v1.2.6</a>{{version|safe}}
                             </p>
                             <p style='font-size:0.8em'>
                                 <a href='admin' style='color:#aaaaaa;'>Admin Area</a>

exoctk/exoctk_app/templates/contam_visibility.html

@@ -26,17 +26,11 @@ <h1>Contamination & Visibility Calculator</h1>
     	observation, thus making it useful to plan observations at the optimal PA. The tool also computes the JWST
     	accessibility windows of the target, along with the corresponding accessible PAs for the chosen instrument/observation mode.
       </p>
-      <p>
-      <b>NIRCam and MIRI options</b>: Users can calculate contamination levels for NIRCam Grism Time Series (F322W2, F444W) and MIRI Low Resolution
-      Spectroscopy mode by calling this tool locally on a terminal. Please keep in mind that the calculation for the
-      NIRCam and MIRI modes can take anywhere from 1-3 hours due to the complexity of their algorithms. For instructions on how to
-      generate the contamination plots for NIRCam and MIRI, please refer to our Contam Visibility <a href="https://jwst-docs.stsci.edu/jwst-other-tools/exoplanet-observations-proposal-tools/contamination-overlap-tool#ContaminationOverlapTool-Contam_nircam_miriContaminationCalculatorforNIRCamandMIRImodes(availablelocally)">JWST-Docs page</a>.
-    	</p>
+
       <p>Potential caveats:</p>
       <ul>
         <li>The field stars used for this analysis are retrieved from the Gaia EDR3 point source catalogue. Contamination from stars missing from this catalog are thus not modelled; this may be important for faint targets.</li>
         <li>Distortion has been observed to create a trace offset as large as ~4 to 5 pixels in both the X and Y direction in the science frame which may contribute to uncertainty in the contamination plots.</li>
-        <li>Traces on the MIRI detector may fold over below 4.5 microns. Our model traces assume no spectral foldover. Depending on the observation, this may lead to inaccurate results.</li>
       </ul>
       <p>If there are any questions regarding these caveats please send us a ticket through the JWST help desk and we will get back to you shortly.</p>
     <form class='form-horizontal' action="/contam_visibility" method="POST" />
@@ -101,6 +95,28 @@ <h1>Contamination & Visibility Calculator</h1>
             </div>
         </div>
 
+        <hr class="col-md-12">
+
+        <div class='form-group'>
+
+            <label class="col-sm-2 control-label">Epoch</label>
+
+            <div class="col-sm-10">
+
+                <div class="input-group">
+                  <div class="input-group-addon" style='width:60px'>Year</div>
+                      {{ form.epoch(value=form.epoch.data, size=10, rows=1, class='form-control') }}
+                  <div class="input-group-addon" style='width:60px'></div>
+                </div>
+                <span id="helpBlock" class="help-block">The 4-digit year of the planned observations</span>
+                <br>
+                {% for error in form.epoch.errors %}
+                    <p style="color: red;">{{ error }}</p>
+                {% endfor %}
+
+            </div>
+        </div>
+
 		<hr class="col-md-12">
 
 		<div class='form-group'>

exoctk/exoctk_app/templates/contam_visibility_results.html

@@ -65,9 +65,9 @@ <h3>Target Visibility</h3>
     	{% if contam_plot %}
             <hr>
             {% if pa_val == -1 %}
-    		    <h3>Target Contamination at all Position Angles</h3>
+    		    <h3>Target Contamination for all Position Angles at Epoch={{ epoch }}</h3>
             {% else %}
-                <h3> Target Contamination at PA={{ pa_val }}</h3>
+                <h3> Target Contamination for PA={{ pa_val }} at Epoch={{ epoch }}</h3>
             {% endif %}
             <br>
             <!-- <p><img src="data:image/png;base64,{{ contam_plot | safe }}" alt="contam" width='1000px'></p> -->
@@ -105,6 +105,8 @@ <h3> Target Contamination at PA={{ pa_val }}</h3>
                         <li>The top plot shows the simulated observation at the given position angle.</li>
                         <li>The circles show the detector location of the 0th order, which you can click to resolve in Vizier.</li>
                         <li>Red lines show the predicted order 1, 2, and 3 trace positions for the target (solid) as well as all contaminant sources (dashed).</li>
+                        <li>If a source's Teff value is listed as "---" on hover, a temperature could not be determined and a 2300K model SED will be used for contamination estimation.</li>
+                        <li>Pink dashed lines show the predicted order 1, 2, and 3 trace positions for contaminant extended sources.</li>
                         <li>The bottom plot shows the fractional contamination of orders 1 (blue), 2 (red), and 3 (green) in each detector column.</li>
                     </ul>
                 {% endif %}

exoctk/exoctk_app/templates/fortney.html

@@ -29,7 +29,6 @@ <h1>Fortney Grid</h1>
                 <div class="col-sm-3">
 
                     <select id="ptemp" name="ptemp" class="form-control" data-placeholder="Select Temp (K)">
-                        <option value=""></option>
                         {% for i in temp %}
                             <option {{ i }} value={{ i }}>{{ i }}</option>
                         {% endfor %}
@@ -45,7 +44,6 @@ <h1>Fortney Grid</h1>
                 <div class="col-sm-3">
 
                     <select id="pchem" name="pchem" class="form-control" data-placeholder="Select Chemistry">
-                        <option value=""></option>
                         <option value='noTiO'>Equilibrium Chemistry</option>
                         <option value='eqchem'>Equilibrium Chemistry, w/ TiO</option>
                     </select>
@@ -60,7 +58,6 @@ <h1>Fortney Grid</h1>
                 <div class="col-sm-3">
 
                     <select id="cloud" name="cloud" class="form-control" data-placeholder="Clouds/Scattering">
-                        <option value=""></option>
                         <option value="0">Nothing</option>
                         <option value="ray10">Weak Rayleigh</option>
                         <option value="ray100">Medium Rayleigh</option>

exoctk/limb_darkening/limb_darkening_fit.py

@@ -1,8 +1,7 @@
 #!/usr/bin/python
 # -*- coding: latin-1 -*-
 """
-A module to calculate limb darkening coefficients from a grid of model
-spectra
+A module to calculate limb darkening coefficients from a grid of model spectra
 """
 
 from copy import copy