Merge pull request #20 from pcubillos/pandeia4

Pandeia 4!
pcubillos · Aug 2, 2024 · 0fa577e · 0fa577e
2 parents 1d695ee + d85fc3a
commit 0fa577e
Show file tree

Hide file tree

Showing 40 changed files with 530 additions and 163 deletions.
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # ✨ Gen TSO ✨
 ### A general ETC interface for time-series observations with JWST
 
-(Getting there...)
+(Nearly at official release...)
 
 <!--
 [![Tests](https://github.com/pcubillos/gen_tso/actions/workflows/python-package.yml/badge.svg?branch=master)](https://github.com/pcubillos/gen_tso/actions/workflows/python-package.yml)
@@ -14,11 +14,9 @@
 
 ### Install as:
 
-Not yet on PyPI or Conda, but for the moment you can get the code from Github:
+Available for Python 3.9+ from PyPI:
 ```
-git clone https://github.com/pcubillos/gen_tso/
-cd gen_tso
-pip install .
+pip install gen_tso
 ```
 
 Then setup the pandeia reference files following these instructions: [https://pcubillos.github.io/gen_tso/install.html](https://pcubillos.github.io/gen_tso/install.html#pandeia-engine-installation)
@@ -40,3 +38,4 @@ tso
 
 Comming soon ...
 
+
diff --git a/docs/get_started.qmd b/docs/get_started.qmd
@@ -1,48 +1,59 @@
 ---
-title: Get started
+title: Getting started
+page-navigation: true
 ---
 
-## Walk through
+With `Gen TSO` you can produce JWST simulated spectra in as few as four simple steps.
 
-You can install `Gen TSO` from [PyPI](https://pypi.org/project/gen_tso/) with the following command:
+## 1 Select target
 
-```bash
-pip install gen_tso
-```
+A drop down menu lets you search/type for confirmed planets and TESS candidates
+(data provided by the NASA Exoplanet Archive).  Once a target is selected:
 
-### Instrument and mode selection
+- [Editable fileds](select_target.qmd) are automatically filled with the system properties
+- A link provides the target's name aliases full system properties
+- A link leads you to the NASA Exoplanet Archive
+- A link displays the exisiting JWST programs on the host star
 
-To use `pandeia` you would need to download some files as per their [documentation](https://outerspace.stsci.edu/display/PEN/Pandeia+Engine+Installation).
+---
+
+{{< video images/select_target.webm width='800'>}}
+
+---
+
+## 2 Set instrument and mode
+
+The top menu lets you select the JWST instrument and mode:
 
-### Target selection
+- All TSO spectroscopic and acquisition modes are available
+- The detector setup panel gets automatically updated for the current instrument
+- The right interactive viewer shows the available filter throughputs of the instrument
 
-First you need to download the pandeia reference data (version 3.0) from
-this folder: [https://stsci.app.box.com/v/pandeia-refdata-v3p0-jwst](https://stsci.app.box.com/v/pandeia-refdata-v3p0-jwst)
+---
+
+{{< video images/select_instrument.webm width='800'>}}
+
+---
 
-### Detector setup
+## 3 Set transit/eclipse model
 
-Unpack the file and set the `$pandeia_refdata` environment variable pointing
-to the top folder of the data (the directory containing the VERSION_PSF file).
+The transit or eclipse depth spectrum encodes the core of a science case,
+so this is the one bit of information that a user has to provide.
+In the `Gen TSO` application users can:
 
-### Stellar atlases:
+- Search and upload specific transit/eclipse depth spectra
+- Pre-load spectra when launching the application
+- Use blackbody or flat-transmission spectra for a quick S/N assessment
+- Interactively view and compare spectra in the viewer panel
 
-Then, you need to download these three reference stellar and calibration files, for example with these commands:
+---
 
-```{.bash filename=run.sh}
-wget https://archive.stsci.edu/hlsps/reference-atlases/hlsp_reference-atlases_hst_multi_kurucz-1993-atlas_multi_v2_synphot4.tar
-wget https://archive.stsci.edu/hlsps/reference-atlases/hlsp_reference-atlases_hst_multi_pheonix-models_multi_v3_synphot5.tar
-wget https://archive.stsci.edu/hlsps/reference-atlases/hlsp_reference-atlases_hst_multi_everything_multi_v15_sed.tar
-```
+{{< video images/select_transit_depth.webm width='800'>}}
 
-Unpack these files and set the environment variable: `$PYSYN_CDBS` pointing to
-the trds directory.
+---
 
-### Vega reference SED:
 
-Lastly, you need to download the Vega reference spectrum:
+## 4 Run Pandeia
 
-```bash
-wget https://ssb.stsci.edu/trds/calspec/alpha_lyr_stis_010.fits
-```
+TBD
 
-and place the file in your `$PYSYN_CDBS` trds/calspec/ folder.
diff --git a/docs/images/select_instrument.webm b/docs/images/select_instrument.webm
diff --git a/docs/images/select_target.webm b/docs/images/select_target.webm
diff --git a/docs/images/select_transit_depth.webm b/docs/images/select_transit_depth.webm
diff --git a/docs/images/status_display.png b/docs/images/status_display.png
diff --git a/docs/images/status_gear.png b/docs/images/status_gear.png
diff --git a/docs/images/target_aliases.png b/docs/images/target_aliases.png
diff --git a/docs/images/target_candidate.png b/docs/images/target_candidate.png
diff --git a/docs/images/target_filter.png b/docs/images/target_filter.png
diff --git a/docs/images/target_magnitude.png b/docs/images/target_magnitude.png
diff --git a/docs/images/target_panel.png b/docs/images/target_panel.png
diff --git a/docs/images/target_programs.png b/docs/images/target_programs.png
diff --git a/docs/images/target_sed_model.png b/docs/images/target_sed_model.png
diff --git a/docs/images/target_sed_type.png b/docs/images/target_sed_type.png
diff --git a/docs/images/target_sed_viewer.png b/docs/images/target_sed_viewer.png
diff --git a/docs/images/target_system_parameters.png b/docs/images/target_system_parameters.png
diff --git a/docs/images/target_upload_sed.png b/docs/images/target_upload_sed.png
diff --git a/docs/index.qmd b/docs/index.qmd
@@ -3,6 +3,7 @@ title: "Gen TSO Documentation"
 author: "Patricio Cubillos"
 date: today
 output: html_document
+page-navigation: true
 ---
 
 ---

diff --git a/docs/install.qmd b/docs/install.qmd
@@ -19,17 +19,27 @@ To use `pandeia` you need to download some files as per their [documentation](ht
 
 ### 2.1 Reference data
 
+If you don't have it yet, download the latest pandeia reference data,
+unzip it, and place it in the folder pointed by `$pandeia_refdata`.
+Here's the current latest version:
+[https://stsci.app.box.com/v/pandeia-refdata-v4p0-jwst](https://stsci.app.box.com/v/pandeia-refdata-v4p0-jwst)
+
 If this is your first time using pandeia, you likely need to setup a
-`$pandeia_refdata` environment variable (e.g., in your `~/.bashrc` file).
+`$pandeia_refdata` environment variable (e.g., in your `~/.bashrc`,
+`~/.bash_profile`, or whichever bash file your machine uses).
+
+Then you will need to start a new prompt terminal or source your bash
+file, e.g.:
+```bash
+source ~/.bashrc
+```
 
-Then, download the pandeia reference data, unzip it, and place
-it in the folder pointed by `$pandeia_refdata`. Here's the current latest version: [https://stsci.app.box.com/v/pandeia-refdata-v3p2-jwst](https://stsci.app.box.com/v/pandeia-refdata-v3p2-jwst)
 
 You should end up with something like this:
 
 ```bash
 echo $pandeia_refdata
-/home/USERNAME/data/pandeia_data-3.2-jwst
+/home/USERNAME/data/pandeia_data-4.0-jwst
 ```
 
 ### 2.2 Atlases data
@@ -71,6 +81,7 @@ wget https://ssb.stsci.edu/trds/calspec/alpha_lyr_stis_010.fits
 If everything went right, then you should see something similar to this:
 
 ```bash
+# (remember to source your bash file or start a new prompt terminal)
 echo $PYSYN_CDBS
 /home/USERNAME/data/pysynphot/trds
 
@@ -92,3 +103,21 @@ current date, you can run this prompt command:
 ```bash
 TSO --update_exo
 ```
+
+<br>
+
+## Live status check
+
+While you are running the `Gen TSO` application, click on this gear icon
+at the top right of the screen:
+
+![](images/status_gear.png){width=375px}
+
+This will pop up a more detailed panel indicating whether any database needs
+to be updated (and if needed, it will give you the instructions to do so):
+
+![](images/status_display.png){width=600px}
+
+
+
+
diff --git a/docs/select_target.qmd b/docs/select_target.qmd
@@ -0,0 +1,106 @@
+---
+title: Setting target properties
+page-navigation: true
+---
+
+## Select target
+
+::: {.column-margin}
+![Target selection panel](images/target_panel.png){width=250px}
+:::
+
+The **Target** panel lets the user select the science target from a
+dropdown menu of known target (from the NASA Exoplanet Archive).  An
+auto-complete feature facilitates searching for specific targets.
+
+The gear icon lets users filter what kind of target to search:
+
+![](images/target_filter.png){width=400px}
+
+
+By selecting a target, the fields with the physical properties needed
+to simulate an observation will be automatically updated.  The values
+in these fields can be edited if desired.  The various information
+links help to make an informed decision (see below).
+
+---
+
+### Info-links
+
+For any given target, info-links on top of the name will provide
+additional information about the target.
+
+The first link (blue) shows any relevant name alias for the target:
+
+![](images/target_aliases.png){width=250px fig-align="left"}
+
+When clicked, `Gen TSO` will display the system parameters extracted
+from the NASA Archive.
+The second link (black) will open the NASA Archive page for the current
+target.
+
+![](images/target_system_parameters.png){width=450px}
+
+
+The third link indicates whether the *host* has JWST observing
+programs (gold color) or not (gray).  For targets with JWST
+programs one can click on the link to display a summary of the
+programs (data from the
+[Trexolists](https://www.stsci.edu/~nnikolov/TrExoLiSTS/JWST/trexolists.html)
+website).  Color coding indicates whether the program was carried out,
+is in proprietary period, or is still to be observed.
+
+![](images/target_programs.png){width=600px}
+
+
+Lastly, unconfirmed candidate targets have an additional icon
+highlighting that:
+
+![](images/target_candidate.png){width=250px fig-align="left"}
+
+
+## Stellar properties
+
+The main stellar values to set for a simulation are the magnitude and
+stellar energy distribution (SED).
+
+
+::: {.column-margin}
+![Target selection panel](images/target_panel.png){width=250px}
+:::
+
+`Gen TSO` provides the Ks magnitude value for the targets.  Users can
+choose among the J, H, Ks, Gaia, and V bands; although these values
+rarely need to be edited since these magnitudes are well established:
+
+![](images/target_magnitude.png){width=250px fig-align="left"}
+
+The stellar effective temperature and log(g) values mainly inform the
+user on the optimal SED to choose.  `Gen TSO` provides a set of
+PHOENIX, Kurucz, and Blackbody models.
+
+::: {layout-ncol=2}
+
+![SED types](images/target_sed_type.png){width=250px}
+
+![Kurucz SED models](images/target_sed_model.png){width=250px}
+
+:::
+
+By clicking the bookmark (star) icon, users can display and compare
+the SEDs on the right viewer panel.  The instrumental observing band
+will be highlighted in light-blue indicating the wavelength range of
+the SED(s) being probed.
+
+![](images/target_sed_viewer.png){width=550px fig-align="left"}
+
+
+Users can also provide their own custom SED models by clicking the
+*upload* icon, which will pop up the following panel:
+
+![](images/target_upload_sed.png){width=350px fig-align="left"}
+
+## Observation configuration
+
+Users can choose between transit and eclipse observation modes.
+
diff --git a/gen_tso/data/throughputs/throughputs_nircam_lw_tsgrism.pickle b/gen_tso/data/throughputs/throughputs_nircam_lw_tsgrism.pickle
diff --git a/gen_tso/data/throughputs/throughputs_nircam_ssgrism.pickle b/gen_tso/data/throughputs/throughputs_nircam_ssgrism.pickle