Homogenise how to instantiate firefly in all 3 notebooks

And headings cleanup in NEOWISE LCs notebook

Author: jaladh-singhal

tutorials/firefly/NEOWISE_light_curve_demo.md

@@ -4,7 +4,7 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.2
+    jupytext_version: 1.16.3
 kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
@@ -19,7 +19,6 @@ By the end of this tutorial, you will:
 
 - Construct a TAP query to download the necessary data and visualize it via the web browser with an instantiated Firefly environment.
 - Plot light curves from NEOWISE data using the Firefly Python API.
-- Format cells containing tables, charts and images viewed in the client.
 - Overlay a catalog of data onto a HiPS image.
 
 +++
@@ -53,26 +52,23 @@ import astropy.utils.data
 import urllib.parse
 ```
 
-## Step 1
+## Instantiate the Firefly client
 
-Instantiate the client and view it in a different tab in the web browser.
+There are two ways to initialize a Firefly client from Python, depending on whether you're running the notebook in JupyterLab or not. Assuming you have `jupyter-firefly-extensions` set up in your environment as explained [here](https://github.com/Caltech-IPAC/jupyter_firefly_extensions/blob/master/README.md), you can use `make_lab_client()` in JupyterLab, which will open the Firefly viewer in a new tab within the Lab. Otherwise, you can use `make_client()` in a Jupyter Notebook (or even a Python shell), which will open the Firefly viewer in a new web browser tab.
 
-In this example, we use the IRSA Viewer - a public firefly server. The firefly server can also be run locally, e.g. via a Firefly Docker image obtained from https://hub.docker.com/r/ipac/firefly/tags/.
+You also need a Firefly server to communicate with your Firefly Python client. In this notebook, we use a public Firefly server: the IRSA Viewer (https://irsa.ipac.caltech.edu/irsaviewer). However, you can also run a local Firefly server via a [Firefly Docker image](https://hub.docker.com/r/ipac/firefly) and access it at `http://localhost:8080/firefly`. The URL of the Firefly server is read by both `make_client()` and `make_lab_client()` through the environment variable `FIREFLY_URL`. However, `make_client()` also allows you to pass the URL directly as the `url` parameter.
 
 ```{code-cell} ipython3
-url = 'https://irsa.ipac.caltech.edu/irsaviewer'
-# url='http://127.0.0.1:8080/firefly'  # if you have firefly server running locally (preferably through docker)
+# Uncomment when using within Jupyter Lab with jupyter_firefly_extensions installed
+# fc = FireflyClient.make_lab_client()
 
-fc = FireflyClient.make_client(url)
-```
-
-You can re-initizialize the viewer to return to a clean state with [`reinit_viewer`](https://caltech-ipac.github.io/firefly_client/api/firefly_client.FireflyClient.html#firefly_client.FireflyClient.reinit_viewer).
+# Uncomment for contexts other than above 
+fc = FireflyClient.make_client(url="https://irsa.ipac.caltech.edu/irsaviewer")
 
-```{code-cell} ipython3
-# fc.reinit_viewer();  # The semi-colon suppresses the output of the method when ran
+fc.reinit_viewer() # to clean the state, if this cell ran earlier
 ```
 
-## Step 2
+## Construct a TAP Query and display the retrieved table in Firefly 
 
 TAP search the 'Known Solar System Object Possible Association List' catalog from the NEOWISE-R database. The specific target we are looking for is minor planet `558 Carmen`. We can query this target using a TAP search through IRSA; the `table_url` is broken down as follows:
 
@@ -110,15 +106,15 @@ Note that along with the table, firefly also displays the coverage and chart ass
 
 +++
 
-## Step 3
+## Plot Light Curves in Firefly
 
 After retrieving the data and displaying it in the client, we can now create a light curve by plotting the Modified Julian Date ('mjd') in the abscissa and the magnitude from band W1 ('w1mpro') in the ordinate. We also flip the ordinate to accurately display magnitude.
 
 ```{code-cell} ipython3
 fc.show_xyplot(tbl_id='tableneo', xCol='mjd', yCol='w1mpro', yOptions='flip')
 ```
 
-## Step 4
+## Overlay the catalog on a HiPS image
 
 Finally, we can overlay the catalog of data in the table onto a HiPS image of our choice, using the method [`show_hips`](https://caltech-ipac.github.io/firefly_client/api/firefly_client.FireflyClient.html#firefly_client.FireflyClient.show_hips). However, this method requires target coordinates for the object you want to analyze.
 
@@ -153,6 +149,6 @@ Firefly allows you to visualize data for specific targets. In conjuction with As
 
 **Author:** Eric Bratton II (IRSA Scientist) in conjunction with the IRSA Science Team
 
-**Updated:** 2024-10-17
+**Updated:** 2024-12-19
 
 **Contact:** [the IRSA Helpdesk](https://irsa.ipac.caltech.edu/docs/help_desk.html) with questions or reporting problems.

tutorials/firefly/OpenUniverse2024Preview_Firefly.md

@@ -373,11 +373,18 @@ Clearly, the simulated Roman coadd has higher spatial resolution than the Rubin
 +++
 
 ### Launch and initialize Firefly
+There are two ways to initialize a Firefly client from Python, depending on whether you're running the notebook in JupyterLab or not. Assuming you have `jupyter-firefly-extensions` set up in your environment as explained [here](https://github.com/Caltech-IPAC/jupyter_firefly_extensions/blob/master/README.md), you can use `make_lab_client()` in JupyterLab, which will open the Firefly viewer in a new tab within the Lab. Otherwise, you can use `make_client()` in a Jupyter Notebook (or even a Python shell), which will open the Firefly viewer in a new web browser tab.
+
+You also need a Firefly server to communicate with your Firefly Python client. In this notebook, we use a public Firefly server: the IRSA Viewer (https://irsa.ipac.caltech.edu/irsaviewer). However, you can also run a local Firefly server via a [Firefly Docker image](https://hub.docker.com/r/ipac/firefly) and access it at `http://localhost:8080/firefly`. The URL of the Firefly server is read by both `make_client()` and `make_lab_client()` through the environment variable `FIREFLY_URL`. However, `make_client()` also allows you to pass the URL directly as the `url` parameter.
 
 ```{code-cell} ipython3
-fc = FireflyClient.make_client()
+# Uncomment when using within Jupyter Lab with jupyter_firefly_extensions installed
+# fc = FireflyClient.make_lab_client()
+
+# Uncomment for contexts other than above 
+fc = FireflyClient.make_client(url="https://irsa.ipac.caltech.edu/irsaviewer")
 
-fc.reinit_viewer() #to clean the state, if this cell ran earlier
+fc.reinit_viewer() # to clean the state, if this cell ran earlier
 ```
 
 ### Send the simulated Rubin coadd to Firefly using show_fits.
@@ -738,6 +745,6 @@ fc.set_stretch(plot_id=coadd_ff_id_roman_3color, stype='sigma', algorithm='squar
 
 **Author:** Jaladh Singhal and Vandana Desai in conjunction with the IRSA Team
 
-**Updated:** 2024-12-18
+**Updated:** 2024-12-19
 
 **Contact:** [the IRSA Helpdesk](https://irsa.ipac.caltech.edu/docs/help_desk.html) with questions or reporting problems.

tutorials/firefly/SEDs_in_Firefly.md

@@ -4,7 +4,7 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.2
+    jupytext_version: 1.16.3
 kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
@@ -62,8 +62,6 @@ The packages needed for this notebook are in the `requirements.txt` file. They c
 * _numpy_ - for working with arrays
 * _pyvo_ - for queries to Virtual Observatory services at the archives
 
-+++
-
 ```{code-cell} ipython3
 # Uncomment the next line to install dependencies if needed.
 # !pip install numpy astropy pyvo firefly_client
@@ -551,16 +549,18 @@ phot_tbl
 
 +++
 
-This notebook assumes that [jupyter_firefly_extensions](https://github.com/Caltech-IPAC/jupyter_firefly_extensions) has been installed, and that the Firefly server to use has been specified before Jupyterlab was started.
+There are two ways to initialize a Firefly client from Python, depending on whether you're running the notebook in JupyterLab or not. Assuming you have `jupyter-firefly-extensions` set up in your environment as explained [here](https://github.com/Caltech-IPAC/jupyter_firefly_extensions/blob/master/README.md), you can use `make_lab_client()` in JupyterLab, which will open the Firefly viewer in a new tab within the Lab. Otherwise, you can use `make_client()` in a Jupyter Notebook (or even a Python shell), which will open the Firefly viewer in a new web browser tab.
 
-If everything has been properly configured, executing the next cell will bring up a Firefly tab in Jupyterlab with the welcome message.
+You also need a Firefly server to communicate with your Firefly Python client. In this notebook, we use a public Firefly server: the IRSA Viewer (https://irsa.ipac.caltech.edu/irsaviewer). However, you can also run a local Firefly server via a [Firefly Docker image](https://hub.docker.com/r/ipac/firefly) and access it at `http://localhost:8080/firefly`. The URL of the Firefly server is read by both `make_client()` and `make_lab_client()` through the environment variable `FIREFLY_URL`. However, `make_client()` also allows you to pass the URL directly as the `url` parameter.
 
 ```{code-cell} ipython3
-# Uncomment to use the jupyter_firefly_extensions
-#fc = FireflyClient.make_lab_client()
+# Uncomment when using within Jupyter Lab with jupyter_firefly_extensions installed
+# fc = FireflyClient.make_lab_client()
 
-# Uncomment to use a separate web browser tab
+# Uncomment for contexts other than above 
 fc = FireflyClient.make_client(url="https://irsa.ipac.caltech.edu/irsaviewer")
+
+fc.reinit_viewer() # to clean the state, if this cell ran earlier
 ```
 
 In the event that there are problems with the tab opened above, run the below command to obtain a web link that can be opened in a browser directly:
@@ -703,6 +703,6 @@ Note that zooming or panning one image will do the same in the other images as w
 
 **Author:** David Shupe (IRSA Scientist) and Joyce Kim (IRSA Scientist) in conjunction with the IRSA Science Team
 
-**Updated:** 2024-12-18
+**Updated:** 2024-12-19
 
 **Contact:** [the IRSA Helpdesk](https://irsa.ipac.caltech.edu/docs/help_desk.html) with questions or reporting problems.