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<img src="../images/icons/question_mark.svg" style="vertical-align: middle; width:1.5em; margin-right:0.25em;"/> [What is the RSP?](../markdown/what-is-rsp.md)

<img src="../images/icons/learning.svg" style="vertical-align: bottom; width:1.5em; margin-right:0.25em;"/> [Roman Science Workflows and Notebook Tutorials](../markdown/tutorials.md)
<img src="../images/icons/learning.svg" style="vertical-align: bottom; width:1.5em; margin-right:0.25em;"/> [Roman Science Workflows](../markdown/workflows.md) and [Notebook Tutorials](../markdown/tutorials.md)

<img src="../images/icons/database.svg" style="vertical-align: bottom; width:1.5em; margin-right:0.25em;"/> [What data are available?](../markdown/simulated-data.md)

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31 changes: 10 additions & 21 deletions markdown/tutorials.md
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# RSP Jupyter Notebooks Tutorials
Jupyter Notebooks offer an efficient and powerful way to interact with Roman datasets. Always save and shut down all notebooks, and log out of JupyterLab when you have finished your work. This is important to preserve resources for other users and to ensure you enter the RSP in a known state every time.
## What are Notebook Tutorials?
In the Roman Science Platform (RSP) framework, a notebook tutorial refers to a Jupyter notebook demonstrating how to use a specific piece of code or tool. A set of predefined Jupyter notebook tutorials is available to demonstrate how to use tools and software for accessing, simulating, processing, visualizing, and analyzing Roman Wide Field Instrument (WFI) data within the science platform. Although the current content primarily focuses on WFI imaging mode, Jupyter notebook tutorials for spectroscopic products will be available by Winter 2024.

## How to Use the Notebook Tutorials
A set of predefined Jupyter Notebook tutorials is available to demonstrate how to use tools and software to access, simulate, process, visualize, and analyze Roman Wide Field Instrument (WFI) data within the science platform. Each tutorial is self-contained, well-documented, and guides users through each step.

Each notebook can also be seen as an individual component or module within a larger science workflow, offering users a complete end-to-end experience. While many different workflows are possible, the current documentation focuses on three main use cases: WFI observation planning, WFI data simulations, and WFI data analysis.

### Summary
- Tutorial: A notebook demonstrating how to use specific code or tools.
- Science Workflow: A combination of documentation and notebook tutorials demonstrating how to achieve a specific science-focused use case.
Each tutorial is self-contained, well-documented, and guides users through every step. While Jupyter notebook tutorials can be used as standalone tools, they also function as individual components or modules within larger science workflows, offering users a complete end-to-end experience.

### Workflows
While users can choose to run any single Jupyter Notebook tutorial as a standalone tool, Science Workflows are designed to offer a complete end-to-end experience. Here, we consider three common workflows focused on the Roman Wide Field Instrument (WFI):

- [WFI Observation Planning](workflows/wfi-obs-plan.md)
- [WFI Data Simulation](workflows/wfi-data-sim.md)
- [WFI Data Analysis](workflows/wfi-data-analysis.md)

There are many potential workflows not covered in this outline; even if you don't see it here, the RSP can likely support your workflow! While the current content primarily focuses on the WFI imaging mode, Jupyter Notebook tutorials and Science Workflows for spectroscopic products will be available by Winter 2024.
## How to Use the Notebook Tutorials
Jupyter notebooks provide an efficient and powerful way to interact with Roman datasets. Always remember to [save and shut down all notebooks and log out](./jupyter.md) of JupyterLab when you finish your work. This is important to preserve resources for other users and to ensure that you enter the Roman Science Platform (RSP) in a known state every time.

## All Notebooks
Below is an outline of the content covered in each notebook and the Science Workflows they are part of. While the current content primarily focuses on the WFI imaging mode, Jupyter Notebook tutorials for spectroscopic products will be available by Winter 2024.
Below is an outline of the content covered in each notebook and the Science Workflows they are part of. While the current content primarily focuses on the WFI imaging mode, Jupyter notebook tutorials for spectroscopic products will be available by Winter 2024.



| Jupyter Notebook Tutorial | Content and Scope | Science Workflow(s) |
|-------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------|------------------------------------------|
| [Data Discovery and Access](../content/notebooks/data_discovery_and_access/data_discovery_and_access.ipynb) | Access data in the cloud archive ("S3 bucket") | WFI Data Analysis |
| [Working with ASDF](../content/notebooks/working_with_asdf/working_with_asdf.ipynb) | Open ASDF files with roman_datamodels, access metadata, manipulate arrays, and save changes to disk | WFI Data Simulation<br>WFI Data Analysis |
| [Data Visualization](../content/notebooks/data_visualization/data_visualization.ipynb) | Use Imviz to display a preview of Roman Level 2 products. | WFI Data Simulation<br>WFI Data Analysis |
| [Data Discovery and Access](../content/notebooks/data_discovery_and_access/data_discovery_and_access.ipynb) | Retrieve data from MAST or access simulated Roman data in the cloud archive ("S3 bucket"). | WFI Data Analysis |
| [Working with ASDF](../content/notebooks/working_with_asdf/working_with_asdf.ipynb) | Open ASDF files with roman_datamodels, access metadata, manipulate arrays, and save changes to disk. | WFI Data Simulation<br>WFI Data Analysis |
| [Data Visualization](../content/notebooks/data_visualization/data_visualization.ipynb) | Use Imviz to display a preview of Roman Level 2 products and run quick analysis tools. | WFI Data Simulation<br>WFI Data Analysis |
| [Roman I-sim](../content/notebooks/romanisim/romanisim.ipynb) | Generate Level 1 and Level 2 WFI imaging products. | WFI Data Simulation |
| [RomanCal](..content/notebooks/romancal/romancal.ipynb) | Process WFI L1 imaging raw data to obtain exposure level products. | WFI Data Simulation<br>WFI Data Analysis |
| [Aperture Photometry](../content/notebooks/aperture_photometry/aperture_photometry.ipynb) | Perform forced aperture photometry on a simulated WFI image. | WFI Data Analysis |
| [Galaxy Shapes](../content/notebooks/measuring_galaxy_shapes/measuring_galaxy_shapes.ipynb) | Perform shape measurements of galaxies on a simulated WFI image. | WFI Data Analysis |
| [Pandeia](../content/notebooks/pandeia/pandeia.ipynb) | Estimate the exposure parameters needed to reach a given SNR for simulated sources in a small area of one WFI detector. | WFI Observations Planning |
| [RIST](../content/notebooks/rist/rist.ipynb) | Simplified, interactive version of Pandeia. Estimate the SNR for a variety of target brightnesses and filters. | WFI Observations Planning |
| [RIST](../content/notebooks/rist/rist.ipynb) | Roman Interactive Sensitivity Tool. Simplified, interactive version of Pandeia. Estimate the SNR for a variety of target brightnesses and filters. | WFI Observations Planning |
| [STIPS](../content/notebooks/stips/stips.ipynb) | Simulate large astronomical scenes with WFI full field-of-view. | WFI Observations Planning |
| [Synphot](../content/notebooks/romanisim_romancal/romanisim_romancal.ipynb) | Synthetic photometry software, estimate the brightness of sources observed with Roman WFI. | WFI Observations Planning |
| [WebbPSF](../content/notebooks/webbpsf/webbpsf.ipynb) | Generate WFI simulated Point Spread Functions using WebbPSF. | WFI Observations Planning |
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# Science Workflows
In the Roman Science Platform (RSP) framework, a Notebook Tutorial refers to a Jupyter Notebook that demonstrates the use of a specific piece of code or tool. A Science Workflow is a combination of multiple Notebook Tutorials, along with accompanying documentation, that guides users through a specific science use case.

Users can run the Jupyter Notebook Tutorials in any order or modify them to suit specific data or science goals. However, following the sequence outlined in the Science Workflows ensures a complete, end-to-end experience. Science Workflows are particularly beneficial for new users unfamiliar with Roman data, tools, and infrastructure, but they also offer a valuable starting point for experienced users aiming to apply them to their own datasets.

We currently support three Science Workflows focused on the Roman Wide Field Instrument (WFI):
- [WFI Data Simulation](./workflows/wfi-data-sim.md)
- [WFI Data Analysis](./workflows/wfi-data-analysis.md)
- [WFI Observation Planning](./workflows/wfi-obs-plan.md)

There are many potential workflows beyond these. Even if yours isn't listed, the RSP can likely support your specific workflow!

Although the current content primarily focuses on WFI imaging mode, Jupyter Notebook Tutorials and Science Workflows for spectroscopic products will be available by Winter 2024.
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# RSP Science Workflows: WFI Data Analysis

This workflow is designed for users that want to analyze their WFI data products for scientific purposes.
![wfi-analysis-flow](../../images/wfi-data-analysis.png)
This science workflow guides users through the discovery and access of data while working in the cloud, as well as the manipulation, visualization, and analysis of simulated Roman WFI imaging data products.



## Workflow Description

- [Access data on the RSP](../../content/notebooks/data_discovery_and_access/data_discovery_and_access.ipynb)
> Stream data from the cloud directly into memory, bypassing the need to download data locally. Learn how to download data from the STScI MAST server, which hosts data for in-flight telescopes including Hubble, TESS, and JWST, or access simulated Roman WFI data stored in AWS cloud containers.
- [Explore Roman WFI Data Files](../../content/notebooks/working_with_asdf/working_with_asdf.ipynb)
> Explore Roman WFI data products by understanding the ASDF format (Advanced Scientific Data Format). Roman WFI data products, including those generated by Roman I-sim, are saved in ASDF format. Learn how to manage ASDF files, read metadata, and access data arrays.
- [Process Roman WFI Raw Data](../../content/notebooks/romancal/romancal.ipynb)
> Process your data in RomanCal, the Roman calibration pipeline. Learn how to use RomanCal to generate L2 data from L1 raw data.
- [Visualize Roman WFI L2 Data Products](../../content/notebooks/data_visualization/data_visualization.ipynb)
> Visualize your L2 data products using Matplotlib and Imviz, a tool for visualization and analysis of 2D astronomical images based on the Jupyter platform with built-in Astropy functionality.
- [Data Discovery and Access](../../content/notebooks/data_discovery_and_access/data_discovery_and_access.ipynb): Access data from MAST or retrieve WFI simulated images
> Stream data directly into memory from the cloud, eliminating the need to download it locally. Access data from the STScI MAST server, which hosts datasets from active missions such as Hubble, TESS, and JWST, or retrieve simulated Roman WFI data stored in AWS.
- [Working with ASDF](../../content/notebooks/working_with_asdf/working_with_asdf.ipynb): Explore Roman WFI Data Files
> Explore WFI data products by understanding the Advanced Scientific Data Format (ASDF). Roman WFI data products, including those generated by Roman-I-Sim, are saved in ASDF format. Learn how to manage ASDF files, read metadata, and access data arrays. To learn more about Roman WFI data levels and products, visit the [RDox pages on the WFI data format](https://roman-docs.stsci.edu/data-handbook-home/wfi-data-format).
- [Data Visualization](../../content/notebooks/data_visualization/data_visualization.ipynb): Visualize Roman WFI L2 Data Products
> Visualize your L2 data products using Matplotlib and Imviz, a tool for visualizing and quickly analyzing 2D astronomical images. Imviz is based on the Jupyter platform and includes built-in Astropy functionality. For additional background, consult the Imviz documentation on ReadTheDocs.
- Analyze Roman WFI images
- > Perform [forced aperture photometry](../../content/notebooks/aperture_photometry/aperture_photometry.ipynb) on a WFI image simulated with Roman I-sim. Learn how to measure the integrated fluxes for a set of specified source positions and aperture sizes.
- > Perform [shape measurements](../../content/notebooks/measuring_galaxy_shapes/measuring_galaxy_shapes.ipynb) of astronomical sources on a WFI image simulated with Roman I-sim. Use galsim to perform ellipticity measurements, and learn how to fit a Sérsic model to a galaxy coutout.
- > [Aperture photometry](../../content/notebooks/aperture_photometry/aperture_photometry.ipynb): Perform forced aperture photometry on a WFI image simulated with Roman I-sim. Learn how to measure the integrated fluxes for a set of specified source positions and aperture sizes.
- > [Galaxy Shapes](../../content/notebooks/measuring_galaxy_shapes/measuring_galaxy_shapes.ipynb): Perform shape measurements of astronomical sources on a WFI image simulated with Roman-I-Sim. Use Galsim to perform ellipticity measurements, and learn how to fit a Sérsic model to a galaxy cutout.
![wfi-analysis-flow](../../images/wfi-data-analysis.png)

## Additional Background Information
Additional documentation is available at the links below:
- [Roman I-Sim on readthedocs](https://romanisim.readthedocs.io/en/latest/)
- [RomanCal on readthedocs](https://roman-pipeline.readthedocs.io/en/latest/)
- [Imviz on readthedocs](https://roman-pipeline.readthedocs.io/en/latest/)

## Caveat and limitations
While the current content primarily focuses on the WFI imaging mode, Jupyter Notebook tutorials and Science Workflows for spectroscopic products will be available by Winter 2024.
- The current content focuses on WFI imaging mode. Jupyter notebook tutorials and Science Workflows for spectroscopic products will be available by winter 2024.
- Content on Level 3 products, including mosaicked images, will be available by Winter 2024.
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