Restructure WFC3 notebooks (#264)

* Update WFC3 README with appropriate hyperlinks and installation

* Remove READMEs from each notebook

* Keep WFC3/dash notebook README until published

* Remove WFC3 legacy environments

* Add WFC3 subsection READMEs

* Add WFC3 subsections to TOC

_toc.yml

@@ -64,20 +64,25 @@ parts:
     - file: notebooks/STIS/extraction/1D_Extraction.ipynb
   - caption: WFC3
     chapters:
-      - file: notebooks/WFC3/README.md
-      - file: notebooks/WFC3/calwf3_recalibration/calwf3_recal_tvb.ipynb
-      - file: notebooks/WFC3/calwf3_v1.0_cte/calwf3_with_v1.0_PCTE.ipynb
-#      - file: notebooks/WFC3/dash/dash.ipynb
-      - file: notebooks/WFC3/exception_report/wfc3_exception_report.ipynb
+    - file: notebooks/WFC3/README.md
+    - file: notebooks/WFC3/general_tools.md
+      sections:
+        - file: notebooks/WFC3/image_displayer_analyzer/wfc3_image_displayer_analyzer.ipynb
+        - file: notebooks/WFC3/exception_report/wfc3_exception_report.ipynb
+        - file: notebooks/WFC3/calwf3_v1.0_cte/calwf3_with_v1.0_PCTE.ipynb
+        - file: notebooks/WFC3/persistence/wfc3_ir_persistence.ipynb
+    - file: notebooks/WFC3/ir_tvb.md
+      sections:
+        - file: notebooks/WFC3/ir_ima_visualization/IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.ipynb
+        - file: notebooks/WFC3/calwf3_recalibration/calwf3_recal_tvb.ipynb
+        - file: notebooks/WFC3/tvb_flattenramp/TVB_flattenramp_notebook.ipynb
+        - file: notebooks/WFC3/ir_scattered_light_calwf3_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_Using_calwf3_to_Mask_Bad_Reads.ipynb
+        - file: notebooks/WFC3/ir_scattered_light_manual_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_by_Manually_Subtracting_Bad_Reads.ipynb
+    - file: notebooks/WFC3/photometry.md
+      sections:
       - file: notebooks/WFC3/filter_transformations/filter_transformations.ipynb
       - file: notebooks/WFC3/flux_conversion_tool/flux_conversion_tool.ipynb
-      - file: notebooks/WFC3/image_displayer_analyzer/wfc3_image_displayer_analyzer.ipynb
-      - file: notebooks/WFC3/ir_ima_visualization/IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.ipynb
-      - file: notebooks/WFC3/ir_scattered_light_calwf3_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_Using_calwf3_to_Mask_Bad_Reads.ipynb
-      - file: notebooks/WFC3/ir_scattered_light_manual_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_by_Manually_Subtracting_Bad_Reads.ipynb
-      - file: notebooks/WFC3/persistence/wfc3_ir_persistence.ipynb
-      - file: notebooks/WFC3/zeropoints/zeropoints.ipynb
-      - file: notebooks/WFC3/tvb_flattenramp/TVB_flattenramp_notebook.ipynb
       - file: notebooks/WFC3/photometry_examples/phot_examples.ipynb
-      - file: notebooks/WFC3/uvis_pam_corrections/WFC3_UVIS_Pixel_Area_Map_Corrections_for_Subarrays.ipynb
       - file: notebooks/WFC3/uvis_time_dependent_photometry/uvis_timedep_phot.ipynb
+      - file: notebooks/WFC3/zeropoints/zeropoints.ipynb
+      - file: notebooks/WFC3/uvis_pam_corrections/WFC3_UVIS_Pixel_Area_Map_Corrections_for_Subarrays.ipynb

notebooks/WFC3/README.md

@@ -1,94 +1,84 @@
 WFC3 Notebooks
 ==============
 
-Here the user will find the latest Python-based software notebooks for the Wide
-Field Camera 3 (WFC3) on the Hubble Space Telescope (HST). For our primary WFC3
-user-support tools, see [wfc3tools](https://github.com/spacetelescope/wfc3tools) and 
-[WFC3 Software Tools](https://www.stsci.edu/hst/instrumentation/wfc3/software-tools).
-
-WFC3Library is the primary repository for Jupyter notebooks, including general tools, 
-WFC3/IR, time variable background (TVB), and photometry. This repository contains the 
-complementary notebooks mentioned in the [WFC3 Data Handbook](https://hst-docs.stsci.edu/wfc3dhb). 
+WFC3 Notebooks is the primary repository for analyzing data from the 
+[Wide Field Camera 3](https://www.stsci.edu/hst/instrumentation/wfc3) on the 
+Hubble Space Telescope. The Jupyter notebooks include tools for general data analysis, 
+WFC3/IR time variable background (TVB), and photometry. This repository contains the 
+complementary notebooks mentioned in the [WFC3 Data Handbook](https://hst-docs.stsci.edu/wfc3dhb).
 These notebooks include:
 
 General Tools:
-- WFC3 Image Displayer and Analyzer
-- Exception Report Checklist - WFC3
-- Processing WFC3/UVIS Data with `calwf3` Using the v1.0 CTE-Correction
-
-WFC3/IR:
-- Masking Persistence in WFC3/IR Images
-- How to use `wfc3_dash` on DASH data
+- [WFC3 Image Displayer and Analyzer](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/image_displayer_analyzer/wfc3_image_displayer_analyzer.html)
+- [Exception Report Checklist - WFC3](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/exception_report/wfc3_exception_report.html)
+- [Processing WFC3/UVIS Data with `calwf3` Using the v1.0 CTE-Correction](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/calwf3_v1.0_cte/calwf3_with_v1.0_PCTE.html)
+- [Masking Persistence in WFC3/IR Images](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/persistence/wfc3_ir_persistence.html)
 
 WFC3/IR Time Variable Background (TVB):
-- WFC3/IR IMA Visualization Tools with an Example of Time Variable Background
-- Manual Recalibration of Images using `calwf3`: Turning off the WFC3/IR Linear Ramp Fit
-- Correcting for Helium Line Emission Background in WFC3/IR Exposures using the "Flatten-Ramp" Technique
-- Correcting for Scattered Light in WFC3/IR Exposures: Manually Subtracting Bad Reads
-- Correcting for Scattered Light in WFC3/IR Exposures: Using `calwf3` to Mask Bad Reads
+- [WFC3/IR IMA Visualization Tools with an Example of Time Variable Background](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/ir_ima_visualization/IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.html)
+- [Manual Recalibration of Images using `calwf3`: Turning off the WFC3/IR Linear Ramp Fit](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/calwf3_recalibration/calwf3_recal_tvb.html)
+- [Correcting for Helium Line Emission Background in WFC3/IR Exposures using the "Flatten-Ramp" Technique](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/tvb_flattenramp/TVB_flattenramp_notebook.html)
+- [Correcting for Scattered Light in WFC3/IR Exposures: Manually Subtracting Bad Reads](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/ir_scattered_light_manual_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_by_Manually_Subtracting_Bad_Reads.html)
+- [Correcting for Scattered Light in WFC3/IR Exposures: Using `calwf3` to Mask Bad Reads](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/ir_scattered_light_calwf3_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_Using_calwf3_to_Mask_Bad_Reads.html)
 
 Photometry:
-- WFC3/UVIS Filter Transformations with `stsynphot`
-- Flux Unit Conversions with `synphot` and `stsynphot`
-- Synthetic Photometry Examples for WFC3
-- WFC3/UVIS Time-dependent Photometry
-- Calculating WFC3 Zeropoints with `stsynphot`
-- WFC3/UVIS Pixel Area Map Corrections for Subarrays
-
-Each folder in `notebooks` has an individual `README.md` with further 
-details and a HTML file that can be opened in a browser after cloning this 
-repository. The HTML file is identical to the notebook, except they contain 
-output plots and tables.
+- [WFC3/UVIS Filter Transformations with `stsynphot`](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/filter_transformations/filter_transformations.html)
+- [Flux Unit Conversions with `synphot` and `stsynphot`](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/flux_conversion_tool/flux_conversion_tool.html)
+- [Synthetic Photometry Examples for WFC3](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/photometry_examples/phot_examples.html)
+- [WFC3/UVIS Time-dependent Photometry](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/uvis_time_dependent_photometry/uvis_timedep_phot.html)
+- [Calculating WFC3 Zeropoints with `stsynphot`](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/zeropoints/zeropoints.html)
+- [WFC3/UVIS Pixel Area Map Corrections for Subarrays](https://spacetelescope.github.io/hst_notebooks/notebooks/WFC3/uvis_pam_corrections/WFC3_UVIS_Pixel_Area_Map_Corrections_for_Subarrays.html)
+
+See the [WFC3 Instrument Handbook](https://hst-docs.stsci.edu/wfc3ihb),
+[WFC3 Data Handbook](https://hst-docs.stsci.edu/wfc3dhb),
+[wfc3tools](https://github.com/spacetelescope/wfc3tools), and 
+[WFC3 Software Tools](https://www.stsci.edu/hst/instrumentation/wfc3/software-tools)
+for more information on instrumentation, data, calibration, and software.
 
 Installation
 ------------
 
-All notebooks require the virtual environment `stenv-stable` (last stable 
-version used for review was December 2022), which contains libraries necessary
-for processing and analyzing data from the Hubble Space Telescope (HST) and the
-James Webb Space Telescope (JWST).
-
-To install, see [stenv readthedocs](https://stenv.readthedocs.io/en/latest/)
-or [stenv GitHub](https://github.com/spacetelescope/stenv). 
-
-In addition, the individual `README.md` files in `notebooks` may have 
-further installation instructions. Please read them to run the notebooks 
-properly.
-
-With the environment activated and additional libraries installed based on the
-individual `README.md` files, you will be able to complete the notebooks.
+It is recommended to clone the entire repository. To do so, run the following
+command in terminal:
 
-Installation (Legacy Environment)
----------------------------------
+```
+git clone https://github.com/spacetelescope/hst_notebooks
+```
 
-**WARNING: `wfc3_env` is a legacy environment, meaning it is deprecated**
-**and no longer maintained. We recommend using `stenv-stable` in all cases.**
+`stenv` is the preferred base virtual environment for running WFC3 Noteboks since 
+it contains libraries necessary for processing and analyzing data from the Hubble 
+Space Telescope (HST) and the James Webb Space Telescope (JWST). To install, see 
+[stenv readthedocs](https://stenv.readthedocs.io/en/latest/) or 
+[stenv GitHub](https://github.com/spacetelescope/stenv). 
 
-All notebooks used to require the same anaconda virtual environment named 
-`wfc3_env`. To create the virtual environment, run this line in a terminal 
-window:
+`hst_notebooks/notebooks_env` is the default virtual environment for HST Notebooks, 
+which contains the same scientific computing libraries in `stenv`, but not the HST and
+JWST libraries. This environment can also be used as a base, but is not recommended.
 
-    conda env create -f wfc3_env_legacy.yml
+In addition, each notebook contains a `requirements.txt` file that needs to be
+installed before running the notebooks. Some notebooks contain a `pre-requirements.sh`
+file, usually to install [HSTCAL](https://github.com/spacetelescope/hstcal), which
+is the calibration software for HST. Here is a common set of commands to run 
+before executing the notebooks (assuming your virtual environment is activated):
 
-To activate `wfc3_env`, run this line in a terminal window:
+```
+bash pre-requirements.sh
+pip install -r requirements.txt
+pip install notebook
+```
 
-    conda activate wfc3_env
-
-You can also create and activate `wfc3_env_no_builds`, which is `wfc3_env` 
-but without the build specifications to avoid platform specific conflicts.
-
-Please read the individual `README.md` files in `notebooks` for further 
-installation instructions.
+With the environment activated and additional libraries installed based on the
+individual requirement files, you will be able to complete the notebooks.
 
 Contributing
 ------------
 
-Please open a new issue or new pull request for bugs, feedback, or new features
-you would like to see. If there is an issue you would like to work on, please
-leave a comment and we will be happy to assist. New contributions and
-contributors are very welcome!
+New contributions and feedback are very welcomed! Please open a new issue or new 
+pull request for bugs, feedback, or new features you would like to see. If there 
+is an issue you would like to work on, please leave a comment and we will be happy 
+to assist. Questions can also be sent through the [HST Help Desk](https://stsci.service-now.com/hst).
 
-WFC3Library follows the 
+WFC3 Notebooks follows the 
 [Astropy Code of Conduct](https://www.astropy.org/code_of_conduct.html)
 and strives to provide a welcoming community to all of our users and 
 contributors.
@@ -99,8 +89,7 @@ the the `astropy`
 and [developer](https://docs.astropy.org/en/stable/index.html#developer-documentation) 
 documentation.
 
-
 License
 -------
 
-WFC3Library is licensed under a 3-clause BSD style license (see the `LICENSE.txt` file).
+WFC3 Notebooks is licensed under a BSD 3-Clause License (see the `LICENSE.txt` file).

notebooks/WFC3/general_tools.md

@@ -0,0 +1,26 @@
+# General Tools
+Here are brief descriptions of WFC3 Notebooks for general tools:
+
+## WFC3 Image Displayer and Analyzer
+We present `display_image`, a tool for displaying full images 
+with metadata, individual WFC3/UVIS chip images, a section of an image with 
+various colormaps/scaling, and individual WFC3/IR `ima` reads. In addition, we 
+present `row_column_stats`, a tool for computing row and column statistics for 
+the types of WFC3 images previously mentioned.
+
+## Exception Report Checklist - WFC3
+We present the steps that should be taken when an observer receives a WFC3 
+Exception Report Email.
+
+## Processing WFC3/UVIS Data with `calwf3` Using the v1.0 CTE-Correction
+We compare `calwf3` v1.0 CTE correction versus v2.0, and explore
+when each version is useful. v1.0 will provide the most up-to-date calibration 
+procedures such as time-dependent photometric corrections and zeropoints, while 
+also including the v1.0 CTE correction.
+
+## Masking Persistence in WFC3/IR Images
+We present how to use the WFC3/IR persistence model to flag pixels affected by 
+persistence in the calibrated (FLT) science images. When the images are 
+sufficiently dithered to step over the observed persistence artifacts, 
+AstroDrizzle may be used to exclude those flagged pixels when combining the FLT 
+frames.