_toc.yml

# Table of contents
# Learn more at https://jupyterbook.org/customize/toc.html
format: jb-book
root: intro
defaults:  # The defaults key will be applied to all chapters and sub-sections
  titlesonly: True
parts:
  - caption: General
    chapters:
    - file: index.rst
      title: Home
    - file: install.rst
      title: Installation
    - file: docs/notebook_development_workflow.rst
      title: Notebook Development Workflow   
  - caption: Development
    chapters:
    - file: docs/submitting_notebooks.rst
      title: Submitting Notebooks
    - file: docs/requirements.rst
      title: Requirements file 
    - file: docs/notebooks.rst
      title: Jupyter Notebooks
    - file: docs/data_files.rst
      title: Data Files 
  - caption: GitHub Guidelines
    chapters:
    - file: docs/github_setup.rst
      title: GitHub Setup
    - file: docs/github_workflow.rst
      title: GitHub Workflow
    - file: docs/github_pr.rst
      title: GitHub PR        
  #- caption: Developers and Staff
    # chapters:     
    # - file : docs/stsci_notebook_leads.rst     
    #   title: STScI Notebook Leads     
  - caption: Cross-Instrument
    chapters:
    - file: notebooks/asdf_example/asdf_example.ipynb
      title: ASDF Example
    - file: notebooks/background_estimation_imaging/Imaging_Sky_Background_Estimation.ipynb
      title: Complex 2D Background
    - file: notebooks/composite_model_fitting/specfit_demo_3.ipynb
      title: Composite Model Spectral Fitting
    - file: notebooks/NIRSpec_MAST_Query/NIRSpec_MAST_Query.ipynb
      title: MAST Query
    - file: notebooks/rgb_imviz/imviz_rgb_carina.ipynb
      title: RGB images with Imviz
    - file: notebooks/specviz_notebookGUI_interaction/specviz_notebook_gui_interaction_redshift.ipynb
      title: Specviz Simple Demo
    #- file: notebooks/cube_fitting/cube_fitting.ipynb
    # title: IFU Cube Line Maps
  - caption: MIRI
    chapters:
    #- file: notebooks/example_notebook
    #  title: TEST SECTION
    #  sections:
    #    - file: notebooks/example_notebook/example_notebook.ipynb
    #      title: Section 1
    - file: notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_runpipeline.ipynb
      title: MRS Mstar - Run Pipeline
    - file: notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_PointSourceDetectorBasedExtraction.ipynb
      title: MRS Mstar - Optimal Extraction
      #sections:
      #- file: notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_runpipeline.ipynb
      #  title: Run Pipeline
    - file: notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_analysis.ipynb
      title: MRS Mstar - Data Analysis
    - file: notebooks/MIRI_IFU_YSOs_in_the_LMC/isha_nayak_ysos_in_the_lmc.ipynb
      title: IFU of YSOs in LMC
    - file: notebooks/MIRI_LRS_spectral_extraction/miri_lrs_advanced_extraction_part1.ipynb
      title: LRS Optimal Spectral Extraction
  - caption: NIRCam
    chapters:
    - file: notebooks/aperture_photometry/NIRCam_Aperture_Photometry_Example.ipynb
      title: Point Source Aperture Photometry
    - file: notebooks/NIRCam_photometry/NIRCam_multiband_photometry.ipynb
      title: Extended Aperture Photometry
    - file: notebooks/NIRCam_PSF-matched_photometry/NIRCam_PSF_matched_multiband_photometry.ipynb
      title: Cross-Filter PSF Matching
    - file: notebooks/psf_photometry/NIRCam_PSF_Photometry_Example.ipynb
      title: PSF Photometry
    #- file: https://github.com/spacetelescope/jdat_notebooks/tree/main/notebooks/preimaging
    #  title: Preimaging - MIRAGE
      #sections:
    #- file: notebooks/preimaging/preimaging_01_mirage.ipynb
    #  title: Preimaging - MIRAGE
    #- file: notebooks/preimaging/preimaging_02_calwebb.ipynb
    #  title: Preimaging - Pipeline Stages 1, 2
    #- file: notebooks/preimaging/preimaging_03_association.ipynb
    #  title: Preimaging - Pipeline Stage 3
  - caption: NIRISS
    chapters:
    - file: notebooks/NIRISS_WFSS_postpipeline/00_Optimal_extraction.ipynb
      title: WFSS Spectra - Optimal Extraction
      #sections:
      #- file: notebooks/NIRISS_WFSS_postpipeline/00. Optimal extraction.ipynb
      #  title: WFSS Spectra - Optimal Extraction
      #  00_Optimal_extraction.ipynb			01_Combine_and_normalize_1D_spectra.ipynb	02_Cross_correlation_template.ipynb		03_Spatially_resolved_emission_line_map.ipynb
    - file: notebooks/NIRISS_WFSS_postpipeline/01_Combine_and_normalize_1D_spectra.ipynb
      title: WFSS Spectra - Combine and Normalize 1D Spectra
    - file: notebooks/NIRISS_WFSS_postpipeline/02_Cross_correlation_template.ipynb 
      title: WFSS Spectra - Cross-Correlation Template
    - file: notebooks/NIRISS_WFSS_postpipeline/03_Spatially_resolved_emission_line_map.ipynb
      title: WFSS Spectra - Emission Line Map
    #- file: notebooks/niriss_ami_binary/1_niriss_ami_binary.ipynb
    #  title: AMI - MIRAGE
      #sections:
      #- file: notebooks/niriss_ami_binary/1_niriss_ami_binary.ipynb
      #  title: Notebook 1
    #- file: notebooks/niriss_ami_binary/2_niriss_ami_binary.ipynb
    #  title:  AMI - Pipeline
    #- file: notebooks/soss-transit-spectroscopy/HAT-P-1b-PART3-data-analysis.ipynb
    #  title: SOSS Transit Spectroscopy
  - caption: NIRSpec
    chapters:
    - file: notebooks/IFU_cube_continuum_fit/NGC4151_FeII_ContinuumFit.ipynb
      title: IFU Background Subtraction
    - file: notebooks/cube_fitting/cube_fitting.ipynb
      title: IFU Cube Modeling
    - file: notebooks/ifu_optimal/ifu_optimal.ipynb
      title: IFU Optimal Spectral Extraction
    - file: notebooks/optimal_extraction/Spectral_Extraction-static.ipynb
      title: MOS Optimal Extraction
    - file: notebooks/mos_spectroscopy_advanced/MOSspec_advanced.ipynb
      title: MOS Spectroscopy of Extragalactic Field
    - file: notebooks/transit_spectroscopy_notebook/Exoplanet_Transmission_Spectra_JWST.ipynb
      title: BOTS Time Series Observations
    - file: notebooks/galaxy_redshift/redshift_fitting.ipynb
      title: Redshift and Template Fitting