Merge pull request #228 from camipacifici/organizing

Organizing notebooks by instrument. Some notebooks are failing but for unrelated reasons. They will be fixed in separate PRs.
spacetelescope · Jul 10, 2024 · 65068ed · 65068ed
2 parents 5087c52 + 967b014
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diff --git a/_toc.yml b/_toc.yml
@@ -12,99 +12,105 @@ parts:
     - file: install.rst
       title: Installation
     - file: docs/notebook_development_workflow.rst
-      title: Notebook Development Workflow   
+      title: Notebook Development Workflow
   - caption: Development
     chapters:
     - file: docs/submitting_notebooks.rst
       title: Submitting Notebooks
     - file: docs/requirements.rst
-      title: Requirements file 
+      title: Requirements file
     - file: docs/notebooks.rst
       title: Jupyter Notebooks
     - file: docs/data_files.rst
-      title: Data Files 
+      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        
+      title: GitHub PR
   #- caption: Developers and Staff
-    # chapters:     
-    # - file : docs/stsci_notebook_leads.rst     
-    #   title: STScI Notebook Leads     
+    # chapters:
+    # - file : docs/stsci_notebook_leads.rst
+    #   title: STScI Notebook Leads
   - caption: Cross-Instrument
     chapters:
-    - file: notebooks/asdf_example/asdf_example.ipynb
+    - file: notebooks/cross_instrument/asdf_example/asdf_example.ipynb
       title: ASDF Example
-    - file: notebooks/background_estimation_imaging/Imaging_Sky_Background_Estimation.ipynb
+    - file: notebooks/cross_instrument/background_estimation_imaging/Imaging_Sky_Background_Estimation.ipynb
       title: Complex 2D Background
-    - file: notebooks/composite_model_fitting/specfit_demo_3.ipynb
+    - file: notebooks/cross_instrument/composite_model_fitting/specfit_demo_3.ipynb
       title: Composite Model Spectral Fitting
-    - file: notebooks/NIRSpec_MAST_Query/NIRSpec_MAST_Query.ipynb
+    - file: notebooks/cross_instrument/NIRSpec_MAST_Query/NIRSpec_MAST_Query.ipynb
       title: MAST Query
-    - file: notebooks/rgb_imviz/imviz_rgb_carina.ipynb
+    - file: notebooks/cross_instrument/rgb_imviz/imviz_rgb_carina.ipynb
       title: RGB images with Imviz
-    - file: notebooks/specviz_notebookGUI_interaction/specviz_notebook_gui_interaction_redshift.ipynb
+    - file: notebooks/cross_instrument/specviz_notebookGUI_interaction/specviz_notebook_gui_interaction_redshift.ipynb
       title: Specviz Simple Demo
   - caption: MIRI
     chapters:
-    - file: notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_runpipeline.ipynb
+    - file: notebooks/MIRI/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_runpipeline.ipynb
       title: MRS Mstar - Run Pipeline
-    - file: notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_PointSourceDetectorBasedExtraction.ipynb
+    - file: notebooks/MIRI/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_PointSourceDetectorBasedExtraction.ipynb
       title: MRS Mstar - Optimal Extraction
-    - file: notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_analysis.ipynb
+    - file: notebooks/MIRI/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
+    - file: notebooks/MIRI/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
+    - file: notebooks/MIRI/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
+    - file: notebooks/NIRCam/aperture_photometry/NIRCam_Aperture_Photometry_Example.ipynb
       title: Point Source Aperture Photometry
-    - file: notebooks/NIRCam_photometry/NIRCam_multiband_photometry.ipynb
+    - file: notebooks/NIRCam/NIRCam_photometry/NIRCam_multiband_photometry.ipynb
       title: Extended Aperture Photometry
-    - file: notebooks/NIRCam_PSF-matched_photometry/NIRCam_PSF_matched_multiband_photometry.ipynb
+    - file: notebooks/NIRCam/NIRCam_PSF-matched_photometry/NIRCam_PSF_matched_multiband_photometry.ipynb
       title: Cross-Filter PSF Matching
-    - file: notebooks/psf_photometry/NIRCam_PSF_Photometry_Example.ipynb
+    - file: notebooks/NIRCam/psf_photometry/NIRCam_PSF_Photometry_Example.ipynb
       title: PSF Photometry
   - caption: NIRISS
     chapters:
-    - file: notebooks/NIRISS_WFSS_postpipeline/00_Optimal_extraction.ipynb
+    - file: notebooks/NIRISS/NIRISS_WFSS_postpipeline/00_Optimal_extraction.ipynb
       title: WFSS Spectra - Optimal Extraction
-    - file: notebooks/NIRISS_WFSS_postpipeline/01_Combine_and_normalize_1D_spectra.ipynb
+    - file: notebooks/NIRISS/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 
+    - file: notebooks/NIRISS/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
+    - file: notebooks/NIRISS/NIRISS_WFSS_postpipeline/03_Spatially_resolved_emission_line_map.ipynb
       title: WFSS Spectra - Emission Line Map
-    - file: notebooks/niriss_imaging/niriss-imaging-tutorial.ipynb
+    - file: notebooks/NIRISS/niriss_imaging/niriss-imaging-tutorial.ipynb
       title: NIRISS Imaging Tutorial
+    - file: notebooks/NIRISS/NIRISS_WFSS_advanced/00_niriss_mast_query_data_setup.ipynb
+      title: NIRISS MAST
+    - file: notebooks/NIRISS/NIRISS_WFSS_advanced/01_niriss_wfss_image2_image3.ipynb
+      title: Direct imaging for WFSS
+    - file: notebooks/NIRISS/NIRISS_WFSS_advanced/02_niriss_wfss_spec2.ipynb
+      title: Spec2 pipeline for WFSS
 
   - caption: NIRSpec
     chapters:
-    - file: notebooks/IFU_cube_continuum_fit/NGC4151_FeII_ContinuumFit.ipynb
+    - file: notebooks/NIRSpec/IFU_cube_continuum_fit/NGC4151_FeII_ContinuumFit.ipynb
       title: IFU Background Subtraction
-    - file: notebooks/cube_fitting/cube_fitting.ipynb
+    - file: notebooks/NIRSpec/cube_fitting/cube_fitting.ipynb
       title: IFU Cube Modeling
-    - file: notebooks/ifu_optimal/ifu_optimal.ipynb
+    - file: notebooks/NIRSpec/ifu_optimal/ifu_optimal.ipynb
       title: IFU Optimal Spectral Extraction
-    - file: notebooks/optimal_extraction/Spectral_Extraction-static.ipynb
+    - file: notebooks/NIRSpec/optimal_extraction/Spectral_Extraction-static.ipynb
       title: MOS Optimal Extraction
-    - file: notebooks/mos_spectroscopy_advanced/MOSspec_advanced.ipynb
+    - file: notebooks/NIRSpec/mos_spectroscopy_advanced/MOSspec_advanced.ipynb
       title: MOS Spectroscopy of Extragalactic Field
-    - file: notebooks/transit_spectroscopy_notebook/Exoplanet_Transmission_Spectra_JWST.ipynb
+    - file: notebooks/NIRSpec/transit_spectroscopy_notebook/Exoplanet_Transmission_Spectra_JWST.ipynb
       title: BOTS Time Series Observations
-    - file: notebooks/galaxy_redshift/redshift_fitting.ipynb
+    - file: notebooks/NIRSpec/galaxy_redshift/redshift_fitting.ipynb
       title: Redshift and Template Fitting
-    - file: notebooks/NIRSpec_NSClean/FS_NSClean_example.ipynb
+    - file: notebooks/NIRSpec/NIRSpec_NSClean/FS_NSClean_example.ipynb
       title: FS Products with NSClean
-    - file: notebooks/NIRSpec_NSClean/IFU_NSClean_example.ipynb
+    - file: notebooks/NIRSpec/NIRSpec_NSClean/IFU_NSClean_example.ipynb
       title: IFU Products with NSClean
-    - file: notebooks/NIRSpec_NSClean/MOS_NSClean_example.ipynb
+    - file: notebooks/NIRSpec/NIRSpec_NSClean/MOS_NSClean_example.ipynb
       title: MOS Products with NSClean
-    - file: notebooks/NIRSpec_NSClean/BOTS_NSClean_example.ipynb
-      title: BOTS Products with NSClean
+    - file: notebooks/NIRSpec/NIRSpec_NSClean/BOTS_NSClean_example.ipynb
+      title: BOTS Products with NSClean
diff --git a/..._the_LMC/isha_nayak_ysos_in_the_lmc.ipynb → ..._the_LMC/isha_nayak_ysos_in_the_lmc.ipynb b/..._the_LMC/isha_nayak_ysos_in_the_lmc.ipynb → ..._the_LMC/isha_nayak_ysos_in_the_lmc.ipynb
@@ -300,7 +300,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Plot the summed image with WCS coordinates and save the figure"
+    "### Plot the summed image with WCS coordinates and save the figure\n",
+    "\n",
+    "**Developer note**: there is a bug in aplpy currently and `show_colorscale` does not work. We skip this cell and come back to this when the bug is fixed."
    ]
   },
   {
@@ -309,8 +311,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "name = '13CO'\n",
-    "\n",
+    "name = '13CO'"
+   ]
+  },
+  {
+   "cell_type": "raw",
+   "metadata": {},
+   "source": [
     "F = aplpy.FITSFigure(cont_img.hdu, north=True)\n",
     "F.show_colorscale()\n",
     "F.add_label(0.1, 0.9, name, relative=True, size=22, weight='bold')\n",
@@ -1157,7 +1164,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

diff --git a/...MIRI_IFU_YSOs_in_the_LMC/requirements.txt → ...MIRI_IFU_YSOs_in_the_LMC/requirements.txt b/...MIRI_IFU_YSOs_in_the_LMC/requirements.txt → ...MIRI_IFU_YSOs_in_the_LMC/requirements.txt
diff --git a/.../miri_lrs_advanced_extraction_part1.ipynb → .../miri_lrs_advanced_extraction_part1.ipynb b/.../miri_lrs_advanced_extraction_part1.ipynb → .../miri_lrs_advanced_extraction_part1.ipynb
diff --git a/..._LRS_spectral_extraction/requirements.txt → ..._LRS_spectral_extraction/requirements.txt b/..._LRS_spectral_extraction/requirements.txt → ..._LRS_spectral_extraction/requirements.txt
diff --git a/..._PointSourceDetectorBasedExtraction.ipynb → ..._PointSourceDetectorBasedExtraction.ipynb b/..._PointSourceDetectorBasedExtraction.ipynb → ..._PointSourceDetectorBasedExtraction.ipynb
diff --git a/...is/JWST_Mstar_dataAnalysis_analysis.ipynb → ...is/JWST_Mstar_dataAnalysis_analysis.ipynb b/...is/JWST_Mstar_dataAnalysis_analysis.ipynb → ...is/JWST_Mstar_dataAnalysis_analysis.ipynb
diff --git a/...JWST_Mstar_dataAnalysis_runpipeline.ipynb → ...JWST_Mstar_dataAnalysis_runpipeline.ipynb b/...JWST_Mstar_dataAnalysis_runpipeline.ipynb → ...JWST_Mstar_dataAnalysis_runpipeline.ipynb
diff --git a/...ointSourceDetectorBasedExtractionFuncs.py → ...ointSourceDetectorBasedExtractionFuncs.py b/...ointSourceDetectorBasedExtractionFuncs.py → ...ointSourceDetectorBasedExtractionFuncs.py
diff --git a/...S_Mstar_analysis/create_distortionMaps.py → ...S_Mstar_analysis/create_distortionMaps.py b/...S_Mstar_analysis/create_distortionMaps.py → ...S_Mstar_analysis/create_distortionMaps.py
diff --git a/...books/MRS_Mstar_analysis/requirements.txt → .../MIRI/MRS_Mstar_analysis/requirements.txt b/...books/MRS_Mstar_analysis/requirements.txt → .../MIRI/MRS_Mstar_analysis/requirements.txt
diff --git a/notebooks/MRS_Mstar_analysis/stpipe-log.cfg → ...ks/MIRI/MRS_Mstar_analysis/stpipe-log.cfg b/notebooks/MRS_Mstar_analysis/stpipe-log.cfg → ...ks/MIRI/MRS_Mstar_analysis/stpipe-log.cfg
diff --git a/...am_PSF_matched_multiband_photometry.ipynb → ...am_PSF_matched_multiband_photometry.ipynb b/...am_PSF_matched_multiband_photometry.ipynb → ...am_PSF_matched_multiband_photometry.ipynb
diff --git a/...m_PSF-matched_photometry/requirements.txt → ...m_PSF-matched_photometry/requirements.txt b/...m_PSF-matched_photometry/requirements.txt → ...m_PSF-matched_photometry/requirements.txt
diff --git a/notebooks/NIRCam_photometry/.gitignore → ...books/NIRCam/NIRCam_photometry/.gitignore b/notebooks/NIRCam_photometry/.gitignore → ...books/NIRCam/NIRCam_photometry/.gitignore
diff --git a/...tometry/NIRCam_multiband_photometry.ipynb → ...tometry/NIRCam_multiband_photometry.ipynb b/...tometry/NIRCam_multiband_photometry.ipynb → ...tometry/NIRCam_multiband_photometry.ipynb
diff --git a/notebooks/NIRCam_photometry/requirements.txt → ...NIRCam/NIRCam_photometry/requirements.txt b/notebooks/NIRCam_photometry/requirements.txt → ...NIRCam/NIRCam_photometry/requirements.txt
diff --git a/.../NIRCam_Aperture_Photometry_Example.ipynb → .../NIRCam_Aperture_Photometry_Example.ipynb b/.../NIRCam_Aperture_Photometry_Example.ipynb → .../NIRCam_Aperture_Photometry_Example.ipynb
diff --git a/...ooks/aperture_photometry/requirements.txt → ...RCam/aperture_photometry/requirements.txt b/...ooks/aperture_photometry/requirements.txt → ...RCam/aperture_photometry/requirements.txt
diff --git a/notebooks/psf_photometry/.gitignore → notebooks/NIRCam/psf_photometry/.gitignore b/notebooks/psf_photometry/.gitignore → notebooks/NIRCam/psf_photometry/.gitignore
diff --git a/...metry/NIRCam_PSF_Photometry_Example.ipynb → ...metry/NIRCam_PSF_Photometry_Example.ipynb b/...metry/NIRCam_PSF_Photometry_Example.ipynb → ...metry/NIRCam_PSF_Photometry_Example.ipynb
diff --git a/notebooks/psf_photometry/requirements.txt → ...ks/NIRCam/psf_photometry/requirements.txt b/notebooks/psf_photometry/requirements.txt → ...ks/NIRCam/psf_photometry/requirements.txt
diff --git a/...ced/00_niriss_mast_query_data_setup.ipynb → ...ced/00_niriss_mast_query_data_setup.ipynb b/...ced/00_niriss_mast_query_data_setup.ipynb → ...ced/00_niriss_mast_query_data_setup.ipynb
diff --git a/...vanced/01_niriss_wfss_image2_image3.ipynb → ...vanced/01_niriss_wfss_image2_image3.ipynb b/...vanced/01_niriss_wfss_image2_image3.ipynb → ...vanced/01_niriss_wfss_image2_image3.ipynb
diff --git a/..._WFSS_advanced/02_niriss_wfss_spec2.ipynb → ..._WFSS_advanced/02_niriss_wfss_spec2.ipynb b/..._WFSS_advanced/02_niriss_wfss_spec2.ipynb → ..._WFSS_advanced/02_niriss_wfss_spec2.ipynb
diff --git a/...anced/extra_niriss_individual_steps.ipynb → ...anced/extra_niriss_individual_steps.ipynb b/...anced/extra_niriss_individual_steps.ipynb → ...anced/extra_niriss_individual_steps.ipynb
diff --git a/...oks/NIRISS_WFSS_advanced/requirements.txt → ...ISS/NIRISS_WFSS_advanced/requirements.txt b/...oks/NIRISS_WFSS_advanced/requirements.txt → ...ISS/NIRISS_WFSS_advanced/requirements.txt
diff --git a/...books/NIRISS_WFSS_postpipeline/.gitignore → ...IRISS/NIRISS_WFSS_postpipeline/.gitignore b/...books/NIRISS_WFSS_postpipeline/.gitignore → ...IRISS/NIRISS_WFSS_postpipeline/.gitignore
diff --git a/..._postpipeline/00_Optimal_extraction.ipynb → ..._postpipeline/00_Optimal_extraction.ipynb b/..._postpipeline/00_Optimal_extraction.ipynb → ..._postpipeline/00_Optimal_extraction.ipynb
diff --git a/...01_Combine_and_normalize_1D_spectra.ipynb → ...01_Combine_and_normalize_1D_spectra.ipynb b/...01_Combine_and_normalize_1D_spectra.ipynb → ...01_Combine_and_normalize_1D_spectra.ipynb
diff --git a/...eline/02_Cross_correlation_template.ipynb → ...eline/02_Cross_correlation_template.ipynb b/...eline/02_Cross_correlation_template.ipynb → ...eline/02_Cross_correlation_template.ipynb
diff --git a/...patially_resolved_emission_line_map.ipynb → ...patially_resolved_emission_line_map.ipynb b/...patially_resolved_emission_line_map.ipynb → ...patially_resolved_emission_line_map.ipynb
diff --git a/...NIRISS_WFSS_postpipeline/requirements.txt → ...NIRISS_WFSS_postpipeline/requirements.txt b/...NIRISS_WFSS_postpipeline/requirements.txt → ...NIRISS_WFSS_postpipeline/requirements.txt
diff --git a/...iss_imaging/niriss-imaging-tutorial.ipynb → ...iss_imaging/niriss-imaging-tutorial.ipynb b/...iss_imaging/niriss-imaging-tutorial.ipynb → ...iss_imaging/niriss-imaging-tutorial.ipynb
diff --git a/notebooks/niriss_imaging/requirements.txt → ...ks/NIRISS/niriss_imaging/requirements.txt b/notebooks/niriss_imaging/requirements.txt → ...ks/NIRISS/niriss_imaging/requirements.txt
diff --git a/notebooks/IFU_cube_continuum_fit/.gitignore → ...NIRSpec/IFU_cube_continuum_fit/.gitignore b/notebooks/IFU_cube_continuum_fit/.gitignore → ...NIRSpec/IFU_cube_continuum_fit/.gitignore
diff --git a/...inuum_fit/NGC4151_FeII_ContinuumFit.ipynb → ...inuum_fit/NGC4151_FeII_ContinuumFit.ipynb b/...inuum_fit/NGC4151_FeII_ContinuumFit.ipynb → ...inuum_fit/NGC4151_FeII_ContinuumFit.ipynb
diff --git a/...cube_continuum_fit/cubeviz2_modelfit1.png → ...cube_continuum_fit/cubeviz2_modelfit1.png b/...cube_continuum_fit/cubeviz2_modelfit1.png → ...cube_continuum_fit/cubeviz2_modelfit1.png
diff --git a/...cube_continuum_fit/cubeviz2_modelfit2.png → ...cube_continuum_fit/cubeviz2_modelfit2.png b/...cube_continuum_fit/cubeviz2_modelfit2.png → ...cube_continuum_fit/cubeviz2_modelfit2.png
diff --git a/...FU_cube_continuum_fit/cubeviz2_subset.png → ...FU_cube_continuum_fit/cubeviz2_subset.png b/...FU_cube_continuum_fit/cubeviz2_subset.png → ...FU_cube_continuum_fit/cubeviz2_subset.png
diff --git a/...e_continuum_fit/cubeviz_model_fitting.png → ...e_continuum_fit/cubeviz_model_fitting.png b/...e_continuum_fit/cubeviz_model_fitting.png → ...e_continuum_fit/cubeviz_model_fitting.png
diff --git a/...um_fit/cubeviz_select_spectral_subset.png → ...um_fit/cubeviz_select_spectral_subset.png b/...um_fit/cubeviz_select_spectral_subset.png → ...um_fit/cubeviz_select_spectral_subset.png
diff --git a/...e_continuum_fit/cubeviz_select_subset.png → ...e_continuum_fit/cubeviz_select_subset.png b/...e_continuum_fit/cubeviz_select_subset.png → ...e_continuum_fit/cubeviz_select_subset.png
diff --git a/...uum_fit/cubeviz_select_subset_outflow.png → ...uum_fit/cubeviz_select_subset_outflow.png b/...uum_fit/cubeviz_select_subset_outflow.png → ...uum_fit/cubeviz_select_subset_outflow.png
diff --git a/...s/IFU_cube_continuum_fit/requirements.txt → ...c/IFU_cube_continuum_fit/requirements.txt b/...s/IFU_cube_continuum_fit/requirements.txt → ...c/IFU_cube_continuum_fit/requirements.txt
diff --git a/...IRSpec_NSClean/BOTS_NSClean_example.ipynb → ...IRSpec_NSClean/BOTS_NSClean_example.ipynb b/...IRSpec_NSClean/BOTS_NSClean_example.ipynb → ...IRSpec_NSClean/BOTS_NSClean_example.ipynb
diff --git a/.../NIRSpec_NSClean/FS_NSClean_example.ipynb → .../NIRSpec_NSClean/FS_NSClean_example.ipynb b/.../NIRSpec_NSClean/FS_NSClean_example.ipynb → .../NIRSpec_NSClean/FS_NSClean_example.ipynb
diff --git a/...NIRSpec_NSClean/IFU_NSClean_example.ipynb → ...NIRSpec_NSClean/IFU_NSClean_example.ipynb b/...NIRSpec_NSClean/IFU_NSClean_example.ipynb → ...NIRSpec_NSClean/IFU_NSClean_example.ipynb
diff --git a/...NIRSpec_NSClean/MOS_NSClean_example.ipynb → ...NIRSpec_NSClean/MOS_NSClean_example.ipynb b/...NIRSpec_NSClean/MOS_NSClean_example.ipynb → ...NIRSpec_NSClean/MOS_NSClean_example.ipynb
diff --git a/notebooks/NIRSpec_NSClean/requirements.txt → .../NIRSpec/NIRSpec_NSClean/requirements.txt b/notebooks/NIRSpec_NSClean/requirements.txt → .../NIRSpec/NIRSpec_NSClean/requirements.txt
diff --git a/notebooks/NIRSpec_NSClean/utils.py → notebooks/NIRSpec/NIRSpec_NSClean/utils.py b/notebooks/NIRSpec_NSClean/utils.py → notebooks/NIRSpec/NIRSpec_NSClean/utils.py
diff --git a/notebooks/cube_fitting/.gitignore → notebooks/NIRSpec/cube_fitting/.gitignore b/notebooks/cube_fitting/.gitignore → notebooks/NIRSpec/cube_fitting/.gitignore
diff --git a/notebooks/cube_fitting/cube_fitting.ipynb → ...s/NIRSpec/cube_fitting/cube_fitting.ipynb b/notebooks/cube_fitting/cube_fitting.ipynb → ...s/NIRSpec/cube_fitting/cube_fitting.ipynb
diff --git a/notebooks/cube_fitting/requirements.txt → ...oks/NIRSpec/cube_fitting/requirements.txt b/notebooks/cube_fitting/requirements.txt → ...oks/NIRSpec/cube_fitting/requirements.txt
diff --git a/...alaxy_redshift/adjust_redshift_slider.png → ...alaxy_redshift/adjust_redshift_slider.png b/...alaxy_redshift/adjust_redshift_slider.png → ...alaxy_redshift/adjust_redshift_slider.png
diff --git a/notebooks/galaxy_redshift/guess_redshift.png → ...IRSpec/galaxy_redshift/guess_redshift.png b/notebooks/galaxy_redshift/guess_redshift.png → ...IRSpec/galaxy_redshift/guess_redshift.png
diff --git a/notebooks/galaxy_redshift/line_list.png → ...oks/NIRSpec/galaxy_redshift/line_list.png b/notebooks/galaxy_redshift/line_list.png → ...oks/NIRSpec/galaxy_redshift/line_list.png
diff --git a/...axy_redshift/precise_adjust_with_zoom.png → ...axy_redshift/precise_adjust_with_zoom.png b/...axy_redshift/precise_adjust_with_zoom.png → ...axy_redshift/precise_adjust_with_zoom.png
diff --git a/...ks/galaxy_redshift/redshift_fitting.ipynb → ...ec/galaxy_redshift/redshift_fitting.ipynb b/...ks/galaxy_redshift/redshift_fitting.ipynb → ...ec/galaxy_redshift/redshift_fitting.ipynb
diff --git a/notebooks/galaxy_redshift/requirements.txt → .../NIRSpec/galaxy_redshift/requirements.txt b/notebooks/galaxy_redshift/requirements.txt → .../NIRSpec/galaxy_redshift/requirements.txt
diff --git a/notebooks/galaxy_redshift/select_list.png → ...s/NIRSpec/galaxy_redshift/select_list.png b/notebooks/galaxy_redshift/select_list.png → ...s/NIRSpec/galaxy_redshift/select_list.png
diff --git a/notebooks/galaxy_redshift/select_region.png → ...NIRSpec/galaxy_redshift/select_region.png b/notebooks/galaxy_redshift/select_region.png → ...NIRSpec/galaxy_redshift/select_region.png
diff --git a/...ks/galaxy_redshift/select_three_lines.png → ...ec/galaxy_redshift/select_three_lines.png b/...ks/galaxy_redshift/select_three_lines.png → ...ec/galaxy_redshift/select_three_lines.png
diff --git a/notebooks/ifu_optimal/ifu_optimal.ipynb → ...oks/NIRSpec/ifu_optimal/ifu_optimal.ipynb b/notebooks/ifu_optimal/ifu_optimal.ipynb → ...oks/NIRSpec/ifu_optimal/ifu_optimal.ipynb
diff --git a/notebooks/ifu_optimal/requirements.txt → ...ooks/NIRSpec/ifu_optimal/requirements.txt b/notebooks/ifu_optimal/requirements.txt → ...ooks/NIRSpec/ifu_optimal/requirements.txt
diff --git a/...optimal/sdssj1652_nirspec_ifu_cubeviz.png → ...optimal/sdssj1652_nirspec_ifu_cubeviz.png b/...optimal/sdssj1652_nirspec_ifu_cubeviz.png → ...optimal/sdssj1652_nirspec_ifu_cubeviz.png
diff --git a/...ctroscopy_advanced/MOSspec_advanced.ipynb → ...ctroscopy_advanced/MOSspec_advanced.ipynb b/...ctroscopy_advanced/MOSspec_advanced.ipynb → ...ctroscopy_advanced/MOSspec_advanced.ipynb
diff --git a/...ectroscopy_advanced/mosviz_screenshot.png → ...ectroscopy_advanced/mosviz_screenshot.png b/...ectroscopy_advanced/mosviz_screenshot.png → ...ectroscopy_advanced/mosviz_screenshot.png
diff --git a/...os_spectroscopy_advanced/requirements.txt → ...os_spectroscopy_advanced/requirements.txt b/...os_spectroscopy_advanced/requirements.txt → ...os_spectroscopy_advanced/requirements.txt
diff --git a/...traction/Spectral_Extraction-static.ipynb → ...traction/Spectral_Extraction-static.ipynb b/...traction/Spectral_Extraction-static.ipynb → ...traction/Spectral_Extraction-static.ipynb
diff --git a/...books/optimal_extraction/requirements.txt → ...RSpec/optimal_extraction/requirements.txt b/...books/optimal_extraction/requirements.txt → ...RSpec/optimal_extraction/requirements.txt
diff --git a/.../transit_spectroscopy_notebook/.gitignore → .../transit_spectroscopy_notebook/.gitignore b/.../transit_spectroscopy_notebook/.gitignore → .../transit_spectroscopy_notebook/.gitignore
diff --git a/...Exoplanet_Transmission_Spectra_JWST.ipynb → ...Exoplanet_Transmission_Spectra_JWST.ipynb b/...Exoplanet_Transmission_Spectra_JWST.ipynb → ...Exoplanet_Transmission_Spectra_JWST.ipynb
diff --git a/...it_spectroscopy_notebook/requirements.txt → ...it_spectroscopy_notebook/requirements.txt b/...it_spectroscopy_notebook/requirements.txt → ...it_spectroscopy_notebook/requirements.txt
diff --git a/...RSpec_MAST_Query/NIRSpec_MAST_Query.ipynb → ...RSpec_MAST_Query/NIRSpec_MAST_Query.ipynb b/...RSpec_MAST_Query/NIRSpec_MAST_Query.ipynb → ...RSpec_MAST_Query/NIRSpec_MAST_Query.ipynb
diff --git a/...books/NIRSpec_MAST_Query/requirements.txt → ...ument/NIRSpec_MAST_Query/requirements.txt b/...books/NIRSpec_MAST_Query/requirements.txt → ...ument/NIRSpec_MAST_Query/requirements.txt
diff --git a/notebooks/asdf_example/asdf_example.ipynb → ...nstrument/asdf_example/asdf_example.ipynb b/notebooks/asdf_example/asdf_example.ipynb → ...nstrument/asdf_example/asdf_example.ipynb
diff --git a/notebooks/asdf_example/requirements.txt → ..._instrument/asdf_example/requirements.txt b/notebooks/asdf_example/requirements.txt → ..._instrument/asdf_example/requirements.txt
diff --git a/...g/Imaging_Sky_Background_Estimation.ipynb → ...g/Imaging_Sky_Background_Estimation.ipynb b/...g/Imaging_Sky_Background_Estimation.ipynb → ...g/Imaging_Sky_Background_Estimation.ipynb
diff --git a/...d_estimation_imaging/pre-requirements.txt → ...d_estimation_imaging/pre-requirements.txt b/...d_estimation_imaging/pre-requirements.txt → ...d_estimation_imaging/pre-requirements.txt
diff --git a/...round_estimation_imaging/requirements.txt → ...round_estimation_imaging/requirements.txt b/...round_estimation_imaging/requirements.txt → ...round_estimation_imaging/requirements.txt
diff --git a/.../composite_model_fitting/custom_models.py → .../composite_model_fitting/custom_models.py b/.../composite_model_fitting/custom_models.py → .../composite_model_fitting/custom_models.py
diff --git a/...te_model_fitting/n5548_lyalpha_sample.dat → ...te_model_fitting/n5548_lyalpha_sample.dat b/...te_model_fitting/n5548_lyalpha_sample.dat → ...te_model_fitting/n5548_lyalpha_sample.dat
diff --git a/...ite_model_fitting/n5548_mean_g130mb4.ecsv → ...ite_model_fitting/n5548_mean_g130mb4.ecsv b/...ite_model_fitting/n5548_mean_g130mb4.ecsv → ...ite_model_fitting/n5548_mean_g130mb4.ecsv
diff --git a/...s/composite_model_fitting/n5548_models.py → ...t/composite_model_fitting/n5548_models.py b/...s/composite_model_fitting/n5548_models.py → ...t/composite_model_fitting/n5548_models.py
diff --git a/.../composite_model_fitting/requirements.txt → .../composite_model_fitting/requirements.txt b/.../composite_model_fitting/requirements.txt → .../composite_model_fitting/requirements.txt
diff --git a/...posite_model_fitting/specfit_demo_3.ipynb → ...posite_model_fitting/specfit_demo_3.ipynb b/...posite_model_fitting/specfit_demo_3.ipynb → ...posite_model_fitting/specfit_demo_3.ipynb
diff --git a/notebooks/cross_instrument/rgb_imviz/carina.png b/notebooks/cross_instrument/rgb_imviz/carina.png