diff --git a/_toc.yml b/_toc.yml index 35a4881a3..d0a6aab14 100644 --- a/_toc.yml +++ b/_toc.yml @@ -12,17 +12,17 @@ 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 @@ -30,81 +30,87 @@ parts: - 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 \ No newline at end of file + - file: notebooks/NIRSpec/NIRSpec_NSClean/BOTS_NSClean_example.ipynb + title: BOTS Products with NSClean diff --git a/notebooks/MIRI_IFU_YSOs_in_the_LMC/isha_nayak_ysos_in_the_lmc.ipynb b/notebooks/MIRI/MIRI_IFU_YSOs_in_the_LMC/isha_nayak_ysos_in_the_lmc.ipynb similarity index 99% rename from notebooks/MIRI_IFU_YSOs_in_the_LMC/isha_nayak_ysos_in_the_lmc.ipynb rename to notebooks/MIRI/MIRI_IFU_YSOs_in_the_LMC/isha_nayak_ysos_in_the_lmc.ipynb index e18cddaf4..8b7e91515 100644 --- a/notebooks/MIRI_IFU_YSOs_in_the_LMC/isha_nayak_ysos_in_the_lmc.ipynb +++ b/notebooks/MIRI/MIRI_IFU_YSOs_in_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/notebooks/MIRI_IFU_YSOs_in_the_LMC/requirements.txt b/notebooks/MIRI/MIRI_IFU_YSOs_in_the_LMC/requirements.txt similarity index 100% rename from notebooks/MIRI_IFU_YSOs_in_the_LMC/requirements.txt rename to notebooks/MIRI/MIRI_IFU_YSOs_in_the_LMC/requirements.txt diff --git a/notebooks/MIRI_LRS_spectral_extraction/miri_lrs_advanced_extraction_part1.ipynb b/notebooks/MIRI/MIRI_LRS_spectral_extraction/miri_lrs_advanced_extraction_part1.ipynb similarity index 100% rename from notebooks/MIRI_LRS_spectral_extraction/miri_lrs_advanced_extraction_part1.ipynb rename to notebooks/MIRI/MIRI_LRS_spectral_extraction/miri_lrs_advanced_extraction_part1.ipynb diff --git a/notebooks/MIRI_LRS_spectral_extraction/requirements.txt b/notebooks/MIRI/MIRI_LRS_spectral_extraction/requirements.txt similarity index 100% rename from notebooks/MIRI_LRS_spectral_extraction/requirements.txt rename to notebooks/MIRI/MIRI_LRS_spectral_extraction/requirements.txt diff --git a/notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_PointSourceDetectorBasedExtraction.ipynb b/notebooks/MIRI/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_PointSourceDetectorBasedExtraction.ipynb similarity index 100% rename from notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_PointSourceDetectorBasedExtraction.ipynb rename to 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notebooks/cross_instrument/rgb_imviz/imviz_rgb_carina.ipynb index 910cedeff..2a0f9bda8 100644 --- a/notebooks/rgb_imviz/imviz_rgb_carina.ipynb +++ b/notebooks/cross_instrument/rgb_imviz/imviz_rgb_carina.ipynb @@ -35,7 +35,9 @@ "\n", "from astroquery.mast import Observations\n", "\n", - "from jdaviz import Imviz" + "from jdaviz import Imviz\n", + "\n", + "from IPython.display import Image" ] }, { @@ -43,6 +45,8 @@ "id": "aaf960cd", "metadata": {}, "source": [ + "## Download images and load Imviz\n", + "\n", "We create an Imviz instance and grab the default viewer instance as well:" ] }, @@ -118,10 +122,8 @@ { "cell_type": "code", "execution_count": null, - "id": "8b754faa", - "metadata": { - "scrolled": false - }, + "id": "48830cc8-997f-4ec7-b278-21e6685ec7cd", + "metadata": {}, "outputs": [], "source": [ "imviz.show()" @@ -132,28 +134,26 @@ "id": "88b7129e", "metadata": {}, "source": [ - "## WCS Linking Controls\n", - "https://jdaviz.readthedocs.io/en/latest/imviz/plugins.html#link-control\n", + "## Align by WCS\n", + "https://jdaviz.readthedocs.io/en/latest/imviz/plugins.html#orientation\n", "\n", "The first thing you will probably notice is that the image doesn't take up the entire viewer area. If you press the \"b\" key to blink to the next image, you will see that this image is zoomed correctly by default. The odd default zoom on the other is because the images are linked by pixel when loaded. We can instead link by WCS (world coordinates) so that the images will be properly aligned." ] }, { "cell_type": "markdown", - "id": "b34dde0c", + "id": "341145e7-e595-4a58-aab8-0e1e24c19c3d", "metadata": {}, "source": [ - "There are two ways to link in Imviz. Firstly, you can do it from within the UI through the Links Control plugin by selecting \"WCS\". Either open the plugin tray to the right and search for \"Links Control\", or execute the following cell to open it automatically:" + "There are two ways to link in Imviz. Firstly, you can do it from within the UI through the Orientation plugin by selecting \"WCS\". Either open the plugin tray to the right and search for \"Orientation\", or execute the following cell to open it automatically:" ] }, { - "cell_type": "code", - "execution_count": null, - "id": "812bbbf5", + "cell_type": "raw", + "id": "19216180-6a20-44cd-a384-981431eb6a3f", "metadata": {}, - "outputs": [], "source": [ - "imviz.plugins['Links Control'].open_in_tray()" + "imviz.plugins['Orientation'].open_in_tray()" ] }, { @@ -171,9 +171,9 @@ "metadata": {}, "outputs": [], "source": [ - "# Link images by WCS (without affine approximation)\n", - "imviz.plugins['Links Control'].link_type = 'WCS'\n", - "imviz.plugins['Links Control'].wcs_use_affine = False" + "# Link images by WCS (without affine approximation).\n", + "imviz.plugins['Orientation'].link_type = 'WCS'\n", + "imviz.plugins['Orientation'].wcs_use_affine = False" ] }, { @@ -208,98 +208,120 @@ "metadata": {}, "outputs": [], "source": [ - "plot_options = imviz.plugins['Plot Options']\n", - "plot_options.open_in_tray()" + "plot_options = imviz.plugins['Plot Options']" ] }, { "cell_type": "markdown", - "id": "3e1285e7", + "id": "a02ea0f6-6101-46f1-a777-2469245fe124", "metadata": {}, "source": [ - "Here you can adjust the color, opacity, contrast, and bias among other things. You can adjust them manually via the UI, or programmatically via the API to make image appear as you'd like:" + "We can use the the Assign RGB Preset button, which can be triggered in the UI or with the following cell." ] }, { "cell_type": "code", "execution_count": null, - "id": "c2211739", + "id": "d9f2aea4-3828-421f-bdaa-cc428a7c8e6b", "metadata": {}, "outputs": [], "source": [ - "plot_options.image_color_mode = 'Monochromatic'\n", - "img_settings = {'f090w': {'image_color': '#cc7ace',\n", - " 'stretch_vmax': 4,\n", - " 'image_opacity': 0.32,\n", - " 'image_contrast': 0.69,\n", - " 'image_bias': 0.39},\n", - " 'f187n': {'image_color': '#66cfef',\n", - " 'stretch_vmin': 0,\n", - " 'stretch_vmax': 16,\n", - " 'image_opacity': 0.4,\n", - " 'image_contrast': 0.94,\n", - " 'image_bias': 0.74},\n", - " 'f200w': {'image_color': '#61d3e1',\n", - " 'stretch_vmax': 6,\n", - " 'image_opacity': 0.31,\n", - " 'image_contrast': 2.15,\n", - " 'image_bias': 0.66},\n", - " 'f335m': {'image_color': '#afff6b',\n", - " 'stretch_vmin': 4,\n", - " 'stretch_vmax': 27,\n", - " 'image_opacity': 0.23,\n", - " 'image_contrast': 3.13,\n", - " 'image_bias': 0.67},\n", - " 'f444w': {'image_color': '#ff767c',\n", - " 'stretch_vmax': 10,\n", - " 'image_opacity': 0.18,\n", - " 'image_contrast': 1.77,\n", - " 'image_bias': 0.56},\n", - " 'f470n': {'image_color': '#f7787d',\n", - " 'stretch_vmin': 1,\n", - " 'stretch_vmax': 11,\n", - " 'image_opacity': 0.4,\n", - " 'image_contrast': 2.53,\n", - " 'image_bias': 0.27}}" + "plot_options.image_color_mode = 'One color per layer'\n", + "plot_options.apply_RGB_presets()" ] }, { "cell_type": "markdown", - "id": "78207a91", + "id": "6bce2a65-953e-436f-b6dc-e81b749cd840", "metadata": {}, "source": [ - "We can now iterate over this dictionary of settings and use the plot options API to set each of the options." + "We just need to adjust the stretch min and max!" ] }, { "cell_type": "code", "execution_count": null, - "id": "c342cd9d", + "id": "04482b8f-89ad-4770-8a4c-9325a72ffbaa", "metadata": {}, "outputs": [], "source": [ - "for layer, settings in img_settings.items():\n", - " plot_options.layer = f'{layer}[DATA]'\n", - " for k, v in settings.items():\n", - " setattr(plot_options, k, v)" + "plot_options.layer = 'f090w[DATA]'\n", + "plot_options.stretch_vmin = 4\n", + "plot_options.stretch_vmax = 16\n", + "plot_options.image_bias = 0.39\n", + "\n", + "plot_options.layer = 'f187n[DATA]'\n", + "plot_options.stretch_vmin = 10\n", + "plot_options.stretch_vmax = 16\n", + "plot_options.image_bias = 0.74\n", + "\n", + "plot_options.layer = 'f200w[DATA]'\n", + "plot_options.stretch_vmin = 1\n", + "plot_options.stretch_vmax = 5\n", + "plot_options.image_bias = 0.66\n", + "\n", + "plot_options.layer = 'f335m[DATA]'\n", + "plot_options.stretch_vmin = 4\n", + "plot_options.stretch_vmax = 27\n", + "plot_options.image_bias = 0.67\n", + "\n", + "plot_options.layer = 'f444w[DATA]'\n", + "plot_options.stretch_vmin = 1\n", + "plot_options.stretch_vmax = 14\n", + "plot_options.image_bias = 0.56\n", + "\n", + "plot_options.layer = 'f470n[DATA]'\n", + "plot_options.stretch_vmin = 1\n", + "plot_options.stretch_vmax = 6\n", + "plot_options.image_bias = 0.60\n" ] }, { "cell_type": "markdown", - "id": "b1ac3c3f", + "id": "9d7821fd-2073-4d1b-8e97-64c46f2e074d", "metadata": {}, "source": [ - "And lastly, we can save to an image using the export plot plugin." + "Let's export the image we just made. This is a placeholder for when the export in the plugin with get the right path." + ] + }, + { + "cell_type": "raw", + "id": "d5266616-c257-4f93-b9d1-11185e0c5fee", + "metadata": {}, + "source": [ + "exportimg = imviz.plugins['Export Plot']\n", + "exportimg.viewer = 'imviz-0'\n", + "exportimg.filename = 'carina_rgb_preset.png'\n", + "exportimg.export()" + ] + }, + { + "cell_type": "markdown", + "id": "ca450e99-04e2-4e08-bbb7-45f6b98843f5", + "metadata": {}, + "source": [ + "We can use the astrowidget API for now." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8193c79d-ae58-469b-a3b0-6ac3497dbb8b", + "metadata": {}, + "outputs": [], + "source": [ + "viewer = imviz.default_viewer\n", + "viewer.save('./carina.png')" ] }, { "cell_type": "code", "execution_count": null, - "id": "fce20b3d", + "id": "501ac813-a160-4180-b3e4-6f03eae3addb", "metadata": {}, "outputs": [], "source": [ - "imviz.plugins['Export Plot'].save_figure('carina_rgb.png')" + "Image('./carina.png')" ] }, { @@ -335,7 +357,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.8" + "version": "3.9.7" } }, "nbformat": 4, diff --git a/notebooks/rgb_imviz/requirements.txt b/notebooks/cross_instrument/rgb_imviz/requirements.txt similarity index 100% rename from notebooks/rgb_imviz/requirements.txt rename to notebooks/cross_instrument/rgb_imviz/requirements.txt diff --git a/notebooks/specviz_notebookGUI_interaction/requirements.txt b/notebooks/cross_instrument/specviz_notebookGUI_interaction/requirements.txt similarity index 100% rename from notebooks/specviz_notebookGUI_interaction/requirements.txt rename to notebooks/cross_instrument/specviz_notebookGUI_interaction/requirements.txt diff --git a/notebooks/specviz_notebookGUI_interaction/specviz_notebook_gui_interaction_redshift.ipynb b/notebooks/cross_instrument/specviz_notebookGUI_interaction/specviz_notebook_gui_interaction_redshift.ipynb similarity index 100% rename from notebooks/specviz_notebookGUI_interaction/specviz_notebook_gui_interaction_redshift.ipynb rename to notebooks/cross_instrument/specviz_notebookGUI_interaction/specviz_notebook_gui_interaction_redshift.ipynb