diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle index a598b67d..3c26cc93 100644 Binary files a/.doctrees/environment.pickle and b/.doctrees/environment.pickle differ diff --git a/.doctrees/forced_photometry/multiband_photometry.doctree b/.doctrees/forced_photometry/multiband_photometry.doctree index 2e882dfe..1ba89ce8 100644 Binary files a/.doctrees/forced_photometry/multiband_photometry.doctree and b/.doctrees/forced_photometry/multiband_photometry.doctree differ diff --git a/_sources/forced_photometry/multiband_photometry.md b/_sources/forced_photometry/multiband_photometry.md index 7a320c69..ffa75ea0 100644 --- a/_sources/forced_photometry/multiband_photometry.md +++ b/_sources/forced_photometry/multiband_photometry.md @@ -115,6 +115,9 @@ except ImportError: print("tractor is missing") pass +# Add ~/.local/bin to path so executables installed with pip are available (needed for nway) +os.environ['PATH'] = f"{os.environ['HOME']}/.local/bin:{os.environ['PATH']}" + %matplotlib inline ``` @@ -794,7 +797,7 @@ nway_write_header('data/multiband_phot.fits', 'OPT', float((2*rad_in_arcmin/60)* ```{code-cell} ipython3 # call nway -!/home/jovyan/.local/bin/nway.py 'data/Chandra/COSMOS_chandra.fits' :ERROR_RADIUS 'data/multiband_phot.fits' 0.1 --out=data/Chandra/chandra_multiband.fits --radius 15 --prior-completeness 0.9 +!nway.py 'data/Chandra/COSMOS_chandra.fits' :ERROR_RADIUS 'data/multiband_phot.fits' 0.1 --out=data/Chandra/chandra_multiband.fits --radius 15 --prior-completeness 0.9 #!/opt/conda/bin/nway.py 'data/Chandra/COSMOS_chandra.fits' :ERROR_RADIUS 'data/multiband_phot.fits' 0.1 --out=data/Chandra/chandra_multiband.fits --radius 15 --prior-completeness 0.9 ``` diff --git a/forced_photometry/multiband_photometry.html b/forced_photometry/multiband_photometry.html index 3b5a8153..16e560ae 100644 --- a/forced_photometry/multiband_photometry.html +++ b/forced_photometry/multiband_photometry.html @@ -574,6 +574,9 @@

Non-standard Dependenciesprint("tractor is missing") pass +# Add ~/.local/bin to path so executables installed with pip are available (needed for nway) +os.environ['PATH'] = f"{os.environ['HOME']}/.local/bin:{os.environ['PATH']}" + %matplotlib inline @@ -1342,7 +1345,7 @@

4b. Run nway 
# call nway
-!/home/jovyan/.local/bin/nway.py 'data/Chandra/COSMOS_chandra.fits' :ERROR_RADIUS 'data/multiband_phot.fits' 0.1 --out=data/Chandra/chandra_multiband.fits --radius 15 --prior-completeness 0.9
+!nway.py 'data/Chandra/COSMOS_chandra.fits' :ERROR_RADIUS 'data/multiband_phot.fits' 0.1 --out=data/Chandra/chandra_multiband.fits --radius 15 --prior-completeness 0.9
 
 #!/opt/conda/bin/nway.py 'data/Chandra/COSMOS_chandra.fits' :ERROR_RADIUS 'data/multiband_phot.fits' 0.1 --out=data/Chandra/chandra_multiband.fits --radius 15 --prior-completeness 0.9
diff --git a/searchindex.js b/searchindex.js index d19f870a..086480cb 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"1) Loading data": [[10, "loading-data"]], "1. Define the Sample": [[20, "define-the-sample"]], "1. Define the sample": [[15, "define-the-sample"], [21, "define-the-sample"]], "1. Get an account on the Fornax Science Console": [[1, "get-an-account-on-the-fornax-science-console"]], "1. Read in a dataset of archival light curves": [[14, "read-in-a-dataset-of-archival-light-curves"]], "1. Retrieve Initial Catalog from IRSA": [[7, "retrieve-initial-catalog-from-irsa"]], "1.1 Build your own sample": [[15, "build-your-own-sample"]], "1.1) What is in this sample": [[10, "what-is-in-this-sample"]], "1.2 Write out your sample to disk": [[15, "write-out-your-sample-to-disk"], [21, "write-out-your-sample-to-disk"]], "1.3 Load the sample table from disk": [[15, "load-the-sample-table-from-disk"], [21, "load-the-sample-table-from-disk"]], "1.4 Initialize data structure to hold the light curves": [[15, "initialize-data-structure-to-hold-the-light-curves"]], "1.4 Initialize data structure to hold the spectra": [[21, "initialize-data-structure-to-hold-the-spectra"]], "1a. Filter Catalog": [[7, "a-filter-catalog"]], "2) Preprocess data for ML (ZTF bands)": [[10, "preprocess-data-for-ml-ztf-bands"]], "2. Data Prep": [[14, "data-prep"]], "2. Find light curves for these targets in NASA catalogs": [[15, "find-light-curves-for-these-targets-in-nasa-catalogs"]], "2. Find spectra for these targets in NASA and other ancillary catalogs": [[21, "find-spectra-for-these-targets-in-nasa-and-other-ancillary-catalogs"]], "2. Log into the Fornax Science Console": [[1, "log-into-the-fornax-science-console"]], "2. Query the Euclid catalog for the sample": [[20, "query-the-euclid-catalog-for-the-sample"]], "2. Retrieve Image Datasets from the Cloud": [[7, "retrieve-image-datasets-from-the-cloud"]], "2.1 HEASARC: FERMI & Beppo SAX": [[15, "heasarc-fermi-beppo-sax"]], "2.1 IRSA Archive": [[21, "irsa-archive"]], "2.1 Remove bands with not enough data": [[14, "remove-bands-with-not-enough-data"]], "2.2 Combine Labels for a Simpler Classification": [[14, "combine-labels-for-a-simpler-classification"]], "2.2 IRSA: ZTF": [[15, "irsa-ztf"]], "2.2 MAST Archive": [[21, "mast-archive"]], "2.3 Data Visualization": [[14, "data-visualization"]], "2.3 ESA Archive": [[21, "esa-archive"]], "2.3 IRSA: WISE": [[15, "irsa-wise"]], "2.4 Clean the dataset of unwanted data": [[14, "clean-the-dataset-of-unwanted-data"]], "2.4 MAST: Pan-STARRS": [[15, "mast-pan-starrs"]], "2.4 SDSS Archive": [[21, "sdss-archive"]], "2.5 DESI Archive": [[21, "desi-archive"]], "2.5 MAST: TESS, Kepler and K2": [[15, "mast-tess-kepler-and-k2"]], "2.5 Missing Data": [[14, "missing-data"]], "2.6 Make all objects and bands have identical time arrays (uniform length and spacing)": [[14, "make-all-objects-and-bands-have-identical-time-arrays-uniform-length-and-spacing"]], "2.6 MAST: Hubble Catalog of Variables (HCV)": [[15, "mast-hubble-catalog-of-variables-hcv"]], "2.7 Restructure dataframe": [[14, "restructure-dataframe"]], "2.8 Normalize": [[14, "normalize"]], "2.9 Cleanup": [[14, "cleanup"]], "3) Learn the Manifold": [[10, "learn-the-manifold"]], "3. Run Forced Photometry": [[7, "run-forced-photometry"]], "3. Find light curves for these targets in relevant, non-NASA catalogs": [[15, "find-light-curves-for-these-targets-in-relevant-non-nasa-catalogs"]], "3. Grab the images, 1D coadded spectrum, & individual spectra": [[20, "grab-the-images-1d-coadded-spectrum-individual-spectra"]], "3. Make plots of luminosity as a function of time": [[21, "make-plots-of-luminosity-as-a-function-of-time"]], "3. Prep for ML algorithms": [[14, "prep-for-ml-algorithms"]], "3. Start a new notebook.": [[1, "start-a-new-notebook"]], "3.1 Gaia": [[15, "gaia"]], "3.1 Train test split": [[14, "train-test-split"]], "3.1) Sample comparison on the UMAP": [[10, "sample-comparison-on-the-umap"]], "3.2) Reduced dimensions on a SOM grid": [[10, "reduced-dimensions-on-a-som-grid"]], "3.3 IceCube neutrinos": [[15, "icecube-neutrinos"]], "3a. Setup": [[7, "a-setup"]], "3b. Main Function to do the Forced Photometry": [[7, "b-main-function-to-do-the-forced-photometry"]], "3c. Calculate Forced Photometry with Straightforward but Slow Method": [[7, "c-calculate-forced-photometry-with-straightforward-but-slow-method"]], "3d. Calculate Forced Photometry - Parallelization": [[7, "d-calculate-forced-photometry-parallelization"]], "3e. Cleanup": [[7, "e-cleanup"]], "3f. Plot to Confirm our Photometry Results": [[7, "f-plot-to-confirm-our-photometry-results"]], "4) Repeating the above, this time with ZTF + WISE manifold": [[10, "repeating-the-above-this-time-with-ztf-wise-manifold"]], "4. Cross Match our New Photometry Catalog with an X-ray archival Catalog": [[7, "cross-match-our-new-photometry-catalog-with-an-x-ray-archival-catalog"]], "4. End your JupyterHub session.": [[1, "end-your-jupyterhub-session"]], "4. Parallel processing the archive calls": [[15, "parallel-processing-the-archive-calls"]], "4. 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Retrieve Initial Catalog from IRSA": [[7, "retrieve-initial-catalog-from-irsa"]], "1.1 Build your own sample": [[15, "build-your-own-sample"]], "1.1) What is in this sample": [[10, "what-is-in-this-sample"]], "1.2 Write out your sample to disk": [[15, "write-out-your-sample-to-disk"], [21, "write-out-your-sample-to-disk"]], "1.3 Load the sample table from disk": [[15, "load-the-sample-table-from-disk"], [21, "load-the-sample-table-from-disk"]], "1.4 Initialize data structure to hold the light curves": [[15, "initialize-data-structure-to-hold-the-light-curves"]], "1.4 Initialize data structure to hold the spectra": [[21, "initialize-data-structure-to-hold-the-spectra"]], "1a. Filter Catalog": [[7, "a-filter-catalog"]], "2) Preprocess data for ML (ZTF bands)": [[10, "preprocess-data-for-ml-ztf-bands"]], "2. Data Prep": [[14, "data-prep"]], "2. Find light curves for these targets in NASA catalogs": [[15, "find-light-curves-for-these-targets-in-nasa-catalogs"]], "2. Find spectra for these targets in NASA and other ancillary catalogs": [[21, "find-spectra-for-these-targets-in-nasa-and-other-ancillary-catalogs"]], "2. Log into the Fornax Science Console": [[1, "log-into-the-fornax-science-console"]], "2. Query the Euclid catalog for the sample": [[20, "query-the-euclid-catalog-for-the-sample"]], "2. Retrieve Image Datasets from the Cloud": [[7, "retrieve-image-datasets-from-the-cloud"]], "2.1 HEASARC: FERMI & Beppo SAX": [[15, "heasarc-fermi-beppo-sax"]], "2.1 IRSA Archive": [[21, "irsa-archive"]], "2.1 Remove bands with not enough data": [[14, "remove-bands-with-not-enough-data"]], "2.2 Combine Labels for a Simpler Classification": [[14, "combine-labels-for-a-simpler-classification"]], "2.2 IRSA: ZTF": [[15, "irsa-ztf"]], "2.2 MAST Archive": [[21, "mast-archive"]], "2.3 Data Visualization": [[14, "data-visualization"]], "2.3 ESA Archive": [[21, "esa-archive"]], "2.3 IRSA: WISE": [[15, "irsa-wise"]], "2.4 Clean the dataset of unwanted data": [[14, "clean-the-dataset-of-unwanted-data"]], "2.4 MAST: Pan-STARRS": [[15, "mast-pan-starrs"]], "2.4 SDSS Archive": [[21, "sdss-archive"]], "2.5 DESI Archive": [[21, "desi-archive"]], "2.5 MAST: TESS, Kepler and K2": [[15, "mast-tess-kepler-and-k2"]], "2.5 Missing Data": [[14, "missing-data"]], "2.6 Make all objects and bands have identical time arrays (uniform length and spacing)": [[14, "make-all-objects-and-bands-have-identical-time-arrays-uniform-length-and-spacing"]], "2.6 MAST: Hubble Catalog of Variables (HCV)": [[15, "mast-hubble-catalog-of-variables-hcv"]], "2.7 Restructure dataframe": [[14, "restructure-dataframe"]], "2.8 Normalize": [[14, "normalize"]], "2.9 Cleanup": [[14, "cleanup"]], "3) Learn the Manifold": [[10, "learn-the-manifold"]], "3. Run Forced Photometry": [[7, "run-forced-photometry"]], "3. Find light curves for these targets in relevant, non-NASA catalogs": [[15, "find-light-curves-for-these-targets-in-relevant-non-nasa-catalogs"]], "3. Grab the images, 1D coadded spectrum, & individual spectra": [[20, "grab-the-images-1d-coadded-spectrum-individual-spectra"]], "3. Make plots of luminosity as a function of time": [[21, "make-plots-of-luminosity-as-a-function-of-time"]], "3. Prep for ML algorithms": [[14, "prep-for-ml-algorithms"]], "3. Start a new notebook.": [[1, "start-a-new-notebook"]], "3.1 Gaia": [[15, "gaia"]], "3.1 Train test split": [[14, "train-test-split"]], "3.1) Sample comparison on the UMAP": [[10, "sample-comparison-on-the-umap"]], "3.2) Reduced dimensions on a SOM grid": [[10, "reduced-dimensions-on-a-som-grid"]], "3.3 IceCube neutrinos": [[15, "icecube-neutrinos"]], "3a. Setup": [[7, "a-setup"]], "3b. 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