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Merge pull request #795 from ojustino/synth-mv-imgs-2
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Updated synthetic image creation notebook
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@pllim
pllim authored Aug 24, 2021
2 parents 055b09d + 9a4503b commit aeb022a
Showing 1 changed file with 53 additions and 19 deletions.
72 changes: 53 additions & 19 deletions notebooks/concepts/generate_mosviz_photometry.ipynb
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Expand Up @@ -27,20 +27,23 @@
"source": [
"### Import packages\n",
"\n",
"- `os` helps us create a new directory for the final cutouts from the synthetic image.\n",
"- `glob.glob` lists local files that match a given pattern.\n",
"- We use `astropy.units` to convert between degrees and arcseconds.\n",
"- `astropy.coordinates.SkyCoord` helps merge lists of right ascensions (RA) and declinations (Dec) into one object.\n",
"- `astropy.convolution.Gaussian2DKernel` smooths two-dimensional data by performing convolutions with two Gaussian functions.\n",
"- We use `astropy.io.fits` to read in existing FITS files and write a new one with the synthetic image.\n",
"- The objects from `astropy.nddata` assist in creating cutouts once we have identified galaxies to take from the field image and also with re-importing our synthetic image.\n",
"- The `sigma_*` methods from `astropy.stats` work with image data that is clipped to within a certain number of deviations from the mean. `gaussian_fwhm_to_sigma` is a float for converting full width at half maximum values to standard deviations from the image mean.\n",
"- The objects from `astropy.table` help with reading an modifiying tabular data.\n",
"- We download a copy of the Artifactory spectra with `astropy.utils.data.download_file`.\n",
"- `astropy.wcs.WCS` creates a World Coordinate System object that is useful for transforming on-sky data from one patch to another.\n",
"- `glob.glob` lists local files that match a given pattern.\n",
"- `pathlib.Path` allows for the creation of file paths that work across operating systems.\n",
"- The objects from `photutils.segmentation` do the work of analytically finding bright sources, separating those that overlap, and creating a catalog of the resulting information.\n",
"- We use `matplotlib.pyplot` to preview the field image, the cutouts, and various stages of our synthetic image.\n",
"- We use `numpy` to facilitate several specialized mathematical and array-related operations.\n",
"- `os` helps us create a new directory for the final cutouts from the synthetic image.\n",
"- `%matplotlib inline` is notebook \"magic\" that helps display in-notebook plots consistently for different users."
"- `zipfile` assists with unzipping the downloaded Artifactory files.\n",
"- Finally, `%matplotlib inline` is notebook \"magic\" that helps display in-notebook plots consistently for different users."
]
},
{
Expand All @@ -53,7 +56,9 @@
"outputs": [],
"source": [
"import os\n",
"import zipfile\n",
"from glob import glob\n",
"from pathlib import Path\n",
"\n",
"from astropy import units as u\n",
"from astropy.coordinates import SkyCoord\n",
Expand All @@ -63,6 +68,7 @@
"from astropy.stats import (gaussian_fwhm_to_sigma,\n",
" sigma_clipped_stats, sigma_clip)\n",
"from astropy.table import Table, join\n",
"from astropy.utils.data import download_file\n",
"from astropy.wcs import WCS\n",
"from photutils.segmentation import (detect_sources, deblend_sources,\n",
" SourceCatalog)\n",
Expand Down Expand Up @@ -417,9 +423,39 @@
"source": [
"### (Try to) Extract destination RA/Dec from spectra files\n",
"\n",
"Note that this section's cells only run on a connection with access to the STScI VPN. They use copies of JWST pipeline files from May 19, 2021.\n",
"We download copies of Level 3 data products from the JWST pipeline dated May 19, 2021 and hosted in a STScI Box folder. (For more current files, visit the [Artifactory](https://bytesalad.stsci.edu/ui/repos/tree/General/jwst-pipeline%2Fdev%2Ftruth%2Ftest_nirspec_mos_spec3.).) The files are saved in this notebook's current location. If you prefer to save them elsewhere, change `filepath`."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "73c7cd0a-1eed-4c1e-a7af-16247d6991b6",
"metadata": {},
"outputs": [],
"source": [
"filepath = Path('./')\n",
"\n",
"# If necessary, download and extract spectra files\n",
"spec_link = 'https://stsci.box.com/shared/static/3rz8g1fizu6dh7zdymxouvdd8usnm3jc.zip'\n",
"spec_zip = filepath / 'artifactory_spectra-2021-05-19.zip'\n",
"spec_path = filepath / spec_zip.stem\n",
"\n",
"To run them elsewhere and/or use more current files, visit the [Artifactory](https://bytesalad.stsci.edu/ui/repos/tree/General/jwst-pipeline%2Fdev%2Ftruth%2Ftest_nirspec_mos_spec3), ensure the `jwst-pipeline/dev/truth/test_nirspec_mos_spec3/` folder is the one selected in the directory tree, and download all files whose names begin with `jw00626-o030` and end with `nirspec_f170lp-g235m_x1d.fits` or `nirspec_f170lp-g235m_s2d.fits`. (The original version of this notebook uses six of these Level 3 data products.) Then, change `filepath` in the next cell to the location where you saved the downloaded files, remembering the trailing slash."
"if spec_path.exists():\n",
" print('Spectra already on disk.')\n",
"else:\n",
" if not (filepath / spec_zip).exists():\n",
" print(f\"Downloading '{spec_zip.name}'.\")\n",
" box_file = download_file(spec_link, cache=True)\n",
" \n",
" # place link to downloaded file in current directory\n",
" os.symlink(box_file, filepath / spec_zip)\n",
" \n",
" print('Extracting spectra.')\n",
" \n",
" # create target directory and extract spectra files \n",
" (filepath / spec_path).mkdir()\n",
" with zipfile.ZipFile(filepath / spec_zip, 'r') as zf:\n",
" zf.extractall(spec_path)"
]
},
{
Expand All @@ -430,9 +466,8 @@
"outputs": [],
"source": [
"# view level 3 spectra FITS header information\n",
"filepath = '/user/jotor/jwst-pipeline-lvl3-copy/'\n",
"x1d_header = fits.getheader(filepath + 'jw00626-o030_s00000_nirspec_f170lp-g235m_x1d.fits', ext=1)\n",
"s2d_header = fits.getheader(filepath + 'jw00626-o030_s00000_nirspec_f170lp-g235m_s2d.fits', ext=1)"
"x1d_header = fits.getheader(spec_path / 'jw00626-o030_s00000_nirspec_f170lp-g235m_x1d.fits', ext=1)\n",
"s2d_header = fits.getheader(spec_path / 'jw00626-o030_s00000_nirspec_f170lp-g235m_s2d.fits', ext=1)"
]
},
{
Expand Down Expand Up @@ -472,7 +507,7 @@
"source": [
"# search for RA/Dec information from Artifactory observation files\n",
"x1d_header_list = [fits.getheader(file, ext=1)\n",
" for file in glob(filepath + 'jw00626*x1d.fits')]\n",
" for file in spec_path.glob('jw00626*x1d.fits')]\n",
"\n",
"_ras, _decs = np.array([[h['SRCRA'], h['SRCDEC']] for h in x1d_header_list]).T\n",
"_ras, _decs"
Expand Down Expand Up @@ -712,7 +747,7 @@
"id": "8b518b39-3d22-42c4-a632-4c17801900a5",
"metadata": {},
"source": [
"We save the image to a local location. The default is this notebook's current directory; you can change that by adjusting `savepath` to your preferred path and remembering the trailing slash.\n",
"We save the image to a local location. The default is this notebook's current directory; you can change that by adjusting `savepath` to your preferred path.\n",
"\n",
"This cell will overwrite a same-named file if it already exists in that location."
]
Expand All @@ -724,10 +759,10 @@
"metadata": {},
"outputs": [],
"source": [
"savepath = './'\n",
"savepath = Path('./')\n",
"synth_file = 'synthetic_mosviz_image.fits'\n",
"\n",
"fits.writeto(savepath + synth_file, synth_image,\n",
"fits.writeto(savepath / synth_file, synth_image,\n",
" header=synth_wcs.to_header(), overwrite=True)"
]
},
Expand All @@ -750,7 +785,7 @@
"metadata": {},
"outputs": [],
"source": [
"ccd_synth_img = CCDData.read(savepath + synth_file, unit='electron/s')"
"ccd_synth_img = CCDData.read(savepath / synth_file, unit='electron/s')"
]
},
{
Expand All @@ -764,7 +799,7 @@
"synth_cutout_list = [Cutout2D(ccd_synth_img, SkyCoord(r, d), synth_cutout_size)\n",
" for r, d in zip(ras * u.deg, decs * u.deg)]\n",
"\n",
"plt.imshow(synth_cutout_list[0].data, **imshow_params,\n",
"plt.imshow(synth_cutout_list[2].data, **imshow_params,\n",
" vmin=0, vmax=ccd_synth_img.data.std())"
]
},
Expand All @@ -788,10 +823,9 @@
},
"outputs": [],
"source": [
"savepath2 = './mosviz-cutouts/'\n",
"\n",
"if not os.path.exists(savepath2):\n",
" os.makedirs(savepath2)\n",
"cutout_dir = savepath / 'mosviz-cutouts/'\n",
"if not (savepath / cutout_dir).exists():\n",
" cutout_dir.mkdir()\n",
"\n",
"for i, cut in enumerate(synth_cutout_list):\n",
" sdt = cut.data\n",
Expand All @@ -802,7 +836,7 @@
" shd['OBJ_DEC'] = (decs[i], 'Source declination')\n",
" shd['OBJ_ROT'] = (0, '')\n",
" \n",
" fits.writeto(savepath2 + f\"synth_cutout{i}.fits\",\n",
" fits.writeto(cutout_dir / f\"synth_cutout{i}.fits\",\n",
" sdt, header=shd, overwrite=True)\n",
" \n",
" plt.imshow(sdt, **imshow_params, vmin=0, vmax=ccd_synth_img.data.std())\n",
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