`Can we load your data file(s)?` | *ers-transit Data Checkpoint:* time-series extracted 1D spectra 🌈

can-we-load-your-data-for-time-series-extracted-1D-spectra.ipynb

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   "source": [
    "# `Can we load your data file(s)?` | *ers-transit Data Checkpoint:* time-series extracted 1D spectra 🌈 \n",
    "*1 March 2022*"
   ]
  },
  {
   "cell_type": "markdown",
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   "source": [
    "This notebook aims to serve as a quick way to visualize and evaluate results produced for the [Spring 2022 Data Challenge with Simulated Data](https://ers-transit.github.io/data-challenge-with-simulated-data.html) for the [Webb Transiting Exoplanet Community Early Release Science Program](https://ers-transit.github.io/index.html)."
   ]
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  {
   "cell_type": "markdown",
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   "source": [
    "*🪐🤩❤️ This test snippet notebook designed to check whether we will be able to read your data files easily. A longer notebook, containing standardized visualizations and quantitative metrics, will be made available by the 21-23 March 2022 meeting.🪐🤩❤️*"
   ]
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   "source": [
    "## 🧑‍💻 Load the Data\n",
    "\n",
    "Can we load in your time-series extracted  1D spectra? \n",
    "\n",
    "This notebook makes use of the `chromatic` toolkit, which can be installed via `pip install chromatic-lightcurves` and is documented [here](https://zkbt.github.io/chromatic/). It's meant to be a handy way to load, visualize, and do calculations with multiwavelength lightcurves."
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   ],
   "source": [
    "from chromatic import *\n",
    "version()"
   ]
  },
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   "source": [
    "`chromatic` can read time-series spectra in a few different file formats. These are the ones that work *so far*:\n",
    "- `*.txt` files that contain columns `wavelength` (in microns), `time` (in days), `flux` (in any units), `uncertainty` (in the same units as `flux`) along with any other columns\n",
    "- `*x1dints.fits` files from the STScI `jwst` pipeline, including all `x1dints` files produced as Stage 2 Data Products for the ers-transit Data Challenge for NIRSpec, NIRCam, MIRI\n",
    "- `spectra_order*.npy` files produced as Stage 2 Data Products for the ers-transit Data Challenge for NIRISS\n",
    "- `S3_*_Table_Save.txt` files from [Eureka!](https://github.com/kevin218/Eureka)\n",
    "- `*.rainbow.npy` files generated by `chromatic` itself\n",
    "\n",
    "Now, let's try to read in that file!"
   ]
  },
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   "cell_type": "code",
   "execution_count": 2,
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   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "🌈 Warning: No times found! Making up imaginary ones!"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The imaginary times assume 47.712 s/integration.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 42/42 [00:05<00:00,  7.39it/s]\n"
     ]
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   ],
   "source": [
    "# define a path pointing to the file(s) for this data product\n",
    "data_path = '/Users/zach/Data/JWST/Spring2022DataChallenge/'\n",
    "file_path = os.path.join(data_path, 'MIRI/Stage 2 Output/*x1dints.fits')\n",
    "data = Rainbow(file_path)"
   ]
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   "cell_type": "code",
   "execution_count": 3,
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   "outputs": [
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     "name": "stdout",
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     "text": [
      "\n",
      "This chromatic light curve <🌈(387w, 1848t)>\n",
      "has 387 wavelengths spanning 3.74 um to 14.4 um \n",
      "and 1848 times spanning 0.00 d to 1.02 d.\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(f'''\n",
    "This chromatic light curve {data}\n",
    "has {data.nwave} wavelengths spanning {min(data.wavelength):.3} to {max(data.wavelength):.3} \n",
    "and {data.ntime} times spanning {min(data.time):.2f} to {max(data.time):.2f}.\n",
    "''')"
   ]
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  {
   "cell_type": "markdown",
   "id": "4e4022b5",
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   "source": [
    "## Did it work?\n",
    "\n",
    "- If you've made it this far without an error, that's spectacular! Huzzah! We should be able to make some snazzy visualizations and calculate some useful metrics from your submitted data.\n",
    "- If you ran into an error, please visit the `chromatic` file [input/output page](https://zkbt.github.io/chromatic/io/) and...\n",
    "    - ...see if your file format could be brought into alignment with one of the existing readers.\n",
    "    - ...try writing a new `chromatic` reader for your particular file format, so others can use it too.\n",
    "    - ...consider sending Zach Berta-Thompson a message on the `ers-transit` slack. He'll be happy to try to help!"
   ]
  }
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