more pep8 changes

spacetelescope · Aug 17, 2023 · 47154f5 · 47154f5
1 parent 75ec6d7
commit 47154f5
Showing 1 changed file with 24 additions and 71 deletions.
diff --git a/notebooks/MIRI_LRS_spectral_extraction/miri_lrs_advanced_extraction_part1.ipynb b/notebooks/MIRI_LRS_spectral_extraction/miri_lrs_advanced_extraction_part1.ipynb
@@ -13,8 +13,7 @@
     "**Data:** Publicly available science data<br>\n",
     "**Tools:** jwst, matplotlib, astropy.<br>\n",
     "**Cross-intrument:** NIRSpec, MIRI.<br>\n",
-    "\n",
-    "\n",
+    "**Documentation:** This notebook is part of a STScI's larger [post-pipeline Data Analysis Tools Ecosystem](https://jwst-docs.stsci.edu/jwst-post-pipeline-data-analysis) and can be [downloaded](https://github.com/spacetelescope/dat_pyinthesky/tree/main/jdat_notebooks/MRS_Mstar_analysis) directly from the [JDAT Notebook Github directory](https://github.com/spacetelescope/jdat_notebooks).<br>\n",
     "\n",
     "### Introduction: Spectral extraction in the JWST calibration pipeline\n",
     "\n",
@@ -61,42 +60,10 @@
   },
   {
    "cell_type": "markdown",
+   "id": "14ff9543",
    "metadata": {},
    "source": [
-    "<p style=\"font-size:200%; color:#e56020; background-color:#1d1160;\"><b><i>Reviewer note:</i> Begin PEP8 check cells (delete below when finished)</b></p>"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# disable all imported packages' loggers\n",
-    "import logging\n",
-    "logging.root.manager.loggerDict = {}"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# enable PEP8 checker for this notebook\n",
-    "%load_ext pycodestyle_magic\n",
-    "%flake8_on --ignore E261,E501,W291,W293\n",
-    "\n",
-    "# only allow the checker to throw warnings when there's a violation\n",
-    "logging.getLogger('flake8').setLevel('ERROR')\n",
-    "logging.getLogger('stpipe').setLevel('ERROR')"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<p style=\"font-size:200%; color:#e56020; background-color:#1d1160;\"><b><i>Reviewer note:</i> Begin PEP8 check cells (delete above when finished)</b></p>"
+    "## Import Packages"
    ]
   },
   {
@@ -130,13 +97,10 @@
     "from astropy.modeling import models, fitting\n",
     "\n",
     "import jwst\n",
-    "from jwst.pipeline import Spec2Pipeline, Spec3Pipeline\n",
     "from jwst import datamodels\n",
     "from jwst.extract_1d import Extract1dStep\n",
     "\n",
     "from matplotlib.patches import Rectangle\n",
-    "from matplotlib.collections import PatchCollection\n",
-    "\n",
     "\n",
     "import json\n",
     "import crds\n",
@@ -166,22 +130,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Download Data\n",
-    "if os.path.exists(\"data.tar.gz\"):\n",
-    "    print(\"Original Data tar.gz Exists\")\n",
-    "else:\n",
-    "    print(\"Downloading Data\")\n",
-    "    url = 'https://data.science.stsci.edu/redirect/JWST/jwst-data_analysis_tools/MIRI_LRS_notebook/data.tar.gz'\n",
-    "    urllib.request.urlretrieve(url, 'data.tar.gz')\n",
+    "data_tar_url = 'https://data.science.stsci.edu/redirect/JWST/jwst-data_analysis_tools/MIRI_LRS_notebook/data.tar.gz'\n",
     "\n",
-    "# Unzip files if they haven't already been unzipped\n",
-    "if os.path.exists(\"data/\"):\n",
-    "    print(\"Data Directory Already Exists\")\n",
-    "else:\n",
+    "# Download and unpack data if needed\n",
+    "if not os.path.exists(\"data.tar.gz\"):\n",
+    "    print(\"Downloading Data\")\n",
+    "    urllib.request.urlretrieve(data_tar_url, 'data.tar.gz')\n",
+    "if not os.path.exists(\"data/\"):\n",
     "    print(\"Unpacking Data\")\n",
-    "    tar = tarfile.open('./data.tar.gz', \"r:gz\")\n",
-    "    tar.extractall()\n",
-    "    tar.close()"
+    "    with tarfile.open('./data.tar.gz', \"r:gz\") as tar:\n",
+    "        tar.extractall()\n"
    ]
   },
   {
@@ -261,7 +219,7 @@
    },
    "outputs": [],
    "source": [
-    "print('Spectral extraction reference file used: {}'.format(l3_spec.meta.ref_file.extract1d.name))"
+    "print(f'Spectral extraction reference file used: {l3_spec.meta.ref_file.extract1d.name}')"
    ]
   },
   {
@@ -273,22 +231,16 @@
    },
    "outputs": [],
    "source": [
-    "hdu = fits.open('data/jw02072-o001_t010_miri_p750l_x1d_1089.fits')\n",
-    "json_ref_default = crds.getreferences(hdu[0].header)['extract1d']"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "50c8ba27",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "with open(json_ref_default) as json_ref:\n",
-    "    x1dref_default = json.load(json_ref)\n",
-    "    print('Settings for SLIT data: {}'.format(x1dref_default['apertures'][0]))\n",
-    "    print('  ')\n",
-    "    print('Settings for SLITLESS data: {}'.format(x1dref_default['apertures'][1]))"
+    "file_path = 'data/jw02072-o001_t010_miri_p750l_x1d_1089.fits'\n",
+    "with fits.open(file_path) as hdul:\n",
+    "    header = hdu[0].header\n",
+    "    json_ref_default = crds.getreferences(header)['extract1d']\n",
+    "    \n",
+    "    with open(json_ref_default) as json_ref:\n",
+    "        x1dref_default = json.load(json_ref)\n",
+    "        print('Settings for SLIT data: {}'.format(x1dref_default['apertures'][0]))\n",
+    "        print('  ')\n",
+    "        print('Settings for SLITLESS data: {}'.format(x1dref_default['apertures'][1])) "
    ]
   },
   {
@@ -705,7 +657,8 @@
     "    ax.set_xlabel('wavelength')\n",
     "    ax.set_ylabel('px')\n",
     "    ax.legend()\n",
-    "    return(fitted_line)\n"
+    "    return(fitted_line)\n",
+    "\n"
    ]
   },
   {