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Update setting of notebook's env. variables for CRDS #262

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merged 4 commits into from
Nov 13, 2024
Merged

Update setting of notebook's env. variables for CRDS #262

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71e24c2
update crds config to match jwst-pipeline-notebooks
gibsongreen Nov 13, 2024
7971ed8
move crds import to be after setting of env variables
gibsongreen Nov 13, 2024
bc8d377
update set server condition
gibsongreen Nov 13, 2024
602fba8
move crds config to right below imports
gibsongreen Nov 13, 2024
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70 changes: 45 additions & 25 deletions notebooks/NIRCam/NIRCam_WFSS_Box_extraction/BoxExtraction_using_Grismconf_CRDS.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -69,13 +69,55 @@
"import requests\n",
"from scipy.stats import sigmaclip\n",
"\n",
"from crds import client\n",
"import grismconf\n",
"from jwst.assign_wcs import AssignWcsStep\n",
"from jwst.flatfield import FlatFieldStep\n",
"from jwst.photom import PhotomStep"
]
},
{
"cell_type": "markdown",
"id": "d6b0fc4b",
"metadata": {},
"source": [
"## Set CRDS Path and Server"
]
},
{
"cell_type": "markdown",
"id": "bb09075d-b0ba-4bee-b6c5-a2f27b767b6a",
"metadata": {},
"source": [
"Before running the pipeline steps, we need to ensure our our CRDS environment is configured. This includes defining a CRDS cache directory in which to keep the reference files that will be used by the calibration pipeline.\n",
"\n",
"If the root directory for the local CRDS cache has not already been set, it will be created in the home directory."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "0ab935ab-a215-4fe3-8aad-b3dae5a017bb",
"metadata": {},
"outputs": [],
"source": [
"# Check whether the local CRDS cache directory has been set.\n",
"# If not, set it to the user home directory\n",
"if (os.getenv('CRDS_PATH') is None):\n",
" os.environ['CRDS_PATH'] = os.path.join(os.path.expanduser('~'), 'crds')\n",
"# Check whether the CRDS server URL has been set. If not, set it.\n",
"if (os.getenv('CRDS_SERVER_URL') is None):\n",
" os.environ['CRDS_SERVER_URL'] = 'https://jwst-crds.stsci.edu'\n",
"\n",
"# Echo CRDS path and context in use\n",
"print('CRDS local filepath:', os.environ['CRDS_PATH'])\n",
"print('CRDS file server:', os.environ['CRDS_SERVER_URL'])\n",
"\n",
"# import crds after setting up the required environment variables\n",
"from crds import client\n",
"if client.get_crds_server() != os.environ['CRDS_SERVER_URL']:\n",
" client.set_crds_server('https://jwst-crds.stsci.edu')"
]
},
{
"cell_type": "markdown",
"id": "117e4ec7-610c-4d11-82f4-756971dc23e0",
Expand Down Expand Up @@ -199,7 +241,7 @@
"id": "41068262-9a54-46c5-a9d2-ca2217ad1fee",
"metadata": {},
"source": [
"## Download Data and Ensure CRDS Configuration"
"## Download Data"
]
},
{
Expand All @@ -224,28 +266,6 @@
"get_jwst_file(wfss_file)"
]
},
{
"cell_type": "markdown",
"id": "faa27c94",
"metadata": {},
"source": [
"If CRDS is not configured, set the CRDS server URL and define a local cache path \n",
"to ensure the pipeline steps can access reference files as needed."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "af7a4057",
"metadata": {},
"outputs": [],
"source": [
"if os.environ.get(\"CRDS_PATH\") is None:\n",
" client.set_crds_server('https://jwst-crds.stsci.edu')\n",
" os.environ[\"CRDS_SERVER_URL\"] = \"https://jwst-crds.stsci.edu\"\n",
" os.environ[\"CRDS_PATH\"] = \"\""
]
},
{
"cell_type": "markdown",
"id": "ab5f3c78-258f-49c4-99c4-87e26f0972cf",
Expand Down Expand Up @@ -1138,7 +1158,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.10"
"version": "3.12.7"
}
},
"nbformat": 4,
Expand Down
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