Updates to Ag 2_ notebook

Fixed the crop type sampling bug, improved workflow & documentation
CU-ESIIL · Jun 9, 2024 · 816d514 · 816d514
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commit 816d514
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diff --git a/notebooks/agriculture/0_Ag_Lands_Search_EMIT.ipynb b/notebooks/agriculture/0_Ag_Lands_Search_EMIT.ipynb
diff --git a/notebooks/agriculture/1_Orthorectify_images.ipynb b/notebooks/agriculture/1_Orthorectify_images.ipynb
@@ -24,7 +24,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "c85f8c1b-c98e-4144-9353-9ccc2c5cf6b7",
    "metadata": {},
    "outputs": [],
@@ -48,7 +48,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "b9904e03-c7e0-4e14-ae86-38033534d227",
    "metadata": {},
    "outputs": [],
@@ -69,24 +69,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "c0e6854f-2505-42fb-8552-42161c9c5622",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "['EMIT_L2A_RFL_001_20230729T205618_2321014_018.nc',\n",
-       " 'EMIT_L2A_RFL_001_20230729T205630_2321014_019.nc',\n",
-       " 'EMIT_L2A_RFL_001_20230729T205642_2321014_020.nc',\n",
-       " 'EMIT_L2A_RFL_001_20230729T205653_2321014_021.nc']"
-      ]
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "### List downloaded files in the directory\n",
     "# Create a file list of the non-ortho images\n",
@@ -106,31 +92,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "fde8b643-1e57-47bf-bfef-dcf5b17622b1",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Input Granule ID: EMIT_L2A_RFL_001_20230729T205618_2321014_018.nc\n",
-      "Output Granule ID: EMIT_L2A_RFL_001_20230729T205618_2321014_018_ortho.nc\n",
-      " \n",
-      "Input Granule ID: EMIT_L2A_RFL_001_20230729T205630_2321014_019.nc\n",
-      "Output Granule ID: EMIT_L2A_RFL_001_20230729T205630_2321014_019_ortho.nc\n",
-      " \n",
-      "Input Granule ID: EMIT_L2A_RFL_001_20230729T205642_2321014_020.nc\n",
-      "Output Granule ID: EMIT_L2A_RFL_001_20230729T205642_2321014_020_ortho.nc\n",
-      " \n",
-      "Input Granule ID: EMIT_L2A_RFL_001_20230729T205653_2321014_021.nc\n",
-      "Output Granule ID: EMIT_L2A_RFL_001_20230729T205653_2321014_021_ortho.nc\n",
-      " \n",
-      "Total time: 31.769140243530273\n",
-      "*** Success! ***\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "### Ortho-mosaic the data granules\n",
     "t0 = time.time()\n",
@@ -168,45 +133,31 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "d542b966-e9c6-4d84-86d6-b72a4f2b2fbe",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "['EMIT_L2A_RFL_001_20230729T205618_2321014_018_ortho.nc',\n",
-       " 'EMIT_L2A_RFL_001_20230729T205630_2321014_019_ortho.nc',\n",
-       " 'EMIT_L2A_RFL_001_20230729T205642_2321014_020_ortho.nc',\n",
-       " 'EMIT_L2A_RFL_001_20230729T205653_2321014_021_ortho.nc']"
-      ]
-     },
-     "execution_count": 5,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "### List ortho-mosaiced files in the working image directory\n",
     "fnmatch.filter(os.listdir(source_file_path), '*ortho.nc')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "ec8dbb62-ac72-4f51-99b9-aa97cb8d5330",
+   "metadata": {},
+   "source": [
+    "### OPTIONAL: Transfer data to your cyverse data store\n",
+    "\n",
+    "Note that this will take a few minutes to complete!"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "ffb5ff5f-b051-4fbf-88cc-89b7ac9ded4b",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "\n",
-      "*** Copying complete! ***\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "### Create backup copy of orthorectified images\n",
     "user_name = os.environ.get(\"IPLANT_USER\")\n",