updated notebooks, not all working

Author: jrcain-usgs

docs/how-to-guides/knoten-notebooks/00-knotebooks-status.md

@@ -0,0 +1,73 @@
+Status:
+
+  No. | Status                           | Notebooks     |                   |                  |                           | notes
+ -----|----------------------------------|---------------|-------------------|------------------|---------------------------|-------------------|
+  16  | Total                            |
+   4  | Working                          | bundle-adjust | sensor-utils      | usgscsm-isis-cmp | reduced-normal-equations* | (* with warnings) |
+   4  | File not Located                 | data-snooping | footprint-control | lm-bundle-adjust |                           |                   |
+   3  | Ale; no driver.to_dict           | cassini-iss   | lrolroc-nac^      | kaguya-tc^       |                           | (^ listed twice)  |
+   1  | Ale; no find_child_frame         | mdis-isis-csm-cmp                 |
+   2  | knoten.create_csm returns None?  | mdis-dem      | mdis-stereo       |
+   1  | Math Error                       | bundle-adjust-distributed         |
+   3  | Not Examined in Depth            | kaguya-tc     | lrolroc-nac       | footprint-comparison |
+
+
+# bundle-adjust-distributed.ipynb
+- result = f.result()
+  - LinAlgError: Singular matrix
+
+# bundle-adjust.ipynb
+- Working!
+
+# cassini-iss.ipynb
+- Had to download and edit spice data for this
+- 'CassiniIssPds3LabelNaifSpiceDriver' object has no attribute 'to_dict'
+
+# data-snooping.ipynb
+- On Hold: File not found: control_network_metrics/registration_quality/cubes.lis
+
+# footprint-comparison.ipynb
+- Download File: data/J03_045994_1986_XN_18N282W_sorted.cub
+- Need 2 ISDs for comparison
+  - example is from 2 different versions of ALE
+  - Produce these and store in repo?
+
+# footprint-control.ipynb
+- On Hold: Files not found: europa/11ESMORPHY01_Island9... _add.net, .net, .lis
+
+# kaguya-tc.ipynb
+- Compressed .sl2 files with spc and ctg files? 
+- Download File: images/TC2W2B0_01_00366S490E1640.img
+
+# lm-bundle-adjust.ipyn
+- On Hold: File not found: /scratch/csm2020/data/cubes2.lis
+
+# lrolroc-nac.ipynb
+- Failed to find metakernels.  (need to download naif spice data)
+
+# mdis-dem.ipynb
+- AttributeError: 'NoneType' object has no attribute 'getImageSize'
+  - knoten.csm.create_csm returns `None`?
+
+# mdis-isis-csm-cmp.ipynb
+- driver.frame_chain has no attribute 'find_child_frame'
+
+# mdis-stereo.ipynb
+- AttributeError: 'NoneType' object has no attribute 'getImageSize'
+  - knoten.csm.create_csm returns `None`?
+
+# reduced-normal-equations.ipynb
+- Working with warning:
+  - FutureWarning: Series.__getitem__ treating keys as positions is deprecated.
+    In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior).
+    To access a value by position, use `ser.iloc[pos]`
+
+# reduced-normal-with-cholesky.ipynb
+- On Hold: File not found: /scratch/csm2020/test_bundles/cubes_smithed_ground.lis
+- requirement: from sksparse.cholmod import cholesky
+
+# sensor-utils.ipynb
+- Working!
+
+# usgscsm-isis-cmp.ipynb
+- Working!

docs/how-to-guides/knoten-notebooks/bundle-adjust-distributed.ipynb

@@ -9,7 +9,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -312,7 +312,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,

docs/how-to-guides/knoten-notebooks/bundle-adjust.ipynb

@@ -13,46 +13,37 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import os\n",
+    "os.environ['ISISROOT'] = '/usr/local/Caskroom/miniconda/base/envs/isis-prod'\n",
+    "os.environ['ISISDATA'] = '/Volumes/usgs-data/isis-data'\n",
+    "import urllib.request\n",
+    "\n",
     "import ale\n",
-    "from ale.drivers.messenger_drivers import MessengerMdisPds3NaifSpiceDriver\n",
+    "from ale.drivers.mess_drivers import MessengerMdisPds3NaifSpiceDriver\n",
     "from ale.formatters.usgscsm_formatter import to_usgscsm\n",
     "import json\n",
     "import os\n",
-    "from pysis import isis\n",
+    "import kalasiris as isis\n",
     "import pvl\n",
     "import numpy as np\n",
     "import knoten\n",
     "import csmapi\n",
-    "from knoten import csm"
+    "from knoten import csm\n",
+    "\n",
+    "ale.spice_root = '/Volumes/usgs-data/spice-data'"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "cassini: data/cassini/kernels/mk/\n",
-      "dawn: spice/dawn-m_a-spice-6-v1.0/dawnsp_1000/extras/mk\n",
-      "kaguya: spice/SELENE/kernels/mk/\n",
-      "lro: spice/lro-l-spice-6-v1.0/lrosp_1000/extras/mk/\n",
-      "mdis: spice/mess-e_v_h-spice-6-v1.0/messsp_1000/extras/mk\n",
-      "mro: spice/mro-m-spice-6-v1.0/mrosp_1000/extras/mk\n",
-      "spice_root: spice/\n",
-      "\n",
-      "MDIS spice directory: spice/mess-e_v_h-spice-6-v1.0/messsp_1000/extras/mk\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# printing config displays the yaml formatted string\n",
-    "print(ale.config)\n",
+    "# print(ale.config) Gone?\n",
     "\n",
     "# config object is a dictionary so it has the same access patterns \n",
-    "print('MDIS spice directory:', ale.config['mdis'])\n",
+    "# print('MDIS spice directory:', ale.config['mdis'])\n",
     "\n",
     "# updating config for new MDIS path in this notebook \n",
     "# Note: this will not change the path in `.ale/config.yml`. This change only lives in the notebook.\n",
@@ -64,9 +55,38 @@
    "execution_count": 3,
    "metadata": {},
    "outputs": [],
+   "source": [
+    "# https://pdsimage2.wr.usgs.gov/Messenger/MSGRMDS_1001/DATA/2015_114/\n",
+    "# https://d3fhgbbgskqro0.cloudfront.net/MSGRMDS_1001/DATA/2015_114/EN1072174528M.IMG\n",
+    "\n",
+    "imgurl = 'https://d3fhgbbgskqro0.cloudfront.net/MSGRMDS_1001/DATA/2015_114/EN1072174528M.IMG'\n",
+    "image_dir = 'data'\n",
+    "EN1072174528M = os.path.join(image_dir, 'EN1072174528M.IMG')\n",
+    "downloader = urllib.request.URLopener()\n",
+    "if not os.path.isfile(EN1072174528M):\n",
+    "    downloader.retrieve(imgurl, EN1072174528M)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "AttributeError",
+     "evalue": "'FrameChain' object has no attribute 'find_child_frame'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[6], line 9\u001b[0m\n\u001b[1;32m      6\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m MessengerMdisPds3NaifSpiceDriver(fileName) \u001b[38;5;28;01mas\u001b[39;00m driver:\n\u001b[1;32m      7\u001b[0m     \u001b[38;5;66;03m# Get rotation from target_frame to j2000\u001b[39;00m\n\u001b[1;32m      8\u001b[0m     j2000 \u001b[38;5;241m=\u001b[39m driver\u001b[38;5;241m.\u001b[39mframe_chain\n\u001b[0;32m----> 9\u001b[0m     target_frame \u001b[38;5;241m=\u001b[39m \u001b[43mj2000\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfind_child_frame\u001b[49m(driver\u001b[38;5;241m.\u001b[39mtarget_frame_id)\n\u001b[1;32m     10\u001b[0m     rotation \u001b[38;5;241m=\u001b[39m target_frame\u001b[38;5;241m.\u001b[39mrotation_to(j2000)\n\u001b[1;32m     12\u001b[0m     \u001b[38;5;66;03m# Apply rotation to sensor position and velocity\u001b[39;00m\n",
+      "\u001b[0;31mAttributeError\u001b[0m: 'FrameChain' object has no attribute 'find_child_frame'"
+     ]
+    }
+   ],
    "source": [
     "# change to desired PDS3 image path \n",
-    "fileName = 'EN1072174528M.IMG'\n",
+    "fileName = EN1072174528M\n",
     "\n",
     "# metakernels are furnsh-ed when entering the context (with block) with a driver instance\n",
     "# most driver constructors simply accept an image path \n",
@@ -322,7 +342,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,