From f349ddeb1f13ae997a2b13fa95cff68271c7dbca Mon Sep 17 00:00:00 2001
From: Summer Stapleton <sgstapleton@usgs.gov>
Date: Wed, 28 Aug 2019 10:00:53 -0700
Subject: [PATCH] Functioning Kernel Split Notebook (#255)
* Notebook for CK/SPK Kernel Slicing
* Initial spkmerged configuration file output
* Functioning kernel split script
---
notebooks/KernelSlice.ipynb | 236 ++++++++++++++++++++++++++++++++++++
1 file changed, 236 insertions(+)
create mode 100644 notebooks/KernelSlice.ipynb
diff --git a/notebooks/KernelSlice.ipynb b/notebooks/KernelSlice.ipynb
new file mode 100644
index 0000000..ebb8963
--- /dev/null
+++ b/notebooks/KernelSlice.ipynb
@@ -0,0 +1,236 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import spiceypy as spice\n",
+ "import pvl\n",
+ "import os\n",
+ "import re\n",
+ "import subprocess\n",
+ "from ale import util\n",
+ "from itertools import chain\n",
+ "import io\n",
+ "import networkx as nx\n",
+ "\n",
+ "\n",
+ "# These should be provided when running this script. \n",
+ "cube = \"/work/users/sgstapleton/kernel_split/EN1072174528M.cub\"\n",
+ "output_dir = \"/work/users/sgstapleton/kernel_split/\" # Output dir for created kernel files\n",
+ "data_dir = \"/usgs/cpkgs/isis3/data/\" # Dir of where to pull original kernels from\n",
+ "\n",
+ " \n",
+ "def get_reference_id(bc_filename):\n",
+ " brief = subprocess.check_output([\"ckbrief\", bc_filename])\n",
+ " reference = None\n",
+ "\n",
+ " for line in brief.splitlines():\n",
+ " line = str(line)\n",
+ " if('Object:' in line):\n",
+ " reference = int(line.strip(\"''\").split()[1])\n",
+ " \n",
+ " return reference\n",
+ "\n",
+ "\n",
+ "def add_light_time_correction(cube_info, kernels):\n",
+ " \n",
+ " furnished_kerns = spice.furnsh(kernels)\n",
+ " \n",
+ " image_start_et = spice.scs2e(cube_info['SpacecraftID'], cube_info['SpacecraftClockCount'])\n",
+ " image_end_et = image_start_et + cube_info['ExposureDuration']\n",
+ " \n",
+ " inst_state, inst_lt = spice.spkez(cube_info['SpacecraftID'], (image_start_et + image_end_et)/2, 'J2000', 'LT+S', 0)\n",
+ " target_state, target_lt = spice.spkez(cube_info['TargetID'], (image_start_et + image_end_et)/2, 'J2000', 'LT+S', 0)\n",
+ " \n",
+ " lt_pad = max(abs(inst_lt), abs(target_lt)) + 15\n",
+ " \n",
+ " # Eph time\n",
+ " padded_start_et = image_start_et - lt_pad\n",
+ " padded_end_et = image_end_et + lt_pad\n",
+ " \n",
+ " # Padded times\n",
+ " padded_start_sclk = spice.sce2s(cube_info['SpacecraftID'], padded_start_et)\n",
+ " padded_end_sclk = spice.sce2s(cube_info['SpacecraftID'], padded_end_et)\n",
+ " padded_start_utc = spice.et2utc(padded_start_et, 'c', 3)\n",
+ " padded_end_utc = spice.et2utc(padded_end_et, 'c', 3)\n",
+ "\n",
+ " cube_info.update(PaddedStartTimeSCLK = padded_start_sclk)\n",
+ " cube_info.update(PaddedEndTimeSCLK = padded_end_sclk)\n",
+ " cube_info.update(PaddedStartTimeUTC = padded_start_utc)\n",
+ " cube_info.update(PaddedEndTimeUTC = padded_end_utc)\n",
+ " \n",
+ "\n",
+ "def get_body_ids(spk_file, body_id):\n",
+ " brief = subprocess.check_output([\"brief\", \"-c {}\".format(spk_file)])\n",
+ " \n",
+ " # Convert from bytes\n",
+ " brief = brief.decode(\"utf-8\")\n",
+ " brief_io = io.StringIO(brief)\n",
+ " line = brief_io.readline()\n",
+ " edge_list = []\n",
+ " \n",
+ " while(line):\n",
+ " \n",
+ " if(\"w.r.t\" in line):\n",
+ " bodies_results = re.findall('\\((.*?)\\)', line)\n",
+ " edge_list.append(bodies_results)\n",
+ " \n",
+ " line = brief_io.readline()\n",
+ " \n",
+ " G = nx.DiGraph()\n",
+ " G.add_edges_from(edge_list)\n",
+ " \n",
+ " body_ids = []\n",
+ " for path in nx.all_simple_paths(G, body_id, '0'):\n",
+ " body_ids = body_ids + path\n",
+ " \n",
+ " body_ids = set(body_ids)\n",
+ "\n",
+ " return body_ids\n",
+ "\n",
+ "\n",
+ "def output_spkmerge_config(config_file, cube_info, output_dir):\n",
+ " \n",
+ " with open(config_file, \"w+\") as config:\n",
+ " config.write('''LEAPSECONDS_KERNEL = {}\\n'''.format(cube_info['LeapSecond'][0]))\n",
+ " \n",
+ " for kern in cube_info['InstrumentPosition']:\n",
+ " \n",
+ " basename = os.path.basename(kern).split('.')[0]\n",
+ " filename, file_extension = os.path.splitext(kern)\n",
+ " new_kern = output_dir + basename + \"_merged\" + file_extension\n",
+ " \n",
+ " config.write(''' SPK_KERNEL = {}\\n'''.format(new_kern))\n",
+ "\n",
+ " body_ids = get_body_ids(kern, str(cube_info['SpacecraftID']))\n",
+ "\n",
+ " for body in body_ids:\n",
+ "\n",
+ " if body != '0':\n",
+ "\n",
+ " config.write(''' SOURCE_SPK_KERNEL = {}\\n'''.format(kern))\n",
+ " config.write(''' INCLUDE_COMMENTS = no\\n''')\n",
+ " config.write(''' BODIES = {}\\n'''.format(body))\n",
+ " config.write(''' BEGIN_TIME = {}\\n'''.format(cube_info['PaddedStartTimeUTC']))\n",
+ " config.write(''' END_TIME = {}\\n'''.format(cube_info['PaddedEndTimeUTC']))\n",
+ " \n",
+ " config.close()\n",
+ " "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# These are the processing steps. This will make use of the cube provided further up to create smaller, \n",
+ "# more manageable kernel files for ale testing purposes. This currently only handles ck and spk files.\n",
+ "\n",
+ "# Get dictionary of kernel lists from cube\n",
+ "cube_info = util.generate_kernels_from_cube(cube, 'dict')\n",
+ "\n",
+ "# Replace path variables with absolute paths for kernels\n",
+ "for kernel_list in cube_info:\n",
+ " for index, kern in enumerate(cube_info[kernel_list]):\n",
+ " if kern is not None:\n",
+ " cube_info[kernel_list][index] = data_dir + kern.strip('$')\n",
+ " \n",
+ "# Create ordered list of kernels for furnishing\n",
+ "kernels = [kernel for kernel in chain.from_iterable(cube_info.values()) if isinstance(kernel, str)]\n",
+ " \n",
+ "# Loads cube as pvl to extract rest of data\n",
+ "cube_pvl = pvl.load(cube)\n",
+ " \n",
+ "# Save other necesary info in cube_info dict\n",
+ "cube_info.update(SpacecraftClockCount = cube_pvl['IsisCube']['Instrument']['SpacecraftClockCount'])\n",
+ "cube_info.update(ExposureDuration = cube_pvl['IsisCube']['Instrument']['ExposureDuration'].value * 0.001)\n",
+ "cube_info.update(TargetID = spice.bods2c(cube_pvl['IsisCube']['Instrument']['TargetName']))\n",
+ "cube_info.update(SpacecraftID = spice.bods2c(cube_pvl['IsisCube']['Instrument']['SpacecraftName']))\n",
+ "\n",
+ "# Add lighttime-corrected SCLK values to cube_info\n",
+ "add_light_time_correction(cube_info, kernels)\n",
+ "\n",
+ "# For each binary ck kernel specified in cube, run the ckslicer, comment and to-transfer commands\n",
+ "for ck in cube_info['InstrumentPointing']:\n",
+ " if ck.endswith('.bc'):\n",
+ " \n",
+ " # Get reference id associated with ck\n",
+ " reference_id = get_reference_id(ck)\n",
+ " \n",
+ " ck_filename = os.path.basename(ck).split('.')[0]\n",
+ " ck_path, ck_file_extension = os.path.splitext(ck)\n",
+ " output_kern = output_dir + ck_filename + '_sliced' + ck_file_extension\n",
+ " \n",
+ " # Create new sliced ck kernel\n",
+ " ckslicer_command = [\"./ckslicer\", \n",
+ " '-LSK {}'.format(cube_info['LeapSecond'][0]), \n",
+ " '-SCLK {}'.format(cube_info['SpacecraftClock'][0]), \n",
+ " '-INPUTCK {}'.format(ck), \n",
+ " '-OUTPUTCK {}'.format(output_kern),\n",
+ " '-ID {}'.format(reference_id),\n",
+ " '-TIMETYPE {}'.format('SCLK'),\n",
+ " '-START {}'.format(cube_info['PaddedStartTimeSCLK']),\n",
+ " '-STOP {}'.format(cube_info['PaddedEndTimeSCLK'])]\n",
+ " subprocess.call(ckslicer_command)\n",
+ " \n",
+ " # Remove old comments from new ck kernel\n",
+ " commnt_command = ['commnt', '-d {}'.format(output_kern)]\n",
+ " subprocess.call(commnt_command)\n",
+ " \n",
+ " # Makes a new txt file for the only comments that should be stored in the new ck file\n",
+ " with open(\"temp_commnts.txt\",\"w+\") as f:\n",
+ " f.write(\"This CK is for testing with the image: {}\\n\".format(cube))\n",
+ " f.write(\"\\nThis CK was generated using the following command: {}\\n\".format(\" \".join(ckslicer_command)))\n",
+ " \n",
+ " # Add new comments to new ck kernel\n",
+ " new_commnts_command = [\"commnt\", \"-a {}\".format(output_kern), \"temp_commnts.txt\"]\n",
+ " subprocess.call(new_commnts_command)\n",
+ " \n",
+ " # Create the transfer file of the new ck kernel\n",
+ " subprocess.call([\"toxfr\", output_kern])\n",
+ "\n",
+ "# Create the config file for the spkmerge command\n",
+ "output_spkmerge_config(output_dir + \"spk.config\", cube_info, output_dir)\n",
+ "\n",
+ "# Run the spkmerge command\n",
+ "spkmerge_command = [\"spkmerge\", output_dir + \"spk.config\"]\n",
+ "subprocess.call(spkmerge_command)\n",
+ "\n",
+ "# Clean up temp config file\n",
+ "os.remove(output_dir + \"spk.config\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
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+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
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+ "nbformat": 4,
+ "nbformat_minor": 2
+}
--
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