Skip to content
Snippets Groups Projects
Commit a9a55c01 authored by Jesse Mapel's avatar Jesse Mapel Committed by GitHub
Browse files

Moved kernel parsing logic from slicing notebook into ale utils. (#259) 

* Moved SPK dependency tree logic to utils

* More tests

* Added ck frame function

* updated notebook

* Updated notebook
parent 9ea482aa
Branches
Tags
No related merge requests found
Show whitespace changes
Inline Side-by-side
notebooks/KernelSlice.ipynb
+ 43
− 107
View file @ a9a55c01
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
import spiceypy as spice import spiceypy as spice
import pvl import pvl
import os import os
import re import re
import subprocess import subprocess
from ale import util from ale import util
from itertools import chain from itertools import chain
import io import io
import networkx as nx import networkx as nx
import tempfile
# These should be provided when running this script. # These should be provided when running this script.
cube = "/work/users/sgstapleton/kernel_split/EN1072174528M.cub" cube = "/work/users/sgstapleton/kernel_split/EN1072174528M.cub"
output_dir = "/work/users/sgstapleton/kernel_split/" # Output dir for created kernel files output_dir = "/Users/jmapel/ale/nb_test" # Output dir for created kernel files
data_dir = "/usgs/cpkgs/isis3/data/" # Dir of where to pull original kernels from data_dir = "/usgs/cpkgs/isis3/data/" # Dir of where to pull original kernels from
ckslicer_loc = "/work/users/sgstapleton/kernel_split/ckslicer" ckslicer_loc = "/Users/jmapel/ale/ckslicer"
def get_reference_id(bc_filename):
brief = subprocess.check_output(["ckbrief", bc_filename])
reference = None
for line in brief.splitlines():
line = str(line)
if('Object:' in line):
reference = int(line.strip("''").split()[1])
return reference
def add_light_time_correction(cube_info): def add_light_time_correction(cube_info):
image_start_et = spice.scs2e(cube_info['SpacecraftID'], cube_info['SpacecraftClockCount']) image_start_et = spice.scs2e(cube_info['SpacecraftID'], cube_info['SpacecraftClockCount'])
image_end_et = image_start_et + cube_info['ExposureDuration'] image_end_et = image_start_et + cube_info['ExposureDuration']
inst_state, inst_lt = spice.spkez(cube_info['SpacecraftID'], (image_start_et + image_end_et)/2, 'J2000', 'LT+S', 0) inst_state, inst_lt = spice.spkez(cube_info['SpacecraftID'], (image_start_et + image_end_et)/2, 'J2000', 'LT+S', 0)
target_state, target_lt = spice.spkez(cube_info['TargetID'], (image_start_et + image_end_et)/2, 'J2000', 'LT+S', 0) target_state, target_lt = spice.spkez(cube_info['TargetID'], (image_start_et + image_end_et)/2, 'J2000', 'LT+S', 0)
lt_pad = max(abs(inst_lt), abs(target_lt)) + 15 lt_pad = max(abs(inst_lt), abs(target_lt)) + 15
# Eph time # Eph time
padded_start_et = image_start_et - lt_pad padded_start_et = image_start_et - lt_pad
padded_end_et = image_end_et + lt_pad padded_end_et = image_end_et + lt_pad
# Padded times # Padded times
padded_start_sclk = spice.sce2s(cube_info['SpacecraftID'], padded_start_et) padded_start_sclk = spice.sce2s(cube_info['SpacecraftID'], padded_start_et)
padded_end_sclk = spice.sce2s(cube_info['SpacecraftID'], padded_end_et) padded_end_sclk = spice.sce2s(cube_info['SpacecraftID'], padded_end_et)
padded_start_utc = spice.et2utc(padded_start_et, 'c', 3) padded_start_utc = spice.et2utc(padded_start_et, 'c', 3)
padded_end_utc = spice.et2utc(padded_end_et, 'c', 3) padded_end_utc = spice.et2utc(padded_end_et, 'c', 3)
cube_info.update(PaddedStartTimeSCLK = padded_start_sclk) cube_info.update(PaddedStartTimeSCLK = padded_start_sclk)
cube_info.update(PaddedEndTimeSCLK = padded_end_sclk) cube_info.update(PaddedEndTimeSCLK = padded_end_sclk)
cube_info.update(PaddedStartTimeUTC = padded_start_utc) cube_info.update(PaddedStartTimeUTC = padded_start_utc)
cube_info.update(PaddedEndTimeUTC = padded_end_utc) cube_info.update(PaddedEndTimeUTC = padded_end_utc)
def get_body_ids(spk_file, body_id):
brief = subprocess.check_output(["brief", "-c {}".format(spk_file)])
# Convert from bytes
brief = brief.decode("utf-8")
brief_io = io.StringIO(brief)
line = brief_io.readline()
edge_list = []
while(line):
if("w.r.t" in line):
bodies_results = re.findall('\((.*?)\)', line)
edge_list.append(bodies_results)
line = brief_io.readline()
G = nx.DiGraph()
G.add_edges_from(edge_list)
body_ids = []
for path in nx.all_simple_paths(G, body_id, '0'):
body_ids = body_ids + path
body_ids = set(body_ids)
return body_ids
def output_spkmerge_config(config_file, cube_info, output_dir):
with open(config_file, "w+") as config:
config.write('''LEAPSECONDS_KERNEL = {}\n'''.format(cube_info['LeapSecond'][0]))
for kern in cube_info['InstrumentPosition']:
basename = os.path.basename(kern).split('.')[0]
filename, file_extension = os.path.splitext(kern)
new_kern = output_dir + basename + "_merged" + file_extension
config.write(''' SPK_KERNEL = {}\n'''.format(new_kern))
body_ids = get_body_ids(kern, str(cube_info['SpacecraftID']))
for body in body_ids:
if body != '0':
config.write(''' SOURCE_SPK_KERNEL = {}\n'''.format(kern))
config.write(''' INCLUDE_COMMENTS = no\n''')
config.write(''' BODIES = {}\n'''.format(body))
config.write(''' BEGIN_TIME = {}\n'''.format(cube_info['PaddedStartTimeUTC']))
config.write(''' END_TIME = {}\n'''.format(cube_info['PaddedEndTimeUTC']))
config.close()
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
# These are the processing steps. This will make use of the cube provided further up to create smaller, # These are the processing steps. This will make use of the cube provided further up to create smaller,
# more manageable kernel files for ale testing purposes. This currently only handles ck and spk files. # more manageable kernel files for ale testing purposes. This currently only handles ck and spk files.
# Get dictionary of kernel lists from cube # Get dictionary of kernel lists from cube
cube_info = util.generate_kernels_from_cube(cube, format_as = 'dict') cube_info = util.generate_kernels_from_cube(cube, format_as = 'dict')
# Replace path variables with absolute paths for kernels # Replace path variables with absolute paths for kernels
for kernel_list in cube_info: for kernel_list in cube_info:
for index, kern in enumerate(cube_info[kernel_list]): for index, kern in enumerate(cube_info[kernel_list]):
if kern is not None: if kern is not None:
cube_info[kernel_list][index] = data_dir + kern.strip('$') cube_info[kernel_list][index] = data_dir + kern.strip('$')
# Create ordered list of kernels for furnishing # Create ordered list of kernels for furnishing
kernels = [kernel for kernel in chain.from_iterable(cube_info.values()) if isinstance(kernel, str)] kernels = [kernel for kernel in chain.from_iterable(cube_info.values()) if isinstance(kernel, str)]
spice.furnsh(kernels) spice.furnsh(kernels)
# Loads cube as pvl to extract rest of data # Loads cube as pvl to extract rest of data
cube_pvl = pvl.load(cube) cube_pvl = pvl.load(cube)
# Save other necesary info in cube_info dict # Save other necesary info in cube_info dict
cube_info.update(SpacecraftClockCount = cube_pvl['IsisCube']['Instrument']['SpacecraftClockCount']) cube_info.update(SpacecraftClockCount = cube_pvl['IsisCube']['Instrument']['SpacecraftClockCount'])
cube_info.update(ExposureDuration = cube_pvl['IsisCube']['Instrument']['ExposureDuration'].value * 0.001) cube_info.update(ExposureDuration = cube_pvl['IsisCube']['Instrument']['ExposureDuration'].value * 0.001)
cube_info.update(TargetID = spice.bods2c(cube_pvl['IsisCube']['Instrument']['TargetName'])) cube_info.update(TargetID = spice.bods2c(cube_pvl['IsisCube']['Instrument']['TargetName']))
cube_info.update(SpacecraftID = spice.bods2c(cube_pvl['IsisCube']['Instrument']['SpacecraftName'])) cube_info.update(SpacecraftID = spice.bods2c(cube_pvl['IsisCube']['Instrument']['SpacecraftName']))
# Add lighttime-corrected SCLK values to cube_info # Add lighttime-corrected SCLK values to cube_info
add_light_time_correction(cube_info) add_light_time_correction(cube_info)
# For each binary ck kernel specified in cube, run the ckslicer, comment and to-transfer commands # For each binary ck kernel specified in cube, run the ckslicer, comment and to-transfer commands
for ck in cube_info['InstrumentPointing']: for ck in [k for k in kernels if k.lower().endswith('.bc')]:
if ck.endswith('.bc'): ck_path, ck_file_extension = os.path.splitext(ck)
ck_basename = os.path.basename(ck_path)
# Get reference id associated with ck for frame in util.get_ck_frames(ck):
reference_id = get_reference_id(ck) output_basename = os.path.join(output_dir, ck_basename + '_sliced' + str(frame))
output_kern = output_basename + ck_file_extension
ck_filename = os.path.basename(ck).split('.')[0] output_comments = output_basename + '.cmt'
ck_path, ck_file_extension = os.path.splitext(ck)
output_kern = output_dir + ck_filename + '_sliced' + ck_file_extension
# Create new sliced ck kernel # Create new sliced ck kernel
ckslicer_command = [ckslicer_loc, ckslicer_command = [ckslicer_loc,
'-LSK {}'.format(cube_info['LeapSecond'][0]), '-LSK {}'.format(cube_info['LeapSecond'][0]),
'-SCLK {}'.format(cube_info['SpacecraftClock'][0]), '-SCLK {}'.format(cube_info['SpacecraftClock'][0]),
'-INPUTCK {}'.format(ck), '-INPUTCK {}'.format(ck),
'-OUTPUTCK {}'.format(output_kern), '-OUTPUTCK {}'.format(output_kern),
'-ID {}'.format(reference_id), '-ID {}'.format(frame),
'-TIMETYPE {}'.format('SCLK'), '-TIMETYPE {}'.format('SCLK'),
'-START {}'.format(cube_info['PaddedStartTimeSCLK']), '-START {}'.format(cube_info['PaddedStartTimeSCLK']),
'-STOP {}'.format(cube_info['PaddedEndTimeSCLK'])] '-STOP {}'.format(cube_info['PaddedEndTimeSCLK'])]
subprocess.call(ckslicer_command) subprocess.run(ckslicer_command, check=True)
# Remove old comments from new ck kernel # Remove old comments from new ck kernel
commnt_command = ['commnt', '-d {}'.format(output_kern)] commnt_command = ['commnt', '-d {}'.format(output_kern)]
subprocess.call(commnt_command) subprocess.run(commnt_command, check=True)
# Makes a new txt file for the only comments that should be stored in the new ck file with open(output_comments, 'w+') as comment_file:
with open(output_dir + "temp_commnts.txt","w+") as f: comment_file.write("This CK is for testing with the image: {}\n".format(cube))
f.write("This CK is for testing with the image: {}\n".format(cube)) comment_file.write("\nThis CK was generated using the following command: {}\n")
f.write("\nThis CK was generated using the following command: {}\n".format(" ".join(ckslicer_command))) comment_file.write(" ".join(ckslicer_command))
# Add new comments to new ck kernel # Add new comments to new ck kernel
new_commnts_command = ["commnt", "-a {}".format(output_kern), "temp_commnts.txt"] new_commnts_command = ["commnt", "-a {}".format(output_kern), output_comments]
subprocess.call(new_commnts_command) subprocess.run(new_commnts_command, check=True)
# Clean up temp comment file
os.remove(output_dir + "temp_commnts.txt")
# Create the transfer file of the new ck kernel # Create the transfer file of the new ck kernel
subprocess.call(["toxfr", output_kern]) subprocess.run(["toxfr", output_kern], check=True)
# Create the config file for the spkmerge command # Create the config file for the spkmerge command
output_spkmerge_config(output_dir + "spk.config", cube_info, output_dir) output_spk_basename = os.path.join(output_dir, os.path.basename(os.path.splitext(cube)[0]))
output_spk = output_spk_basename + '.bsp'
spk_dep_tree = util.create_spk_dependency_tree([k for k in kernels if k.lower().endswith('.bsp')])
config_string = util.spkmerge_config_string(spk_dep_tree,
output_spk,
[cube_info['TargetID'], cube_info['SpacecraftID'], 10],
cube_info['LeapSecond'][0],
cube_info['PaddedStartTimeUTC'],
cube_info['PaddedEndTimeUTC'])
with open(output_spk_basename + '.conf', 'w+') as spk_config:
spk_config.write(config_string)
# Create the new SPK
spkmerge_command = ["spkmerge", spk_config.name]
subprocess.run(spkmerge_command, check=True)
# Run the spkmerge command # Create the transfer file of the new SPK kernel
spkmerge_command = ["spkmerge", output_dir + "spk.config"] subprocess.run(["toxfr", output_spk], check=True)
subprocess.call(spkmerge_command)
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
``` ```
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment