Updated LRO test (#262)

# Binary Kernels

*.bsp

*.BSP

*.bc

*.BC

*.bpc

*.BPC

# Binary Images

*.cub

*.CUB

*.img

*.IMG

        sun_state, _ = spice.spkezr("SUN",

                                     self.center_ephemeris_time,

                                     self.reference_frame,

                                     'NONE',

                                     'LT+S',

                                     self.target_name)

        positions = 1000 * np.asarray([sun_state[:3]])

        velocities = 1000 * np.asarray([sun_state[3:6]])

%% Cell type:code id: tags:

``` python

import spiceypy as spice

import pvl

import os

import re

import subprocess

from ale import util

from itertools import chain

import io

import networkx as nx

# These should be provided when running this script.

cube = "/work/users/sgstapleton/kernel_split/EN1072174528M.cub"

cube = "/home/acpaquette/B10_013341_1010_XN_79S172W.cub"

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

ckslicer_loc = "/Users/jmapel/ale/ckslicer"

def add_light_time_correction(cube_info):

def merge_intervals(intervals):

    """

    Merge a set of intervals. The intervals are assumed to be closed, that is they include the end-points.

    Parameters

    ----------

    intervals : list

                The input list of intrvals where each interval is a tuple of (start, end)

    Returns

    -------

    : list

      A sorted list of the merged intervals

    """

    sorted_intervals = sorted(intervals, key=lambda tup: tup[0])

    merged = [sorted_intervals[0]]

    for interval in sorted_intervals[1:]:

        # No intersection

        if interval[0] > merged[-1][1]:

            merged.append(interval)

        # Intersection, but new interval isn't wholey contained

        elif interval[1] > merged[-1][1]:

            merged[-1] = (merged[-1][0], interval[1])

    return merged

def add_light_time_correction(cube_info, padding=5):

    """

    Compute the time intervals for the image and any light time correction

    Parameters

    ----------

    cube_info : ordered dict

                The cube info from ale.util.generate_kernels_from_cube

    padding : float

              Time padding in seconds to add to each interval

    Returns

    -------

    : list

      A sorted list of the intervals as (start_et, stop_et)

    """

    image_start_et = spice.scs2e(cube_info['SpacecraftID'], cube_info['SpacecraftClockCount'])

    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)

    target_state, target_lt = spice.spkez(cube_info['TargetID'], (image_start_et + image_end_et)/2, 'J2000', 'LT+S', 0)

    image_end_et = image_start_et + cube_info['ExposureDuration'] * cube_info['Lines']

    lt_pad = max(abs(inst_lt), abs(target_lt)) + 15

    inst_state, inst_lt = spice.spkez(cube_info['SpacecraftID'], image_start_et, 'J2000', 'LT+S', 0)

    target_state, target_lt = spice.spkez(cube_info['TargetID'], image_start_et, 'J2000', 'LT+S', 0)

    sun_state, sun_lt = spice.spkez(10, image_start_et, 'J2000', 'LT+S', cube_info['TargetID'])

    intervals = [

        (image_start_et - padding, image_end_et + padding),

        (image_start_et - padding - inst_lt, image_end_et + padding - inst_lt),

        (image_start_et - padding - target_lt, image_end_et + padding - target_lt),

        (image_start_et - padding - sun_lt, image_end_et + padding - sun_lt)]

    # Eph time

    padded_start_et = image_start_et - lt_pad

    padded_end_et = image_end_et + lt_pad

    # Padded times

    padded_start_sclk = spice.sce2s(cube_info['SpacecraftID'], padded_start_et)

    padded_end_sclk = spice.sce2s(cube_info['SpacecraftID'], padded_end_et)

    padded_start_utc = spice.et2utc(padded_start_et, 'c', 3)

    padded_end_utc = spice.et2utc(padded_end_et, 'c', 3)

    cube_info.update(PaddedStartTimeSCLK = padded_start_sclk)

    cube_info.update(PaddedEndTimeSCLK = padded_end_sclk)

    cube_info.update(PaddedStartTimeUTC = padded_start_utc)

    cube_info.update(PaddedEndTimeUTC = padded_end_utc)

    return merge_intervals(intervals)

```

%% Cell type:code id: tags:

``` python

# 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.

# Get dictionary of kernel lists from cube

cube_info = util.generate_kernels_from_cube(cube, format_as = 'dict')

# Replace path variables with absolute paths for kernels

for kernel_list in cube_info:

    for index, kern in enumerate(cube_info[kernel_list]):

        if kern is not None:

            cube_info[kernel_list][index] = data_dir + kern.strip('$')

# Create ordered list of kernels for furnishing

kernels = [kernel for kernel in chain.from_iterable(cube_info.values()) if isinstance(kernel, str)]

spice.furnsh(kernels)

# Loads cube as pvl to extract rest of data

cube_pvl = pvl.load(cube)

# Save other necesary info in cube_info dict

cube_info.update(Lines = cube_pvl['IsisCube']['Core']['Dimensions']['Lines'])

cube_info.update(Lines = 400)

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']['LineExposureDuration'].value * 0.001)

cube_info.update(TargetID = spice.bods2c(cube_pvl['IsisCube']['Instrument']['TargetName']))

cube_info.update(SpacecraftID = spice.bods2c(cube_pvl['IsisCube']['Instrument']['SpacecraftName']))

# Add lighttime-corrected SCLK values to cube_info

add_light_time_correction(cube_info)

# Account for light time correction

intervals = add_light_time_correction(cube_info)

# For each binary ck kernel specified in cube, run the ckslicer, comment and to-transfer commands

for ck in [k for k in kernels if k.lower().endswith('.bc')]:

    ck_path, ck_file_extension = os.path.splitext(ck)

    ck_basename = os.path.basename(ck_path)

    for frame in util.get_ck_frames(ck):

        output_basename = os.path.join(output_dir, ck_basename + '_sliced' + str(frame))

        output_kern = output_basename + ck_file_extension

        output_comments = output_basename + '.cmt'

        # Create new sliced ck kernel

        ckslicer_command = [ckslicer_loc,

                                '-LSK {}'.format(cube_info['LeapSecond'][0]),

                                '-SCLK {}'.format(cube_info['SpacecraftClock'][0]),

                                '-INPUTCK {}'.format(ck),

                                '-OUTPUTCK {}'.format(output_kern),

                                '-ID {}'.format(frame),

                                '-TIMETYPE {}'.format('SCLK'),

                                '-START {}'.format(cube_info['PaddedStartTimeSCLK']),

                                '-STOP {}'.format(cube_info['PaddedEndTimeSCLK'])]

        subprocess.run(ckslicer_command, check=True)

        # Remove old comments from new ck kernel

        commnt_command = ['commnt', '-d {}'.format(output_kern)]

        subprocess.run(commnt_command, check=True)

        with open(output_comments, 'w+') as comment_file:

            comment_file.write("This CK is for testing with the image: {}\n".format(cube))

            comment_file.write("\nThis CK was generated using the following command: {}\n")

            comment_file.write(" ".join(ckslicer_command))

        # Add new comments to new ck kernel

        new_commnts_command = ["commnt", "-a {}".format(output_kern), output_comments]

        subprocess.run(new_commnts_command, check=True)

    for index, interval in enumerate(intervals):

        for frame in util.get_ck_frames(ck):

            output_basename = os.path.join(output_dir, ck_basename + '_' + str(index) + '_sliced_' + str(frame))

            output_kern = output_basename + ck_file_extension

            output_comments = output_basename + '.cmt'

            start_sclk = spice.sce2s(cube_info['SpacecraftID'], interval[0])

            end_sclk = spice.sce2s(cube_info['SpacecraftID'], interval[1])

            # Create new sliced ck kernel

            ckslicer_command = [ckslicer_loc,

                                    '-LSK {}'.format(cube_info['LeapSecond'][0]),

                                    '-SCLK {}'.format(cube_info['SpacecraftClock'][0]),

                                    '-INPUTCK {}'.format(ck),

                                    '-OUTPUTCK {}'.format(output_kern),

                                    '-ID {}'.format(frame),

                                    '-TIMETYPE {}'.format('SCLK'),

                                    '-START {}'.format(start_sclk),

                                    '-STOP {}'.format(end_sclk)]

            subprocess.run(ckslicer_command, check=True)

            # Remove old comments from new ck kernel

            commnt_command = ['commnt', '-d {}'.format(output_kern)]

            subprocess.run(commnt_command, check=True)

            with open(output_comments, 'w+') as comment_file:

                comment_file.write("This CK is for testing with the image: {}\n".format(cube))

                comment_file.write("\nThis CK was generated using the following command: {}\n")

                comment_file.write(" ".join(ckslicer_command))

            # Add new comments to new ck kernel

            new_commnts_command = ["commnt", "-a {}".format(output_kern), output_comments]

            subprocess.run(new_commnts_command, check=True)

        # Create the transfer file of the new ck kernel

        subprocess.run(["toxfr", output_kern], check=True)

            # Create the transfer file of the new ck kernel

            subprocess.run(["toxfr", output_kern], check=True)

# Create the config file for the spkmerge command

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)

for index, interval in enumerate(intervals):

    output_spk_basename = os.path.join(output_dir, os.path.basename(os.path.splitext(cube)[0]) + '_' + str(index))

    output_spk = output_spk_basename + '.bsp'

    start_utc = spice.et2utc(interval[0], 'c', 3)

    end_utc = spice.et2utc(interval[1], 'c', 3)

    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],

                                                start_utc,

                                                end_utc)

    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)

# Create the transfer file of the new SPK kernel

subprocess.run(["toxfr", output_spk], check=True)

    # Create the transfer file of the new SPK kernel

    subprocess.run(["toxfr", output_spk], check=True)

```

%% Cell type:code id: tags:

``` python

```

DAFETF NAIF DAF ENCODED TRANSFER FILE

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'2'

'6'

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 ~NAIF/SPC BEGIN COMMENTS~

; /Users/jmapel/ale/nb_test/B10_013341_1010_XN_79S172W_0.bsp LOG FILE

; Created 2019-09-04/13:08:37.00.

;

; BEGIN SPKMERGE COMMANDS

LEAPSECONDS_KERNEL   = /usgs/cpkgs/isis3/data/base/kernels/lsk/naif0012.tls

SPK_KERNEL         = /Users/jmapel/ale/nb_test/B10_013341_1010_XN_79S172W_0.bsp

  SOURCE_SPK_KERNEL  = /usgs/cpkgs/isis3/data/base/kernels/spk/mar097.bsp

    INCLUDE_COMMENTS = NO

    BODIES           = 4, 10, 499

    BEGIN_TIME       = 2009 JUN 01 00:26:35.913

    END_TIME         = 2009 JUN 01 00:26:48.055

SOURCE_SPK_KERNEL = /usgs/cpkgs/isis3/data/mro/kernels/spk/mro_psp11_ssd_mro110c.bsp

    INCLUDE_COMMENTS = NO

    BODIES           = -74

    BEGIN_TIME       = 2009 JUN 01 00:26:35.913

    END_TIME         = 2009 JUN 01 00:26:48.055

; END SPKMERGE COMMANDS

 ~NAIF/SPC END COMMENTS~