Unverified Commit 650d42ee authored by Amy Stamile's avatar Amy Stamile Committed by GitHub
Browse files

Leisa driver (#474) 

* Initial Leisa Driver

* Updated nh tests

* Added sensor_name

* Removed Jupiter test data and added Pluto test data.

* Removed light time correction and increased padding in KernelSlice

* Fixed exposure and increased padding in KernelSlice

* fixed exposure duration int error

* Fixes CI failures. Updated isd.

* separated load tests for lorri and leisa.

* Added Leisa unit tests
parent 88c48c01

ale/drivers/nh_drivers.py

+123 −0
Original line number Diff line number Diff line
@@ -11,6 +11,7 @@ from ale.base.type_distortion import NoDistortion 
from ale.base.data_naif import NaifSpice

from ale.base.label_isis import IsisLabel

from ale.base.type_sensor import Framer

from ale.base.type_sensor import LineScanner



class NewHorizonsLorriIsisLabelNaifSpiceDriver(Framer, IsisLabel, NaifSpice, NoDistortion, Driver):

    """
@@ -65,3 +66,125 @@ class NewHorizonsLorriIsisLabelNaifSpiceDriver(Framer, IsisLabel, NaifSpice, NoD 
    @property

    def sensor_name(self):

        return self.label['IsisCube']['Instrument']['SpacecraftName']





class NewHorizonsLeisaIsisLabelNaifSpiceDriver(LineScanner, IsisLabel, NaifSpice, NoDistortion, Driver):

    """

    Driver for reading New Horizons LEISA ISIS3 Labels.

    """



    @property

    def instrument_id(self):

        """

        Returns an instrument id for uniquely identifying the instrument, but often

        also used to be piped into Spice Kernels to acquire IKIDs. Therefore they

        the same ID the Spice expects in bods2c calls.



        Returns

        -------

        : str

          instrument id

        """

        id_lookup = {

            "LEISA" : "NH_RALPH_LEISA"

        }

        return id_lookup[super().instrument_id]



    @property

    def ikid(self):

        """

        Overridden to grab the ikid from the Isis Cube since there is no way to

        obtain this value with a spice bods2c call. Isis sets this value during

        ingestion, based on the original fits file.



        Returns

        -------

        : int

          Naif ID used to for identifying the instrument in Spice kernels

        """

        return self.label['IsisCube']['Kernels']['NaifFrameCode'][0]





    @property

    def ephemeris_start_time(self):

        """

        Returns the ephemeris start time of the image.

        Expects spacecraft_id to be defined. This should be the integer

        Naif ID code for the spacecraft.



        Returns

        -------

        : float

          ephemeris start time of the image

        """

        return spice.scs2e(self.spacecraft_id, self.spacecraft_clock_start_count)



    @property

    def ephemeris_stop_time(self):

        """

        ISIS doesn't preserve the spacecraft stop count that we can use to get

        the ephemeris stop time of the image, so compute the ephemeris stop time

        from the start time and the exposure duration.

        """

        return self.ephemeris_start_time + self.exposure_duration * self.image_lines



    @property

    def detector_center_line(self):

        """

        Returns the center detector line. Expects ikid to be defined. This should

        be an integer containing the Naif Id code of the instrument.



        Returns

        -------

        : float

          Detector line of the principal point

        """

        return 0



    @property

    def detector_center_sample(self):

        """

        Returns the center detector sample. Expects ikid to be defined. This should

        be an integer containing the Naif Id code of the instrument.



        Returns

        -------

        : float

          Detector sample of the principal point

        """

        return 0



    @property

    def sensor_name(self):

        """

        Returns the name of the instrument. Need to over-ride isis_label because

        InstrumentName is not defined in the ISIS label for NH Leisa cubes.



        Returns

        -------

        : str

        Name of the sensor

        """

        return self.instrument_id



    @property

    def sensor_model_version(self):

        """

        Returns

        -------

        : int

          ISIS sensor model version

        """

        return 1



    @property

    def exposure_duration(self):

        """

        The exposure duration of the image, in seconds



        Returns

        -------

        : float

          Exposure duration in seconds

        """

        return self.label['IsisCube']['Instrument']['ExposureDuration']

notebooks/KernelSlice.ipynb

+11 −14
Original line number Diff line number Diff line 
%% 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 = "/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"

cube = "leisa/lsb_0296962438_0x53c_eng/lsb_0296962438_0x53c_eng-spiced.cub"

output_dir = "leisa/lsb_0296962438_0x53c_eng/" # Output dir for created kernel files

data_dir = "isis3/isis_data/" # Dir of where to pull original kernels from



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):

def add_light_time_correction(cube_info, padding=120):

    """

    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'] * cube_info['Lines']



    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'])

    inst_state, inst_lt = spice.spkez(cube_info['SpacecraftID'], image_start_et, 'J2000', 'NONE', 0)

    target_state, target_lt = spice.spkez(cube_info['TargetID'], image_start_et, 'J2000', 'NONE', 0)

    sun_state, sun_lt = spice.spkez(10, image_start_et, 'J2000', 'NONE', 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)]



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

cube_info.update(SpacecraftClockCount = cube_pvl['IsisCube']['Instrument']['SpacecraftClockStartCount'])

cube_info.update(ExposureDuration = cube_pvl['IsisCube']['Instrument']['ExposureDuration'])

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

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



# 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 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,

            ckslicer_command = ["ckslicer",

                                    '-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 config file for the spkmerge command

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)

```



%% Cell type:code id: tags:



``` python

```

notebooks/write_NHLeisaIsisLabelNaifSpiceDriver.ipynb

0 → 100644
+54 −0
Original line number Diff line number Diff line 
%% Cell type:code id: tags:



``` python

fileName = 'ale/leisa/lsb_0296962438_0x53c_eng/lsb_0296962438_0x53c_eng-spiced.cub'



import os

os.environ["ISISDATA"] = "isis3/isis_data"

os.environ["ISISTESTDATA"] = "isis_testData"

os.environ["ISISROOT"] = "isis/ISIS3/build"



import ale

from ale.drivers.nh_drivers import NewHorizonsLeisaIsisLabelNaifSpiceDriver

from ale.formatters.formatter import to_isd

import spiceypy as spice

from ale.drivers import AleJsonEncoder

```



%% Cell type:code id: tags:



``` python

from ale.util import generate_kernels_from_cube

kernels = generate_kernels_from_cube(fileName, expand=True, format_as='list')

```



%% Cell type:code id: tags:



``` python

with NewHorizonsLeisaIsisLabelNaifSpiceDriver(fileName, props = {"kernels": kernels}) as driver:

    isisString = to_isd(driver)

```



%% Cell type:code id: tags:



``` python

isisString

```



%% Cell type:code id: tags:



``` python

import json



isis_dict = isisString



json_file = os.path.splitext(fileName)[0] + '.json'



with open(json_file, 'w') as fp:

    json.dump(isis_dict, fp, cls = AleJsonEncoder)



with open(json_file, 'r') as fp:

    isis_dict = json.load(fp)



isis_dict.keys()

```

tests/pytests/data/isds/nhleisa_isd.json

0 → 100644
+1 −0
Original line number Diff line number Diff line 
{"isis_camera_version": 1, "image_lines": 368, "image_samples": 256, "name_platform": "NEW HORIZONS", "name_sensor": "NH_RALPH_LEISA", "reference_height": {"maxheight": 1000, "minheight": -1000, "unit": "m"}, "name_model": "USGS_ASTRO_LINE_SCANNER_SENSOR_MODEL", "interpolation_method": "lagrange", "line_scan_rate": [[0.5, -157.50400000810623, 0.856]], "starting_ephemeris_time": 487928588.0336103, "center_ephemeris_time": 487928745.5376103, "radii": {"semimajor": 1188.3, "semiminor": 1188.3, "unit": "km"}, "body_rotation": {"time_dependent_frames": [10019, 1], "ck_table_start_time": 487928588.0336103, "ck_table_end_time": 487928903.0416103, "ck_table_original_size": 5, "ephemeris_times": [487928588.0336103, 487928666.7856103, 487928745.5376103, 487928824.28961027, 487928903.0416103], "quaternions": [[-0.2447405651322848, 0.2727488147412229, -0.6923053902236965, -0.6216296216423436], [-0.24501922793442102, 0.27243841475512237, -0.6924275986998515, -0.6215198377098623], [-0.2452978414907075, 0.27212796001179584, -0.6925496680060897, -0.6214099288589402], [-0.24557640574494083, 0.2718174505738702, -0.6926715981177864, -0.6212998951117484], [-0.24585492064113273, 0.27150688650375393, -0.6927933890104353, -0.6211897364904025]], "angular_velocities": [[-7.719038104508623e-06, 8.279682752122315e-06, -1.2223224358447397e-06], [-7.719038104508623e-06, 8.279682752122315e-06, -1.22232243584474e-06], [-7.719038104508622e-06, 8.279682752122315e-06, -1.222322435844739e-06], [-7.719038104508623e-06, 8.279682752122315e-06, -1.2223224358447393e-06], [-7.719038104508623e-06, 8.279682752122316e-06, -1.2223224358447386e-06]], "reference_frame": 1}, "instrument_pointing": {"time_dependent_frames": [-98000, 1], "ck_table_start_time": 487928588.0336103, "ck_table_end_time": 487928903.0416103, "ck_table_original_size": 5, "ephemeris_times": [487928588.0336103, 487928666.7856103, 487928745.5376103, 487928824.28961027, 487928903.0416103], "quaternions": [[-0.6894448798229785, -0.13288333554010637, -0.30018901711893975, 0.645673548182655], [-0.687721087896909, -0.13374109956420746, -0.29978054587038167, 0.6475219284834335], [-0.6859672573646195, -0.13441668765411288, -0.2995880589786557, 0.6493289388446816], [-0.6843925306207158, -0.13520640845056833, -0.2991531939769342, 0.6510249286147723], [-0.68280490039217, -0.13588350538291064, -0.2989481901333484, 0.6526431801384941]], "angular_velocities": [[-6.0016600701510346e-05, -3.4315085391481984e-05, 3.616461098110838e-05], [-2.9998984431665234e-05, -2.9941950083650682e-05, 5.4011064302860286e-05], [-5.7451833433989726e-05, -2.640886089874711e-05, 3.345134823897179e-05], [-2.2375968791183237e-05, -2.5852223731490175e-05, 5.491960013111816e-05], [-1.3816947750491701e-05, -3.320701389161546e-05, 5.328198819154163e-05]], "reference_frame": 1, "constant_frames": [-98901, -98201, -98000], "constant_rotation": [-0.001805871124864633, 0.0037494052664166673, 0.9999913403573196, 0.018161770046999218, 0.9998281559785996, -0.0037159953166251633, -0.999833430596437, 0.01815490216391774, -0.001873656632970122]}, "naif_keywords": {"BODY999_RADII": [1188.3, 1188.3, 1188.3], "BODY_FRAME_CODE": 10019, "BODY_CODE": 999, "FRAME_-98901_CLASS": 4.0, "INS-98901_TRANSX": [0.0, 0.04, 0.0], "INS-98901_TRANSY": [0.04, 0.0, 0.04], "TKFRAME_-98901_UNITS": "DEGREES", "INS-98901_PIXEL_PITCH": 0.04, "INS-98901_FOCAL_LENGTH": 644.486, "FRAME_-98901_NAME": "ISIS_NH_RALPH_LEISA", "INS-98901_ITRANSL": [-1.0, 0.0, 25.0], "FRAME_-98901_CLASS_ID": -98901.0, "INS-98901_ITRANSS": [0.0, 25.0, 0.0], "TKFRAME_-98901_ANGLES": [0.0, 90.0, 0.0], "TKFRAME_-98901_AXES": [1.0, 2.0, 3.0], "TKFRAME_-98901_SPEC": "ANGLES", "FRAME_-98901_CENTER": -98.0, "TKFRAME_-98901_RELATIVE": "NH_RALPH_LEISA", "BODY999_PM": [302.695, 56.3625225, 0.0], "BODY999_POLE_RA": [132.993, 0.0, 0.0], "BODY999_POLE_DEC": [-6.163, 0.0, 0.0], "BODY999_LONG_AXIS": 0.0}, "detector_sample_summing": 1, "detector_line_summing": 1, "focal_length_model": {"focal_length": 644.486}, "detector_center": {"line": 0, "sample": 0}, "starting_detector_line": 0, "starting_detector_sample": 0, "focal2pixel_lines": [-1.0, 0.0, 25.0], "focal2pixel_samples": [0.0, 25.0, 0.0], "optical_distortion": {"radial": {"coefficients": [0.0, 0.0, 0.0]}}, "instrument_position": {"spk_table_start_time": 487928588.0336103, "spk_table_end_time": 487928903.0416103, "spk_table_original_size": 5, "ephemeris_times": [487928588.0336103, 487928666.7856103, 487928745.5376103, 487928824.28961027, 487928903.0416103], "positions": [[-341893.24779512954, 29580910.11543975, 7720840.361930893], [-341880.7808565185, 29579860.06353102, 7720567.900988498], [-341868.3126599601, 29578810.0127891, 7720295.440004236], [-341855.84320573055, 29577759.963213038, 7720022.97897548], [-341843.3724940212, 29576709.914803796, 7719750.517901289]], "velocities": [[0.15829834503568418, -13.333661290526594, -3.4597333648983915], [0.15831431122399225, -13.333646475303395, -3.4597338961260395], [0.15833027850391226, -13.333631661980828, -3.459734446767892], [0.1583462468689395, -13.333616850568019, -3.4597350168341365], [0.15836221629776992, -13.333602041080965, -3.4597356063085027]], "reference_frame": 1}, "sun_position": {"spk_table_start_time": 487928745.5376103, "spk_table_end_time": 487928745.5376103, "spk_table_original_size": 1, "ephemeris_times": [487928745.5376103], "positions": [[-1185193768.8247254, 4445753700.58781, 1744608601.9356186]], "velocities": [[-5.384652174342424, -0.7983186588678509, 1.3987335963733494]], "reference_frame": 1}}
 
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