Unverified Commit 77cf5d9e authored by Tim Giroux's avatar Tim Giroux Committed by GitHub
Browse files

ciss2isis - Set validmax global to input label value (#4589) 



* set validmax to inputlabel value

* Converted ciss2isis app and added gtests

* Addressed PR feedback and updated test

* Added test data for ciss2isis tests

Co-authored-by: default avataracpaquette <acp263@nau.edu>
parent 4763bf4f

isis/notebooks/crop_cassiniIss.ipynb

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%% Cell type:code id:b6c4ed37 tags:



``` python

import pvl

import struct

import matplotlib.pyplot as plt

import numpy as np

import datetime

import os

import binascii

```



%% Cell type:code id:e45c31fe tags:



``` python

label_file = "/Users/acpaquette/repos/ISIS3/build/N1472853667_1.LBL"

```



%% Cell type:code id:4eccdc86 tags:



``` python

pvl_label = pvl.load(label_file)

img_file = os.path.join(os.path.split(label_file)[0], pvl_label["^IMAGE"][0])

pvl_label

```



%% Output



    PVLModule([

      ('PDS_VERSION_ID', 'PDS3')

      ('RECORD_TYPE', 'FIXED_LENGTH')

      ('RECORD_BYTES', 1048)

      ('FILE_RECORDS', 1028)

      ('^IMAGE_HEADER', ['N1472853667_1.IMG', 1])

      ('^TELEMETRY_TABLE', ['N1472853667_1.IMG', 4])

      ('^LINE_PREFIX_TABLE', ['N1472853667_1.IMG', 5])

      ('^IMAGE', ['N1472853667_1.IMG', 5])

      ('ANTIBLOOMING_STATE_FLAG', 'ON')

      ('BIAS_STRIP_MEAN', 17.25049)

      ('CALIBRATION_LAMP_STATE_FLAG', 'N/A')

      ('COMMAND_FILE_NAME', 'trigger_6510_6.ioi')

      ('COMMAND_SEQUENCE_NUMBER', 6510)

      ('DARK_STRIP_MEAN', 0.0)

      ('DATA_CONVERSION_TYPE', 'TABLE')

      ('DATA_SET_ID', 'CO-S-ISSNA/ISSWA-2-EDR-V1.0')

      ('DELAYED_READOUT_FLAG', 'NO')

      ('DESCRIPTION', 'Incomplete product finalized due to truncated lines.')

      ('DETECTOR_TEMPERATURE', Quantity(value=-89.243546, units='DEGC'))

      ('EARTH_RECEIVED_START_TIME',

       datetime.datetime(2004, 9, 3, 9, 54, 37, 232000, tzinfo=datetime.timezone.utc))

      ('EARTH_RECEIVED_STOP_TIME',

       datetime.datetime(2004, 9, 3, 9, 57, 12, 966000, tzinfo=datetime.timezone.utc))

      ('ELECTRONICS_BIAS', 112)

      ('EXPECTED_MAXIMUM', [0.756496, 1.9487])

      ('EXPECTED_PACKETS', 519)

      ('EXPOSURE_DURATION', 220000.0)

      ('FILTER_NAME', ['CL1', 'CL2'])

      ('FILTER_TEMPERATURE', -0.468354)

      ('FLIGHT_SOFTWARE_VERSION_ID', '1.3')

      ('GAIN_MODE_ID', '12 ELECTRONS PER DN')

      ('IMAGE_MID_TIME',

       datetime.datetime(2004, 9, 2, 21, 34, 26, 410000, tzinfo=datetime.timezone.utc))

      ('IMAGE_NUMBER', '1472853667')

      ('IMAGE_OBSERVATION_TYPE', frozenset({'SCIENCE'}))

      ('IMAGE_TIME',

       datetime.datetime(2004, 9, 2, 21, 36, 16, 410000, tzinfo=datetime.timezone.utc))

      ('INSTRUMENT_DATA_RATE', 182.783997)

      ('INSTRUMENT_HOST_NAME', 'CASSINI ORBITER')

      ('INSTRUMENT_ID', 'ISSNA')

      ('INSTRUMENT_MODE_ID', 'FULL')

      ('INSTRUMENT_NAME', 'IMAGING SCIENCE SUBSYSTEM NARROW ANGLE')

      ('INST_CMPRS_PARAM', ['N/A', 'N/A', 'N/A', 'N/A'])

      ('INST_CMPRS_RATE', [3.6, 4.333807])

      ('INST_CMPRS_RATIO', 1.845952)

      ('INST_CMPRS_TYPE', 'LOSSLESS')

      ('LIGHT_FLOOD_STATE_FLAG', 'ON')

      ('METHOD_DESC', 'ISSPT2.5.3;Saturn-Ering;ISS_00ARI_DIFFUSRNG003_PRIME_4')

      ('MISSING_LINES', 511)

      ('MISSING_PACKET_FLAG', 'NO')

      ('MISSION_NAME', 'CASSINI-HUYGENS')

      ('MISSION_PHASE_NAME', 'TOUR PRE-HUYGENS')

      ('OBSERVATION_ID', 'ISS_00ARI_DIFFUSRNG003_PRIME')

      ('OPTICS_TEMPERATURE', [0.712693, 1.905708])

      ('ORDER_NUMBER', 2)

      ('PARALLEL_CLOCK_VOLTAGE_INDEX', 9)

      ('PREPARE_CYCLE_INDEX', 12)

      ('PRODUCT_CREATION_TIME',

       datetime.datetime(2004, 9, 3, 10, 39, 14, tzinfo=datetime.timezone.utc))

      ('PRODUCT_ID', '1_N1472853667.118')

      ('PRODUCT_VERSION_TYPE', 'FINAL')

      ('READOUT_CYCLE_INDEX', 10)

      ('RECEIVED_PACKETS', 576)

      ('SENSOR_HEAD_ELEC_TEMPERATURE', 1.633024)

      ('SEQUENCE_ID', 'S03')

      ('SEQUENCE_NUMBER', 2)

      ('SEQUENCE_TITLE', 'ISS_00ARI_DIFFUSRNG003_PRIME')

      ('SHUTTER_MODE_ID', 'NACONLY')

      ('SHUTTER_STATE_ID', 'ENABLED')

      ('SOFTWARE_VERSION_ID', 'ISS 9.00 02-05-2004')

      ('SPACECRAFT_CLOCK_CNT_PARTITION', 1)

      ('SPACECRAFT_CLOCK_START_COUNT', '1472853447.118')

      ('SPACECRAFT_CLOCK_STOP_COUNT', '1472853667.118')

      ('START_TIME',

       datetime.datetime(2004, 9, 2, 21, 32, 36, 410000, tzinfo=datetime.timezone.utc))

      ('STOP_TIME',

       datetime.datetime(2004, 9, 2, 21, 36, 16, 410000, tzinfo=datetime.timezone.utc))

      ('TARGET_DESC', 'Saturn-Ering')

      ('TARGET_LIST', 'N/A')

      ('TARGET_NAME', 'SATURN')

      ('TELEMETRY_FORMAT_ID', 'UNK')

      ('VALID_MAXIMUM', [9896, 4095])

      ('IMAGE_HEADER',

       {'BYTES': 3144,

        'HEADER_TYPE': 'VICAR2',

        'INTERCHANGE_FORMAT': 'ASCII',

        'RECORDS': 1,

        '^DESCRIPTION': 'VICAR2.TXT'})

      ('TELEMETRY_TABLE',

       {'COLUMN': {'BYTES': 987,

                   'DATA_TYPE': 'MSB_UNSIGNED_INTEGER',

                   'NAME': 'NULL_PADDING',

                   'START_BYTE': 61},

        'COLUMNS': 2,

        'INTERCHANGE_FORMAT': 'BINARY',

        'ROWS': 1,

        'ROW_BYTES': 1048,

        '^STRUCTURE': 'TLMTAB.FMT'})

      ('LINE_PREFIX_TABLE',

       {'COLUMNS': 7,

        'INTERCHANGE_FORMAT': 'BINARY',

        'ROWS': 1024,

        'ROW_BYTES': 24,

        'ROW_SUFFIX_BYTES': 1024,

        '^LINE_PREFIX_STRUCTURE': 'PREFIX2.FMT'})

      ('IMAGE',

       {'LINES': 1024,

        'LINE_PREFIX_BYTES': 24,

        'LINE_SAMPLES': 1024,

        'SAMPLE_BITS': 8,

        'SAMPLE_TYPE': 'SUN_INTEGER'})

    ])



%% Cell type:code id:616e7622 tags:



``` python

with open(img_file, 'rb') as fp:

    byte_position = ((pvl_label["^IMAGE"][1] - 1) * pvl_label["RECORD_BYTES"])

    b_original_header = fp.read(byte_position)

    b_image_data = fp.read()

```



%% Cell type:code id:10f0680b tags:



``` python

lut_list = [1, 3, 5, 7, 9, 11, 14, 16, 19, 22, 25, 28, 31, 35, 38, 42, 46, 49, 53, 57,

61, 65, 70, 74, 79, 83, 88, 93, 98, 103, 108, 113, 119, 125, 130, 136, 142,

148, 154, 160, 166, 173, 179, 186, 193, 199, 206, 213, 221, 228, 236, 243,

251, 259, 267, 275, 283, 291, 299, 307, 316, 324, 333, 342, 351, 360, 369,

379, 388, 398, 407, 417, 427, 437, 447, 457, 467, 478, 488, 499, 509, 520,

531, 542, 554, 565, 576, 588, 600, 611, 623, 635, 647, 659, 672, 684, 697,

709, 722, 735, 747, 761, 774, 787, 801, 814, 828, 842, 856, 870, 884, 898,

912, 926, 941, 955, 970, 985, 1000, 1015, 1030, 1045, 1061, 1076, 1092, 1108,

1124, 1140, 1156, 1172, 1188, 1204, 1221, 1237, 1254, 1271, 1288, 1305, 1322,

1339, 1357, 1374, 1392, 1410, 1428, 1446, 1464, 1482, 1500, 1518, 1537, 1555,

1574, 1593, 1612, 1631, 1650, 1669, 1689, 1708, 1728, 1748, 1768, 1788, 1808,

1828, 1848, 1868, 1889, 1909, 1930, 1951, 1971, 1993, 2014, 2035, 2057, 2078,

2100, 2121, 2143, 2165, 2187, 2209, 2232, 2254, 2276, 2299, 2322, 2344, 2367,

2390, 2413, 2437, 2460, 2484, 2507, 2531, 2555, 2579, 2603, 2627, 2651, 2676,

2700, 2725, 2749, 2774, 2799, 2824, 2849, 2874, 2900, 2925, 2951, 2977, 3003,

3029, 3055, 3081, 3107, 3133, 3160, 3186, 3213, 3239, 3266, 3293, 3321, 3348,

3375, 3403, 3430, 3458, 3486, 3514, 3542, 3570, 3598, 3627, 3655, 3684, 3712,

3741, 3770, 3799, 3828, 3857, 3887, 3916, 3946, 3976, 4005, 4035, 4065, 4095]

```



%% Cell type:code id:4c26e15b tags:



``` python

sampling = (pvl_label['IMAGE']['SAMPLE_BITS']//8)

line_length = (pvl_label['IMAGE']['LINE_SAMPLES'] * sampling) + pvl_label['IMAGE']['LINE_PREFIX_BYTES']

print(line_length)

n_lines = 10





image_data = []

for j in range(n_lines):

    start, stop = j*(line_length), (j+1)*(line_length)

    if (sampling == 2):

        dtype = np.int16

    elif (sampling == 4):

        dtype = np.float32

    else:

        dtype=np.int8

    image_sample = np.frombuffer(b_image_data[start:stop], dtype=dtype, count=int((line_length)/sampling))

    image_data.append(image_sample)

image_data = np.array(image_data)



# Uncomment the following to compare with an ISIS cube

# if pvl_label["^IMAGE"][0][0] == 'W':

#     image_data = image_data.byteswap()

# else:

#     image_data = np.reshape(np.array(list(map(lambda x: lut_list[x], image_data.flatten()))), (n_lines, line_length))

```



%% Output



    1048



%% Cell type:code id:3815ac94 tags:



``` python

path_cropped_label = os.path.splitext(label_file)[0] + ".cropped.lbl"

path_cropped_file = os.path.splitext(img_file)[0] + ".cropped.img"

cropped_file = os.path.split(path_cropped_file)[1]



new_label = pvl_label.copy()

new_label["IMAGE"]["LINES"] = n_lines

new_label["^IMAGE"][0] = cropped_file

new_label["^IMAGE_HEADER"][0] = cropped_file

new_label["^TELEMETRY_TABLE"][0] = cropped_file

new_label["^LINE_PREFIX_TABLE"][0] = cropped_file



with open(path_cropped_file, 'wb') as fp:

    fp.write(b_original_header)

    fp.write(image_data)



pvl.dump(new_label, path_cropped_label)

```



%% Output



    4620



%% Cell type:code id:28a7937d tags:



``` python

# Below lines used to compare the ISIS cube to the original label since qt 15.0 doesn't work on big sur

# as of 01/28/2022

```



%% Cell type:code id:31bd22d4 tags:



``` python

cube_file = "/Path/to/test/output.cub"

cube_label = pvl.load(cube_file)

```



%% Cell type:code id:d3ea86dc tags:



``` python

with open(cube_file, 'rb') as fp:

    fp.seek(cube_label["IsisCube"]["Core"]["StartByte"] - 1)

    b_cube_data = fp.read()

```



%% Cell type:code id:2b175905 tags:



``` python

line_length = cube_label["IsisCube"]["Core"]["Dimensions"]["Samples"] * 2

n_lines = cube_label["IsisCube"]["Core"]["Dimensions"]["Lines"]



cube_data = []

for j in range(n_lines):

    start, stop = j*(line_length), (j+1)*(line_length)



    cube_sample = np.frombuffer(b_cube_data[start:stop], dtype=np.int16, count=int(line_length/2))

    cube_data.append(cube_sample)



cube_data = np.array(cube_data)

# cube_data = np.where(cube_data == -32764, 4095, cube_data)

cube_data = np.where(cube_data < -32764, 1, cube_data)

```



%% Cell type:code id:f8d8c29c tags:



``` python

plt.figure(0, figsize=(20, 20))

plt.imshow(cube_data)

plt.show()

```



%% Cell type:code id:6db691e3 tags:



``` python

```

isis/src/cassini/apps/ciss2isis/ciss2isis.cpp

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isis/src/cassini/apps/ciss2isis/ciss2isis.h

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#ifndef ciss2isis_h

#define ciss2isis_h



/** This is free and unencumbered software released into the public domain.



The authors of ISIS do not claim copyright on the contents of this file.

For more details about the LICENSE terms and the AUTHORS, you will

find files of those names at the top level of this repository. **/



/* SPDX-License-Identifier: CC0-1.0 */



#include "Cube.h"

#include "UserInterface.h"



namespace Isis {

  extern void ciss2isis(UserInterface &ui, Pvl *log=nullptr);

}



#endif

isis/src/cassini/apps/ciss2isis/main.cpp

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isis/src/cassini/apps/ciss2isis/tsts/narrowAngle/Makefile

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APPNAME = ciss2isis



labels.txt.IGNORELINES = Bytes StartByte TileSamples TileLines



include $(ISISROOT)/make/isismake.tsts



commands:

	$(APPNAME) from=$(INPUT)/N1472853667_1.LBL \

	to=$(OUTPUT)/N1472853667_1.truth.cub > /dev/null;

	catlab from=$(OUTPUT)/N1472853667_1.truth.cub to=$(OUTPUT)/labels.txt > /dev/null;