Unverified Commit 74da682d authored by AustinSanders's avatar AustinSanders Committed by GitHub
Browse files

Cleaned up cropping notebooks (#4211) 



Co-authored-by: default avatarAdam Paquette <acpaquette@usgs.gov>
parent 7914ba0c

isis/notebooks/crop_chandrayaan.ipynb

+93 −113

File changed.

Preview size limit exceeded, changes collapsed.

isis/notebooks/crop_crism.ipynb

+2 −130
Original line number Diff line number Diff line 
%% Cell type:code id: tags:



``` python

import pvl

import struct

import matplotlib.pyplot as plt

import numpy as np

import datetime

import os.path

import binascii

```



%% Cell type:code id: tags:



``` python

crism_file = '/home/arsanders/testData/crism/tsts/mrdr/input/t1865_mrrde_70n185_0256_1.lbl'

image_file = crism_file

```



%% Cell type:code id: tags:



``` python

header = pvl.load(crism_file)

```



%% Cell type:code id: tags:



``` python

header

```



%% Output



    PVLModule([

      ('PDS_VERSION_ID', 'PDS3')

      ('RECORD_TYPE', 'FIXED_LENGTH')

      ('RECORD_BYTES', 3920)

      ('FILE_RECORDS', 30720)

      ('LABEL_REVISION_NOTE',

       '2003-11-19, S. Slavney (GEO); 2005-09-25, S. Murchie (JHU/APL); 2007-03-09, '

       'E. Malaret (ACT Corp.); 2007-09-14, C. Hash (ACT Corp)')

      ('^IMAGE', 'T1865_MRRDE_70N185_0256_1.IMG')

      ('DATA_SET_ID', 'MRO-M-CRISM-5-RDR-MULTISPECTRAL-V1.0')

      ('PRODUCT_ID', 'T1865_MRRDE_70N185_0256_1')

      ('INSTRUMENT_HOST_NAME', 'MARS RECONNAISSANCE ORBITER')

      ('SPACECRAFT_ID', 'MRO')

      ('INSTRUMENT_NAME', 'COMPACT RECONNAISSANCE IMAGING SPECTROMETER FOR MARS')

      ('INSTRUMENT_ID', 'CRISM')

      ('TARGET_NAME', 'MARS')

      ('PRODUCT_TYPE', 'MAP_PROJECTED_MULTISPECTRAL_RDR')

      ('PRODUCT_CREATION_TIME',

       datetime.datetime(2007, 12, 22, 16, 50, 47, 432000, tzinfo=datetime.timezone.utc))

      ('START_TIME', 'N/A')

      ('STOP_TIME', 'N/A')

      ('SPACECRAFT_CLOCK_START_COUNT', 'N/A')

      ('SPACECRAFT_CLOCK_STOP_COUNT', 'N/A')

      ('PRODUCT_VERSION_ID', '1')

      ('PRODUCER_INSTITUTION_NAME', 'APPLIED PHYSICS LABORATORY')

      ('SOFTWARE_NAME', 'PIPE_create_crism_mrdr_product')

      ('SOFTWARE_VERSION_ID', '12.21.07')

      ('MRO:WAVELENGTH_FILE_NAME', 'T1865_MRRWV_70N185_0256_1.TAB')

      ('IMAGE',

       {'BANDS': 24,

        'BAND_NAME': ['Solar longitude, deg',

                      'Solar distance, AU',

                      'Observation ID, VNIR',

                      'Observation ID, IR',

                      'Ordinal counter, VNIR',

                      'Ordinal counter, IR',

                      'Column number, VNIR',

                      'Column number, IR',

                      'Line, or frame number, VNIR',

                      'Line, or frame number, IR',

                      'INA at areoid, deg',

                      'EMA at areoid, deg',

                      'Phase angle, deg',

                      'Latitude, areocentric, deg N',

                      'Longitude, areocentric, deg E',

                      'INA at surface from MOLA, deg',

                      'EMA at surface from MOLA, deg',

                      'Slope magnitude from MOLA, deg',

                      'MOLA slope azimuth, deg clkwise from N',

                      'Elevation, meters relative to MOLA',

                      'Thermal inertia, J m^-2 K^-1 s^-0.5',

                      'Bolometic albedo',

                      'Local solar time, hours',

                      'Spare'],

        'BAND_STORAGE_TYPE': 'BAND_SEQUENTIAL',

        'LINES': 1280,

        'LINE_SAMPLES': 980,

        'SAMPLE_BITS': 32,

        'SAMPLE_TYPE': 'PC_REAL'})

      ('IMAGE_MAP_PROJECTION',

       {'A_AXIS_RADIUS': Quantity(value=3396, units='KM'),

        'B_AXIS_RADIUS': Quantity(value=3396, units='KM'),

        'CENTER_LATITUDE': Quantity(value=67.5000001, units='DEGREE'),

        'CENTER_LONGITUDE': Quantity(value=185.0, units='DEGREE'),

        'COORDINATE_SYSTEM_NAME': 'PLANETOCENTRIC',

        'COORDINATE_SYSTEM_TYPE': 'BODY-FIXED ROTATING',

        'C_AXIS_RADIUS': Quantity(value=3396, units='KM'),

        'EASTERNMOST_LONGITUDE': Quantity(value=9.9999999, units='DEGREE'),

        'FIRST_STANDARD_PARALLEL': 'N/A',

        'LINE_FIRST_PIXEL': 1,

        'LINE_LAST_PIXEL': 1280,

        'LINE_PROJECTION_OFFSET': 18560.0,

        'MAP_PROJECTION_ROTATION': 0.0,

        'MAP_PROJECTION_TYPE': 'EQUIRECTANGULAR',

        'MAP_RESOLUTION': Quantity(value=256, units='PIXEL/DEGREE'),

        'MAP_SCALE': Quantity(value=0.231528833585, units='KM/PIXEL'),

        'MAXIMUM_LATITUDE': Quantity(value=72.5, units='DEGREE'),

        'MINIMUM_LATITUDE': Quantity(value=67.5000001, units='DEGREE'),

        'POSITIVE_LONGITUDE_DIRECTION': 'EAST',

        'REFERENCE_LATITUDE': 'N/A',

        'REFERENCE_LONGITUDE': 'N/A',

        'SAMPLE_FIRST_PIXEL': 1,

        'SAMPLE_LAST_PIXEL': 980,

        'SAMPLE_PROJECTION_OFFSET': 47360.0,

        'SECOND_STANDARD_PARALLEL': 'N/A',

        'WESTERNMOST_LONGITUDE': Quantity(value=360.0, units='DEGREE'),

        '^DATA_SET_MAP_PROJECTION': 'MRR_MAP.CAT'})

    ])



%% Cell type:code id: tags:



``` python

with open(crism_file, 'rb') as f:

    # If detached label, "^IMAGE" will be a list.

    image_file = os.path.dirname(crism_file) + "/" + header["^IMAGE"].lower()

    with open(image_file, 'rb') as im_f:

        b_image_data = im_f.read()

```



%% Cell type:code id: tags:



``` python

n_lines = 10

line_length = header['IMAGE']['LINE_SAMPLES'] * (header['IMAGE']['SAMPLE_BITS']//8)

```



%% Cell type:code id: tags:



``` python

image_data = []

for j in range(n_lines):

    image_sample = np.frombuffer(b_image_data[j*line_length:(j+1)*line_length], dtype=np.float32, count=int(line_length/4))

    image_data.append(image_sample)

image_data = np.array(image_data)

```



%% Cell type:code id: tags:



``` python

plt.imshow(image_data, cmap='magma')

plt.imshow(image_data)

```



%% Output



    <matplotlib.image.AxesImage at 0x2aff238d0850>





%% Cell type:code id: tags:



``` python

image_fn, image_ext = os.path.splitext(image_file)

mini_image_fn = image_fn + '_cropped' + image_ext

mini_image_bn = os.path.basename(mini_image_fn)



# Overwrite the number of lines in the label

header['IMAGE']['LINES'] = n_lines

header['IMAGE']['BANDS'] = 1

header['^IMAGE'] = mini_image_bn

header['FILE_RECORDS'] = n_lines -1

```



%% Cell type:code id: tags:



``` python

class RealIsisCubeLabelEncoder(pvl.encoder.ISISEncoder):

    def encode_time(self, value):

        if value.microsecond:

            second = u'%02d.%06d' % (value.second, value.microsecond)

        else:

            second = u'%02d' % value.second



        time = u'%02d:%02d:%s' % (value.hour, value.minute, second)

        return time

```



%% Cell type:code id: tags:



``` python

label_fn, label_ext = os.path.splitext(crism_file)

out_label = label_fn + '_cropped' + label_ext



grammar = pvl.grammar.ISISGrammar()

grammar.comments+=(("#", "\n"), )

encoder = RealIsisCubeLabelEncoder()

encoder = pvl.encoder.ISISEncoder()

pvl.dump(header, out_label, encoder=encoder, grammar=grammar)

```



%% Output



    3539



%% Cell type:code id: tags:



``` python

with open(mini_image_fn, 'wb+') as f:

    b_reduced_image_data = image_data.tobytes()

    f.seek(0, 2)

    f.write(b_reduced_image_data)

```
 


%% Cell type:code id: tags:



``` python

```



%% Cell type:code id: tags:



``` python

header = pvl.load(out_label)

```



%% Cell type:code id: tags:



``` python

header

```



%% Output



    PVLModule([

      ('PDS_VERSION_ID', 'PDS3')

      ('RECORD_TYPE', 'FIXED_LENGTH')

      ('RECORD_BYTES', 3920)

      ('FILE_RECORDS', 9)

      ('LABEL_REVISION_NOTE',

       '2003-11-19, S. Slavney (GEO); 2005-09-25, S. Murchie (JHU/APL); 2007-03-09, '

       'E. Malaret (ACT Corp.); 2007-09-14, C. Hash (ACT Corp)')

      ('^IMAGE', 't1865_mrrde_70n185_0256_1_cropped.img')

      ('DATA_SET_ID', 'MRO-M-CRISM-5-RDR-MULTISPECTRAL-V1.0')

      ('PRODUCT_ID', 'T1865_MRRDE_70N185_0256_1')

      ('INSTRUMENT_HOST_NAME', 'MARS RECONNAISSANCE ORBITER')

      ('SPACECRAFT_ID', 'MRO')

      ('INSTRUMENT_NAME', 'COMPACT RECONNAISSANCE IMAGING SPECTROMETER FOR MARS')

      ('INSTRUMENT_ID', 'CRISM')

      ('TARGET_NAME', 'MARS')

      ('PRODUCT_TYPE', 'MAP_PROJECTED_MULTISPECTRAL_RDR')

      ('PRODUCT_CREATION_TIME',

       datetime.datetime(2007, 12, 22, 16, 50, 47, 432000, tzinfo=datetime.timezone.utc))

      ('START_TIME', 'N/A')

      ('STOP_TIME', 'N/A')

      ('SPACECRAFT_CLOCK_START_COUNT', 'N/A')

      ('SPACECRAFT_CLOCK_STOP_COUNT', 'N/A')

      ('PRODUCT_VERSION_ID', '1')

      ('PRODUCER_INSTITUTION_NAME', 'APPLIED PHYSICS LABORATORY')

      ('SOFTWARE_NAME', 'PIPE_create_crism_mrdr_product')

      ('SOFTWARE_VERSION_ID', '12.21.07')

      ('MRO:WAVELENGTH_FILE_NAME', 'T1865_MRRWV_70N185_0256_1.TAB')

      ('IMAGE',

       {'BANDS': 1,

        'BAND_NAME': ['Solar longitude, deg',

                      'Solar distance, AU',

                      'Observation ID, VNIR',

                      'Observation ID, IR',

                      'Ordinal counter, VNIR',

                      'Ordinal counter, IR',

                      'Column number, VNIR',

                      'Column number, IR',

                      'Line, or frame number, VNIR',

                      'Line, or frame number, IR',

                      'INA at areoid, deg',

                      'EMA at areoid, deg',

                      'Phase angle, deg',

                      'Latitude, areocentric, deg N',

                      'Longitude, areocentric, deg E',

                      'INA at surface from MOLA, deg',

                      'EMA at surface from MOLA, deg',

                      'Slope magnitude from MOLA, deg',

                      'MOLA slope azimuth, deg clkwise from N',

                      'Elevation, meters relative to MOLA',

                      'Thermal inertia, J m^-2 K^-1 s^-0.5',

                      'Bolometic albedo',

                      'Local solar time, hours',

                      'Spare'],

        'BAND_STORAGE_TYPE': 'BAND_SEQUENTIAL',

        'LINES': 10,

        'LINE_SAMPLES': 980,

        'SAMPLE_BITS': 32,

        'SAMPLE_TYPE': 'PC_REAL'})

      ('IMAGE_MAP_PROJECTION',

       {'A_AXIS_RADIUS': Quantity(value=3396, units='KM'),

        'B_AXIS_RADIUS': Quantity(value=3396, units='KM'),

        'CENTER_LATITUDE': Quantity(value=67.5000001, units='DEGREE'),

        'CENTER_LONGITUDE': Quantity(value=185.0, units='DEGREE'),

        'COORDINATE_SYSTEM_NAME': 'PLANETOCENTRIC',

        'COORDINATE_SYSTEM_TYPE': 'BODY-FIXED ROTATING',

        'C_AXIS_RADIUS': Quantity(value=3396, units='KM'),

        'EASTERNMOST_LONGITUDE': Quantity(value=9.9999999, units='DEGREE'),

        'FIRST_STANDARD_PARALLEL': 'N/A',

        'LINE_FIRST_PIXEL': 1,

        'LINE_LAST_PIXEL': 1280,

        'LINE_PROJECTION_OFFSET': 18560.0,

        'MAP_PROJECTION_ROTATION': 0.0,

        'MAP_PROJECTION_TYPE': 'EQUIRECTANGULAR',

        'MAP_RESOLUTION': Quantity(value=256, units='PIXEL/DEGREE'),

        'MAP_SCALE': Quantity(value=0.231528833585, units='KM/PIXEL'),

        'MAXIMUM_LATITUDE': Quantity(value=72.5, units='DEGREE'),

        'MINIMUM_LATITUDE': Quantity(value=67.5000001, units='DEGREE'),

        'POSITIVE_LONGITUDE_DIRECTION': 'EAST',

        'REFERENCE_LATITUDE': 'N/A',

        'REFERENCE_LONGITUDE': 'N/A',

        'SAMPLE_FIRST_PIXEL': 1,

        'SAMPLE_LAST_PIXEL': 980,

        'SAMPLE_PROJECTION_OFFSET': 47360.0,

        'SECOND_STANDARD_PARALLEL': 'N/A',

        'WESTERNMOST_LONGITUDE': Quantity(value=360.0, units='DEGREE'),

        '^DATA_SET_MAP_PROJECTION': 'MRR_MAP.CAT'})

    ])



%% Cell type:code id: tags:



``` python

```

isis/notebooks/crop_crism_trdr.ipynb

+2 −209
Original line number Diff line number Diff line 
%% Cell type:code id: tags:



``` python

import pvl

import struct

import matplotlib.pyplot as plt

import numpy as np

import datetime

import os.path

import binascii

```



%% Cell type:code id: tags:



``` python

crism_file = '/home/arsanders/testData/crism/tsts/trdr/input/frt0001e5c3_07_if124s_trr3.lbl'

image_file = crism_file

```



%% Cell type:code id: tags:



``` python

header = pvl.load(crism_file)

```



%% Cell type:code id: tags:



``` python

header

```



%% Output



    PVLModule([

      ('PDS_VERSION_ID', 'PDS3')

      ('LABEL_REVISION_NOTE',

       '2004-11-22, S. Slavney (GEO); 2005-12-20, H. Taylor (JHU/APL); 2006-04-05, '

       'S. Murchie (JHU/APL); 2006-09-18, P. Cavender (JHU/APL); 2007-02-19, P. '

       'Cavender (JHU/APL); Version 2, new stray light subtraction 2010-06-01, D. '

       'Humm (JHU/APL); Version 3, shutter mirror correction 2010-10-12, C. Hash '

       '(ACT); Version 3, Added data filter control parameters')

      ('DATA_SET_ID', 'MRO-M-CRISM-3-RDR-TARGETED-V1.0')

      ('PRODUCT_ID', 'FRT0001E5C3_07_IF124S_TRR3')

      ('INSTRUMENT_HOST_NAME', 'MARS RECONNAISSANCE ORBITER')

      ('SPACECRAFT_ID', 'MRO')

      ('INSTRUMENT_NAME', 'COMPACT RECONNAISSANCE IMAGING SPECTROMETER FOR MARS')

      ('INSTRUMENT_ID', 'CRISM')

      ('TARGET_NAME', 'MARS')

      ('PRODUCT_TYPE', 'TARGETED_RDR')

      ('PRODUCT_CREATION_TIME',

       datetime.datetime(2011, 6, 8, 10, 52, 30, tzinfo=datetime.timezone.utc))

      ('START_TIME',

       datetime.datetime(2011, 6, 2, 4, 3, 9, 29000, tzinfo=datetime.timezone.utc))

      ('STOP_TIME',

       datetime.datetime(2011, 6, 2, 4, 5, 0, 763000, tzinfo=datetime.timezone.utc))

      ('SPACECRAFT_CLOCK_START_COUNT', '10/0991454621.14521')

      ('SPACECRAFT_CLOCK_STOP_COUNT', '10/0991454732.62633')

      ('ORBIT_NUMBER', 'NULL')

      ('OBSERVATION_TYPE', 'FRT')

      ('OBSERVATION_ID', '16#0001E5C3#')

      ('MRO:OBSERVATION_NUMBER', 7)

      ('MRO:ACTIVITY_ID', 'IF124')

      ('MRO:SENSOR_ID', 'S')

      ('MRO:DETECTOR_TEMPERATURE', -53.663)

      ('MRO:OPTICAL_BENCH_TEMPERATURE', -42.348)

      ('MRO:SPECTROMETER_HOUSING_TEMP', -65.178)

      ('MRO:SPHERE_TEMPERATURE', -42.484)

      ('MRO:FPE_TEMPERATURE', 5.269)

      ('PRODUCT_VERSION_ID', '3')

      ('SOURCE_PRODUCT_ID',

       frozenset({'CDR400991452611_SP0042501S_3',

                  'CDR400991452639_BP0042500S_3',

                  'CDR400991452639_BP1018400S_3',

                  'CDR400991454611_BI1018400S_3',

                  'CDR400991454611_UB1018400S_3',

                  'CDR400991454737_BI1018400S_3',

                  'CDR400991454737_UB1018400S_3',

                  'CDR410000000000_SH0000001S_4',

                  'CDR410000000000_SS0000001S_2',

                  'CDR450924300802_DM0000000S_3',

                  'CDR450924300802_NU1000001S_3',

                  'CDR450924300802_SF0000000S_2',

                  'CDR450924300802_TD0000000S_2',

                  'CDR6_0_0991440032_ST_J_0',

                  'CDR6_1_0000000000_AS_S_0',

                  'CDR6_1_0000000000_DB_S_0',

                  'CDR6_1_0000000000_EB_S_0',

                  'CDR6_1_0000000000_GH_S_1',

                  'CDR6_1_0000000000_HD_J_1',

                  'CDR6_1_0000000000_HK_J_1',

                  'CDR6_1_0000000000_HV_J_1',

                  'CDR6_1_0000000000_LC_S_1',

                  'CDR6_1_0000000000_LI_J_0',

                  'CDR6_1_0000000000_VL_S_0',

                  'CDR6_2_0835294537_PP_S_0',

                  'FRT0001E5C3_07_SC124S_EDR0'}))

      ('MRO:INVALID_PIXEL_LOCATION', frozenset())

      ('PRODUCER_INSTITUTION_NAME',

       'JOHNS HOPKINS UNIVERSITY APPLIED PHYSICS LABORATORY')

      ('SOFTWARE_NAME', 'crism_imagecal')

      ('SOFTWARE_VERSION_ID', '2.5.3')

      ('TARGET_CENTER_DISTANCE', Quantity(value='NULL', units='KM'))

      ('SOLAR_DISTANCE', Quantity(value=213788591.232902, units='KM'))

      ('SOLAR_LONGITUDE', 303.590051)

      ('SHUTTER_MODE_ID', 'OPEN')

      ('LIGHT_SOURCE_NAME', 'NONE')

      ('MRO:CALIBRATION_LAMP_STATUS', 'OFF')

      ('MRO:CALIBRATION_LAMP_LEVEL', 'N/A')

      ('PIXEL_AVERAGING_WIDTH', 1)

      ('MRO:INSTRUMENT_POINTING_MODE', 'DYNAMIC POINTING')

      ('SCAN_MODE_ID', 'SHORT')

      ('MRO:FRAME_RATE', Quantity(value=3.75, units='HZ'))

      ('MRO:EXPOSURE_PARAMETER', 184)

      ('SAMPLING_MODE_ID', 'HYPERSPEC')

      ('COMPRESSION_TYPE', 'NONE')

      ('MRO:WAVELENGTH_FILTER', '0')

      ('MRO:WAVELENGTH_FILE_NAME', 'CDR450924300802_WA0000000S_2.IMG')

      ('MRO:PIXEL_PROC_FILE_NAME', 'CDR6_2_0835294537_PP_S_0.TAB')

      ('MRO:INV_LOOKUP_TABLE_FILE_NAME', 'CDR6_1_0000000000_LI_J_0.TAB')

      ('MRO:ATMO_CORRECTION_FLAG', 'OFF')

      ('MRO:THERMAL_CORRECTION_MODE', 'OFF')

      ('MRO:PHOTOCLIN_CORRECTION_FLAG', 'OFF')

      ('MRO:SPATIAL_RESAMPLING_FLAG', 'OFF')

      ('MRO:SPATIAL_RESAMPLING_FILE', 'N/A')

      ('MRO:SPATIAL_RESCALING_FLAG', 'OFF')

      ('MRO:SPATIAL_RESCALING_FILE', 'N/A')

      ('MRO:SPECTRAL_RESAMPLING_FLAG', 'OFF')

      ('MRO:SPECTRAL_RESAMPLING_FILE', 'N/A')

      ('MRO:HDF_SOFTWARE_NAME', 'crismhdf')

      ('MRO:HDF_SOFTWARE_VERSION_ID', '1.0.5')

      ('MRO:IF_MIN_VALUE', 0.0)

      ('MRO:IF_MAX_VALUE', 1.0)

      ('MRO:TRACE_MIN_VALUE', 0.01)

      ('MRO:TRACE_MAX_VALUE', 100.0)

      ('MRO:REFZ_MEDIAN_BOX_WIDTH', 15)

      ('MRO:REFZ_SMOOTH_BOX_WIDTH', 5)

      ('MRO:FRAM_STAT_MEDIAN_BOX_WIDTH', 5)

      ('MRO:FRAM_STAT_MIN_DEVIATION', 0.005)

      ('MRO:FRAM_STAT_MEDIAN_CONF_LVL', 0.999999)

      ('MRO:FRAM_STAT_IQR_CONF_LVL', 0.999999)

      ('MRO:RSC_REF_XY_MEDIAN_WIDTH', 15)

      ('MRO:RSC_REF_XY_SMOOTH_WIDTH', 5)

      ('MRO:RSC_REF_YZ_MEDIAN_WIDTH', 15)

      ('MRO:RSC_REF_YZ_SMOOTH_WIDTH', 5)

      ('MRO:RSC_RATIO_XY_MEDIAN_WIDTH', 25)

      ('MRO:RSC_RATIO_XY_SMOOTH_WIDTH', 13)

      ('MRO:RSC_RES_XY_PLY_ORDER', 5)

      ('MRO:RSC_RES_XY_PLY_EXTND_WIDTH', 38)

      ('MRO:LOG_XFORM_NEG_CLIP_VALUE', 'N/A')

      ('MRO:IKF_NUM_REGIONS', 'N/A')

      ('MRO:IKF_START_CHANNEL', ['N/A', 'N/A'])

      ('MRO:IKF_STOP_CHANNEL', ['N/A', 'N/A'])

      ('MRO:IKF_CONFIDENCE_LEVEL', ['N/A', 'N/A'])

      ('MRO:IKF_WEIGHTING_STDDEV', ['N/A', 'N/A'])

      ('MRO:IKF_KERNEL_SIZE_X', ['N/A', 'N/A'])

      ('MRO:IKF_KERNEL_SIZE_Y', ['N/A', 'N/A'])

      ('MRO:IKF_KERNEL_SIZE_Z', ['N/A', 'N/A'])

      ('MRO:IKF_MODEL_ORDER_X', ['N/A', 'N/A'])

      ('MRO:IKF_MODEL_ORDER_Y', ['N/A', 'N/A'])

      ('MRO:IKF_MODEL_ORDER_Z', ['N/A', 'N/A'])

      ('FILE',

       {'FILE_RECORDS': 44941,

        'IMAGE': {'BANDS': 107,

                  'BAND_STORAGE_TYPE': 'LINE_INTERLEAVED',

                  'LINES': 420,

                  'LINE_SAMPLES': 640,

                  'SAMPLE_BITS': 32,

                  'SAMPLE_TYPE': 'PC_REAL',

                  'UNIT': 'I_OVER_F'},

        'RECORD_BYTES': 2560,

        'RECORD_TYPE': 'FIXED_LENGTH',

        'ROWNUM_TABLE': {'COLUMN': {'BIT_MASK': 511,

                                    'BYTES': 2,

                                    'COLUMN_NUMBER': 1,

                                    'DATA_TYPE': 'MSB_UNSIGNED_INTEGER',

                                    'DESCRIPTION': 'Detector row number from which '

                                                   'the data was taken.',

                                    'NAME': 'DETECTOR_ROW_NUMBER',

                                    'START_BYTE': 1},

                         'COLUMNS': 1,

                         'DESCRIPTION': 'The detector is subsampled in the spectral '

                                        'direction by selecting specific rows to be '

                                        'downlinked. This table provides a list of '

                                        'the rows selected for all frames in this '

                                        'multidimensional image cube.',

                         'INTERCHANGE_FORMAT': 'BINARY',

                         'NAME': 'SELECTED ROWS FROM DETECTOR',

                         'ROWS': 107,

                         'ROW_BYTES': 2},

        '^IMAGE': 'FRT0001E5C3_07_IF124S_TRR3.IMG',

        '^ROWNUM_TABLE': ['FRT0001E5C3_07_IF124S_TRR3.IMG', 44941]})

      ('FILE',

       {'FILE_RECORDS': 420,

        'RECORD_BYTES': 1221,

        'RECORD_TYPE': 'FIXED_LENGTH',

        'TRDR_HK_TABLE': {'COLUMNS': 233,

                          'INTERCHANGE_FORMAT': 'ASCII',

                          'NAME': 'TARGETED RDR HOUSEKEEPING TABLE',

                          'ROWS': 420,

                          'ROW_BYTES': 1221,

                          '^STRUCTURE': 'TRDRHK.FMT'},

        '^TRDR_HK_TABLE': 'FRT0001E5C3_07_RA124S_HKP3.TAB'})

    ])



%% Cell type:code id: tags:



``` python

with open(crism_file, 'rb') as f:

    # If detached label, "^IMAGE" will be a list.

    image_file = os.path.dirname(crism_file) + "/" + header['FILE']["^IMAGE"].lower()

    with open(image_file, 'rb') as im_f:

        b_image_data = im_f.read()

```



%% Cell type:code id: tags:



``` python

n_lines = 1

line_length = header['FILE']['IMAGE']['LINE_SAMPLES'] * (header['FILE']['IMAGE']['SAMPLE_BITS']//8)

```



%% Cell type:code id: tags:



``` python

def read_crism_trdr(b_image_data, line_length, n_lines, n_bands):

    image_data = []

    for j in range(n_lines*n_bands):

        image_sample = np.frombuffer(b_image_data[j*line_length:(j+1)*line_length],

                                     dtype=np.float32, count=int(line_length/4))

        image_data.append(image_sample)

    return np.array(image_data)

```



%% Cell type:code id: tags:



``` python

#

n_output_bands = 107

n_bands = header['FILE']['IMAGE']['BANDS']

image_data = read_crism_trdr(b_image_data, line_length, n_lines, n_bands)

#cropped_image_data = image_data[np.where(np.arange(image_data.shape[0]) % n_bands < n_output_bands)]



cropped_image_data = image_data

```



%% Cell type:code id: tags:



``` python

plt.imshow(cropped_image_data)

```



%% Output



    <matplotlib.image.AxesImage at 0x2ab7ccf77f10>





%% Cell type:code id: tags:



``` python

image_fn, image_ext = os.path.splitext(image_file)

mini_image_fn = image_fn + '_cropped' + image_ext

mini_image_bn = os.path.basename(mini_image_fn)



# Overwrite the number of lines in the label

header['FILE']['IMAGE']['LINES'] = n_lines

header['FILE']['IMAGE']['BANDS'] = n_output_bands

header['FILE']['^IMAGE'] = mini_image_bn

header['FILE']['FILE_RECORDS'] = n_lines * n_output_bands + 1

header['FILE']['^ROWNUM_TABLE'][0] = mini_image_bn

header['FILE']['^ROWNUM_TABLE'][1] = n_lines * n_output_bands + 1

header['FILE']['ROWNUM_TABLE']['ROWS'] = n_output_bands

# Access the second instance of "FILE", which can't be accessed by name

header[-1][1]['TRDR_HK_TABLE'] = 0

header[-1][1]['^TRDR_HK_TABLE'] = 0

#header[-1][1]['FILE_RECORDS'] = n_lines

#header[-1][1]['TRDR_HK_TABLE']['ROWS'] = n_lines

```



%% Cell type:code id: tags:



``` python

class RealIsisCubeLabelEncoder(pvl.encoder.ISISEncoder):

    def encode_time(self, value):

        if value.microsecond:

            second = u'%02d.%06d' % (value.second, value.microsecond)

        else:

            second = u'%02d' % value.second



        time = u'%02d:%02d:%s' % (value.hour, value.minute, second)

        return time

```



%% Cell type:code id: tags:



``` python

label_fn, label_ext = os.path.splitext(crism_file)

out_label = label_fn + '_cropped' + label_ext



grammar = pvl.grammar.ISISGrammar()

grammar.comments+=(("#", "\n"), )

encoder = RealIsisCubeLabelEncoder()

encoder = pvl.encoder.ISISEncoder()

pvl.dump(header, out_label, encoder=encoder, grammar=grammar)

```



%% Output



    6596



%% Cell type:code id: tags:



``` python

with open(mini_image_fn, 'wb+') as f:

    b_reduced_image_data = cropped_image_data.tobytes()

    f.seek(0, 2)

    f.write(b_reduced_image_data)

```
 


%% Cell type:code id: tags:



``` python

```



%% Cell type:code id: tags:



``` python

header = pvl.load(out_label)

```



%% Cell type:code id: tags:



``` python

header

```



%% Output



    PVLModule([

      ('PDS_VERSION_ID', 'PDS3')

      ('LABEL_REVISION_NOTE',

       '2004-11-22, S. Slavney (GEO); 2005-12-20, H. Taylor (JHU/APL); 2006-04-05, '

       'S. Murchie (JHU/APL); 2006-09-18, P. Cavender (JHU/APL); 2007-02-19, P. '

       'Cavender (JHU/APL); Version 2, new stray light subtraction 2010-06-01, D. '

       'Humm (JHU/APL); Version 3, shutter mirror correction 2010-10-12, C. Hash '

       '(ACT); Version 3, Added data filter control parameters')

      ('DATA_SET_ID', 'MRO-M-CRISM-3-RDR-TARGETED-V1.0')

      ('PRODUCT_ID', 'FRT0001E5C3_07_IF124S_TRR3')

      ('INSTRUMENT_HOST_NAME', 'MARS RECONNAISSANCE ORBITER')

      ('SPACECRAFT_ID', 'MRO')

      ('INSTRUMENT_NAME', 'COMPACT RECONNAISSANCE IMAGING SPECTROMETER FOR MARS')

      ('INSTRUMENT_ID', 'CRISM')

      ('TARGET_NAME', 'MARS')

      ('PRODUCT_TYPE', 'TARGETED_RDR')

      ('PRODUCT_CREATION_TIME',

       datetime.datetime(2011, 6, 8, 10, 52, 30, tzinfo=datetime.timezone.utc))

      ('START_TIME',

       datetime.datetime(2011, 6, 2, 4, 3, 9, 29000, tzinfo=datetime.timezone.utc))

      ('STOP_TIME',

       datetime.datetime(2011, 6, 2, 4, 5, 0, 763000, tzinfo=datetime.timezone.utc))

      ('SPACECRAFT_CLOCK_START_COUNT', '10/0991454621.14521')

      ('SPACECRAFT_CLOCK_STOP_COUNT', '10/0991454732.62633')

      ('ORBIT_NUMBER', None)

      ('OBSERVATION_TYPE', 'FRT')

      ('OBSERVATION_ID', '16#0001E5C3#')

      ('MRO:OBSERVATION_NUMBER', 7)

      ('MRO:ACTIVITY_ID', 'IF124')

      ('MRO:SENSOR_ID', 'S')

      ('MRO:DETECTOR_TEMPERATURE', -53.663)

      ('MRO:OPTICAL_BENCH_TEMPERATURE', -42.348)

      ('MRO:SPECTROMETER_HOUSING_TEMP', -65.178)

      ('MRO:SPHERE_TEMPERATURE', -42.484)

      ('MRO:FPE_TEMPERATURE', 5.269)

      ('PRODUCT_VERSION_ID', '3')

      ('SOURCE_PRODUCT_ID',

       frozenset({'CDR400991452611_SP0042501S_3',

                  'CDR400991452639_BP0042500S_3',

                  'CDR400991452639_BP1018400S_3',

                  'CDR400991454611_BI1018400S_3',

                  'CDR400991454611_UB1018400S_3',

                  'CDR400991454737_BI1018400S_3',

                  'CDR400991454737_UB1018400S_3',

                  'CDR410000000000_SH0000001S_4',

                  'CDR410000000000_SS0000001S_2',

                  'CDR450924300802_DM0000000S_3',

                  'CDR450924300802_NU1000001S_3',

                  'CDR450924300802_SF0000000S_2',

                  'CDR450924300802_TD0000000S_2',

                  'CDR6_0_0991440032_ST_J_0',

                  'CDR6_1_0000000000_AS_S_0',

                  'CDR6_1_0000000000_DB_S_0',

                  'CDR6_1_0000000000_EB_S_0',

                  'CDR6_1_0000000000_GH_S_1',

                  'CDR6_1_0000000000_HD_J_1',

                  'CDR6_1_0000000000_HK_J_1',

                  'CDR6_1_0000000000_HV_J_1',

                  'CDR6_1_0000000000_LC_S_1',

                  'CDR6_1_0000000000_LI_J_0',

                  'CDR6_1_0000000000_VL_S_0',

                  'CDR6_2_0835294537_PP_S_0',

                  'FRT0001E5C3_07_SC124S_EDR0'}))

      ('MRO:INVALID_PIXEL_LOCATION', frozenset())

      ('PRODUCER_INSTITUTION_NAME',

       'JOHNS HOPKINS UNIVERSITY APPLIED PHYSICS LABORATORY')

      ('SOFTWARE_NAME', 'crism_imagecal')

      ('SOFTWARE_VERSION_ID', '2.5.3')

      ('TARGET_CENTER_DISTANCE', Quantity(value=None, units='KM'))

      ('SOLAR_DISTANCE', Quantity(value=213788591.232902, units='KM'))

      ('SOLAR_LONGITUDE', 303.590051)

      ('SHUTTER_MODE_ID', 'OPEN')

      ('LIGHT_SOURCE_NAME', 'NONE')

      ('MRO:CALIBRATION_LAMP_STATUS', 'OFF')

      ('MRO:CALIBRATION_LAMP_LEVEL', 'N/A')

      ('PIXEL_AVERAGING_WIDTH', 1)

      ('MRO:INSTRUMENT_POINTING_MODE', 'DYNAMIC POINTING')

      ('SCAN_MODE_ID', 'SHORT')

      ('MRO:FRAME_RATE', Quantity(value=3.75, units='HZ'))

      ('MRO:EXPOSURE_PARAMETER', 184)

      ('SAMPLING_MODE_ID', 'HYPERSPEC')

      ('COMPRESSION_TYPE', 'NONE')

      ('MRO:WAVELENGTH_FILTER', '0')

      ('MRO:WAVELENGTH_FILE_NAME', 'CDR450924300802_WA0000000S_2.IMG')

      ('MRO:PIXEL_PROC_FILE_NAME', 'CDR6_2_0835294537_PP_S_0.TAB')

      ('MRO:INV_LOOKUP_TABLE_FILE_NAME', 'CDR6_1_0000000000_LI_J_0.TAB')

      ('MRO:ATMO_CORRECTION_FLAG', 'OFF')

      ('MRO:THERMAL_CORRECTION_MODE', 'OFF')

      ('MRO:PHOTOCLIN_CORRECTION_FLAG', 'OFF')

      ('MRO:SPATIAL_RESAMPLING_FLAG', 'OFF')

      ('MRO:SPATIAL_RESAMPLING_FILE', 'N/A')

      ('MRO:SPATIAL_RESCALING_FLAG', 'OFF')

      ('MRO:SPATIAL_RESCALING_FILE', 'N/A')

      ('MRO:SPECTRAL_RESAMPLING_FLAG', 'OFF')

      ('MRO:SPECTRAL_RESAMPLING_FILE', 'N/A')

      ('MRO:HDF_SOFTWARE_NAME', 'crismhdf')

      ('MRO:HDF_SOFTWARE_VERSION_ID', '1.0.5')

      ('MRO:IF_MIN_VALUE', 0.0)

      ('MRO:IF_MAX_VALUE', 1.0)

      ('MRO:TRACE_MIN_VALUE', 0.01)

      ('MRO:TRACE_MAX_VALUE', 100.0)

      ('MRO:REFZ_MEDIAN_BOX_WIDTH', 15)

      ('MRO:REFZ_SMOOTH_BOX_WIDTH', 5)

      ('MRO:FRAM_STAT_MEDIAN_BOX_WIDTH', 5)

      ('MRO:FRAM_STAT_MIN_DEVIATION', 0.005)

      ('MRO:FRAM_STAT_MEDIAN_CONF_LVL', 0.999999)

      ('MRO:FRAM_STAT_IQR_CONF_LVL', 0.999999)

      ('MRO:RSC_REF_XY_MEDIAN_WIDTH', 15)

      ('MRO:RSC_REF_XY_SMOOTH_WIDTH', 5)

      ('MRO:RSC_REF_YZ_MEDIAN_WIDTH', 15)

      ('MRO:RSC_REF_YZ_SMOOTH_WIDTH', 5)

      ('MRO:RSC_RATIO_XY_MEDIAN_WIDTH', 25)

      ('MRO:RSC_RATIO_XY_SMOOTH_WIDTH', 13)

      ('MRO:RSC_RES_XY_PLY_ORDER', 5)

      ('MRO:RSC_RES_XY_PLY_EXTND_WIDTH', 38)

      ('MRO:LOG_XFORM_NEG_CLIP_VALUE', 'N/A')

      ('MRO:IKF_NUM_REGIONS', 'N/A')

      ('MRO:IKF_START_CHANNEL', ['N/A', 'N/A'])

      ('MRO:IKF_STOP_CHANNEL', ['N/A', 'N/A'])

      ('MRO:IKF_CONFIDENCE_LEVEL', ['N/A', 'N/A'])

      ('MRO:IKF_WEIGHTING_STDDEV', ['N/A', 'N/A'])

      ('MRO:IKF_KERNEL_SIZE_X', ['N/A', 'N/A'])

      ('MRO:IKF_KERNEL_SIZE_Y', ['N/A', 'N/A'])

      ('MRO:IKF_KERNEL_SIZE_Z', ['N/A', 'N/A'])

      ('MRO:IKF_MODEL_ORDER_X', ['N/A', 'N/A'])

      ('MRO:IKF_MODEL_ORDER_Y', ['N/A', 'N/A'])

      ('MRO:IKF_MODEL_ORDER_Z', ['N/A', 'N/A'])

      ('FILE',

       {'FILE_RECORDS': 108,

        'IMAGE': {'BANDS': 107,

                  'BAND_STORAGE_TYPE': 'LINE_INTERLEAVED',

                  'LINES': 1,

                  'LINE_SAMPLES': 640,

                  'SAMPLE_BITS': 32,

                  'SAMPLE_TYPE': 'PC_REAL',

                  'UNIT': 'I_OVER_F'},

        'RECORD_BYTES': 2560,

        'RECORD_TYPE': 'FIXED_LENGTH',

        'ROWNUM_TABLE': {'COLUMN': {'BIT_MASK': 511,

                                    'BYTES': 2,

                                    'COLUMN_NUMBER': 1,

                                    'DATA_TYPE': 'MSB_UNSIGNED_INTEGER',

                                    'DESCRIPTION': 'Detector row number from which '

                                                   'the data was taken.',

                                    'NAME': 'DETECTOR_ROW_NUMBER',

                                    'START_BYTE': 1},

                         'COLUMNS': 1,

                         'DESCRIPTION': 'The detector is subsampled in the spectral '

                                        'direction by selecting specific rows to be '

                                        'downlinked. This table provides a list of '

                                        'the rows selected for all frames in this '

                                        'multidimensional image cube.',

                         'INTERCHANGE_FORMAT': 'BINARY',

                         'NAME': 'SELECTED ROWS FROM DETECTOR',

                         'ROWS': 107,

                         'ROW_BYTES': 2},

        '^IMAGE': 'frt0001e5c3_07_if124s_trr3_cropped.img',

        '^ROWNUM_TABLE': ['frt0001e5c3_07_if124s_trr3_cropped.img', 108]})

      ('FILE',

       {'FILE_RECORDS': 420,

        'RECORD_BYTES': 1221,

        'RECORD_TYPE': 'FIXED_LENGTH',

        'TRDR_HK_TABLE': 0,

        '^TRDR_HK_TABLE': 0})

    ])



%% Cell type:code id: tags:



``` python

```

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