Added themis notebook to crop themis images (#4204)

%% Cell type:code id: tags:

``` python

import os.path

import datetime

import pvl

import numpy as np

import matplotlib.pyplot as plt

```

%% Cell type:code id: tags:

``` python

themis_file = '/Path/to/themis/raw_data.QUB'

image_file = themis_file

```

%% Cell type:code id: tags:

``` python

header = pvl.load(image_file)

header

```

%% Cell type:code id: tags:

``` python

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

    # -1 offset obtained from ISIS, record offset likely one based

    # so subtract one as we need it to be zero based

    image_offset = int((header['^SPECTRAL_QUBE'] - 1) * header['RECORD_BYTES'])

    f.seek(image_offset)

    b_image_data = f.read()

```

%% Cell type:code id: tags:

``` python

n_bands = header['SPECTRAL_QUBE']['CORE_ITEMS'][header['SPECTRAL_QUBE']['AXIS_NAME'].index('BAND')]

# n_bands = 5

n_lines = header['SPECTRAL_QUBE']['CORE_ITEMS'][header['SPECTRAL_QUBE']['AXIS_NAME'].index('LINE')]

n_lines = 10

if 'LINE_SUFFIX_ITEM_BYTES' in header['SPECTRAL_QUBE'].keys():

    n_lines += 2

line_length = header['RECORD_BYTES']

# Add line suffix offset to handle reading two extra lines from each band

if 'LINE_SUFFIX_ITEM_BYTES' in header['SPECTRAL_QUBE'].keys():

    bytes_per_band = ((header['SPECTRAL_QUBE']['CORE_ITEMS'][header['SPECTRAL_QUBE']['AXIS_NAME'].index('LINE')]) + header['SPECTRAL_QUBE']['LINE_SUFFIX_ITEM_BYTES']) * line_length

else:

    bytes_per_band = (header['SPECTRAL_QUBE']['CORE_ITEMS'][1]) * line_length

```

%% Cell type:code id: tags:

``` python

image_data = []

# Custom numpy data type to handle appropriate DN conversion

# Not necessary but was done for debugging purposes

dt = np.dtype(np.int16)

dt = dt.newbyteorder('>')

for i in range(n_bands):

#     image_data.append([])

    for j in range(n_lines):

        start = (j*line_length) + (bytes_per_band * i)

        stop = ((j+1)*line_length) + (bytes_per_band * i)

        image_sample = np.frombuffer(b_image_data[start:stop], dtype=dt, count=line_length//2)

        image_data.append(image_sample)

image_data = np.array(image_data, dtype=dt)

```

%% Cell type:code id: tags:

``` python

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

plt.imshow(image_data)

plt.show()

```

%% 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

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

crop = '_cropped'

themis_image_fn = image_fn + crop + image_ext

themis_image_bn = os.path.basename(themis_image_fn)

grammar = pvl.grammar.ISISGrammar()

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

encoder = RealIsisCubeLabelEncoder()

if header['SPECTRAL_QUBE']['DESCRIPTION'] == '':

    header['SPECTRAL_QUBE']['DESCRIPTION'] = " "

# Overwrite the number of lines in the label

if 'LINE_SUFFIX_ITEM_BYTES' in header['SPECTRAL_QUBE'].keys():

    n_lines -= 2

header['SPECTRAL_QUBE']['CORE_ITEMS'][header['SPECTRAL_QUBE']['AXIS_NAME'].index('LINE')] = n_lines

# Calculate the new offset

# Run this twice as the change to the header will change the headers length.

# Then add two to handle an extra new line character later on

header['^SPECTRAL_QUBE'] = pvl.collections.Units(len(pvl.dumps(header, encoder=encoder, grammar=grammar)), 'BYTES')

header['^SPECTRAL_QUBE'] = pvl.collections.Units(len(pvl.dumps(header, encoder=encoder, grammar=grammar)) + 2, 'BYTES')

```

%% Cell type:code id: tags:

``` python

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

out_label = label_fn + crop + label_ext

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

```

%% Cell type:code id: tags:

``` python

with open(themis_image_fn, 'ab+') as f:

    b_reduced_image_data = image_data.tobytes()

    f.seek(0, 2)

    f.write(b'\n')

    f.write(b_reduced_image_data)

```

%% Cell type:code id: tags:

``` python

new_header = pvl.load(out_label)

new_header

```

%% Cell type:code id: tags:

``` python

```