Added themis notebook to crop themis images (#4204)

isis/notebooks/crop_themis.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os.path\n",
+    "import datetime\n",
+    "\n",
+    "import pvl\n",
+    "import numpy as np\n",
+    "\n",
+    "import matplotlib.pyplot as plt"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "themis_file = '/Path/to/themis/raw_data.QUB'\n",
+    "image_file = themis_file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "header = pvl.load(image_file)\n",
+    "header"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with open(image_file, 'rb') as f:\n",
+    "    # -1 offset obtained from ISIS, record offset likely one based \n",
+    "    # so subtract one as we need it to be zero based\n",
+    "    image_offset = int((header['^SPECTRAL_QUBE'] - 1) * header['RECORD_BYTES'])\n",
+    "\n",
+    "    f.seek(image_offset)\n",
+    "    b_image_data = f.read()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "n_bands = header['SPECTRAL_QUBE']['CORE_ITEMS'][header['SPECTRAL_QUBE']['AXIS_NAME'].index('BAND')]\n",
+    "# n_bands = 5\n",
+    "n_lines = header['SPECTRAL_QUBE']['CORE_ITEMS'][header['SPECTRAL_QUBE']['AXIS_NAME'].index('LINE')]\n",
+    "n_lines = 10\n",
+    "\n",
+    "if 'LINE_SUFFIX_ITEM_BYTES' in header['SPECTRAL_QUBE'].keys():\n",
+    "    n_lines += 2\n",
+    "        \n",
+    "line_length = header['RECORD_BYTES']\n",
+    "# Add line suffix offset to handle reading two extra lines from each band\n",
+    "if 'LINE_SUFFIX_ITEM_BYTES' in header['SPECTRAL_QUBE'].keys():\n",
+    "    bytes_per_band = ((header['SPECTRAL_QUBE']['CORE_ITEMS'][header['SPECTRAL_QUBE']['AXIS_NAME'].index('LINE')]) + header['SPECTRAL_QUBE']['LINE_SUFFIX_ITEM_BYTES']) * line_length\n",
+    "else:\n",
+    "    bytes_per_band = (header['SPECTRAL_QUBE']['CORE_ITEMS'][1]) * line_length\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "image_data = []\n",
+    "# Custom numpy data type to handle appropriate DN conversion\n",
+    "# Not necessary but was done for debugging purposes\n",
+    "dt = np.dtype(np.int16)\n",
+    "dt = dt.newbyteorder('>')\n",
+    "\n",
+    "for i in range(n_bands):\n",
+    "#     image_data.append([])\n",
+    "    for j in range(n_lines):\n",
+    "        start = (j*line_length) + (bytes_per_band * i)\n",
+    "        stop = ((j+1)*line_length) + (bytes_per_band * i)\n",
+    "        image_sample = np.frombuffer(b_image_data[start:stop], dtype=dt, count=line_length//2)\n",
+    "        image_data.append(image_sample)\n",
+    "image_data = np.array(image_data, dtype=dt)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plt.figure(0, figsize=(20, 20))\n",
+    "plt.imshow(image_data)\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "class RealIsisCubeLabelEncoder(pvl.encoder.ISISEncoder):    \n",
+    "    def encode_time(self, value):\n",
+    "        if value.microsecond:\n",
+    "            second = u'%02d.%06d' % (value.second, value.microsecond)\n",
+    "        else:\n",
+    "            second = u'%02d' % value.second\n",
+    "\n",
+    "        time = u'%02d:%02d:%s' % (value.hour, value.minute, second)\n",
+    "        return time"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "image_fn, image_ext = os.path.splitext(image_file)\n",
+    "crop = '_cropped'\n",
+    "themis_image_fn = image_fn + crop + image_ext\n",
+    "themis_image_bn = os.path.basename(themis_image_fn)\n",
+    "\n",
+    "grammar = pvl.grammar.ISISGrammar()\n",
+    "grammar.comments+=((\"#\", \"\\n\"), )\n",
+    "encoder = RealIsisCubeLabelEncoder()\n",
+    "\n",
+    "if header['SPECTRAL_QUBE']['DESCRIPTION'] == '':\n",
+    "    header['SPECTRAL_QUBE']['DESCRIPTION'] = \" \"\n",
+    "\n",
+    "# Overwrite the number of lines in the label\n",
+    "if 'LINE_SUFFIX_ITEM_BYTES' in header['SPECTRAL_QUBE'].keys():\n",
+    "    n_lines -= 2\n",
+    "header['SPECTRAL_QUBE']['CORE_ITEMS'][header['SPECTRAL_QUBE']['AXIS_NAME'].index('LINE')] = n_lines\n",
+    "\n",
+    "# Calculate the new offset\n",
+    "# Run this twice as the change to the header will change the headers length.\n",
+    "# Then add two to handle an extra new line character later on\n",
+    "header['^SPECTRAL_QUBE'] = pvl.collections.Units(len(pvl.dumps(header, encoder=encoder, grammar=grammar)), 'BYTES')\n",
+    "header['^SPECTRAL_QUBE'] = pvl.collections.Units(len(pvl.dumps(header, encoder=encoder, grammar=grammar)) + 2, 'BYTES')\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "label_fn, label_ext = os.path.splitext(themis_file)\n",
+    "out_label = label_fn + crop + label_ext\n",
+    "\n",
+    "pvl.dump(header, out_label, encoder=encoder, grammar=grammar)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with open(themis_image_fn, 'ab+') as f:\n",
+    "    b_reduced_image_data = image_data.tobytes()\n",
+    "    f.seek(0, 2)\n",
+    "    f.write(b'\\n')\n",
+    "    f.write(b_reduced_image_data)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "new_header = pvl.load(out_label)\n",
+    "new_header"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}