EXP: Load large 4D cube

example_notebooks/cube_4d.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Reading a 4D Data Cube with Astrowidgets\n",
+    "\n",
+    "This is an example of reading a four dimensional data cube using Astrowidgets."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from astropy.nddata import NDData\n",
+    "from astropy.wcs import WCS\n",
+    "from ginga.misc.log import get_logger\n",
+    "from matplotlib import pyplot as plt\n",
+    "\n",
+    "import ipywidgets as ipyw\n",
+    "from IPython.display import display, clear_output\n",
+    "\n",
+    "from astrowidgets import ImageWidget\n",
+    "\n",
+    "%matplotlib inline\n",
+    "\n",
+    "# To prevent automatic figure display when execution of the cell ends\n",
+    "# https://github.com/jupyter-widgets/ipywidgets/issues/1940\n",
+    "%config InlineBackend.close_figures=False \n",
+    "\n",
+    "plt.ioff()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Subclass `ImageWidget` to implement cube-specific behavior."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "class CubeWidget(ImageWidget):\n",
+    "    def __init__(self, *args, **kwargs):\n",
+    "        super().__init__(*args, **kwargs)\n",
+    "        self._4d_idx = 0  # Lock 4th dim to this for now\n",
+    "        self.line_out = ipyw.Output()\n",
+    "        self.line_plot = None\n",
+    "\n",
+    "    def load_nddata(self, nddata, naxispath=None):\n",
+    "        from ginga.AstroImage import AstroImage\n",
+    "        image = AstroImage()\n",
+    "        image.load_nddata(nddata, naxispath=[0, self._4d_idx])\n",
+    "        self._viewer.set_image(image)\n",
+    "        \n",
+    "    def _mouse_click_cb(self, viewer, event, data_x, data_y):\n",
+    "        super()._mouse_click_cb(viewer, event, data_x, data_y)\n",
+    "        \n",
+    "        # Plot line profile\n",
+    "        image = self._viewer.get_image()\n",
+    "        if image is not None and self.line_plot is not None:\n",
+    "            mddata = image.get_mddata()\n",
+    "            ix = int(round(data_x))\n",
+    "            iy = int(round(data_y))\n",
+    "            with self.line_out:\n",
+    "                self.line_plot.clear()\n",
+    "                self.line_plot.plot(mddata[self._4d_idx, :, iy, ix])\n",
+    "                clear_output(wait=True)\n",
+    "                display(self.line_plot.figure)\n",
+    "\n",
+    "    def show_slice(self, n):\n",
+    "        image = self._viewer.get_image()\n",
+    "        image.set_naxispath([n, self._4d_idx])\n",
+    "        self._viewer.redraw(whence=0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "logger = get_logger('my viewer', log_stderr=True, log_file=None, level=30)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "w = CubeWidget(logger=logger)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Generate a fake 4D data cube."
+   ]
+  },
+  {
+   "cell_type": "raw",
+   "metadata": {},
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "pf = None  # Not using FITS file pointer\n",
+    "cube4d = np.random.random((2, 5, 100, 200))\n",
+    "n_3d = cube4d.shape[1]\n",
+    "\n",
+    "# Convert to NDData.\n",
+    "im = NDData(cube4d, wcs=WCS(naxis=4))\n",
+    "\n",
+    "# Loading a fake WCS into widget sometimes gives error. Try reload before giving up.\n",
+    "w.load_nddata(im)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**--- OR ---**\n",
+    "\n",
+    "Load an existing data cube."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import dask.array as da\n",
+    "from astropy.io import fits\n",
+    "\n",
+    "# This is a larger-than-memory cube that is 43GB.\n",
+    "filename = '/redkeep/dungeons/tess_big_cubes/tess-s0001-1-1-cube.fits'\n",
+    "pf = fits.open(filename, memmap=True)\n",
+    "im = da.from_array(pf[1].data, name='mytesscube')\n",
+    "im = im.T  # TESS cube is transposed by ASB\n",
+    "# Shape now is (2, 1282, 2136, 2078)\n",
+    "n_3d = im.shape[1]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# This needs https://github.com/ejeschke/ginga/pull/805\n",
+    "# TODO: Why is it taking so long?\n",
+    "w.load_array(im)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Create a slider for third dimension."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def show_slice(n):\n",
+    "    w.show_slice(n - 1)\n",
+    "\n",
+    "slider = ipyw.interactive(\n",
+    "    show_slice,\n",
+    "    n=ipyw.IntSlider(min=1, max=n_3d, step=1, value=0, continuous_update=False))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Set up the plot and hook to widget."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Semicolon to avoid plot showing here.\n",
+    "# If plot shows, rerun cell to hide it.\n",
+    "ax = plt.gca();\n",
+    "\n",
+    "w.line_plot = ax"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Display the widgets."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "display(ipyw.HBox([ipyw.VBox([slider, w]), w.line_out]))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Close the file pointer, if open."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "if pf is not None:\n",
+    "    pf.close()"
+   ]
+  }
+ ],
+ "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": "3.7.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}