{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import tomopy\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "rec = dict()  # Store all of the different reconstructions here"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Data import\n",
    "\n",
    "Common tomography data formats are imported through [DXchange](http://dxchange.readthedocs.org/en/latest/source/api/dxchange.exchange.html) (available through Conda):\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import dxchange as dx"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "prj, flat, dark, ang = dx.read_aps_32id('data/data-simulated.h5')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "rec = dict()\n",
    "rec['before'] = tomopy.recon(prj, ang, algorithm='gridrec', num_gridx=128, num_gridy=128)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Poisson noise and zinger removal"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "z = 1  # slice that has the poisson noise\n",
    "prj_corrected = tomopy.median_filter(prj, axis=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "z = 1\n",
    "plt.figure(dpi=150)\n",
    "plt.subplot(1, 2, 1)\n",
    "plt.title('before')\n",
    "plt.imshow(prj[:, z, :])\n",
    "plt.subplot(1, 2, 2)\n",
    "plt.title('after')\n",
    "plt.imshow(prj_corrected[:, z, :])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "rec['after'] = tomopy.recon(prj_corrected, ang, algorithm='gridrec', num_gridx=128, num_gridy=128)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plt.figure(dpi=150)\n",
    "plt.subplot(1, 2, 1)\n",
    "plt.title('before')\n",
    "plt.imshow(rec['before'][z], vmin=0, vmax=255)\n",
    "plt.subplot(1, 2, 2)\n",
    "plt.title('after')\n",
    "plt.imshow(rec['after'][z], vmin=0, vmax=255)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "z = 2  # slice that has the zingers"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plt.figure(dpi=150)\n",
    "plt.subplot(1, 2, 1)\n",
    "plt.title('before')\n",
    "plt.imshow(prj[:, z, :])\n",
    "plt.subplot(1, 2, 2)\n",
    "plt.title('after')\n",
    "plt.imshow(prj_corrected[:, z, :])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plt.figure(dpi=150)\n",
    "plt.subplot(1, 2, 1)\n",
    "plt.title('before')\n",
    "plt.imshow(rec['before'][z], vmin=0, vmax=255)\n",
    "plt.subplot(1, 2, 2)\n",
    "plt.title('after')\n",
    "plt.imshow(rec['after'][z], vmin=0, vmax=255)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Ring Removal"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "z = 3  # slice that has the rings\n",
    "prj_corrected = tomopy.remove_stripe_based_filtering(prj)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plt.figure(dpi=150)\n",
    "plt.subplot(1, 2, 1)\n",
    "plt.title('before')\n",
    "plt.imshow(prj[:, z, :])\n",
    "plt.subplot(1, 2, 2)\n",
    "plt.title('after')\n",
    "plt.imshow(prj_corrected[:, z, :])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "rec['after'] = tomopy.recon(prj_corrected, ang, algorithm='gridrec', num_gridx=128, num_gridy=128)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plt.figure(dpi=150)\n",
    "plt.subplot(1, 2, 1)\n",
    "plt.title('before')\n",
    "plt.imshow(rec['before'][z], vmin=0, vmax=255)\n",
    "plt.subplot(1, 2, 2)\n",
    "plt.title('after')\n",
    "plt.imshow(rec['after'][z], vmin=0, vmax=255)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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