jupyter_tutorials/jupyter_tutorials_tutorial_CPM_multiWavelength.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "370de90d",
   "metadata": {},
   "source": [
    "# multiWavelength ptychography\n",
    " - This tutorial shows a reconstruction with a multiwavelength dataset measusred with a mouse brain sample, which is used in the publication: \"L. Loetgering, X. Liu, A. C. C. De Beurs, M. Du, G. Kuijper, K. S. E. Eikema, and S. Witte, “Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography,” Optica 8, 130 (2021)\".\n",
    " - Download the dataset from figshare: https://figshare.com/articles/dataset/Brain_smoothBeam_poly_bin8_hdf5/19107068\n",
    " - A kind suggestion: check out general tutorials for CPM (conventional ptychographic microscopy) before diving into this one."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "5030d712",
   "metadata": {},
   "outputs": [],
   "source": [
    "# %matplotlib notebook\n",
    "%matplotlib qt\n",
    "import matplotlib\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "from pathlib import Path\n",
    "import h5py"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "8b61d2da",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\ProgramData\\Anaconda3\\lib\\site-packages\\cupy\\_environment.py:213: UserWarning: CUDA path could not be detected. Set CUDA_PATH environment variable if CuPy fails to load.\n",
      "  warnings.warn(\n"
     ]
    }
   ],
   "source": [
    "# import the fracPy module\n",
    "import PtyLab\n",
    "from PtyLab import ExperimentalData\n",
    "from PtyLab import Reconstruction\n",
    "from PtyLab import Monitor\n",
    "from PtyLab import Params\n",
    "from PtyLab import Engines"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "113f3499",
   "metadata": {},
   "outputs": [],
   "source": [
    "from PtyLab.utils.visualisation import hsvplot, hsvmodeplot, absplot, absmodeplot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "f3398ba3",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Step 1: Download the preprocessed data from surfdrive (https://figshare.com/articles/dataset/Brain_smoothBeam_poly_bin8_hdf5/19107068)\n",
    "\n",
    "# set your data folder as fileFolder \n",
    "fileFolder = Path(r\"D:\\Du\\FigshareData\")\n",
    "# select the hdf5 file\n",
    "fileName = \"Brain_smoothBeam_poly_bin8.hdf5\"\n",
    "# create the complete filePath\n",
    "filePath = Path.joinpath(fileFolder,fileName)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "52251565",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\"Unable to open object (object 'orientation' doesn't exist)\"\n"
     ]
    }
   ],
   "source": [
    "# Step 2: Initialize the ExperimentalData class \n",
    "\n",
    "# Initialize the ExperimentalData using the filePath, and choose the operation Mode (default is 'CPM')\n",
    "experimentalData = ExperimentalData(filePath, operationMode='CPM')\n",
    "backgroundOffset = 10\n",
    "experimentalData.entrancePupilDiameter = 0.2e-3\n",
    "from PtyLab.utils.utils import posit\n",
    "experimentalData.ptychogram = posit(experimentalData.ptychogram-backgroundOffset)\n",
    "# show measured ptychogram in log scale. Need to close the window to continue\n",
    "# experimentalData.showPtychogram()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "371b80ef",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Set monitor properties\n",
    "monitor = Monitor()\n",
    "monitor.figureUpdateFrequency = 1\n",
    "monitor.objectPlot = 'angle'  # complex abs angle\n",
    "monitor.verboseLevel = 'high'  # high: plot two figures, low: plot only one figure\n",
    "monitor.probeZoom = 1  # control probe plot FoV\n",
    "monitor.objectZoom = 1   # control object plot FoV\n",
    "monitor.objectPlotContrast = 8\n",
    "monitor.probePlotContrast = 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "7dd91c14",
   "metadata": {},
   "outputs": [],
   "source": [
    "params = Params()\n",
    "params.gpuSwitch = True\n",
    "params.positionOrder = 'random'  # 'sequential' or 'random'\n",
    "params.propagatorType = 'Fraunhofer'  # Fraunhofer Fresnel ASP scaledASP polychromeASP scaledPolychromeASP\n",
    "params.probePowerCorrectionSwitch = False\n",
    "params.modulusEnforcedProbeSwitch = True\n",
    "params.comStabilizationSwitch = True\n",
    "params.orthogonalizationSwitch = True\n",
    "params.orthogonalizationFrequency = 5\n",
    "params.intensityConstraint = 'standard'  # standard fluctuation exponential poission\n",
    "params.couplingObjectSwitch = True\n",
    "params.couplingObjectAleph = 0.5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "309376a0",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Copying attribute wavelength\n",
      "Copying attribute dxd\n",
      "Copying attribute theta\n",
      "Copying attribute spectralDensity\n",
      "Copying attribute entrancePupilDiameter\n"
     ]
    }
   ],
   "source": [
    "# now, all our experimental data is loaded into experimental_data and we don't have to worry about it anymore.\n",
    "# now create an object to hold everything we're eventually interested in\n",
    "reconstruction = Reconstruction(experimentalData, params)\n",
    "reconstruction.No = 2**10\n",
    "reconstruction.nlambdaObject = 1\n",
    "reconstruction.nlambdaProbe = len(reconstruction.spectralDensity)\n",
    "\n",
    "# initialize probe and object and related params\n",
    "reconstruction.initialProbe = 'circ'\n",
    "reconstruction.initialObject = 'ones'\n",
    "reconstruction.initializeObjectProbe()\n",
    "\n",
    "# # customize initial probe quadratic phase\n",
    "reconstruction.probe = reconstruction.probe*np.exp(1.j*2*np.pi/reconstruction.wavelength *\n",
    "                                             (reconstruction.Xp**2+reconstruction.Yp**2)/(1*2e-2))\n",
    "\n",
    "hsvmodeplot(np.squeeze(reconstruction.probe), pixelSize = reconstruction.dxp, axisUnit = 'mm')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "911f11ce",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                                                                                                                       \n",
      "iteration: 0                                                                                                           \n",
      "error: 19.4                                                                                                            \n",
      "estimated linear overlap: 60.9 %                                                                                       \n",
      "estimated area overlap: 76.5 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 1                                                                                                           \n",
      "error: 19.4                                                                                                            \n",
      "estimated linear overlap: 60.8 %                                                                                       \n",
      "estimated area overlap: 76.3 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 2                                                                                                           \n",
      "error: 19.1                                                                                                            \n",
      "estimated linear overlap: 60.7 %                                                                                       \n",
      "estimated area overlap: 76.2 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 3                                                                                                           \n",
      "error: 19.0                                                                                                            \n",
      "estimated linear overlap: 60.7 %                                                                                       \n",
      "estimated area overlap: 75.9 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 4                                                                                                           \n",
      "error: 19.1                                                                                                            \n",
      "estimated linear overlap: 60.6 %                                                                                       \n",
      "estimated area overlap: 75.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 5                                                                                                           \n",
      "error: 18.8                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 75.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 6                                                                                                           \n",
      "error: 19.0                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 75.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 7                                                                                                           \n",
      "error: 19.0                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 75.5 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 8                                                                                                           \n",
      "error: 19.1                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 75.1 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 9                                                                                                           \n",
      "error: 18.9                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 75.2 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 10                                                                                                          \n",
      "error: 19.0                                                                                                            \n",
      "estimated linear overlap: 60.6 %                                                                                       \n",
      "estimated area overlap: 74.8 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 11                                                                                                          \n",
      "error: 19.0                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 74.7 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 12                                                                                                          \n",
      "error: 19.1                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 74.8 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 13                                                                                                          \n",
      "error: 19.3                                                                                                            \n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 74.8 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 14                                                                                                          \n",
      "error: 19.2                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 75.0 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 15                                                                                                          \n",
      "error: 19.3                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 74.7 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 16                                                                                                          \n",
      "error: 19.3                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 74.8 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 17                                                                                                          \n",
      "error: 19.3                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 74.7 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 18                                                                                                          \n",
      "error: 19.4                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 74.5 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 19                                                                                                          \n",
      "error: 19.4                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 74.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 20                                                                                                          \n",
      "error: 19.5                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 74.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 21                                                                                                          \n",
      "error: 19.7                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 74.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 22                                                                                                          \n",
      "error: 19.7                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 74.8 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 23                                                                                                          \n",
      "error: 19.7                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 74.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 24                                                                                                          \n",
      "error: 19.8                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 74.3 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 25                                                                                                          \n",
      "error: 19.8                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 73.9 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 26                                                                                                          \n",
      "error: 19.7                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 74.3 %                                                                                         \n",
      "                                                                                                                       \n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "iteration: 27                                                                                                          \n",
      "error: 19.7                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 74.2 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 28                                                                                                          \n",
      "error: 19.7                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 73.7 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 29                                                                                                          \n",
      "error: 20.1                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 73.9 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 30                                                                                                          \n",
      "error: 20.0                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 79.5 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 31                                                                                                          \n",
      "error: 20.0                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 79.5 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 32                                                                                                          \n",
      "error: 20.2                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 79.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 33                                                                                                          \n",
      "error: 20.2                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 79.5 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 34                                                                                                          \n",
      "error: 20.2                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 79.8 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 35                                                                                                          \n",
      "error: 20.4                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 79.5 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 36                                                                                                          \n",
      "error: 20.2                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 79.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 37                                                                                                          \n",
      "error: 20.4                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 79.3 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 38                                                                                                          \n",
      "error: 20.3                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 79.2 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 39                                                                                                          \n",
      "error: 20.5                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 79.1 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 40                                                                                                          \n",
      "error: 20.6                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "estimated area overlap: 79.6 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 41                                                                                                          \n",
      "error: 20.7                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 79.2 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 42                                                                                                          \n",
      "error: 20.7                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 79.1 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 43                                                                                                          \n",
      "error: 20.9                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 79.1 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 44                                                                                                          \n",
      "error: 20.8                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 79.0 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 45                                                                                                          \n",
      "error: 20.8                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.5 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 46                                                                                                          \n",
      "error: 21.0                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.8 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 47                                                                                                          \n",
      "error: 21.0                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 79.0 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 48                                                                                                          \n",
      "error: 21.1                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.5 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 49                                                                                                          \n",
      "error: 21.1                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.9 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 50                                                                                                          \n",
      "error: 21.0                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.5 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 51                                                                                                          \n",
      "error: 21.1                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 78.9 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 52                                                                                                          \n",
      "error: 21.2                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 78.7 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 53                                                                                                          \n",
      "error: 21.0                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.5 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 54                                                                                                          \n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "error: 21.3                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.6 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 55                                                                                                          \n",
      "error: 21.4                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.3 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 56                                                                                                          \n",
      "error: 21.3                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.1 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 57                                                                                                          \n",
      "error: 21.5                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 78.5 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 58                                                                                                          \n",
      "error: 21.5                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 78.1 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 59                                                                                                          \n",
      "error: 21.5                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.7 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 60                                                                                                          \n",
      "error: 21.7                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.1 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 61                                                                                                          \n",
      "error: 21.6                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.2 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 62                                                                                                          \n",
      "error: 21.6                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 77.8 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 63                                                                                                          \n",
      "error: 21.6                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.1 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 64                                                                                                          \n",
      "error: 21.4                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 77.8 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 65                                                                                                          \n",
      "error: 21.7                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 77.9 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 66                                                                                                          \n",
      "error: 22.1                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 77.8 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 67                                                                                                          \n",
      "error: 21.8                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 77.8 %                                                                                         \n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                                                                                                                       \n",
      "iteration: 68                                                                                                          \n",
      "error: 21.8                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 77.3 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 69                                                                                                          \n",
      "error: 21.9                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 77.9 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 70                                                                                                          \n",
      "error: 21.9                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 77.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 71                                                                                                          \n",
      "error: 21.7                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 77.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 72                                                                                                          \n",
      "error: 22.1                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 77.3 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 73                                                                                                          \n",
      "error: 22.1                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 77.3 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 74                                                                                                          \n",
      "error: 22.1                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 77.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 75                                                                                                          \n",
      "error: 22.4                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 77.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 76                                                                                                          \n",
      "error: 22.2                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 77.2 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 77                                                                                                          \n",
      "error: 22.1                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 77.3 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 78                                                                                                          \n",
      "error: 22.4                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 77.2 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 79                                                                                                          \n",
      "error: 22.5                                                                                                            \n",
      "estimated linear overlap: 60.3 %                                                                                       \n",
      "estimated area overlap: 77.0 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 80                                                                                                          \n",
      "error: 22.2                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 76.8 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 81                                                                                                          \n",
      "error: 22.2                                                                                                            \n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 79.3 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 82                                                                                                          \n",
      "error: 22.4                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 79.5 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 83                                                                                                          \n",
      "error: 22.4                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 79.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 84                                                                                                          \n",
      "error: 22.4                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 79.2 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 85                                                                                                          \n",
      "error: 22.5                                                                                                            \n",
      "estimated linear overlap: 60.3 %                                                                                       \n",
      "estimated area overlap: 79.5 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 86                                                                                                          \n",
      "error: 22.5                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 79.4 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 87                                                                                                          \n",
      "error: 22.5                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 79.1 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 88                                                                                                          \n",
      "error: 22.7                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 78.9 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 89                                                                                                          \n",
      "error: 22.7                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 79.1 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 90                                                                                                          \n",
      "error: 22.6                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.9 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 91                                                                                                          \n",
      "error: 22.6                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 79.2 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 92                                                                                                          \n",
      "error: 22.7                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.9 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 93                                                                                                          \n",
      "error: 22.8                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 79.1 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 94                                                                                                          \n",
      "error: 22.8                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 78.9 %                                                                                         \n",
      "                                                                                                                       \n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "iteration: 95                                                                                                          \n",
      "error: 22.7                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.9 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 96                                                                                                          \n",
      "error: 23.0                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 79.2 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 97                                                                                                          \n",
      "error: 22.9                                                                                                            \n",
      "estimated linear overlap: 60.5 %                                                                                       \n",
      "estimated area overlap: 78.9 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 98                                                                                                          \n",
      "error: 22.9                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.6 %                                                                                         \n",
      "                                                                                                                       \n",
      "iteration: 99                                                                                                          \n",
      "error: 22.9                                                                                                            \n",
      "estimated linear overlap: 60.4 %                                                                                       \n",
      "estimated area overlap: 78.4 %                                                                                         \n",
      "multiPIE: 100%|██████████████████████████████████████████████████████████████████████| 100/100 [03:36<00:00,  2.17s/it]\n"
     ]
    }
   ],
   "source": [
    "# Run the reconstruction\n",
    "## choose engine\n",
    "# mPIE\n",
    "multiPIE = Engines.multiPIE(reconstruction, experimentalData, params, monitor)\n",
    "multiPIE.numIterations = 100\n",
    "multiPIE.betaProbe = 0.25\n",
    "multiPIE.betaObject = 0.25\n",
    "multiPIE.reconstruct()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "id": "cfed4f32",
   "metadata": {},
   "outputs": [],
   "source": [
    "# now save the data\n",
    "# reconstruction.saveResults('reconstruction.hdf5')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c0120b14",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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