python/examples/notebooks/experimenting with real_domain option.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "from flowdec.nb import utils as nbutils \n",
    "from flowdec import data as fd_data\n",
    "from scipy import ndimage\n",
    "import tensorflow as tf\n",
    "from flowdec.restoration import RichardsonLucyDeconvolver"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "def create_data_and_kernel(shape):\n",
    "    data=np.random.uniform(size=shape).astype(np.float32)\n",
    "    # create a gaussian kernel\n",
    "    kernel = np.zeros_like(data)\n",
    "    for offset in [0, 1]:\n",
    "        kernel[tuple((np.array(kernel.shape) - offset) // 2)] = 1\n",
    "    kernel = ndimage.gaussian_filter(kernel, sigma=1.)\n",
    "    return data, kernel"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Test real domain vs complex FFT with different shapes"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# all dimensions have at least one factor of 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "shape = (2*2*5,2*5, 2*5*3)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### real domain"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "algo = RichardsonLucyDeconvolver(3, pad_mode=\"None\", real_domain_fft=True)\n",
    "data, kernel = create_data_and_kernel(shape)\n",
    "tmp = algo.initialize().run(fd_data.Acquisition(data=data, kernel=kernel), niter=3, session_config=tf.ConfigProto(device_count={'GPU': 0}))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### complex domain"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "algo = RichardsonLucyDeconvolver(3, pad_mode=\"None\", real_domain_fft=False)\n",
    "data, kernel = create_data_and_kernel(shape)\n",
    "tmp = algo.initialize().run(fd_data.Acquisition(data=data, kernel=kernel), niter=3, session_config=tf.ConfigProto(device_count={'GPU': 0}))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# one dimension does not have a factor of 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "shape = (2*2*5,2*5, 5*3*3)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### real domain"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "ename": "InvalidArgumentError",
     "evalue": "Incompatible shapes: [20,10,45] vs. [20,10,44]\n\t [[Node: while/truediv = RealDiv[T=DT_FLOAT, _device=\"/job:localhost/replica:0/task:0/device:CPU:0\"](while/zeros_like/Enter, while/irfft3d)]]\n\nCaused by op 'while/truediv', defined at:\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\runpy.py\", line 193, in _run_module_as_main\n    \"__main__\", mod_spec)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\runpy.py\", line 85, in _run_code\n    exec(code, run_globals)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\ipykernel_launcher.py\", line 16, in <module>\n    app.launch_new_instance()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\traitlets\\config\\application.py\", line 658, in launch_instance\n    app.start()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\ipykernel\\kernelapp.py\", line 497, in start\n    self.io_loop.start()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tornado\\platform\\asyncio.py\", line 132, in start\n    self.asyncio_loop.run_forever()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\asyncio\\base_events.py\", line 422, in run_forever\n    self._run_once()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\asyncio\\base_events.py\", line 1434, in _run_once\n    handle._run()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\asyncio\\events.py\", line 145, in _run\n    self._callback(*self._args)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tornado\\ioloop.py\", line 758, in _run_callback\n    ret = callback()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tornado\\stack_context.py\", line 300, in null_wrapper\n    return fn(*args, **kwargs)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\zmq\\eventloop\\zmqstream.py\", line 536, in <lambda>\n    self.io_loop.add_callback(lambda : self._handle_events(self.socket, 0))\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\zmq\\eventloop\\zmqstream.py\", line 450, in _handle_events\n    self._handle_recv()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\zmq\\eventloop\\zmqstream.py\", line 480, in _handle_recv\n    self._run_callback(callback, msg)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\zmq\\eventloop\\zmqstream.py\", line 432, in _run_callback\n    callback(*args, **kwargs)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tornado\\stack_context.py\", line 300, in null_wrapper\n    return fn(*args, **kwargs)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\ipykernel\\kernelbase.py\", line 283, in dispatcher\n    return self.dispatch_shell(stream, msg)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\ipykernel\\kernelbase.py\", line 233, in dispatch_shell\n    handler(stream, idents, msg)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\ipykernel\\kernelbase.py\", line 399, in execute_request\n    user_expressions, allow_stdin)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\ipykernel\\ipkernel.py\", line 208, in do_execute\n    res = shell.run_cell(code, store_history=store_history, silent=silent)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\ipykernel\\zmqshell.py\", line 537, in run_cell\n    return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\IPython\\core\\interactiveshell.py\", line 2843, in run_cell\n    raw_cell, store_history, silent, shell_futures)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\IPython\\core\\interactiveshell.py\", line 2869, in _run_cell\n    return runner(coro)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\IPython\\core\\async_helpers.py\", line 67, in _pseudo_sync_runner\n    coro.send(None)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\IPython\\core\\interactiveshell.py\", line 3044, in run_cell_async\n    interactivity=interactivity, compiler=compiler, result=result)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\IPython\\core\\interactiveshell.py\", line 3209, in run_ast_nodes\n    if (yield from self.run_code(code, result)):\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\IPython\\core\\interactiveshell.py\", line 3291, in run_code\n    exec(code_obj, self.user_global_ns, self.user_ns)\n  File \"<ipython-input-7-37045d047079>\", line 3, in <module>\n    tmp = algo.initialize().run(fd_data.Acquisition(data=data, kernel=kernel), niter=3, session_config=tf.ConfigProto(device_count={'GPU': 0}))\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\flowdec\\restoration.py\", line 62, in initialize\n    self.graph = self._get_tf_graph()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\flowdec\\restoration.py\", line 58, in _get_tf_graph\n    inputs, outputs = self._build_tf_graph()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\flowdec\\restoration.py\", line 316, in _build_tf_graph\n    result = tf.while_loop(cond, body, [1, decon], parallel_iterations=1)[1]\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\ops\\control_flow_ops.py\", line 3209, in while_loop\n    result = loop_context.BuildLoop(cond, body, loop_vars, shape_invariants)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\ops\\control_flow_ops.py\", line 2941, in BuildLoop\n    pred, body, original_loop_vars, loop_vars, shape_invariants)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\ops\\control_flow_ops.py\", line 2878, in _BuildLoop\n    body_result = body(*packed_vars_for_body)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\flowdec\\restoration.py\", line 301, in body\n    blur1 = tf.where(conv1 < self.epsilon, tf.zeros_like(datat), datat / conv1, name='blur1')\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\ops\\math_ops.py\", line 847, in binary_op_wrapper\n    return func(x, y, name=name)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\ops\\math_ops.py\", line 955, in _truediv_python3\n    return gen_math_ops.real_div(x, y, name=name)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\ops\\gen_math_ops.py\", line 5703, in real_div\n    \"RealDiv\", x=x, y=y, name=name)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\framework\\op_def_library.py\", line 787, in _apply_op_helper\n    op_def=op_def)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\framework\\ops.py\", line 3414, in create_op\n    op_def=op_def)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\framework\\ops.py\", line 1740, in __init__\n    self._traceback = self._graph._extract_stack()  # pylint: disable=protected-access\n\nInvalidArgumentError (see above for traceback): Incompatible shapes: [20,10,45] vs. [20,10,44]\n\t [[Node: while/truediv = RealDiv[T=DT_FLOAT, _device=\"/job:localhost/replica:0/task:0/device:CPU:0\"](while/zeros_like/Enter, while/irfft3d)]]\n",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mInvalidArgumentError\u001b[0m                      Traceback (most recent call last)",
      "\u001b[1;32mc:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\client\\session.py\u001b[0m in \u001b[0;36m_do_call\u001b[1;34m(self, fn, *args)\u001b[0m\n\u001b[0;32m   1321\u001b[0m     \u001b[1;32mtry\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1322\u001b[1;33m       \u001b[1;32mreturn\u001b[0m \u001b[0mfn\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m*\u001b[0m\u001b[0margs\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m   1323\u001b[0m     \u001b[1;32mexcept\u001b[0m \u001b[0merrors\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mOpError\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0me\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mc:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\client\\session.py\u001b[0m in \u001b[0;36m_run_fn\u001b[1;34m(feed_dict, fetch_list, target_list, options, run_metadata)\u001b[0m\n\u001b[0;32m   1306\u001b[0m       return self._call_tf_sessionrun(\n\u001b[1;32m-> 1307\u001b[1;33m           options, feed_dict, fetch_list, target_list, run_metadata)\n\u001b[0m\u001b[0;32m   1308\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mc:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\client\\session.py\u001b[0m in \u001b[0;36m_call_tf_sessionrun\u001b[1;34m(self, options, feed_dict, fetch_list, target_list, run_metadata)\u001b[0m\n\u001b[0;32m   1408\u001b[0m           \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_session\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0moptions\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfeed_dict\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfetch_list\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtarget_list\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1409\u001b[1;33m           run_metadata)\n\u001b[0m\u001b[0;32m   1410\u001b[0m     \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mInvalidArgumentError\u001b[0m: Incompatible shapes: [20,10,45] vs. [20,10,44]\n\t [[Node: while/truediv = RealDiv[T=DT_FLOAT, _device=\"/job:localhost/replica:0/task:0/device:CPU:0\"](while/zeros_like/Enter, while/irfft3d)]]",
      "\nDuring handling of the above exception, another exception occurred:\n",
      "\u001b[1;31mInvalidArgumentError\u001b[0m                      Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-7-37045d047079>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[0malgo\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mRichardsonLucyDeconvolver\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;36m3\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mpad_mode\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m\"None\"\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mreal_domain_fft\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;32mTrue\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      2\u001b[0m \u001b[0mdata\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mkernel\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mcreate_data_and_kernel\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mshape\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 3\u001b[1;33m \u001b[0mtmp\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0malgo\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0minitialize\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfd_data\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mAcquisition\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mdata\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mkernel\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mkernel\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mniter\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;36m3\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0msession_config\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mtf\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mConfigProto\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdevice_count\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;33m{\u001b[0m\u001b[1;34m'GPU'\u001b[0m\u001b[1;33m:\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m}\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;32mc:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\flowdec\\restoration.py\u001b[0m in \u001b[0;36mrun\u001b[1;34m(self, acquisition, niter, session_config)\u001b[0m\n\u001b[0;32m    214\u001b[0m     \u001b[1;32mdef\u001b[0m \u001b[0mrun\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0macquisition\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mniter\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0msession_config\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;32mNone\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    215\u001b[0m         \u001b[0minput_kwargs\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mdict\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mniter\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mniter\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mpad_mode\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mpad_mode\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mpad_min\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mpad_min\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mstart_mode\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mstart_mode\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 216\u001b[1;33m         \u001b[0mres\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_run\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0macquisition\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0minput_kwargs\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0msession_config\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0msession_config\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    217\u001b[0m         \u001b[1;32mreturn\u001b[0m \u001b[0mDeconvolutionResult\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mres\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'result'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0minfo\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;33m{\u001b[0m\u001b[0mk\u001b[0m\u001b[1;33m:\u001b[0m \u001b[0mv\u001b[0m \u001b[1;32mfor\u001b[0m \u001b[0mk\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mv\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mres\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mitems\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mk\u001b[0m \u001b[1;33m!=\u001b[0m \u001b[1;34m'result'\u001b[0m\u001b[1;33m}\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    218\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mc:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\flowdec\\restoration.py\u001b[0m in \u001b[0;36m_run\u001b[1;34m(self, acquisition, input_kwargs, session_config)\u001b[0m\n\u001b[0;32m     81\u001b[0m             \u001b[0mdata_dict\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;33m{\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mgraph\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0minputs\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mk\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m:\u001b[0m \u001b[0mv\u001b[0m \u001b[1;32mfor\u001b[0m \u001b[0mk\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mv\u001b[0m \u001b[1;32min\u001b[0m \u001b[0macquisition\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mto_feed_dict\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mitems\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m}\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     82\u001b[0m             \u001b[0margs_dict\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;33m{\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mgraph\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0minputs\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mk\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m:\u001b[0m \u001b[0mv\u001b[0m \u001b[1;32mfor\u001b[0m \u001b[0mk\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mv\u001b[0m \u001b[1;32min\u001b[0m \u001b[0minput_kwargs\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mitems\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mv\u001b[0m \u001b[1;32mis\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[1;32mNone\u001b[0m\u001b[1;33m}\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 83\u001b[1;33m             \u001b[0mres\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0msess\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mgraph\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0moutputs\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfeed_dict\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;33m{\u001b[0m\u001b[1;33m**\u001b[0m\u001b[0mdata_dict\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m**\u001b[0m\u001b[0margs_dict\u001b[0m\u001b[1;33m}\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m     84\u001b[0m             \u001b[1;32mreturn\u001b[0m \u001b[0mres\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     85\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mc:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\client\\session.py\u001b[0m in \u001b[0;36mrun\u001b[1;34m(self, fetches, feed_dict, options, run_metadata)\u001b[0m\n\u001b[0;32m    898\u001b[0m     \u001b[1;32mtry\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    899\u001b[0m       result = self._run(None, fetches, feed_dict, options_ptr,\n\u001b[1;32m--> 900\u001b[1;33m                          run_metadata_ptr)\n\u001b[0m\u001b[0;32m    901\u001b[0m       \u001b[1;32mif\u001b[0m \u001b[0mrun_metadata\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    902\u001b[0m         \u001b[0mproto_data\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mtf_session\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mTF_GetBuffer\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mrun_metadata_ptr\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mc:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\client\\session.py\u001b[0m in \u001b[0;36m_run\u001b[1;34m(self, handle, fetches, feed_dict, options, run_metadata)\u001b[0m\n\u001b[0;32m   1133\u001b[0m     \u001b[1;32mif\u001b[0m \u001b[0mfinal_fetches\u001b[0m \u001b[1;32mor\u001b[0m \u001b[0mfinal_targets\u001b[0m \u001b[1;32mor\u001b[0m \u001b[1;33m(\u001b[0m\u001b[0mhandle\u001b[0m \u001b[1;32mand\u001b[0m \u001b[0mfeed_dict_tensor\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1134\u001b[0m       results = self._do_run(handle, final_targets, final_fetches,\n\u001b[1;32m-> 1135\u001b[1;33m                              feed_dict_tensor, options, run_metadata)\n\u001b[0m\u001b[0;32m   1136\u001b[0m     \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1137\u001b[0m       \u001b[0mresults\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;33m[\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mc:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\client\\session.py\u001b[0m in \u001b[0;36m_do_run\u001b[1;34m(self, handle, target_list, fetch_list, feed_dict, options, run_metadata)\u001b[0m\n\u001b[0;32m   1314\u001b[0m     \u001b[1;32mif\u001b[0m \u001b[0mhandle\u001b[0m \u001b[1;32mis\u001b[0m \u001b[1;32mNone\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1315\u001b[0m       return self._do_call(_run_fn, feeds, fetches, targets, options,\n\u001b[1;32m-> 1316\u001b[1;33m                            run_metadata)\n\u001b[0m\u001b[0;32m   1317\u001b[0m     \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1318\u001b[0m       \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_do_call\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0m_prun_fn\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mhandle\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfeeds\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfetches\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mc:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\client\\session.py\u001b[0m in \u001b[0;36m_do_call\u001b[1;34m(self, fn, *args)\u001b[0m\n\u001b[0;32m   1333\u001b[0m         \u001b[1;32mexcept\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1334\u001b[0m           \u001b[1;32mpass\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1335\u001b[1;33m       \u001b[1;32mraise\u001b[0m \u001b[0mtype\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0me\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mnode_def\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mop\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mmessage\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m   1336\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1337\u001b[0m   \u001b[1;32mdef\u001b[0m \u001b[0m_extend_graph\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mInvalidArgumentError\u001b[0m: Incompatible shapes: [20,10,45] vs. [20,10,44]\n\t [[Node: while/truediv = RealDiv[T=DT_FLOAT, _device=\"/job:localhost/replica:0/task:0/device:CPU:0\"](while/zeros_like/Enter, while/irfft3d)]]\n\nCaused by op 'while/truediv', defined at:\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\runpy.py\", line 193, in _run_module_as_main\n    \"__main__\", mod_spec)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\runpy.py\", line 85, in _run_code\n    exec(code, run_globals)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\ipykernel_launcher.py\", line 16, in <module>\n    app.launch_new_instance()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\traitlets\\config\\application.py\", line 658, in launch_instance\n    app.start()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\ipykernel\\kernelapp.py\", line 497, in start\n    self.io_loop.start()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tornado\\platform\\asyncio.py\", line 132, in start\n    self.asyncio_loop.run_forever()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\asyncio\\base_events.py\", line 422, in run_forever\n    self._run_once()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\asyncio\\base_events.py\", line 1434, in _run_once\n    handle._run()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\asyncio\\events.py\", line 145, in _run\n    self._callback(*self._args)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tornado\\ioloop.py\", line 758, in _run_callback\n    ret = callback()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tornado\\stack_context.py\", line 300, in null_wrapper\n    return fn(*args, **kwargs)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\zmq\\eventloop\\zmqstream.py\", line 536, in <lambda>\n    self.io_loop.add_callback(lambda : self._handle_events(self.socket, 0))\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\zmq\\eventloop\\zmqstream.py\", line 450, in _handle_events\n    self._handle_recv()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\zmq\\eventloop\\zmqstream.py\", line 480, in _handle_recv\n    self._run_callback(callback, msg)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\zmq\\eventloop\\zmqstream.py\", line 432, in _run_callback\n    callback(*args, **kwargs)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tornado\\stack_context.py\", line 300, in null_wrapper\n    return fn(*args, **kwargs)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\ipykernel\\kernelbase.py\", line 283, in dispatcher\n    return self.dispatch_shell(stream, msg)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\ipykernel\\kernelbase.py\", line 233, in dispatch_shell\n    handler(stream, idents, msg)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\ipykernel\\kernelbase.py\", line 399, in execute_request\n    user_expressions, allow_stdin)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\ipykernel\\ipkernel.py\", line 208, in do_execute\n    res = shell.run_cell(code, store_history=store_history, silent=silent)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\ipykernel\\zmqshell.py\", line 537, in run_cell\n    return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\IPython\\core\\interactiveshell.py\", line 2843, in run_cell\n    raw_cell, store_history, silent, shell_futures)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\IPython\\core\\interactiveshell.py\", line 2869, in _run_cell\n    return runner(coro)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\IPython\\core\\async_helpers.py\", line 67, in _pseudo_sync_runner\n    coro.send(None)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\IPython\\core\\interactiveshell.py\", line 3044, in run_cell_async\n    interactivity=interactivity, compiler=compiler, result=result)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\IPython\\core\\interactiveshell.py\", line 3209, in run_ast_nodes\n    if (yield from self.run_code(code, result)):\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\IPython\\core\\interactiveshell.py\", line 3291, in run_code\n    exec(code_obj, self.user_global_ns, self.user_ns)\n  File \"<ipython-input-7-37045d047079>\", line 3, in <module>\n    tmp = algo.initialize().run(fd_data.Acquisition(data=data, kernel=kernel), niter=3, session_config=tf.ConfigProto(device_count={'GPU': 0}))\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\flowdec\\restoration.py\", line 62, in initialize\n    self.graph = self._get_tf_graph()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\flowdec\\restoration.py\", line 58, in _get_tf_graph\n    inputs, outputs = self._build_tf_graph()\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\flowdec\\restoration.py\", line 316, in _build_tf_graph\n    result = tf.while_loop(cond, body, [1, decon], parallel_iterations=1)[1]\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\ops\\control_flow_ops.py\", line 3209, in while_loop\n    result = loop_context.BuildLoop(cond, body, loop_vars, shape_invariants)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\ops\\control_flow_ops.py\", line 2941, in BuildLoop\n    pred, body, original_loop_vars, loop_vars, shape_invariants)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\ops\\control_flow_ops.py\", line 2878, in _BuildLoop\n    body_result = body(*packed_vars_for_body)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\flowdec\\restoration.py\", line 301, in body\n    blur1 = tf.where(conv1 < self.epsilon, tf.zeros_like(datat), datat / conv1, name='blur1')\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\ops\\math_ops.py\", line 847, in binary_op_wrapper\n    return func(x, y, name=name)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\ops\\math_ops.py\", line 955, in _truediv_python3\n    return gen_math_ops.real_div(x, y, name=name)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\ops\\gen_math_ops.py\", line 5703, in real_div\n    \"RealDiv\", x=x, y=y, name=name)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\framework\\op_def_library.py\", line 787, in _apply_op_helper\n    op_def=op_def)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\framework\\ops.py\", line 3414, in create_op\n    op_def=op_def)\n  File \"c:\\users\\volker\\anaconda3\\envs\\spimenv\\lib\\site-packages\\tensorflow\\python\\framework\\ops.py\", line 1740, in __init__\n    self._traceback = self._graph._extract_stack()  # pylint: disable=protected-access\n\nInvalidArgumentError (see above for traceback): Incompatible shapes: [20,10,45] vs. [20,10,44]\n\t [[Node: while/truediv = RealDiv[T=DT_FLOAT, _device=\"/job:localhost/replica:0/task:0/device:CPU:0\"](while/zeros_like/Enter, while/irfft3d)]]\n"
     ]
    }
   ],
   "source": [
    "algo = RichardsonLucyDeconvolver(3, pad_mode=\"None\", real_domain_fft=True)\n",
    "data, kernel = create_data_and_kernel(shape)\n",
    "tmp = algo.initialize().run(fd_data.Acquisition(data=data, kernel=kernel), niter=3, session_config=tf.ConfigProto(device_count={'GPU': 0}))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### complex domain"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "algo = RichardsonLucyDeconvolver(3, pad_mode=\"None\", real_domain_fft=False)\n",
    "data, kernel = create_data_and_kernel(shape)\n",
    "tmp = algo.initialize().run(fd_data.Acquisition(data=data, kernel=kernel), niter=3, session_config=tf.ConfigProto(device_count={'GPU': 0}))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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