add minimal notebook (no MRzeroCore!)

Author: J-Endres

test/demo_notebook_minimal.ipynb

@@ -0,0 +1,127 @@
+{
+  "cells": [
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/"
+        },
+        "collapsed": true,
+        "id": "GiA85Mp8NnVR",
+        "outputId": "18f17ceb-69a3-4c39-a146-0c900d11441d"
+      },
+      "outputs": [],
+      "source": [
+        "!pip install toolapi\n",
+        "!wget -q --show-progress https://github.com/mrx-org/toolapi-py/releases/download/v0.1.0/gre.seq"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "gXB-6EyNuDOO"
+      },
+      "outputs": [],
+      "source": [
+        "# @title Define tools\n",
+        "import toolapi\n",
+        "from functools import cache\n",
+        "\n",
+        "def on_message(msg):\n",
+        "    print(f\"\\r > {msg}\", end=\"\")\n",
+        "    return True\n",
+        "\n",
+        "def call(url, **kwargs):\n",
+        "    from time import time\n",
+        "    start = time()\n",
+        "    result = toolapi.call(url, on_message, **kwargs)\n",
+        "    print(f\"\\n --- done ({time() - start:.2f} s) ---\")\n",
+        "    return result\n",
+        "\n",
+        "# .seq loader: uses disseqt to convert sequence to instant events\n",
+        "def load_seq(path, exact_trajectories=True):\n",
+        "    with open(path) as f:\n",
+        "        file_content = f.read()\n",
+        "    return call(\n",
+        "        \"wss://tool-seqloader-flyio.fly.dev/tool\",\n",
+        "        seq_file=file_content,\n",
+        "        exact_trajectory=exact_trajectories\n",
+        "    )[\"seq\"]\n",
+        "\n",
+        "# phantom library: returns rescaled brainweb multi-tissue phantoms (slow)\n",
+        "@cache\n",
+        "def load_phantom(subject, res, slice):\n",
+        "    return call(\n",
+        "        \"wss://tool-phantomlib-flyio.fly.dev/tool\",\n",
+        "        subject=subject,  # BrainWeb subject 1-20\n",
+        "        res_x=res[0],     # X resolution (1-434)\n",
+        "        res_y=res[1],     # Y resolution (1-362)\n",
+        "        res_z=res[2],     # Z resolution (1-434)\n",
+        "        slice=slice,      # Axial slice index\n",
+        "    )[\"phantom\"]\n",
+        "\n",
+        "# not-yet-quite segmented PDG\n",
+        "def sim_spdg(sequence, phantom):\n",
+        "    return call(\n",
+        "        \"wss://tool-spdg-flyio.fly.dev/tool\",\n",
+        "        sequence=sequence,\n",
+        "        phantom=phantom,\n",
+        "    )[\"signal\"]"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/",
+          "height": 475
+        },
+        "id": "G-39fS3ygxen",
+        "outputId": "e26eef10-da33-45a8-b8c1-00ec23cef04e"
+      },
+      "outputs": [],
+      "source": [
+        "# @title **load .seq + load phantom + run sim** |  _with tools hosted on fly.io_\n",
+        "import numpy as np\n",
+        "import matplotlib.pyplot as plt\n",
+        "\n",
+        "seq = load_seq(\"gre.seq\", exact_trajectories=False)\n",
+        "phantom = load_phantom(4, (64, 64, 64), 30)\n",
+        "signal = np.array(sim_spdg(seq, phantom))[0, :]\n",
+        "\n",
+        "# Reconstruction is done here (not via some tool)\n",
+        "kspace = signal.reshape(256, 256)\n",
+        "reco = np.fft.fftshift(np.fft.fft2(np.fft.fftshift(kspace)))\n",
+        "\n",
+        "plt.figure()\n",
+        "plt.subplot(211)\n",
+        "plt.plot(np.abs(signal))\n",
+        "plt.grid()\n",
+        "plt.subplot(223)\n",
+        "plt.imshow(np.abs(reco), origin=\"lower\", vmin=0)\n",
+        "plt.axis(\"off\")\n",
+        "plt.subplot(224)\n",
+        "plt.imshow(np.angle(reco), origin=\"lower\", vmin=-np.pi, vmax=np.pi, cmap=\"twilight\")\n",
+        "plt.axis(\"off\")\n",
+        "plt.show()\n"
+      ]
+    }
+  ],
+  "metadata": {
+    "colab": {
+      "provenance": []
+    },
+    "kernelspec": {
+      "display_name": "Python 3",
+      "name": "python3"
+    },
+    "language_info": {
+      "name": "python"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 0
+}