toolapi 0.1.0__tar.gz → 0.1.1__tar.gz

{toolapi-0.1.0 → toolapi-0.1.1}/Cargo.lock

@@ -86,15 +86,15 @@ dependencies = [
 
 [[package]]
 name = "bytes"
-version = "1.11.0"
+version = "1.11.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b35204fbdc0b3f4446b89fc1ac2cf84a8a68971995d0bf2e925ec7cd960f9cb3"
+checksum = "1e748733b7cbc798e1434b6ac524f0c1ff2ab456fe201501e6497c8417a4fc33"
 
 [[package]]
 name = "cc"
-version = "1.2.54"
+version = "1.2.55"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6354c81bbfd62d9cfa9cb3c773c2b7b2a3a482d569de977fd0e961f6e7c00583"
+checksum = "47b26a0954ae34af09b50f0de26458fa95369a0d478d8236d3f93082b219bd29"
 dependencies = [
  "find-msvc-tools",
  "shlex",
@@ -143,9 +143,9 @@ dependencies = [
 
 [[package]]
 name = "find-msvc-tools"
-version = "0.1.8"
+version = "0.1.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8591b0bcc8a98a64310a2fae1bb3e9b8564dd10e381e6e28010fde8e8e8568db"
+checksum = "5baebc0774151f905a1a2cc41989300b1e6fbb29aff0ceffa1064fdd3088d582"
 
 [[package]]
 name = "form_urlencoded"
@@ -304,12 +304,11 @@ dependencies = [
 
 [[package]]
 name = "hyper-util"
-version = "0.1.19"
+version = "0.1.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "727805d60e7938b76b826a6ef209eb70eaa1812794f9424d4a4e2d740662df5f"
+checksum = "96547c2556ec9d12fb1578c4eaf448b04993e7fb79cbaad930a656880a6bdfa0"
 dependencies = [
  "bytes",
- "futures-core",
  "http",
  "http-body",
  "hyper",
@@ -428,9 +427,9 @@ checksum = "8b870d8c151b6f2fb93e84a13146138f05d02ed11c7e7c54f8826aaaf7c9f184"
 
 [[package]]
 name = "portable-atomic"
-version = "1.13.0"
+version = "1.13.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f89776e4d69bb58bc6993e99ffa1d11f228b839984854c7daeb5d37f87cbe950"
+checksum = "c33a9471896f1c69cecef8d20cbe2f7accd12527ce60845ff44c153bb2a21b49"
 
 [[package]]
 name = "ppv-lite86"
@@ -570,6 +569,25 @@ dependencies = [
  "windows-sys 0.52.0",
 ]
 
+[[package]]
+name = "rmp"
+version = "0.8.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4ba8be72d372b2c9b35542551678538b562e7cf86c3315773cae48dfbfe7790c"
+dependencies = [
+ "num-traits",
+]
+
+[[package]]
+name = "rmp-serde"
+version = "1.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "72f81bee8c8ef9b577d1681a70ebbc962c232461e397b22c208c43c04b67a155"
+dependencies = [
+ "rmp",
+ "serde",
+]
+
 [[package]]
 name = "rustls"
 version = "0.23.36"
@@ -701,9 +719,9 @@ checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64"
 
 [[package]]
 name = "slab"
-version = "0.4.11"
+version = "0.4.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a2ae44ef20feb57a68b23d846850f861394c2e02dc425a50098ae8c90267589"
+checksum = "0c790de23124f9ab44544d7ac05d60440adc586479ce501c1d6d7da3cd8c9cf5"
 
 [[package]]
 name = "smallvec"
@@ -824,14 +842,14 @@ dependencies = [
 
 [[package]]
 name = "toolapi"
-version = "0.1.0"
-source = "git+https://github.com/mrx-org/toolapi.git#c4a30afcd3a64d1a752c12d1d8f0c20d3f5f9613"
+version = "0.1.1"
+source = "git+https://github.com/mrx-org/toolapi.git#0bf4075575b48abb8d0844433d5581aa2d81b72d"
 dependencies = [
  "axum",
  "num-complex",
+ "rmp-serde",
  "rustls",
  "serde",
- "serde_json",
  "thiserror",
  "tokio",
  "tokio-tungstenite",
@@ -840,7 +858,7 @@ dependencies = [
 
 [[package]]
 name = "toolapi-py"
-version = "0.1.0"
+version = "0.1.1"
 dependencies = [
  "num-complex",
  "pyo3",
@@ -1154,18 +1172,18 @@ checksum = "d7249219f66ced02969388cf2bb044a09756a083d0fab1e566056b04d9fbcaa5"
 
 [[package]]
 name = "zerocopy"
-version = "0.8.35"
+version = "0.8.37"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fdea86ddd5568519879b8187e1cf04e24fce28f7fe046ceecbce472ff19a2572"
+checksum = "7456cf00f0685ad319c5b1693f291a650eaf345e941d082fc4e03df8a03996ac"
 dependencies = [
  "zerocopy-derive",
 ]
 
 [[package]]
 name = "zerocopy-derive"
-version = "0.8.35"
+version = "0.8.37"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0c15e1b46eff7c6c91195752e0eeed8ef040e391cdece7c25376957d5f15df22"
+checksum = "1328722bbf2115db7e19d69ebcc15e795719e2d66b60827c6a69a117365e37a0"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1180,6 +1198,6 @@ checksum = "b97154e67e32c85465826e8bcc1c59429aaaf107c1e4a9e53c8d8ccd5eff88d0"
 
 [[package]]
 name = "zmij"
-version = "1.0.17"
+version = "1.0.19"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "02aae0f83f69aafc94776e879363e9771d7ecbffe2c7fbb6c14c5e00dfe88439"
+checksum = "3ff05f8caa9038894637571ae6b9e29466c1f4f829d26c9b28f869a29cbe3445"

{toolapi-0.1.0 → toolapi-0.1.1}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "toolapi-py"
-version = "0.1.0"
+version = "0.1.1"
 edition = "2024"
 readme = "README.md"
 

{toolapi-0.1.0 → toolapi-0.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: toolapi
-Version: 0.1.0
+Version: 0.1.1
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy

toolapi-0.1.1/test/demo_notebook.ipynb

@@ -0,0 +1,324 @@
+{
+  "cells": [
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/"
+        },
+        "collapsed": true,
+        "id": "GiA85Mp8NnVR",
+        "outputId": "6480281e-518e-4d94-9632-9ce6159eb9a6"
+      },
+      "outputs": [],
+      "source": [
+        "!pip install MRzeroCore\n",
+        "!pip install toolapi"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/"
+        },
+        "collapsed": true,
+        "id": "G8exhuriPqYH",
+        "outputId": "987874de-1ab3-4021-bc42-ed35f27aaab2"
+      },
+      "outputs": [],
+      "source": [
+        "# @title Download sequence and phantom data\n",
+        "\n",
+        "!wget -q --show-progress https://github.com/mrx-org/toolapi-py/releases/download/v0.1.0/gre.seq\n",
+        "!wget -q --show-progress https://github.com/mrx-org/toolapi-py/releases/download/v0.1.0/brainweb-subj05-3T.json\n",
+        "!wget -q --show-progress https://github.com/mrx-org/toolapi-py/releases/download/v0.1.0/brainweb-subj05.nii.gz\n",
+        "!wget -q --show-progress https://github.com/mrx-org/toolapi-py/releases/download/v0.1.0/brainweb-subj05_dB0.nii.gz\n",
+        "!wget -q --show-progress https://github.com/mrx-org/toolapi-py/releases/download/v0.1.0/brainweb-subj05_B1+.nii.gz"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "opV_JcaANzPs"
+      },
+      "outputs": [],
+      "source": [
+        "import MRzeroCore as mr0\n",
+        "import torch\n",
+        "import matplotlib.pyplot as plt\n",
+        "from time import time\n",
+        "\n",
+        "import toolapi"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "ifDoRtEHWoQz"
+      },
+      "outputs": [],
+      "source": [
+        "# @title Helpers to convert between `toolapi` and `MRzeroCore`\n",
+        "def phantom_dict_to_toolapi(phantom: mr0.TissueDict) -> toolapi.value.MultiTissuePhantom:\n",
+        "    tissues = list(phantom.values())\n",
+        "    voxel_size = (tissues[0].size / torch.as_tensor(tissues[0].PD.shape)).tolist()\n",
+        "\n",
+        "    return toolapi.value.MultiTissuePhantom(\n",
+        "        \"AASinc\",  # voxel shape type\n",
+        "        voxel_size,  # voxel shape data\n",
+        "        voxel_size,  # grid spacing\n",
+        "        list(tissues[0].PD.shape),  # grid size\n",
+        "        # We assume that all tissues have the same B1 and coil_sens\n",
+        "        tissues[0].B1.reshape(tissues[0].B1.shape[0], -1).tolist(),\n",
+        "        tissues[0].coil_sens.reshape(tissues[0].coil_sens.shape[0], -1).tolist(),\n",
+        "        [\n",
+        "            (\n",
+        "                tissue.PD.flatten().tolist(),\n",
+        "                tissue.B0.flatten().tolist(),\n",
+        "                toolapi.value.TissueProperties(\n",
+        "                    float(tissue.T1[tissue.PD > 0].mean()),\n",
+        "                    float(tissue.T2[tissue.PD > 0].mean()),\n",
+        "                    float(tissue.T2dash[tissue.PD > 0].mean()),\n",
+        "                    float(tissue.D[tissue.PD > 0].mean()),\n",
+        "                )\n",
+        "            )\n",
+        "            for tissue in tissues\n",
+        "        ]\n",
+        "    )\n",
+        "\n",
+        "\n",
+        "def to_instant_events(seq: mr0.Sequence) -> toolapi.value.EventSeq:\n",
+        "    ie_seq = []\n",
+        "\n",
+        "    Event = toolapi.value.Event\n",
+        "    for rep in seq:\n",
+        "        ie_seq.append(Event.Pulse(rep.pulse.angle, rep.pulse.phase))\n",
+        "        for ev in range(rep.event_count):\n",
+        "            ie_seq.append(Event.Fid([\n",
+        "                rep.gradm[ev, 0],\n",
+        "                rep.gradm[ev, 1],\n",
+        "                rep.gradm[ev, 2],\n",
+        "                rep.event_time[ev]\n",
+        "            ]))\n",
+        "            if rep.adc_usage[ev] != 0:\n",
+        "                ie_seq.append(Event.Adc(torch.pi / 2 - rep.adc_phase[ev]))\n",
+        "\n",
+        "    ie_seq = toolapi.value.EventSeq(ie_seq)\n",
+        "    return ie_seq"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "gXB-6EyNuDOO"
+      },
+      "outputs": [],
+      "source": [
+        "# @title Define tools\n",
+        "def on_message(msg):\n",
+        "    print(f\"\\r > {msg}\", end=\"\")\n",
+        "    return True\n",
+        "\n",
+        "def load_seq(path, exact_trajectories=True):\n",
+        "    with open(path) as f:\n",
+        "        file_content = f.read()\n",
+        "    result = toolapi.call(\n",
+        "        \"wss://tool-seqloader-flyio.fly.dev/tool\",\n",
+        "        on_message,\n",
+        "        seq_file=file_content,\n",
+        "        exact_trajectory=exact_trajectories\n",
+        "    )\n",
+        "    print(\"\\n --- done ---\")\n",
+        "    return result[\"seq\"]\n",
+        "\n",
+        "# Define the simulation tool\n",
+        "def sim_spdg(sequence, phantom):\n",
+        "    result = toolapi.call(\n",
+        "        \"wss://tool-spdg-flyio.fly.dev/tool\",\n",
+        "        on_message,\n",
+        "        sequence=sequence,\n",
+        "        phantom=phantom,\n",
+        "    )\n",
+        "    print(\"\\n --- done ---\")\n",
+        "    return result[\"signal\"]"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/"
+        },
+        "collapsed": true,
+        "id": "h1cWrGG5XXm8",
+        "outputId": "36890490-d999-4aac-d105-a45ba237f070"
+      },
+      "outputs": [],
+      "source": [
+        "# @title Load phantom\n",
+        "seq_tool = load_seq(\"gre.seq\")\n",
+        "seq_mr0 = to_instant_events(mr0.Sequence.import_file(\"gre.seq\", exact_trajectories=False))\n",
+        "\n",
+        "# Colab can't handle the phantom at full resolution; reduce data a bit\n",
+        "config = mr0.NiftiPhantom.load(\"brainweb-subj05-3T.json\")\n",
+        "config.tissues.pop(\"fat\")\n",
+        "for tissue in config.tissues.values():\n",
+        "    tissue.B1_tx = [1.0]\n",
+        "    tissue.B1_rx = [1.0]\n",
+        "\n",
+        "phantom = mr0.TissueDict.load(\".\", config)\n",
+        "phantom = phantom.interpolate(64, 64, 64).slices([30])\n",
+        "phantom = phantom_dict_to_toolapi(phantom)"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/"
+        },
+        "id": "UD-euke_qLoN",
+        "outputId": "1dbea27d-b919-4754-d3d9-a7bc442759fc"
+      },
+      "outputs": [],
+      "source": [
+        "# @title Load sequence\n",
+        "seq_tool = load_seq(\"gre.seq\", exact_trajectories=True)\n",
+        "seq_mr0 = to_instant_events(mr0.Sequence.import_file(\"gre.seq\", exact_trajectories=True))"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/"
+        },
+        "id": "IUm9Zj6ijq00",
+        "outputId": "2973c887-b998-4726-f422-051d8e80b115"
+      },
+      "outputs": [],
+      "source": [
+        "# @title compare parsed sequences for differences\n",
+        "print(f\"event count: tool={len(seq_tool.events)}, mr0={len(seq_tool.events)}\")\n",
+        "\n",
+        "rf_angles = []\n",
+        "rf_phases = []\n",
+        "kt_x = []\n",
+        "kt_y = []\n",
+        "kt_z = []\n",
+        "kt_t = []\n",
+        "adc_phases = []\n",
+        "\n",
+        "for ev_tool, ev_mr0 in zip(seq_tool.events, seq_mr0.events):\n",
+        "    if ev_tool.variant == 'Pulse':\n",
+        "        rf_angles.append((ev_tool.fields['angle'], ev_mr0.fields['angle']))\n",
+        "        rf_phases.append((ev_tool.fields['phase'], ev_mr0.fields['phase']))\n",
+        "    elif ev_tool.variant == 'Fid':\n",
+        "        kt_x.append((ev_tool.fields['kt'][0], ev_mr0.fields['kt'][0]))\n",
+        "        kt_y.append((ev_tool.fields['kt'][1], ev_mr0.fields['kt'][1]))\n",
+        "        kt_z.append((ev_tool.fields['kt'][2], ev_mr0.fields['kt'][2]))\n",
+        "        kt_t.append((ev_tool.fields['kt'][3], ev_mr0.fields['kt'][3]))\n",
+        "    elif ev_tool.variant == 'Adc':\n",
+        "        adc_phases.append((ev_tool.fields['phase'], ev_mr0.fields['phase']))\n",
+        "\n",
+        "\n",
+        "print(f\"max diff in angle: {max(abs(x[0] - x[1]) for x in rf_angles)}\")\n",
+        "print(f\"max diff in phase: {max(abs(x[0] - x[1]) for x in rf_phases)}\")\n",
+        "print(f\"max diff in kt_x: {max(abs(x[0] - x[1]) for x in kt_x)}\")\n",
+        "print(f\"max diff in kt_y: {max(abs(x[0] - x[1]) for x in kt_y)}\")\n",
+        "print(f\"max diff in kt_z: {max(abs(x[0] - x[1]) for x in kt_z)}\")\n",
+        "print(f\"max diff in kt_t: {max(abs(x[0] - x[1]) for x in kt_t)}\")\n",
+        "print(f\"max diff in adc phase: {max(abs(x[0] - x[1]) for x in adc_phases)}\")\n",
+        "\n",
+        "# plt.figure()\n",
+        "# plt.plot([x[0] - x[1] for x in rf_angles], label=\"angle\")\n",
+        "# plt.plot([x[0] - x[1] for x in rf_phases], label=\"phase\")\n",
+        "# plt.plot([x[0] - x[1] for x in kt_x], label=\"kt_x\")\n",
+        "# plt.plot([x[0] - x[1] for x in kt_y], label=\"kt_y\")\n",
+        "# plt.plot([x[0] - x[1] for x in kt_z], label=\"kt_z\")\n",
+        "# plt.plot([x[0] - x[1] for x in kt_t], label=\"kt_t\")\n",
+        "# plt.legend()\n",
+        "# plt.grid()\n",
+        "# plt.show()"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/",
+          "height": 1000
+        },
+        "id": "G-39fS3ygxen",
+        "outputId": "f9e1d12b-2460-47e5-93d1-f8e58ad172ad"
+      },
+      "outputs": [],
+      "source": [
+        "# @title Run simulation on fly.io\n",
+        "start = time()\n",
+        "signal_tool = torch.tensor(sim_spdg(seq_tool, phantom))[0, :]\n",
+        "print(f\"took {time() - start:.3} s\")\n",
+        "start = time()\n",
+        "signal_mr0 = torch.tensor(sim_spdg(seq_mr0, phantom))[0, :]\n",
+        "print(f\"took {time() - start:.3} s\")\n",
+        "\n",
+        "reco_tool = torch.fft.fftshift(torch.fft.fft2(torch.fft.fftshift(signal_tool.reshape(256, 256))))\n",
+        "reco_mr0 = torch.fft.fftshift(torch.fft.fft2(torch.fft.fftshift(signal_mr0.reshape(256, 256))))\n",
+        "\n",
+        "# Small difference due to small deviations (order of 1e-7) between adc phases\n",
+        "plt.figure()\n",
+        "plt.suptitle(\"Difference\")\n",
+        "plt.subplot(121)\n",
+        "plt.imshow((reco_tool - reco_mr0).abs(), origin=\"lower\", vmin=0)\n",
+        "plt.axis(\"off\")\n",
+        "plt.colorbar()\n",
+        "plt.subplot(122)\n",
+        "plt.imshow((reco_tool - reco_mr0).angle(), origin=\"lower\", vmin=-torch.pi, vmax=torch.pi, cmap=\"twilight\")\n",
+        "plt.axis(\"off\")\n",
+        "plt.colorbar()\n",
+        "plt.show()\n",
+        "\n",
+        "for signal, title in [(signal_tool, \"Tool\"), (signal_mr0, \"MR0\")]:\n",
+        "    kspace = signal.reshape(256, 256)\n",
+        "    reco = torch.fft.fftshift(torch.fft.fft2(torch.fft.fftshift(kspace)))\n",
+        "\n",
+        "    plt.figure()\n",
+        "    plt.suptitle(title)\n",
+        "    plt.subplot(211)\n",
+        "    plt.plot(signal.abs())\n",
+        "    plt.grid()\n",
+        "    plt.subplot(223)\n",
+        "    plt.imshow(reco.abs(), origin=\"lower\", vmin=0)\n",
+        "    plt.axis(\"off\")\n",
+        "    plt.subplot(224)\n",
+        "    plt.imshow(reco.angle(), origin=\"lower\", vmin=-torch.pi, vmax=torch.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
+}

toolapi-0.1.1/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
+}