Bug fix in ext_test_report()

README.md

@@ -8,10 +8,6 @@
 
 `Compatible with Pulseq 1.4.0`
 
-
-🚨🚨🚨 **NOTE:** This is the `dev` branch which hosts the bleeding edge version. For the most recent, stable release,
-switch to the `master` branch by clicking [here](https://github.com/imr-framework/pypulseq/tree/master). 🚨🚨🚨
-
 ## Table of contents 🧾
 1. [👥 Contributors][section-contributors]
 2. [📚 Citations][section-relevant-literature]

pypulseq/Sequence/ext_test_report.py

@@ -68,7 +68,8 @@ def ext_test_report(self) -> str:
             TR = t_ex_tmp1[0] - t_ex_tmp[-1]
 
     # Check sequence dimensionality and spatial resolution
-    k_extent = np.max(np.abs(k_traj_adc), axis=1)
+    # Small error made for non-symmetric k-space, e.g. if you sample from -32 to +31 with 64 samples
+    k_extent = 0.5 * (np.max(k_traj_adc, axis=1) -  np.min(k_traj_adc, axis=1)) 
     k_scale = np.max(k_extent)
     is_cartesian = False
     if k_scale != 0:

pypulseq/seq_examples/notebooks/ESMRMB_DEMO_GRE_20211215.ipynb

@@ -0,0 +1,258 @@
+{
+  "nbformat": 4,
+  "nbformat_minor": 0,
+  "metadata": {
+    "colab": {
+      "name": "ESMRMB_DEMO_20211215.ipynb",
+      "provenance": [],
+      "collapsed_sections": [],
+      "toc_visible": true
+    },
+    "kernelspec": {
+      "name": "python3",
+      "display_name": "Python 3"
+    },
+    "language_info": {
+      "name": "python"
+    }
+  },
+  "cells": [
+    {
+      "cell_type": "markdown",
+      "source": [
+        "# **ESMRMB 2021 PyPulseq LIVE DEMO** - 12/15/2021"
+      ],
+      "metadata": {
+        "id": "hc3VbKKCOidq"
+      }
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "AuVzrkgEaVTG"
+      },
+      "outputs": [],
+      "source": [
+        "!pip install pypulseq"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "import pypulseq"
+      ],
+      "metadata": {
+        "id": "hZqtcYtQXhGN"
+      },
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "source": [
+        "### **IMPORT PACKAGES**"
+      ],
+      "metadata": {
+        "id": "dXeeFq6Bc5-9"
+      }
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "import math\n",
+        "\n",
+        "import numpy as np\n",
+        "from matplotlib import pyplot as plt\n",
+        "\n",
+        "import pypulseq as pp"
+      ],
+      "metadata": {
+        "id": "cwuaHdp_a8ub"
+      },
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "source": [
+        "#### **SETUP**"
+      ],
+      "metadata": {
+        "id": "qQ7uenQcdAWA"
+      }
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "# ======\n",
+        "# SETUP\n",
+        "# ======\n",
+        "# Create a new sequence object\n",
+        "seq = pp.Sequence()\n",
+        "\n",
+        "# Define FOV and resolution\n",
+        "fov = 256e-3\n",
+        "Nx = 256\n",
+        "Ny = 256\n",
+        "alpha = 10  # flip angle\n",
+        "slice_thickness = 3e-3  # slice\n",
+        "# TE = np.array([7.38]) * 1e-3  # give a vector here to have multiple TEs (e.g. for field mapping)\n",
+        "TE = np.array([4.3e-3])\n",
+        "TR = 10e-3\n",
+        "\n",
+        "rf_spoiling_inc = 117  # RF spoiling increment\n",
+        "\n",
+        "system = pp.Opts(max_grad=28, grad_unit='mT/m', max_slew=150, slew_unit='T/m/s', rf_ringdown_time=20e-6,\n",
+        "                 rf_dead_time=100e-6, adc_dead_time=10e-6)"
+      ],
+      "metadata": {
+        "id": "EnvyC9kDbHwE"
+      },
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "source": [
+        "#### **CREATE EVENTS**"
+      ],
+      "metadata": {
+        "id": "JEUIGiM0dZqG"
+      }
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "# ======\n",
+        "# CREATE EVENTS\n",
+        "# ======\n",
+        "rf, gz, gzr = pp.make_sinc_pulse(flip_angle=alpha * math.pi / 180, duration=3e-3, slice_thickness=slice_thickness,\n",
+        "                                 apodization=0.5, time_bw_product=4, system=system, return_gz=True)\n",
+        "# Define other gradients and ADC events\n",
+        "delta_k = 1 / fov\n",
+        "gx = pp.make_trapezoid(channel='x', flat_area=Nx * delta_k, flat_time=3.2e-3, system=system)\n",
+        "adc = pp.make_adc(num_samples=Nx, duration=gx.flat_time, delay=gx.rise_time, system=system)\n",
+        "gx_pre = pp.make_trapezoid(channel='x', area=-gx.area / 2, duration=1e-3, system=system)\n",
+        "gz_reph = pp.make_trapezoid(channel='z', area=-gz.area / 2, duration=1e-3, system=system)\n",
+        "phase_areas = (np.arange(Ny) - Ny / 2) * delta_k\n",
+        "\n",
+        "# gradient spoiling\n",
+        "gx_spoil = pp.make_trapezoid(channel='x', area=2 * Nx * delta_k, system=system)\n",
+        "gz_spoil = pp.make_trapezoid(channel='z', area=4 / slice_thickness, system=system)\n",
+        "\n",
+        "# Calculate timing\n",
+        "delay_TE = np.ceil((TE - pp.calc_duration(gx_pre) - gz.fall_time - gz.flat_time / 2 - pp.calc_duration(\n",
+        "    gx) / 2) / seq.grad_raster_time) * seq.grad_raster_time\n",
+        "delay_TR = np.ceil((TR - pp.calc_duration(gz) - pp.calc_duration(gx_pre) - pp.calc_duration(\n",
+        "    gx) - delay_TE) / seq.grad_raster_time) * seq.grad_raster_time\n",
+        "\n",
+        "assert np.all(delay_TE >= 0)\n",
+        "assert np.all(delay_TR >= pp.calc_duration(gx_spoil, gz_spoil))\n",
+        "\n",
+        "rf_phase = 0\n",
+        "rf_inc = 0\n"
+      ],
+      "metadata": {
+        "id": "2TXWjpBkdVMm"
+      },
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "source": [
+        "#### **CONSTRUCT SEQUENCE**"
+      ],
+      "metadata": {
+        "id": "zBlSefhqdhix"
+      }
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "# ======\n",
+        "# CONSTRUCT SEQUENCE\n",
+        "# ======\n",
+        "# Loop over phase encodes and define sequence blocks\n",
+        "for i in range(Ny):\n",
+        "    for j in range(len(TE)):\n",
+        "        rf.phase_offset = rf_phase / 180 * np.pi\n",
+        "        adc.phase_offset = rf_phase / 180 * np.pi\n",
+        "        rf_inc = divmod(rf_inc + rf_spoiling_inc, 360.0)[1]\n",
+        "        rf_phase = divmod(rf_phase + rf_inc, 360.0)[1]\n",
+        "\n",
+        "        seq.add_block(rf, gz)\n",
+        "        gy_pre = pp.make_trapezoid(channel='y', area=phase_areas[i], duration=pp.calc_duration(gx_pre), system=system)\n",
+        "        seq.add_block(gx_pre, gy_pre, gz_reph)\n",
+        "        seq.add_block(pp.make_delay(delay_TE[j]))\n",
+        "        seq.add_block(gx, adc)\n",
+        "        gy_pre.amplitude = -gy_pre.amplitude\n",
+        "        seq.add_block(pp.make_delay(delay_TR[j]), gx_spoil, gy_pre, gz_spoil)"
+      ],
+      "metadata": {
+        "id": "rOM1mAKfdb2t"
+      },
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "source": [
+        "#### **VISUALIZE**"
+      ],
+      "metadata": {
+        "id": "i5zQHVxadmTa"
+      }
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "# ======\n",
+        "# VISUALIZATION\n",
+        "# ======\n",
+        "seq.plot(time_range=[0, TR])"
+      ],
+      "metadata": {
+        "id": "jI-QNyKkdpO7"
+      },
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "source": [
+        "#### **DOWNLOAD `.SEQ` FILE**"
+      ],
+      "metadata": {
+        "id": "YkctaLKud8uV"
+      }
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "from google.colab import files\n",
+        "\n",
+        "seq.write('esmrmb_demo_20211215.seq')\n",
+        "\n",
+        "files.download('esmrmb_demo_20211215.seq')"
+      ],
+      "metadata": {
+        "id": "Kr1KW5JkdqcS"
+      },
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        ""
+      ],
+      "metadata": {
+        "id": "l9IZS6R-eN_j"
+      },
+      "execution_count": null,
+      "outputs": []
+    }
+  ]
+}