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docs/source/generated/examples/aif/plot_aif_parker.ipynb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,113 +1,97 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "\n# The Parker AIF - a play with variables\n\nSimulating a Parker AIF with different settings. \n" | ||
| ] | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "\n# The Parker AIF - a play with variables\n\nSimulating a Parker AIF with different settings.\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import matplotlib.pyplot as plt" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Import necessary packages\n\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import numpy as np\nimport osipi" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Generate synthetic AIF with default settings and plot the result.\n\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Define time points in units of seconds - in this case we use a time\n# resolution of 0.5 sec and a total duration of 6 minutes.\nt = np.arange(0, 6 * 60, 0.5)\n\n# Create an AIF with default settings\nca = osipi.aif_parker(t)\n\n# Plot the AIF over the full range\nplt.plot(t, ca, \"r-\")\nplt.plot(t, 0 * t, \"k-\")\nplt.xlabel(\"Time (sec)\")\nplt.ylabel(\"Plasma concentration (mM)\")\nplt.show()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "The bolus arrival time (BAT) defaults to 0s. What happens if we\nchange it? Let's try, by changing it in steps of 30s:\n\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "ca = osipi.aif_parker(t, BAT=0)\nplt.plot(t, ca, \"b-\", label=\"BAT = 0s\")\nca = osipi.aif_parker(t, BAT=30)\nplt.plot(t, ca, \"r-\", label=\"BAT = 30s\")\nca = osipi.aif_parker(t, BAT=60)\nplt.plot(t, ca, \"g-\", label=\"BAT = 60s\")\nca = osipi.aif_parker(t, BAT=90)\nplt.plot(t, ca, \"m-\", label=\"BAT = 90s\")\nplt.xlabel(\"Time (sec)\")\nplt.ylabel(\"Plasma concentration (mM)\")\nplt.legend()\nplt.show()\n\n# Choose the last image as a thumbnail for the gallery\n# sphinx_gallery_thumbnail_number = -1" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.10.8" | ||
| } | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Import necessary packages\n\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import numpy as np\n", | ||
| "import matplotlib.pyplot as plt\n", | ||
| "import osipi" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Generate synthetic AIF with default settings and plot the result.\n\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Define time points in units of seconds - in this case we use a time resolution of 0.5 sec and a total duration of 6 minutes.\n", | ||
| "t = np.arange(0, 6 * 60, 0.5)\n", | ||
| "\n", | ||
| "# Create an AIF with default settings\n", | ||
| "ca = osipi.aif_parker(t)\n", | ||
| "\n", | ||
| "# Plot the AIF over the full range\n", | ||
| "plt.plot(t, ca, \"r-\")\n", | ||
| "plt.plot(t, 0 * t, \"k-\")\n", | ||
| "plt.xlabel(\"Time (sec)\")\n", | ||
| "plt.ylabel(\"Plasma concentration (mM)\")\n", | ||
| "plt.show()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "The bolus arrival time (BAT) defaults to 0s. What happens if we change it? Let's try, by changing it in steps of 30s:\n\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "ca = osipi.aif_parker(t, BAT=0)\n", | ||
| "plt.plot(t, ca, \"b-\", label=\"BAT = 0s\")\n", | ||
| "ca = osipi.aif_parker(t, BAT=30)\n", | ||
| "plt.plot(t, ca, \"r-\", label=\"BAT = 30s\")\n", | ||
| "ca = osipi.aif_parker(t, BAT=60)\n", | ||
| "plt.plot(t, ca, \"g-\", label=\"BAT = 60s\")\n", | ||
| "ca = osipi.aif_parker(t, BAT=90)\n", | ||
| "plt.plot(t, ca, \"m-\", label=\"BAT = 90s\")\n", | ||
| "plt.xlabel(\"Time (sec)\")\n", | ||
| "plt.ylabel(\"Plasma concentration (mM)\")\n", | ||
| "plt.legend()\n", | ||
| "plt.show()\n", | ||
| "\n", | ||
| "# Choose the last image as a thumbnail for the gallery\n", | ||
| "# sphinx_gallery_thumbnail_number = -1" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.9.16" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 0 | ||
| "nbformat": 4, | ||
| "nbformat_minor": 0 | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| 2ad42a0f8a1b8aa8ec46f9a5f66e86e4 | ||
| e93d51ea52bd242140d5fb616a34364e |
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