DEMO_Getcutout_SciServer.ipynb

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    "<hr style = \"height:6px;border:none;background-color:sienna\">\n",
    "\n",
    "<h2 style = \"font-weight:bold;font-style:italic\">\n",
    "    Getcutout demo notebook\n",
    "</h2>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    &emsp;n.b. requires python 3.9+\n",
    "</p>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>purpose</u> :\n",
    "    <br>\n",
    "    &emsp;- SciServer processing of JHTDB datasets.\n",
    "    <br><br>\n",
    "    <u>supported datasets</u> :\n",
    "</p>\n",
    "\n",
    "<ul>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        isotropic1024coarse &ensp;: &ensp;isotropic 1024-cube (coarse).\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        isotropic1024fine &ensp;: &ensp;isotropic 1024-cube (fine).\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        isotropic4096 &ensp;: &ensp;isotropic 4096-cube.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        isotropic8192 &ensp;: &ensp;isotropic 8192-cube.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        sabl2048low &ensp;: &ensp;stable atmospheric boundary layer 2048-cube, low-rate timestep.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        sabl2048high &ensp;: &ensp;stable atmospheric boundary layer 2048-cube, high-rate timestep.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        rotstrat4096 &ensp;: &ensp;rotating stratified 4096-cube.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        mhd1024 &ensp;: &ensp;magneto-hydrodynamic isotropic 1024-cube.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        mixing &ensp;: &ensp;homogeneous buoyancy driven 1024-cube.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        channel &ensp;: &ensp;channel flow.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        channel5200 &ensp;: &ensp;channel flow (reynolds number 5200).\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        transition_bl &ensp;: &ensp;transitional boundary layer.\n",
    "    </li>\n",
    "</ul>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>functions</u> :\n",
    "</p>\n",
    "\n",
    "<ul>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        getCutout &ensp;: &ensp;read data for a user-specified box.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        write_cutout_hdf5_and_xmf_files &ensp;: &ensp;write getCutout results to .h5 and .xmf files.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        cutout_values &ensp;: &ensp;see values for specific point(s) in the getCutout data.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        contour_plot &ensp;: &ensp;create a contour plot of getCutout data.\n",
    "    </li>\n",
    "</ul>"
   ]
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    "<hr style = \"height:6px;border:none;background-color:sienna\">\n",
    "\n",
    "<h4 style = \"font-weight:bold;font-style:italic\">\n",
    "    instantiate dataset\n",
    "</h4>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>purpose</u> : \n",
    "    <br>\n",
    "    &emsp;- instantiate the dataset and cache the metadata.\n",
    "    <br>\n",
    "\n",
    "</p>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>parameters</u> :\n",
    "</p>\n",
    "\n",
    "<ul>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        auth_token &ensp;: &ensp;turbulence user authorization token.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        dataset_title &ensp;: &ensp;name of the turbulence dataset.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        output_path &ensp;: &ensp;folder path in the \"scratch\" folder of the \"Temporary\" directory of the user's SciServer container.\n",
    "        <br>\n",
    "        &emsp;- default (if left blank) &ensp;: &ensp;/home/idies/workspace/Temporary/USERNAME/scratch/turbulence_output\n",
    "        <br>\n",
    "        &emsp;- output files will be saved in this folder.\n",
    "    </li>\n",
    "</ul>\n",
    "\n",
    "<hr style = \"height:6px;border:none;background-color:sienna\">"
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    "\"\"\"\n",
    "instantiate dataset\n",
    "\"\"\"\n",
    "from giverny.turbulence_dataset import *\n",
    "from giverny.turbulence_toolkit import *\n",
    "\n",
    "auth_token = 'edu.jhu.pha.turbulence.testing-201406'\n",
    "dataset_title = 'channel'\n",
    "output_path = ''\n",
    "\n",
    "# instantiate the dataset.\n",
    "dataset = turb_dataset(dataset_title = dataset_title, output_path = output_path, auth_token = auth_token)"
   ]
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   "cell_type": "markdown",
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   "source": [
    "<hr style = \"height:6px;border:none;background-color:sienna\">\n",
    "\n",
    "<h4 style = \"font-weight:bold;font-style:italic\">\n",
    "    getCutout\n",
    "</h4>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>purpose</u> : \n",
    "    <br>\n",
    "    &emsp;- retrieve the user-requested box.\n",
    "    <br>\n",
    "</p>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>steps</u> :\n",
    "</p>\n",
    "\n",
    "<ul>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        step 1 &ensp;: &ensp;identify the database files to be read.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        step 2 &ensp;: &ensp;read the database files and store the data in a matrix.\n",
    "    </li>\n",
    "</ul>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>parameters</u> :\n",
    "</p>\n",
    "\n",
    "<ul>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        x_range, y_range, z_range &ensp;: &ensp;axes ranges defining the box for which data values will be read.\n",
    "        <br>\n",
    "        &emsp;- specify each axis range as [minimum, maximum].\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        x_stride, y_stride, z_stride &ensp;: &ensp;axes strides, i.e. the number of points between each step along the axes.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        variable &ensp;: &ensp;type of data (velocity, pressure, energy, temperature, force, magneticfield, vectorpotential, density).\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        time &ensp;: &ensp;snapshot number.\n",
    "    </li>\n",
    "</ul>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>output</u> :\n",
    "</p>\n",
    "\n",
    "<ul>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        result &ensp;: &ensp;matrix corresponding to variable at time in axes_ranges with strides.\n",
    "    </li>\n",
    "</ul>\n",
    "\n",
    "<hr style = \"height:6px;border:none;background-color:sienna\">"
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    "\"\"\"\n",
    "process getCutout data\n",
    "\"\"\"\n",
    "variable = 'velocity'\n",
    "time = 1\n",
    "\n",
    "x_range = [1, 4]\n",
    "y_range = [1, 32]\n",
    "z_range = [1, 32]\n",
    "\n",
    "x_stride = 1\n",
    "y_stride = 1\n",
    "z_stride = 1\n",
    "\n",
    "\"\"\"\n",
    "use the tools and processing gizmos.\n",
    "\"\"\"\n",
    "# combine all of the axis data together for simplicity.\n",
    "axes_ranges = np.array([x_range, y_range, z_range])\n",
    "strides = np.array([x_stride, y_stride, z_stride])\n",
    "\n",
    "# process a brick cutout.\n",
    "result = getCutout(dataset, variable, time, axes_ranges, strides)"
   ]
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   "cell_type": "markdown",
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   "source": [
    "<hr style = \"height:6px;border:none;background-color:sienna\">\n",
    "\n",
    "<h4 style = \"font-weight:bold;font-style:italic\">\n",
    "    save cutout results\n",
    "</h4>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>purpose</u> : \n",
    "    <br>\n",
    "    &emsp;- save the cutout retrieved by the getCutout function.\n",
    "    <br>\n",
    "</p>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>parameters</u> :\n",
    "</p>\n",
    "\n",
    "<ul>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "         dataset &ensp;: &ensp;the instantiated dataset.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "         axes_ranges &ensp;: &ensp;parameter used by getCutout.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "         result &ensp;: &ensp;output from getCutout.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        output_filename &ensp;: &ensp;filename for the tsv file to be saved in the output_path folder.\n",
    "    </li>\n",
    "</ul>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>output</u> :\n",
    "</p>\n",
    "\n",
    "<ul>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        hdf5, xmf files &ensp;: &ensp;saved to output_filename in the output_path folder.\n",
    "    </li>\n",
    "</ul>\n",
    "\n",
    "<hr style = \"height:6px;border:none;background-color:sienna\">"
   ]
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   "cell_type": "code",
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    "\"\"\"\n",
    "write the cutout results to hdf5 and xmf files\n",
    "\"\"\"\n",
    "output_filename = 'turbulence-cutout'\n",
    "\n",
    "\"\"\"\n",
    "use the hdf5 and xmf writing gizmo.\n",
    "\"\"\"\n",
    "# writes the output hdf5 and xmf files.\n",
    "write_cutout_hdf5_and_xmf_files(dataset, result, axes_ranges, output_filename)"
   ]
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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<hr style = \"height:6px;border:none;background-color:sienna\">\n",
    "\n",
    "<h4 style = \"font-weight:bold;font-style:italic\">\n",
    "    cutout values\n",
    "</h4>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>purpose</u> : \n",
    "    <br>\n",
    "    &emsp;- retrieve the data value(s) for a datapoint (x, y, z), or a range of datapoints, e.g. x = range(1, 5), in the getCutout data.\n",
    "    <br>\n",
    "    &emsp;- note: range(min, max) will retrieve data values for points \"min\" through (\"max\" - 1).\n",
    "    <br>\n",
    "</p>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>parameters</u> :\n",
    "</p>\n",
    "\n",
    "<ul>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        dataset &ensp;: &ensp;the instantiated dataset.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "         axes_ranges, strides &ensp;: &ensp;parameters used by getCutout.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "         result &ensp;: &ensp;output from getCutout.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        x &ensp;: &ensp;x-axis datapoint(s).\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        y &ensp;: &ensp;y-axis datapoint(s).\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        z &ensp;: &ensp;z-axis datapoint(s).\n",
    "    </li>\n",
    "</ul>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>output</u> :\n",
    "</p>\n",
    "\n",
    "<ul>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        cutout_value &ensp;: &ensp;data value(s) of the requested datapoint(s).\n",
    "    </li>\n",
    "</ul>\n",
    "\n",
    "<hr style = \"height:6px;border:none;background-color:sienna\">"
   ]
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    "\"\"\"\n",
    "data values\n",
    "\"\"\"\n",
    "x = 4\n",
    "y = 5\n",
    "z = 8\n",
    "\n",
    "\"\"\"\n",
    "use the data values gizmo.\n",
    "\"\"\"\n",
    "cutout_value = cutout_values(dataset, x, y, z, result, axes_ranges, strides)\n",
    "\n",
    "cutout_value"
   ]
  },
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   "metadata": {},
   "source": [
    "<hr style = \"height:6px;border:none;background-color:sienna\">\n",
    "\n",
    "<h4 style = \"font-weight:bold;font-style:italic\">\n",
    "    contour plot\n",
    "</h4>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>purpose</u> : \n",
    "    <br>\n",
    "    &emsp;- create a contour plot from the getCutout data.\n",
    "    <br>\n",
    "    &emsp;- note: one of the axis ranges should be a single point, e.g. z_plot_range = [3, 3], since the contour plot is 2-dimensional.\n",
    "    <br>\n",
    "</p>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>parameters</u> :\n",
    "</p>\n",
    "\n",
    "<ul>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        dataset &ensp;: &ensp;the instantiated dataset.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "         axes_ranges, strides &ensp;: &ensp;parameters used by getCutout.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "         result &ensp;: &ensp;output from getCutout.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        x_plot_range &ensp;: &ensp;x-axis plot range.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        y_plot_range &ensp;: &ensp;y-axis plot range.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        z_plot_range &ensp;: &ensp;z-axis plot range.\n",
    "    </li>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "         plot_ranges &ensp;: &ensp;combined array of x_plot_range, y_plot_range, and z_plot_range.\n",
    "    </li>\n",
    "    <br>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        plot_component &ensp;: &ensp;the component (column) of the values to plot.\n",
    "        <br>\n",
    "        &emsp;- 0 corresponds to the \"ux\" component of the velocity data or the scalar magnitude of the scalar data (e.g. pressure).\n",
    "        <br>\n",
    "        &emsp;- 1 corresponds to the \"uy\" component of the velocity data.\n",
    "        <br>\n",
    "        &emsp;- 2 corresponds to the \"uz\" component of the velocity data.\n",
    "    </li>\n",
    "    <br>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        output_filename &ensp;: &ensp;filename for the contour plot to be saved in the output_path folder.\n",
    "    </li>\n",
    "</ul>\n",
    "\n",
    "<p style = \"font-weight:bold;font-size:13px\">\n",
    "    <u>output</u> :\n",
    "</p>\n",
    "\n",
    "<ul>\n",
    "    <li style = \"font-weight:bold;font-size:13px\">\n",
    "        contour plot &ensp;: &ensp;displayed in the notebook and saved to output_filename in the output_path folder.\n",
    "    </li>\n",
    "</ul>\n",
    "\n",
    "<hr style = \"height:6px;border:none;background-color:sienna\">"
   ]
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    "\"\"\"\n",
    "contour plot\n",
    "\"\"\"\n",
    "x_plot_range = [1, 1]\n",
    "y_plot_range = [1, 32]\n",
    "z_plot_range = [1, 32]\n",
    "\n",
    "plot_component = 0\n",
    "\n",
    "output_filename = 'turbulence-plane_contour_plot'\n",
    "\n",
    "\"\"\"\n",
    "use the tools and contour plot gizmo.\n",
    "\"\"\"\n",
    "# combine all of the plot axis ranges together for simplicity.\n",
    "plot_ranges = np.array([x_plot_range, y_plot_range, z_plot_range])\n",
    "\n",
    "# create the contour plot.\n",
    "contour_plot(dataset, plot_component, result, plot_ranges, axes_ranges, strides, output_filename)"
   ]
  },
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