add nexus compatibility testign notebook

Author: Rama Vasudevan

notebooks/00_basic_usage/sippy_Nexus_testing.ipynb

@@ -0,0 +1,193 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "d9e1079f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "import sidpy as sid\n",
+    "import pyNSID as nsid\n",
+    "import h5py"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4c562c94",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def axis_generator(start_letter='i', prefix='axis_'):\n",
+    "    \"\"\"\n",
+    "    Generates strings with prefix + letters from start_letter to 'z'.\n",
+    "    \n",
+    "    Args:\n",
+    "        start_letter (str): starting letter (default 'i')\n",
+    "        prefix (str): string prefix (default 'axis_')\n",
+    "    \n",
+    "    Yields:\n",
+    "        str: e.g. \"axis_i\", \"axis_j\", ...\n",
+    "    \"\"\"\n",
+    "    start_ord = ord(start_letter.lower())\n",
+    "    end_ord = ord('z')\n",
+    "    \n",
+    "    for c in range(start_ord, end_ord + 1):\n",
+    "        yield prefix + chr(c)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "f51806e7",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(50, 2, 80, 128)\n",
+      "(50, 80, 128)\n"
+     ]
+    }
+   ],
+   "source": [
+    "all_results = np.load('all_results.npy')\n",
+    "\n",
+    "amp_mat = all_results[:,0,:,:]\n",
+    "phase_mat = all_results[:,1,:,:]\n",
+    "pr_mat = amp_mat*np.cos(phase_mat)\n",
+    "\n",
+    "print(pr_mat.shape) #line_number, time step, x\n",
+    "#Make sidpy dataset from the amplitude, phase and PR mats\n",
+    "\n",
+    "pr_mat_sid = sid.Dataset.from_array(pr_mat, name='pr_mat')\n",
+    "amp_mat_sid = sid.Dataset.from_array(amp_mat, name='amp_mat')\n",
+    "phase_mat_sid = sid.Dataset.from_array(phase_mat, name='phase_mat')\n",
+    "\n",
+    "#make the dimension vectors\n",
+    "line_vector = 2.0E-6*np.linspace(-1,1,pr_mat.shape[0]) #position in y for the line\n",
+    "time_step_vector = np.arange(pr_mat.shape[1])\n",
+    "x_vector = np.linspace(0, 2.0E-6, pr_mat.shape[2])\n",
+    "\n",
+    "for sid_dset in [pr_mat_sid, amp_mat_sid, phase_mat_sid]:\n",
+    "    sid_dset.data_type = 'spectral_image'  # supported\n",
+    "    sid_dset.units = 'a.u.'\n",
+    "    sid_dset.quantity = 'Piezoresponse'\n",
+    "    sid_dset.set_dimension(0, sid.Dimension(line_vector,\n",
+    "                                          name='y', units='um', quantity='Width',\n",
+    "                                          dimension_type='spatial'))\n",
+    "    sid_dset.set_dimension(1, sid.Dimension(time_step_vector,\n",
+    "                                          'time', units='Time Step', quantity='Time',\n",
+    "                                          dimension_type='spectral'))\n",
+    "    sid_dset.set_dimension(2, sid.Dimension(x_vector,\n",
+    "                                          'x', units='um', quantity = 'Length', dimension_type='spatial' ))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8aa44d48",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data = {'piezoresponse': pr_mat_sid}\n",
+    "h5_name = 'test_h5_file2.h5'\n",
+    "\n",
+    "with h5py.File(h5_name, 'w') as h5_f:\n",
+    "    h5_group = h5_f.create_group('Measurement_Nexus')\n",
+    "    my_str = \"NXsidpy\"\n",
+    "    def_dset = h5_group.create_dataset('definition', data=my_str)\n",
+    "    \n",
+    "    for key in list(data.keys()):\n",
+    "        h5_g = h5_group.create_group(key)\n",
+    "        nsid.hdf_io.write_nsid_dataset(data[key], h5_g)\n",
+    "    "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5ac219bb",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "h5_g = h5_f['Measurement_Nexus/piezoresponse/generic']\n",
+    "dset_dims = []\n",
+    "[dset_dims.append(dim) for dim in h5_g if dim !='generic']\n",
+    "print(dset_dims)\n",
+    "\n",
+    "# Example usage:\n",
+    "gen = axis_generator()\n",
+    "axis_ij_names = []\n",
+    "for ind,dset in enumerate(dset_dims):\n",
+    "    axis_name = next(gen)\n",
+    "    axis_ij_names.append(axis_name)\n",
+    "    h5_g.copy(dset, axis_name)\n",
+    "\n",
+    "axes_refs = np.array(\n",
+    "            axis_ij_names,\n",
+    "            dtype='object'\n",
+    "        )\n",
+    "h5_g.attrs[\"NX_class\"] = \"NXdata\"\n",
+    "h5_g.attrs[\"axes\"] = axes_refs\n",
+    "\n",
+    "for ind in range(len(axis_ij_names)):\n",
+    "    lab = axis_ij_names[ind]+\"_indices\"\n",
+    "    h5_g.attrs[lab]=ind\n",
+    "\n",
+    "for ind,axis in enumerate(axis_ij_names):\n",
+    "    h5_g[axis].attrs[\"units\"] = h5_g[dset_dims[ind]].attrs['units']\n",
+    "    h5_g[axis].attrs[\"long_name\"] = h5_g[dset_dims[ind]].attrs['name']\n",
+    "\n",
+    "h5_g.attrs[\"default\"] = \"generic\"\n",
+    "h5_f.attrs[\"default\"] = key\n",
+    "       \n",
+    "del h5_f['Measurement_Nexus'][key]['generic']['generic'].attrs[\"DIMENSION_LIST\"] #delete dimension list attribute\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "000e0ce6",
+   "metadata": {},
+   "source": [
+    "#Reminder:\n",
+    "1. pyNSID shoudl only write to a Nexus compatible file format\n",
+    "2. When we read the file back, we shoudl read it back as a sidpy dataset format. We need to make sure to be able to read back files that are NSID-NExus compatible and the older (standard) NSID format."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c44123ae",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.11.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}