example.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Create test files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "%run make_test_files.py"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Load file and show its info"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Filename is: linked_file.h5 \n",
      "Keys are:\n",
      "link1/group1/data1\n",
      "link1/group1/data2\n",
      "link2/group2/data1\n",
      "link2/group2/data2\n",
      "link2/group2/data3\n",
      "link2/group2/data4\n",
      "link2/group2/data5\n",
      "non_linked_data/data5\n",
      "\n"
     ]
    }
   ],
   "source": [
    "from h5file import h5file\n",
    "h = h5file('linked_file.h5')\n",
    "print(h)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Get dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<HDF5 dataset \"data4\": shape (10,), type \"<i8\">"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "h['data4']"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Get the array"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([ 2,  3,  4,  5,  6,  7,  8,  9, 10, 11])"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "h['data4'][()]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Show all keys"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['link1/group1/data1',\n",
       " 'link1/group1/data2',\n",
       " 'link2/group2/data1',\n",
       " 'link2/group2/data2',\n",
       " 'link2/group2/data3',\n",
       " 'link2/group2/data4',\n",
       " 'link2/group2/data5',\n",
       " 'non_linked_data/data5']"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "h.keys()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Get a subset of keys"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Anything with data1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['link1/group1/data1', 'link2/group2/data1']"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "h.keys(getkey='data1')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "data2 or data5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['link1/group1/data2', 'link2/group2/data2', 'link2/group2/data4']"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "h.keys(getkey=r'data2|data4')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "from link1 with data between 2 and 4"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['link2/group2/data2', 'link2/group2/data3', 'link2/group2/data4']"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "h.keys(getkey=r'link2.*data[2-4]')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "key starts with n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['non_linked_data/data5']"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "h.keys(getkey=r'^n')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Within IPython keys starting with n can be typing `h['n` and pressing `tab`."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## sum data in link 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 49 reference 49\n"
     ]
    }
   ],
   "source": [
    "total = sum(dataset[:].sum() for key, dataset in h.items(getkey='^link1'))\n",
    "print(\"total {} reference {}\".format(total, np.sum(np.arange(1, 5)).sum() + np.arange(4,10).sum()))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "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": "3.10.3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}