{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Using HDF5 with Python"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Import the required libraries"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from pandas import (\n",
" DataFrame, HDFStore\n",
")\n",
"import pandas as pd\n",
"import numpy as np"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Create a dataframe"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"df = DataFrame(np.random.randn(5,3), columns=['A', 'B', 'C',])"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
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" A B C\n",
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"3 0.729817 -0.042234 0.229410\n",
"4 -1.117705 -0.778368 -1.280790"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Create a HDF5 format file for saving th dataframe"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"store = HDFStore('dataset.h5')"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"\n",
"File path: dataset.h5\n",
"Empty"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"store"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Add the dataframe to the HDF5 file"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"store.put('d1', df, format='table', data_columns=True)"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"\n",
"File path: dataset.h5\n",
"/d1 frame_table (typ->appendable,nrows->5,ncols->3,indexers->[index],dc->[A,B,C])"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"store"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Accessing the dataframe from HDF5 file"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
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"text/plain": [
" A B C\n",
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"3 0.729817 -0.042234 0.229410\n",
"4 -1.117705 -0.778368 -1.280790"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"store['d1']"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Appending another dataframe to already exisiting dataframe in HDF5 file"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"store.append('d1', DataFrame(np.random.randn(5,3), columns=['A', 'B', 'C']))"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"\n",
"File path: dataset.h5\n",
"/d1 frame_table (typ->appendable,nrows->10,ncols->3,indexers->[index],dc->[A,B,C])"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"store"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
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"4 1.442614 0.818815 -0.378552"
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},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"store['d1']"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Closing the HDF5 file"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"store.close()"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"\n",
"File path: dataset.h5\n",
"File is CLOSED"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"store"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Opening HDF5 file - Method 1 (not advised)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"df = pd.read_hdf('dataset.h5')"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
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" A B C\n",
"0 -0.092894 0.480401 -0.967241\n",
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"3 0.729817 -0.042234 0.229410\n",
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"4 1.442614 0.818815 -0.378552"
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},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Opening HDF5 file - Method 2 (recommended way)"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"store = HDFStore('dataset.h5')"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"\n",
"File path: dataset.h5\n",
"/d1 frame_table (typ->appendable,nrows->10,ncols->3,indexers->[index],dc->[A,B,C])"
]
},
"execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"store"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Adding dataframe to the opened HDF5, using the default format"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"store.put('d2', DataFrame(np.random.randn(7,4)))\n",
"store.put('d3', DataFrame(np.random.randn(14,3)))"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"\n",
"File path: dataset.h5\n",
"/d1 frame_table (typ->appendable,nrows->10,ncols->3,indexers->[index],dc->[A,B,C])\n",
"/d2 frame (shape->[7,4]) \n",
"/d3 frame (shape->[14,3]) "
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"store"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Difference between frame_table and frame formats"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### frame_table format"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"store.append('d1', pd.DataFrame(np.random.randn(3,3), columns=['A', 'B', 'C']))"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
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"execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"store['d1']"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### frame format"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {
"collapsed": false
},
"outputs": [
{
"ename": "ValueError",
"evalue": "Can only append to Tables",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mstore\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'd2'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mpd\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mDataFrame\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mrandom\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mrandn\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;36m4\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;36m4\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32mC:\\Users\\Jeri_Dabba\\pandas\\io\\pytables.pyc\u001b[0m in \u001b[0;36mappend\u001b[0;34m(self, key, value, format, append, columns, dropna, **kwargs)\u001b[0m\n\u001b[1;32m 917\u001b[0m \u001b[0mkwargs\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_validate_format\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mformat\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m 918\u001b[0m self._write_to_group(key, value, append=append, dropna=dropna,\n\u001b[0;32m--> 919\u001b[0;31m **kwargs)\n\u001b[0m\u001b[1;32m 920\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m 921\u001b[0m def append_to_multiple(self, d, value, selector, data_columns=None,\n",
"\u001b[0;32mC:\\Users\\Jeri_Dabba\\pandas\\io\\pytables.pyc\u001b[0m in \u001b[0;36m_write_to_group\u001b[0;34m(self, key, value, format, index, append, complib, encoding, **kwargs)\u001b[0m\n\u001b[1;32m 1250\u001b[0m if (not s.is_table or\n\u001b[1;32m 1251\u001b[0m (s.is_table and format == 'fixed' and s.is_exists)):\n\u001b[0;32m-> 1252\u001b[0;31m \u001b[1;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'Can only append to Tables'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1253\u001b[0m \u001b[1;32mif\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[0ms\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mis_exists\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m 1254\u001b[0m \u001b[0ms\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mset_object_info\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[0;31mValueError\u001b[0m: Can only append to Tables"
]
}
],
"source": [
"store.append('d2', pd.DataFrame(np.random.randn(4,4)))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### The frame format (default) is faster than frame_table format"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### To view the dataframe with ordered index"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {
"collapsed": false
},
"outputs": [
{
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"execution_count": 23,
"metadata": {},
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}
],
"source": [
"store['d1/table']"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### To get the dataframe from the HDF5 file"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"df = store['d1']"
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{
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"execution_count": 25,
"metadata": {},
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"source": [
"df"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"store.close()"
]
}
],
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