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Example usage of interface

Here is an example of how to read, write, modify and inspect a HDF5 dataset from a kdb+ session. The associated repository has examples with more functionality.

KxSystems/hdf5-kdb/examples

A typical workflow when dealing with HDF5 data:

Create a .h5 file

Create a .h5 file to house experimental datasets.

//create a file named appropriately
q)fname:"experiments.h5"
q).hdf5.createFile fname

//Check that this file exists
q).hdf5.ishdf5 fname
1b

Create a dataset

Create a dataset containing experimental information and write to a file.

// Create a dataset of floating point data and write to HDF5
q)show dset:dims#prd[dims:5*1+til 5]?10f
3.927524  5.170911 5.159796  4.066642  1.780839  3.017723 7.85033    5.347096..
1.572794   4.25421    2.573062  1.30827   1.930758  6.585985   3.227891 3.888..
9.822297  8.278122  6.610537 5.013077  8.215865 2.360797  6.881804 1.411613  ..
9.674024   9.491312  8.290642  8.987704  6.497505  1.057242   4.66386   8.425..
5.260983  4.556574   9.517531 5.659605  0.864824  0.8628434 4.824764  3.95274..
q)dset_name:"experiment1_data"
q).hdf5.writeData[fname;dset_name;dset]

// Inspect the content of the file to ensure the data has been written to file
q).hdf5.ls fname
type | dataset
name | `experiment1_data
value| (`symbol$())!()

Add attributes to the dataset

Add attributes to the dataset indicating who collected the dataset and the temperature of the room at the start and end of data collection.

// Add an attribute named for the scientists collecting data
q)user_attr:"Completed by"
q).hdf5.writeAttr[fname;dset_name;user_attr;"Alice and Bob"]

// Add an attribute indicating room temperature
q)temp_attr:"Temperatures"
q).hdf5.writeAttr[fname;dset_name;temp_attr;21.7 20.3]

Create a group

Create a group to contain tables related to another experiment.

// Create a group within the dataset
q)gname:"experiment2_tables"
q).hdf5.createGroup[fname;gname]

// Inspect the content of the file
q).hdf5.ls fname
type | dataset           group
name | `experiment1_data `experiment2_tables
value| (`symbol$())!()   (`symbol$())!()

Write a set of tabular data

Write a set of tabular data collected from sensors into the experiment2_tables group

// Create a kdb+ table and write this to a dataset in the appropriate group
q)N:10000
q)tname:gname,"/tab_dset"
q)5#dset_tab:([]tstamp:asc N?0p;voltage:N?1f;volume:N?100;class:N?10h;on_off:N?0b)
tstamp                        voltage   volume class on_off
-----------------------------------------------------------
2000.01.01D01:03:27.925513386 0.1458085 85     0     0     
2000.01.01D05:46:27.469021975 0.4981235 99     9     0     
2000.01.01D06:14:44.435858577 0.1976848 75     8     0     
2000.01.01D09:38:22.896863222 0.2246491 63     4     0     
2000.01.01D11:13:14.535212963 0.82371   45     1     0     
q).hdf5.writeData[fname;tname;dset_tab]

// Inspect the content of the file
q).hdf5.ls fname
type | dataset           group                                               ..
name | `experiment1_data `experiment2_tables                                 ..
value| (`symbol$())!()   `type`name`value!(,`group;,`tab_dset;,`type`name`val..

Read data and attributes back into kdb+

Read the data and attributes written to the file back into kdb+.

// Read back the dataset "experiment1_data"
q).hdf5.readData[fname;"experiment1_data"]
3.927524  5.170911 5.159796  4.066642  1.780839  3.017723 7.85033    5.347096..
1.572794   4.25421    2.573062  1.30827   1.930758  6.585985   3.227891 3.888..
9.822297  8.278122  6.610537 5.013077  8.215865 2.360797  6.881804 1.411613  ..
9.674024   9.491312  8.290642  8.987704  6.497505  1.057242   4.66386   8.425..
5.260983  4.556574   9.517531 5.659605  0.864824  0.8628434 4.824764  3.95274..

// Read the attributes outlining the scientists and temperatures at the time of the experiment
q).hdf5.readAttr[fname;dset_name;]each(user_attr;temp_attr)
"Alice and Bob"
21.7 20.3

// Read the table stored for in "experiment2_tables" back to kdb+
q)5#.hdf5.readData[fname;"experiment2_tables/tab_dset"]
tstamp                        fdata     jdata                hdata bdata
------------------------------------------------------------------------
2000.01.01D02:36:49.894041717 0.6629197 7562568519879588350  0     1    
2000.01.01D03:40:09.942953288 0.5822169 3403572723019440513  1     0    
2000.01.01D08:39:00.615521371 0.2564546 4273682761033353527  0     0    
2000.01.01D12:09:27.866282165 0.1936573 3462325873973710832  4     1    
2000.01.02D05:48:47.516824007 0.1653556 110707218304197100   3     1    
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