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.. _working_with_waveform_data:
.. title:: Working with Waveform Data
Working with Waveform Data
==========================
.. currentmodule:: pydicom
.. rubric:: How to work with waveform data in pydicom.
Introduction
------------
Some DICOM SOP classes such as :dcm:`Basic Voice Audio Waveform
<part03/sect_A.34.2.html>` and :dcm:`12-Lead ECG<part03/sect_A.34.3.html>`
contain a (5400,0100) *Waveform Sequence* element,
where each item in the sequence is a related group of waveforms (a multiplex).
The requirements of the sequence is given by the :dcm:`Waveform
module <part03/sect_C.10.9.html>` in Part 3, Annex C.10.9 of the DICOM
Standard.
Each multiplex consists of one or more channels synchronised at a
common sampling frequency (in Hz), which is given by the (003A,001A) *Sampling
Frequency*. The waveform data for each multiplex is encoded in the
corresponding (5400,1010) *Waveform Data* element.
>>> from pydicom import dcmread
>>> from pydicom.data import get_testdata_file
>>> fpath = get_testdata_file("waveform_ecg.dcm")
>>> ds = dcmread(fpath)
>>> ds.WaveformSequence
<Sequence, length 2>
>>> multiplex = ds.WaveformSequence[0]
>>> multiplex.NumberOfWaveformChannels
12
>>> multiplex.SamplingFrequency
"1000.0"
>>> multiplex['WaveformData']
(5400, 1010) Waveform Data OW: Array of 240000 elements
``Dataset.waveform_array()``
----------------------------
.. warning::
:attr:`Dataset.waveform_array<pydicom.dataset.Dataset.waveform_array>`
requires `NumPy <http://numpy.org/>`_.
The *Waveform Data* element contains the raw bytes exactly as found in the
file. To get the waveforms in a more useful form you can use the
:attr:`~pydicom.dataset.Dataset.waveform_array` method to return a
a :class:`numpy.ndarray` with shape (samples, channels) for the multiplex
group at `index` in the *Waveform Sequence*.
>>> multiplex_1 = ds.waveform_array(0)
>>> multiplex_1
array([[ 100. , 112.5 , 12.5 , ..., -25. , -68.75, -50. ],
[ 81.25, 106.25, 25. , ..., -25. , -75. , -50. ],
[ 62.5 , 100. , 37.5 , ..., -25. , -81.25, -50. ],
...,
[ 25. , 131.25, 106.25, ..., -137.5 , -150. , -100. ],
[ 21.25, 137.5 , 116.25, ..., -137.5 , -150. , -106.25],
[ 25. , 137.5 , 112.5 , ..., -137.5 , -150. , -112.5 ]])
>>> multiplex_1.shape
(10000, 12)
>>> multiplex_2 = ds.waveform_array(1)
>>> multiplex_2.shape
(1200, 12)
If the *Channel Sensitivity Correction Factor* is available for a given channel
then it will be applied to the raw channel data. If you need the raw data
without any corrections then you can use the
:func:`~pydicom.waveforms.numpy_handler.multiplex_array`
function with the *as_raw* keyword parameter instead:
>>> from pydicom.waveforms import multiplex_array
>>> arr = multiplex_array(ds, 0, as_raw=True)
>>> arr
array([[ 80, 90, 10, ..., -20, -55, -40],
[ 65, 85, 20, ..., -20, -60, -40],
[ 50, 80, 30, ..., -20, -65, -40],
...,
[ 20, 105, 85, ..., -110, -120, -80],
[ 17, 110, 93, ..., -110, -120, -85],
[ 20, 110, 90, ..., -110, -120, -90]], dtype=int16)
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