├── README.md
└── ECGXMLReader.py


/README.md:
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 1 | # ECGXMLReader
 2 | 
 3 | Python class for reading ECG XML files. Extracts lead voltages, and optionally augments 12L from 8L (common in GE MUSE XML).
 4 | 
 5 | ## Dependencies
 6 | Requires the following libraries:
 7 | 
 8 | - xmltodict
 9 | - numpy
10 | 
11 | ## Usage
12 | ECGXMLReader can be called by other Python scripts and used to get raw voltage values from compressed formats.
13 | ```
14 | from ECGXMLReader import ECGXMLReader
15 | 
16 | ecg = ECGXMLReader('ecg_file.xml', augmentLeads=True)
17 | 
18 | print( ecg.getLeadVoltages('I') )
19 | ```
20 | 
21 | ## Structure
22 | * ECGXMLReader
23 |   * PatientDemographics
24 |     * PatientID
25 |     * DateOfBirth
26 |     * Gender
27 |     * HeightCM
28 |     * WeightKG
29 |     * PatientLastName
30 |   * TestDemographics
31 |     * DataType
32 |     * Site
33 |     * AcquisitionDevice
34 |     * Status
35 |     * AcquisitionTime
36 |     * AcquisitionDate
37 |     * CartNumber
38 |     * AcquisitionSoftwareVersion
39 |   * RestingECGMeasurements
40 |     * ECGSampleBase
41 |     * ECGSampleExponent
42 |   * Waveform
43 |     * WaveformType
44 |     * WaveformStartTime
45 |     * NumberOfLeads
46 |     * SampleType
47 |     * SampleBase
48 |     * SampleExponent
49 |     * LeadData
50 |       * LeadByteCountTotal
51 |       * LeadTimeOffset
52 |       * LeadSampleCountTotal
53 |       * LeadAmplitudeUnitsPerBit
54 |       * LeadAmplitudeUnits
55 |       * LeadHighLimit
56 |       * LeadLowLimit
57 |       * LeadID
58 |       * LeadOffsetFirstSample
59 |       * FirstSampleBaseline
60 |       * LeadSampleSize
61 |       * LeadOff
62 |       * BaselineSway
63 |       * LeadDataCRC32
64 |       * WaveFormData
65 | 


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/ECGXMLReader.py:
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 1 | import os
 2 | import csv
 3 | import array
 4 | import base64
 5 | import xmltodict
 6 | 
 7 | import numpy as np
 8 | 
 9 | __author__ = "Will Hewitt"
10 | __credits__ = ["Will Hewitt"]
11 | __version__ = "1.0.0"
12 | __maintainer__ = "Will Hewitt"
13 | __email__ = "me@hewittwill.com"
14 | __status__ = "Development"
15 | 
16 | class ECGXMLReader:
17 |     """ Extract voltage data from a ECG XML file """
18 |     def __init__(self, path, augmentLeads=False):
19 |         try: 
20 |             with open(path, 'rb') as xml:
21 |                 self.ECG = xmltodict.parse(xml.read().decode('utf8'))
22 |             
23 |             self.augmentLeads           = augmentLeads
24 |             self.path                   = path
25 | 
26 |             self.PatientDemographics    = self.ECG['RestingECG']['PatientDemographics']
27 |             self.TestDemographics       = self.ECG['RestingECG']['TestDemographics']
28 |             self.RestingECGMeasurements = self.ECG['RestingECG']['RestingECGMeasurements']
29 |             self.Waveforms              = self.ECG['RestingECG']['Waveform']
30 | 
31 |             self.LeadVoltages           = self.makeLeadVoltages()
32 |         
33 |         except Exception as e:
34 |             print(str(e))
35 |     
36 |     def makeLeadVoltages(self):
37 | 
38 |         num_leads = 0
39 | 
40 |         leads = {}
41 | 
42 |         for lead in self.Waveforms['LeadData']:
43 |             num_leads += 1
44 |             
45 |             lead_data = lead['WaveFormData']
46 |             lead_b64  = base64.b64decode(lead_data)
47 |             lead_vals = np.array(array.array('h', lead_b64))
48 | 
49 |             leads[ lead['LeadID'] ] = lead_vals
50 |         
51 |         if num_leads == 8 and self.augmentLeads:
52 | 
53 |             leads['III'] = np.subtract(leads['II'], leads['I'])
54 |             leads['aVR'] = np.add(leads['I'], leads['II'])*(-0.5)
55 |             leads['aVL'] = np.subtract(leads['I'], 0.5*leads['II'])
56 |             leads['aVF'] = np.subtract(leads['II'], 0.5*leads['I'])
57 |         
58 |         return leads
59 | 
60 |     def getLeadVoltages(self, LeadID):
61 |         return self.LeadVoltages[LeadID]
62 |     
63 |     def getAllVoltages(self):
64 |         return self.LeadVoltages


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