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musexmlex.py
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#!/usr/bin/env python
"""_______________________________________________________________________________
xmlecgex: An utility to extract an ECG rhythm strip from a MUSE(R) XML file
Copyright (C) 2009 GE Healthcare
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program (it is embedded in the text of this script).
If not, see <http://www.gnu.org/licenses/>.
You may contact the author by e-mail ([email protected]) or postal
mail (Anthony D. Ricke, GE Healthcare, RP 2122, 9900 Innovation Drive,
Wauwatosa, WI 53226 USA). For updates to this software, please visit the
Source Forge project site (http://sourceforge.net/projects/musexmlexport/)
- MUSE is a registered trademark of GE Healthcare, Inc.
_______________________________________________________________________________
This script reads a MUSE(R) XML ECG file and writes two output files:
1. A binary ZCG buffer that contains all of the discovered independent leads in the XML
2. A CSV (comma seperated value) file, suitable for import into a spreadsheet program
DISCLAIMER: This is not a GE Healthcare product. Neither this tool, nor its
output, can it be used to make medical diagnosis or treatment.
Usage:
python musexmlex.py [-h|-w|-c] file.xml
Example:
python musexmlex.py MUSE_20080702_120153_57000.xml
Known Bugs:
- Error checking is essentially ignored
NOTE ON PYTHON.
Python is a free scripting language, available at www.python.org.
For best results, use a Python-aware IDE when editing this script. I prefer
Komodo Edit 4.4, but may others are available.
"""
WARRANTY = """
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
DISCLAIMER.
THIS IS NOT A MEDICAL DEVICE, NOR IS IT A GE HEALTHCARE PRODUCT!
NEITHER THIS TOOL, NOR ITS OUTPUT, CAN IT BE USED TO MAKE MEDICAL DIAGNOSIS
OR TREATMENT.
-=NOT FOR PATIENT USE=-
"""
GNU_GPL = """
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"""
###############################################################################
# Information about the program
###############################################################################
__author__ = "Anthony D. Ricke"
__date__ = "22 Jul 2009"
__version__ = "0.1.0"
__credits__ = "Guido van Rossum, for the Python language"
__copyright__ = "Copyright (C) 2009 GE Healthcare"
###############################################################################
# Imports
# Modules needed by the script.
###############################################################################
import sys # For system information
import optparse
import string
import xml.parsers.expat
import base64
import struct
import array
import os
import io
# Globals
# The following are the element tags for the XML document
#WAVEFORM_ELEM = "Waveform"
#WAVETYPE_ELEM = "WaveformType"
#RHYTHM_TAG = "Rhythm"
#LEAD_DATA_ELEM = "LeadData"
#LEAD_ID_ELEM = "LeadID"
#WAVEFORM_DATA_ELEM = "WaveFormData"
#SAMPLE_BASE_ELEM = "SampleBase"
#LEAD_ADU_ELEM = "LeadAmplitudeUnitsPerBit"
#LEAD_UNIT_ELEM = "LeadAmplitudeUnits"
INDEPENDENT_LEADS = ("I", "II", "V1", "V2", "V3", "V4", "V5", "V6")
###############################################################################
# Classes
###############################################################################
class XmlElementParser:
"""Abstract base class for a XML Parsing State. It contains methods for
restoring the previous state and for tracking the character data between
tags."""
def __init__(self, old_State = None):
self.__old_State = old_State
self.__data_Text = ""
def restoreState(self, context):
"""This method restores the previous state in the XML parser."""
if self.__old_State:
context.setState(self.__old_State)
def clearData(self):
"""This method clears the character data that was collected during parsing"""
self.__data_Text = ""
def getData(self):
"""This method returns the character data that was collected during
parsing and it strips any leading or trailing whitespace"""
return self.__data_Text.strip()
def start_element(self, name, attrs, context):
print ("""abstract method, called at the start of an XML element""")
sys.exit(0)
def end_element(self, name, context):
print ("""abstract method, called at the end of an XML element""")
sys.exit(0)
def char_data(self, data, context):
"""This method accumulates any character data"""
self.__data_Text = self.__data_Text + data
class IdleParser(XmlElementParser):
"""State for handling the Idle condition"""
def __init__(self):
XmlElementParser.__init__(self)
def start_element(self, name, attrs, context):
if name == WaveformElementParser.Tag:
context.setState(WaveformElementParser(self))
def end_element(self, name, context):
self.clearData()
class WaveformElementParser(XmlElementParser):
"""State for handling the Waveform element"""
Tag = "Waveform"
def __init__(self, old_State):
XmlElementParser.__init__(self, old_State)
def start_element(self, name, attrs, context):
self.clearData()
if name == WaveformTypeElementParser.Tag:
context.setState(WaveformTypeElementParser(self))
elif name == LeadDataElementParser.Tag:
context.setState(LeadDataElementParser(self))
elif name == SampleBaseElementParser.Tag:
context.setState(SampleBaseElementParser(self))
def end_element(self, name, context):
if name == self.Tag:
self.restoreState(context)
class SampleBaseElementParser(XmlElementParser):
"""State for handling the SampleBase element"""
Tag = "SampleBase"
def __init__(self, old_State):
XmlElementParser.__init__(self, old_State)
def start_element(self, name, attrs, context):
self.clearData()
def end_element(self, name, context):
if name == self.Tag:
self.restoreState(context)
if context.found_Rhythm:
context.setSampleBase(self.getData())
print( "Sampling rate for rhythm is %s sps..." % (context.sample_Rate))
class LeadUnitsPerBitElementParser(XmlElementParser):
"""State for handling the LeadAmplitudeUnitsPerBit element"""
Tag = "LeadAmplitudeUnitsPerBit"
def __init__(self, old_State):
XmlElementParser.__init__(self, old_State)
def start_element(self, name, attrs, context):
self.clearData()
def end_element(self, name, context):
if name == self.Tag:
self.restoreState(context)
context.setAdu(float(self.getData().strip()))
class LeadUnitsElementParser(XmlElementParser):
"""State for handling the LeadAmplitudeUnits element"""
Tag = "LeadAmplitudeUnits"
def __init__(self, old_State):
XmlElementParser.__init__(self, old_State)
def start_element(self, name, attrs, context):
self.clearData()
def end_element(self, name, context):
if name == self.Tag:
self.restoreState(context)
context.setUnits(self.getData().strip())
class WaveformTypeElementParser(XmlElementParser):
"""State for handling the WaveformType element"""
Tag = "WaveformType"
def __init__(self, old_State):
XmlElementParser.__init__(self, old_State)
def start_element(self, name, attrs, context):
self.clearData()
def end_element(self, name, context):
if name == self.Tag:
self.restoreState(context)
if self.getData().find("Rhythm") >= 0:
context.setRhythmFound(1)
print( "ECG %s object found." % self.getData())
else:
context.setRhythmFound(0)
class LeadDataElementParser(XmlElementParser):
"""State for handling the LeadData element"""
Tag = "LeadData"
def __init__(self, old_State):
XmlElementParser.__init__(self, old_State)
def start_element(self, name, attrs, context):
self.clearData()
if name == LeadIdElementParser.Tag:
context.setState(LeadIdElementParser(self))
if name == WaveformDataElementParser.Tag:
context.setState(WaveformDataElementParser(self))
if name == LeadUnitsPerBitElementParser.Tag:
context.setState(LeadUnitsPerBitElementParser(self))
if name == LeadUnitsElementParser.Tag:
context.setState(LeadUnitsElementParser(self))
def end_element(self, name, context):
if name == self.Tag:
self.restoreState(context)
class LeadIdElementParser(XmlElementParser):
"""State for handling the LeadID element"""
Tag = "LeadID"
def __init__(self, old_State):
XmlElementParser.__init__(self, old_State)
def start_element(self, name, attrs, context):
self.clearData()
def end_element(self, name, context):
if name == self.Tag:
self.restoreState(context)
if context.found_Rhythm:
sys.stdout.write(" Lead %2s found..." % self.getData())
context.addLeadId(self.getData())
class WaveformDataElementParser(XmlElementParser):
"""State for handling the WaveformData element"""
Tag = "WaveFormData"
def __init__(self, old_State):
XmlElementParser.__init__(self, old_State)
def start_element(self, name, attrs, context):
self.clearData()
def end_element(self, name, context):
if name == self.Tag:
self.restoreState(context)
if context.found_Rhythm:
print( " Adding data for lead %2s." % context.lead_Id)
context.addWaveformData(self.getData())
class MuseXmlParser:
"""This class is the parsing context in the object-oriented State pattern."""
def __init__(self):
self.ecg_Data = dict()
self.ecg_Leads = list()
self.__state = IdleParser()
self.found_Rhythm = 0
self.sample_Rate = 0
self.adu_Gain = 1
self.units = ""
def setState(self, s):
self.__state = s
def getState(self):
return self.__state
def setSampleBase(self, text):
if self.found_Rhythm:
self.sample_Rate = int(text)
def setAdu(self, gain):
self.adu_Gain = gain
def setUnits(self, units):
self.units = units
def setRhythmFound(self, v):
self.found_Rhythm = v
def addLeadId(self, id):
self.lead_Id = id
def addWaveformData(self, text):
self.ecg_Data[self.lead_Id] = base64.b64decode(text)
self.ecg_Leads.append(self.lead_Id)
def start_element(self, name, attrs):
"""This function trackes the start elements found in the XML file with a
simple state machine"""
self.__state.start_element(name, attrs, self)
def end_element(self, name):
self.__state.end_element(name, self)
def char_data(self, data):
self.__state.char_data(data, self)
def makeZcg(self):
"""This function converts the data read from the XML file into a ZCG buffer
suitable for storage in binary format."""
# All of the leads should have the same number of samples
n = len(self.ecg_Data[self.ecg_Leads[0]])
# We have 2 bytes per ECG sample, so make our buffer size n * DATAMUX
self.zcg = array.array('d')