Gnumed.business.gmDevices API documentation

# Module `Gnumed.business.gmDevices`

Expand source code

    # -*- coding: utf-8 -*-
    #======================================================================
    # GNUmed Device handling
    #
    # @copyright: author
    #======================================================================
    __author__ = "Sebastian Hilbert"
    __license__ = 'GPL v2 or later (details at https://www.gnu.org)'

    import sys, logging

    if __name__ == '__main__':
            sys.path.insert(0, '../../')
            _ = lambda x:x

    _log = logging.getLogger('gm.dev')
    #======================================================================
    # XML cardiac device description parsing
    #----------------------------------------------------------------------

    # since those methods appear in a top-level generic file (gmDevices.py)
    # they need more specific names because things like drivers for
    # urinalyzers, ecg, spiro, ... all conceptually belong into gmDevices.py

    # Devices holds a list of all cardiac devices in the xml
    # each list item holds a device context ( generator and one or more leads )
    ##Devices = []
    # DeviceParts is the device context and holds one or more device parts. Each list item
    # is a device part such as lead , generator which in turn can consist of
    # device parts such as mainboard or battery
    ##DeviceParts = []

    def extractDevices(DevicesTree=None):
            Devices = []
            # sort device list, first ICD, then pacemaker, then disconnected devices
            for Device in DevicesTree:
                    Devices.append(Device)
            return Devices

    def sortDevicesByTypeAndStatus(Devices=None):
            # todo: sort later, for now return like order gotten from XML
            return Devices

    def extractDeviceParts(Device=None,Type=None):
            DeviceParts = []
            for DevicePart in Device:
                    if DevicePart.get("type") == Type:
                            DeviceParts.append(DevicePart)
            return DeviceParts

    def sortLeadsByPosition(Leads=None):
            #skips sorting for now
            return Leads

    def extractActions(DevicePart=None,Type=None):
            Actions = []
            # get a list of all procedures for this DevicePart
            for tag in DevicePart.getchildren():
                    if tag.get("type") == Type:
                            Actions.append(tag)
            return Actions

    def extractTagData(start_node=None,SearchTag=None):
            #tag = None
            for tag in start_node.getchildren():
                    if tag.tag==SearchTag:
                            return tag.text

    def extractTagAttribute(start_node=None,SearchTag=None,Attribute=None):
            for tag in start_node.getchildren():
                    if tag.tag == SearchTag:
                            return tag.get(Attribute)

    def device_status_as_text(tree=None):
            DevicesDisplayed = []

            """ In this area GNUmed will place the status of all cardiac devices and device parts.
            There can be more than one device at a time\n\n
            It potentially looks like this\n
            ----------------------------------------------------------------------------------------------------------------\n
            Device: SJM Atlas DR (active)     Battery: 2.4V (MOL)      Implanted:  Feb 09 2008\n\n
            RA: Medtronic Sprint fidelis (active, flaky, replacement)             Implanted: Feb 09 2008\n
            Sensing: 2 (1.5) mV    Threshold: 0.7/0.5 (1/0.4) V/ms       Impedance: 800 (900) Ohm\n\n
            RV: Medtronic Sprint fidelis (active, flaky, replacement)             Implanted: Feb 09 2008\n
            Sensing: 7 (15) mV    Threshold: 0.7/0.5 (1/0.4) V/ms       Impedance: 800 (900) Ohm\n\n
            LV: Medtronic Sprint fidelis (active, flaky, Y-connector)             Implanted: Feb 09 2008\n
            Sensing: 7 ( ?) mV    Threshold: 1/1.5 (1/1) V/ms       Impedance: 800 (900) Ohm\n
            ----------------------------------------------------------------------------------------------------------------\n
            Device: Medtronic Relia SR (inactive)     Battery 2.1V (EOL)   Implanted: Jan 23 2000\n\n
            Device: Medtronic Kappa SR (explanted)     Battery 2.1V (EOL)   Explanted: Jan 23 2000 (Jan 23 1995)\n
            -----------------------------------------------------------------------------------------------------------------\n
            RA Lead: Medtronic ? (inactive, capped)             Implanted: Jan 23 2000\n
            RV Lead: Medtronic ? (explanted)                        Explanted: Feb 09 2008
            """
            """
            first search for devices, produce a list,
            sort in active devices first, ICD befor pacemaker before disconnted devices
            per convention a single generator or lead which is not connected is a self contained device
            there are virtual devices such as 'ICD' or 'pacemaker' which consist of parts such as leads and generator
            there are true devices such as inactive leads or non-explanted generators
            class will be 'lead' instead of type 'lead' for DeviceParts
            """

            DevicesTree = tree.getroot()
            Devices = extractDevices(DevicesTree)
            DevicesSorted = sortDevicesByTypeAndStatus(Devices)
            #print 'Number of devices: %s' %len(Devices)

            for Device in DevicesSorted:
                    DevicesDisplayed.append('-------------------------------------------------------------\n')
                    # check for class
                    DeviceClass=Device.get("class")
                    if DeviceClass == 'ICD':
                            # get generator xml node
                            Generator = extractDeviceParts(Device=Device,Type='generator')[0]
                            # get generator vendor, model, devicestate
                            vendor = extractTagData(start_node=Generator,SearchTag='vendor')
                            model = extractTagData(start_node=Generator,SearchTag='model')
                            devicestate = extractTagData(start_node=Generator,SearchTag='devicestate')
                            # get subpart battery
                            battery = extractDeviceParts(Device=Generator,Type='battery')[0]
                            action = extractActions(DevicePart=battery,Type='interrogation')[0]
                            battery_voltage = extractTagData(start_node=action,SearchTag='voltage')
                            battery_voltage_unit = extractTagAttribute(start_node=action,SearchTag='voltage',Attribute='unit')
                            battery_status = extractTagData(start_node=action,SearchTag='status')
                            implantation_date= extractTagData(start_node=Generator,SearchTag='doi')
                            line = _('Device(%s):') %DeviceClass + ' ' + vendor + ' ' + model + ' ' + '('+ devicestate + ')'+'   '+_('Battery:')+' '+battery_voltage+' '+battery_voltage_unit+'('+battery_status+')'+'  '+_('Implanted:')+' '+implantation_date+'\n\n'
                            # append each line to a list, later produce display string by parsing list
                            DevicesDisplayed.append(line)
                            #DevicesDisplayed.append('\n')
                            # now get the leads, RA then RV and last LV if they exist
                            # todo: think about four leads : pace/sense but on another thought they both simply show up as RV leads
                            Leads = extractDeviceParts(Device=Device,Type='lead')
                            LeadsSorted = sortLeadsByPosition(Leads)
                            for Lead in LeadsSorted:
                                    leadposition = extractTagData(start_node=Lead,SearchTag='leadposition')
                                    leadslot = extractTagData(start_node=Lead,SearchTag='leadslot')
                                    vendor = extractTagData(start_node=Lead,SearchTag='manufacturer')
                                    model = extractTagData(start_node=Lead,SearchTag='model')
                                    devicestate = extractTagData(start_node=Lead,SearchTag='devicestate')
                                    comment = extractTagData(start_node=Lead,SearchTag='comment')
                                    implantation_date = extractTagData(start_node=Lead,SearchTag='doi')
                                    line = '%s-lead in %s-position:' %(leadposition,leadslot) + ' ' + vendor + ' ' + model + ' ' + '(' + devicestate + ',' + comment + ')' + ' ' + 'Implanted:' + ' ' + implantation_date +'\n'
                                    DevicesDisplayed.append(line)
                                    #now get the newest interrogation
                                    action = extractActions(DevicePart=Lead,Type='interrogation')[0]
                                    action_date = extractTagData(start_node=action,SearchTag='dop')
                                    sensing = extractTagData(start_node=action,SearchTag='sensing')
                                    sensingunit = extractTagAttribute(start_node=action,SearchTag='sensing',Attribute='unit')
                                    threshold = extractTagData(start_node=action,SearchTag='thresholdvoltage')
                                    thresholdunit = extractTagAttribute(start_node=action,SearchTag='thresholdvoltage',Attribute='unit')
                                    impedance = extractTagData(start_node=action,SearchTag='impedance')
                                    impedanceunit = extractTagAttribute(start_node=action,SearchTag='impedance',Attribute='unit')
                                    line = _('last check:')+' '+action_date+' '+_('Sensing:')+' '+sensing+sensingunit+' '+_('Threshold')+' '+threshold+thresholdunit+' '+_('Impedance:')+' '+impedance+' '+impedanceunit+'\n\n'
                                    DevicesDisplayed.append(line)

            return DevicesDisplayed

    #======================================================================
    # main - unit testing
    #----------------------------------------------------------------------
    if __name__ == '__main__':

            from lxml import etree

            from Gnumed.pycommon import gmI18N
            gmI18N.activate_locale()
            gmI18N.install_domain()

            if len(sys.argv) > 1 and sys.argv[1] == 'test':

                    #----------------------------------------------------
                    def test_parsing_cardio_dev_state():
                            # for now assume that the xml file provide the cardiac device context.
                            # that pretty much means logical connection of leads and generator is provided in the xml
                            print("parsing device status from XML file:", sys.argv[2])
                            xml_device_desc = etree.parse(sys.argv[2])
                            formatted_device_status = device_status_as_text(xml_device_desc)
                            for line in formatted_device_status:
                                    print(line)
                    #----------------------------------------------------

                    test_parsing_cardio_dev_state()

## Functions

`def device_status_as_text(tree=None)`
  Expand source code

      def device_status_as_text(tree=None):
              DevicesDisplayed = []

              """ In this area GNUmed will place the status of all cardiac devices and device parts.
              There can be more than one device at a time\n\n
              It potentially looks like this\n
              ----------------------------------------------------------------------------------------------------------------\n
              Device: SJM Atlas DR (active)     Battery: 2.4V (MOL)      Implanted:  Feb 09 2008\n\n
              RA: Medtronic Sprint fidelis (active, flaky, replacement)             Implanted: Feb 09 2008\n
              Sensing: 2 (1.5) mV    Threshold: 0.7/0.5 (1/0.4) V/ms       Impedance: 800 (900) Ohm\n\n
              RV: Medtronic Sprint fidelis (active, flaky, replacement)             Implanted: Feb 09 2008\n
              Sensing: 7 (15) mV    Threshold: 0.7/0.5 (1/0.4) V/ms       Impedance: 800 (900) Ohm\n\n
              LV: Medtronic Sprint fidelis (active, flaky, Y-connector)             Implanted: Feb 09 2008\n
              Sensing: 7 ( ?) mV    Threshold: 1/1.5 (1/1) V/ms       Impedance: 800 (900) Ohm\n
              ----------------------------------------------------------------------------------------------------------------\n
              Device: Medtronic Relia SR (inactive)     Battery 2.1V (EOL)   Implanted: Jan 23 2000\n\n
              Device: Medtronic Kappa SR (explanted)     Battery 2.1V (EOL)   Explanted: Jan 23 2000 (Jan 23 1995)\n
              -----------------------------------------------------------------------------------------------------------------\n
              RA Lead: Medtronic ? (inactive, capped)             Implanted: Jan 23 2000\n
              RV Lead: Medtronic ? (explanted)                        Explanted: Feb 09 2008
              """
              """
              first search for devices, produce a list,
              sort in active devices first, ICD befor pacemaker before disconnted devices
              per convention a single generator or lead which is not connected is a self contained device
              there are virtual devices such as 'ICD' or 'pacemaker' which consist of parts such as leads and generator
              there are true devices such as inactive leads or non-explanted generators
              class will be 'lead' instead of type 'lead' for DeviceParts
              """

              DevicesTree = tree.getroot()
              Devices = extractDevices(DevicesTree)
              DevicesSorted = sortDevicesByTypeAndStatus(Devices)
              #print 'Number of devices: %s' %len(Devices)

              for Device in DevicesSorted:
                      DevicesDisplayed.append('-------------------------------------------------------------\n')
                      # check for class
                      DeviceClass=Device.get("class")
                      if DeviceClass == 'ICD':
                              # get generator xml node
                              Generator = extractDeviceParts(Device=Device,Type='generator')[0]
                              # get generator vendor, model, devicestate
                              vendor = extractTagData(start_node=Generator,SearchTag='vendor')
                              model = extractTagData(start_node=Generator,SearchTag='model')
                              devicestate = extractTagData(start_node=Generator,SearchTag='devicestate')
                              # get subpart battery
                              battery = extractDeviceParts(Device=Generator,Type='battery')[0]
                              action = extractActions(DevicePart=battery,Type='interrogation')[0]
                              battery_voltage = extractTagData(start_node=action,SearchTag='voltage')
                              battery_voltage_unit = extractTagAttribute(start_node=action,SearchTag='voltage',Attribute='unit')
                              battery_status = extractTagData(start_node=action,SearchTag='status')
                              implantation_date= extractTagData(start_node=Generator,SearchTag='doi')
                              line = _('Device(%s):') %DeviceClass + ' ' + vendor + ' ' + model + ' ' + '('+ devicestate + ')'+'   '+_('Battery:')+' '+battery_voltage+' '+battery_voltage_unit+'('+battery_status+')'+'  '+_('Implanted:')+' '+implantation_date+'\n\n'
                              # append each line to a list, later produce display string by parsing list
                              DevicesDisplayed.append(line)
                              #DevicesDisplayed.append('\n')
                              # now get the leads, RA then RV and last LV if they exist
                              # todo: think about four leads : pace/sense but on another thought they both simply show up as RV leads
                              Leads = extractDeviceParts(Device=Device,Type='lead')
                              LeadsSorted = sortLeadsByPosition(Leads)
                              for Lead in LeadsSorted:
                                      leadposition = extractTagData(start_node=Lead,SearchTag='leadposition')
                                      leadslot = extractTagData(start_node=Lead,SearchTag='leadslot')
                                      vendor = extractTagData(start_node=Lead,SearchTag='manufacturer')
                                      model = extractTagData(start_node=Lead,SearchTag='model')
                                      devicestate = extractTagData(start_node=Lead,SearchTag='devicestate')
                                      comment = extractTagData(start_node=Lead,SearchTag='comment')
                                      implantation_date = extractTagData(start_node=Lead,SearchTag='doi')
                                      line = '%s-lead in %s-position:' %(leadposition,leadslot) + ' ' + vendor + ' ' + model + ' ' + '(' + devicestate + ',' + comment + ')' + ' ' + 'Implanted:' + ' ' + implantation_date +'\n'
                                      DevicesDisplayed.append(line)
                                      #now get the newest interrogation
                                      action = extractActions(DevicePart=Lead,Type='interrogation')[0]
                                      action_date = extractTagData(start_node=action,SearchTag='dop')
                                      sensing = extractTagData(start_node=action,SearchTag='sensing')
                                      sensingunit = extractTagAttribute(start_node=action,SearchTag='sensing',Attribute='unit')
                                      threshold = extractTagData(start_node=action,SearchTag='thresholdvoltage')
                                      thresholdunit = extractTagAttribute(start_node=action,SearchTag='thresholdvoltage',Attribute='unit')
                                      impedance = extractTagData(start_node=action,SearchTag='impedance')
                                      impedanceunit = extractTagAttribute(start_node=action,SearchTag='impedance',Attribute='unit')
                                      line = _('last check:')+' '+action_date+' '+_('Sensing:')+' '+sensing+sensingunit+' '+_('Threshold')+' '+threshold+thresholdunit+' '+_('Impedance:')+' '+impedance+' '+impedanceunit+'\n\n'
                                      DevicesDisplayed.append(line)

              return DevicesDisplayed

`def extractActions(DevicePart=None, Type=None)`
  Expand source code

      def extractActions(DevicePart=None,Type=None):
              Actions = []
              # get a list of all procedures for this DevicePart
              for tag in DevicePart.getchildren():
                      if tag.get("type") == Type:
                              Actions.append(tag)
              return Actions

`def extractDeviceParts(Device=None, Type=None)`
  Expand source code

      def extractDeviceParts(Device=None,Type=None):
              DeviceParts = []
              for DevicePart in Device:
                      if DevicePart.get("type") == Type:
                              DeviceParts.append(DevicePart)
              return DeviceParts

`def extractDevices(DevicesTree=None)`
  Expand source code

      def extractDevices(DevicesTree=None):
              Devices = []
              # sort device list, first ICD, then pacemaker, then disconnected devices
              for Device in DevicesTree:
                      Devices.append(Device)
              return Devices

`def extractTagAttribute(start_node=None, SearchTag=None, Attribute=None)`
  Expand source code

      def extractTagAttribute(start_node=None,SearchTag=None,Attribute=None):
              for tag in start_node.getchildren():
                      if tag.tag == SearchTag:
                              return tag.get(Attribute)

`def extractTagData(start_node=None, SearchTag=None)`
  Expand source code

      def extractTagData(start_node=None,SearchTag=None):
              #tag = None
              for tag in start_node.getchildren():
                      if tag.tag==SearchTag:
                              return tag.text

`def sortDevicesByTypeAndStatus(Devices=None)`
  Expand source code

      def sortDevicesByTypeAndStatus(Devices=None):
              # todo: sort later, for now return like order gotten from XML
              return Devices

`def sortLeadsByPosition(Leads=None)`
  Expand source code

      def sortLeadsByPosition(Leads=None):
              #skips sorting for now
              return Leads