biosignal-device-interface 0.1.1a0__py3-none-any.whl → 0.1.4a1__py3-none-any.whl

biosignal_device_interface/devices/otb/otb_syncstation.py

@@ -0,0 +1,407 @@
+"""
+Device class for real-time interfacing the OTB Syncstation device.
+Developer: Dominik I. Braun
+Contact: dome.braun@fau.de
+Last Update: 2025-01-09
+"""
+
+from __future__ import annotations
+from typing import TYPE_CHECKING, Union, Dict
+from PySide6.QtNetwork import QTcpSocket, QHostAddress
+from PySide6.QtCore import QIODevice
+import numpy as np
+
+# Local Libraries
+from biosignal_device_interface.constants.devices.otb.otb_syncstation_constants import (
+    PROBE_CHARACTERISTICS_DICT,
+    SYNCSTATION_CHARACTERISTICS_DICT,
+    SYNCSTATION_CONVERSION_FACTOR_DICT,
+    SyncStationDetectionMode,
+    SyncStationProbeConfigMode,
+    SyncStationRecOnMode,
+    SyncStationWorkingMode,
+)
+from biosignal_device_interface.devices.core.base_device import BaseDevice
+from biosignal_device_interface.constants.devices.core.base_device_constants import (
+    DeviceType,
+    DeviceChannelTypes,
+)
+
+
+if TYPE_CHECKING:
+    from PySide6.QtWidgets import QMainWindow, QWidget
+    from aenum import Enum
+
+
+class OTBSyncStation(BaseDevice):
+    """
+    Device class for real-time interfacing the OTB Syncstation device.
+    The SyncStation class is using a TCP/IP protocol to communicate with the device.
+    """
+
+    def __init__(self, parent: Union[QMainWindow, QWidget] = None) -> None:
+        """
+        Constructor of the OTBSyncStation class.
+
+        Args:
+            parent (Union[QMainWindow, QWidget]): The parent object of the device. Defaults to None.
+        """
+        super().__init__(parent)
+
+        # Device Parameters
+        self._device_type = DeviceType.OTB_SYNCSTATION
+
+        # Connection Parameters
+        self._interface: QTcpSocket = QTcpSocket()
+
+        # Configuration Parameters
+        self._configuration_command_A: bytearray = None
+        self._configuration_command_B: bytearray = None
+
+        # Configuration Parameters A
+        self._rec_on_mode: SyncStationRecOnMode = None
+        self._working_mode: SyncStationWorkingMode = None
+        self._number_of_probes: int = None
+        self._bytes_configuration_A: Dict[
+            SyncStationProbeConfigMode, Dict[str, SyncStationDetectionMode | bool]
+        ] = None
+
+        # Configuration Parameters B
+        self._bytes_configuration_B: Dict[str, int] = None
+
+    def _connect_to_device(self) -> bool:
+        super()._connect_to_device()
+
+        self._received_bytes: bytearray = bytearray()
+        self._make_request()
+
+    def _make_request(self) -> bool:
+        super()._make_request()
+
+        self._interface.connectToHost(
+            QHostAddress(self._connection_settings[0]),
+            self._connection_settings[1],
+            QIODevice.ReadWrite,
+        )
+
+        if not self._interface.waitForConnected(1000):
+            self._disconnect_from_device()
+            return False
+
+        self.is_connected = True
+        self.connect_toggled.emit(True)
+
+        self._interface.readyRead.connect(self._read_data)
+        return True
+
+    def _disconnect_from_device(self) -> None:
+        super()._disconnect_from_device()
+
+        self._interface.disconnectFromHost()
+        self._interface.readyRead.disconnect(self._read_data)
+        self._interface.close()
+
+        self.is_connected = False
+        self.connect_toggled.emit(False)
+
+    def configure_device(self, params) -> None:
+        super().configure_device(params)
+
+        success = self._configure_byte_sequence_A()
+
+        if not success:
+            print("Unable to configure device.")
+            return
+
+        self._send_configuration_to_device()
+
+        self._is_configured = True
+        self.configure_toggled.emit(True)
+
+    def _configure_byte_sequence_A(self) -> None:
+        start_byte = 0
+        start_byte += (self._rec_on_mode.value - 1) << 6
+
+        self._sampling_frequency = SYNCSTATION_CHARACTERISTICS_DICT[
+            "channel_information"
+        ][self._working_mode]["sampling_frequency"]
+        self._bytes_per_sample = SYNCSTATION_CHARACTERISTICS_DICT[
+            "channel_information"
+        ][self._working_mode]["bytes_per_sample"]
+
+        self._configuration_command_A = bytearray()
+        self._number_of_channels = 0
+        self._number_of_bytes = 0
+
+        self._number_of_biosignal_channels = 0
+        self._number_of_auxiliary_channels = 0
+        self._biosignal_channel_indices = []
+        self._auxiliary_channel_indices = []
+
+        for key, value in self._bytes_configuration_A.items():
+            probe_command = 0
+            probe_command += (key.value - 1) << 4
+            probe_command += (self._working_mode.value - 1) << 3
+            probe_command += (value["detection_mode"].value - 1) << 1
+            probe_command += int(value["probe_status"])
+
+            if value["probe_status"]:
+                self._configuration_command_A.append(probe_command)
+                channels = PROBE_CHARACTERISTICS_DICT[key][DeviceChannelTypes.ALL]
+                biosignal_channels = PROBE_CHARACTERISTICS_DICT[key][
+                    DeviceChannelTypes.BIOSIGNAL
+                ]
+                auxiliary_channels = PROBE_CHARACTERISTICS_DICT[key][
+                    DeviceChannelTypes.AUXILIARY
+                ]
+
+                self._biosignal_channel_indices.append(
+                    np.arange(
+                        self._number_of_channels,
+                        self._number_of_channels + biosignal_channels,
+                    )
+                )
+
+                self._auxiliary_channel_indices.append(
+                    np.arange(
+                        self._number_of_channels + biosignal_channels,
+                        self._number_of_channels + channels,
+                    )
+                )
+
+                self._number_of_channels += channels
+                self._number_of_biosignal_channels += biosignal_channels
+                self._number_of_auxiliary_channels += auxiliary_channels
+
+        self._conversion_factor_biosignal = SYNCSTATION_CONVERSION_FACTOR_DICT[
+            value["detection_mode"]
+        ]
+        self._conversion_factor_auxiliary = self._conversion_factor_biosignal
+
+        self._biosignal_channel_indices = np.hstack(self._biosignal_channel_indices)
+        self._auxiliary_channel_indices = np.hstack(self._auxiliary_channel_indices)
+        self._number_of_bytes = self._number_of_channels * self._bytes_per_sample
+
+        # Add SyncStation Channels
+        self._number_of_channels += SYNCSTATION_CHARACTERISTICS_DICT[
+            DeviceChannelTypes.ALL
+        ]
+        self._number_of_auxiliary_channels += SYNCSTATION_CHARACTERISTICS_DICT[
+            DeviceChannelTypes.ALL
+        ]
+
+        self._number_of_bytes += (
+            SYNCSTATION_CHARACTERISTICS_DICT[DeviceChannelTypes.ALL]
+            * SYNCSTATION_CHARACTERISTICS_DICT["bytes_per_sample"]
+        )
+
+        self._samples_per_frame = int(
+            (1 / SYNCSTATION_CHARACTERISTICS_DICT["FPS"]) * self._sampling_frequency
+        )
+
+        self._buffer_size = int(self._number_of_bytes * self._samples_per_frame)
+
+        num_probes = len(self._configuration_command_A)
+        start_byte += num_probes << 1
+        self._configuration_command_A.insert(0, start_byte)
+        start_byte_ckc8 = self._crc_check(
+            self._configuration_command_A, len(self._configuration_command_A)
+        )
+        self._configuration_command_A.append(start_byte_ckc8)
+
+        return True
+
+    def _crc_check(self, command_bytes: bytearray, command_length: int) -> bytes:
+        """
+        Performs the Cyclic Redundancy Check (CRC) of the transmitted bytes.
+
+        Translated function from example code provided by OT Bioelettronica.
+
+        Args:
+            command_bytes (bytearray):
+                Bytearray of the transmitted bytes.
+
+            command_length (int):
+                Length of the transmitted bytes.
+
+        Returns:
+            bytes:
+                CRC of the transmitted bytes.
+        """
+
+        crc = 0
+        j = 0
+
+        while command_length > 0:
+            extracted_byte = command_bytes[j]
+            for i in range(8, 0, -1):
+                sum = crc % 2 ^ extracted_byte % 2
+                crc = crc // 2
+
+                if sum > 0:
+                    crc_bin = format(crc, "08b")
+                    a_bin = format(140, "08b")
+
+                    str_list = []
+
+                    for k in range(8):
+                        str_list.append("0" if crc_bin[k] == a_bin[k] else "1")
+
+                    crc = int("".join(str_list), 2)
+
+                extracted_byte = extracted_byte // 2
+
+            command_length -= 1
+            j += 1
+
+        return crc
+
+    def _configure_byte_sequence_B(self) -> None:
+        # TODO: Implement this method
+        ...
+
+    def _send_configuration_to_device(self) -> None:
+        print(
+            f"Device configuration sent: {[int.from_bytes(self._configuration_command_A[i : i + 1], 'big') for i in range(len(self._configuration_command_A))]}"
+        )
+        self._interface.write(self._configuration_command_A)
+
+    def _stop_streaming(self):
+        self._configuration_command_A[0] -= 1
+        self._configuration_command_A[-1] = self._crc_check(
+            self._configuration_command_A, len(self._configuration_command_A) - 1
+        )
+
+        self._send_configuration_to_device()
+
+        self._is_streaming = False
+        self.stream_toggled.emit(False)
+
+    def _start_streaming(self):
+        self._configuration_command_A[0] += 1
+        self._configuration_command_A[-1] = self._crc_check(
+            self._configuration_command_A, len(self._configuration_command_A) - 1
+        )
+
+        self._send_configuration_to_device()
+
+        self._is_streaming = True
+        self.stream_toggled.emit(True)
+
+    def _clear_socket(self) -> None:
+        """
+        Clears the socket from any remaining data.
+        """
+        self._interface.readAll()
+        self._received_bytes = bytearray()
+
+    def _read_data(self) -> None:
+        if not self._is_streaming:
+            packet = self._interface.readAll()
+
+        else:
+            if self._interface.bytesAvailable() > 0:
+
+                packet = self._interface.readAll()
+                packet_bytearray = bytearray(packet.data())
+
+                if not packet_bytearray:
+                    return
+
+                self._received_bytes.extend(packet_bytearray)
+
+                while len(self._received_bytes) >= self._buffer_size:
+                    self._process_data(
+                        bytearray(self._received_bytes)[: self._buffer_size]
+                    )
+                    self._received_bytes = bytearray(self._received_bytes)[
+                        self._buffer_size :
+                    ]
+
+    def _process_data(self, input: bytearray) -> None:
+        data: np.ndarray = np.frombuffer(input, dtype=np.uint8).astype(np.float32)
+
+        samples = self._samples_per_frame
+        data = np.reshape(data, (samples, self._number_of_bytes)).T
+        processed_data = self._bytes_to_integers(data)
+
+        # Emit the data
+        self.data_available.emit(processed_data)
+        self.biosignal_data_available.emit(self._extract_biosignal_data(processed_data))
+        self.auxiliary_data_available.emit(self._extract_auxiliary_data(processed_data))
+
+    def _integer_to_bytes(self, command: int) -> bytes:
+        return int(command).to_bytes(1, byteorder="big")
+
+    # Convert channels from bytes to integers
+    def _bytes_to_integers(
+        self,
+        data: np.ndarray,
+    ) -> np.ndarray:
+        samples = self._samples_per_frame
+        frame_data = np.zeros((self._number_of_channels, samples), dtype=np.float32)
+        channels_to_read = 0
+        for device in list(SyncStationProbeConfigMode)[1:]:
+            if self._bytes_configuration_A[device]["probe_status"]:
+                channel_number = PROBE_CHARACTERISTICS_DICT[device][
+                    DeviceChannelTypes.ALL
+                ]
+                # Convert channel's byte value to integer
+                if self._working_mode == SyncStationWorkingMode.EMG:
+                    channel_indices = (
+                        np.arange(0, channel_number * 2, 2) + channels_to_read * 2
+                    )
+                    data_sub_matrix = self._decode_int16(data, channel_indices)
+                    frame_data[
+                        channels_to_read : channels_to_read + channel_number, :
+                    ] = data_sub_matrix
+
+                elif self._working_mode == SyncStationWorkingMode.EEG:
+                    channel_indices = (
+                        np.arange(0, channel_number * 3, 3) + channels_to_read * 2
+                    )
+                    data_sub_matrix = self._decode_int24(data, channel_indices)
+                    frame_data[
+                        channels_to_read : channels_to_read + channel_number, :
+                    ] = data_sub_matrix
+
+                channels_to_read += channel_number
+                del data_sub_matrix
+                del channel_indices
+
+        syncstation_aux_bytes_number = (
+            SYNCSTATION_CHARACTERISTICS_DICT[DeviceChannelTypes.ALL]
+            * SYNCSTATION_CHARACTERISTICS_DICT["bytes_per_sample"]
+        )
+        syncstation_aux_starting_byte = (
+            self._number_of_bytes - syncstation_aux_bytes_number
+        )
+        channel_indices = np.arange(
+            syncstation_aux_starting_byte,
+            syncstation_aux_starting_byte + syncstation_aux_bytes_number,
+            2,
+        )
+        data_sub_matrix = self._decode_int16(data, channel_indices)
+        frame_data[channels_to_read : channels_to_read + 6, :] = data_sub_matrix
+        return np.array(frame_data)
+
+    def _decode_int24(
+        self, data: np.ndarray, channel_indices: np.ndarray
+    ) -> np.ndarray:
+        data_sub_matrix = (
+            data[channel_indices, :] * 2**16
+            + data[channel_indices + 1, :] * 2**8
+            + data[channel_indices + 2, :]
+        )
+        negative_indices = np.where(data_sub_matrix >= 2**23)
+        data_sub_matrix[negative_indices] -= 2**24
+
+        return data_sub_matrix
+
+    def _decode_int16(
+        self, data: np.ndarray, channel_indices: np.ndarray
+    ) -> np.ndarray:
+        data_sub_matrix = data[channel_indices, :] * 2**8 + data[channel_indices + 1, :]
+        negative_indices = np.where(data_sub_matrix >= 2**15)
+        data_sub_matrix[negative_indices] -= 2**16
+        return data_sub_matrix

biosignal_device_interface/gui/device_template_widgets/__init__.py

@@ -1,6 +0,0 @@
-# OTB Devices
-from biosignal_device_interface.gui.device_template_widgets.otb import (
-    MuoviWidget,
-    MuoviPlusWidget,
-    QuattrocentoLightWidget,
-)

biosignal_device_interface/gui/device_template_widgets/all_devices_widget.py

@@ -14,10 +14,20 @@ from biosignal_device_interface.gui.device_template_widgets.core.base_multiple_d
 from biosignal_device_interface.constants.devices.core.base_device_constants import (
     DeviceType,
 )
-from biosignal_device_interface.gui.device_template_widgets import (
-    MuoviPlusWidget,
-    MuoviWidget,
-    QuattrocentoLightWidget,
+from biosignal_device_interface.gui.device_template_widgets.otb.otb_muovi_plus_widget import (
+    OTBMuoviPlusWidget,
+)
+from biosignal_device_interface.gui.device_template_widgets.otb.otb_muovi_widget import (
+    OTBMuoviWidget,
+)
+from biosignal_device_interface.gui.device_template_widgets.otb.otb_quattrocento_light_widget import (
+    OTBQuattrocentoLightWidget,
+)
+from biosignal_device_interface.gui.device_template_widgets.otb.otb_quattrocento_widget import (
+    OTBQuattrocentoWidget,
+)
+from biosignal_device_interface.gui.device_template_widgets.otb.otb_syncstation_widget import (
+    OTBSyncStationWidget,
 )
 
 if TYPE_CHECKING:
@@ -32,8 +42,10 @@ class AllDevicesWidget(BaseMultipleDevicesWidget):
         super().__init__(parent)
 
         self._device_selection: Dict[DeviceType, BaseDeviceWidget] = {
-            DeviceType.OTB_QUATTROCENTO_LIGHT: QuattrocentoLightWidget(self),
-            DeviceType.OTB_MUOVI: MuoviWidget(self),
-            DeviceType.OTB_MUOVI_PLUS: MuoviPlusWidget(self),
+            DeviceType.OTB_QUATTROCENTO: OTBQuattrocentoWidget(self),
+            DeviceType.OTB_QUATTROCENTO_LIGHT: OTBQuattrocentoLightWidget(self),
+            DeviceType.OTB_MUOVI: OTBMuoviWidget(self),
+            DeviceType.OTB_MUOVI_PLUS: OTBMuoviPlusWidget(self),
+            DeviceType.OTB_SYNCSTATION: OTBSyncStationWidget(self),
         }
         self._set_devices(self._device_selection)

biosignal_device_interface/gui/device_template_widgets/core/base_device_widget.py

@@ -19,6 +19,7 @@ from biosignal_device_interface.devices.core.base_device import BaseDevice
 
 if TYPE_CHECKING:
     from enum import Enum
+    from PySide6.QtWidgets import QLineEdit
 
 
 class BaseDeviceWidget(QWidget):
@@ -36,7 +37,7 @@ class BaseDeviceWidget(QWidget):
         self.parent_widget: QWidget | QMainWindow | None = parent
 
         # Device Setup
-        self.device: BaseDevice | None = None
+        self._device: BaseDevice | None = None
         self._device_params: Dict[str, Union[str, int, float]] = {}
 
         # GUI setup
@@ -90,16 +91,16 @@ class BaseDeviceWidget(QWidget):
     def _set_device(self, device: BaseDevice) -> None:
         """ """
         # Device Setup
-        self.device: BaseDevice = device
+        self._device: BaseDevice = device
         self._initialize_device_params()
         self._set_signals()
         self._initialize_ui()
 
     def _set_signals(self) -> None:
         """ """
-        self.device.data_available.connect(self.data_arrived.emit)
-        self.device.biosignal_data_available.connect(self.biosignal_data_arrived.emit)
-        self.device.auxiliary_data_available.connect(self.auxiliary_data_arrived.emit)
+        self._device.data_available.connect(self.data_arrived.emit)
+        self._device.biosignal_data_available.connect(self.biosignal_data_arrived.emit)
+        self._device.auxiliary_data_available.connect(self.auxiliary_data_arrived.emit)
 
     def get_device_information(self) -> Dict[str, Enum | int | float | str]:
         """
@@ -110,12 +111,20 @@ class BaseDeviceWidget(QWidget):
                 Dictionary that holds information about the
                 current device configuration and status.
         """
-        return self.device.get_device_information()
+        return self._device.get_device_information()
 
     def disconnect_device(self) -> None:
         """ """
-        if self.device._is_connected or self.device._is_streaming:
-            self.device.toggle_connection()
+        if self._device.is_connected or self._device._is_streaming:
+            self._device.toggle_connection()
+
+    def _check_ip_input(self, line_edit: QLineEdit, default: str) -> None:
+        if not self._device.check_valid_ip(line_edit.text()):
+            line_edit.setText(default)
+
+    def _check_port_input(self, line_edit: QLineEdit, default: str) -> None:
+        if not self._device.check_valid_port(line_edit.text()):
+            line_edit.setText(default)
 
     def closeEvent(self, event: QCloseEvent) -> None:
         self.disconnect_device()

biosignal_device_interface/gui/device_template_widgets/core/base_multiple_devices_widget.py

@@ -49,9 +49,6 @@ class BaseMultipleDevicesWidget(QWidget):
 
         self.device_stacked_widget = self.ui.deviceStackedWidget
         self.device_selection_combo_box = self.ui.deviceSelectionComboBox
-        self.device_selection_combo_box.currentIndexChanged.connect(
-            self._update_stacked_widget
-        )
 
     def get_device_information(self) -> Dict[str, Union[str, int]]:
         return self._get_current_widget().get_device_information()
@@ -76,13 +73,16 @@ class BaseMultipleDevicesWidget(QWidget):
                 current_widget.stream_toggled.disconnect(self.stream_toggled)
 
             except (TypeError, RuntimeError):
-                pass
+                ...
 
         self.device_stacked_widget.setCurrentIndex(index)
         current_widget = self._get_current_widget()
 
+        # Data arrived
         current_widget.data_arrived.connect(self.data_arrived.emit)
+        # Biosignal data arrived
         current_widget.biosignal_data_arrived.connect(self.biosignal_data_arrived.emit)
+        # Auxiliary data arrived
         current_widget.auxiliary_data_arrived.connect(self.auxiliary_data_arrived.emit)
 
         current_widget.connect_toggled.connect(self.connect_toggled)
@@ -97,6 +97,9 @@ class BaseMultipleDevicesWidget(QWidget):
             self.device_selection_combo_box.addItem(DEVICE_NAME_DICT[device_type])
 
         self._update_stacked_widget(0)
+        self.device_selection_combo_box.currentIndexChanged.connect(
+            self._update_stacked_widget
+        )
 
     def _get_current_widget(self) -> BaseDeviceWidget:
         return self.device_stacked_widget.currentWidget()

biosignal_device_interface/gui/device_template_widgets/otb/__init__.py

@@ -1,10 +0,0 @@
-# OTB Devices
-from biosignal_device_interface.gui.device_template_widgets.otb.otb_muovi_widget import (
-    MuoviWidget,
-)
-from biosignal_device_interface.gui.device_template_widgets.otb.otb_muovi_plus_widget import (
-    OTBMuoviWidget as MuoviPlusWidget,
-)
-from biosignal_device_interface.gui.device_template_widgets.otb.otb_quattrocento_light_widget import (
-    QuattrocentoLightWidget,
-)

biosignal_device_interface/gui/device_template_widgets/otb/otb_devices_widget.py

@@ -7,10 +7,20 @@ from biosignal_device_interface.gui.device_template_widgets.core.base_multiple_d
 from biosignal_device_interface.constants.devices.core.base_device_constants import (
     DeviceType,
 )
-from biosignal_device_interface.gui.device_template_widgets.otb import (
-    MuoviPlusWidget,
-    MuoviWidget,
-    QuattrocentoLightWidget,
+from biosignal_device_interface.gui.device_template_widgets.otb.otb_muovi_plus_widget import (
+    OTBMuoviPlusWidget,
+)
+from biosignal_device_interface.gui.device_template_widgets.otb.otb_muovi_widget import (
+    OTBMuoviWidget,
+)
+from biosignal_device_interface.gui.device_template_widgets.otb.otb_quattrocento_light_widget import (
+    OTBQuattrocentoLightWidget,
+)
+from biosignal_device_interface.gui.device_template_widgets.otb.otb_quattrocento_widget import (
+    OTBQuattrocentoWidget,
+)
+from biosignal_device_interface.gui.device_template_widgets.otb.otb_syncstation_widget import (
+    OTBSyncStationWidget,
 )
 
 if TYPE_CHECKING:
@@ -20,13 +30,15 @@ if TYPE_CHECKING:
     )
 
 
-class AllDevicesWidget(BaseMultipleDevicesWidget):
+class OTBDevicesWidget(BaseMultipleDevicesWidget):
     def __init__(self, parent: QWidget | QMainWindow | None = None):
         super().__init__(parent)
 
         self._device_selection: Dict[DeviceType, BaseDeviceWidget] = {
-            DeviceType.OTB_QUATTROCENTO_LIGHT: QuattrocentoLightWidget(self),
-            DeviceType.OTB_MUOVI: MuoviWidget(self),
-            DeviceType.OTB_MUOVI_PLUS: MuoviPlusWidget(self),
+            DeviceType.OTB_QUATTROCENTO: OTBQuattrocentoWidget(self),
+            DeviceType.OTB_QUATTROCENTO_LIGHT: OTBQuattrocentoLightWidget(self),
+            DeviceType.OTB_MUOVI: OTBMuoviWidget(self),
+            DeviceType.OTB_MUOVI_PLUS: OTBMuoviPlusWidget(self),
+            DeviceType.OTB_SYNCSTATION: OTBSyncStationWidget(self),
         }
         self._set_devices(self._device_selection)