Logging

.vscode/launch.json

@@ -9,7 +9,7 @@
       "type": "debugpy",
       "request": "launch",
       // "program": "__main__.py",
-      "module": "examples.mid_level.example_mid_level",
+      "module": "examples.dyscom.example_dyscom_write_csv",
       "justMyCode": false,
       // "args": ["COM3"],
       "console": "integratedTerminal"

HINTS.md

@@ -24,6 +24,12 @@ This page describes implementation details.
   - The acknowledge needs to handled manually by using _PacketBuffer_ object from device
   - _PacketBuffer_ reads data from connection and separates packets from data stream
 
+## Logging
+- Library creates a custom logger, see class _Logger_
+- By default some information is logged to console
+- Set log level to DEBUG to get more detailed information
+- For more performance, disable logger
+
 ## General layer
 - Contains functions to get common information like device serial or firmware version
 
@@ -57,6 +63,7 @@ This page describes implementation details.
     - Device sends now _DlSendLiveData_ packets with measurement data
   - Call _stop()_ to end measurement
   - Call _power_module()_ to power off measurement module
+- Important: all storage related functions are untested
 
 # Deviation from Instruction for Use
 
@@ -66,8 +73,12 @@ This page describes implementation details.
 - Strings are 1 byte less long (null termination is not an extra byte) in acknowledge packets
 - Datetime parameters have a different order
 
+### DL_init
+- Init state seems always be UNUSED
+- Output data rate depends on init params filter property
+
 ### DL_get_ack for type file by name
-- Addition parameter mode (1 byte)
+- Additional parameter mode (1 byte)
   - Undefined = 0
   - Multiblock = 1
   - Singleblock = 2

README.md

@@ -48,6 +48,8 @@ Python 3.11 or higher
 - Located in folder `examples`
 - Run examples with `python -m examples.<layer>.<example>`
   - Example: `python -m examples.dyscom.example_dyscom_fastplotlib`
+  - All examples try to find the serial port that a science mode device is connected to automatically
+  - If that fails, provide serial port name as parameter, e.g. `python -m examples.<layer>.<example> COM3`
 - Examples have own dependencies, see [Dependencies for examples](#dependencies-for-examples)
 - General layer
   - `example_general.py`

__main__.py

@@ -4,139 +4,27 @@
 import sys
 import asyncio
 
-import matplotlib.pyplot as plt
-import numpy as np
+from science_mode_4.device_p24 import DeviceP24
+from science_mode_4.utils.serial_port_connection import SerialPortConnection
 
-from src.science_mode_4 import LayerDyscom, LayerLowLevel,\
-    Commands, Connector, Channel, ChannelPoint,\
-    SerialPortConnection,\
-    DeviceI24,\
-    Ads129xOutputDataRate, Ads129xPowerMode,\
-    PacketDyscomGetAckOperationMode, PacketDyscomSendLiveData,\
-    DyscomInitParams, DyscomPowerModulePowerType, DyscomPowerModuleType, DyscomSignalType
 
 
-
-# print(science_mode_4.__version__)
-
-def send_channel_config(low_level_layer: LayerLowLevel, connector: Connector):
-    """Sends channel update"""
-    # device can store up to 10 channel config commands
-    for channel in Channel:
-        # send_channel_config does not wait for an acknowledge
-        low_level_layer.send_channel_config(True, channel, connector,
-                                            [ChannelPoint(4000, 20), ChannelPoint(4000, -20),
-                                            ChannelPoint(4000, 0)])
-
 async def main() -> int:
     """Main function"""
 
-    connection = SerialPortConnection("COM6")
+    devices = SerialPortConnection.list_science_mode_device_ports()
+    connection = SerialPortConnection(devices[0].device)
     # devices = UsbConnection.list_science_mode_devices()
     # connection = UsbConnection(devices[0])
     # connection = NullConnection()
     connection.open()
 
-    device = DeviceI24(connection)
+    device = DeviceP24(connection)
     await device.initialize()
-    # general = device.get_layer_general()
-    # print(f"device id: {general.device_id}")
-    # print(f"firmware version: {general.firmware_version}")
-    # print(f"science mode version: {general.science_mode_version}")
-
-    dyscom: LayerDyscom = device.get_layer_dyscom()
-    # fss: DyscomGetFileSystemStatusResult = await dyscom.get_file_system_status()
-    # print(f"Ready {fss.file_system_ready}, used size {fss.used_size}, free size {fss.free_size}")
-    # fbn: DyscomGetFileByNameResult = await dyscom.get_file_by_name()
-    # print(f"Filename {fbn.filename}, block offset {fbn.block_offset}, filesize {fbn.filesize}, nr of blocks {fbn.number_of_blocks}")
-    # fv: str = await dyscom.get_firmware_version()
-    # print(f"Firmware version {fv}")
-    # nrof = await dyscom.get_list_of_measurement_meta_info()
-    # print(f"Number of measurement meta info {nrof}")
-    # did = await dyscom.get_device_id()
-    # print(f"Device ID {did}")
-    # fi = await dyscom.get_file_info()
-    # print(f"File info {fi.filename} {fi.filesize} {fi.checksum}")
-    # b = await dyscom.get_battery()
-    # print(f"Battery {b.voltage} {b.current} {b.percentage} {b.temperature} {b.energy_state}")
-
-    # sys_ack: DyscomSysResult = await dyscom.sys(DyscomSysType.DEVICE_STORAGE)
-    # print(f"Sys {sys_ack.sys_type} {sys_ack.state} {sys_ack.filename}")
-
-    await dyscom.power_module(DyscomPowerModuleType.MEASUREMENT, DyscomPowerModulePowerType.SWITCH_ON)
-    init_params = DyscomInitParams()
-    init_params.register_map_ads129x.config_register_1.output_data_rate = Ads129xOutputDataRate.HR_MODE_500_SPS__LP_MODE_250_SPS
-    init_params.register_map_ads129x.config_register_1.power_mode = Ads129xPowerMode.LOW_POWER
-    await dyscom.init(init_params)
-
-    fig, ax = plt.subplots()
-    ax.set(xlabel="Sample Time (µs)", ylabel="Current (mA)",
-        title="Current measurement")
-    ax.grid()
-    plt.ion()
-    plt.show()
-
-    def update_ylim(data: list[float]):
-        if len(data) == 0:
-            return
-
-        new_min = data[0]
-        new_max = data[0]
-        for x in data:
-            new_min = min(new_min, x)
-            new_max = max(new_max, x)
-
-        offset = (new_max - new_min) * 0.1
-        plt.ylim(new_min - offset, new_max + offset)
-
-    plot_buffer: list[float] = []
-    plot_data, = ax.plot(np.linspace(0, 100, len(plot_buffer)), plot_buffer)
-    update_ylim(plot_buffer)
-    used_signals: set[DyscomSignalType] = set()
-    await dyscom.start()
-
-    for x in range(1000):
-        if x % 100 == 0:
-            dyscom.send_get_operation_mode()
-
-        while True:
-            ack = dyscom.packet_buffer.get_packet_from_buffer()
-            if ack:
-                if ack.command == Commands.DlGetAck:
-                    om_ack: PacketDyscomGetAckOperationMode = ack
-                    print(f"Operation mode {om_ack.operation_mode}")
-                elif ack.command == Commands.DlSendLiveData:
-                    sld: PacketDyscomSendLiveData = ack
-                    if sld.status_error:
-                        print(f"SendLiveData status error {sld.samples}")
-                        break
-                    if sld.number % 50 == 0:
-                        # print(f"Append {sld.value} {sld.signal_type}")
-                        for s in sld.samples:
-                            used_signals.add(s.signal_type)
-                        if len(plot_buffer) > 250:
-                            plot_buffer.pop(0)
-                        plot_buffer.append(sld.time_offset) # samples[1].value
-                        plot_data.remove()
-                        plot_data, = ax.plot(np.linspace(0, len(plot_buffer), len(plot_buffer)), plot_buffer, color = "b")
-                        # plot_data.set_xdata(np.linspace(0, 100, len(plot_buffer)))
-                        # plot_data.set_ydata(plot_buffer)
-                        # update_ylim(plot_buffer)
-                        fig.canvas.draw()
-                        fig.canvas.flush_events()
-
-            else:
-                break
-
-        await asyncio.sleep(0.01)
-
-    # wait until all acknowledges are received
-    await asyncio.sleep(0.5)
-
-    await dyscom.stop()
-    await dyscom.power_module(DyscomPowerModuleType.MEASUREMENT, DyscomPowerModulePowerType.SWITCH_OFF)
-
-    print(used_signals)
+    general = device.get_layer_general()
+    print(f"Device id: {general.device_id}")
+    print(f"Firmware version: {general.firmware_version}")
+    print(f"Science mode version: {general.science_mode_version}")
 
     connection.close()
 

examples/dyscom/example_dyscom_fastplotlib.py

@@ -79,13 +79,13 @@ async def device_communication() -> int:
                 if ack:
                     # because there are multiple get commands, we need to additionally check kind,
                     # which is always associated DyscomGetType
-                    if ack.command == Commands.DlGetAck and ack.kind == DyscomGetType.OPERATION_MODE:
+                    if ack.command == Commands.DL_GET_ACK and ack.kind == DyscomGetType.OPERATION_MODE:
                         om_ack: PacketDyscomGetAckOperationMode = ack
-                        print(f"Operation mode {om_ack.operation_mode}")
+                        print(f"Operation mode {om_ack.operation_mode.name}")
                         # check if measurement is still active
                         if om_ack.result_error != ResultAndError.NO_ERROR:
                             break
-                    elif ack.command == Commands.DlSendLiveData:
+                    elif ack.command == Commands.DL_SEND_LIVE_DATA:
                         live_data_counter += 1
 
                         sld: PacketDyscomSendLiveData = ack
@@ -111,9 +111,6 @@ async def device_communication() -> int:
 
             await asyncio.sleep(0.01)
 
-        # wait until all acknowledges are received
-        await asyncio.sleep(0.5)
-
         # stop measurement
         await dyscom.stop()
         # turn power module off

examples/dyscom/example_dyscom_pyplot.py

@@ -9,6 +9,7 @@
 from science_mode_4.dyscom.dyscom_get_operation_mode import PacketDyscomGetAckOperationMode
 from science_mode_4.dyscom.dyscom_send_live_data import PacketDyscomSendLiveData
 from science_mode_4.dyscom.dyscom_types import DyscomInitParams, DyscomPowerModulePowerType, DyscomPowerModuleType, DyscomSignalType
+from science_mode_4.utils.logger import logger
 from examples.utils.example_utils import ExampleUtils
 from examples.utils.pyplot_utils import PyPlotHelper
 
@@ -18,6 +19,9 @@ async def main() -> int:
 
     plot_helper = PyPlotHelper({0: ["BI", "blue"]}, 250)
 
+    # disable logger to increase performance
+    logger().disabled = True
+
     # get comport from command line argument
     com_port = ExampleUtils.get_comport_from_commandline_argument()
     # create serial port connection
@@ -55,10 +59,10 @@ async def main() -> int:
         while True:
             ack = dyscom.packet_buffer.get_packet_from_buffer(live_data_counter == 0)
             if ack:
-                if ack.command == Commands.DlGetAck:
+                if ack.command == Commands.DL_GET_ACK:
                     om_ack: PacketDyscomGetAckOperationMode = ack
-                    print(f"Operation mode {om_ack.operation_mode}")
-                elif ack.command == Commands.DlSendLiveData:
+                    print(f"Operation mode {om_ack.operation_mode.name}")
+                elif ack.command == Commands.DL_SEND_LIVE_DATA:
                     live_data_counter += 1
 
                     sld: PacketDyscomSendLiveData = ack
@@ -77,9 +81,6 @@ async def main() -> int:
 
         await asyncio.sleep(0.01)
 
-    # wait until all acknowledges are received
-    await asyncio.sleep(0.5)
-
     # stop measurement
     await dyscom.stop()
     # turn power module off

examples/dyscom/example_dyscom_write_csv.py

@@ -11,9 +11,10 @@
 from science_mode_4.dyscom.ads129x.ads129x_config_register_1 import Ads129xOutputDataRate, Ads129xPowerMode
 from science_mode_4.dyscom.dyscom_get_operation_mode import PacketDyscomGetAckOperationMode
 from science_mode_4.dyscom.dyscom_send_live_data import PacketDyscomSendLiveData
-from science_mode_4.dyscom.dyscom_types import DyscomGetType, DyscomInitParams, DyscomPowerModulePowerType,\
+from science_mode_4.dyscom.dyscom_types import DyscomFilterType, DyscomGetType, DyscomInitParams, DyscomPowerModulePowerType,\
     DyscomPowerModuleType, DyscomSignalType
 from science_mode_4.protocol.types import ResultAndError
+from science_mode_4.utils.logger import logger
 from examples.utils.example_utils import ExampleUtils
 from examples.utils.csv_utils import CsvHelper
 
@@ -27,6 +28,9 @@ def main():
     async def device_communication() -> int:
         """Communication with science mode device"""
 
+        # disable logger to increase performance
+        logger().disabled = True
+
         # get comport from command line argument
         com_port = ExampleUtils.get_comport_from_commandline_argument()
         # create serial port connection
@@ -47,6 +51,7 @@ async def device_communication() -> int:
         await dyscom.power_module(DyscomPowerModuleType.MEASUREMENT, DyscomPowerModulePowerType.SWITCH_ON)
         # call init with 4k sample rate and enable signal types
         init_params = DyscomInitParams()
+        init_params.filter = DyscomFilterType.PREDEFINED_FILTER_3
         init_params.signal_type = [DyscomSignalType.BI, DyscomSignalType.EMG_1,\
                                 DyscomSignalType.EMG_2, DyscomSignalType.BREATHING, DyscomSignalType.TEMPERATURE]
         init_params.register_map_ads129x.config_register_1.output_data_rate = Ads129xOutputDataRate.HR_MODE_4_KSPS__LP_MODE_2_KSPS
@@ -73,13 +78,13 @@ async def device_communication() -> int:
                 if ack:
                     # because there are multiple get commands, we need to additionally check kind,
                     # which is always associated DyscomGetType
-                    if ack.command == Commands.DlGetAck and ack.kind == DyscomGetType.OPERATION_MODE:
+                    if ack.command == Commands.DL_GET_ACK and ack.kind == DyscomGetType.OPERATION_MODE:
                         om_ack: PacketDyscomGetAckOperationMode = ack
-                        print(f"Operation mode {om_ack.operation_mode}")
+                        print(f"Operation mode {om_ack.operation_mode.name}")
                         # check if measurement is still active
                         if om_ack.result_error != ResultAndError.NO_ERROR:
                             break
-                    elif ack.command == Commands.DlSendLiveData:
+                    elif ack.command == Commands.DL_SEND_LIVE_DATA:
                         live_data_counter += 1
                         total_count += 1
 
@@ -90,7 +95,7 @@ async def device_communication() -> int:
 
                         csv_helper.append_values(ack.number, [sld.samples[0].value, sld.samples[1].value,\
                                                               sld.samples[2].value, sld.samples[3].value,\
-                                                                sld.samples[4].value], sld.time_offset)
+                                                              sld.samples[4].value], sld.time_offset)
 
                 else:
                     # print(f"Live data acknowledges per iteration {live_data_counter}")
@@ -101,8 +106,6 @@ async def device_communication() -> int:
         # print stats
         end_time = timer()
         print(f"Samples: {total_count}, duration: {end_time - start_time}, sample rate: {total_count / (end_time - start_time)}")
-        # wait until all acknowledges are received
-        await asyncio.sleep(0.5)
 
         # stop measurement
         await dyscom.stop()

examples/low_level/example_low_level_plot.py

@@ -50,7 +50,7 @@ async def main() -> int:
     # get new data from connection
     ack = low_level_layer.packet_buffer.get_packet_from_buffer()
     if ack:
-        if ack.command == Commands.LowLevelChannelConfigAck:
+        if ack.command == Commands.LOW_LEVEL_CHANNEL_CONFIG_ACK:
             ll_config_ack: PacketLowLevelChannelConfigAck = ack
             measurement_sample_time = ll_config_ack.sampling_time_in_microseconds
             measurement_samples.extend(ll_config_ack.measurement_samples)

examples/utils/fastplotlib_utils.py

@@ -19,7 +19,7 @@ def __init__(self, sub_plot, max_value_count: int, color: str):
         self._sub_plot = sub_plot
 
         # we use an array with zero as start data
-        y_data = np.array([0] * max_value_count)
+        y_data = np.array([0.0] * max_value_count, dtype=np.float32)
         self._line = sub_plot.add_line(y_data, name="values", colors=color)
 
         # this queue is used to synchronize data between background and main thread
@@ -88,7 +88,7 @@ def __init__(self, channels: dict[int, tuple[str, str]], max_value_count: int):
 
             sub_plot_counter += 1
 
-        # set animation function that is called regulary to update plots
+        # set animation function that is called regularly to update plots
         self._figure.add_animations(self._animation)
         # show figure
         self._figure.show(maintain_aspect=False)

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "science_mode_4"
-version = "0.0.9"
+version = "0.0.10"
 authors = [
   { name="Marc Hofmann", email="marc-hofmann@gmx.de" },
 ]

src/science_mode_4/__init__.py

@@ -15,3 +15,4 @@
 from .device_i24 import *
 
 __version__ = version("science_mode_4")
+logger().info("Library version %s", __version__)

src/science_mode_4/device.py

@@ -74,7 +74,7 @@ def capabilities(self) -> set[DeviceCapability]:
 
     async def initialize(self):
         """Initialize device to get basic information (serial, versions) and stop any active stimulation/measurement"""
-        if [DeviceCapability.LOW_LEVEL, DeviceCapability.MID_LEVEL] in self._capabilities:
+        if {DeviceCapability.LOW_LEVEL, DeviceCapability.MID_LEVEL}.issubset(self._capabilities):
             # get stim status to see if low/mid level is initialized or running
             stim_status = await self.get_layer_general().get_stim_status()
             if stim_status.stim_status == StimStatus.LOW_LEVEL_INITIALIZED: