seemoo-lab / pyshimmer Goto Github PK

Hi, I'm trying to deploying and end to end system, so I don't want that the user interact with Consensys or other Shimmer software.
The data I'm downloading it through the dock station.
Following your examples I could access to the raw data, but I can't access to the calibration one. Can you help me?

Hi thank you for this code. Could you explain how this could be intergrated with PyLSL to set up data streaming?
This would be a great merge with the LSL project to combine GSR with other sensors.

Hi, thanks for the great work with this API.

We are trying to integrate shimmer with a Psychopy https://www.psychopy.org/ experiment where we present some images and want to record the physiological signals using the shimmer kit.

Is there a way to send a "trigger"/ event marker using the API, such that I can synchronise the image presentation with the recording afterwards?

I hope this makes sense

After successful firmware flashing, and rfcomm bind,
The test code provides below error.
'device reports readiness to read but returned no data'.
Should I do something between binding and run the testcode provided in repository?

Dear Lukas,
first thank you for this library, I have been looking for a long time for a simpler way to access the shimmer via python.
One thing is missing is the possibility to set configure the Shimmer before starting to stream.

One should be able to select which channels are active (e.g., AC13, RAW GSR, SRC, etc) and the streaming frequency.
Maybe the features is already there, if that's the case, could you please provide me a snippet on how to use it?

Thank you!
Dario

Hello,

Thank you for your impressive work on Shimmer devices.
I would like to know if you were able to test the compatibility of pyshimmer with the new version of the LogAndStream v0.16.000 firmware.
I await your feedback before updating my IMUs.

Thank you in advance,
Sincerely

Hey,
I followed the instructions of the readme. I also patched LogAndStream Firmware on my Shimmer3 EXG.
Everything work till the example Program of the BT API. I am working on an Ubuntu 18.04.4 LTS.
I got the Error:
My name is: Shimmer_86A5
Exception in thread Thread-1:
Traceback (most recent call last):
File "/usr/lib/python3.8/threading.py", line 932, in _bootstrap_inner
self.run()
File "/usr/lib/python3.8/threading.py", line 870, in run
self._target(*self._args, **self._kwargs)
File "/home/z-fcc/PycharmProjects/Test/pyshimmer/pyshimmer/bluetooth/bt_api.py", line 294, in _run_readloop
self._bluetooth.process_single_input_event()
File "/home/z-fcc/PycharmProjects/Test/pyshimmer/pyshimmer/bluetooth/bt_api.py", line 206, in process_single_input_event
self._process_data_packet()
File "/home/z-fcc/PycharmProjects/Test/pyshimmer/pyshimmer/bluetooth/bt_api.py", line 148, in _process_data_packet
cb(packet)
File "/home/z-fcc/PycharmProjects/Test/pyshimmer/test_hallo.py", line 26, in handler
cur_value = pkt[EChannelType.INTERNAL_ADC_13]
File "/home/z-fcc/PycharmProjects/Test/pyshimmer/pyshimmer/bluetooth/bt_commands.py", line 60, in getitem
return self._values[item]
KeyError: <EChannelType.INTERNAL_ADC_13: 19>

After that i have to keyinterrupt the session:

Traceback (most recent call last):
File "/home/z-fcc/PycharmProjects/Test/pyshimmer/test_hallo.py", line 43, in
shim_dev.stop_streaming()
File "/home/z-fcc/PycharmProjects/Test/pyshimmer/pyshimmer/bluetooth/bt_api.py", line 480, in stop_streaming
self._process_and_wait(StopStreamingCommand())
File "/home/z-fcc/PycharmProjects/Test/pyshimmer/pyshimmer/bluetooth/bt_api.py", line 301, in _process_and_wait
compl_obj.wait()
File "/home/z-fcc/PycharmProjects/Test/pyshimmer/pyshimmer/bluetooth/bt_api.py", line 50, in wait
self.__event.wait()
File "/usr/lib/python3.8/threading.py", line 558, in wait
signaled = self._cond.wait(timeout)
File "/usr/lib/python3.8/threading.py", line 302, in wait
waiter.acquire()
KeyboardInterrupt

I can't find the mistake by my own. Can you help me pls?

Dear StudentofGermany

Hello lumagi,

I use your Python API for my Shimmer3 EXG Unit and it works well. Thank you for that :)
Now I want to get the data from the Shimmer SD with Consensys. Sometimes it works, but more often an error occur.
Also I use your Reader API, but with the reader API the data have a different shape, like the streaming data. And i would prefer to have the data in the shape of the output from Consensys.
Could it be that the data got damaged or not closed with the Python API? Even if i use the stop() and shutdown() command?

Best StudentofGermany

Hi Lukas,

I think the realign functionality when loading data is incorrect. From my understanding it does the following right now:

1. take the first timestamp as an initial offset for the new timestamps
2. extrapolate from the first timestamp assuming a constant sampling rate while preserving the total number of observations
3. interpolate the sensor data to match the newly generated timestamps

If the original timestamps are assumed to be correct, keeping the total number of observations in the second step will lead to an too early final timestamp. Instead, the correct approach would be to impute missing timestamps and interpolate new sensor values. Otherwise, if the timestamps are assumed to be incorrect, interpolating the sensor values in the third steps is wrong.

Working with the raw data from the Shimmer devices, I have made the following observations:

• the difference between consecutive observations is almost always an integer multiple of the sample time (inverse of the sampling frequency)
• the only exception I have seen so far is the time difference between the first and second sample: often this one is not an integer multiple of the sampling time

Using this observations, my current approach is to disable the realign functionality, drop the first sample and impute missing values by linear interpolation as outlined below.

import pandas as pd
import numpy as np
from pyshimmer import ShimmerReader, EChannelType

with open("ECG.sb3", "rb") as ecg_file:
    ecg_reader = ShimmerReader(ecg_file, realign=False)
    ecg_reader.load_file_data()
    ecg_fs = ecg_reader.sample_rate

    # convert to pandas dataframe and drop the first sample
    ecg_df = pd.DataFrame({
        "ecg1": ecg_reader[EChannelType.EXG_ADS1292R_1_CH1_24BIT][1:],
        "ecg2": ecg_reader[EChannelType.EXG_ADS1292R_1_CH2_24BIT][1:],
    }, index=ecg_reader[EChannelType.TIMESTAMP][1:])

    # add empty rows for the missing timestamps and interpolate the sensor values
    ecg_ts = pd.Index(np.arange(ecg_df.index[0], ecg_df.index[-1], 1/ecg_fs), name="timestamps")
    ecg_df = ecg_df.reindex(ecg_ts).reset_index().interpolate()

Concluding, I think it would be better to remove the realign functionality and let the users decide on how to deal with the presumably missing observations. Though, it may be helpful to raise a warning on detecting such gaps in the recording and, in particular, on detecting those which are are not an integer multiple of the sample time.

Cheers,
Matthias

See ShimmerResearch/shimmer3#10