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Example for message parser
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‎examples/EIT-16-256-MessageParser.ipynb‎

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{
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"cells": [
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{
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"metadata": {},
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"cell_type": "markdown",
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"source": "# Example code for connecting a Sciospec EIT device",
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"id": "8e6ea1591f787a86"
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},
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{
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"metadata": {},
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"cell_type": "markdown",
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"source": [
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"This script gives an example how to use this updated version of sciopy. \n",
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" \n",
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"Central new feature is an automated USB messaage parser, that parses incoming messages immediately and upon request saves data frames while running. For burst measurements AND continuous measurements with burst_count = 0"
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],
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"id": "e443e180ad6c1dfd"
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},
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{
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"metadata": {},
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"cell_type": "code",
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"outputs": [],
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"execution_count": null,
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"source": [
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"# Initialization\n",
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"import matplotlib.pyplot as plt\n",
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"import numpy as np\n",
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"import time\n",
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"from sciopy.sciopy import EIT_16_32_64_128, EitMeasurementSetup, available_serial_ports\n",
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"from sciopy.sciopy import make_results_folder\n",
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"# create a 'sciospec' EIT device\n",
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"n_el = 16\n",
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"sciospec = EIT_16_32_64_128(n_el)\n",
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"# connect device via USB-FS port\n",
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"print(available_serial_ports())\n",
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"sciospec.connect_device_FS(\"COM3\")\n",
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"savepath = \"../../data/\""
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],
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"id": "91983d17281c7ff1"
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},
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{
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"metadata": {},
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"cell_type": "code",
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"outputs": [],
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"execution_count": null,
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"source": [
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"# read system message buffer\n",
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"sciospec.SystemMessageCallback()"
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],
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"id": "1a8832c9510b72c9"
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},
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{
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"metadata": {},
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"cell_type": "code",
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"outputs": [],
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"execution_count": null,
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"source": [
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"# create a measurement setup\n",
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"setup = EitMeasurementSetup(\n",
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" burst_count=4,\n",
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" n_el=n_el,\n",
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" exc_freq=125_000,\n",
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" framerate=3,\n",
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" amplitude=0.01,\n",
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" inj_skip=n_el // 2,\n",
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" gain=1,\n",
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" adc_range=1\n",
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")\n",
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"sciospec.SetMeasurementSetup(setup)\n",
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"# look inside the docstring of the function and manual\n",
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"sciospec.GetMeasurementSetup(2)"
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],
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"id": "c1dbc04960e403ab"
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},
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{
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"metadata": {},
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"cell_type": "markdown",
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"source": [
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"### Usage of the \"old\" measure data command \n",
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"\n",
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"Here, the message parser is not utilized, technically faster processing of incoming messages. Messages are solely appended and processed into EITFrames and bursts"
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],
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"id": "890b0096ca6b8bb"
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},
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{
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"metadata": {},
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"cell_type": "code",
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"outputs": [],
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"execution_count": null,
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"source": [
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"data = sciospec.StartStopMeasurementFast(return_as=\"hex\")\n",
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"print(data.shape)"
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],
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"id": "initial_id"
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},
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{
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"metadata": {},
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"cell_type": "markdown",
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"source": [
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"\n",
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"### New measure-data function\n"
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],
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"id": "3301812b2d53b956"
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},
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{
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"metadata": {},
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"cell_type": "code",
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"outputs": [],
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"execution_count": null,
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"source": [
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"# 1) With burstcount\n",
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"sciospec.update_BurstCount(3) \n",
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"data= sciospec.StartStopMeasurement(return_as=\"eitframe\", bSaveData=False, bDeleteData=False,\n",
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" sSavePath=savepath, bResultsFolder=False)\n",
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"print(data.shape)\n",
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"\n",
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"# 2) Continuous measurement\n",
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"sciospec.update_BurstCount(0)\n",
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"data= sciospec.StartStopMeasurement(timeout= 5,return_as=\"eitframe\", bSaveData=False, bDeleteData=False,\n",
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" sSavePath=savepath,bResultsFolder=False) # measured for five seconds\n",
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"print(data.shape)\n",
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"\n",
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"\n",
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"\n",
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"# 3) Save data in real time and create an additional folder for storage\n",
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"data= sciospec.StartStopMeasurement(timeout= 5,return_as=\"eitframe\", bSaveData=True, bDeleteData=False,\n",
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" sSavePath=savepath,bResultsFolder=True) # measured for five seconds\n",
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"print(data.shape)\n",
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"\n",
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"\n",
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"\n",
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"\n",
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"# 4) For continuous saving results in the same folder, create a folder before and then pass it along\n",
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"sCurrPath= make_results_folder(bCreateResultsFolder=True, bSaveData=True, sSavePath=savepath)\n",
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"sciospec.StartStopMeasurement(timeout= 5,return_as=\"eitframe\", bSaveData=True, bDeleteData=True,\n",
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" sSavePath=sCurrPath,bResultsFolder=False) # measured for five seconds\n",
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"time.sleep(3)\n",
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"sciospec.StartStopMeasurement(timeout= 5,return_as=\"eitframe\", bSaveData=True, bDeleteData=True,\n",
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" sSavePath=sCurrPath,bResultsFolder=False) # measured for five seconds\n",
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"time.sleep(3)\n",
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"sciospec.StartStopMeasurement(timeout= 5,return_as=\"eitframe\", bSaveData=True, bDeleteData=True,\n",
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" sSavePath=sCurrPath,bResultsFolder=False) # measured for five seconds\n",
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"\n",
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"\n",
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"\n",
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"# Arguments:\n",
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"# bDeleteData: Data is not returned but if bSaveData=True saved, and is deleted from an internal buffer. For False, data is returned according to return_as\n",
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"# bSaveData: if Data should be saved in-time with the measurements. Data is saved at sSavePath, \n"
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],
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"id": "143a513757acfe71"
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},
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{
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"metadata": {},
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"cell_type": "markdown",
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"source": [
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"### Example on how to change the measurement mode with boundary conditions is updated\n",
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"\n",
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"Recommended is for every change of the measurement mode\n",
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"1. Restart Device\n",
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"2. Set new measurement mode"
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],
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"id": "e48b23b1ed247a39"
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},
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{
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"metadata": {},
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"cell_type": "code",
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"outputs": [],
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"execution_count": null,
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"source": [
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"# Standard setting \"singleended\" -> potential measurement\n",
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"sciospec.GetMeasurementSetup(2)\n",
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"sciospec.update_BurstCount(3) \n",
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"data= sciospec.StartStopMeasurement(return_as=\"eitframe\", bSaveData=False, bDeleteData=False,\n",
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" sSavePath=savepath, bResultsFolder=False)\n",
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"data_pot=np.abs(data[2])\n",
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"\n"
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],
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"id": "5db0b9e7255bf10b"
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},
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{
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"metadata": {},
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"cell_type": "code",
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"outputs": [],
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"execution_count": null,
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"source": [
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"# For updated setting, restart device\n",
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"sciospec.SoftwareReset()\n",
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"sciospec = EIT_16_32_64_128(16)\n",
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"print(available_serial_ports())\n",
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"sciospec.connect_device_FS(\"COM3\")\n",
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"sciospec.SetMeasurementSetup(setup)\n",
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"sciospec.update_measurement_mode(\"skip4\", \"internal\")\n",
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"sciospec.GetMeasurementSetup(2)\n",
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"# look inside the docstring of the function and manual\n",
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"\n",
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"sciospec.update_BurstCount(3) \n",
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"data= sciospec.StartStopMeasurement(return_as=\"eitframe\", bSaveData=False, bDeleteData=False,\n",
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" sSavePath=savepath, bResultsFolder=False)\n",
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"data_skip4= np.abs(data[2])\n",
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"\n",
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"\n",
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"fig, ax = plt.subplots(ncols=2)\n",
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"ax[0].imshow(data_pot, cmap=\"viridis\")\n",
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"ax[0].set_title(\"Singleended\")\n",
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"ax[1].imshow(data_skip4, cmap=\"viridis\")\n",
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"ax[1].set_title(\"Skip4\")\n",
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"plt.tight_layout()\n",
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"plt.show()"
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],
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"id": "72e8b4e384c52b7"
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},
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{
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"metadata": {},
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"cell_type": "code",
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"outputs": [],
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"execution_count": null,
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"source": [
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"\n",
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"# Alternatively,\n",
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"setup = EitMeasurementSetup(\n",
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" burst_count=4,\n",
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" n_el=n_el,\n",
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" exc_freq=125_000,\n",
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" framerate=3,\n",
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" amplitude=0.01,\n",
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" inj_skip=n_el // 2,\n",
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" gain=1,\n",
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" adc_range=1,\n",
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" mea_mode=\"skip2\",\n",
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" mea_mode_boundary=\"external\"\n",
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")\n",
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"sciospec.SetMeasurementSetup(setup)\n",
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"\n",
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"\n",
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"\n"
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],
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"id": "a026d514146eb1f0"
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 2
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.6"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎sciopy/EIT_16_32_64_128.py‎

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print("TBD: Translation")
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self.print_msg = False
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# todo
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def StartStopMeasurementFast(self, return_as="pot_mat"):
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"""
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Starts and stops a measurement process using the configured serial protocol (HS or FS).
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bSaveData (bool): Specifies if the measured data is saved in NPZ format
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bDeleteData (bool): Specifies if the measured data is deleted out of memory after each EITframe, with
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bSaveData=True, measured data is saved and then removed from RAM
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sSavepath (str): Specifies the sPath where the measured data is saved.
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sSavePath (str): Specifies the sPath where the measured data is saved.
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bResultsFolder (bool): Specifies if additionally a folder in sSavePath is created to store the data in
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Returns:
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list or matrix: The measurement data in the format specified by `return_as`.

‎sciopy/__init__.py‎

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from .EIT_16_32_64_128 import EIT_16_32_64_128, EitMeasurementSetup
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from .ISX_3 import ISX_3, EisMeasurementSetup
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from .usb_message_parser import make_results_folder
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__all__ = [
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"EitMeasurementSetup",
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"ISX_3",
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"EisMeasurementSetup",
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"make_results_folder",
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]

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