Merge Develop2 into master

README.md

@@ -9,3 +9,7 @@ This package offers the serial interface for communication with an EIT device fr
 If you have any ideas or other suggestions, please don't hesitate to contact me.
 
 Email: jacob.thoenes@uni-rostock.de
+
+___
+
+- FTDI Driver installation: https://www.ftdichip.com/old2020/Drivers/D2XX.htm

citation.cff

@@ -13,6 +13,11 @@ authors:
     email: jacob.thoenes@uni-rostock.de
     affiliation: Universität Rostock
     orcid: 'https://orcid.org/0000-0003-2826-5281'
+  - given-names: Patricia
+    family-names: Fuchs
+    email: pat.fuchs@uni-rostock.de
+    affiliation: Universität Rostock
+    orcid: 'https://orcid.org/0009-0006-4647-633X
   - given-names: Oveys
     family-names: Javanmardtilaki
     email: oveys@javanmardtilaki@uni-rostock.de
@@ -23,6 +28,6 @@ keywords:
   - EIT
   - Sciospec
 license: MIT
-version: 0.8.0
+version: 0.9.0
 doi: 10.5281/zenodo.7766305
 date-released: '2024-11-14'

docs/conf.py

@@ -7,7 +7,7 @@
 
 project = "sciopy"
 author = "Jacob P. Thönes"
-release = "0.8.2.2"
+release = "0.8.2.3"
 
 extensions = [
     "sphinx.ext.autodoc",

examples/EIT-16-256-MessageParser.ipynb

@@ -0,0 +1,300 @@
+{
+ "cells": [
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "# Example code for connecting a Sciospec EIT device",
+   "id": "8e6ea1591f787a86"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "This script gives an example how to use this updated version of sciopy.   \n",
+    "  \n",
+    "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"
+   ],
+   "id": "e443e180ad6c1dfd"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "# Initialization\n",
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "import time\n",
+    "from sciopy.sciopy import EIT_16_32_64_128, EitMeasurementSetup, available_serial_ports\n",
+    "from sciopy.sciopy import make_results_folder\n",
+    "\n",
+    "# create a 'sciospec' EIT device\n",
+    "n_el = 16\n",
+    "sciospec = EIT_16_32_64_128(n_el)\n",
+    "# connect device via USB-FS port\n",
+    "print(available_serial_ports())\n",
+    "sciospec.connect_device_FS(\"COM3\")\n",
+    "savepath = \"../../data/\""
+   ],
+   "id": "91983d17281c7ff1"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "# read system message buffer\n",
+    "sciospec.SystemMessageCallback()"
+   ],
+   "id": "1a8832c9510b72c9"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "# create a measurement setup\n",
+    "setup = EitMeasurementSetup(\n",
+    "    burst_count=4,\n",
+    "    n_el=n_el,\n",
+    "    exc_freq=125_000,\n",
+    "    framerate=3,\n",
+    "    amplitude=0.01,\n",
+    "    inj_skip=n_el // 2,\n",
+    "    gain=1,\n",
+    "    adc_range=1,\n",
+    ")\n",
+    "sciospec.SetMeasurementSetup(setup)\n",
+    "# look inside the docstring of the function and manual\n",
+    "sciospec.GetMeasurementSetup(2)"
+   ],
+   "id": "c1dbc04960e403ab"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "### Usage of the \"old\" measure data command \n",
+    "\n",
+    "Here, the message parser is not utilized, technically faster processing of incoming messages. Messages are solely appended and processed into EITFrames and bursts"
+   ],
+   "id": "890b0096ca6b8bb"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "data = sciospec.StartStopMeasurementFast(return_as=\"hex\")\n",
+    "print(data.shape)"
+   ],
+   "id": "initial_id"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "\n",
+    "### New measure-data function\n"
+   ],
+   "id": "3301812b2d53b956"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "# 1) With burstcount\n",
+    "sciospec.update_BurstCount(3)\n",
+    "data = sciospec.StartStopMeasurement(\n",
+    "    return_as=\"eitframe\",\n",
+    "    bSaveData=False,\n",
+    "    bDeleteData=False,\n",
+    "    sSavePath=savepath,\n",
+    "    bResultsFolder=False,\n",
+    ")\n",
+    "print(data.shape)\n",
+    "\n",
+    "# 2) Continuous measurement\n",
+    "sciospec.update_BurstCount(0)\n",
+    "data = sciospec.StartStopMeasurement(\n",
+    "    timeout=5,\n",
+    "    return_as=\"eitframe\",\n",
+    "    bSaveData=False,\n",
+    "    bDeleteData=False,\n",
+    "    sSavePath=savepath,\n",
+    "    bResultsFolder=False,\n",
+    ")  # measured for five seconds\n",
+    "print(data.shape)\n",
+    "\n",
+    "\n",
+    "# 3) Save data in real time and create an additional folder for storage\n",
+    "data = sciospec.StartStopMeasurement(\n",
+    "    timeout=5,\n",
+    "    return_as=\"eitframe\",\n",
+    "    bSaveData=True,\n",
+    "    bDeleteData=False,\n",
+    "    sSavePath=savepath,\n",
+    "    bResultsFolder=True,\n",
+    ")  # measured for five seconds\n",
+    "print(data.shape)\n",
+    "\n",
+    "\n",
+    "# 4) For continuous saving results in the same folder, create a folder before and then pass it along\n",
+    "sCurrPath = make_results_folder(\n",
+    "    bCreateResultsFolder=True, bSaveData=True, sSavePath=savepath\n",
+    ")\n",
+    "sciospec.StartStopMeasurement(\n",
+    "    timeout=5,\n",
+    "    return_as=\"eitframe\",\n",
+    "    bSaveData=True,\n",
+    "    bDeleteData=True,\n",
+    "    sSavePath=sCurrPath,\n",
+    "    bResultsFolder=False,\n",
+    ")  # measured for five seconds\n",
+    "time.sleep(3)\n",
+    "sciospec.StartStopMeasurement(\n",
+    "    timeout=5,\n",
+    "    return_as=\"eitframe\",\n",
+    "    bSaveData=True,\n",
+    "    bDeleteData=True,\n",
+    "    sSavePath=sCurrPath,\n",
+    "    bResultsFolder=False,\n",
+    ")  # measured for five seconds\n",
+    "time.sleep(3)\n",
+    "sciospec.StartStopMeasurement(\n",
+    "    timeout=5,\n",
+    "    return_as=\"eitframe\",\n",
+    "    bSaveData=True,\n",
+    "    bDeleteData=True,\n",
+    "    sSavePath=sCurrPath,\n",
+    "    bResultsFolder=False,\n",
+    ")  # measured for five seconds\n",
+    "\n",
+    "\n",
+    "# Arguments:\n",
+    "# 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",
+    "# bSaveData: if Data should be saved in-time with the measurements. Data is saved at sSavePath,"
+   ],
+   "id": "143a513757acfe71"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "### Example on how to change the measurement mode with boundary conditions is updated\n",
+    "\n",
+    "Recommended is for every change of the measurement mode\n",
+    "1. Restart Device\n",
+    "2. Set new measurement mode"
+   ],
+   "id": "e48b23b1ed247a39"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "# Standard setting \"singleended\" -> potential measurement\n",
+    "sciospec.GetMeasurementSetup(2)\n",
+    "sciospec.update_BurstCount(3)\n",
+    "data = sciospec.StartStopMeasurement(\n",
+    "    return_as=\"eitframe\",\n",
+    "    bSaveData=False,\n",
+    "    bDeleteData=False,\n",
+    "    sSavePath=savepath,\n",
+    "    bResultsFolder=False,\n",
+    ")\n",
+    "data_pot = np.abs(data[2])"
+   ],
+   "id": "5db0b9e7255bf10b"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "# For updated setting, restart device\n",
+    "sciospec.SoftwareReset()\n",
+    "sciospec = EIT_16_32_64_128(16)\n",
+    "print(available_serial_ports())\n",
+    "sciospec.connect_device_FS(\"COM3\")\n",
+    "sciospec.SetMeasurementSetup(setup)\n",
+    "sciospec.update_measurement_mode(\"skip4\", \"internal\")\n",
+    "sciospec.GetMeasurementSetup(2)\n",
+    "# look inside the docstring of the function and manual\n",
+    "\n",
+    "sciospec.update_BurstCount(3)\n",
+    "data = sciospec.StartStopMeasurement(\n",
+    "    return_as=\"eitframe\",\n",
+    "    bSaveData=False,\n",
+    "    bDeleteData=False,\n",
+    "    sSavePath=savepath,\n",
+    "    bResultsFolder=False,\n",
+    ")\n",
+    "data_skip4 = np.abs(data[2])\n",
+    "\n",
+    "\n",
+    "fig, ax = plt.subplots(ncols=2)\n",
+    "ax[0].imshow(data_pot, cmap=\"viridis\")\n",
+    "ax[0].set_title(\"Singleended\")\n",
+    "ax[1].imshow(data_skip4, cmap=\"viridis\")\n",
+    "ax[1].set_title(\"Skip4\")\n",
+    "plt.tight_layout()\n",
+    "plt.show()"
+   ],
+   "id": "72e8b4e384c52b7"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "# Alternatively,\n",
+    "setup = EitMeasurementSetup(\n",
+    "    burst_count=4,\n",
+    "    n_el=n_el,\n",
+    "    exc_freq=125_000,\n",
+    "    framerate=3,\n",
+    "    amplitude=0.01,\n",
+    "    inj_skip=n_el // 2,\n",
+    "    gain=1,\n",
+    "    adc_range=1,\n",
+    "    mea_mode=\"skip2\",\n",
+    "    mea_mode_boundary=\"external\",\n",
+    ")\n",
+    "sciospec.SetMeasurementSetup(setup)"
+   ],
+   "id": "a026d514146eb1f0"
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}