Merge Develop2 into master

.github/workflows/docs.yml

@@ -0,0 +1,27 @@
+name: Build docs
+
+on:
+  push:
+    branches: [ main, master, develop ]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.12'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r docs/requirements.txt
+          pip install -e .
+
+      - name: Build Sphinx docs
+        working-directory: docs
+        run: make html

.gitignore

@@ -1,8 +1,5 @@
-__pycache__/
 manuals
 error_device_logs
-build/
-dist/
 .update_package.sh.swp
 .eggs/
 sciopy.egg-info/
@@ -22,3 +19,40 @@ examples/measuremet_16/*
 examples/measuremet_32/*
 sciopy/eth_*
 Driver
+ISX3-dev.ipynb
+update_docu.md
+
+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+dist/
+build/
+
+# virtualenvs
+.env/
+.venv/
+.docs-venv/
+docs-venv/
+venv/
+venv*/
+
+# Sphinx build outputs & doctrees
+docs/_build/
+docs/_doctrees/
+_build/
+.doctrees/
+
+# Sphinx cache / temp
+docs/.doctrees/
+*.doctree
+
+# OS / editor files
+.DS_Store
+Thumbs.db
+.idea/
+.vscode/
+
+# pip / wheel cache (optional)
+pip-wheel-metadata/
+*.whl

.readthedocs.yml

@@ -0,0 +1,12 @@
+version: 2
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+python:
+  install:
+    - method: pip
+      path: .
+    - requirements: docs/requirements.txt
+requests:
+  - type: github

README.md

@@ -1,10 +1,15 @@
-<img src="https://raw.githubusercontent.com/spatialaudio/sciopy/main/doc/images/logo_sciopy.jpg" alt="Bildbeschreibung" width="200"/>
+<img src="https://raw.githubusercontent.com/EITLabworks/sciopy/develop/docs/_static/logo_sciopy.jpg" alt="Sciopy-logo" width="200"/>
 
 This package offers the serial interface for communication with an EIT device from ScioSpec. Commands can be written serially and the system response can be read out. With the current version, it is possible to start and stop measurements with defined burst counts and to read out the measurement data. In addition, the measurement data is packed into a data class for better further processing.
 
+**WIP** Communication with ISX-3
 
 ## Contact
 
-If you have ideas or other advice don't hesitate to contact me!
+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

docs/Makefile

@@ -0,0 +1,18 @@
+# Minimal Makefile for Sphinx
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+.PHONY: help html clean
+
+help:
+	@echo "Please use 'make <target>' where <target> is one of"
+	@echo "  html     to build the documentation"
+	@echo "  clean    to remove build artifacts"
+
+html:
+	$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" -a -E
+
+clean:
+	@rm -rf $(BUILDDIR)/*
+	@echo "Cleaned build artifacts"

docs/_autosummary/sciopy.EIT_16_32_64_128.rst

@@ -0,0 +1,45 @@
+sciopy.EIT\_16\_32\_64\_128
+===========================
+
+.. currentmodule:: sciopy
+
+.. autoclass:: EIT_16_32_64_128
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~EIT_16_32_64_128.GetDeviceInfo
+      ~EIT_16_32_64_128.GetFirmwareIDs
+      ~EIT_16_32_64_128.GetMeasurementSetup
+      ~EIT_16_32_64_128.GetOutputConfiguration
+      ~EIT_16_32_64_128.PowerPlugDetect
+      ~EIT_16_32_64_128.ResetMeasurementSetup
+      ~EIT_16_32_64_128.SaveSettings
+      ~EIT_16_32_64_128.SetMeasurementSetup
+      ~EIT_16_32_64_128.SetOutputConfiguration
+      ~EIT_16_32_64_128.SoftwareReset
+      ~EIT_16_32_64_128.StartStopMeasurement
+      ~EIT_16_32_64_128.SystemMessageCallback
+      ~EIT_16_32_64_128.SystemMessageCallback_usb_fs
+      ~EIT_16_32_64_128.SystemMessageCallback_usb_hs
+      ~EIT_16_32_64_128.__init__
+      ~EIT_16_32_64_128.connect_device_FS
+      ~EIT_16_32_64_128.connect_device_HS
+      ~EIT_16_32_64_128.disconnect_device
+      ~EIT_16_32_64_128.get_data_as_matrix
+      ~EIT_16_32_64_128.init_channel_group
+      ~EIT_16_32_64_128.update_BurstCount
+      ~EIT_16_32_64_128.update_ExcitationFrequency
+      ~EIT_16_32_64_128.update_FrameRate
+      ~EIT_16_32_64_128.write_command_string
+
+
+
+
+
+

docs/_autosummary/sciopy.ISX_3.rst

@@ -0,0 +1,45 @@
+sciopy.ISX\_3
+=============
+
+.. currentmodule:: sciopy
+
+.. autoclass:: ISX_3
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~ISX_3.Action
+      ~ISX_3.GetDeviceID
+      ~ISX_3.GetExtensionPortChannel
+      ~ISX_3.GetExtensionPortModule
+      ~ISX_3.GetFE_Settings
+      ~ISX_3.GetFPGAfirmwareID
+      ~ISX_3.GetOptions
+      ~ISX_3.GetSetup
+      ~ISX_3.GetSyncTime
+      ~ISX_3.ResetSystem
+      ~ISX_3.SetExtensionPortChannel
+      ~ISX_3.SetFE_Settings
+      ~ISX_3.SetMeasurementSetup
+      ~ISX_3.SetOptions
+      ~ISX_3.SetSetup
+      ~ISX_3.SetSyncTime
+      ~ISX_3.StartMeasure
+      ~ISX_3.SystemMessageCallback
+      ~ISX_3.__init__
+      ~ISX_3.connect_device_FTDI
+      ~ISX_3.disconnect_device_FTDI
+      ~ISX_3.info
+      ~ISX_3.list_usb_devices
+      ~ISX_3.write_command_string
+
+
+
+
+
+

docs/_autosummary/sciopy.com_util.rst

@@ -0,0 +1,22 @@
+sciopy.com\_util
+================
+
+.. automodule:: sciopy.com_util
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      available_serial_ports
+      bytesarray_to_byteslist
+      bytesarray_to_float
+      bytesarray_to_int
+      clTbt_dp
+      clTbt_sp
+      del_hex_in_list
+      parse_single_frame
+      reshape_full_message_in_bursts
+      single_hex_to_int
+      split_bursts_in_frames
+

docs/_autosummary/sciopy.doteit.rst

@@ -0,0 +1,18 @@
+sciopy.doteit
+=============
+
+.. automodule:: sciopy.doteit
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      convert_fulldir_doteit_to_npz
+      convert_fulldir_doteit_to_pickle
+      doteit_in_SingleEitFrame
+      list_all_files
+      list_eit_files
+      load_pickle_to_dict
+      single_eit_in_pickle
+

docs/_autosummary/sciopy.meshing.rst

@@ -0,0 +1,15 @@
+sciopy.meshing
+==============
+
+.. automodule:: sciopy.meshing
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      add_circle_anomaly
+      create_empty_2d_mesh
+      mesh_sample
+      plot_mesh
+

docs/_autosummary/sciopy.rst

@@ -0,0 +1,6 @@
+sciopy
+======
+
+.. automodule:: sciopy
+
+

docs/_autosummary/sciopy.sciopy_dataclasses.rst

@@ -0,0 +1,17 @@
+sciopy.sciopy\_dataclasses
+==========================
+
+.. automodule:: sciopy.sciopy_dataclasses
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      EisMeasurementSetup
+      EitMeasurementSetup
+      PreperationConfig
+      ScioSpecMeasurementConfig
+      SingleEitFrame
+      SingleFrame
+

docs/_autosummary/sciopy.visualization.rst

@@ -0,0 +1,14 @@
+sciopy.visualization
+====================
+
+.. automodule:: sciopy.visualization
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      norm_data
+      plot_el_sign
+      plot_potential_matrix
+

docs/api.rst

@@ -0,0 +1,14 @@
+API reference
+=============
+
+.. autosummary::
+   :toctree: _autosummary
+
+   sciopy
+   sciopy.com_util
+   sciopy.doteit
+   sciopy.EIT_16_32_64_128
+   sciopy.ISX_3
+   sciopy.meshing
+   sciopy.sciopy_dataclasses
+   sciopy.visualization