[project] make it a package

Reviewed-on: Awendt/pyrelacs#1

.gitignore

@@ -161,3 +161,5 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
+# ignore created data files
+*.nix

poetry.lock

@@ -1,4 +1,22 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
+
+[[package]]
+name = "asttokens"
+version = "2.4.1"
+description = "Annotate AST trees with source code positions"
+optional = false
+python-versions = "*"
+files = [
+    {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
+    {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
+]
+
+[package.dependencies]
+six = ">=1.12.0"
+
+[package.extras]
+astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
+test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
 
 [[package]]
 name = "click"
@@ -124,6 +142,31 @@ files = [
 docs = ["ipython", "matplotlib", "numpydoc", "sphinx"]
 tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
+[[package]]
+name = "decorator"
+version = "5.1.1"
+description = "Decorators for Humans"
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"},
+    {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
+]
+
+[[package]]
+name = "executing"
+version = "2.1.0"
+description = "Get the currently executing AST node of a frame, and other information"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "executing-2.1.0-py2.py3-none-any.whl", hash = "sha256:8d63781349375b5ebccc3142f4b30350c0cd9c79f921cde38be2be4637e98eaf"},
+    {file = "executing-2.1.0.tar.gz", hash = "sha256:8ea27ddd260da8150fa5a708269c4a10e76161e2496ec3e587da9e3c0fe4b9ab"},
+]
+
+[package.extras]
+tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich"]
+
 [[package]]
 name = "fonttools"
 version = "4.53.1"
@@ -189,6 +232,99 @@ ufo = ["fs (>=2.2.0,<3)"]
 unicode = ["unicodedata2 (>=15.1.0)"]
 woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 
+[[package]]
+name = "h5py"
+version = "3.12.1"
+description = "Read and write HDF5 files from Python"
+optional = false
+python-versions = ">=3.9"
+files = [
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+]
+
+[package.dependencies]
+numpy = ">=1.19.3"
+
+[[package]]
+name = "ipython"
+version = "8.27.0"
+description = "IPython: Productive Interactive Computing"
+optional = false
+python-versions = ">=3.10"
+files = [
+    {file = "ipython-8.27.0-py3-none-any.whl", hash = "sha256:f68b3cb8bde357a5d7adc9598d57e22a45dfbea19eb6b98286fa3b288c9cd55c"},
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+]
+
+[package.dependencies]
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+decorator = "*"
+jedi = ">=0.16"
+matplotlib-inline = "*"
+pexpect = {version = ">4.3", markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""}
+prompt-toolkit = ">=3.0.41,<3.1.0"
+pygments = ">=2.4.0"
+stack-data = "*"
+traitlets = ">=5.13.0"
+
+[package.extras]
+all = ["ipython[black,doc,kernel,matplotlib,nbconvert,nbformat,notebook,parallel,qtconsole]", "ipython[test,test-extra]"]
+black = ["black"]
+doc = ["docrepr", "exceptiongroup", "intersphinx-registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli", "typing-extensions"]
+kernel = ["ipykernel"]
+matplotlib = ["matplotlib"]
+nbconvert = ["nbconvert"]
+nbformat = ["nbformat"]
+notebook = ["ipywidgets", "notebook"]
+parallel = ["ipyparallel"]
+qtconsole = ["qtconsole"]
+test = ["packaging", "pickleshare", "pytest", "pytest-asyncio (<0.22)", "testpath"]
+test-extra = ["curio", "ipython[test]", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.23)", "pandas", "trio"]
+
+[[package]]
+name = "jedi"
+version = "0.19.1"
+description = "An autocompletion tool for Python that can be used for text editors."
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "jedi-0.19.1-py2.py3-none-any.whl", hash = "sha256:e983c654fe5c02867aef4cdfce5a2fbb4a50adc0af145f70504238f18ef5e7e0"},
+    {file = "jedi-0.19.1.tar.gz", hash = "sha256:cf0496f3651bc65d7174ac1b7d043eff454892c708a87d1b683e57b569927ffd"},
+]
+
+[package.dependencies]
+parso = ">=0.8.3,<0.9.0"
+
+[package.extras]
+docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"]
+qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
+testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
+
 [[package]]
 name = "kiwisolver"
 version = "1.4.7"
@@ -399,6 +535,20 @@ python-dateutil = ">=2.7"
 [package.extras]
 dev = ["meson-python (>=0.13.1)", "numpy (>=1.25)", "pybind11 (>=2.6)", "setuptools (>=64)", "setuptools_scm (>=7)"]
 
+[[package]]
+name = "matplotlib-inline"
+version = "0.1.7"
+description = "Inline Matplotlib backend for Jupyter"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "matplotlib_inline-0.1.7-py3-none-any.whl", hash = "sha256:df192d39a4ff8f21b1895d72e6a13f5fcc5099f00fa84384e0ea28c2cc0653ca"},
+    {file = "matplotlib_inline-0.1.7.tar.gz", hash = "sha256:8423b23ec666be3d16e16b60bdd8ac4e86e840ebd1dd11a30b9f117f2fa0ab90"},
+]
+
+[package.dependencies]
+traitlets = "*"
+
 [[package]]
 name = "mdurl"
 version = "0.1.2"
@@ -410,66 +560,65 @@ files = [
     {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"},
 ]
 
+[[package]]
+name = "nixio"
+version = "1.5.3"
+description = "Python reimplementation of NIXIO (http://g-node.github.io/nix/)"
+optional = false
+python-versions = ">=3.6"
+files = [
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+    {file = "nixio-1.5.3.tar.gz", hash = "sha256:0ba7a65148297bd43a5ddaf143c4faad1c999771aa1d7e690aa0a5e31f368608"},
+]
+
+[package.dependencies]
+h5py = "*"
+numpy = "*"
+six = "*"
+
 [[package]]
 name = "numpy"
-version = "2.1.1"
+version = "1.26.4"
 description = "Fundamental package for array computing in Python"
 optional = false
-python-versions = ">=3.10"
+python-versions = ">=3.9"
 files = [
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 typing = ["typing-extensions"]
 xmp = ["defusedxml"]
 
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+    {file = "scipy-1.14.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:fef8c87f8abfb884dac04e97824b61299880c43f4ce675dd2cbeadd3c9b466d2"},
+    {file = "scipy-1.14.1-cp311-cp311-musllinux_1_2_x86_64.whl", hash = "sha256:b05d43735bb2f07d689f56f7b474788a13ed8adc484a85aa65c0fd931cf9ccd2"},
+    {file = "scipy-1.14.1-cp311-cp311-win_amd64.whl", hash = "sha256:716e389b694c4bb564b4fc0c51bc84d381735e0d39d3f26ec1af2556ec6aad94"},
+    {file = "scipy-1.14.1-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:631f07b3734d34aced009aaf6fedfd0eb3498a97e581c3b1e5f14a04164a456d"},
+    {file = "scipy-1.14.1-cp312-cp312-macosx_12_0_arm64.whl", hash = "sha256:af29a935803cc707ab2ed7791c44288a682f9c8107bc00f0eccc4f92c08d6e07"},
+    {file = "scipy-1.14.1-cp312-cp312-macosx_14_0_arm64.whl", hash = "sha256:2843f2d527d9eebec9a43e6b406fb7266f3af25a751aa91d62ff416f54170bc5"},
+    {file = "scipy-1.14.1-cp312-cp312-macosx_14_0_x86_64.whl", hash = "sha256:eb58ca0abd96911932f688528977858681a59d61a7ce908ffd355957f7025cfc"},
+    {file = "scipy-1.14.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:30ac8812c1d2aab7131a79ba62933a2a76f582d5dbbc695192453dae67ad6310"},
+    {file = "scipy-1.14.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8f9ea80f2e65bdaa0b7627fb00cbeb2daf163caa015e59b7516395fe3bd1e066"},
+    {file = "scipy-1.14.1-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:edaf02b82cd7639db00dbff629995ef185c8df4c3ffa71a5562a595765a06ce1"},
+    {file = "scipy-1.14.1-cp312-cp312-win_amd64.whl", hash = "sha256:2ff38e22128e6c03ff73b6bb0f85f897d2362f8c052e3b8ad00532198fbdae3f"},
+    {file = "scipy-1.14.1-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:1729560c906963fc8389f6aac023739ff3983e727b1a4d87696b7bf108316a79"},
+    {file = "scipy-1.14.1-cp313-cp313-macosx_12_0_arm64.whl", hash = "sha256:4079b90df244709e675cdc8b93bfd8a395d59af40b72e339c2287c91860deb8e"},
+    {file = "scipy-1.14.1-cp313-cp313-macosx_14_0_arm64.whl", hash = "sha256:e0cf28db0f24a38b2a0ca33a85a54852586e43cf6fd876365c86e0657cfe7d73"},
+    {file = "scipy-1.14.1-cp313-cp313-macosx_14_0_x86_64.whl", hash = "sha256:0c2f95de3b04e26f5f3ad5bb05e74ba7f68b837133a4492414b3afd79dfe540e"},
+    {file = "scipy-1.14.1-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b99722ea48b7ea25e8e015e8341ae74624f72e5f21fc2abd45f3a93266de4c5d"},
+    {file = "scipy-1.14.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5149e3fd2d686e42144a093b206aef01932a0059c2a33ddfa67f5f035bdfe13e"},
+    {file = "scipy-1.14.1-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:e4f5a7c49323533f9103d4dacf4e4f07078f360743dec7f7596949149efeec06"},
+    {file = "scipy-1.14.1-cp313-cp313-win_amd64.whl", hash = "sha256:baff393942b550823bfce952bb62270ee17504d02a1801d7fd0719534dfb9c84"},
+    {file = "scipy-1.14.1.tar.gz", hash = "sha256:5a275584e726026a5699459aa72f828a610821006228e841b94275c4a7c08417"},
+]
+
+[package.dependencies]
+numpy = ">=1.23.5,<2.3"
+
+[package.extras]
+dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy (==1.10.0)", "pycodestyle", "pydevtool", "rich-click", "ruff (>=0.0.292)", "types-psutil", "typing_extensions"]
+doc = ["jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.13.1)", "jupytext", "matplotlib (>=3.5)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0,<=7.3.7)", "sphinx-design (>=0.4.0)"]
+test = ["Cython", "array-api-strict (>=2.0)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+
 [[package]]
 name = "shellingham"
 version = "1.5.4"
@@ -727,16 +1008,50 @@ files = [
 ]
 
 [[package]]
-name = "tomli"
+name = "stack-data"
-version = "2.0.1"
+version = "0.6.3"
-description = "A lil' TOML parser"
+description = "Extract data from python stack frames and tracebacks for informative displays"
 optional = false
-python-versions = ">=3.7"
+python-versions = "*"
 files = [
-    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
+    {file = "stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695"},
-    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
+    {file = "stack_data-0.6.3.tar.gz", hash = "sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9"},
 ]
 
+[package.dependencies]
+asttokens = ">=2.1.0"
+executing = ">=1.2.0"
+pure-eval = "*"
+
+[package.extras]
+tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
+
+[[package]]
+name = "tomlkit"
+version = "0.13.2"
+description = "Style preserving TOML library"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "tomlkit-0.13.2-py3-none-any.whl", hash = "sha256:7a974427f6e119197f670fbbbeae7bef749a6c14e793db934baefc1b5f03efde"},
+    {file = "tomlkit-0.13.2.tar.gz", hash = "sha256:fff5fe59a87295b278abd31bec92c15d9bc4a06885ab12bcea52c71119392e79"},
+]
+
+[[package]]
+name = "traitlets"
+version = "5.14.3"
+description = "Traitlets Python configuration system"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"},
+    {file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"},
+]
+
+[package.extras]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
+test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.2)", "pytest-mock", "pytest-mypy-testing"]
+
 [[package]]
 name = "typer"
 version = "0.12.5"
@@ -776,7 +1091,18 @@ files = [
     {file = "uldaq-1.2.3.tar.gz", hash = "sha256:2d405ead334bb4e37c20b72d8ec498f0e372b08f1d3323f622abe0581ac28b98"},
 ]
 
+[[package]]
+name = "wcwidth"
+version = "0.2.13"
+description = "Measures the displayed width of unicode strings in a terminal"
+optional = false
+python-versions = "*"
+files = [
+    {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"},
+    {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"},
+]
+
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.12"
-content-hash = "6b680c385942c0a2c0eef934f3fb37fdc3d2e1dc058a7f2d891d4f2f0607d9c6"
+content-hash = "b1076b7f750e8f7e66542918ec746e74544fbfdb376875158f083fb573d18107"

pyproject.toml

@@ -1,20 +1,42 @@
+[project]
+organization = "de.uni-tuebingen.neuroetho"
+copyright = "(c) 2020, Neuroethology lab, Uni Tuebingen"
+
 [tool.poetry]
 name = "pyrelacs"
 version = "0.1.0"
 description = "Relaxed ELectrophysiology Acquisition, Control, and Stimulation in python"
 authors = ["wendtalexander <wendtalexander@protonmail.com>"]
+repository = "https://whale.am28.uni-tuebingen.de/git/awendt/pyrelacs"
 readme = "README.md"
+license = "MIT"
+classifiers = [
+    "Topic :: Scientific/Engineering",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: End Users/Desktop",
+]
+include = [
+    { path = "pyproject.toml" }
+]
 
 [tool.poetry.dependencies]
 python = "^3.12"
 uldaq = "^1.2.3"
 typer = "^0.12.5"
 matplotlib = "^3.9.2"
-numpy = "^2.1.1"
+numpy = "^1.9"
 pyqt6 = "^6.7.1"
-tomli = "^2.0.1"
+tomlkit = "^0.13.2"
+scipy = "^1.14.1"
+nixio = "^1.5.3"
+pyqtgraph = "^0.13.7"
 
+[tool.poetry.scripts]
+pyrelacs = "pyrelacs.app:main"
+
+[tool.poetry.group.dev.dependencies]
+ipython = "^8.27.0"
 
 [build-system]
-requires = ["poetry-core"]
+requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"

pyrelacs/app.py

@@ -1,144 +1,44 @@
-from PyQt6.QtGui import QAction
 import sys
 import pathlib
-import ctypes
 
-from PyQt6.QtCore import QProcess, QSize, QThreadPool, Qt
+from PyQt6.QtCore import QSettings
-from PyQt6.QtWidgets import (
+from PyQt6.QtWidgets import QApplication
-    QApplication,
-    QGridLayout,
-    QPushButton,
-    QToolBar,
-    QWidget,
-    QMainWindow,
-    QPlainTextEdit,
-)
-import tomli
-import uldaq
-from IPython import embed
-import numpy as np
-
-from pyrelacs.util.logging import config_logging
 
+from . import info
+from .ui.mainwindow import PyRelacs
+from .util.logging import config_logging
 log = config_logging()
 
 
-class PyRelacs(QMainWindow):
+def main():
-    def __init__(self):
+    app = QApplication(sys.argv)
-        super().__init__()
+    app.setApplicationName(info.NAME)
-        self.setWindowTitle("PyRelacs")
+    app.setApplicationVersion(str(info.VERSION))
-        self.setMinimumSize(1000, 1000)
+    app.setOrganizationDomain(info.ORGANIZATION)
 
-        self.threadpool = QThreadPool()
+    # read window settings
-        # for starting a Qprocess
+    settings = QSettings(info.ORGANIZATION, info.NAME)
-        self.p = None
+    width = int(settings.value("app/width", 1024))
+    height = int(settings.value("app/height", 768))
+    x = int(settings.value("app/pos_x", 100))
+    y = int(settings.value("app/pos_y", 100))
 
-        self.daq_connect_button = QPushButton("Connect Daq")
+    window = PyRelacs()
-        self.daq_connect_button.setCheckable(True)
+    window.setMinimumWidth(200)
-        self.daq_connect_button.clicked.connect(self.connect_dac)
+    window.setMinimumHeight(200)
+    window.resize(width, height)
+    window.move(x, y)
+    window.show()
+    exit_code = app.exec()
 
-        self.daq_disconnect_button = QPushButton("Disconnect Daq")
+    # store window position and size
-        self.daq_disconnect_button.setCheckable(True)
+    pos = window.pos()
-        self.daq_disconnect_button.clicked.connect(self.disconnect_dac)
+    settings.setValue("app/width", window.width())
-
+    settings.setValue("app/height", window.height())
-        self.text = QPlainTextEdit()
+    settings.setValue("app/pos_x", pos.x())
-        self.text.setReadOnly(True)
+    settings.setValue("app/pos_y", pos.y())
-
+    sys.exit(exit_code)
-        layout = QGridLayout()
-        layout.addWidget(self.daq_connect_button, 0, 0)
-        layout.addWidget(self.daq_disconnect_button, 0, 1)
-        layout.addWidget(self.text, 2, 0, 1, 2)
-
-        self.toolbar = QToolBar("Repros")
-        self.addToolBar(self.toolbar)
-        self.repro()
-
-        self.setFixedSize(QSize(400, 300))
-        widget = QWidget()
-        widget.setLayout(layout)
-        self.setCentralWidget(widget)
-
-    def connect_dac(self):
-        devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
-        try:
-            self.daq_device = uldaq.DaqDevice(devices[0])
-            log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
-            self.daq_device.connect()
-            log.debug("Connected")
-        except IndexError:
-            log.debug("DAQ is not connected, closing")
-            QApplication.quit()
-        self.daq_connect_button.setDisabled(True)
-
-    def disconnect_dac(self):
-        try:
-            log.debug(f"{self.daq_device}")
-            self.daq_device.disconnect()
-            self.daq_device.release()
-            log.debug(f"{self.daq_device}")
-            self.daq_disconnect_button.setDisabled(True)
-            self.daq_connect_button.setEnabled(True)
-        except AttributeError:
-            log.debug("DAQ was not connected")
-
-    def repro(self):
-        repos_path = pathlib.Path(__file__).parent / "repros"
-        repos_names = list(repos_path.glob("*.py"))
-        # exclude the repos.py file
-        repos_names = [
-            f.with_suffix("").name for f in repos_names if not f.name == "repos.py"
-        ]
-        for rep in repos_names:
-            individual_repro_button = QAction(rep, self)
-            individual_repro_button.setStatusTip("Button")
-            individual_repro_button.triggered.connect(
-                lambda checked, n=rep: self.run_repro(n)
-            )
-            self.toolbar.addAction(individual_repro_button)
-
-    def message(self, s):
-        self.text.appendPlainText(s)
-
-    def run_repro(self, name_of_repo):
-        if self.p is None:
-            self.message(f"Executing process {name_of_repo}")
-            self.p = QProcess()
-            self.p.setWorkingDirectory(str(pathlib.Path(__file__).parent / "repros/"))
-            # log.debug(pathlib.Path(__file__).parent / "repos")
-            self.p.readyReadStandardOutput.connect(self.handle_stdout)
-            self.p.readyReadStandardError.connect(self.handle_stderr)
-            self.p.stateChanged.connect(self.handle_state)
-            self.p.finished.connect(self.process_finished)
-            self.p.start("python3", [f"{name_of_repo}" + ".py"])
-
-    def handle_stderr(self):
-        if self.p is not None:
-            data = self.p.readAllStandardError()
-            stderr = bytes(data).decode("utf8")
-            self.message(stderr)
-
-    def handle_stdout(self):
-        if self.p is not None:
-            data = self.p.readAllStandardOutput()
-            stdout = bytes(data).decode("utf8")
-            self.message(stdout)
-
-    def handle_state(self, state):
-        states = {
-            QProcess.ProcessState.NotRunning: "Not running",
-            QProcess.ProcessState.Starting: "Starting",
-            QProcess.ProcessState.Running: "Running",
-        }
-        state_name = states[state]
-        self.message(f"State changed: {state_name}")
-
-    def process_finished(self):
-        self.text.appendPlainText("Process finished")
-        self.p = None
 
 
 if __name__ == "__main__":
-    app = QApplication(sys.argv)
+    main()
-    window = PyRelacs()
-    window.show()
-    app.exec()

pyrelacs/devices/mccdac.py

@@ -0,0 +1,291 @@
+from ctypes import Array, c_double
+import time
+from typing import Union
+from IPython import embed
+import numpy.typing as npt
+import uldaq
+import numpy as np
+
+from pyrelacs.util.logging import config_logging
+
+log = config_logging()
+
+
+class MccDac:
+    def __init__(self) -> None:
+        devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
+        log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
+        if len(devices) == 0:
+            log.error("Did not found daq devices, please connect one")
+            exit(1)
+        self.daq_device = uldaq.DaqDevice(devices[0])
+        try:
+            self.daq_device.connect()
+        except uldaq.ul_exception.ULException:
+            self.disconnect_dac()
+            self.connect_dac()
+        self.ai_device = self.daq_device.get_ai_device()
+        self.ao_device = self.daq_device.get_ao_device()
+        self.dio_device = self.daq_device.get_dio_device()
+        log.debug("Connected")
+
+    def connect_dac(self):
+        devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
+        log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
+        if len(devices) == 0:
+            log.error("Did not found daq devices, please connect one")
+            exit(1)
+        self.daq_device = uldaq.DaqDevice(devices[0])
+        self.daq_device.connect()
+        self.ai_device = self.daq_device.get_ai_device()
+        self.ao_device = self.daq_device.get_ao_device()
+        self.dio_device = self.daq_device.get_dio_device()
+        log.debug("Connected")
+
+    def read_analog(
+        self,
+        channels: list[int],
+        duration: int,
+        samplerate: float,
+        AiInputMode: uldaq.AiInputMode = uldaq.AiInputMode.SINGLE_ENDED,
+        Range: uldaq.Range = uldaq.Range.BIP10VOLTS,
+        ScanOption: uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO,
+        AInScanFlag: uldaq.AInScanFlag = uldaq.AInScanFlag.DEFAULT,
+    ) -> Array[c_double]:
+        assert len(channels) == 2, log.error("You can only provide two channels [0, 1]")
+
+        if channels[0] != channels[1]:
+            buffer_len_channels = 2
+        else:
+            buffer_len_channels = 1
+
+        buffer_len = np.shape(np.arange(0, duration, 1 / samplerate))[0]
+        data_analog_input = uldaq.create_float_buffer(buffer_len_channels, buffer_len)
+
+        er = self.ai_device.a_in_scan(
+            channels[0],
+            channels[1],
+            AiInputMode,
+            Range,
+            buffer_len,
+            samplerate,
+            ScanOption,
+            AInScanFlag,
+            data=data_analog_input,
+        )
+
+        return data_analog_input
+
+    def write_analog(
+        self,
+        data: Union[list, npt.NDArray],
+        channels: list[int],
+        samplerate: float,
+        Range: uldaq.Range = uldaq.Range.BIP10VOLTS,
+        ScanOption: uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO,
+        AOutScanFlag: uldaq.AOutScanFlag = uldaq.AOutScanFlag.DEFAULT,
+    ) -> Array[c_double]:
+        assert len(channels) == 2, log.error("You can only provide two channels [0, 1]")
+
+        buffer = c_double * len(data)
+        data_analog_output = buffer(*data)
+        log.debug(f"Created C_double data {data_analog_output}")
+
+        try:
+            err = self.ao_device.a_out_scan(
+                channels[0],
+                channels[1],
+                Range,
+                int(len(data)),
+                samplerate,
+                ScanOption,
+                AOutScanFlag,
+                data_analog_output,
+            )
+        except Exception as e:
+            print(f"{e}")
+            self.set_analog_to_zero()
+            self.disconnect_dac()
+
+        return data_analog_output
+
+    def set_analog_to_zero(self, channels: list[int] = [0, 1]):
+        try:
+            err = self.ao_device.a_out_list(
+                channels[0],
+                channels[1],
+                [
+                    uldaq.Range.BIP10VOLTS,
+                    uldaq.Range.BIP10VOLTS,
+                ],
+                uldaq.AOutListFlag.DEFAULT,
+                [0, 0],
+            )
+        except Exception as e:
+            log.error("f{e}")
+            log.error("disconnection dac")
+            self.disconnect_dac()
+
+    def diggital_trigger(self) -> None:
+        data = self.read_bit(channel=0)
+        if data:
+            self.write_bit(channel=0, bit=0)
+            time.time_ns()
+            self.write_bit(channel=0, bit=1)
+        else:
+            self.write_bit(channel=0, bit=1)
+
+    def write_bit(self, channel: int = 0, bit: int = 1) -> None:
+        self.dio_device.d_config_bit(
+            uldaq.DigitalPortType.AUXPORT, channel, uldaq.DigitalDirection.OUTPUT
+        )
+        self.dio_device.d_bit_out(
+            uldaq.DigitalPortType.AUXPORT, bit_number=channel, data=bit
+        )
+
+    def read_bit(self, channel: int = 0):
+        bit = self.dio_device.d_bit_in(uldaq.DigitalPortType.AUXPORT, channel)
+        return bit
+
+    def read_digitalio(
+        self,
+        channels: list[int],
+        duration,
+        samplerate,
+        ScanOptions: uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO,
+        DInScanFlag: uldaq.DInScanFlag = uldaq.DInScanFlag.DEFAULT,
+    ):
+        if channels[0] == channels[1]:
+            channel_len = 1
+        else:
+            channel_len = len(channels)
+
+        buffer_len = np.shape(np.arange(0, duration, 1 / samplerate))[0]
+        data_digital_input = uldaq.create_int_buffer(channel_len, buffer_len)
+
+        self.dio_device.d_config_port(
+            uldaq.DigitalPortType.AUXPORT, uldaq.DigitalDirection.INPUT
+        )
+        scan_rate = self.dio_device.d_in_scan(
+            uldaq.DigitalPortType.AUXPORT0,
+            uldaq.DigitalPortType.AUXPORT0,
+            len(data_digital_input),
+            samplerate,
+            ScanOptions,
+            DInScanFlag,
+            data_digital_input,
+        )
+        return data_digital_input
+
+    def disconnect_dac(self):
+        self.daq_device.disconnect()
+        self.daq_device.release()
+
+    def check_attenuator(self):
+        """
+        ident     : attdev-1
+        strobepin : 6
+        datainpin : 5
+        dataoutpin: -1
+        cspin     : 4
+        mutepin   : 7
+        zcenpin   : -1
+        """
+
+        SAMPLERATE = 40_000.0
+        DURATION = 5
+        AMPLITUDE = 1
+        SINFREQ = 1
+        t = np.arange(0, DURATION, 1 / SAMPLERATE)
+        data = AMPLITUDE * np.sin(2 * np.pi * SINFREQ * t)
+        # data_channels = np.concatenate((data, data))
+
+        db_values = [0, 0, -2, -5, -10, -20, -50]
+        db_values = [0, -10, -20]
+        for i, db_value in enumerate(db_values):
+            log.info(f"Attenuating the Channels, with {db_value}")
+            if i == 1:
+                log.info("Muting the Channels")
+                self.set_attenuation_level(
+                    db_value, db_value, mute_channel1=True, mute_channel2=True
+                )
+            else:
+                self.set_attenuation_level(db_value, db_value)
+
+            _ = self.write_analog(
+                data,
+                [0, 0],
+                SAMPLERATE,
+                ScanOption=uldaq.ScanOption.EXTTRIGGER,
+                Range=uldaq.Range.BIP10VOLTS,
+            )
+            self.diggital_trigger()
+
+            try:
+                self.ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 15)
+                self.write_bit(channel=0, bit=0)
+                self.set_analog_to_zero()
+            except uldaq.ul_exception.ULException:
+                log.debug("Operation timed out")
+                self.write_bit(channel=0, bit=0)
+                self.disconnect_dac()
+                self.connect_dac()
+                self.set_analog_to_zero()
+            finally:
+                self.write_bit(channel=0, bit=0)
+                self.disconnect_dac()
+                self.connect_dac()
+                self.set_analog_to_zero()
+
+            log.info("Sleeping for 1 second, before next attenuation")
+            time.sleep(1)
+
+    def set_attenuation_level(
+        self,
+        db_channel1: float = 5.0,
+        db_channel2: float = 5.0,
+        mute_channel1: bool = False,
+        mute_channel2: bool = False,
+    ):
+        """
+        ident     : attdev-1
+        strobepin : 6
+        datainpin : 5
+        dataoutpin: -1
+        cspin     : 4
+        mutepin   : 7
+        zcenpin   : -1
+        """
+
+        self.activate_attenuator()
+        hardware_possible_db = np.arange(-95.5, 32.0, 0.5)
+        byte_number = np.arange(1, 256)
+        byte_number_db1 = byte_number[hardware_possible_db == db_channel1][0]
+        binary_db1 = np.binary_repr(byte_number_db1, width=8)
+        byte_number_db2 = byte_number[hardware_possible_db == db_channel2][0]
+        binary_db2 = np.binary_repr(byte_number_db2, width=8)
+        if mute_channel1:
+            log.info("Muting channel one")
+            binary_db1 = "00000000"
+        if mute_channel2:
+            log.info("Muting channel one")
+            binary_db2 = "00000000"
+
+        channels_db = binary_db2 + binary_db1
+        self.write_bit(channel=4, bit=0)
+        for b in channels_db:
+            self.write_bit(channel=5, bit=int(b))
+            time.time_ns()
+            self.write_bit(channel=6, bit=1)
+            time.time_ns()
+            self.write_bit(channel=6, bit=0)
+            time.time_ns()
+        self.write_bit(channel=4, bit=1)
+
+    def activate_attenuator(self):
+        for ch, b in zip([4, 5, 6, 7], [1, 0, 0, 1]):
+            self.write_bit(channel=ch, bit=b)
+
+    def deactivate_attenuator(self):
+        # mute should be enabled for starting calibration
+        self.write_bit(channel=7, bit=0)

pyrelacs/info.py

@@ -0,0 +1,38 @@
+import tomlkit
+import pathlib
+
+
+def load_project_settings(project_root):
+    # Read the pyproject.toml file
+    with open(pathlib.Path.joinpath(project_root, "pyproject.toml"), "r") as f:
+        pyproject_content = f.read()
+
+    # Parse the toml content
+    pyproject = tomlkit.parse(pyproject_content)
+
+    # Access project settings
+    return {
+        "name": pyproject["tool"]["poetry"]["name"],
+        "version": pyproject["tool"]["poetry"]["version"],
+        "description": pyproject["tool"]["poetry"]["description"],
+        "authors": pyproject["tool"]["poetry"]["authors"],
+        "readme": pyproject["tool"]["poetry"]["authors"],
+        "licence": pyproject["tool"]["poetry"]["license"],
+        "organization": pyproject["project"]["organization"],
+        "classifiers": pyproject["tool"]["poetry"]["classifiers"],
+        "copyright": pyproject["project"]["copyright"],
+        "repository": pyproject["tool"]["poetry"]["repository"],
+    }
+
+
+_root = pathlib.Path(__file__).parent.parent
+_infodict = load_project_settings(_root)
+
+NAME = _infodict["name"]
+VERSION = _infodict["version"]
+AUTHORS = _infodict["authors"]
+COPYRIGHT = _infodict["copyright"]
+HOMEPAGE = _infodict["repository"]
+CLASSIFIERS = _infodict["classifiers"]
+DESCRIPTION = _infodict["description"]
+ORGANIZATION = _infodict["organization"]

pyrelacs/repros/calbi.py

@@ -1,42 +1,272 @@
-import ctypes
+import signal
+import sys
+import faulthandler
+import time
 
+import nixio as nix
 import uldaq
 from IPython import embed
-from pyrelacs.repros.repos import Repos
-from pyrelacs.util.logging import config_logging
 import numpy as np
 import matplotlib.pyplot as plt
+from scipy.signal import welch, csd
+from scipy.signal import find_peaks
+
+from pyrelacs.devices.mccdac import MccDac
+from pyrelacs.util.logging import config_logging
 
 log = config_logging()
+faulthandler.enable()
 
 
-class Calibration(Repos):
+class Calibration(MccDac):
     def __init__(self) -> None:
         super().__init__()
+        self.SAMPLERATE = 40_000.0
+        self.DURATION = 5
+        self.AMPLITUDE = 1
+        self.SINFREQ = 750
+
+    @staticmethod
+    def run(nix_file: nix.File):
+        calb = Calibration()
+        calb.check_beat(nix_file)
+
+    def check_amplitude(self):
+        db_values = [0.0, -5.0, -10.0, -20.0, -50.0]
+        colors = ["red", "green", "blue", "black", "yellow"]
+        self.set_attenuation_level(db_channel1=0.0, db_channel2=0.0)
+        # write to ananlog 1
+        t = np.arange(0, self.DURATION, 1 / self.SAMPLERATE)
+        data = self.AMPLITUDE * np.sin(2 * np.pi * self.SINFREQ * t)
+        fig, ax = plt.subplots()
+
+        for i, db_value in enumerate(db_values):
+            self.set_attenuation_level(db_channel1=db_value, db_channel2=db_value)
+            log.debug(f"{db_value}")
+
+            stim = self.write_analog(
+                data,
+                [0, 0],
+                self.SAMPLERATE,
+                ScanOption=uldaq.ScanOption.EXTTRIGGER,
+            )
+
+            data_channel_one = self.read_analog(
+                [0, 0],
+                self.DURATION,
+                self.SAMPLERATE,
+                ScanOption=uldaq.ScanOption.EXTTRIGGER,
+            )
+            time.sleep(1)
+
+            log.debug("Starting the Scan")
+            self.diggital_trigger()
+
+            try:
+                self.ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 15)
+                log.debug("Scan finished")
+                self.write_bit(channel=0, bit=0)
+                time.sleep(1)
+                self.set_analog_to_zero()
+            except uldaq.ul_exception.ULException:
+                log.debug("Operation timed out")
+                # reset the diggital trigger
+                self.write_bit(channel=0, bit=0)
+                time.sleep(1)
+                self.set_analog_to_zero()
+                self.disconnect_dac()
+
+            if i == 0:
+                ax.plot(t, stim, label=f"Input_{db_value}", color=colors[i])
+            ax.plot(t, data_channel_one, label=f"Reaout {db_value}", color=colors[i])
+
+        ax.legend()
+        plt.show()
 
-    def run_calibration(self):
-        # Stimulus
-        time = np.arange(0, DURATION, 1 / SAMPLERATE)
-        data = AMPLITUDE * np.sin(2 * np.pi * SINFREQ * time)
-        # sending stimulus
-        stim, ao_device = self.send_analog_dac(
-            data, [0, 0], SAMPLERATE, ScanOption=uldaq.ScanOption.EXTTRIGGER
-        )
-        read_data = self.read_analog_daq(
-            [0, 1], DURATION, SAMPLERATE, ScanOption=uldaq.ScanOption.EXTTRIGGER
-        )
-        self.digital_trigger()
-        ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 11)
-        self.digital_trigger(data=0)
         self.disconnect_dac()
-        embed()
+
-        exit()
+    def check_beat(self, nix_file: nix.File):
+        self.set_attenuation_level(db_channel1=-10.0, db_channel2=0.0)
+        t = np.arange(0, self.DURATION, 1 / self.SAMPLERATE)
+        data = self.AMPLITUDE * np.sin(2 * np.pi * self.SINFREQ * t)
+        # data = np.concatenate((data, data))
+        db_values = [0.0, -5.0, -8.5, -10.0]
+        colors = ["red", "blue", "black", "green"]
+        colors_in = ["lightcoral", "lightblue", "grey", "lightgreen"]
+        block = nix_file.create_block("Calibration", "data")
+        # fig, axes = plt.subplots(2, 2, sharex="col")
+        for i, db_value in enumerate(db_values):
+            self.set_attenuation_level(db_channel1=db_value)
+            stim = self.write_analog(
+                data,
+                [0, 0],
+                self.SAMPLERATE,
+                ScanOption=uldaq.ScanOption.EXTTRIGGER,
+            )
+            readout = self.read_analog(
+                [0, 1],
+                self.DURATION,
+                self.SAMPLERATE,
+                ScanOption=uldaq.ScanOption.EXTTRIGGER,
+            )
+            self.diggital_trigger()
+            log.info(self.ao_device)
+            ai_status = uldaq.ScanStatus.RUNNING
+            ao_status = uldaq.ScanStatus.RUNNING
+
+            log.debug(
+                f"Status Analog_output {ao_status}\n, Status Analog_input {ai_status}"
+            )
+            while (ai_status != uldaq.ScanStatus.IDLE) and (
+                ao_status != uldaq.ScanStatus.IDLE
+            ):
+                # log.debug("Scanning")
+                time.time_ns()
+                ai_status = self.ai_device.get_scan_status()[0]
+                ao_status = self.ao_device.get_scan_status()[0]
+
+            self.write_bit(channel=0, bit=0)
+            log.debug(
+                f"Status Analog_output {ao_status}\n, Status Analog_input {ai_status}"
+            )
+
+            channel1 = np.array(readout[::2])
+            channel2 = np.array(readout[1::2])
+
+            block.create_data_array(
+                f"stimulus_{db_value}",
+                "Array",
+                shape=data.shape,
+                data=channel1,
+                label="Voltage",
+                unit="V",
+            )
+            block.create_data_array(
+                f"fish_{db_value}",
+                "Array",
+                shape=data.shape,
+                data=channel2,
+                label="Voltage",
+                unit="V",
+            )
+
+            beat = channel1 + channel2
+            beat_square = beat**2
+
+            f, powerspec = welch(beat, fs=self.SAMPLERATE)
+            powerspec = decibel(powerspec)
+
+            f_sq, powerspec_sq = welch(beat_square, fs=self.SAMPLERATE)
+            powerspec_sq = decibel(powerspec_sq)
+            peaks = find_peaks(powerspec_sq, prominence=20)[0]
+
+            f_stim, powerspec_stim = welch(channel1, fs=self.SAMPLERATE)
+            powerspec_stim = decibel(powerspec_stim)
+
+            f_in, powerspec_in = welch(channel2, fs=self.SAMPLERATE)
+            powerspec_in = decibel(powerspec_in)
+
+        #     axes[0, 0].plot(
+        #         t,
+        #         channel1,
+        #         label=f"{db_value} Readout Channel0",
+        #         color=colors[i],
+        #     )
+        #     axes[0, 0].plot(
+        #         t,
+        #         channel2,
+        #         label=f"{db_value} Readout Channel1",
+        #         color=colors_in[i],
+        #     )
+        #
+        #     axes[0, 1].plot(
+        #         f_stim,
+        #         powerspec_stim,
+        #         label=f"{db_value} powerspec Channel0",
+        #         color=colors[i],
+        #     )
+        #     axes[0, 1].plot(
+        #         f_in,
+        #         powerspec_in,
+        #         label=f"{db_value} powerspec Channel2",
+        #         color=colors_in[i],
+        #     )
+        #     axes[0, 1].set_xlabel("Freq [HZ]")
+        #     axes[0, 1].set_ylabel("dB")
+        #
+        #     axes[1, 0].plot(
+        #         t,
+        #         beat,
+        #         label="Beat",
+        #         color=colors[i],
+        #     )
+        #     axes[1, 0].plot(
+        #         t,
+        #         beat**2,
+        #         label="Beat squared",
+        #         color=colors_in[i],
+        #     )
+        #     axes[1, 0].legend()
+        #
+        #     axes[1, 1].plot(
+        #         f,
+        #         powerspec,
+        #         color=colors[i],
+        #     )
+        #     axes[1, 1].plot(
+        #         f_sq,
+        #         powerspec_sq,
+        #         color=colors_in[i],
+        #         label=f"dB {db_value}, first peak {np.min(f_sq[peaks])}",
+        #     )
+        #     axes[1, 1].scatter(
+        #         f_sq[peaks],
+        #         powerspec_sq[peaks],
+        #         color="maroon",
+        #     )
+        #     axes[1, 1].set_xlabel("Freq [HZ]")
+        #     axes[1, 1].set_ylabel("dB")
+        #     axes[0, 0].legend()
+        #     axes[1, 1].legend()
+        # plt.show()
+        self.set_analog_to_zero()
+        self.disconnect_dac()
 
 
-if __name__ == "__main__":
+def decibel(power, ref_power=1.0, min_power=1e-20):
-    SAMPLERATE = 40_000.0
+    """Transform power to decibel relative to ref_power.
-    DURATION = 5
+
-    AMPLITUDE = 3
+    \\[ decibel = 10 \\cdot \\log_{10}(power/ref\\_power) \\]
-    SINFREQ = 1
+    Power values smaller than `min_power` are set to `-np.inf`.
-    daq_input = Calibration()
+
-    daq_input.run_calibration()
+    Parameters
+    ----------
+    power: float or array
+        Power values, for example from a power spectrum or spectrogram.
+    ref_power: float or None or 'peak'
+        Reference power for computing decibel.
+        If set to `None` or 'peak', the maximum power is used.
+    min_power: float
+        Power values smaller than `min_power` are set to `-np.inf`.
+
+    Returns
+    -------
+    decibel_psd: array
+        Power values in decibel relative to `ref_power`.
+    """
+    if np.isscalar(power):
+        tmp_power = np.array([power])
+        decibel_psd = np.array([power])
+    else:
+        tmp_power = power
+        decibel_psd = power.copy()
+    if ref_power is None or ref_power == "peak":
+        ref_power = np.max(decibel_psd)
+    decibel_psd[tmp_power <= min_power] = float("-inf")
+    decibel_psd[tmp_power > min_power] = 10.0 * np.log10(
+        decibel_psd[tmp_power > min_power] / ref_power
+    )
+    if np.isscalar(power):
+        return decibel_psd[0]
+    else:
+        return decibel_psd

pyrelacs/repros/inandout.py

@@ -1,86 +0,0 @@
-import ctypes
-
-import uldaq
-from IPython import embed
-import matplotlib.pyplot as plt
-import numpy as np
-
-
-from pyrelacs.util.logging import config_logging
-
-log = config_logging()
-
-
-class ReadWrite:
-    def __init__(self) -> None:
-        devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
-        log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
-        self.daq_device = uldaq.DaqDevice(devices[0])
-        self.daq_device.connect()
-        log.debug("Connected")
-        # self.daq_device.enable_event(
-        #     uldaq.DaqEventType.ON_DATA_AVAILABLE,
-        #     1,
-        #     self.read_write,
-        #     (uldaq.DaqEventType.ON_DATA_AVAILABLE, 1, 1),
-        # )
-
-    def read_write(self) -> None:
-        # event_type = callback_args.event_type
-        # event_data = callback_args.event_data
-        # user_data = callback_args.user_data
-
-        FS = 30_000.0
-        DURATION = 10
-        FREQUENCY = 100
-
-        time = np.arange(0, DURATION, 1 / FS)
-        data = 2 * np.sin(2 * np.pi * FREQUENCY * time)
-
-        buffer = ctypes.c_double * len(time)
-        data_c = buffer(*data)
-        buf = uldaq.create_float_buffer(1, len(time))
-
-        # Get the Ananlog In device and Analog Info
-        ai_device = self.daq_device.get_ai_device()
-        ai_info = ai_device.get_info()
-
-        # Get the Analog Out device
-        ao_device = self.daq_device.get_ao_device()
-        ao_info = ao_device.get_info()
-
-        er_ao = ao_device.a_out_scan(
-            0,
-            0,
-            uldaq.Range.BIP10VOLTS,
-            int(len(data)),
-            30_000.0,
-            uldaq.ScanOption.DEFAULTIO,
-            uldaq.AOutScanFlag.DEFAULT,
-            data_c,
-        )
-
-        er_ai = ai_device.a_in_scan(
-            1,
-            1,
-            uldaq.AiInputMode.SINGLE_ENDED,
-            uldaq.Range.BIP10VOLTS,
-            len(time),
-            FS,
-            uldaq.ScanOption.DEFAULTIO,
-            uldaq.AInScanFlag.DEFAULT,
-            data=buf,
-        )
-        ai_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, timeout=-1)
-        log.debug("Scanning")
-
-        self.daq_device.disconnect()
-        self.daq_device.release()
-        plt.plot(buf)
-        plt.plot(data_c)
-        plt.show()
-
-
-if __name__ == "__main__":
-    daq_input = ReadWrite()
-    daq_input.read_write()

pyrelacs/repros/input.py

@@ -1,28 +0,0 @@
-import uldaq
-import matplotlib.pyplot as plt
-
-from pyrelacs.util.logging import config_logging
-from .repos import Repos
-
-log = config_logging()
-
-
-class ReadData(Repos):
-    def __init__(self) -> None:
-        super().__init__()
-
-    def analog_in(self) -> None:
-        # Get the Ananlog In device and Analog Info
-        data = self.read_analog_daq(
-            [0, 0],
-            10,
-            3000.0,
-        )
-        plt.plot(data)
-        plt.show()
-        self.disconnect_dac()
-
-
-if __name__ == "__main__":
-    daq_input = ReadData()
-    daq_input.analog_in()

pyrelacs/repros/output.py

@@ -1,37 +0,0 @@
-import ctypes
-
-import uldaq
-from IPython import embed
-from pyrelacs.repros.repos import Repos
-from pyrelacs.util.logging import config_logging
-import numpy as np
-import matplotlib.pyplot as plt
-
-log = config_logging()
-
-
-class Output_daq(Repos):
-    def __init__(self) -> None:
-        super().__init__()
-        # devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
-        # self.daq_device = uldaq.DaqDevice(devices[0])
-        # self.daq_device.connect()
-
-    def write_daq(self):
-        log.debug("running repro")
-        time = np.arange(0, 10, 1 / 30_000.0)
-        data = 2 * np.sin(2 * np.pi * 1 * time)
-        self.send_analog_dac(
-            data, [0, 0], 30_000, ScanOption=uldaq.ScanOption.EXTTRIGGER
-        )
-
-    def trigger(self):
-        self.digital_trigger(1)
-        self.daq_device.disconnect()
-        self.daq_device.release()
-
-
-if __name__ == "__main__":
-    daq_input = Output_daq()
-    daq_input.write_daq()
-    # daq_input.trigger()

pyrelacs/repros/repos.py

@@ -1,142 +0,0 @@
-from ctypes import Array, c_double
-from typing import Union
-from IPython import embed
-import numpy.typing as npt
-import uldaq
-import numpy as np
-
-from pyrelacs.util.logging import config_logging
-
-log = config_logging()
-
-
-class Repos:
-    def __init__(self) -> None:
-        devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
-        log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
-        if len(devices) == 0:
-            log.error("Did not found daq devices, please connect one")
-            exit(1)
-        self.daq_device = uldaq.DaqDevice(devices[0])
-        self.daq_device.connect()
-        log.debug("Connected")
-
-    def read_analog_daq(
-        self,
-        channels: list[int],
-        duration: int,
-        samplerate: float,
-        AiInputMode: uldaq.AiInputMode = uldaq.AiInputMode.SINGLE_ENDED,
-        Range: uldaq.Range = uldaq.Range.BIP10VOLTS,
-        ScanOption: uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO,
-        AInScanFlag: uldaq.AInScanFlag = uldaq.AInScanFlag.DEFAULT,
-    ) -> Array[c_double]:
-        if channels[0] == channels[1]:
-            channel_len = 1
-        else:
-            channel_len = len(channels)
-        assert len(channels) == 2, log.error("Please provide a list with two ints")
-
-        ai_device = self.daq_device.get_ai_device()
-        buffer_len = np.shape(np.arange(0, duration, 1 / samplerate))[0]
-        data_analog_input = uldaq.create_float_buffer(channel_len, buffer_len)
-
-        er = ai_device.a_in_scan(
-            channels[0],
-            channels[1],
-            AiInputMode,
-            Range,
-            buffer_len,
-            samplerate,
-            ScanOption,
-            AInScanFlag,
-            data=data_analog_input,
-        )
-        # ai_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, timeout=-1)
-
-        return data_analog_input
-
-    def send_analog_dac(
-        self,
-        data: Union[list, npt.NDArray],
-        channels: list[int],
-        samplerate: float,
-        Range: uldaq.Range = uldaq.Range.BIP10VOLTS,
-        ScanOption: uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO,
-        AOutScanFlag: uldaq.AOutScanFlag = uldaq.AOutScanFlag.DEFAULT,
-    ):
-        """
-
-        Parameters
-        ----------
-        data : Union[list, npt.NDArray]
-
-        channels : list[int]
-
-        duration : int
-
-        samplerate : float
-
-        AiInputMode : uldaq.AiInputMode
-
-        Range : uldaq.Range
-
-        ScanOption : uldaq.ScanOption
-
-        AInScanFlag : uldaq.AOutScanFlag
-
-
-        Returns
-        -------
-        Array[c_double]
-        ao_device
-
-
-        """
-        buffer = c_double * len(data)
-        data_analog_output = buffer(*data)
-
-        log.debug(f"Created C_double data {data_analog_output}")
-        ao_device = self.daq_device.get_ao_device()
-        ao_info = ao_device.get_info()
-
-        err = ao_device.a_out_scan(
-            channels[0],
-            channels[1],
-            Range,
-            int(len(data)),
-            samplerate,
-            ScanOption,
-            AOutScanFlag,
-            data_analog_output,
-        )
-        log.info(f"The actual scan rate was {err}")
-        # ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 11)
-
-        return data_analog_output, ao_device
-
-    def digital_trigger(self, portn: int = 0, data: int = 1) -> None:
-        log.info(f"{self.daq_device}")
-        dio_device = self.daq_device.get_dio_device()
-
-        dio_device.d_config_bit(
-            uldaq.DigitalPortType.AUXPORT, portn, uldaq.DigitalDirection.OUTPUT
-        )
-
-        dio_device.d_bit_out(uldaq.DigitalPortType.AUXPORT, bit_number=portn, data=data)
-
-    def disconnect_dac(self):
-        self.daq_device.disconnect()
-        self.daq_device.release()
-
-    def clean_up():
-        pass
-
-    def run_repo(self) -> None:
-        pass
-
-    def stop_repo(self) -> None:
-        pass
-
-    def reload_repo(self) -> None:
-        pass

pyrelacs/repros/repros.py

@@ -0,0 +1,55 @@
+import sys
+import importlib.util
+import ast
+import pathlib
+
+from IPython import embed
+import nixio as nix
+from pyrelacs.util.logging import config_logging
+
+log = config_logging()
+
+
+class Repro:
+    def __init__(self) -> None:
+        pass
+
+    def run_repro(
+        self, nix_file: nix.File, name: str, file: pathlib.Path, *args, **kwargs
+    ) -> None:
+        spec = importlib.util.spec_from_file_location("rep", file)
+        if not spec:
+            log.error("Could not load the file")
+        else:
+            module = importlib.util.module_from_spec(spec)
+            if not module:
+                log.error("Could not load the module of the repro")
+            else:
+                sys.modules[name] = module
+                spec.loader.exec_module(module)
+                if hasattr(module, name):
+                    rep_class = getattr(module, name)
+                    rep_class.run(nix_file)
+                else:
+                    raise AttributeError(f"{file.name} has no {name} class")
+
+    def names_of_repros(self):
+        file_path_cur = pathlib.Path(__file__).parent
+        python_files = list(file_path_cur.glob("**/*.py"))
+        exclude_files = ["repros.py", "__init__.py"]
+        python_files = [f for f in python_files if f.name not in exclude_files]
+        repro_names = []
+        file_names = []
+        for python_file in python_files:
+            with open(python_file, "r") as file:
+                file_content = file.read()
+                tree = ast.parse(file_content)
+                class_name = [
+                    node.name
+                    for node in ast.walk(tree)
+                    if isinstance(node, ast.ClassDef)
+                ]
+                repro_names.extend(class_name)
+                file_names.append(python_file)
+            file.close()
+        return repro_names, file_names

pyrelacs/ui/mainwindow.py

@@ -0,0 +1,178 @@
+from PyQt6.QtGui import QAction
+from PyQt6.QtCore import QSize, QThreadPool
+from PyQt6.QtWidgets import (
+    QApplication,
+    QGridLayout,
+    QPushButton,
+    QToolBar,
+    QWidget,
+    QMainWindow,
+    QPlainTextEdit,
+)
+import uldaq
+import pathlib
+import numpy as np
+import nixio as nix
+import pyqtgraph as pg
+
+from scipy.signal import welch, find_peaks
+
+from ..worker import Worker
+from ..repros.repros import Repro
+from ..util.logging import config_logging
+log = config_logging()
+
+from IPython import embed
+
+class PyRelacs(QMainWindow):
+    def __init__(self):
+        super().__init__()
+        self.setWindowTitle("PyRelacs")
+        self.setMinimumSize(1000, 1000)
+        self.plot_graph = pg.PlotWidget()
+
+        self.threadpool = QThreadPool()
+        self.repros = Repro()
+
+        self.daq_connect_button = QPushButton("Connect Daq")
+        self.daq_connect_button.setCheckable(True)
+        self.daq_connect_button.clicked.connect(self.connect_dac)
+
+        self.daq_disconnect_button = QPushButton("Disconnect Daq")
+        self.daq_disconnect_button.setCheckable(True)
+        self.daq_disconnect_button.clicked.connect(self.disconnect_dac)
+
+        self.plot_calibration_button = QPushButton("Plot Calibration")
+        self.plot_calibration_button.setCheckable(True)
+        self.plot_calibration_button.clicked.connect(self.plot_calibration)
+
+        self.text = QPlainTextEdit()
+        self.text.setReadOnly(True)
+
+        layout = QGridLayout()
+        layout.addWidget(self.plot_calibration_button, 0, 0)
+        layout.addWidget(self.daq_disconnect_button, 0, 1)
+        layout.addWidget(self.text, 3, 0, 1, 2)
+        layout.addWidget(self.plot_graph, 2, 0, 1, 2)
+
+        self.toolbar = QToolBar("Repros")
+        self.addToolBar(self.toolbar)
+        self.repros_to_toolbar()
+
+        # self.setFixedSize(QSize(400, 300))
+        widget = QWidget()
+        widget.setLayout(layout)
+        self.setCentralWidget(widget)
+
+        filename = pathlib.Path.joinpath(pathlib.Path.cwd(), "data.nix")
+        self.nix_file = nix.File.open(
+            str(filename), nix.FileMode.Overwrite
+        )
+
+    def plot_calibration(self):
+        def decibel(power, ref_power=1.0, min_power=1e-20):
+            """Transform power to decibel relative to ref_power.
+
+            \\[ decibel = 10 \\cdot \\log_{10}(power/ref\\_power) \\]
+            Power values smaller than `min_power` are set to `-np.inf`.
+
+            Parameters
+            ----------
+            power: float or array
+                Power values, for example from a power spectrum or spectrogram.
+            ref_power: float or None or 'peak'
+                Reference power for computing decibel.
+                If set to `None` or 'peak', the maximum power is used.
+            min_power: float
+                Power values smaller than `min_power` are set to `-np.inf`.
+
+            Returns
+            -------
+            decibel_psd: array
+                Power values in decibel relative to `ref_power`.
+            """
+            if np.isscalar(power):
+                tmp_power = np.array([power])
+                decibel_psd = np.array([power])
+            else:
+                tmp_power = power
+                decibel_psd = power.copy()
+            if ref_power is None or ref_power == "peak":
+                ref_power = np.max(decibel_psd)
+            decibel_psd[tmp_power <= min_power] = float("-inf")
+            decibel_psd[tmp_power > min_power] = 10.0 * np.log10(
+                decibel_psd[tmp_power > min_power] / ref_power
+            )
+            if np.isscalar(power):
+                return decibel_psd[0]
+            else:
+                return decibel_psd
+
+        block = self.nix_file.blocks[0]
+        for stim, fish in zip(
+            list(block.data_arrays)[::2], list(block.data_arrays)[1::2]
+        ):
+            beat = stim[:] + fish[:]
+            beat_squared = beat**2
+
+            f, powerspec = welch(beat, fs=40_000.0)
+            powerspec = decibel(powerspec)
+
+            f_sq, powerspec_sq = welch(beat_squared, fs=40_000.0)
+            powerspec_sq = decibel(powerspec_sq)
+            peaks = find_peaks(powerspec_sq, prominence=20)[0]
+            pen = pg.mkPen()
+            self.plot_graph.plot(
+                np.arange(0, len(beat)) / 40_000.0, beat_squared, pen=pen
+            )
+
+    def connect_dac(self):
+        devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
+        try:
+            self.daq_device = uldaq.DaqDevice(devices[0])
+            log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
+            self.daq_device.connect()
+            log.debug("Connected")
+        except IndexError:
+            log.debug("DAQ is not connected, closing")
+            QApplication.quit()
+        self.daq_connect_button.setDisabled(True)
+
+    def disconnect_dac(self):
+        try:
+            log.debug(f"{self.daq_device}")
+            self.daq_device.disconnect()
+            self.daq_device.release()
+            log.debug(f"{self.daq_device}")
+            self.daq_disconnect_button.setDisabled(True)
+            self.daq_connect_button.setEnabled(True)
+        except AttributeError:
+            log.debug("DAQ was not connected")
+
+    def repros_to_toolbar(self):
+        repro_names, file_names = self.repros.names_of_repros()
+        for rep, fn in zip(repro_names, file_names):
+            individual_repro_button = QAction(rep, self)
+            individual_repro_button.setStatusTip("Button")
+            individual_repro_button.triggered.connect(
+                lambda checked, n=rep, f=fn: self.run_repro(n, f)
+            )
+            self.toolbar.addAction(individual_repro_button)
+
+    def run_repro(self, n, fn):
+        self.text.appendPlainText(f"started Repro {n}, {fn}")
+        worker = Worker(self.repros.run_repro, self.nix_file, n, fn)
+        worker.signals.result.connect(self.print_output)
+        worker.signals.finished.connect(self.thread_complete)
+        worker.signals.progress.connect(self.progress_fn)
+
+        self.threadpool.start(worker)
+
+    def print_output(self, s):
+        print(s)
+
+    def thread_complete(self):
+        print("THREAD COMPLETE!")
+
+    def progress_fn(self, n):
+        print("%d%% done" % n)

pyrelacs/worker.py

@@ -0,0 +1,75 @@
+import sys
+import traceback
+
+from PyQt6.QtCore import QRunnable, pyqtSlot, QObject, pyqtSignal
+
+
+class WorkerSignals(QObject):
+    """
+    Defines the signals available from a running worker thread.
+
+    Supported signals are:
+
+    finished
+        No data
+
+    error
+        tuple (exctype, value, traceback.format_exc() )
+
+    result
+        object data returned from processing, anything
+
+    progress
+        int indicating % progress
+
+    """
+
+    finished = pyqtSignal()
+    error = pyqtSignal(tuple)
+    result = pyqtSignal(object)
+    progress = pyqtSignal(int)
+
+
+class Worker(QRunnable):
+    """
+    Worker thread
+
+    Inherits from QRunnable to handler worker thread setup, signals and wrap-up.
+
+    :param callback: The function callback to run on this worker thread. Supplied args and
+                     kwargs will be passed through to the runner.
+    :type callback: function
+    :param args: Arguments to pass to the callback function
+    :param kwargs: Keywords to pass to the callback function
+
+    """
+
+    def __init__(self, fn, *args, **kwargs):
+        super(Worker, self).__init__()
+
+        # Store constructor arguments (re-used for processing)
+        self.fn = fn
+        self.args = args
+        self.kwargs = kwargs
+        self.signals = WorkerSignals()
+
+        # Add the callback to our kwargs
+        self.kwargs["progress_callback"] = self.signals.progress
+
+    @pyqtSlot()
+    def run(self):
+        """
+        Initialise the runner function with passed args, kwargs.
+        """
+
+        # Retrieve args/kwargs here; and fire processing using them
+        try:
+            result = self.fn(*self.args, **self.kwargs)
+        except:
+            traceback.print_exc()
+            exctype, value = sys.exc_info()[:2]
+            self.signals.error.emit((exctype, value, traceback.format_exc()))
+        else:
+            self.signals.result.emit(result)  # Return the result of the processing
+        finally:
+            self.signals.finished.emit()  # Done