[plotting] move calibrtion plot outside of main window

.gitignore

@@ -161,3 +161,8 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
+# ignore created data files
+*.nix
+
+# ignore reource.py as it is created by pyside6-rcc resources.qrc -o resources.py
+resources.py

README.md

@@ -5,9 +5,13 @@ Relaxed ELectrophysiology Acquisition, Control, and Stimulation in python
 Implementing [relacs](https://github.com/relacs/relacs) with MCC USB 1608GX-2AO / 1808X devices ([multifunction-usb-daq-devices](https://digilent.com/shop/mcc-daq/data-acquisition/low-cost-daq/))
 
 # Installation 
-You have to install the MCC library (follow the installing instructions for [linux](https://github.com/mccdaq/uldaq) or [windows](https://github.com/mccdaq/mcculw)). 
+You have to install the MCC library (follow the installing instructions for [linux/macOS](https://github.com/mccdaq/uldaq) or [windows](https://github.com/mccdaq/mcculw)).
 
-After successful installing, you can use clone the reposity and install it with 
+For MacOs if you run into problems with the libusb library if installed with homebrew, there is an issue thread on the uldaq repository.
+
+[https://github.com/mccdaq/uldaq/issues/44](https://github.com/mccdaq/uldaq/issues/44)
+
+After successful installing, you can use clone the repository and install it with
 
 ```sh
 pip install -e .

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"
@@ -227,6 +270,61 @@ files = [
 [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"},
+    {file = "ipython-8.27.0.tar.gz", hash = "sha256:0b99a2dc9f15fd68692e898e5568725c6d49c527d36a9fb5960ffbdeaa82ff7e"},
+]
+
+[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"
@@ -437,6 +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"
@@ -520,6 +632,35 @@ files = [
     {file = "packaging-24.1.tar.gz", hash = "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002"},
 ]
 
+[[package]]
+name = "parso"
+version = "0.8.4"
+description = "A Python Parser"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "parso-0.8.4-py2.py3-none-any.whl", hash = "sha256:a418670a20291dacd2dddc80c377c5c3791378ee1e8d12bffc35420643d43f18"},
+    {file = "parso-0.8.4.tar.gz", hash = "sha256:eb3a7b58240fb99099a345571deecc0f9540ea5f4dd2fe14c2a99d6b281ab92d"},
+]
+
+[package.extras]
+qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
+testing = ["docopt", "pytest"]
+
+[[package]]
+name = "pexpect"
+version = "4.9.0"
+description = "Pexpect allows easy control of interactive console applications."
+optional = false
+python-versions = "*"
+files = [
+    {file = "pexpect-4.9.0-py2.py3-none-any.whl", hash = "sha256:7236d1e080e4936be2dc3e326cec0af72acf9212a7e1d060210e70a47e253523"},
+    {file = "pexpect-4.9.0.tar.gz", hash = "sha256:ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f"},
+]
+
+[package.dependencies]
+ptyprocess = ">=0.5"
+
 [[package]]
 name = "pillow"
 version = "10.4.0"
@@ -617,6 +758,45 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa
 typing = ["typing-extensions"]
 xmp = ["defusedxml"]
 
+[[package]]
+name = "prompt-toolkit"
+version = "3.0.48"
+description = "Library for building powerful interactive command lines in Python"
+optional = false
+python-versions = ">=3.7.0"
+files = [
+    {file = "prompt_toolkit-3.0.48-py3-none-any.whl", hash = "sha256:f49a827f90062e411f1ce1f854f2aedb3c23353244f8108b89283587397ac10e"},
+    {file = "prompt_toolkit-3.0.48.tar.gz", hash = "sha256:d6623ab0477a80df74e646bdbc93621143f5caf104206aa29294d53de1a03d90"},
+]
+
+[package.dependencies]
+wcwidth = "*"
+
+[[package]]
+name = "ptyprocess"
+version = "0.7.0"
+description = "Run a subprocess in a pseudo terminal"
+optional = false
+python-versions = "*"
+files = [
+    {file = "ptyprocess-0.7.0-py2.py3-none-any.whl", hash = "sha256:4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35"},
+    {file = "ptyprocess-0.7.0.tar.gz", hash = "sha256:5c5d0a3b48ceee0b48485e0c26037c0acd7d29765ca3fbb5cb3831d347423220"},
+]
+
+[[package]]
+name = "pure-eval"
+version = "0.2.3"
+description = "Safely evaluate AST nodes without side effects"
+optional = false
+python-versions = "*"
+files = [
+    {file = "pure_eval-0.2.3-py3-none-any.whl", hash = "sha256:1db8e35b67b3d218d818ae653e27f06c3aa420901fa7b081ca98cbedc874e0d0"},
+    {file = "pure_eval-0.2.3.tar.gz", hash = "sha256:5f4e983f40564c576c7c8635ae88db5956bb2229d7e9237d03b3c0b0190eaf42"},
+]
+
+[package.extras]
+tests = ["pytest"]
+
 [[package]]
 name = "pygments"
 version = "2.18.0"
@@ -827,6 +1007,25 @@ files = [
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
 ]
 
+[[package]]
+name = "stack-data"
+version = "0.6.3"
+description = "Extract data from python stack frames and tracebacks for informative displays"
+optional = false
+python-versions = "*"
+files = [
+    {file = "stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695"},
+    {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"
@@ -838,6 +1037,21 @@ files = [
     {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"
@@ -877,7 +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 = "7321f58bda2e65a4a0674d43997ce31402e0fed876a77b37a1b86d83d569707a"
+content-hash = "b1076b7f750e8f7e66542918ec746e74544fbfdb376875158f083fb573d18107"

pyproject.toml

@@ -16,11 +16,12 @@ classifiers = [
     "Intended Audience :: End Users/Desktop",
 ]
 include = [
-    { path = "pyproject.toml" }
+    { path = "pyproject.toml" },
+    "pyrelacs/resources.py"
 ]
 
 [tool.poetry.dependencies]
-python = "^3.12"
+python = "^3.10"
 uldaq = "^1.2.3"
 typer = "^0.12.5"
 matplotlib = "^3.9.2"
@@ -34,6 +35,9 @@ 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>=1.0.0"]
 build-backend = "poetry.core.masonry.api"

pyrelacs/app.py

@@ -1,183 +1,17 @@
-import pathlib
-from PyQt6.QtGui import QAction
 import sys
 
-from PyQt6.QtCore import QSize, QThreadPool, QSettings
-from PyQt6.QtWidgets import (
-    QApplication,
-    QGridLayout,
-    QPushButton,
-    QToolBar,
-    QWidget,
-    QMainWindow,
-    QPlainTextEdit,
-)
-import pyqtgraph as pg
-import uldaq
-from IPython import embed
-from scipy.signal import welch, find_peaks
-import numpy as np
-import nixio as nix
+from PyQt6.QtCore import QSettings
+from PyQt6.QtWidgets import QApplication
 
+from pyrelacs import info
+from pyrelacs.ui.mainwindow import PyRelacs
 from pyrelacs.util.logging import config_logging
-import pyrelacs.info as info
-from pyrelacs.worker import Worker
-from pyrelacs.repros.repros import Repro
 
 log = config_logging()
 
-
-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)
-
-        self.nix_file = nix.File.open(
-            str(pathlib.Path(__file__).parent / "data"), nix.FileMode.ReadOnly
-        )
-
-    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)
+from pyrelacs import (
+    resources,
+)  # best created with pyside6-rcc resources.qrc -o resources.py (rcc produces an error...)
 
 
 def main():
@@ -185,6 +19,7 @@ def main():
     app.setApplicationName(info.NAME)
     app.setApplicationVersion(str(info.VERSION))
     app.setOrganizationDomain(info.ORGANIZATION)
+    # app.setAttribute(Qt.ApplicationAttribute.AA_DontShowIconsInMenus, False)
 
     # read window settings
     settings = QSettings(info.ORGANIZATION, info.NAME)

pyrelacs/devices/mccdac.py

@@ -12,13 +12,32 @@ log = config_logging()
 
 
 class MccDac:
+    """
+    Represents the Digital/Analog Converter from Meassuring Computing.
+    provides methods for writing and reading the Analog / Digital input and output.
+
+    Connects to the DAC device.
+
+    Attributes
+    ----------
+    daq_device : uldaq.DaqDevice
+        DaqDevice for handling connecting, releasing and disconnecting
+    ai_device : uldaq.AiDevice
+        The Analog input Device
+    ao_device :
+        Analog output Device
+    dio_device :
+        Digital Input Output
+    """
+
     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:
+        try:
+            self.daq_device = uldaq.DaqDevice(devices[0])
+        except uldaq.ul_exception.ULException as e:
             log.error("Did not found daq devices, please connect one")
-            exit(1)
-        self.daq_device = uldaq.DaqDevice(devices[0])
+            raise e
         try:
             self.daq_device.connect()
         except uldaq.ul_exception.ULException:
@@ -30,6 +49,10 @@ class MccDac:
         log.debug("Connected")
 
     def connect_dac(self):
+        """
+        Connecting to the DAQ device
+
+        """
         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:
@@ -52,6 +75,40 @@ class MccDac:
         ScanOption: uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO,
         AInScanFlag: uldaq.AInScanFlag = uldaq.AInScanFlag.DEFAULT,
     ) -> Array[c_double]:
+        """
+        Reading the analog input of the DAC device
+        Creates a c_double Array for storing the acquired data
+
+        Parameters
+        ----------
+        channels : list[int]
+            channels to read from, provide only two int's in a list (ex [0, 1] or [0, 4])
+            for sampling from the range(channel0, channel4)
+
+        duration : int
+            duration of sampling period
+
+        samplerate : float
+            samplerate for the duration of sampling
+
+        AiInputMode : uldaq.AiInputMode = uldaq.AiInputMode.SINGLE_ENDED
+            Contains attributes indicating A/D channel input modes.
+            Compares to Ground
+
+        Range : uldaq.Range = uldaq.Range.BIP10VOLTS
+            Range of the output
+
+        ScanOption : uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO
+            Specific Flags for acuiring the input
+
+        AInScanFlag : uldaq.AInScanFlag = uldaq.AInScanFlag.DEFAULT
+            Scaling of the data
+
+        Returns
+        -------
+        Array[c_double]
+
+        """
         assert len(channels) == 2, log.error("You can only provide two channels [0, 1]")
 
         if channels[0] != channels[1]:
@@ -85,6 +142,37 @@ class MccDac:
         ScanOption: uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO,
         AOutScanFlag: uldaq.AOutScanFlag = uldaq.AOutScanFlag.DEFAULT,
     ) -> Array[c_double]:
+        """
+        Writes data to the DAC device.
+        Creates a c_double Array for writing the data
+
+        Parameters
+        ----------
+        data : Union[list, npt.NDArray]
+            data which should be written to the DAC
+
+        channels : list[int]
+            channels to read from, provide only two int's in a list (ex [0, 1])
+            for sampling from the range(channel0, channel1)
+            DAC USB 1608GX-2AO has only 2 output channels
+
+        samplerate : float
+            samplerate for the duration of sampling
+
+        Range : uldaq.Range = uldaq.Range.BIP10VOLTS
+            Range of the output
+
+        ScanOption : uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO
+            Specific Flags for acuiring the input
+
+        AOutScanFlag : uldaq.AOutScanFlag = uldaq.AOutScanFlag.DEFAULT
+            For Scaling the data
+
+        Returns
+        -------
+        Array[c_double]
+        """
+
         assert len(channels) == 2, log.error("You can only provide two channels [0, 1]")
 
         buffer = c_double * len(data)
@@ -109,7 +197,18 @@ class MccDac:
 
         return data_analog_output
 
-    def set_analog_to_zero(self, channels: list[int] = [0, 1]):
+    def set_analog_to_zero(self, channels: list[int] = [0, 1]) -> None:
+        """
+        Sets all analog outputs to zero
+
+        Parameters
+        ----------
+        channels : list[int]
+            channels to read from, provide only two int's in a list (ex [0, 1])
+            for sampling from the range(channel0, channel1)
+            DAC USB 1608GX-2AO has only 2 output channels
+
+        """
         try:
             err = self.ao_device.a_out_list(
                 channels[0],
@@ -126,16 +225,37 @@ class MccDac:
             log.error("disconnection dac")
             self.disconnect_dac()
 
-    def diggital_trigger(self) -> None:
-        data = self.read_bit(channel=0)
+    def digital_trigger(self, ch: int = 0) -> None:
+        """
+        Writes a 1 to a specified digital channel, if the channel is already on 1 switches it to
+        0 and after Nano second it writes a 1 to the specified digital channel
+
+        Parameters
+        ----------
+        ch : int
+            Channel to trigger
+        """
+        data = self.read_bit(channel=ch)
         if data:
-            self.write_bit(channel=0, bit=0)
+            self.write_bit(channel=ch, bit=0)
             time.time_ns()
-            self.write_bit(channel=0, bit=1)
+            self.write_bit(channel=ch, bit=1)
         else:
-            self.write_bit(channel=0, bit=1)
+            self.write_bit(channel=ch, bit=1)
 
     def write_bit(self, channel: int = 0, bit: int = 1) -> None:
+        """
+        Writes a 0 / 1 to a specified digitial channel
+
+        Parameters
+        ----------
+        channel : int
+            Digital channel to write
+
+        bit : int
+            0 / 1 for writing to the digital channel
+
+        """
         self.dio_device.d_config_bit(
             uldaq.DigitalPortType.AUXPORT, channel, uldaq.DigitalDirection.OUTPUT
         )
@@ -143,55 +263,36 @@ class MccDac:
             uldaq.DigitalPortType.AUXPORT, bit_number=channel, data=bit
         )
 
-    def read_bit(self, channel: int = 0):
+    def read_bit(self, channel: int = 0) -> int:
+        """
+        Reads a 0 / 1 from the specified digital channel
+
+        Parameters
+        ----------
+        channel : int
+            Digital channel to read from
+
+        Returns
+        -------
+        bit : int
+            0 or 1 from the digital channel
+        """
         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
+    def check_attenuator(self) -> None:
         """
+        For checking the attenuator in the DAC device that was implemented to attenuate the
+        analog signal to mV.
 
+        Writes to Channel 0 of the analog output with different attenuation levels
+        0, 0, -2, -5, -10, -20, -50 dB and the second 0 has a software mute
+
+        """
         SAMPLERATE = 40_000.0
         DURATION = 5
         AMPLITUDE = 1
@@ -201,7 +302,6 @@ class MccDac:
         # 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:
@@ -219,7 +319,7 @@ class MccDac:
                 ScanOption=uldaq.ScanOption.EXTTRIGGER,
                 Range=uldaq.Range.BIP10VOLTS,
             )
-            self.diggital_trigger()
+            self.digital_trigger()
 
             try:
                 self.ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 15)
@@ -248,6 +348,16 @@ class MccDac:
         mute_channel2: bool = False,
     ):
         """
+        Setting the attenuation level of the chip that is connected to the DAQ
+        The attenuation level is set by writing to the connected digital output pin 5
+        where the strobepin 6 is signaling the when the bit was send.
+        The cspin is set from 1 to 0 for the start and 0 to 1 for signaling the end
+        of the data write process.
+
+        The mute pin should be set to 1 for the device to be working.
+
+        More information in the AttCS3310.pdf in the doc
+
         ident     : attdev-1
         strobepin : 6
         datainpin : 5
@@ -255,8 +365,23 @@ class MccDac:
         cspin     : 4
         mutepin   : 7
         zcenpin   : -1
-        """
 
+        Parameters
+        ----------
+        db_channel1 : float
+            dB Attenuation level for the first channel
+
+        db_channel2 : float
+            dB Attenuation level for the second channel
+
+        mute_channel1 : bool
+            Software mute for the first channel
+
+        mute_channel2 : bool
+            Software mute for the second channel
+
+
+        """
         self.activate_attenuator()
         hardware_possible_db = np.arange(-95.5, 32.0, 0.5)
         byte_number = np.arange(1, 256)
@@ -283,9 +408,18 @@ class MccDac:
         self.write_bit(channel=4, bit=1)
 
     def activate_attenuator(self):
+        """
+        Activation of the attenuator, where the cspin and mute pin is set to 1,
+        and the datapin and strobpin to 0
+
+        """
         for ch, b in zip([4, 5, 6, 7], [1, 0, 0, 1]):
             self.write_bit(channel=ch, bit=b)
 
     def deactivate_attenuator(self):
+        """
+        Writes a 0 to the mute pin, which is deactivating the attenuator
+
+        """
         # mute should be enabled for starting calibration
         self.write_bit(channel=7, bit=0)

pyrelacs/info.py

@@ -3,6 +3,7 @@ import pathlib
 
 
 def load_project_settings(project_root):
+    print(project_root)
     # Read the pyproject.toml file
     with open(pathlib.Path.joinpath(project_root, "pyproject.toml"), "r") as f:
         pyproject_content = f.read()

pyrelacs/repros/calbi.py

@@ -1,5 +1,3 @@
-import signal
-import sys
 import faulthandler
 import time
 
@@ -8,13 +6,14 @@ import uldaq
 from IPython import embed
 import numpy as np
 import matplotlib.pyplot as plt
-from scipy.signal import welch, csd
+from scipy.signal import welch
 from scipy.signal import find_peaks
 
 from pyrelacs.devices.mccdac import MccDac
 from pyrelacs.util.logging import config_logging
 
 log = config_logging()
+# for more information on seg faults
 faulthandler.enable()
 
 
@@ -60,7 +59,7 @@ class Calibration(MccDac):
             time.sleep(1)
 
             log.debug("Starting the Scan")
-            self.diggital_trigger()
+            self.digital_trigger()
 
             try:
                 self.ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 15)
@@ -109,7 +108,7 @@ class Calibration(MccDac):
                 self.SAMPLERATE,
                 ScanOption=uldaq.ScanOption.EXTTRIGGER,
             )
-            self.diggital_trigger()
+            self.digital_trigger()
             log.info(self.ao_device)
             ai_status = uldaq.ScanStatus.RUNNING
             ao_status = uldaq.ScanStatus.RUNNING
@@ -133,15 +132,20 @@ class Calibration(MccDac):
             channel1 = np.array(readout[::2])
             channel2 = np.array(readout[1::2])
 
-            block.create_data_array(
+            stim_data = block.create_data_array(
                 f"stimulus_{db_value}",
-                "Array",
+                "nix.regular_sampled",
                 shape=data.shape,
                 data=channel1,
                 label="Voltage",
                 unit="V",
             )
-            block.create_data_array(
+            stim_data.append_sampled_dimension(
+                self.SAMPLERATE,
+                label="time",
+                unit="s",
+            )
+            fish_data = block.create_data_array(
                 f"fish_{db_value}",
                 "Array",
                 shape=data.shape,
@@ -149,88 +153,13 @@ class Calibration(MccDac):
                 label="Voltage",
                 unit="V",
             )
+            fish_data.append_sampled_dimension(
+                self.SAMPLERATE,
+                label="time",
+                unit="s",
+            )
 
-            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()
 
 
 def decibel(power, ref_power=1.0, min_power=1e-20):

pyrelacs/repros/repros.py

@@ -1,16 +1,24 @@
 import sys
-import importlib.util
 import ast
 import pathlib
+from typing import Tuple
 
 from IPython import embed
 import nixio as nix
+import importlib.util
+
 from pyrelacs.util.logging import config_logging
 
 log = config_logging()
 
 
 class Repro:
+    """
+    Repro Class that searches in the repro folder for classes instances and executes the
+    the run function in the searched class
+
+    """
+
     def __init__(self) -> None:
         pass
 
@@ -26,14 +34,27 @@ class Repro:
                 log.error("Could not load the module of the repro")
             else:
                 sys.modules[name] = module
-                spec.loader.exec_module(module)
+                if spec.loader is not None:
+                    spec.loader.exec_module(module)
+                else:
+                    log.error(f"{spec.loader} is None")
                 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):
+    def names_of_repros(self) -> Tuple[list, list]:
+        """
+        Searches for class names in the repro folder in all python files
+
+        Returns
+        -------
+        Tuple[list, list]
+            list of class names
+            list of file names from the class names
+        """
+
         file_path_cur = pathlib.Path(__file__).parent
         python_files = list(file_path_cur.glob("**/*.py"))
         exclude_files = ["repros.py", "__init__.py"]

pyrelacs/resources.qrc

@@ -0,0 +1,10 @@
+<!DOCTYPE RCC><RCC version="1.0">
+<qresource>
+    <file>icons/exit.png</file>
+    <file>icons/connect.png</file>
+    <file>icons/disconnect.png</file>
+    <file>icons/record.png</file>
+    <file>icons/stop.png</file>
+    <file>icons/relacstuxheader.png</file>
+</qresource>
+</RCC>

pyrelacs/ui/about.py

@@ -0,0 +1,54 @@
+from PyQt6.QtGui import QPixmap
+from PyQt6.QtWidgets import QDialog, QDialogButtonBox, QLabel, QVBoxLayout, QWidget
+from PyQt6.QtCore import Qt
+
+
+class AboutDialog(QDialog):
+
+    def __init__(self, parent=None) -> None:
+        super().__init__(parent=parent)
+        self.setModal(True)
+        about = About(self)
+        self.setLayout(QVBoxLayout())
+        self.layout().addWidget(about)
+        bbox = QDialogButtonBox(QDialogButtonBox.StandardButton.Ok)
+        bbox.accepted.connect(self.accept)
+        self.layout().addWidget(bbox)
+
+
+class About(QWidget):
+
+    def __init__(self, parent=None) -> None:
+        super().__init__(parent=parent)
+        self.setLayout(QVBoxLayout())
+
+        heading = QLabel("pyRelacs")
+        font = heading.font()
+        font.setPointSize(18)
+        font.setBold(True)
+        heading.setFont(font)
+        heading.setAlignment(Qt.AlignmentFlag.AlignCenter)
+        subheading = QLabel("relacsed electrophysiological recordings")
+        subheading.setAlignment(Qt.AlignmentFlag.AlignCenter)
+        nix_link = QLabel("https://github.com/relacs")
+        nix_link.setOpenExternalLinks(True)
+        nix_link.setAlignment(Qt.AlignmentFlag.AlignCenter)
+        rtd_link = QLabel("https://relacs.net")
+        rtd_link.setOpenExternalLinks(True)
+        rtd_link.setAlignment(Qt.AlignmentFlag.AlignCenter)
+
+        iconlabel = QLabel()
+        pixmap = QPixmap(":/icons/relacstuxheader.png")
+        s = pixmap.size()
+        new_height = int(s.height() * 300/s.width())
+        pixmap = pixmap.scaled(300, new_height, Qt.AspectRatioMode.KeepAspectRatio, Qt.TransformationMode.FastTransformation)
+        iconlabel.setPixmap(pixmap)
+        iconlabel.setMaximumWidth(300)
+        iconlabel.setAlignment(Qt.AlignmentFlag.AlignCenter)
+        iconlabel.setScaledContents(True)
+
+        self.layout().addWidget(heading)
+        self.layout().addWidget(subheading)
+        self.layout().addWidget(iconlabel)
+        self.layout().addWidget(nix_link)
+        self.layout().addWidget(rtd_link)

pyrelacs/ui/mainwindow.py

@@ -0,0 +1,227 @@
+from PyQt6.QtGui import QAction, QIcon, QKeySequence
+from PyQt6.QtCore import Qt, QSize, QThreadPool
+from PyQt6.QtWidgets import (
+    QGridLayout,
+    QPushButton,
+    QToolBar,
+    QWidget,
+    QMainWindow,
+    QPlainTextEdit,
+    QMenuBar,
+    QStatusBar,
+)
+import uldaq
+import numpy as np
+import nixio as nix
+import pyqtgraph as pg
+
+from pathlib import Path as path
+from scipy.signal import welch, find_peaks
+
+from pyrelacs.worker import Worker
+from pyrelacs.repros.repros import Repro
+from pyrelacs.util.logging import config_logging
+from pyrelacs.ui.about import AboutDialog
+from pyrelacs.ui.plots.calibration import CalibrationPlot
+
+log = config_logging()
+_root = path(__file__).parent.parent
+
+from IPython import embed
+
+
+class PyRelacs(QMainWindow):
+    def __init__(self):
+        super().__init__()
+        self.setToolButtonStyle(
+            Qt.ToolButtonStyle.ToolButtonTextBesideIcon
+        )  # Ensure icons are displayed with text
+        self.setWindowTitle("PyRelacs")
+
+        self.figure = pg.GraphicsLayoutWidget()
+
+        filename = path.joinpath(path.cwd(), "data.nix")
+        if filename.exists():
+            self.nix_file = nix.File.open(str(filename), nix.FileMode.ReadOnly)
+        else:
+            self.nix_file = nix.File.open(str(filename), nix.FileMode.Overwrite)
+
+        self.calibration_plot = CalibrationPlot(self.figure, self.nix_file)
+
+        self.threadpool = QThreadPool()
+        self.repros = Repro()
+
+        self.text = QPlainTextEdit()
+        self.text.setReadOnly(True)
+
+        self.setMenuBar(QMenuBar(self))
+        self.setStatusBar(QStatusBar(self))
+        self.create_actions()
+        self.create_buttons()
+        self.create_toolbars()
+
+        layout = QGridLayout()
+        layout.addWidget(self.figure, 0, 0, 2, 2)
+        layout.addWidget(self.text, 2, 0, 1, 2)
+
+        widget = QWidget()
+        widget.setLayout(layout)
+        self.setCentralWidget(widget)
+
+    def create_actions(self):
+        self._rlx_exitaction = QAction(QIcon(":/icons/exit.png"), "Exit", self)
+        self._rlx_exitaction.setStatusTip("Close relacs")
+        self._rlx_exitaction.setShortcut(QKeySequence("Alt+q"))
+        self._rlx_exitaction.triggered.connect(self.on_exit)
+
+        self._rlx_aboutaction = QAction("about")
+        self._rlx_aboutaction.setStatusTip("Show about dialog")
+        self._rlx_aboutaction.setEnabled(True)
+        self._rlx_aboutaction.triggered.connect(self.on_about)
+
+        self._daq_connectaction = QAction(
+            QIcon(":icons/connect.png"), "Connect DAQ", self
+        )
+        self._daq_connectaction.setStatusTip("Connect to daq device")
+        # self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
+        self._daq_connectaction.triggered.connect(self.connect_dac)
+
+        self._daq_disconnectaction = QAction(
+            QIcon(":/icons/disconnect.png"), "Disconnect DAQ", self
+        )
+        self._daq_disconnectaction.setStatusTip("Disconnect the DAQ device")
+        # self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
+        self._daq_disconnectaction.triggered.connect(self.disconnect_dac)
+
+        self._daq_calibaction = QAction(
+            QIcon(":/icons/calibration.png"), "Plot calibration", self
+        )
+        self._daq_calibaction.setStatusTip("Calibrate the attenuator device")
+        # self._daq_calibaction.setShortcut(QKeySequence("Alt+d"))
+        self._daq_calibaction.triggered.connect(self.calibration_plot.plot)
+        self.create_menu()
+
+    def create_menu(self):
+        menu = self.menuBar()
+        if menu is not None:
+            file_menu = menu.addMenu("&File")
+            device_menu = menu.addMenu("&DAQ")
+            help_menu = menu.addMenu("&Help")
+
+            if file_menu is not None:
+                file_menu.addAction(self._rlx_exitaction)
+                file_menu.addAction(self._rlx_aboutaction)
+
+            if device_menu is not None:
+                device_menu.addAction(self._daq_connectaction)
+                device_menu.addAction(self._daq_disconnectaction)
+                device_menu.addSeparator()
+                device_menu.addAction(self._daq_calibaction)
+
+            if help_menu is not None:
+                help_menu.addSeparator()
+                # help_menu.addAction(self._help_action)
+        else:
+            log.error("could not create file menu and device menu")
+            self.on_exit()
+
+        self.setMenuBar(menu)
+
+    def create_toolbars(self):
+        rlx_toolbar = QToolBar("Relacs")
+        rlx_toolbar.addAction(self._rlx_exitaction)
+        rlx_toolbar.setIconSize(QSize(24, 24))
+
+        self.addToolBar(Qt.ToolBarArea.TopToolBarArea, rlx_toolbar)
+        daq_toolbar = QToolBar("DAQ")
+        daq_toolbar.addAction(self._daq_connectaction)
+        daq_toolbar.addAction(self._daq_disconnectaction)
+        daq_toolbar.addAction(self._daq_calibaction)
+        self.addToolBar(Qt.ToolBarArea.TopToolBarArea, daq_toolbar)
+
+        repro_toolbar = QToolBar("Repros")
+        repro_names, file_names = self.repros.names_of_repros()
+        for rep, fn in zip(repro_names, file_names):
+            repro_action = QAction(rep, self)
+            repro_action.setStatusTip(rep)
+            repro_action.triggered.connect(
+                lambda checked, n=rep, f=fn: self.run_repro(n, f)
+            )
+            repro_toolbar.addAction(repro_action)
+        self.addToolBar(Qt.ToolBarArea.TopToolBarArea, repro_toolbar)
+
+    def create_buttons(self):
+        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.calibration_plot.plot)
+
+    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")
+        except IndexError:
+            log.error("DAQ is not connected")
+            log.error("Please connect a DAQ device to the system")
+
+        if hasattr(PyRelacs, "daq_device"):
+            try:
+                self.daq_device.connect()
+                log.debug("Connected")
+            except uldaq.ul_exception.ULException as e:
+                log.error(f"Could not Connect to DAQ: {e}")
+            self.daq_connect_button.setDisabled(True)
+        else:
+            log.debug("Already handeld the error")
+            pass
+
+    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 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 add_to_textfield(self, s: str):
+        self.text.appendPlainText(s)
+
+    def on_exit(self):
+        log.info("exit button!")
+        self.add_to_textfield("exiting")
+        self.close()
+
+    def on_about(self, e):
+        about = AboutDialog(self)
+        about.show()
+
+    def print_output(self, s):
+        log.info(s)
+        self.add_to_textfield(s)
+
+    def thread_complete(self):
+        log.info("Thread complete!")
+        self.add_to_textfield("Thread complete!")
+
+    def progress_fn(self, n):
+        print("%d%% done" % n)

pyrelacs/ui/plots/calibration.py

@@ -0,0 +1,113 @@
+from IPython import embed
+import pyqtgraph as pg
+import numpy as np
+from scipy.signal import welch, find_peaks
+from scipy.integrate import romb
+
+
+class CalibrationPlot:
+    def __init__(self, figure: pg.GraphicsLayoutWidget, nix_file):
+        self.figure = figure
+        self.nix_file = nix_file
+
+    def plot(self):
+        self.figure.setBackground("w")
+        self.beat_plot = self.figure.addPlot(row=0, col=0)
+        self.power_plot = self.figure.addPlot(row=1, col=0)
+        self.beat_plot.addLegend()
+        self.power_plot.addLegend()
+        # self.power_plot.setLogMode(x=False, y=True)
+
+        block = self.nix_file.blocks[0]
+        colors = ["red", "green", "blue", "black", "yellow"]
+        for i, (stim, fish) in enumerate(
+            zip(list(block.data_arrays)[::2], list(block.data_arrays)[1::2])
+        ):
+            f_stim, stim_power = welch(
+                stim[:],
+                fs=40_000.0,
+                window="flattop",
+                nperseg=100_000,
+            )
+            stim_power = self.decibel(stim_power)
+            stim_max_power_index = np.argmax(stim_power)
+            freq_stim = f_stim[stim_max_power_index]
+
+            f_fish, fish_power = welch(
+                fish[:],
+                fs=40_000.0,
+                window="flattop",
+                nperseg=100_000,
+            )
+            fish_power = self.decibel(fish_power)
+            fish_max_power_index = np.argmax(fish_power)
+            freq_fish = f_fish[fish_max_power_index]
+
+            beat_frequency = np.abs(freq_fish - freq_stim)
+
+            beat = stim[:] + fish[:]
+            beat_squared = beat**2
+
+            f, powerspec = welch(
+                beat_squared,
+                window="flattop",
+                fs=40_000.0,
+                nperseg=100_000,
+            )
+            powerspec = self.decibel(powerspec)
+
+            padding = 20
+            integration_window = powerspec[
+                (f > beat_frequency - padding) & (f < beat_frequency + padding)
+            ]
+
+            peaks = find_peaks(powerspec, prominence=40)[0]
+
+            pen = pg.mkPen(colors[i])
+
+            self.beat_plot.plot(
+                np.arange(0, len(beat)) / 40_000.0,
+                beat,
+                pen=pen,
+                name=stim.name,
+            )
+            self.power_plot.plot(f, powerspec, pen=pen, name=stim.name)
+            self.power_plot.plot(f[peaks], powerspec[peaks], pen=None, symbol="x")
+
+    def decibel(self, 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