Merge pull request 'main' (#1) from jgrewe/minipyrelacs:main into main

Reviewed-on: Awendt/pyrelacs#1

poetry.lock

@@ -704,6 +704,56 @@ pygments = ">=2.13.0,<3.0.0"
 [package.extras]
 jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
+[[package]]
+name = "scipy"
+version = "1.14.1"
+description = "Fundamental algorithms for scientific computing in Python"
+optional = false
+python-versions = ">=3.10"
+files = [
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+    {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"
@@ -779,4 +829,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.12"
-content-hash = "6b680c385942c0a2c0eef934f3fb37fdc3d2e1dc058a7f2d891d4f2f0607d9c6"
+content-hash = "477748fbc18bde095d13dea548108541c1b584242099398155787361b1dc31fe"

pyproject.toml

@@ -3,7 +3,20 @@ 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"
+organization = "de.uni-tuebingen.neuroetho"
+classifiers = [
+    "Topic :: Scientific/Engineering",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: End Users/Desktop",
+]
+copyright = "(c) 2020, Neuroethology lab, Uni Tuebingen"
+
+include = [
+    { path = "pyproject.toml" }
+]
 
 [tool.poetry.dependencies]
 python = "^3.12"
@@ -13,7 +26,11 @@ matplotlib = "^3.9.2"
 numpy = "^2.1.1"
 pyqt6 = "^6.7.1"
 tomli = "^2.0.1"
+tomlkit = "^0.13.2"
+scipy = "^1.14.1"
 
+[tool.poetry.scripts]
+pyrelacs = "pyrelacs.app:main"
 
 [build-system]
 requires = ["poetry-core"]

pyrelacs/app.py

@@ -1,9 +1,8 @@
 from PyQt6.QtGui import QAction
 import sys
 import pathlib
-import ctypes
 
-from PyQt6.QtCore import QProcess, QSize, QThreadPool, Qt
+from PyQt6.QtCore import QProcess, QSize, QThreadPool, Qt, QSettings
 from PyQt6.QtWidgets import (
     QApplication,
     QGridLayout,
@@ -13,12 +12,14 @@ from PyQt6.QtWidgets import (
     QMainWindow,
     QPlainTextEdit,
 )
-import tomli
 import uldaq
 from IPython import embed
 import numpy as np
 
 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()
 
@@ -30,8 +31,7 @@ class PyRelacs(QMainWindow):
         self.setMinimumSize(1000, 1000)
 
         self.threadpool = QThreadPool()
-        # for starting a Qprocess
+        self.repros = Repro()
-        self.p = None
 
         self.daq_connect_button = QPushButton("Connect Daq")
         self.daq_connect_button.setCheckable(True)
@@ -51,7 +51,7 @@ class PyRelacs(QMainWindow):
 
         self.toolbar = QToolBar("Repros")
         self.addToolBar(self.toolbar)
-        self.repro()
+        self.repros_to_toolbar()
 
         self.setFixedSize(QSize(400, 300))
         widget = QWidget()
@@ -81,64 +81,49 @@ class PyRelacs(QMainWindow):
         except AttributeError:
             log.debug("DAQ was not connected")
 
-    def repro(self):
+    def repros_to_toolbar(self):
-        repos_path = pathlib.Path(__file__).parent / "repros"
+        repro_names, file_names = self.repros.names_of_repros()
-        repos_names = list(repos_path.glob("*.py"))
+        for rep, fn in zip(repro_names, file_names):
-        # 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)
+                lambda checked, n=rep, f=fn: self.run_repro(n, f)
             )
             self.toolbar.addAction(individual_repro_button)
 
-    def message(self, s):
+    def run_repro(self, n, fn):
-        self.text.appendPlainText(s)
+        self.text.appendPlainText(f"started Repro {n}, {fn}")
 
-    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):
+def main():
-        if self.p is not None:
+    app = QApplication(sys.argv)
-            data = self.p.readAllStandardError()
+    app.setApplicationName(info.NAME)
-            stderr = bytes(data).decode("utf8")
+    app.setApplicationVersion(str(info.VERSION))
-            self.message(stderr)
+    app.setOrganizationDomain(info.ORGANIZATION)
 
-    def handle_stdout(self):
+    # read window settings
-        if self.p is not None:
+    settings = QSettings(info.ORGANIZATION, info.NAME)
-            data = self.p.readAllStandardOutput()
+    width = int(settings.value("app/width", 1024))
-            stdout = bytes(data).decode("utf8")
+    height = int(settings.value("app/height", 768))
-            self.message(stdout)
+    x = int(settings.value("app/pos_x", 100))
+    y = int(settings.value("app/pos_y", 100))
 
-    def handle_state(self, state):
+    window = PyRelacs()
-        states = {
+    window.setMinimumWidth(200)
-            QProcess.ProcessState.NotRunning: "Not running",
+    window.setMinimumHeight(200)
-            QProcess.ProcessState.Starting: "Starting",
+    window.resize(width, height)
-            QProcess.ProcessState.Running: "Running",
+    window.move(x, y)
-        }
+    window.show()
-        state_name = states[state]
+    app.exec()
-        self.message(f"State changed: {state_name}")
 
-    def process_finished(self):
+    # store window position and size
-        self.text.appendPlainText("Process finished")
+    pos = window.pos()
-        self.p = None
+    settings.setValue("app/width", window.width())
+    settings.setValue("app/height", window.height())
+    settings.setValue("app/pos_x", pos.x())
+    settings.setValue("app/pos_y", pos.y())
+    sys.exit(exit_code)
 
 
 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 +1,37 @@
+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['tool']['poetry']['organization'],
+        'classifiers': pyproject['tool']['poetry']['classifiers'],
+        'copyright': pyproject['tool']['poetry']['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 +1,251 @@
-import ctypes
+import signal
+import sys
+import faulthandler
+import time
 
 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
 
-    def run_calibration(self):
+    def run(self):
-        # Stimulus
+
-        time = np.arange(0, DURATION, 1 / SAMPLERATE)
+    def segfault_handler(self, signum, frame):
-        data = AMPLITUDE * np.sin(2 * np.pi * SINFREQ * time)
+        print(f"Segmentation fault caught! Signal number: {signum}")
-        # sending stimulus
+        self.disconnect_dac()
-        stim, ao_device = self.send_analog_dac(
+        sys.exit(1)  # Gracefully exit the program
-            data, [0, 0], SAMPLERATE, ScanOption=uldaq.ScanOption.EXTTRIGGER
+
-        )
+    def check_amplitude(self):
-        read_data = self.read_analog_daq(
+        db_values = [0.0, -5.0, -10.0, -20.0, -50.0]
-            [0, 1], DURATION, SAMPLERATE, ScanOption=uldaq.ScanOption.EXTTRIGGER
+        colors = ["red", "green", "blue", "black", "yellow"]
-        )
+        self.set_attenuation_level(db_channel1=0.0, db_channel2=0.0)
-        self.digital_trigger()
+        # write to ananlog 1
-        ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 11)
+        t = np.arange(0, self.DURATION, 1 / self.SAMPLERATE)
-        self.digital_trigger(data=0)
+        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()
+
+        self.disconnect_dac()
+
+    def check_beat(self):
+        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"]
+        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()
+            signal.signal(signal.SIGSEGV, self.segfault_handler)
+            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])
+            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()
-        embed()
-        exit()
 
 
-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 +1,33 @@
+import ast
+import pathlib
+
+from IPython import embed
+
+
+class Repro:
+    def __init__(self) -> None:
+        pass
+
+    def run_repro(self, name: str, *args, **kwargs) -> None:
+        pass
+
+    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/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