diff --git a/pyrelacs/app.py b/pyrelacs/app.py index af76544..db65e36 100644 --- a/pyrelacs/app.py +++ b/pyrelacs/app.py @@ -1,185 +1,15 @@ -import pathlib -from PyQt6.QtGui import QAction import sys +import pathlib -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 pyrelacs.util.logging import config_logging -import pyrelacs.info as info -from pyrelacs.worker import Worker -from pyrelacs.repros.repros import Repro +from PyQt6.QtCore import QSettings +from PyQt6.QtWidgets import QApplication +from . import info +from .ui.mainwindow import PyRelacs +from .util.logging import config_logging 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) - - def main(): app = QApplication(sys.argv) app.setApplicationName(info.NAME) diff --git a/pyrelacs/ui/mainwindow.py b/pyrelacs/ui/mainwindow.py new file mode 100644 index 0000000..6f1d2d0 --- /dev/null +++ b/pyrelacs/ui/mainwindow.py @@ -0,0 +1,178 @@ +from PyQt6.QtGui import QAction +from PyQt6.QtCore import QSize, QThreadPool +from PyQt6.QtWidgets import ( + QApplication, + QGridLayout, + QPushButton, + QToolBar, + QWidget, + QMainWindow, + QPlainTextEdit, +) +import uldaq +import pathlib +import numpy as np +import nixio as nix +import pyqtgraph as pg + +from scipy.signal import welch, find_peaks + +from ..worker import Worker +from ..repros.repros import Repro +from ..util.logging import config_logging +log = config_logging() + +from IPython import embed + +class PyRelacs(QMainWindow): + def __init__(self): + super().__init__() + self.setWindowTitle("PyRelacs") + self.setMinimumSize(1000, 1000) + self.plot_graph = pg.PlotWidget() + + self.threadpool = QThreadPool() + self.repros = Repro() + + self.daq_connect_button = QPushButton("Connect Daq") + self.daq_connect_button.setCheckable(True) + self.daq_connect_button.clicked.connect(self.connect_dac) + + self.daq_disconnect_button = QPushButton("Disconnect Daq") + self.daq_disconnect_button.setCheckable(True) + self.daq_disconnect_button.clicked.connect(self.disconnect_dac) + + self.plot_calibration_button = QPushButton("Plot Calibration") + self.plot_calibration_button.setCheckable(True) + self.plot_calibration_button.clicked.connect(self.plot_calibration) + + self.text = QPlainTextEdit() + self.text.setReadOnly(True) + + layout = QGridLayout() + layout.addWidget(self.plot_calibration_button, 0, 0) + layout.addWidget(self.daq_disconnect_button, 0, 1) + layout.addWidget(self.text, 3, 0, 1, 2) + layout.addWidget(self.plot_graph, 2, 0, 1, 2) + + self.toolbar = QToolBar("Repros") + self.addToolBar(self.toolbar) + self.repros_to_toolbar() + + # self.setFixedSize(QSize(400, 300)) + widget = QWidget() + widget.setLayout(layout) + self.setCentralWidget(widget) + + filename = pathlib.Path.joinpath(pathlib.Path.cwd(), "data.nix") + self.nix_file = nix.File.open( + str(filename), nix.FileMode.Overwrite + ) + + def plot_calibration(self): + def decibel(power, ref_power=1.0, min_power=1e-20): + """Transform power to decibel relative to ref_power. + + \\[ decibel = 10 \\cdot \\log_{10}(power/ref\\_power) \\] + Power values smaller than `min_power` are set to `-np.inf`. + + Parameters + ---------- + power: float or array + Power values, for example from a power spectrum or spectrogram. + ref_power: float or None or 'peak' + Reference power for computing decibel. + If set to `None` or 'peak', the maximum power is used. + min_power: float + Power values smaller than `min_power` are set to `-np.inf`. + + Returns + ------- + decibel_psd: array + Power values in decibel relative to `ref_power`. + """ + if np.isscalar(power): + tmp_power = np.array([power]) + decibel_psd = np.array([power]) + else: + tmp_power = power + decibel_psd = power.copy() + if ref_power is None or ref_power == "peak": + ref_power = np.max(decibel_psd) + decibel_psd[tmp_power <= min_power] = float("-inf") + decibel_psd[tmp_power > min_power] = 10.0 * np.log10( + decibel_psd[tmp_power > min_power] / ref_power + ) + if np.isscalar(power): + return decibel_psd[0] + else: + return decibel_psd + + block = self.nix_file.blocks[0] + for stim, fish in zip( + list(block.data_arrays)[::2], list(block.data_arrays)[1::2] + ): + beat = stim[:] + fish[:] + beat_squared = beat**2 + + f, powerspec = welch(beat, fs=40_000.0) + powerspec = decibel(powerspec) + + f_sq, powerspec_sq = welch(beat_squared, fs=40_000.0) + powerspec_sq = decibel(powerspec_sq) + peaks = find_peaks(powerspec_sq, prominence=20)[0] + pen = pg.mkPen() + self.plot_graph.plot( + np.arange(0, len(beat)) / 40_000.0, beat_squared, pen=pen + ) + + def connect_dac(self): + devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB) + try: + self.daq_device = uldaq.DaqDevice(devices[0]) + log.debug(f"Found daq devices {len(devices)}, connecting to the first one") + self.daq_device.connect() + log.debug("Connected") + except IndexError: + log.debug("DAQ is not connected, closing") + QApplication.quit() + self.daq_connect_button.setDisabled(True) + + def disconnect_dac(self): + try: + log.debug(f"{self.daq_device}") + self.daq_device.disconnect() + self.daq_device.release() + log.debug(f"{self.daq_device}") + self.daq_disconnect_button.setDisabled(True) + self.daq_connect_button.setEnabled(True) + except AttributeError: + log.debug("DAQ was not connected") + + def repros_to_toolbar(self): + repro_names, file_names = self.repros.names_of_repros() + for rep, fn in zip(repro_names, file_names): + individual_repro_button = QAction(rep, self) + individual_repro_button.setStatusTip("Button") + individual_repro_button.triggered.connect( + lambda checked, n=rep, f=fn: self.run_repro(n, f) + ) + self.toolbar.addAction(individual_repro_button) + + def run_repro(self, n, fn): + self.text.appendPlainText(f"started Repro {n}, {fn}") + worker = Worker(self.repros.run_repro, self.nix_file, n, fn) + worker.signals.result.connect(self.print_output) + worker.signals.finished.connect(self.thread_complete) + worker.signals.progress.connect(self.progress_fn) + + self.threadpool.start(worker) + + def print_output(self, s): + print(s) + + def thread_complete(self): + print("THREAD COMPLETE!") + + def progress_fn(self, n): + print("%d%% done" % n) \ No newline at end of file