[plotting] move calibrtion plot outside of main window

pyrelacs/app.py

@@ -3,12 +3,16 @@ import sys
 from PyQt6.QtCore import QSettings
 from PyQt6.QtWidgets import QApplication
 
-from . import info
+from pyrelacs import info
-from .ui.mainwindow import PyRelacs
+from pyrelacs.ui.mainwindow import PyRelacs
-from .util.logging import config_logging
+from pyrelacs.util.logging import config_logging
+
 log = config_logging()
 
-from . import resources  # best created with pyside6-rcc resources.qrc -o resources.py (rcc produces an error...)
+from pyrelacs import (
+    resources,
+)  # best created with pyside6-rcc resources.qrc -o resources.py (rcc produces an error...)
+
 
 def main():
     app = QApplication(sys.argv)

pyrelacs/repros/calbi.py

@@ -159,87 +159,7 @@ class Calibration(MccDac):
                 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

@@ -8,9 +8,9 @@ import nixio as nix
 import importlib.util
 
 from pyrelacs.util.logging import config_logging
+
 log = config_logging()
 
-from IPython import embed
 
 class Repro:
     """
@@ -25,7 +25,6 @@ class Repro:
     def run_repro(
         self, nix_file: nix.File, name: str, file: pathlib.Path, *args, **kwargs
     ) -> None:
-
         spec = importlib.util.spec_from_file_location("rep", file)
         if not spec:
             log.error("Could not load the file")
@@ -35,7 +34,10 @@ 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)

pyrelacs/ui/mainwindow.py

@@ -8,7 +8,7 @@ from PyQt6.QtWidgets import (
     QMainWindow,
     QPlainTextEdit,
     QMenuBar,
-    QStatusBar
+    QStatusBar,
 )
 import uldaq
 import numpy as np
@@ -18,22 +18,35 @@ import pyqtgraph as pg
 from pathlib import Path as path
 from scipy.signal import welch, find_peaks
 
-from ..worker import Worker
+from pyrelacs.worker import Worker
-from ..repros.repros import Repro
+from pyrelacs.repros.repros import Repro
-from ..util.logging import config_logging
+from pyrelacs.util.logging import config_logging
-from .about import AboutDialog
+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.setToolButtonStyle(
+            Qt.ToolButtonStyle.ToolButtonTextBesideIcon
+        )  # Ensure icons are displayed with text
         self.setWindowTitle("PyRelacs")
-        self.beat_plot = pg.PlotWidget()
+
-        self.power_plot = pg.PlotWidget()
+        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()
@@ -48,67 +61,70 @@ class PyRelacs(QMainWindow):
         self.create_toolbars()
 
         layout = QGridLayout()
-        layout.addWidget(self.plot_calibration_button, 0, 0)
+        layout.addWidget(self.figure, 0, 0, 2, 2)
-        layout.addWidget(self.daq_disconnect_button, 0, 1)
+        layout.addWidget(self.text, 2, 0, 1, 2)
-        layout.addWidget(self.beat_plot, 2, 0, 1, 2)
-        layout.addWidget(self.power_plot, 3, 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 = path.joinpath(path.cwd(), "data.nix")
-        self.nix_file = nix.File.open(
-            str(filename), nix.FileMode.Overwrite
-        )
-
     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 = 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 = 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 = 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.plot_calibration)
+        self._daq_calibaction.triggered.connect(self.calibration_plot.plot)
         self.create_menu()
 
     def create_menu(self):
         menu = self.menuBar()
-        file_menu = menu.addMenu("&File")
+        if menu is not None:
-        file_menu.addAction(self._rlx_exitaction)
+            file_menu = menu.addMenu("&File")
-        file_menu.addAction(self._rlx_aboutaction)
+            device_menu = menu.addMenu("&DAQ")
+            help_menu = menu.addMenu("&Help")
 
-        device_menu = menu.addMenu("&DAQ")
+            if file_menu is not None:
-        device_menu.addAction(self._daq_connectaction)
+                file_menu.addAction(self._rlx_exitaction)
-        device_menu.addAction(self._daq_disconnectaction)
+                file_menu.addAction(self._rlx_aboutaction)
-        device_menu.addSeparator()
+
-        device_menu.addAction(self._daq_calibaction)
+            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()
 
-        help_menu = menu.addMenu("&Help")
-        help_menu.addSeparator()
-        # help_menu.addAction(self._help_action)
         self.setMenuBar(menu)
 
     def create_toolbars(self):
@@ -145,82 +161,27 @@ class PyRelacs(QMainWindow):
 
         self.plot_calibration_button = QPushButton("Plot Calibration")
         self.plot_calibration_button.setCheckable(True)
-        self.plot_calibration_button.clicked.connect(self.plot_calibration)
+        self.plot_calibration_button.clicked.connect(self.calibration_plot.plot)
-
-    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]
-        colors = ["red", "green", "blue", "black", "yellow"]
-        for i, (stim, fish) in enumerate(
-            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(colors[i])
-            self.beat_plot.plot(
-                np.arange(0, len(beat)) / 40_000.0,
-                beat_squared,
-                pen=pen,
-                # name=stim.name,
-            )
-            self.power_plot.plot(f_sq, powerspec_sq, pen=pen)
-            self.power_plot.plot(f[peaks], powerspec_sq[peaks], pen=None, symbol="x")
 
     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")
+            log.error("DAQ is not connected")
-            self.on_exit()
+            log.error("Please connect a DAQ device to the system")
-        self.daq_connect_button.setDisabled(True)
+
+        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:
@@ -233,16 +194,6 @@ class PyRelacs(QMainWindow):
         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)
@@ -252,19 +203,25 @@ class PyRelacs(QMainWindow):
 
         self.threadpool.start(worker)
 
+    def add_to_textfield(self, s: str):
+        self.text.appendPlainText(s)
+
     def on_exit(self):
-        print("exit button!")
+        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):
-        print(s)
+        log.info(s)
+        self.add_to_textfield(s)
 
     def thread_complete(self):
-        print("THREAD COMPLETE!")
+        log.info("Thread complete!")
+        self.add_to_textfield("Thread complete!")
 
     def progress_fn(self, n):
-        print("%d%% done" % 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