[ui/structure] updating repros to tab bar with individual plots and nix blocks

pyrelacs/devices/mccdaq.py

@@ -224,10 +224,10 @@ class MccDaq:
                 uldaq.AOutListFlag.DEFAULT,
                 [0, 0],
             )
-        except Exception as e:
+        except Exception as er:
-            log.error("f{e}")
+            log.error(f"{er}")
             log.error("disconnection dac")
-            self.disconnect_daq()
+            # self.disconnect_daq()
 
     def digital_trigger(self, ch: int = 0) -> None:
         """

pyrelacs/repros/calibration/calibration.py

@@ -6,6 +6,8 @@ import uldaq
 from IPython import embed
 import numpy as np
 import matplotlib.pyplot as plt
+from scipy.signal import welch, find_peaks
+import pyqtgraph as pg
 
 from pyrelacs.devices.mccdaq import MccDaq
 from pyrelacs.util.logging import config_logging
@@ -15,40 +17,50 @@ log = config_logging()
 faulthandler.enable()
 
 
-class Calibration(MccDaq):
+class Calibration:
-    def __init__(self) -> None:
+    def __init__(self, config, mccdaq: MccDaq) -> None:
-        super().__init__()
+        self.config = config
+        self.mccdaq = mccdaq
         self.SAMPLERATE = 40_000.0
         self.DURATION = 5
         self.AMPLITUDE = 1
         self.SINFREQ = 750
 
     @staticmethod
-    def run(nix_file: nix.File):
+    def run(*args, **kwargs):
-        calb = Calibration()
+        nix_block = args[0]
-        calb.check_beat(nix_file)
+        figure = args[1]
+        mccdaq = args[2]
+        config = args[3]
+        calb = Calibration(config, mccdaq)
+        calb.check_beat(nix_block)
+        calb.plot(figure, nix_block)
+
+        return "finished"
 
     def check_amplitude(self):
         db_values = [0.0, -5.0, -10.0, -20.0, -50.0]
         colors = ["red", "green", "blue", "black", "yellow"]
-        self.set_attenuation_level(db_channel1=0.0, db_channel2=0.0)
+        self.mccdaq.set_attenuation_level(db_channel1=0.0, db_channel2=0.0)
         # write to ananlog 1
         t = np.arange(0, self.DURATION, 1 / self.SAMPLERATE)
         data = self.AMPLITUDE * np.sin(2 * np.pi * self.SINFREQ * t)
         fig, ax = plt.subplots()
 
         for i, db_value in enumerate(db_values):
-            self.set_attenuation_level(db_channel1=db_value, db_channel2=db_value)
+            self.mccdaq.set_attenuation_level(
+                db_channel1=db_value, db_channel2=db_value
+            )
             log.debug(f"{db_value}")
 
-            stim = self.write_analog(
+            stim = self.mccdaq.write_analog(
                 data,
                 [0, 0],
                 self.SAMPLERATE,
                 ScanOption=uldaq.ScanOption.EXTTRIGGER,
             )
 
-            data_channel_one = self.read_analog(
+            data_channel_one = self.mccdaq.read_analog(
                 [0, 0],
                 self.DURATION,
                 self.SAMPLERATE,
@@ -57,21 +69,21 @@ class Calibration(MccDaq):
             time.sleep(1)
 
             log.debug("Starting the Scan")
-            self.digital_trigger()
+            self.mccdaq.digital_trigger()
 
             try:
-                self.ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 15)
+                self.mccdaq.ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 15)
                 log.debug("Scan finished")
-                self.write_bit(channel=0, bit=0)
+                self.mccdaq.write_bit(channel=0, bit=0)
                 time.sleep(1)
-                self.set_analog_to_zero()
+                self.mccdaq.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)
+                self.mccdaq.write_bit(channel=0, bit=0)
                 time.sleep(1)
-                self.set_analog_to_zero()
+                self.mccdaq.set_analog_to_zero()
-                self.disconnect_daq()
+                # self.mccdaq.disconnect_daq()
 
             if i == 0:
                 ax.plot(t, stim, label=f"Input_{db_value}", color=colors[i])
@@ -80,34 +92,33 @@ class Calibration(MccDaq):
         ax.legend()
         plt.show()
 
-        self.disconnect_daq()
+        # self.mccdaq.disconnect_daq()
 
-    def check_beat(self, nix_file: nix.File):
+    def check_beat(self, nix_block: nix.Block):
-        self.set_attenuation_level(db_channel1=-10.0, db_channel2=0.0)
+        self.mccdaq.set_attenuation_level(db_channel1=-10.0, db_channel2=0.0)
         t = np.arange(0, self.DURATION, 1 / self.SAMPLERATE)
         data = self.AMPLITUDE * np.sin(2 * np.pi * self.SINFREQ * t)
         # data = np.concatenate((data, data))
         db_values = [0.0, -5.0, -8.5, -10.0]
         colors = ["red", "blue", "black", "green"]
         colors_in = ["lightcoral", "lightblue", "grey", "lightgreen"]
-        block = nix_file.create_block("Calibration", "data")
         # fig, axes = plt.subplots(2, 2, sharex="col")
         for i, db_value in enumerate(db_values):
-            self.set_attenuation_level(db_channel1=db_value)
+            self.mccdaq.set_attenuation_level(db_channel1=db_value)
-            stim = self.write_analog(
+            stim = self.mccdaq.write_analog(
                 data,
                 [0, 0],
                 self.SAMPLERATE,
                 ScanOption=uldaq.ScanOption.EXTTRIGGER,
             )
-            readout = self.read_analog(
+            readout = self.mccdaq.read_analog(
                 [0, 1],
                 self.DURATION,
                 self.SAMPLERATE,
                 ScanOption=uldaq.ScanOption.EXTTRIGGER,
             )
-            self.digital_trigger()
+            self.mccdaq.digital_trigger()
-            log.info(self.ao_device)
+            log.info(self.mccdaq.ao_device)
             ai_status = uldaq.ScanStatus.RUNNING
             ao_status = uldaq.ScanStatus.RUNNING
 
@@ -119,10 +130,10 @@ class Calibration(MccDaq):
             ):
                 # log.debug("Scanning")
                 time.time_ns()
-                ai_status = self.ai_device.get_scan_status()[0]
+                ai_status = self.mccdaq.ai_device.get_scan_status()[0]
-                ao_status = self.ao_device.get_scan_status()[0]
+                ao_status = self.mccdaq.ao_device.get_scan_status()[0]
 
-            self.write_bit(channel=0, bit=0)
+            self.mccdaq.write_bit(channel=0, bit=0)
             log.debug(
                 f"Status Analog_output {ao_status}\n, Status Analog_input {ai_status}"
             )
@@ -130,7 +141,7 @@ class Calibration(MccDaq):
             channel1 = np.array(readout[::2])
             channel2 = np.array(readout[1::2])
 
-            stim_data = block.create_data_array(
+            stim_data = nix_block.create_data_array(
                 f"stimulus_{db_value}",
                 "nix.regular_sampled",
                 shape=data.shape,
@@ -143,7 +154,7 @@ class Calibration(MccDaq):
                 label="time",
                 unit="s",
             )
-            fish_data = block.create_data_array(
+            fish_data = nix_block.create_data_array(
                 f"fish_{db_value}",
                 "Array",
                 shape=data.shape,
@@ -157,7 +168,72 @@ class Calibration(MccDaq):
                 unit="s",
             )
 
-        self.set_analog_to_zero()
+        time.time_ns()
+        self.mccdaq.set_analog_to_zero()
+
+    def plot(self, figure, block):
+        self.figure = figure
+        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)
+
+        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 = 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 = 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 = 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(power, ref_power=1.0, min_power=1e-20):

pyrelacs/repros/repros.py

@@ -22,9 +22,7 @@ class Repro:
     def __init__(self) -> None:
         pass
 
-    def run_repro(
+    def run_repro(self, name: str, file: pathlib.Path, *args, **kwargs) -> None:
-        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")
@@ -40,7 +38,7 @@ class Repro:
                     log.error(f"{spec.loader} is None")
                 if hasattr(module, name):
                     rep_class = getattr(module, name)
-                    rep_class.run(nix_file)
+                    rep_class.run(*args, **kwargs)
                 else:
                     raise AttributeError(f"{file.name} has no {name} class")
 

pyrelacs/repros/sinus.py

@@ -1,3 +0,0 @@
-class Sinus:
-    def __init__(self) -> None:
-        pass

pyrelacs/repros/sinus/sinus.py

@@ -0,0 +1,17 @@
+import nixio
+from pyrelacs.util.logging import config_logging
+
+
+log = config_logging()
+
+
+class Sinus:
+    def __init__(self) -> None:
+        pass
+
+    @staticmethod
+    def run(config, mccdaq, nix_block: nixio.Block, figure) -> None:
+        log.debug(config)
+        log.debug(mccdaq)
+        log.debug(nix_block)
+        log.debug(figure)

pyrelacs/ui/mainwindow.py

@@ -7,7 +7,10 @@ from PyQt6.QtGui import QAction, QIcon, QKeySequence
 from PyQt6.QtCore import Qt, QSize, QThreadPool, QMutex
 from PyQt6.QtWidgets import (
     QGridLayout,
+    QPushButton,
+    QTabWidget,
     QToolBar,
+    QVBoxLayout,
     QWidget,
     QMainWindow,
     QPlainTextEdit,
@@ -52,6 +55,8 @@ class PyRelacs(QMainWindow):
             self.mccdaq = MccDaq()
             end = time.time()
             log.debug(f"Connection to DAQ took {end - start}")
+        else:
+            self.mccdaq = None
 
         self.repros = Repro()
 
@@ -60,6 +65,8 @@ class PyRelacs(QMainWindow):
         )  # Ensure icons are displayed with text
         self.setWindowTitle("PyRelacs")
 
+        self.create_nix_file(f"{_root}/test.nix", self.config.metadata)
+
         self.mutex = QMutex()
 
         self.figure = pg.GraphicsLayoutWidget()
@@ -73,10 +80,13 @@ class PyRelacs(QMainWindow):
         self.setStatusBar(QStatusBar(self))
         self.create_actions()
         self.create_toolbars()
+        self.repro_tabs = QTabWidget()
+        self.create_repros_tabs()
 
         layout = QGridLayout()
         layout.addWidget(self.figure, 0, 0, 2, 2)
-        layout.addWidget(self.text, 2, 0, 1, 2)
+        layout.addWidget(self.repro_tabs, 2, 0, 2, 2)
+        layout.addWidget(self.text, 4, 0, 1, 1)
 
         widget = QWidget()
         widget.setLayout(layout)
@@ -104,14 +114,13 @@ class PyRelacs(QMainWindow):
         self.continously_plot = Continously(self.figure, self.buffer)
         # self.continously_plot.plot()
 
-        if self.config.settings.daq:
+        if self.mccdaq:
             log.debug("Creating Daq Generator")
             self.daq_producer = DaqProducer(self.buffer, self.mccdaq.daq_device, [1, 1])
         log.debug("Creating Sinus Generator")
         self.sinus_producer = SinProducer(self.buffer)
 
         self.nix_writer = NixWriter(self.buffer)
-        self.create_nix_file(f"{_root}/test.nix", self.config.metadata)
 
     def create_actions(self):
         self._rlx_exitaction = QAction(QIcon(":/icons/exit.png"), "Exit", self)
@@ -127,7 +136,7 @@ class PyRelacs(QMainWindow):
         self._daq_connectaction = QAction(
             QIcon(":icons/connect.png"), "Connect DAQ", self
         )
-        if self.config.settings.daq:
+        if self.mccdaq:
             self._daq_connectaction.setStatusTip("Connect to daq device")
             # self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
             self._daq_connectaction.triggered.connect(self.mccdaq.connect_dac)
@@ -146,7 +155,7 @@ class PyRelacs(QMainWindow):
         # # self._daq_calibaction.setShortcut(QKeySequence("Alt+d"))
         # self._daq_calibaction.triggered.connect(self.calibration_plot.plot)
 
-        self._run_action = QAction(QIcon(":/icons/record.png"), "Run", self)
+        self._run_action = QAction(QIcon(":/icons/record.png"), "RunDAQ", self)
         self._run_action.triggered.connect(self.run_daq)
 
         self._run_sinus_action = QAction(QIcon(":/icons/record.png"), "Sinus", self)
@@ -211,18 +220,60 @@ class PyRelacs(QMainWindow):
         daq_toolbar.addAction(self._record)
         self.addToolBar(Qt.ToolBarArea.TopToolBarArea, daq_toolbar)
 
-        repro_toolbar = QToolBar("Repros")
+    def create_repros_tabs(self):
         repro_names, file_names = self.repros.names_of_repros(
             include_repros=self.config.settings.repros
         )
+        nix_blocks = {
+            rep: self.nix_file.create_block(f"{rep}", "Data Repro")
+            for rep in repro_names
+        }
+        figures_repros = {rep: pg.GraphicsLayoutWidget() for rep in repro_names}
         for rep, fn in zip(repro_names, file_names):
-            repro_action = QAction(rep, self)
+            tab = QWidget()
-            repro_action.setStatusTip(rep)
+            tab_layout = QGridLayout()
-            repro_action.triggered.connect(
+
-                lambda checked, n=rep, f=fn: self.run_repro(n, f)
+            run_repro_button = QPushButton(f"Run {rep}")
+            run_repro_button.setCheckable(True)
+            run_repro_button.clicked.connect(
+                lambda checked, n=rep, f=fn: self.run_repro(
+                    n,
+                    f,
+                    nix_blocks,
+                    figures_repros,
+                    self.mccdaq,
+                    self.config,
+                )
             )
-            repro_toolbar.addAction(repro_action)
+            tab_layout.addWidget(run_repro_button, 0, 0, 1, 0)
-        self.addToolBar(Qt.ToolBarArea.BottomToolBarArea, repro_toolbar)
+            tab_layout.addWidget(figures_repros[rep], 1, 0, 1, 1)
+            tab.setLayout(tab_layout)
+            self.repro_tabs.addTab(tab, f"{rep}")
+
+    def run_repro(
+        self,
+        name_of_repro: str,
+        file_of_repro: str,
+        nix_block,
+        figures,
+        *args,
+    ):
+        self.text.appendPlainText(f"started Repro {name_of_repro}, {file_of_repro}")
+        nix_block_repro = nix_block[name_of_repro]
+        figure_repro = figures[name_of_repro]
+        worker = Worker(
+            self.repros.run_repro,
+            name_of_repro,
+            file_of_repro,
+            nix_block_repro,
+            figure_repro,
+            *args[-2:],
+        )
+        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 create_nix_file(self, file_path, metadata):
         self.nix_file = nixio.File.open(
@@ -311,17 +362,6 @@ class PyRelacs(QMainWindow):
         if hasattr(PyRelacs, "daq_device"):
             log.debug("Stopping DAQ")
             self.daq_producer.stop_aquisition()
-        embed()
-        exit()
-
-    def run_repro(self, n, fn):
-        self.text.appendPlainText(f"started Repro {n}, {fn}")
-        worker = Worker(self.repros.run_repro, self.nix_calibration, 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)
@@ -330,7 +370,7 @@ class PyRelacs(QMainWindow):
         log.info("exit button!")
         self.stop_recording()
         self.add_to_textfield("exiting")
-        if self.config.settings.daq:
+        if self.mccdaq:
             self.mccdaq.disconnect_daq()
         log.info("closing GUI")
         self.close()

pyrelacs/ui/plots/continously.py

@@ -16,6 +16,7 @@ class Continously:
         self.figure = figure
         self.buffer = buffer
         self.last_plotted_index = 0
+        self.timer = QTimer()
 
     def plot(self, *args, **kwargs):
         self.figure.setBackground("w")
@@ -36,7 +37,6 @@ class Continously:
         )
 
         # self.plot_index = 0
-        self.timer = QTimer()
         self.CHUNK_PLOT = int(self.buffer.samplerate / 6)
         self.PLOT_HISTORY = 500_000  # The amount of data you want to keep on screen
         self.timer.setInterval(150)
@@ -70,18 +70,19 @@ class Continously:
 
     def stop_plotting(self):
         self.timer.stop()
-        total_count = self.buffer.totalcount()
+        if self.last_plotted_index > 0:
-        times, items = self.buffer.read(
+            total_count = self.buffer.totalcount()
-            self.last_plotted_index,
+            times, items = self.buffer.read(
-            extend=total_count - self.last_plotted_index,
+                self.last_plotted_index,
-        )
+                extend=total_count - self.last_plotted_index,
-        self.time = np.concatenate((self.time, times))[-self.PLOT_HISTORY :]
+            )
-        self.data = np.concatenate((self.data, items))[-self.PLOT_HISTORY :]
+            self.time = np.concatenate((self.time, times))[-self.PLOT_HISTORY :]
-        self.line.setData(
+            self.data = np.concatenate((self.data, items))[-self.PLOT_HISTORY :]
-            self.time,
+            self.line.setData(
-            self.data,
+                self.time,
-        )
+                self.data,
-        self.last_plotted_index += total_count - self.last_plotted_index
+            )
+            self.last_plotted_index += total_count - self.last_plotted_index
 
     def refresh(self):
         self.continous_ax.enableAutoRange()