Merge pull request #5 from hoodlabpurdue/make-more-streamlined

Speed up rendering

src/qudi/gui/data_analysis/data_analysis_gui.py

@@ -0,0 +1,187 @@
+# -*- coding: utf-8 -*-
+__all__ = ['DataAnalysisGui']
+
+import os
+import numpy as np
+from PySide2 import QtCore, QtWidgets, QtGui
+import pyqtgraph as pg
+from qudi.core.module import GuiBase
+from qudi.core.connector import Connector
+from qudi.core.configoption import ConfigOption
+from qudi.util.paths import get_artwork_dir
+
+class DataAnalysisMainWindow(QtWidgets.QMainWindow):
+    """ Main window for the Data Analysis GUI """
+    def __init__(self, data_color, fit_color, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.setWindowTitle('Data Analysis')
+        self.resize(1250, 500)
+
+        # Menu bar
+        menu_bar = QtWidgets.QMenuBar()
+        file_menu = menu_bar.addMenu('File')
+        self.action_load_data = QtWidgets.QAction('Load Data', self)
+        path = os.path.join(get_artwork_dir(), 'icons', 'document-open')
+        self.action_load_data.setIcon(QtGui.QIcon(path))
+        file_menu.addAction(self.action_load_data)
+        self.action_copy_plot = QtWidgets.QAction('Copy Plot to Clipboard', self)
+        path = os.path.join(get_artwork_dir(), 'icons', 'edit-copy')
+        self.action_copy_plot.setIcon(QtGui.QIcon(path))
+        file_menu.addAction(self.action_copy_plot)
+        self.setMenuBar(menu_bar)
+
+        # Plot widget
+        self.plot_widget = pg.PlotWidget()
+        self.plot_widget.setLabel('bottom', 'Wavelength / Frequency')
+        self.plot_widget.setLabel('left', 'Counts')
+        self.data_item = pg.PlotDataItem(pen=pg.mkPen(data_color))
+        self.plot_widget.addItem(self.data_item)
+
+        # Control panel
+        self.load_button = QtWidgets.QPushButton('Load Most Recent Data')
+        self.home_button = QtWidgets.QPushButton('Home Plot')
+        self.window_size_spin = QtWidgets.QSpinBox()
+        self.window_size_spin.setRange(1, 100)
+        self.window_size_spin.setValue(5)
+        self.height_spin = QtWidgets.QDoubleSpinBox()
+        self.height_spin.setRange(0, 10000)
+        self.height_spin.setValue(4)
+        self.distance_spin = QtWidgets.QDoubleSpinBox()
+        self.distance_spin.setRange(0, 100)
+        self.distance_spin.setValue(1)
+        self.prominence_spin = QtWidgets.QDoubleSpinBox()
+        self.prominence_spin.setRange(0, 10000)
+        self.prominence_spin.setValue(0.3)
+        self.unit_combo = QtWidgets.QComboBox()
+        self.unit_combo.addItems(['um', 'nm', 'THz', 'GHz', 'MHz'])
+        self.fit_button = QtWidgets.QPushButton('Fit Peaks')
+
+        # Layout
+        control_layout = QtWidgets.QFormLayout()
+        control_layout.addRow('Running Avg Window:', self.window_size_spin)
+        control_layout.addRow('Min Peak Height:', self.height_spin)
+        control_layout.addRow('Min Distance (GHz):', self.distance_spin)
+        control_layout.addRow('Min Prominence:', self.prominence_spin)
+        control_layout.addRow('X-Axis Unit:', self.unit_combo)
+        control_layout.addWidget(self.fit_button)
+        control_layout.addWidget(self.load_button)
+        control_layout.addWidget(self.home_button)  # New Home Plot button
+
+        main_layout = QtWidgets.QHBoxLayout()
+        main_layout.addWidget(self.plot_widget)
+        main_layout.addLayout(control_layout)
+
+        central_widget = QtWidgets.QWidget()
+        central_widget.setLayout(main_layout)
+        self.setCentralWidget(central_widget)
+
+        # Store fit color for use in update_plot
+        self.fit_color = fit_color
+
+class DataAnalysisGui(GuiBase):
+    """ Qudi GUI module for data analysis """
+    _data_analysis_logic = Connector(name='data_analysis_logic', interface='DataAnalysisLogic')
+    data_color = ConfigOption('data_color', default='#00CED1')
+    fit_color = ConfigOption('fit_color', default='#FF6F61')
+    data_dir = ConfigOption('data_dir', default='C:\\Users\\hoodl\\qudi\\Data')  # Default data directory
+
+    def on_activate(self):
+        self._mw = DataAnalysisMainWindow(data_color=self.data_color, fit_color=self.fit_color)
+        self._mw.action_load_data.triggered.connect(self.load_data)
+        self._mw.action_copy_plot.triggered.connect(self.copy_plot_to_clipboard)
+        self._mw.load_button.clicked.connect(self.load_most_recent_data)
+        self._mw.fit_button.clicked.connect(self.fit_peaks)
+        self._mw.home_button.clicked.connect(self.home_plot)  # Connect Home Plot button
+        self._mw.unit_combo.currentTextChanged.connect(self.update_plot_units)
+        self._data_analysis_logic().sigPlotUpdated.connect(self.update_plot)
+        # Initialize current file location as empty
+        self.current_file_path = ""
+        self.show()
+
+    def on_deactivate(self):
+        self._mw.close()
+
+    def show(self):
+        self._mw.show()
+
+    @QtCore.Slot()
+    def load_data(self):
+        file_path, _ = QtWidgets.QFileDialog.getOpenFileName(self._mw, 'Load Data', self.data_dir, 'Data files (*.dat)')
+        if file_path:
+            self.current_file_path = file_path
+            self._data_analysis_logic().load_data(file_path)
+            # Immediately update the plot title to show the data location.
+            self._mw.plot_widget.setTitle(file_path)
+
+    @QtCore.Slot()
+    def load_most_recent_data(self):
+        # For most recent data, if the logic module does not return the location,
+        # we use a default string.
+        self.current_file_path = self._data_analysis_logic()._get_most_recent_data_file()
+        self._data_analysis_logic().load_most_recent_data()
+
+    @QtCore.Slot()
+    def fit_peaks(self):
+        params = {
+            'window_size': self._mw.window_size_spin.value(),
+            'height': self._mw.height_spin.value(),
+            'distance': self._mw.distance_spin.value(),
+            'prominence': self._mw.prominence_spin.value(),
+            'unit': self._mw.unit_combo.currentText()
+        }
+        self._data_analysis_logic().analyze_data(params)
+
+    @QtCore.Slot(str)
+    def update_plot_units(self, unit):
+        if self._data_analysis_logic()._data is not None:
+            params = {
+                'window_size': self._mw.window_size_spin.value(),
+                'height': self._mw.height_spin.value(),
+                'distance': self._mw.distance_spin.value(),
+                'prominence': self._mw.prominence_spin.value(),
+                'unit': unit
+            }
+            self._data_analysis_logic().analyze_data(params)
+
+    @QtCore.Slot(object)
+    def update_plot(self, plot_data):
+        x_data, y_data, fits = plot_data
+        self._mw.plot_widget.setLabel('bottom', f'Wavelength / Frequency ({self._mw.unit_combo.currentText()})')
+        self._mw.data_item.setData(x=x_data, y=y_data)
+        # Clear previous fits
+        for item in self._mw.plot_widget.listDataItems():
+            if item != self._mw.data_item:
+                self._mw.plot_widget.removeItem(item)
+        for text in self._mw.plot_widget.items():
+            if isinstance(text, pg.TextItem):
+                self._mw.plot_widget.removeItem(text)
+        # Add new fits
+        for fit in fits:
+            fit_item = pg.PlotDataItem(x=fit['x_fit'], y=fit['y_fit'], pen=pg.mkPen(self._mw.fit_color))
+            self._mw.plot_widget.addItem(fit_item)
+            # Add FWHM annotation
+            text = pg.TextItem(text=f"{np.abs(fit['fwhm_mhz']):.1f} MHz", anchor=(0.5, 1))
+            self._mw.plot_widget.addItem(text)
+            text.setPos(fit['center'], fit['amplitude'] + fit['offset'])
+        # Auto-home the plot after new data is loaded
+        self.home_plot()
+        # Update the title with the current file location.
+        self._mw.plot_widget.setTitle(self.current_file_path)
+
+    @QtCore.Slot()
+    def home_plot(self):
+        # Get the current data from the plot data item.
+        x_data, y_data = self._mw.data_item.getData()
+        if x_data is None or y_data is None or len(x_data) == 0:
+            return
+        xmin, xmax = np.min(x_data), np.max(x_data)
+        ymin, ymax = np.min(y_data), np.max(y_data)
+        # Set x range to exactly span the data.
+        self._mw.plot_widget.setXRange(xmin, xmax)
+        # Set y range from y min to y max scaled by 1.1.
+        self._mw.plot_widget.setYRange(ymin, ymax * 1.1)
+
+    @QtCore.Slot()
+    def copy_plot_to_clipboard(self):
+        pixmap = self._mw.plot_widget.grab()
+        QtWidgets.QApplication.clipboard().setPixmap(pixmap)

src/qudi/gui/terascan/terascan_gui.py

@@ -10,6 +10,7 @@
 from qudi.util.datastorage import TextDataStorage
 from qudi.core.module import GuiBase
 from qudi.core.connector import Connector
+from qudi.core.configoption import ConfigOption
 from qudi.core.statusvariable import StatusVar
 from qudi.gui.terascan.terascan_main_window import TerascanMainWindow
 from qudi.util.paths import get_artwork_dir
@@ -35,6 +36,7 @@ class TerascanGui(GuiBase):
 
     # Connector to the logic module
     _terascan_logic = Connector(name='terascan_logic', interface='TerascanLogic')
+    save_dir = ConfigOption('save_dir', default='C:\\Users\\hoodl\\qudi\\Data')
 
     # Status variables saved in the AppStatus:
     _start_wavelength = StatusVar(name='start_wavelength', default=0.775)
@@ -186,7 +188,7 @@ def _wavelength_changed(self, wave: float) -> None:
     @QtCore.Slot()
     def _save_data(self) -> None:
         ds = TextDataStorage(
-            root_dir=self.module_default_data_dir,
+            root_dir=self.save_dir,  # Use the configurable save directory
             column_formats='.15e'
         )
         array = np.array([(d.wavelength, d.counts) for d in self._data])

src/qudi/gui/terascan/terascan_main_window.py

@@ -4,6 +4,7 @@
 import os
 from PySide2 import QtGui, QtCore, QtWidgets
 import pyqtgraph as pg
+pg.setConfigOption('useOpenGL', True)  # Add this at the top of your file
 
 from qudi.util.widgets.plotting.image_widget import ImageWidget
 from qudi.util.paths import get_artwork_dir
@@ -16,6 +17,7 @@ class TerascanMainWindow(QtWidgets.QMainWindow):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.setWindowTitle('Terascan Measurement')
+        self.resize(1250, 500)
 
         # Create menu bar
         menu_bar = QtWidgets.QMenuBar()
@@ -68,6 +70,7 @@ def __init__(self, *args, **kwargs):
         self.scan_type = QtWidgets.QComboBox()
 
         self.plot_widget = pg.PlotWidget()
+        self.plot_widget.setAntialiasing(False)
         self.plot_widget.getPlotItem().setContentsMargins(1, 1, 1, 1)
         self.plot_widget.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
                                        QtWidgets.QSizePolicy.Expanding)
@@ -76,15 +79,14 @@ def __init__(self, *args, **kwargs):
         self.plot_widget.setLabel('left', text='Counts')
 
         self.data_item = pg.PlotDataItem(
-            pen=pg.mkPen(palette.c1, style=QtCore.Qt.DotLine),
-            symbol='o',
-            symbolPen=palette.c1,
-            symbolBrush=palette.c1,
-            symbolSize=7
+            pen=pg.mkPen(palette.c1, style=QtCore.Qt.SolidLine),
+            # downsampling if you want
+            # downsample=10,  # Render 1 out of every 10 points
+            # downsampleMethod='mean'  # Average points for smoother results
         )
         self.plot_widget.addItem(self.data_item)
 
-        # New Running Average controls
+        # Running Average controls
         self.checkbox_running_avg = QtWidgets.QCheckBox("Enable Running Average")
         self.checkbox_running_avg.setChecked(False)
         self.label_avg_points = QtWidgets.QLabel("Points in Rolling Average:")

src/qudi/logic/data_analysis_logic/data_analysis_logic.py

@@ -0,0 +1,139 @@
+# -*- coding: utf-8 -*-
+__all__ = ['DataAnalysisLogic']
+
+import os
+import glob
+import numpy as np
+from scipy.signal import find_peaks
+from scipy.optimize import curve_fit
+from qudi.core.module import LogicBase
+from qudi.core.configoption import ConfigOption
+from qudi.util.mutex import RecursiveMutex
+from PySide2 import QtCore
+
+class DataAnalysisLogic(LogicBase):
+    """ Logic module for data analysis """
+    sigPlotUpdated = QtCore.Signal(object)
+
+    _base_path = ConfigOption('base_path', default=os.getcwd())
+    _max_peaks_to_fit = ConfigOption('max_peaks_to_fit', default=10)
+    _maxfev = ConfigOption('maxfev', default=10000)
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self._thread_lock = RecursiveMutex()
+        self._data = None
+
+    def on_activate(self):
+        pass
+
+    def on_deactivate(self):
+        pass
+
+    def load_data(self, file_path):
+        with self._thread_lock:
+            self._data = self._load_data(file_path)
+            self.sigPlotUpdated.emit((self._data[:, 0], self._data[:, 1], []))
+
+    def load_most_recent_data(self):
+        with self._thread_lock:
+            file_path = self._get_most_recent_data_file()
+            if file_path:
+                self._data = self._load_data(file_path)
+                self.sigPlotUpdated.emit((self._data[:, 0], self._data[:, 1], []))
+
+        return file_path
+
+    def analyze_data(self, params):
+        with self._thread_lock:
+            if self._data is None:
+                return
+            x_nm = self._data[:, 0]
+            y_counts = self._data[:, 1]
+            y_smooth = self._running_average(y_counts, params['window_size'])
+            peaks, _ = find_peaks(y_smooth, height=params['height'], distance=self._distance_to_points(x_nm, params['distance']), prominence=params['prominence'])
+            fits = self._fit_peaks(x_nm, y_smooth, peaks)
+            x_plot = self._convert_units(x_nm, params['unit'])
+            fit_x_converted = [dict(fit, x_fit=self._convert_units(fit['x_fit'], params['unit']), center=self._convert_units(np.array([fit['center']]), params['unit'])[0]) for fit in fits]
+            self.sigPlotUpdated.emit((x_plot, y_smooth, fit_x_converted))
+
+    def _load_data(self, file_path):
+        with open(file_path, 'r') as f:
+            lines = [line for line in f if not line.startswith('#') and line.strip()]
+        data = np.array([list(map(float, line.split())) for line in lines])
+        return data
+
+    def _get_most_recent_data_file(self):
+        search_path = os.path.join(self._base_path, '**', '*.dat')
+        files = glob.glob(search_path, recursive=True)
+        if not files:
+            return None
+        return max(files, key=os.path.getmtime)
+
+    def _running_average(self, y, window_size):
+        return np.convolve(y, np.ones(window_size)/window_size, mode='same')
+
+    def _distance_to_points(self, x_nm, distance_ghz):
+        dx_nm = np.mean(np.diff(x_nm))
+        x_ref = np.median(x_nm)
+        separation_nm = distance_ghz / (2.99792458e17 / (x_ref**2 * 1e9))
+        return max(1, int(round(separation_nm / dx_nm)))
+
+    def _lorentzian(self, x, amplitude, center, gamma, offset):
+        return offset + amplitude * (gamma**2) / ((x - center)**2 + gamma**2)
+
+    def _fit_peaks(self, x_nm, y_smooth, peaks):
+        fits = []
+        fit_width_nm = 0.01
+        for pk in peaks[:self._max_peaks_to_fit]:
+            pk_x = x_nm[pk]
+            left = np.searchsorted(x_nm, pk_x - fit_width_nm)
+            right = np.searchsorted(x_nm, pk_x + fit_width_nm)
+
+            # Skip if the slice is empty or too small
+            if right - left < 3:
+                continue
+
+            x_slice = x_nm[left:right]
+            y_slice = y_smooth[left:right]
+
+            # Now it's safe to call y_slice.max(), etc.
+            p0 = [
+                y_slice.max() - y_slice.min(),
+                pk_x,
+                0.001,
+                y_slice.min()
+            ]
+
+            try:
+                popt, _ = curve_fit(self._lorentzian, x_slice, y_slice, p0=p0, maxfev=self._maxfev)
+                fits.append({
+                    'x_fit': x_slice,
+                    'y_fit': self._lorentzian(x_slice, *popt),
+                    'center': popt[1],
+                    'amplitude': popt[0],
+                    'offset': popt[3],
+                    'fwhm_mhz': self._fwhm_nm_to_mhz(popt[1], 2 * popt[2])
+                })
+            except Exception as exc:
+                # If the fit fails, just skip it
+                self.log.warning(f'Peak fit failed: {exc}')
+                pass
+
+        return fits
+
+    def _fwhm_nm_to_mhz(self, center_nm, fwhm_nm):
+        return (2.99792458e17 / (center_nm**2)) * fwhm_nm / 1e6
+
+    def _convert_units(self, x_nm, unit):
+        if unit == 'nm':
+            return x_nm
+        elif unit == 'um':
+            return x_nm / 1000
+        elif unit == 'GHz':
+            return 2.99792458e17 / (x_nm * 1e9)
+        elif unit == 'THz':
+            return 2.99792458e17 / (x_nm * 1e12)
+        elif unit == 'MHz':
+            return 2.99792458e17 / (x_nm * 1e6)
+        return x_nm