temp update (currently has issues)

app.py

@@ -9,7 +9,6 @@ import pathlib
 
 class AppWindow(QtWidgets.QMainWindow, Ui_MainWindow):
 
-    csv_selected = QtCore.pyqtSignal()
     correlation_complete = QtCore.pyqtSignal()
     fitting_complete = QtCore.pyqtSignal()
 
@@ -17,14 +16,6 @@ class AppWindow(QtWidgets.QMainWindow, Ui_MainWindow):
         super(AppWindow, self).__init__()
         self.setupUi(self)
 
-        # Graphing actions
-
-        self.csv_selected.connect(self.raw_data_graph.plot)
-        def corr_act():
-            self.groups_graph.plot()
-            self.graph_tabs.setCurrentIndex(1)
-        self.correlation_complete.connect(corr_act)
-
         # Helpers
 
         def display_warning(message: str):
@@ -52,15 +43,24 @@ class AppWindow(QtWidgets.QMainWindow, Ui_MainWindow):
                 return
             mem['x_data'] = data.transpose()[0]
             mem['y_data'] = data.transpose()[1]
+            mem['timestep'] = mem['x_data'][1] - mem['x_data'][0]
+            self.raw_data_graph.plot() # Graph new stuff
+
+            # self.groups_graph.clear() # Clear old stuff
+            self.voltage_graph.clear()
+            self.added_peaks_graph.clear()
+            # self.tau_graph.clear()
+
+            mem['ymin'], mem['ymax'] = crds_calc.minmax(mem['y_data'])
+
             try:
                 mem['v_data'] = data.transpose()[2]
+                self.voltage_graph.plot()
+                self.graph_tabs.setCurrentIndex(1)
             except IndexError:
                 display_warning('No voltage column detected. VThreshold algo will not work.')
-
+                self.voltage.setVisible(False)
-            self.groups_graph.clear()
+                self.graph_tabs.setCurrentIndex(0)
-            self.tau_graph.clear()
-            self.graph_tabs.setCurrentIndex(0)
-            self.csv_selected.emit()
 
 
         # Universal Actions stuff
@@ -68,6 +68,11 @@ class AppWindow(QtWidgets.QMainWindow, Ui_MainWindow):
         self.actionOpen_CSV_File.triggered.connect(select_csv)
         self.actionGithub_Repository.triggered.connect(lambda: QtGui.QDesktopServices.openUrl(QtCore.QUrl('https://github.com/turtlebasket/crds_analyze')))
 
+        # NOTE: Do later, use QDialog
+        # def check_if_quit():
+        #   <stuff here>
+        self.actionQuit_2.triggered.connect(sys.exit)
+
         # Inputs
 
         def switch_grouping_algo():
@@ -86,40 +91,121 @@ class AppWindow(QtWidgets.QMainWindow, Ui_MainWindow):
             if self.check_custom_end.isChecked():
                 self.spin_end_time.setDisabled(False)
             else:
-                # mem['end_time'] = self.spin_end_time.value()
                 self.spin_end_time.setDisabled(True)
         self.check_custom_end.stateChanged.connect(set_end_time)
 
+        # Sync up peak detection settings between input locations
+        self.spin_min_peakheight.valueChanged.connect(lambda x: self.spin_min_peakheight_2.setValue(x))
+        self.spin_min_peakheight_2.valueChanged.connect(lambda x: self.spin_min_peakheight.setValue(x))
+        self.spin_min_peakprominence.valueChanged.connect(lambda x: self.spin_min_peakprominence_2.setValue(x))
+        self.spin_min_peakprominence_2.valueChanged.connect(lambda x: self.spin_min_peakprominence.setValue(x))
+        self.spin_moving_average_denom.valueChanged.connect(lambda x: self.spin_moving_average_denom_2.setValue(x))
+        self.spin_moving_average_denom_2.valueChanged.connect(lambda x: self.spin_moving_average_denom.setValue(x))
+        
+        # Make advanced peak detection optional
+        def update_advanced_peak_detection_setting():
+            enabled = self.check_advanced_peak_detection.isChecked()
+            self.spin_min_peakheight_2.setEnabled(enabled)
+            self.spin_min_peakprominence_2.setEnabled(enabled)
+            self.spin_moving_average_denom_2.setEnabled(enabled)
+        self.check_advanced_peak_detection.stateChanged.connect(update_advanced_peak_detection_setting)
+
+
         def init_correlate():
             groups_raw = None
             algo = self.combo_grouping_algo.currentIndex()
             try:
                 if algo == 0:
-                    display_error('VThreshold not yet implemented.')
+                    groups_raw = crds_calc.vthreshold(
-                    return
+                        mem['x_data'],
+                        mem['y_data'],
+                        mem['v_data'],
+                        self.spin_min_voltage.value(),
+                        self.spin_max_voltage.value(),
+                        mirrored=False if self.check_skip_groups.checkState() == 0 else True,
+                        start=self.spin_start_time.value() if self.check_custom_start.isChecked() else None,
+                        end=self.spin_end_time.value() if self.check_custom_end.isChecked() else None
+                    )
+                    # display_error('VThreshold not yet implemented.')
+                    # return
+
                 elif algo == 1:
-                    try:
+                    groups_raw = crds_calc.spaced_groups(
-                        groups_raw = crds_calc.spaced_groups(
+                        mem['x_data'],
-                            mem['x_data'],
+                        mem['y_data'],
-                            mem['y_data'],
+                        self.spin_group_len.value(),
-                            self.spin_group_len.value(),
+                        self.spin_min_peakheight.value(),
-                            self.spin_min_peakheight.value(),
+                        self.spin_min_peakprominence.value(),
-                            self.spin_min_peakprominence.value(),
+                        self.spin_moving_average_denom.value(),
-                            self.spin_moving_average_denom.value(),
+                        mirrored=False if self.check_skip_groups.checkState() == 0 else True,
-                            mirrored=False if self.check_skip_groups.checkState() == 0 else True,
+                        start=self.spin_start_time.value() if self.check_custom_start.isChecked() else None,
-                            start=self.spin_start_time.value() if self.check_custom_start.isChecked() else None,
+                        end=self.spin_end_time.value() if self.check_custom_end.isChecked() else None
-                            end=self.spin_end_time.value() if self.check_custom_end.isChecked() else None
+                    )
-                        )
+
-                    except (ValueError, TypeError):
+                if groups_raw == None or len(groups_raw) < 1:
-                        display_error('Failed to correlate. This could be because no groups are being detected.')
+                    display_error("No groups were detected. Try adjusting grouping parameters.")
 
                 mem['groups_correlated'] = crds_calc.correlate_groups(groups_raw)
-                self.correlation_complete.emit()
+
+                # Graphing action
+                self.groups_graph.plot()
+                self.graph_tabs.setCurrentIndex(2)
 
             except KeyError:
                 display_error('Failed to correlate. Did you import a data file & set parameters?')
         self.correlate_button.pressed.connect(init_correlate)
 
+        def init_add_simple():
+            try:
+                mem['added_peaks'] = crds_calc.add_peaks_only(mem['groups_correlated'])
+
+                self.added_peaks_graph.set_params(None, shift_over=None)
+                self.added_peaks_graph.plot()
+                self.graph_tabs.setCurrentIndex(3)
+
+            except KeyError:
+                display_error("Correlated groups not found. Group peaks first.")
+        self.peak_add_button.pressed.connect(init_add_simple)
+            
+
+        def init_add():
+            try:
+                mem['added_peaks'], mem['peak_indices'], mem['isolated_peaks'] = crds_calc.isolate_peaks(
+                    mem['groups_correlated'],
+                    self.spin_peak_overlap.value(),
+                    self.spin_moving_average_denom.value(),
+                    peak_prominence=self.spin_min_peak_height_added.value(),
+                    peak_minheight=self.spin_peak_prominence_added.value(),
+                    shift_over=self.spin_shift_over.value()
+                )
+                self.added_peaks_graph.set_params(self.spin_peak_overlap.value(), shift_over=self.spin_shift_over.value())
+                self.added_peaks_graph.plot()
+                self.graph_tabs.setCurrentIndex(3)
+
+            except KeyError:
+                display_error("Correlated groups not found. Group peaks first.")
+        self.isolate_button.pressed.connect(init_add)
+
+        def init_fit():
+            if not 'isolated_peaks' in mem:
+                display_error('Peaks not yet isolated.')
+                return
+            mem['fit_equations'] = crds_calc.fit_peaks(
+                mem['isolated_peaks'],
+                mem['peak_indices'],
+                self.spin_min_peakheight_2.value(),
+                self.spin_min_peakprominence_2.value(),
+                self.spin_moving_average_denom_2.value(),
+                self.spin_var_a.value(),
+                self.spin_var_tau.value(),
+                self.spin_var_y0.value(),
+                self.spin_shift_over_fit.value(),
+                self.check_advanced_peak_detection.isChecked()
+            )
+            # print(mem['fit_equations'])
+            self.peak_fits_graph.plot()
+        self.fit_button.pressed.connect(init_fit)
+
         # Show equation
 
         pix = QtGui.QPixmap(f"{pathlib.Path(__file__).parent.resolve()}/assets/eq3.png")

build.cmd

@@ -3,13 +3,26 @@
 set compileUI=0
 set build=0
 
+IF "%~1" == "" (
+	echo --------------
+	echo  BUILD SCRIPT 
+	echo --------------
+	echo -compileUI	Generate main window class from .UI file
+	echo -build		Build standalone desktop app with embedded python runtime
+	exit
+)
+
 FOR %%A IN (%*) DO (
     IF "%%A"=="-compileUI" set compileUI=1
     IF "%%A"=="-build" set build=1
 )
 
-if %compileUI%==1 pyuic5.exe -x .\ui\mainwin.ui -o mainwin.py
+if %compileUI%==1 (
+	pyuic5.exe -x .\ui\mainwin.ui -o mainwin.py
+	if %ERRORLEVEL% EQU 0 echo Generated mainwin.py.
+	if %ERRORLEVEL% EQU 1 echo Generation failed. 
+)
 
 if %build%==1 pyinstaller --onefile --windowed --icon=favicon.ico app.py 
 
-exit
+exit

crds_calc.py

@@ -1,7 +1,14 @@
 import numpy as np
 from scipy.signal import find_peaks, correlate
+from scipy.optimize import curve_fit
 from memdb import mem
 
+def minmax(data):
+    return np.min(data), np.max(data)
+
+def exp_func(x, x0, a, y0, tau): # NOTE: X is not something we pass in 🤦‍♂️
+    return y0 + a*np.exp(-(x-x0)/tau)
+
 def spaced_groups(
     x_data: np.array,
     y_data: np.array,
@@ -16,7 +23,9 @@ def spaced_groups(
     """
     Use SpacedGroups algo to separate groups
 
-    Returns 2D array of raw data; every other group
+    Returns
+    -------
+    2D array of raw data; every other group
     """
 
     # Helpers
@@ -107,11 +116,44 @@ def spaced_groups(
     return groups_raw
 
 
+def vthreshold(
+    x_data: np.array,
+    y_data: np.array,
+    v_data: np.array,
+    vmin: float,
+    vmax: float,
+    mirrored: bool=True,
+    start=None,
+    end=None
+):
+    """
+    Voltage-threshold grouping algorithm
+
+    Returns
+    -------
+    A `list` of all peak groups
+    """
+
+    # Helpers
+    def t2i(t):
+        delta_t = abs(x_data[0] - t)
+        timestep = abs(x_data[1] - x_data[0])
+        return int(delta_t / timestep)
+
+    def t2i_range(t):
+        timestep = abs(x_data[1] - x_data[0])
+        return int(t / timestep)
+
+    groups_raw = []
+    return groups_raw
+
 def correlate_groups(groups_raw):
     """
     Overlay groups using `scipy.correlate`.
 
-    Returns 2D array of overlayed groups
+    Returns
+    -------
+    2D array of overlayed groups
     """
 
     # Compare groups (scipy correlate)
@@ -135,19 +177,121 @@ def correlate_groups(groups_raw):
 
     return groups_adjusted
 
+def add_peaks_only(groups_adjusted: list):
+
+    def unequal_add_truncation(a,b): # Instead of padding with 0, truncate
+        if len(a) < len(b):
+            c = b.copy()
+            c = c[:len(a)]
+            c += a
+        else:
+            c = a.copy()
+            c = c[:len(b)]
+            c += b
+        return(c)
+
+    added_peaks = np.array(groups_adjusted[0])
+
+    for g in groups_adjusted[1:]:
+        g1 = np.array(g)
+        g0 = added_peaks
+        added_peaks = unequal_add_truncation(g0, g1)
+
+    return added_peaks
+
 def isolate_peaks(
+    groups_adjusted: list,
     peak_width: int, 
-    groups_adjusted: list, 
+    sma_denom: int,
-    peak_minheight: int,
+    peak_minheight: int = None,
-    peak_prominence: int,
+    peak_prominence: int = None,
-    sma_denom: int
+    shift_over: int = 0
 ):
 
+    def unequal_add(a,b): # NOTE: See https://www.delftstack.com/howto/numpy/vector-addition-in-numpy/
+        if len(a) < len(b):
+            c = b.copy()
+            c[:len(a)] += a
+        else:
+            c = a.copy()
+            c[:len(b)] += b
+        return(c)
+
+    def unequal_add_truncation(a,b): # Instead of padding with 0, truncate
+        if len(a) < len(b):
+            c = b.copy()
+            c = c[:len(a)]
+            c += a
+        else:
+            c = a.copy()
+            c = c[:len(b)]
+            c += b
+        return(c)
+
     def moving_average(x, w):
         return np.convolve(x, np.ones(w), 'valid') / w
 
-    group_peaks = []
+    added_peaks = np.array(groups_adjusted[0])
+
+    for g in groups_adjusted[1:]:
+        g1 = np.array(g)
+        g0 = added_peaks
+        added_peaks = unequal_add_truncation(g0, g1)
+
+    added_peaks_av = moving_average(added_peaks, sma_denom)
+    peak_indices = find_peaks(added_peaks_av, height=peak_minheight, prominence=peak_prominence, distance=peak_width/2)[0] # Get indices of all peaks
+
+    isolated_peaks = []
+    delta = peak_width/2
+
     for g in groups_adjusted:
-        y_data_av = moving_average(g, sma_denom)
+        peaks_cut = []
-        peak_indices = find_peaks(y_data_av, height=peak_minheight, prominence=peak_prominence) # Get indices of all peaks
+        for i in peak_indices:
-        group_peaks.append(peak_indices)
+            peak = g[int(i-delta+shift_over):int(i+delta+shift_over)]
+            peaks_cut.append(peak)
+        isolated_peaks.append(peaks_cut)
+
+    return added_peaks, peak_indices, isolated_peaks
+
+
+def fit_peaks(
+    isolated_peaks: list,
+    peak_indices: list,
+    min_peak_height: float,
+    min_peak_prominence: float,
+    moving_avg_size: int,
+    a: float,
+    tau: float,
+    y0: float,
+    shift_over: int,
+    use_advanced: bool
+):
+    
+    print(f'{use_advanced=}')
+
+    """
+    Returns
+    -------
+    Peak fit equations. Linked to `mem['isolated_peaks']`.
+    """
+
+    params_guess = (0.0000, a, y0, tau)
+    equations = []
+    for peaks_cut in isolated_peaks:
+        row = []
+        for peak_data in peaks_cut:
+            x_data = np.arange(len(peak_data)) # just placeholder indices
+            if not use_advanced:
+                peak_index = np.argmax(peak_data, axis=0)
+            else:
+                peak_index = find_peaks(peak_data, height=min_peak_height, prominence=min_peak_prominence)[0][0]
+            # print(peak_index)
+            params_guess = (peak_index+shift_over, a, y0, tau)
+            x_data_target = x_data[peak_index+shift_over:]
+            peak_data_target = peak_data[peak_index+shift_over:]
+            # popt, pcov = curve_fit(exp_func, x_data_target, peak_data_target, bounds=([-np.inf, 0.0, -np.inf, 0.0], np.inf))
+            popt, pcov = curve_fit(exp_func, x_data_target, peak_data_target, bounds=([-np.inf, 0.0, -np.inf, 0.0], np.inf), p0=params_guess, maxfev=10000000)
+            row.append({'popt': popt, 'pcov': pcov})
+        equations.append(row)
+
+    return equations # list linked with isolated_peaks

memdb.py

@@ -1,4 +1,5 @@
 from sqlitedict import SqliteDict
+from varname.core import nameof
 
 class ModSqliteDict(SqliteDict):
     def __init__(self):
@@ -7,4 +8,8 @@ class ModSqliteDict(SqliteDict):
         self.filename = ':memory:'
         super().__init__()
 
+    def set_key(self, item):
+        name = nameof(item)
+        self[name] = item
+
 mem = ModSqliteDict()

requirements.txt

@@ -3,3 +3,5 @@ pandas
 numpy
 pyinstaller==4.4
 sqlitedict
+scipy
+varname

widgets.py

@@ -1,17 +1,32 @@
+import numpy as np
 from PyQt5 import QtWidgets
 import matplotlib
 matplotlib.use('Qt5Agg')
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg, NavigationToolbar2QT as NavigationToolbar
 from matplotlib.figure import Figure
 from memdb import mem
+from crds_calc import exp_func
 
 class MplCanvas(FigureCanvasQTAgg):
     def __init__(self, parent=None, width=5, height=4, dpi=100):
         fig = Figure(figsize=(width, height), dpi=dpi)
         self.axes = fig.add_subplot(111)
         fig.tight_layout()
+        self.fig_width = width
+        self.fig_height = height
+        self.fig_dpi = dpi
         super(MplCanvas, self).__init__(fig)
 
+    def reset(self):
+        self.axes.remove()
+        self.axes = self.figure.add_subplot(111)
+        self.figure.tight_layout()
+        # fig = Figure(figsize=(self.fig_width, self.fig_height), dpi=self.fig_dpi)
+        # self.axes = fig.add_subplot(111)
+        # self.figure.clear()
+        # self.figure.axes.remove()
+        # fig.tight_layout()
+
 class BaseGraph(QtWidgets.QWidget):
     """
     Widget with embedded matplotlib graph & navigation toolbar
@@ -31,27 +46,87 @@ class BaseGraph(QtWidgets.QWidget):
         layout.addWidget(toolbar)
         layout.addWidget(self.canv)
         self.setLayout(layout)
-
+        
     def plot_data(self):
         self.canv.axes.plot(mem['x_data'], mem['y_data'])
 
     def plot(self):
-        self.canv.axes.clear()
+        try:
+            self.canv.axes.clear()
+        except AttributeError:
+            pass
         self.plot_data()
         self.canv.draw()
-        print("attempted plot")
 
     def clear(self):
         self.canv.axes.clear()
-        self.canv.draw()
 
 class RawDataGraph(BaseGraph):
     pass
 
+class VoltageGraph(BaseGraph):
+    def plot_data(self):
+        if not mem['v_data'][0] == None:
+            self.canv.axes.plot(mem['x_data'], mem['v_data'], color='orange')
+
 class PeaksGraph(BaseGraph):
     def plot_data(self):
         for i in mem['groups_correlated']:
             self.canv.axes.plot(i)
 
+class AddedPeaksGraph(BaseGraph):
+
+    params = {
+        'peak_width': None,
+        'shift_over': None
+    }
+
+    def set_params(self, peak_width, shift_over=0):
+        self.params['peak_width'] = peak_width
+        self.params['shift_over'] = shift_over
+
+    def plot_data(self):
+        self.canv.axes.plot(mem['added_peaks'], color='green') # plot added peaks
+
+        if not self.params['peak_width'] == None: # plot peak indices
+            for i in mem['peak_indices']: 
+                self.canv.axes.axvspan(int(i-self.params['peak_width']/2+self.params['shift_over']), int(i+self.params['peak_width']/2+self.params['shift_over']), color='red', alpha=0.4)
+
+class FitsGraph(BaseGraph):
+    
+    def __init__(self, x):
+        super(FitsGraph, self).__init__(x)
+        
+    def plot_data(self):
+        
+        for g_i in range(len(mem['isolated_peaks'])):
+            for p_i in range(len(mem['isolated_peaks'][g_i])):
+                peak = mem['isolated_peaks'][g_i][p_i]
+                x_data = np.arange(len(peak))
+                popt = mem['fit_equations'][g_i][p_i]['popt']
+                self.canv.axes.plot(peak)
+                self.canv.axes.plot(x_data, exp_func(x_data, *popt), color='red')
+    
+    # def plot_data(self):
+
+    #     try:
+    #         self.canv.axes.remove()
+    #     except AttributeError:
+    #         pass
+
+    #     subplots_stacked = len(mem['isolated_peaks'][0]) # should all be same length
+    #     axes = self.canv.figure.subplots(subplots_stacked, 1, sharex=True)
+        
+    #     for g_i in range(len(mem['isolated_peaks'])):
+    #         for p_i in range(subplots_stacked):
+    #             peak = mem['isolated_peaks'][g_i][p_i]
+    #             axes[p_i].plot(peak)
+    #             x_data = np.arange(len(peak))
+    #             popt = mem['fit_equations'][g_i][p_i]['popt']
+    #             axes[p_i].plot(x_data, exp_func(x_data, *popt), color='red')
+
+        # for ax in axs.flat:
+        #     ax.set(xlabel='x-label', ylabel='y-label')
+
 class TimeConstantGraph(BaseGraph):
-    pass # no modifications thus far
+    pass