fix fitting
factor in peak index + shift while graphing, only fit relevant data (peak & afterward), fix default A and Tau values to use tick scale, NOT timemaster
parent
d8b0b6d0fd
commit
04b549d106
2
app.py
2
app.py
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@ -94,6 +94,7 @@ class AppWindow(QtWidgets.QMainWindow, Ui_MainWindow):
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self.spin_end_time.setDisabled(True)
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self.check_custom_end.stateChanged.connect(set_end_time)
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# Sync up peak detection settings between input locations
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self.spin_min_peakheight.valueChanged.connect(lambda x: self.spin_min_peakheight_2.setValue(x))
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self.spin_min_peakheight_2.valueChanged.connect(lambda x: self.spin_min_peakheight.setValue(x))
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@ -202,6 +203,7 @@ class AppWindow(QtWidgets.QMainWindow, Ui_MainWindow):
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self.spin_shift_over_fit.value(),
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self.check_advanced_peak_detection.isChecked()
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)
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mem['shift_over_fit'] = self.spin_shift_over_fit.value()
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# print(mem['fit_equations'])
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self.peak_fit_viewer.plot()
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self.graph_tabs.setCurrentIndex(4)
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34
crds_calc.py
34
crds_calc.py
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@ -267,8 +267,6 @@ def fit_peaks(
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use_advanced: bool
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):
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print(f'{use_advanced=}')
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"""
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Returns
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-------
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@ -277,8 +275,10 @@ def fit_peaks(
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params_guess = (0.0000, a, y0, tau)
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equations = []
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overlayed_peak_indices = []
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for peaks_cut in isolated_peaks:
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row = []
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equation_row = []
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overlayed_peak_row = []
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for peak_data in peaks_cut:
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x_data = np.arange(len(peak_data)) # just placeholder indices
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if not use_advanced:
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@ -291,7 +291,31 @@ def fit_peaks(
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peak_data_target = peak_data[peak_index+shift_over:]
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# popt, pcov = curve_fit(exp_func, x_data_target, peak_data_target, bounds=([-np.inf, 0.0, -np.inf, 0.0], np.inf))
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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)
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row.append({'popt': popt, 'pcov': pcov})
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equations.append(row)
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equation_row.append({'popt': popt, 'pcov': pcov})
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overlayed_peak_row.append(peak_index)
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equations.append(equation_row)
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overlayed_peak_indices.append(overlayed_peak_row)
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mem['overlayed_peak_indices'] = overlayed_peak_indices
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return equations # list linked with isolated_peaks
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def get_tau_data(equation_data):
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"""
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Extracts time constant from all equations (2d array)
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Returns
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-------
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Tau data in same dimensions as `equation_data`
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"""
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tau_data = []
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for r in equation_data:
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row = []
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for e in r:
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tau = e['popt'][3]
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row.append(tau)
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equation_data.append(row)
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return tau_data
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@ -39,9 +39,9 @@
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<property name="geometry">
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<rect>
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<x>0</x>
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<y>0</y>
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<y>-158</y>
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<width>261</width>
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<height>812</height>
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<height>818</height>
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</rect>
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</property>
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<layout class="QVBoxLayout" name="verticalLayout_2">
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@ -141,8 +141,8 @@
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<rect>
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<x>0</x>
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<y>0</y>
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<width>221</width>
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<height>108</height>
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<width>222</width>
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<height>101</height>
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</rect>
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</property>
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<layout class="QFormLayout" name="formLayout">
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@ -268,8 +268,8 @@
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<rect>
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<x>10</x>
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<y>160</y>
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<width>230</width>
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<height>52</height>
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<width>235</width>
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<height>53</height>
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</rect>
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</property>
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<layout class="QFormLayout" name="formLayout_5">
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@ -371,7 +371,7 @@
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<x>9</x>
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<y>20</y>
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<width>221</width>
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<height>108</height>
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<height>111</height>
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</rect>
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</property>
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<layout class="QFormLayout" name="formLayout_2">
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@ -531,7 +531,7 @@
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<x>10</x>
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<y>90</y>
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<width>221</width>
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<height>106</height>
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<height>111</height>
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</rect>
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</property>
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<layout class="QFormLayout" name="formLayout_3">
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@ -542,19 +542,6 @@
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</property>
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</widget>
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</item>
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<item row="2" column="1">
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<widget class="QDoubleSpinBox" name="spin_var_tau">
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<property name="suffix">
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<string/>
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</property>
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<property name="decimals">
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<number>8</number>
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</property>
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<property name="value">
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<double>0.000002000000000</double>
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</property>
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</widget>
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</item>
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<item row="3" column="0">
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<widget class="QLabel" name="label_13">
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<property name="text">
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@ -582,7 +569,7 @@
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<number>6</number>
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</property>
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<property name="value">
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<double>1.000500000000000</double>
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<double>0.000500000000000</double>
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</property>
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</widget>
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</item>
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@ -603,6 +590,16 @@
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</property>
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</widget>
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</item>
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<item row="2" column="1">
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<widget class="QSpinBox" name="spin_var_tau">
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<property name="maximum">
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<number>10000</number>
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</property>
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<property name="value">
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<number>150</number>
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</property>
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</widget>
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</item>
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</layout>
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</widget>
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<widget class="QGraphicsView" name="equation_view">
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@ -641,8 +638,8 @@
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<rect>
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<x>10</x>
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<y>260</y>
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<width>221</width>
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<height>81</height>
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<width>222</width>
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<height>82</height>
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</rect>
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</property>
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<layout class="QFormLayout" name="formLayout_6">
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@ -833,7 +830,7 @@
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<x>0</x>
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<y>0</y>
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<width>279</width>
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<height>641</height>
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<height>633</height>
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</rect>
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</property>
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<widget class="QGroupBox" name="groupBox_3">
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@ -103,9 +103,10 @@ class FitGraph(BaseGraph):
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for g_i in range(len(mem['isolated_peaks'])):
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peak = mem['isolated_peaks'][g_i][self.peak_index]
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x_data = np.arange(len(peak))
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x_data_target = x_data[mem['overlayed_peak_indices'][g_i][self.peak_index]+mem['shift_over_fit']:]
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popt = mem['fit_equations'][g_i][self.peak_index]['popt']
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self.canv.axes.plot(peak)
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self.canv.axes.plot(x_data, exp_func(x_data, *popt), color='red')
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self.canv.axes.plot(x_data_target, exp_func(x_data_target, *popt), color='red')
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class FitsGraphViewer(QtWidgets.QTabWidget):
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def __init__(self, x):
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