From 04b549d106c7d5756e8e1c093e60936f074c8ec6 Mon Sep 17 00:00:00 2001
From: turtlebasket <turtlebasket@gmail.com>
Date: Mon, 9 Aug 2021 09:55:29 -0700
Subject: [PATCH] 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 time
---
 app.py        |  2 ++
 crds_calc.py  | 36 ++++++++++++++++++++++++++++++------
 ui/mainwin.ui | 47 ++++++++++++++++++++++-------------------------
 widgets.py    |  3 ++-
 4 files changed, 56 insertions(+), 32 deletions(-)

diff --git a/app.py b/app.py
index 38ba1d2..861ce5c 100644
--- a/app.py
+++ b/app.py
@@ -94,6 +94,7 @@ class AppWindow(QtWidgets.QMainWindow, Ui_MainWindow):
                 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))
@@ -202,6 +203,7 @@ class AppWindow(QtWidgets.QMainWindow, Ui_MainWindow):
                 self.spin_shift_over_fit.value(),
                 self.check_advanced_peak_detection.isChecked()
             )
+            mem['shift_over_fit'] = self.spin_shift_over_fit.value()
             # print(mem['fit_equations'])
             self.peak_fit_viewer.plot()
             self.graph_tabs.setCurrentIndex(4)
diff --git a/crds_calc.py b/crds_calc.py
index 179c30d..d9d1298 100644
--- a/crds_calc.py
+++ b/crds_calc.py
@@ -267,8 +267,6 @@ def fit_peaks(
     use_advanced: bool
 ):
     
-    print(f'{use_advanced=}')
-
     """
     Returns
     -------
@@ -277,8 +275,10 @@ def fit_peaks(
 
     params_guess = (0.0000, a, y0, tau)
     equations = []
+    overlayed_peak_indices = []
     for peaks_cut in isolated_peaks:
-        row = []
+        equation_row = []
+        overlayed_peak_row = []
         for peak_data in peaks_cut:
             x_data = np.arange(len(peak_data)) # just placeholder indices
             if not use_advanced:
@@ -291,7 +291,31 @@ def fit_peaks(
             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)
+            equation_row.append({'popt': popt, 'pcov': pcov})
+            overlayed_peak_row.append(peak_index)
+        equations.append(equation_row)
+        overlayed_peak_indices.append(overlayed_peak_row)
+        mem['overlayed_peak_indices'] = overlayed_peak_indices
 
-    return equations # list linked with isolated_peaks
\ No newline at end of file
+    return equations # list linked with isolated_peaks
+
+
+def get_tau_data(equation_data):
+    """
+    Extracts time constant from all equations (2d array)
+    
+    Returns
+    -------
+
+    Tau data in same dimensions as `equation_data`
+    """
+    
+    tau_data = []
+    for r in equation_data:
+        row = []
+        for e in r:
+            tau = e['popt'][3]
+            row.append(tau)
+        equation_data.append(row)
+
+    return tau_data
diff --git a/ui/mainwin.ui b/ui/mainwin.ui
index a09ff75..8ad2873 100644
--- a/ui/mainwin.ui
+++ b/ui/mainwin.ui
@@ -39,9 +39,9 @@
        <property name="geometry">
         <rect>
          <x>0</x>
-         <y>0</y>
+         <y>-158</y>
          <width>261</width>
-         <height>812</height>
+         <height>818</height>
         </rect>
        </property>
        <layout class="QVBoxLayout" name="verticalLayout_2">
@@ -141,8 +141,8 @@
               <rect>
                <x>0</x>
                <y>0</y>
-               <width>221</width>
-               <height>108</height>
+               <width>222</width>
+               <height>101</height>
               </rect>
              </property>
              <layout class="QFormLayout" name="formLayout">
@@ -268,8 +268,8 @@
             <rect>
              <x>10</x>
              <y>160</y>
-             <width>230</width>
-             <height>52</height>
+             <width>235</width>
+             <height>53</height>
             </rect>
            </property>
            <layout class="QFormLayout" name="formLayout_5">
@@ -371,7 +371,7 @@
              <x>9</x>
              <y>20</y>
              <width>221</width>
-             <height>108</height>
+             <height>111</height>
             </rect>
            </property>
            <layout class="QFormLayout" name="formLayout_2">
@@ -531,7 +531,7 @@
              <x>10</x>
              <y>90</y>
              <width>221</width>
-             <height>106</height>
+             <height>111</height>
             </rect>
            </property>
            <layout class="QFormLayout" name="formLayout_3">
@@ -542,19 +542,6 @@
               </property>
              </widget>
             </item>
-            <item row="2" column="1">
-             <widget class="QDoubleSpinBox" name="spin_var_tau">
-              <property name="suffix">
-               <string/>
-              </property>
-              <property name="decimals">
-               <number>8</number>
-              </property>
-              <property name="value">
-               <double>0.000002000000000</double>
-              </property>
-             </widget>
-            </item>
             <item row="3" column="0">
              <widget class="QLabel" name="label_13">
               <property name="text">
@@ -582,7 +569,7 @@
                <number>6</number>
               </property>
               <property name="value">
-               <double>1.000500000000000</double>
+               <double>0.000500000000000</double>
               </property>
              </widget>
             </item>
@@ -603,6 +590,16 @@
               </property>
              </widget>
             </item>
+            <item row="2" column="1">
+             <widget class="QSpinBox" name="spin_var_tau">
+              <property name="maximum">
+               <number>10000</number>
+              </property>
+              <property name="value">
+               <number>150</number>
+              </property>
+             </widget>
+            </item>
            </layout>
           </widget>
           <widget class="QGraphicsView" name="equation_view">
@@ -641,8 +638,8 @@
             <rect>
              <x>10</x>
              <y>260</y>
-             <width>221</width>
-             <height>81</height>
+             <width>222</width>
+             <height>82</height>
             </rect>
            </property>
            <layout class="QFormLayout" name="formLayout_6">
@@ -833,7 +830,7 @@
              <x>0</x>
              <y>0</y>
              <width>279</width>
-             <height>641</height>
+             <height>633</height>
             </rect>
            </property>
            <widget class="QGroupBox" name="groupBox_3">
diff --git a/widgets.py b/widgets.py
index 77fdf35..e98900f 100644
--- a/widgets.py
+++ b/widgets.py
@@ -103,9 +103,10 @@ class FitGraph(BaseGraph):
         for g_i in range(len(mem['isolated_peaks'])):
             peak = mem['isolated_peaks'][g_i][self.peak_index]
             x_data = np.arange(len(peak))
+            x_data_target = x_data[mem['overlayed_peak_indices'][g_i][self.peak_index]+mem['shift_over_fit']:]
             popt = mem['fit_equations'][g_i][self.peak_index]['popt']
             self.canv.axes.plot(peak)
-            self.canv.axes.plot(x_data, exp_func(x_data, *popt), color='red')
+            self.canv.axes.plot(x_data_target, exp_func(x_data_target, *popt), color='red')
 
 class FitsGraphViewer(QtWidgets.QTabWidget):
     def __init__(self, x):