Add FitData.py, modified python GUI for fitting. work but not perfect
This commit is contained in:
parent
3a41e13fdf
commit
f1b2d4a580
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@ -9,17 +9,27 @@ class PythonHighlighter(QSyntaxHighlighter):
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super().__init__(document)
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# Define formatting for comments
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self.comment_format = QTextCharFormat()
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self.comment_format.setForeground(Qt.GlobalColor.darkGreen)
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self.comment_format1 = QTextCharFormat()
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self.comment_format1.setForeground(Qt.GlobalColor.darkGreen)
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self.comment_format2 = QTextCharFormat()
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self.comment_format2.setForeground(Qt.GlobalColor.blue)
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self.comment_format2.setBackground(Qt.GlobalColor.yellow)
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self.comment_format3 = QTextCharFormat()
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self.comment_format3.setForeground(Qt.GlobalColor.magenta)
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def highlightBlock(self, text):
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# Highlight comments
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if text.startswith("#"):
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self.setFormat(0, len(text), self.comment_format)
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if text.startswith("#") and text.startswith("#=") == False:
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self.setFormat(0, len(text), self.comment_format1)
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if text.startswith("$"):
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self.setFormat(0, len(text), self.comment_format)
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self.setFormat(0, len(text), self.comment_format1)
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if text.startswith("0"):
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self.setFormat(0, len(text), self.comment_format)
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self.setFormat(0, len(text), self.comment_format1)
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if text.startswith("fit"):
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self.setFormat(0, len(text), self.comment_format2)
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if text.startswith("#="):
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self.setFormat(0, len(text), self.comment_format3)
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class CustomTextEdit(QTextEdit):
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def __init__(self, parent=None):
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@ -35,9 +45,8 @@ class CustomTextEdit(QTextEdit):
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# Check if Ctrl+D is pressed
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if event.key() == Qt.Key.Key_D and event.modifiers() == Qt.KeyboardModifier.ControlModifier:
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self.duplicate_line()
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event.accept() # Prevent the default behavior of Ctrl+D
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else:
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super().keyPressEvent(event) # Call the base class to handle other keys
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super().keyPressEvent(event) # Call the base class to handle other keys
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def duplicate_line(self):
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cursor = self.textCursor()
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178
Cleopatra/FitExData.py
Normal file
178
Cleopatra/FitExData.py
Normal file
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@ -0,0 +1,178 @@
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#!/usr/bin/python3
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import numpy as np
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from scipy.optimize import curve_fit
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import matplotlib.pyplot as plt
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from ExtractXsecPy import read_DWBA
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class Fitting:
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def __init__(self):
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self.ExList = []
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self.fitOption = []
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self.expData = []
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self.dataX = []
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self.data = [] # is a 2D array
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self.headers = []
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def read_data(self,file_path):
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self.headers, self.dataX, self.data = read_DWBA(file_path)
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print(self.headers)
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def read_expData(self, fileName):
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self.ExList = []
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self.fitOption = []
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self.expData = []
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current_data = []
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with open(fileName, "r") as file:
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for line in file:
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line = line.strip()
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if not line:
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continue
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# Check for excitation energy lines
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if line.startswith("#======================"):
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# If there's an existing data block, save it
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if current_data:
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self.expData.append(np.array(current_data, dtype=float))
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current_data = []
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# Extract excitation energy
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Ex_energy = line.split()[1]
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self.ExList.append(float(Ex_energy))
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# Check for fit option lines
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elif line.startswith("fit"):
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# Add fit option parameters
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fit_params = [x.strip(',') for x in line.split()[1:]]
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self.fitOption.append(fit_params)
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# Parse data lines
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elif not line.startswith("#"):
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values = [float(x) for x in line.split()]
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current_data.append(values)
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# Append the last block
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if current_data:
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self.expData.append(np.array(current_data, dtype=float))
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# Convert to numpy arrays
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self.ExList = np.array(self.ExList)
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self.expData = [np.array(data) for data in self.expData]
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# Output the result
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print("=========== Number of data set:", len(self.ExList))
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for i in range(0, len(self.ExList)):
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print("-------------------------")
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print(" ExList:", self.ExList[i])
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print("Fit Options:", self.fitOption[i])
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print(" Data List:\n", self.expData[i])
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def FitData(self):
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# Set initial offset values
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x_offset, y_offset = 2000, 100
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figure = []
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for expDataID in range(len(self.expData)):
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# Get the number of fit options and cross-sections
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nFit = len(self.fitOption[expDataID])
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nXsec = len(self.data)
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# Extract experimental data (x, y, and errors)
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x_exp = self.expData[expDataID][:, 0] # x positions
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x_err = self.expData[expDataID][:, 1] # x uncertainties (errors)
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y_exp = self.expData[expDataID][:, 2] # y positions
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y_err = self.expData[expDataID][:, 3] # y errors
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fitTheory = []
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fitTheory_lower = []
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fitTheory_upper = []
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for k in range(nFit):
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# Get the cross-section IDs for the current fit option and strip extra spaces
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xsecIDStr = self.fitOption[expDataID][k].strip()
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xsecID = [int(part.strip()) for part in xsecIDStr.split('+')] if '+' in xsecIDStr else [int(xsecIDStr)]
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# Ensure all cross-section IDs are valid
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processFlag = True
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for id in range(len(xsecID)):
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if xsecID[id] >= nXsec:
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print(f"Error: Requested Xsec-{xsecID[id]} exceeds the number of available cross-sections ({nXsec})")
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processFlag = False
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if processFlag == False :
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continue
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# Define the fitting function: a weighted sum of the selected data
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def fit_func(x, *scale):
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y = np.zeros_like(x)
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for p, id in enumerate(xsecID):
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y += scale[p] * np.interp(x, self.dataX, self.data[id])
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return y
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lower_bounds = [1e-6] * len(xsecID) # Setting a small positive lower bound
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upper_bounds = [np.inf] * len(xsecID) # No upper bound
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# Perform curve fitting using the fit_func and experimental data with y-errors as weights
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popt, pcov = curve_fit(fit_func, x_exp, y_exp, sigma=y_err, absolute_sigma=True,
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p0=np.ones(len(xsecID)), # Initial guess for scale parameters
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bounds=(lower_bounds, upper_bounds))
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perr = np.sqrt(np.diag(pcov)) # Standard deviation of the parameters
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print(f"Fitted scale for fit {k+1}: {popt} +/- {perr}")
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# Append the theoretical fit for this fit option
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fitTheory.append(np.zeros_like(self.dataX))
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for p, id in enumerate(xsecID):
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fitTheory[k] += popt[p] * np.interp(self.dataX, self.dataX, self.data[id])
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# Optionally, you can plot the uncertainty as shaded regions (confidence intervals)
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# Create the upper and lower bounds of the theoretical model with uncertainties
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fitTheory_upper.append(np.zeros_like(self.dataX))
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fitTheory_lower.append(np.zeros_like(self.dataX))
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for p, id in enumerate(xsecID):
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fitTheory_upper[k] += (popt[p] + perr[p]) * np.interp(self.dataX, self.dataX, self.data[id])
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fitTheory_lower[k] += (popt[p] - perr[p]) * np.interp(self.dataX, self.dataX, self.data[id])
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fig = plt.figure()
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figure.append(fig)
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# Plot results
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plt.errorbar(x_exp, y_exp, xerr=x_err, yerr=y_err, fmt='o', label='Experimental Data', color='blue')
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# Plot all fit theories
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for i, fit in enumerate(fitTheory):
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plt.plot(self.dataX, fit, label=f'Xsec:{self.fitOption[expDataID][i]} Fit')
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plt.fill_between(self.dataX, fitTheory_lower[i], fitTheory_upper[i], alpha=0.2)
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# Customize plot
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plt.xlabel('Angle_CM [deg]')
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plt.ylabel('X-Sec [a.u.]')
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plt.legend()
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plt.autoscale(enable=True, axis='x', tight=True)
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plt.tight_layout()
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plt.yscale('log')
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# Replace plt.title() with plt.text() to position the title inside the plot
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plt.text(0.05, 0.05, f'Fit for Exp Data : {self.ExList[expDataID]} MeV', transform=plt.gca().transAxes,
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fontsize=12, verticalalignment='bottom', horizontalalignment='left', color='black')
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manager = plt.get_current_fig_manager()
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# manager.window.wm_geometry(f"+{x_offset}+{y_offset}")
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manager.set_window_title(f"Exp Data : {self.ExList[expDataID]} MeV")
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x_offset += 100
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y_offset += 100
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plt.show()
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@ -17,7 +17,7 @@ from CustomTextEdit import CustomTextEdit
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from ExtractXsecPy import extract_xsec
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from ExWindow import ExWindow
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from MatPlotLibWindow import MatPlotLibWindow
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from FitExData import Fitting
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################################################## MainWindow
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class MyWindow(QMainWindow):
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@ -25,15 +25,17 @@ class MyWindow(QMainWindow):
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super().__init__()
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self.setWindowTitle("Ptolemy GUI")
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self.setGeometry(100, 100, 1000, 700)
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self.setMinimumSize(400, 600)
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self.setGeometry(100, 100, 1000, 800)
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self.setMinimumSize(1000, 800)
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self.lastDWBARecord = "lastDWBA.txt"
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self.DWBAFileName = ""
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self.ExpDataFileName = ""
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self.LoadLastOpenDWBASource()
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self.bashResult = ""
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self.plot_window = MatPlotLibWindow()
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self.Ex_window = ExWindow()
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self.fitting = Fitting()
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# Set up Group Box for DWBA Control
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self.gbDWBA = QGroupBox("DWBA")
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@ -146,6 +148,21 @@ class MyWindow(QMainWindow):
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Ex_layout.addWidget(self.sbMaXEx, 1, 1)
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Ex_layout.addWidget(buEx, 2, 0, 1, 2)
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# ExpData Group
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self.gbExpFit = QGroupBox("Exp Data Fit")
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fit_layout = QVBoxLayout()
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fit_layout.setAlignment(Qt.AlignmentFlag.AlignTop)
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self.gbExpFit.setLayout(fit_layout)
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bnOpenExpData = QPushButton("Open ExpData")
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bnOpenExpData.clicked.connect(self.LoadExpDataToTextBox)
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bnFit = QPushButton("Fit")
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bnFit.clicked.connect(self.fitData)
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fit_layout.addWidget(bnOpenExpData)
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fit_layout.addWidget(bnFit)
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# Set up the Right Side
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self.bnOpenDWBASource = QPushButton("Open DWBA Source")
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@ -158,6 +175,16 @@ class MyWindow(QMainWindow):
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self.bnSaveFile = QPushButton("Save File")
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self.bnSaveFile.clicked.connect(self.SaveFile)
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self.bnOpenExpData = QPushButton("Open Exp Data")
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self.bnOpenExpData.clicked.connect(self.OpenExpDataFile)
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self.leExpDataFileName = QLineEdit("")
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self.leExpDataFileName.setReadOnly(True)
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self.leExpDataFileName.setText(self.ExpDataFileName)
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self.bnSaveExpDataFile = QPushButton("Save Exp Data File")
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self.bnSaveExpDataFile.clicked.connect(self.SaveExpDataFile)
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self.text_edit = CustomTextEdit(self)
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self.leStatus = QLineEdit("")
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@ -165,17 +192,25 @@ class MyWindow(QMainWindow):
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self.LoadFileToTextBox(self.DWBAFileName, True)
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self.bnSaveExpDataFile.setEnabled(False)
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# Set up the layout
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layout = QGridLayout()
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# layout.addWidget(self.gbDWBA, 0, 0, 7, 1)
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layout.addWidget(self.gbDWBA, 0, 0, 5, 1)
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layout.addWidget(self.gbEx, 5, 0, 2, 1)
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layout.addWidget(self.gbExpFit, 7, 0, 2, 1)
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layout.addWidget(self.bnOpenDWBASource, 0, 1)
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layout.addWidget(self.leFileName, 0, 2, 1, 3)
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layout.addWidget(self.bnSaveFile, 0, 5)
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layout.addWidget(self.text_edit, 1, 1, 5, 5)
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layout.addWidget(self.leStatus, 6, 1, 1, 5)
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layout.addWidget(self.bnOpenExpData, 1, 1)
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layout.addWidget(self.leExpDataFileName, 1, 2, 1, 3)
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layout.addWidget(self.bnSaveExpDataFile, 1, 5)
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layout.addWidget(self.text_edit, 2, 1, 6, 5)
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layout.addWidget(self.leStatus, 8, 1, 1, 5)
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for i in range(layout.columnCount()) :
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layout.setColumnStretch(i, 1)
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@ -192,12 +227,16 @@ class MyWindow(QMainWindow):
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try :
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with open(self.lastDWBARecord, 'r') as file:
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self.DWBAFileName = file.readline().strip()
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self.ExpDataFileName = file.readline().strip()
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except:
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self.DWBAFileName = "DWBA"
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self.ExpDataFileName = ""
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def SaveLastOpenDWBASource(self):
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with open(self.lastDWBARecord, 'w') as file:
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file.write(self.DWBAFileName)
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file.write("\n")
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file.write(self.ExpDataFileName)
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def OnOffXsecOption(self):
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self.cbXsec.setEnabled(self.chkExtracrXsec.isChecked())
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@ -209,6 +248,20 @@ class MyWindow(QMainWindow):
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self.leFileName.setText(self.DWBAFileName)
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self.LoadFileToTextBox(self.DWBAFileName)
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self.SaveLastOpenDWBASource()
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self.bnSaveExpDataFile.setEnabled(False)
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def OpenExpDataFile(self):
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file_path, _ = QFileDialog.getOpenFileName(self, "Open File", "", "Text File (*.txt)")
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if file_path:
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self.ExpDataFileName = file_path
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self.leExpDataFileName.setText(self.ExpDataFileName)
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self.LoadFileToTextBox(self.ExpDataFileName)
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self.bnSaveExpDataFile.setEnabled(True)
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self.SaveLastOpenDWBASource()
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def LoadExpDataToTextBox(self):
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self.LoadFileToTextBox(self.ExpDataFileName)
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self.bnSaveExpDataFile.setEnabled(True)
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def LoadFileToTextBox(self, fileName, moveToButton = False):
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# print(fileName)
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@ -227,12 +280,20 @@ class MyWindow(QMainWindow):
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except Exception as e:
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self.text_edit.setText(f"Failed to load file:\n{e}")
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self.leStatus.setText(f"Failed to load file:\n{e}")
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self.bnSaveExpDataFile.setEnabled(False)
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def SaveFile(self):
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file_path = self.leFileName.text()
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with open(file_path, 'w') as file:
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file.write(self.text_edit.toPlainText())
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self.leStatus.setText(f"File saved to: {file_path}")
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def SaveExpDataFile(self):
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file_path = self.leExpDataFileName.text()
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with open(file_path, 'w') as file:
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file.write(self.text_edit.toPlainText())
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self.leStatus.setText(f"File saved to: {file_path}")
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def DeleteinOutXsecFiles(self):
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if os.path.exists(self.DWBAFileName + ".in"):
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@ -303,6 +364,10 @@ class MyWindow(QMainWindow):
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self.Ex_window.plot_Ex_graph()
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self.Ex_window.show()
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def fitData(self):
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self.fitting.read_expData(self.ExpDataFileName)
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self.fitting.read_data(self.DWBAFileName + ".Xsec.txt")
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self.fitting.FitData()
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def closeEvent(self, event):
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if self.plot_window:
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