rubycond_cb 0.2.0__tar.gz

rubycond_cb-0.2.0/PKG-INFO

@@ -0,0 +1,85 @@
+Metadata-Version: 2.3
+Name: rubycond_cb
+Version: 0.2.0
+Summary: Tool for calibrating a spectrometer wavelengths 
+License: GPL-3.0-or-later
+Author: Yiuri Garino
+Author-email: yiuri.garino@cnrs.fr
+Requires-Python: >=3.11
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: configparser (>=6,<7)
+Requires-Dist: lmfit (>=1.3,<2.0)
+Requires-Dist: matplotlib (>=3.8.2,<4.0.0)
+Requires-Dist: numpy (>=2.1,<3.0.0)
+Requires-Dist: pillow (>=10.1.0)
+Requires-Dist: pyqt5 (>=5.15.11,<6.0.0)
+Requires-Dist: rubycond_of (>=0.1.0)
+Project-URL: Repository, https://github.com/CelluleProjet/Rubycond_CB
+Description-Content-Type: text/markdown
+
+# Rubycond_CB
+Tool for calibrating the spectrometer wavelengths 
+  
+<img width="1282" height="702" alt="1_open_file" src="https://github.com/user-attachments/assets/3d744deb-cf81-4d27-aae1-8c685986c98d" />
+
+# Manual
+  
+1) Select the Neon line on the left graph and the corresponding peak on the right graph.  
+The program automatically performs a peak fit within the pixel window defined in Delta (pixels), default 20 pixels.
+
+2) Add the pair of points using the **ADD** button.  The points used for calibration are indicated on both the graphs and the table on the left.  
+<img width="1920" height="1032" alt="2_1_point" src="https://github.com/user-attachments/assets/7078a113-a26a-4ff4-9c1e-c06ab30deee6" />  
+  
+3) Repeat the operation, adding as many peaks as possible.  
+<img width="1920" height="1032" alt="3_n_point" src="https://github.com/user-attachments/assets/d46ac124-a0f3-407e-87d8-41a6133e65b5" />  
+  
+4) Use the **Simple Calib** button to perform the calibration.  
+The calibration result is displayed in the left graph, and the fit result is shown in the Fit Output window.
+<img width="1920" height="1032" alt="4_output" src="https://github.com/user-attachments/assets/689a1baa-e4ec-4fb9-97c4-5956a9384e15" />  
+  
+5) Use the **Accept** button to send the calibration parameters to the main program  
+# Install
+Use pip to install the program **within a virtual environment (strongly recommended).**  
+[Here's a short tutorial on installing a virtual environment.](https://github.com/CelluleProjet/Install/tree/main?tab=readme-ov-file#install-virtual-environment)
+```bash
+pip install rubycond_CB
+```
+# About
+## Author
+
+**Yiuri Garino**  
+
+## Contacts
+
+**Yiuri Garino**  
+- yiuri.garino@cnrs.fr
+   
+**Silvia Boccato**
+- silvia.boccato@cnrs.fr
+  
+<img src="https://github.com/CelluleProjet/Rubycond/assets/83216683/b728fe64-2752-4ecd-843b-09d335cf4f93" width="100" height="100">
+<img src="https://github.com/CelluleProjet/Rubycond/assets/83216683/0a81ce1f-089f-49d8-ae65-d19af8078492" width="100" height="100">
+
+
+[Cellule Projet](http://impmc.sorbonne-universite.fr/fr/plateformes-et-equipements/cellule-projet.html) @ [IMPMC](http://impmc.sorbonne-universite.fr/en/index.html)
+
+
+## License
+**Rubycond_CB**: Tool for calibrating the spectrometer wavelengths 
+
+
+Copyright (c) 2022-2026 Yiuri Garino
+
+**Rubycond_CB** is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+## Release notes
+
+Version 0.2.0 Release 260301: First release  
+

rubycond_cb-0.2.0/README.md

@@ -0,0 +1,61 @@
+# Rubycond_CB
+Tool for calibrating the spectrometer wavelengths 
+  
+<img width="1282" height="702" alt="1_open_file" src="https://github.com/user-attachments/assets/3d744deb-cf81-4d27-aae1-8c685986c98d" />
+
+# Manual
+  
+1) Select the Neon line on the left graph and the corresponding peak on the right graph.  
+The program automatically performs a peak fit within the pixel window defined in Delta (pixels), default 20 pixels.
+
+2) Add the pair of points using the **ADD** button.  The points used for calibration are indicated on both the graphs and the table on the left.  
+<img width="1920" height="1032" alt="2_1_point" src="https://github.com/user-attachments/assets/7078a113-a26a-4ff4-9c1e-c06ab30deee6" />  
+  
+3) Repeat the operation, adding as many peaks as possible.  
+<img width="1920" height="1032" alt="3_n_point" src="https://github.com/user-attachments/assets/d46ac124-a0f3-407e-87d8-41a6133e65b5" />  
+  
+4) Use the **Simple Calib** button to perform the calibration.  
+The calibration result is displayed in the left graph, and the fit result is shown in the Fit Output window.
+<img width="1920" height="1032" alt="4_output" src="https://github.com/user-attachments/assets/689a1baa-e4ec-4fb9-97c4-5956a9384e15" />  
+  
+5) Use the **Accept** button to send the calibration parameters to the main program  
+# Install
+Use pip to install the program **within a virtual environment (strongly recommended).**  
+[Here's a short tutorial on installing a virtual environment.](https://github.com/CelluleProjet/Install/tree/main?tab=readme-ov-file#install-virtual-environment)
+```bash
+pip install rubycond_CB
+```
+# About
+## Author
+
+**Yiuri Garino**  
+
+## Contacts
+
+**Yiuri Garino**  
+- yiuri.garino@cnrs.fr
+   
+**Silvia Boccato**
+- silvia.boccato@cnrs.fr
+  
+<img src="https://github.com/CelluleProjet/Rubycond/assets/83216683/b728fe64-2752-4ecd-843b-09d335cf4f93" width="100" height="100">
+<img src="https://github.com/CelluleProjet/Rubycond/assets/83216683/0a81ce1f-089f-49d8-ae65-d19af8078492" width="100" height="100">
+
+
+[Cellule Projet](http://impmc.sorbonne-universite.fr/fr/plateformes-et-equipements/cellule-projet.html) @ [IMPMC](http://impmc.sorbonne-universite.fr/en/index.html)
+
+
+## License
+**Rubycond_CB**: Tool for calibrating the spectrometer wavelengths 
+
+
+Copyright (c) 2022-2026 Yiuri Garino
+
+**Rubycond_CB** is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+## Release notes
+
+Version 0.2.0 Release 260301: First release  

rubycond_cb-0.2.0/pyproject.toml

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+[project]
+name = "rubycond_cb"
+version = "0.2.0"
+description = "Tool for calibrating a spectrometer wavelengths "
+authors = [
+    {name = "Yiuri Garino", email = "yiuri.garino@cnrs.fr"}
+]
+license = "GPL-3.0-or-later"
+readme = "README.md"
+requires-python = ">=3.11"
+dependencies = [
+    "numpy (>=2.1,<3.0.0)",
+    "configparser (>=6,<7)",
+    "matplotlib (>=3.8.2,<4.0.0)",
+    "lmfit (>=1.3,<2.0)",
+    "pyqt5 (>=5.15.11,<6.0.0)",
+    "pillow (>=10.1.0)",
+    "rubycond_of (>=0.1.0)"
+]
+
+[tool.poetry]
+packages = [{ include = "rubycond_CB" }]
+
+[project.urls]
+repository = "https://github.com/CelluleProjet/Rubycond_CB"
+
+[project.scripts]
+rubycond_CB = "rubycond_CB.rubycond_CB:main"
+
+[build-system]
+requires = ["poetry-core>=2.0.0,<3.0.0"]
+build-backend = "poetry.core.masonry.api"

rubycond_cb-0.2.0/rubycond_CB/model/CB_Model.py

@@ -0,0 +1,277 @@
+# -*- coding: utf-8 -*-
+"""
+
+Title: Rubycond_CB: tool for calibrating the wavelength of the spectrometer
+
+This file is part of Rubycond: Pressure by Ruby Luminescence (PRL) software to determine pressure in diamond anvil cell experiments.
+
+Version 0.2.0
+Release 260301
+
+Author:
+
+Yiuri Garino
+    yiuri.garino@cnrs.fr
+
+Copyright (c) 2023-2026 Yiuri Garino
+
+Download: 
+    https://github.com/CelluleProjet/Rubycond_calc
+
+License: GPLv3
+
+This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+You should have received a copy of the GNU General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+"""
+
+def reset():
+    import sys
+    
+    if hasattr(sys, 'ps1'):
+        
+        #clean Console and Memory
+        from IPython import get_ipython
+        get_ipython().run_line_magic('clear','/')
+        get_ipython().run_line_magic('reset','-sf')
+        print("Running interactively")
+        print()
+        terminal = False
+    else:
+        print("Running in terminal")
+        print()
+        terminal = True
+
+if __name__ == '__main__':
+    reset()
+
+import configparser as cp
+from pathlib import Path
+import numpy as np
+import matplotlib.pyplot as plt
+import os
+from datetime import datetime
+from lmfit.models import LinearModel, GaussianModel, PolynomialModel
+from PyQt5 import QtWidgets, QtCore, QtGui
+from scipy.special import wofz
+from scipy.interpolate import Akima1DInterpolator
+from pathlib import Path
+
+SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
+
+class my_model():
+    def __init__(self, debug = False):
+        self.debug = debug
+        self.version = 'RC_Model_11.py'
+        if self.debug: print('\nModel\n')
+        try:
+            #file_NEON = Path("Neon_Astrosurf.csv")
+            file_NEON = Path("Neon_PI.csv")
+            path_NEON = Path(__file__).parent.resolve() / file_NEON
+        except:
+            path_NEON = file_NEON
+
+            
+        self.Neon_lines = np.loadtxt(path_NEON, delimiter=',')
+        self.peaks_data_x = np.zeros((2,2)) #Data from open file
+        self.peaks_data_y = np.zeros((2,2)) #Data from open file
+        self.peaks_data_x_simple_calib = np.zeros((2,2))
+        
+        self.fit_delta_pixel = .6
+        
+        self.Last_peaks_pixel_clicked = 0
+    
+        
+        self.delta = 20
+        self.calib_cn = [0,0,0,0] #max poly degree = 3
+        
+        #
+        self.statusbar_message_ref = [print] #List of messages method (print, label, statusbar, etc)
+    
+    def statusbar_message_add(self, method):
+        #print(method)
+        self.statusbar_message_ref.append(method)
+        
+    def nearest_neon(self, value):
+        if value is not None:
+            i = abs(self.Neon_lines[:,0]-value).argmin()
+            data = self.Neon_lines[i]
+            #print(self.Neon_lines)
+            #print(abs(self.Neon_lines-value))
+            if self.debug :
+                print(f'input {i}: {value}')
+                print(f'output : {data}')
+        else:
+            data = 0
+        return data
+    
+    def peaks_data_pixel(self, value):
+        if value is not None:
+            data = abs(self.peaks_data_x-value).argmin()
+            
+            
+            #print(abs(self.Neon_lines-value))
+            if self.debug :
+                print(self.peaks_data_x)
+                print(f'input : {value}')
+                print(f'output : {data}')
+        else:
+            data = 0
+        return data
+
+    def button_calc_simple_calib(self):
+        y1 = self.Neon_Left_reference
+        y2 = self.Neon_Right_reference
+        x1 = self.Peaks_Left_reference
+        x2 = self.Peaks_Right_reference
+        s = (y2 - y1)/(x2 - x1)
+        i = y1 - s*x1
+        size = len(self.peaks_data_x)
+        pixels = np.arange(0,size,1)
+        if self.debug :
+            print(f'slope : {s}')
+            print(f'intercept : {i}')
+        self.peaks_data_x_simple_calib = i + s*pixels
+    
+    def format_fit_results(self, degree, res):
+        message = 'Fit Output\n'
+        message+= '\n'
+        # message+= 'Wavelengths (nm) = c0 + c1 * pixels + c2 * pixels\u00B2 + c3 * pixels\u00B3\n'
+        # message+= '\n\n'
+        for i in range(degree+1):
+            
+            message+= f'c{i} = ' 
+            message+= f"{res.params[f'line_c{i}'].value:.5e}"
+            message+= '\n'
+            self.calib_cn[i] = res.params[f'line_c{i}'].value
+        for j in range(3 - degree):
+            message+= f'c{j + degree +1} = 0'
+            message+= '\n'
+            self.calib_cn[j + degree +1] = 0
+        print(message)
+        print(self.calib_cn)
+        self.print_message_output = message
+        
+    def calib_poly_3(self, data_x, data_y):
+        degree = min(len(data_x)-1, 3)
+        model = PolynomialModel(degree=degree, prefix='line_')
+        pars = model.guess(data_y, data_x)
+        res = model.fit(data_y, pars, x = data_x)
+        if self.debug: pars.pretty_print()
+        #if self.debug: res.fit_report()#TODO restore in next version
+        print(res.fit_report()) #TODO cut in next version
+        size = len(self.peaks_data_x)
+        pixels = np.arange(0,size,1)
+        
+        self.peaks_data_x_simple_calib = model.eval(res.params, x = pixels)
+        
+        #prepare message to be used in layout_Output
+        self.format_fit_results(degree, res)
+    
+    def fit_peak_range(self):
+        try:
+            center = self.Last_peaks_pixel_clicked
+            delta = self.delta
+            data_x_graph = self.peaks_data_x[center - delta: center + delta + 1]
+            data_x_pixel = np.linspace(center - delta, center + delta, delta*2+1)
+            data_y = self.peaks_data_y[center - delta: center + delta + 1]
+            data_x, data_y, init, fit_x, fit_y, res = self.fit_peak(data_x_pixel, data_y)
+            
+            spl = Akima1DInterpolator(data_x_pixel, data_x_graph)
+    
+            data_x = spl(data_x)
+            fit_x = spl(fit_x)
+            center_pixel = res.params['center'].value
+            center_graph = spl(center_pixel)
+            return data_x, data_y, init, fit_x, fit_y, center_graph, center_pixel
+        except:
+            return None
+        
+    def fit_peak(self, data_x, data_y):
+        model = LinearModel() + GaussianModel()
+        pars = model.make_params()
+        
+        y1 = data_y[0]
+        y2 = data_y[-1]
+        x1 = data_x[0]
+        x2 = data_x[-1]
+        slope = (y2 - y1)/(x2 - x1)
+        intercept = y1 - slope*x1
+        pars['slope'].value = slope
+        pars['intercept'].value = intercept
+        center = data_x[data_y.argmax()]
+        pars['center'].value = center
+        sigma = 5 * abs(data_x[1] - data_x[0])
+        pars['sigma'].value = sigma
+        height = data_y.max() - (intercept + slope * center)
+        pars['amplitude'].value = self.Gauss_amplitude(height, sigma)
+        
+        init = model.eval(pars, x = data_x)
+        if self.debug: pars.pretty_print()
+        res = model.fit(data_y, pars, x = data_x)
+        
+        if self.debug: print(res.fit_report())
+        size = len(self.peaks_data_x)
+        fit_x = np.linspace(data_x.min(),data_x.max(),500)
+        fit_y = model.eval(res.params, x = fit_x)
+        
+        return data_x, data_y, init, fit_x, fit_y, res
+    
+    def x_2_nm(self, x, i, c1, c2, c3):
+        return i +c1*x + c2*x**2 +c3*x**3 
+
+    def Voigt(self, x, c0, c1, c2, c3, amplitude, center, sigma, gamma):
+        """
+        Return the Voigt line shape at x with Lorentzian component HWHM gamma
+        and Gaussian component sigma.
+        sigma = HWHM / sqrt(2 * log(2))
+
+        """
+        nm = c0 +c1*x + c2*x**2 +c3*x**3
+        return amplitude*np.real(wofz((nm - center + 1j*gamma)/sigma/np.sqrt(2))) / sigma /np.sqrt(2*np.pi)
+
+    def Voigt_amplitude(self, height, gamma, sigma):
+        
+        return height*(sigma*np.sqrt(2*np.pi))/wofz((1j*gamma)/(sigma*np.sqrt(2))).real
+
+    def Gauss(self, x, c0, c1, c2, c3, amplitude, center, sigma):
+        #x pixel
+        nm = c0 +c1*x + c2*x**2 +c3*x**3
+        cm = 1e7/nm
+        center_cm = 1e7/center
+        return amplitude / sigma / np.sqrt(2*np.pi) * np.exp( - (cm -center_cm) **2 / 2 / sigma**2 )
+
+    def Gauss_amplitude(self, height, sigma):
+        return sigma * np.sqrt(2*np.pi) * height
+    
+    #
+    def statusbar_message(self, message):
+        now = datetime.now()
+        text = now.strftime("%H:%M:%S : ") + message
+        for method in self.statusbar_message_ref:
+            method(text)
+
+    def error_box(self, error):
+        msgBox = QtWidgets.QMessageBox()
+        msgBox.setIcon(QtWidgets.QMessageBox.Critical)
+        msgBox.setWindowTitle("Script Error")
+        msgBox.setText(str(error))
+        msgBox.setStandardButtons(QtWidgets.QMessageBox.Ok)
+        msgBox.exec()
+'''
+#%%
+data_x = np.array((300,400,500,600))
+data_y = np.array((300,400,500,600))
+model = PolynomialModel(degree=2, prefix='line_')
+pars = model.guess(data_y, data_x)
+res = model.fit(data_y, pars, x = data_x)
+pars.pretty_print()
+res.params.pretty_print()
+res.fit_report()
+
+Fit = self.model.eval(self.out.params, x = x_fit_lmfit)
+self.center_pk = self.out.params['pk_center'].value
+self.out = self.model.fit(y_fit, self.pars, x = x, max_nfev = self.Fit_iter_lim.get()) 
+comps = self.out.eval_components(x = x_fit_lmfit)
+'''

rubycond_cb-0.2.0/rubycond_CB/model/Neon_Astrosurf.csv

@@ -0,0 +1,25 @@
+585.0936329588015, 0.9920106524633822
+588.1179775280899, 0.1238348868175766
+594.3258426966293, 0.23435419440745675
+597.3501872659176, 0.0679094540612517
+602.9213483146068, 0.06924101198402122
+607.059925093633, 0.18375499334221035
+609.2883895131087, 0.2583222370173103
+614.0636704119851, 0.4194407456724367
+616.1329588014981, 0.14647137150466039
+621.3857677902622, 0.118508655126498
+626.3202247191011, 0.2250332889480693
+630.1404494382023, 0.07589880159786955
+632.8464419475656, 0.18242343541944084
+637.7808988764045, 0.2663115845539281
+639.8501872659176, 0.29693741677762975
+650.3558052434457, 0.16644474034620504
+652.9026217228464, 0.07589880159786955
+659.5880149812734, 0.0732356857523303
+667.5468164794008, 0.11584553928095864
+671.5262172284645, 0.1131824234354194
+692.6966292134832, 0.09986684420772307
+703.0430711610487, 0.2809587217043942
+717.368913857678, 0.011984021304926706
+724.5318352059926, 0.08655126498002663
+744.1104868913858, 0.01464713715046595

rubycond_cb-0.2.0/rubycond_CB/model/Neon_PI.csv

@@ -0,0 +1,20 @@
+607.43377, 0.18375499334221035
+609.61631, 0.2583222370173103
+614.30626, 0.4194407456724367
+616.35939, 0.14647137150466039
+621.72812, 0.118508655126498
+626.6495, 0.2250332889480693
+630.4789, 0.07589880159786955
+633.44278, 0.18242343541944084
+638.29917, 0.2663115845539281
+640.2246, 0.29693741677762975
+650.65281, 0.16644474034620504
+653.28822, 0.07589880159786955
+659.89529, 0.0732356857523303
+667.82764, 0.11584553928095864
+671.7043, 0.1131824234354194
+692.94673, 0.09986684420772307
+703.24131, 0.2809587217043942
+717.39381, 0.011984021304926706
+724.51666, 0.08655126498002663
+743.8899, 0.01464713715046595