pyspectrace 2.0.0__tar.gz

pyspectrace-2.0.0/LICENSE

@@ -0,0 +1,178 @@
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pyspectrace-2.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pyspectrace
+Version: 2.0.0
+Summary: **PySpecTrace** is an open-source, Python-based graphical user interface (GUI) designed for real-time UV-visible-NIR spectroscopy data analysis. It addresses the limitations of proprietary spectrometer software by providing advanced, customizable, and real-time spectral tracking and analysis tools suitable for a wide range of scientific disciplines
+Author-email: Iwan Darmadi <iwan.darmadi@alumni.ui.ac.id>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: <3.13,>=3.9
+Requires-Dist: matplotlib==3.9.4
+Requires-Dist: numpy==1.26.4
+Requires-Dist: pandas==2.3.3
+Requires-Dist: pyqt5==5.15.11
+Requires-Dist: pyqtgraph==0.13.7
+Requires-Dist: scipy==1.13.1
+Requires-Dist: seabreeze==2.11.0
+Requires-Dist: seatease==0.4.0
+Description-Content-Type: text/markdown
+
+# PySpecTrace: Python-based Graphical User Interface (GUI) for Real-time UV-Vis-NIR Spectroscopy Analysis
+
+**PySpecTrace** is an open-source, Python-based graphical user interface (GUI) designed for real-time UV-visible-NIR spectroscopy data analysis. It addresses the limitations of proprietary spectrometer software by providing advanced, customizable, and real-time spectral tracking and analysis tools suitable for a wide range of scientific disciplines.
+
+![PySpecTrace Application](https://github.com/anamsigit/pyspectrace/blob/main/GUI_snapshot.png?raw=true)
+
+## Installation
+Open a terminal or Command Prompt
+then run the following command to install the latest version from PyPI:
+```
+pip install pyspectrace
+```
+
+### Run the Application 
+After installation is complete, start the program with open terminal and write:
+```
+pyspectrace
+```
+
+### Spectrometer SDK Setup
+To connect the software with supported spectrometers, you must manually provide the required SDK files (DLLs/shared libraries). These SDKs are proprietary and must be obtained directly from the hardware manufacturers.
+
+You can add SDK files from the application menu:
+1. Open PySpecTrace.
+2. Click menu bar ```SDK```.
+3. Choose the vendor: ```Ocean Optics```, ```CNI Laser```, or ```Avantes```.
+4. Select ```Add ... DLL``` and choose the required ```.dll``` file.
+5. Close PySpecTrace then run again
+
+PySpecTrace stores user-provided SDK files in the user data directory. This keeps the PyPI package free from proprietary SDK files.
+
+### Requirements
+* Python 3.9 – 3.12
+
+***Notes for Avantes Spectrometer***: If the spectrometer is still not detected after placing the SDK, please Install the official Avantes interface software from https://www.avantes.com/products/software/
+
+> Detailed steps for running documented in the Manual: [PySpecTrace_Manual.pdf](https://github.com/anamsigit/pyspectrace/blob/main/PySpecTrace_Manual.pdf)
+
+_If you encounter any issues or need assistance, we will do our best to help. Please feel free to contact us via the **Corresponding Contact**_
+
+
+## Extra Documentation
+- **Zenodo archive:** [doi.org/10.5281/zenodo.18920460](https://doi.org/10.5281/zenodo.18920460)
+- **Repository:** [https://github.com/anamsigit/pyspectrace](https://github.com/anamsigit/pyspectrace)
+- **Supporting information:** [PySpecTrace_SI.pdf](https://github.com/anamsigit/pyspectrace/blob/main/PySpecTrace_SI.pdf)
+- **Demonstration video:** [Google drive](https://drive.google.com/file/d/1Tj6Fig017nFhzMavVcG9cRoBS5tbMKVn/view?usp=sharing)
+
+
+
+## Key Features
+- **Real-time spectral visualization:** Enables immediate monitoring of spectral changes during experiments.
+- **Dynamic spectral tracing and peak tracking:** Utilizes adaptive fitting routines to identify and track spectral features live.
+- **Flexible configuration:** User-friendly GUI includes panels for spectrometer connection, settings, data display, and analysis.
+- **Spectral post-processing:** Offers robust data analysis capabilities for in-depth interpretation.
+- **Spectrometer Simulator:** Supports testing without physical hardware, facilitating development and training.
+- **Modular and adaptable:** Compatible with any spectrometer via appropriate driver interfaces; easily customizable for various experimental needs.
+
+## Architecture
+- Built on a **Model-View-Presenter (MVP)** pattern for maintainability and scalability.
+- Uses popular Python libraries including **PyQt5, NumPy, SciPy, Pandas, Matplotlib, and PyQtGraph**.
+- This project has been tested with **Python 3.9.13**.
+
+## List of working spectrometers
+PySpecTrace has been tested and working seamlessly with these commercial spectrometers (on Windows OS). Testing was performed using some instruments available from several research laboratories: Photonics Research Center of Indonesia; Chemistry Dept. of Chulalongkorn University; Electrical Eng. Dept. of Universiti Teknologi Malaysia; IMRAN, Tohoku University, Physics Dept. of Universitas Indonesia.
+
+| Ocean Optics           | Avantes                      | CNI          |
+|-----------------------|------------------------------|--------------|
+| Maya PRO2000          | AvaSpec-ULS4096CL-EVO        | Aurora 4000  |
+| HR 4000CG-UV-NIR      | AvaSpec-2048-USB2            |              |
+| USB4000               |                              |              |
+
+Please add to the list if you have found that it works in your spectrometer. It will be a nice information for new user.
+
+## Corresponding contact
+- Feel free to contact us via Iwan Darmadi (email:iwan.darmadi@alumni.ui.ac.id) for technical support, bug reports, feature requests, or questions regarding PySpecTrace.
+
+
+---
+
+

pyspectrace-2.0.0/README.md

@@ -0,0 +1,80 @@
+# PySpecTrace: Python-based Graphical User Interface (GUI) for Real-time UV-Vis-NIR Spectroscopy Analysis
+
+**PySpecTrace** is an open-source, Python-based graphical user interface (GUI) designed for real-time UV-visible-NIR spectroscopy data analysis. It addresses the limitations of proprietary spectrometer software by providing advanced, customizable, and real-time spectral tracking and analysis tools suitable for a wide range of scientific disciplines.
+
+![PySpecTrace Application](https://github.com/anamsigit/pyspectrace/blob/main/GUI_snapshot.png?raw=true)
+
+## Installation
+Open a terminal or Command Prompt
+then run the following command to install the latest version from PyPI:
+```
+pip install pyspectrace
+```
+
+### Run the Application 
+After installation is complete, start the program with open terminal and write:
+```
+pyspectrace
+```
+
+### Spectrometer SDK Setup
+To connect the software with supported spectrometers, you must manually provide the required SDK files (DLLs/shared libraries). These SDKs are proprietary and must be obtained directly from the hardware manufacturers.
+
+You can add SDK files from the application menu:
+1. Open PySpecTrace.
+2. Click menu bar ```SDK```.
+3. Choose the vendor: ```Ocean Optics```, ```CNI Laser```, or ```Avantes```.
+4. Select ```Add ... DLL``` and choose the required ```.dll``` file.
+5. Close PySpecTrace then run again
+
+PySpecTrace stores user-provided SDK files in the user data directory. This keeps the PyPI package free from proprietary SDK files.
+
+### Requirements
+* Python 3.9 – 3.12
+
+***Notes for Avantes Spectrometer***: If the spectrometer is still not detected after placing the SDK, please Install the official Avantes interface software from https://www.avantes.com/products/software/
+
+> Detailed steps for running documented in the Manual: [PySpecTrace_Manual.pdf](https://github.com/anamsigit/pyspectrace/blob/main/PySpecTrace_Manual.pdf)
+
+_If you encounter any issues or need assistance, we will do our best to help. Please feel free to contact us via the **Corresponding Contact**_
+
+
+## Extra Documentation
+- **Zenodo archive:** [doi.org/10.5281/zenodo.18920460](https://doi.org/10.5281/zenodo.18920460)
+- **Repository:** [https://github.com/anamsigit/pyspectrace](https://github.com/anamsigit/pyspectrace)
+- **Supporting information:** [PySpecTrace_SI.pdf](https://github.com/anamsigit/pyspectrace/blob/main/PySpecTrace_SI.pdf)
+- **Demonstration video:** [Google drive](https://drive.google.com/file/d/1Tj6Fig017nFhzMavVcG9cRoBS5tbMKVn/view?usp=sharing)
+
+
+
+## Key Features
+- **Real-time spectral visualization:** Enables immediate monitoring of spectral changes during experiments.
+- **Dynamic spectral tracing and peak tracking:** Utilizes adaptive fitting routines to identify and track spectral features live.
+- **Flexible configuration:** User-friendly GUI includes panels for spectrometer connection, settings, data display, and analysis.
+- **Spectral post-processing:** Offers robust data analysis capabilities for in-depth interpretation.
+- **Spectrometer Simulator:** Supports testing without physical hardware, facilitating development and training.
+- **Modular and adaptable:** Compatible with any spectrometer via appropriate driver interfaces; easily customizable for various experimental needs.
+
+## Architecture
+- Built on a **Model-View-Presenter (MVP)** pattern for maintainability and scalability.
+- Uses popular Python libraries including **PyQt5, NumPy, SciPy, Pandas, Matplotlib, and PyQtGraph**.
+- This project has been tested with **Python 3.9.13**.
+
+## List of working spectrometers
+PySpecTrace has been tested and working seamlessly with these commercial spectrometers (on Windows OS). Testing was performed using some instruments available from several research laboratories: Photonics Research Center of Indonesia; Chemistry Dept. of Chulalongkorn University; Electrical Eng. Dept. of Universiti Teknologi Malaysia; IMRAN, Tohoku University, Physics Dept. of Universitas Indonesia.
+
+| Ocean Optics           | Avantes                      | CNI          |
+|-----------------------|------------------------------|--------------|
+| Maya PRO2000          | AvaSpec-ULS4096CL-EVO        | Aurora 4000  |
+| HR 4000CG-UV-NIR      | AvaSpec-2048-USB2            |              |
+| USB4000               |                              |              |
+
+Please add to the list if you have found that it works in your spectrometer. It will be a nice information for new user.
+
+## Corresponding contact
+- Feel free to contact us via Iwan Darmadi (email:iwan.darmadi@alumni.ui.ac.id) for technical support, bug reports, feature requests, or questions regarding PySpecTrace.
+
+
+---
+
+

pyspectrace-2.0.0/pyproject.toml

@@ -0,0 +1,38 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "pyspectrace"
+version = "2.0.0"
+description = "**PySpecTrace** is an open-source, Python-based graphical user interface (GUI) designed for real-time UV-visible-NIR spectroscopy data analysis. It addresses the limitations of proprietary spectrometer software by providing advanced, customizable, and real-time spectral tracking and analysis tools suitable for a wide range of scientific disciplines"
+readme = "README.md"
+requires-python = ">=3.9,<3.13"
+license = "Apache-2.0"
+
+authors = [
+  { name = "Iwan Darmadi", email = "iwan.darmadi@alumni.ui.ac.id" }
+]
+
+classifiers = [
+  "License :: OSI Approved :: Apache Software License",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+]
+
+dependencies = [
+  "numpy==1.26.4",
+  "pandas==2.3.3",
+  "matplotlib==3.9.4",
+  "PyQt5==5.15.11",
+  "pyqtgraph==0.13.7",
+  "scipy==1.13.1",
+  "seatease==0.4.0",
+  "seabreeze==2.11.0"
+]
+
+[project.gui-scripts]
+pyspectrace = "pyspectrace.main:main"

pyspectrace-2.0.0/src/pyspectrace/Control/Configuration/Acquisition/Communication/communicationcontrol.py

@@ -0,0 +1,34 @@
+
+class CommunicationControl:
+    def __init__(self, model, view):
+        self.model = model
+        self.view = view
+        
+        self.delay_time = 250
+
+        self.view.configurationlayout.acquisitionlayout.communicationlayout.time_integration_button.clicked.connect(
+            lambda: self.integration_time_change(
+                self.view.configurationlayout.acquisitionlayout.communicationlayout.time_integration_spinbox.value()
+                )
+            )
+        self.view.configurationlayout.acquisitionlayout.communicationlayout.acquisitiondelay_button.clicked.connect(
+            lambda: self.acquisition_delay_change(
+                self.view.configurationlayout.acquisitionlayout.communicationlayout.acquisitiondelay_spinbox.value()
+                )
+            )
+    
+    def mainloop(self):
+        self.acquire()
+
+    def acquire(self):
+        cumulative_plot = [self.model.acquire_spectrum()]       
+        self.view.plottinglayout.spectrumlayout.num_spectrum = [None]
+        self.view.plottinglayout.spectrumlayout.plot_spectrum(cumulative_plot, cumulative_plot)
+
+    def integration_time_change(self, slot_integration_value):
+        self.model.set_integration_time(slot_integration_value)
+
+    def acquisition_delay_change(self, slot_delay_value):
+        self.delay_time = slot_delay_value
+        self.model.set_acquisition_delay(slot_delay_value)
+

pyspectrace-2.0.0/src/pyspectrace/Control/Configuration/Acquisition/Saving/savingcontrol.py

@@ -0,0 +1,190 @@
+import numpy as np
+from datetime import datetime, timedelta
+import os
+
+class SavingControl:
+    def __init__(self, model, view):
+        self.model = model
+        self.view = view
+        self.mainpath = self.view.configurationlayout.acquisitionlayout.savinglayout.combined_path_text
+        self.processed_wavelengths = None
+        self.processed_intensities = None
+
+        self.raw_wavelengths = None
+        self.raw_intensities = None
+
+        self.stateresume = True
+
+        self.current_forprogress = 0
+        self.elapsed_time = 0
+
+        # self.current_progress = 0
+        self.count_saved = 0
+
+        self.cumulative_delta_time = 0
+        self.frame_list_txt = 0
+        self.cumulative_delta_time_raw = 0
+
+        self.cumulative_delta_time_list = []
+        self.cumulative_delta_time_list_raw = []
+
+        self.delta_timestart = datetime.now()   
+        # self.delta_timestart_raw = datetime.now()
+        # self.delta_timestart = time.perf_counter()      
+        # self.delta_timestart_raw = time.perf_counter()
+        self.start_time = datetime.now()
+        self.start_time_progress = datetime.now()
+
+        self.view.configurationlayout.acquisitionlayout.savinglayout.enable_record_checkbox.stateChanged.connect(self.inittime_save_slot)
+        self.view.configurationlayout.acquisitionlayout.savinglayout.apply_button.clicked.connect(self.init_time_save)
+        self.view.configurationlayout.acquisitionlayout.savinglayout.pauseresumebuttom.clicked.connect(self.pauseresumestate)
+
+    def mainloop(self):
+        if self.view.configurationlayout.acquisitionlayout.savinglayout.status_saving:     
+            if self.stateresume:
+                _current_time = datetime.now()
+                self.elapsed_time = (_current_time - self.start_time).total_seconds()
+                
+                interval = self.view.configurationlayout.acquisitionlayout.savinglayout.interval_saving.value()
+                progress_percent = min(int((self.elapsed_time / interval) * 100), 100)
+                self.view.configurationlayout.acquisitionlayout.savinglayout.progress.setValue(progress_percent)
+                
+                
+                if self.elapsed_time >= self.view.configurationlayout.acquisitionlayout.savinglayout.interval_saving.value():
+                    self.intervalstart()
+                    self.savingtxt()
+                    self.start_time = _current_time
+                    self.current_progress = 0
+                    self.view.record_value_saved.setText(f"{self.count_saved}")
+                    self.view.configurationlayout.acquisitionlayout.savinglayout.progress.setValue(0)
+                    self.intervalend()
+            else:
+                _current_time = datetime.now()
+                self.start_time = _current_time - timedelta(seconds=self.elapsed_time)
+
+                self.delta_timestart =  _current_time - timedelta(seconds=self.elapsed_time)
+                # self.delta_timestart_raw =  _current_time - timedelta(seconds=self.elapsed_time)
+
+
+    def pauseresumestate(self):
+        if self.view.configurationlayout.acquisitionlayout.savinglayout.pauseresumebuttom.text() == "Pause":
+            self.stateresume = False
+            self.view.configurationlayout.acquisitionlayout.savinglayout.pauseresumebuttom.setText("Resume")
+
+        elif self.view.configurationlayout.acquisitionlayout.savinglayout.pauseresumebuttom.text() == "Resume":
+            self.stateresume = True
+            self.view.configurationlayout.acquisitionlayout.savinglayout.pauseresumebuttom.setText("Pause")
+
+    def intervalstart(self):
+        self.current_time = datetime.now()
+        self.current_time_raw = datetime.now()
+
+    def intervalend(self):
+        self.delta_timestart = self.delta_timeend 
+        # self.delta_timestart_raw = self.delta_timeend_raw
+    
+    def savingtxt(self):
+        processed_wavelengths, processed_intensities = self.model.acquire_spectrum()
+        raw_wavelengths, raw_intensities = self.model.acquire_spectrum_for_normalization()
+
+        self.delta_timeend = datetime.now()
+        self.delta_timeend_raw = datetime.now()
+        # self.delta_timeend = time.perf_counter()
+        # self.delta_timeend_raw = time.perf_counter()
+
+        self.delta_time = (self.delta_timeend - self.delta_timestart).total_seconds()
+        self.delta_time = np.array(self.delta_time)
+        self.delta_time = np.full(len(processed_intensities), self.delta_time)
+        
+        self.frame_list_txt = self.frame_list_txt + 1
+
+        processed_data = [processed_wavelengths, processed_intensities, self.delta_time]
+        raw_data = [raw_wavelengths, raw_intensities, self.delta_time]
+
+        processed_data_transposed = list(map(list, zip(*processed_data)))
+        raw_data_transposed = list(map(list, zip(*raw_data)))
+
+        filename = self.current_time.strftime("%Y-%m-%d_%H-%M-%S")
+
+        self.mainpath = self.view.configurationlayout.acquisitionlayout.savinglayout.combined_path_text
+        os.makedirs(os.path.join(self.mainpath, 'processed'), exist_ok=True)
+        os.makedirs(os.path.join(self.mainpath, 'raw'), exist_ok=True)
+
+        save_path_processed = os.path.join(self.mainpath, 'processed', f'{self.frame_list_txt}-index-processed_spectrum_{filename}.txt')
+        save_path_raw = os.path.join(self.mainpath, 'raw', f'{self.frame_list_txt}-index-raw_spectrum_{filename}.txt')
+
+        for sublist in processed_data_transposed:
+            sublist.append(self.current_time.strftime("%Y-%m-%d %H-%M-%S-%f"))
+        try:
+            with open(save_path_processed, "w") as file:
+                file.write(("[wavelength, intensities, timedelta, date, time]") + "\n")
+                file.write((">>>>>Begin Processed Spectral Data<<<<<") + "\n")
+                for sublist in processed_data_transposed:
+                    file.write(" ".join(map(str, sublist)) + "\n")
+                file.write((">>>>>End Processed Spectral Data<<<<<") + "\n")
+                self.count_saved = self.count_saved + 1
+        except:
+            print("error txt processed saved")
+            pass
+
+        for sublist in raw_data_transposed:
+            sublist.append(self.current_time.strftime("%Y-%m-%d %H-%M-%S-%f"))
+        try:
+            with open(save_path_raw, "w") as file:
+                file.write(("[wavelength, intensities, timedelta, date, time]") + "\n")
+                file.write((">>>>>Begin Processed Spectral Data<<<<<") + "\n")
+                for sublist in raw_data_transposed:
+                    file.write(" ".join(map(str, sublist)) + "\n")
+                file.write((">>>>>End Processed Spectral Data<<<<<") + "\n")
+            self.count_saved = self.count_saved + 1
+        except:
+            print("error txt raw saved")
+            pass
+
+
+    def inittime_save_slot(self, state):
+        if state == 2:
+            self.view.configurationlayout.acquisitionlayout.savinglayout.inittime_save = datetime.now().strftime("%Y-%m-%d_%H-%M-%S_%f")
+            self.view.configurationlayout.acquisitionlayout.savinglayout.update_combined_text()
+            self.mainpath = self.view.configurationlayout.acquisitionlayout.savinglayout.combined_path_text
+
+        if state == 0:
+            self.count_saved = 0
+            self.view.record_value_saved.setText(f"{self.count_saved}")
+    
+    def init_time_save(self):
+            if self.view.configurationlayout.acquisitionlayout.savinglayout.syncsensorgram.isChecked():
+                self.view.configurationlayout.plottinglayout.sensorgramlayout.reset_button.click()
+
+            self.processed_wavelengths = None
+            self.processed_intensities = None
+
+            self.raw_wavelengths = None
+            self.raw_intensities = None
+
+            # self.current_progress = 0
+            self.current_forprogress = 0
+            self.count_saved = 0
+            
+
+            self.cumulative_delta_time = 0
+            self.frame_list_txt = 0
+            self.cumulative_delta_time_raw = 0
+
+            self.delta_timestart = datetime.now()     
+            # self.delta_timestart = time.perf_counter()      
+            self.cumulative_delta_time_list = []
+            # self.delta_timestart_raw = datetime.now()
+            # self.delta_timestart_raw = time.perf_counter()
+            self.cumulative_delta_time_list_raw = []
+            self.start_time = datetime.now()
+            self.start_time_progress = datetime.now()
+        
+            
+
+    def onesecond_left(self, start_time):
+        current_time = datetime.now()
+        elapsed_time = (current_time - start_time).total_seconds()
+        if elapsed_time >= 0.1:
+            return True
+        return False

pyspectrace-2.0.0/src/pyspectrace/Control/Configuration/Acquisition/acquisitioncontrol.py

@@ -0,0 +1,10 @@
+from pyspectrace.Control.Configuration.Acquisition.Communication.communicationcontrol import CommunicationControl
+from pyspectrace.Control.Configuration.Acquisition.Saving.savingcontrol import SavingControl
+class AcquisitionControl:
+    def __init__(self, 
+                 model, 
+                 view):
+        self.model = model
+        self.view = view
+        self.communicationcontrol = CommunicationControl(model, view)
+        self.savingcontrol = SavingControl(model, view)

pyspectrace-2.0.0/src/pyspectrace/Control/Configuration/Plotting/Sensorgramcontrol/__init__.py

@@ -0,0 +1,6 @@
+from PyQt5.QtCore import QTimer
+
+class SpectrumControl:
+    def __init__(self, model, view):
+        self.model = model
+        self.view = view