phasor-handler 2.3.0__tar.gz → 3.1.0__tar.gz

{phasor_handler-2.3.0/phasor_handler.egg-info → phasor_handler-3.1.0}/PKG-INFO

@@ -1,136 +1,176 @@
-Metadata-Version: 2.4
-Name: phasor-handler
-Version: 2.3.0
-Summary: A PyQt6 GUI toolbox for processing two-photon phasor imaging data
-Author-email: Josia Shemuel <joshemuel@users.noreply.github.com>
-License: MIT License
-        
-        Copyright (c) 2025 Josia Shemuel
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy
-        of this software and associated documentation files (the "Software"), to deal
-        in the Software without restriction, including without limitation the rights
-        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        copies of the Software, and to permit persons to whom the Software is
-        furnished to do so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in all
-        copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-        SOFTWARE.
-Project-URL: Homepage, https://github.com/joshemuel/Phasor-Handler
-Project-URL: Repository, https://github.com/joshemuel/Phasor-Handler
-Project-URL: Issues, https://github.com/joshemuel/Phasor-Handler/issues
-Keywords: two-photon,phasor,imaging,calcium,neuroscience,suite2p
-Classifier: Development Status :: 4 - Beta
-Classifier: Intended Audience :: Science/Research
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Topic :: Scientific/Engineering :: Image Processing
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Operating System :: Microsoft :: Windows
-Classifier: Environment :: X11 Applications :: Qt
-Requires-Python: <3.10,>=3.9.23
-Description-Content-Type: text/markdown
-License-File: LICENSE.md
-Requires-Dist: PyQt6>=6.4.0
-Requires-Dist: numpy<2.0.0,>=1.21.0
-Requires-Dist: matplotlib>=3.5.0
-Requires-Dist: tifffile>=2021.11.2
-Requires-Dist: pyyaml>=6.0
-Requires-Dist: suite2p>=0.14.0
-Requires-Dist: pyqtdarktheme>=1.0.0
-Requires-Dist: Pillow>=9.0.0
-Requires-Dist: scikit-image>=0.19.0
-Requires-Dist: scipy>=1.7.0
-Requires-Dist: npTDMS>=1.2.0
-Requires-Dist: pandas>=1.3.0
-Provides-Extra: dev
-Requires-Dist: pytest>=7.0.0; extra == "dev"
-Requires-Dist: black>=22.0.0; extra == "dev"
-Requires-Dist: flake8>=4.0.0; extra == "dev"
-Dynamic: license-file
-
-# Phasor-Handler (Windows)
-
-Phasor Handler is a toolbox for processing raw two-photon phasor imaging data: **convert → register → explore → extract calcium traces**.  
-It provides a PyQt6 GUI for viewing registered or raw stacks (Ch1/Ch2), z-projections (std/max/mean), drawing/storing ROIs, overlaying stimulated ROIs from metadata, and exporting ROI traces.
-
-> ⚠️ **Platform:** Windows 10/11 only  
-> 🧪 Status: actively developed (Brightness & Contrast dialog is WIP)
-
----
-
-## Features
-
-- Load **registered TIFF** (`Ch1-reg.tif`, `Ch2-reg.tif`) or **raw NPY** fallbacks (`ImageData_Ch0_TP0000000.npy`, `ImageData_Ch1_TP0000000.npy`)
-- Linear and non-linear motion-correct **TIFF images** using Suite2p
-- Automated cell detection using Suite2p
-- Channel switching (Ch1/Ch2) and **Composite (G/R)**
-- **Z-projections**: standard deviation, max, mean
-- **ROI tools**: draw elliptical ROIs, translate or rotate ROIs, save/load as JSON, quick-select saved ROIs
-- **Stimulus overlay**: show stimulated ROI locations from experiment metadata and add to the saved ROIs
-- **Trace plotting**: configurable formula, custom y-limits, frame/time (s) x-axis
-- **Export**: write per-ROI traces for all frames to `.txt` (tab-separated)
-- Keyboard: `R` save/add ROI, `Delete` remove selected ROI, `Esc` clear selection, `Alt+S` load stimulated ROIs, `Right Click + drag` translate selected ROI, `Y` toggle right click to rotation mode
-
----
-
-## Input data layout
-
-For each dataset directory, Phasor Handler looks for any of:
-
-- Ch1-reg.tif
-- Ch2-reg.tif                 # optional
-- ImageData_Ch0_TP0000000.npy # raw fallback for Ch1
-- ImageData_Ch1_TP0000000.npy # optional raw fallback for Ch2
-- experiment_summary.pkl      # optional metadata (or .json)
-
-Registered TIFFs are preferred when available; raw NPYs are used as fallback.
-
----
-
-## Installation (Windows, Conda)
-
-This project provides an `environment.yml` for Windows. The environment is large (GUI, image I/O, napari/suite2p), so **mamba** is recommended, but `conda` works too.
-
-### 1) Install Conda/Mamba (if needed)
-- Install **Miniconda** or **Mambaforge** on Windows.
-- (Optional) Add mamba for faster solves:
-  ```powershell
-  conda install -n base -c conda-forge mamba
-
-### 2) Get the code
-- Clone the repo and change it into
-  ```powershell
-  git clone https://github.com/joshemuel/Phasor-Handler.git
-  chdir Phasor-Handler
-- Alternatively, you can download the entire project as a zip file, unzip it, then open that directory in **Miniconda**
-  cd Phasor-Handler
-
-### 3) Create the environment
-- Using mamba:
-  ```powershell
-  mamba env create -f environment.yml
-- Using conda:
-  ```powershell
-  conda env create -f environment.yml
-
-# 4) Activate and run
-- Before running the toolbox, activate the environment
-  ```powershell
-  conda activate suite2p
-  python app.py
-## Update (Windows, Conda)
-
-### 1) Go to your local repo and pull the latest code from the branch you use
-```powershell
-chdir Phasor-Handler
-git pull --ff-only
+Metadata-Version: 2.4
+Name: phasor-handler
+Version: 3.1.0
+Summary: A PyQt6 GUI toolbox for processing two-photon phasor imaging data
+Author-email: Josia Shemuel <joshemuel@users.noreply.github.com>
+License: MIT License
+        
+        Copyright (c) 2025 Josia Shemuel
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+Project-URL: Homepage, https://github.com/joshemuel/Phasor-Handler
+Project-URL: Repository, https://github.com/joshemuel/Phasor-Handler
+Project-URL: Issues, https://github.com/joshemuel/Phasor-Handler/issues
+Keywords: two-photon,phasor,imaging,calcium,neuroscience,suite2p
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Environment :: X11 Applications :: Qt
+Requires-Python: <3.10,>=3.9.23
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: PyQt6>=6.4.0
+Requires-Dist: numpy<2.0.0,>=1.21.0
+Requires-Dist: matplotlib>=3.5.0
+Requires-Dist: tifffile>=2021.11.2
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: suite2p>=0.14.0
+Requires-Dist: pyqtdarktheme>=1.0.0
+Requires-Dist: Pillow>=9.0.0
+Requires-Dist: scikit-image>=0.19.0
+Requires-Dist: scipy>=1.7.0
+Requires-Dist: npTDMS>=1.2.0
+Requires-Dist: pandas>=1.3.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: black>=22.0.0; extra == "dev"
+Requires-Dist: flake8>=4.0.0; extra == "dev"
+Dynamic: license-file
+
+# Phasor-Handler (Windows)
+
+Phasor Handler is a toolbox for processing raw two-photon phasor imaging data:  **convert → register → explore → extract calcium traces**.  
+It provides a PyQt6 GUI for viewing registered or raw stacks (Ch1/Ch2), z-projections (std/max/mean), drawing/storing ROIs, overlaying stimulated ROIs from metadata, and exporting ROI traces.
+
+> ⚠️ **Platform:** Windows 10/11 only  
+> 🚀 **Version 3.0** — Latest stable release
+
+---
+
+## Features
+
+- Load **registered TIFF** (`Ch1-reg.tif`, `Ch2-reg.tif`) or **raw NPY** fallbacks (`ImageData_Ch0_TP0000000.npy`, `ImageData_Ch1_TP0000000.npy`)
+- Linear and non-linear motion-correct **TIFF images** using Suite2p
+- Automated cell detection using Suite2p
+- Channel switching (Ch1/Ch2) and **Composite (G/R)**
+- **Z-projections**: standard deviation, max, mean
+- **Brightness & Contrast (BnC)**: adjust image display settings
+- **ROI tools**: draw elliptical ROIs, **freehand drawing tool**, translate or rotate ROIs, **move multiple ROIs**, save/load as JSON, quick-select saved ROIs
+- **Metadata viewer**: inspect experiment metadata directly in the application
+- **Second-level analysis viewer**: explore and visualize second-level analysis results
+- **Stimulus overlay**: show stimulated ROI locations from experiment metadata and add to the saved ROIs
+- **Trace plotting**: configurable formula, custom y-limits, frame/time (s) x-axis
+- **Export**: write per-ROI traces for all frames to `.txt` (tab-separated)
+- Keyboard: `R` save/add ROI, `Delete` remove selected ROI, `Esc` clear selection, `Alt+S` load stimulated ROIs, `Right Click + drag` translate selected ROI, `Y` toggle right click to rotation mode
+
+---
+
+## Input data layout
+
+For each dataset directory, Phasor Handler looks for any of: 
+
+- Ch1-reg.tif
+- Ch2-reg. tif                 # optional
+- ImageData_Ch0_TP0000000.npy # raw fallback for Ch1
+- ImageData_Ch1_TP0000000.npy # optional raw fallback for Ch2
+- experiment_summary.pkl      # optional metadata (or .json)
+
+Registered TIFFs are preferred when available; raw NPYs are used as fallback.
+
+---
+
+## Installation
+
+Phasor Handler is now available on **PyPI** and can be installed via pip or from source using Conda/Mamba. 
+
+### Option 1: Install via pip (Recommended)
+
+The easiest way to install Phasor Handler is through pip:
+
+```powershell
+pip install phasor-handler
+```
+
+After installation, you can run the application: 
+
+```powershell
+phasor-handler
+```
+
+**PyPI Package:** [https://pypi.org/project/phasor-handler/](https://pypi.org/project/phasor-handler/)
+
+### Option 2: Install from source (Windows, Conda)
+
+This project provides an `environment.yml` for Windows. The environment is large (GUI, image I/O, napari/suite2p), so **mamba** is recommended, but `conda` works too.
+
+#### 1) Install Conda/Mamba (if needed)
+- Install **Miniconda** or **Mambaforge** on Windows.
+- (Optional) Add mamba for faster solves:
+  ```powershell
+  conda install -n base -c conda-forge mamba
+  ```
+
+#### 2) Get the code
+- Clone the repo and change into it:
+  ```powershell
+  git clone https://github.com/joshemuel/Phasor-Handler.git
+  cd Phasor-Handler
+  ```
+- Alternatively, you can download the entire project as a zip file, unzip it, then open that directory in **Miniconda**
+
+#### 3) Create the environment
+- Using mamba:
+  ```powershell
+  mamba env create -f environment.yml
+  ```
+- Using conda:
+  ```powershell
+  conda env create -f environment.yml
+  ```
+
+#### 4) Activate and run
+- Before running the toolbox, activate the environment:
+  ```powershell
+  conda activate suite2p
+  python app.py
+  ```
+
+---
+
+## Update (Windows, Conda)
+
+### If installed via pip: 
+```powershell
+pip install --upgrade phasor-handler
+```
+
+### If installed from source: 
+
+#### 1) Go to your local repo and pull the latest code from the branch you use
+```powershell
+cd Phasor-Handler
+git pull --ff-only
+```
+
+---

{phasor_handler-2.3.0 → phasor_handler-3.1.0}/README.md

@@ -1,10 +1,10 @@
 # Phasor-Handler (Windows)
 
-Phasor Handler is a toolbox for processing raw two-photon phasor imaging data: **convert → register → explore → extract calcium traces**.  
+Phasor Handler is a toolbox for processing raw two-photon phasor imaging data:  **convert → register → explore → extract calcium traces**.  
 It provides a PyQt6 GUI for viewing registered or raw stacks (Ch1/Ch2), z-projections (std/max/mean), drawing/storing ROIs, overlaying stimulated ROIs from metadata, and exporting ROI traces.
 
 > ⚠️ **Platform:** Windows 10/11 only  
-> 🧪 Status: actively developed (Brightness & Contrast dialog is WIP)
+> 🚀 **Version 3.0** — Latest stable release
 
 ---
 
@@ -15,7 +15,10 @@ It provides a PyQt6 GUI for viewing registered or raw stacks (Ch1/Ch2), z-projec
 - Automated cell detection using Suite2p
 - Channel switching (Ch1/Ch2) and **Composite (G/R)**
 - **Z-projections**: standard deviation, max, mean
-- **ROI tools**: draw elliptical ROIs, translate or rotate ROIs, save/load as JSON, quick-select saved ROIs
+- **Brightness & Contrast (BnC)**: adjust image display settings
+- **ROI tools**: draw elliptical ROIs, **freehand drawing tool**, translate or rotate ROIs, **move multiple ROIs**, save/load as JSON, quick-select saved ROIs
+- **Metadata viewer**: inspect experiment metadata directly in the application
+- **Second-level analysis viewer**: explore and visualize second-level analysis results
 - **Stimulus overlay**: show stimulated ROI locations from experiment metadata and add to the saved ROIs
 - **Trace plotting**: configurable formula, custom y-limits, frame/time (s) x-axis
 - **Export**: write per-ROI traces for all frames to `.txt` (tab-separated)
@@ -25,10 +28,10 @@ It provides a PyQt6 GUI for viewing registered or raw stacks (Ch1/Ch2), z-projec
 
 ## Input data layout
 
-For each dataset directory, Phasor Handler looks for any of:
+For each dataset directory, Phasor Handler looks for any of: 
 
 - Ch1-reg.tif
-- Ch2-reg.tif                 # optional
+- Ch2-reg. tif                 # optional
 - ImageData_Ch0_TP0000000.npy # raw fallback for Ch1
 - ImageData_Ch1_TP0000000.npy # optional raw fallback for Ch2
 - experiment_summary.pkl      # optional metadata (or .json)
@@ -37,40 +40,77 @@ Registered TIFFs are preferred when available; raw NPYs are used as fallback.
 
 ---
 
-## Installation (Windows, Conda)
+## Installation
+
+Phasor Handler is now available on **PyPI** and can be installed via pip or from source using Conda/Mamba. 
+
+### Option 1: Install via pip (Recommended)
+
+The easiest way to install Phasor Handler is through pip:
+
+```powershell
+pip install phasor-handler
+```
+
+After installation, you can run the application: 
+
+```powershell
+phasor-handler
+```
+
+**PyPI Package:** [https://pypi.org/project/phasor-handler/](https://pypi.org/project/phasor-handler/)
+
+### Option 2: Install from source (Windows, Conda)
 
 This project provides an `environment.yml` for Windows. The environment is large (GUI, image I/O, napari/suite2p), so **mamba** is recommended, but `conda` works too.
 
-### 1) Install Conda/Mamba (if needed)
+#### 1) Install Conda/Mamba (if needed)
 - Install **Miniconda** or **Mambaforge** on Windows.
 - (Optional) Add mamba for faster solves:
   ```powershell
   conda install -n base -c conda-forge mamba
+  ```
 
-### 2) Get the code
-- Clone the repo and change it into
+#### 2) Get the code
+- Clone the repo and change into it:
   ```powershell
   git clone https://github.com/joshemuel/Phasor-Handler.git
-  chdir Phasor-Handler
-- Alternatively, you can download the entire project as a zip file, unzip it, then open that directory in **Miniconda**
   cd Phasor-Handler
+  ```
+- Alternatively, you can download the entire project as a zip file, unzip it, then open that directory in **Miniconda**
 
-### 3) Create the environment
+#### 3) Create the environment
 - Using mamba:
   ```powershell
   mamba env create -f environment.yml
+  ```
 - Using conda:
   ```powershell
   conda env create -f environment.yml
+  ```
 
-# 4) Activate and run
-- Before running the toolbox, activate the environment
+#### 4) Activate and run
+- Before running the toolbox, activate the environment:
   ```powershell
   conda activate suite2p
   python app.py
+  ```
+
+---
+
 ## Update (Windows, Conda)
 
-### 1) Go to your local repo and pull the latest code from the branch you use
+### If installed via pip: 
 ```powershell
-chdir Phasor-Handler
+pip install --upgrade phasor-handler
+```
+
+### If installed from source: 
+
+#### 1) Go to your local repo and pull the latest code from the branch you use
+```powershell
+cd Phasor-Handler
 git pull --ff-only
+```
+
+---

{phasor_handler-2.3.0 → phasor_handler-3.1.0}/phasor_handler/__init__.py

@@ -4,6 +4,6 @@ Phasor Handler - Two-Photon Phasor Imaging Data Processor
 A PyQt6 GUI toolbox for processing two-photon phasor imaging data.
 """
 
-__version__ = "2.3.0"
+__version__ = "3.1.0"
 __author__ = "Josia Shemuel"
 __all__ = ["app", "widgets", "workers", "models", "scripts", "tools", "themes"]

{phasor_handler-2.3.0 → phasor_handler-3.1.0}/phasor_handler/app.py

@@ -14,7 +14,7 @@ from PyQt6.QtCore import Qt
 from PyQt6.QtCore import QThread
 
 from .widgets import ConversionWidget, RegistrationWidget, AnalysisWidget, SecondLevelWidget
-from .workers import RegistrationWorker, ConversionWorker
+from .workers import RegistrationWorker, ConversionWorker, ConvertRegisterWorker
 from .models.dir_manager import DirManager
 from .themes import apply_dark_theme
 import qdarktheme
@@ -109,26 +109,29 @@ class MainWindow(QMainWindow):
         if hasattr(self, 'analysis_list_widget'):
             self.analysis_list_widget.clear()
 
-        from PyQt6.QtWidgets import QListWidgetItem
-        for full_path, display_name in self.dir_manager.get_display_names():
-            if hasattr(self, 'conv_list_widget'):
-                item = QListWidgetItem(display_name)
-                item.setToolTip(full_path)
-                item.setData(Qt.ItemDataRole.UserRole, full_path)
-                self.conv_list_widget.addItem(item)
-            if hasattr(self, 'reg_list_widget'):
-                try:
-                    item = QListWidgetItem(display_name)
-                    item.setToolTip(full_path)
-                    item.setData(Qt.ItemDataRole.UserRole, full_path)
-                    self.reg_list_widget.addItem(item)
-                except RuntimeError:
-                    pass
-            if hasattr(self, 'analysis_list_widget'):
-                item = QListWidgetItem(display_name)
-                item.setToolTip(full_path)
-                item.setData(Qt.ItemDataRole.UserRole, full_path)
-                self.analysis_list_widget.addItem(item)
+        from PyQt6.QtWidgets import QListWidgetItem
+        # Conversion and Registration tabs keep insertion order
+        for full_path, display_name in self.dir_manager.get_display_names():
+            if hasattr(self, 'conv_list_widget'):
+                item = QListWidgetItem(display_name)
+                item.setToolTip(full_path)
+                item.setData(Qt.ItemDataRole.UserRole, full_path)
+                self.conv_list_widget.addItem(item)
+            if hasattr(self, 'reg_list_widget'):
+                try:
+                    item = QListWidgetItem(display_name)
+                    item.setToolTip(full_path)
+                    item.setData(Qt.ItemDataRole.UserRole, full_path)
+                    self.reg_list_widget.addItem(item)
+                except RuntimeError:
+                    pass
+        # Analysis list is sorted by capture time
+        if hasattr(self, 'analysis_list_widget'):
+            for full_path, display_name in self.dir_manager.get_display_names(sort_by_time=True):
+                item = QListWidgetItem(display_name)
+                item.setToolTip(full_path)
+                item.setData(Qt.ItemDataRole.UserRole, full_path)
+                self.analysis_list_widget.addItem(item)
 
     def on_tab_changed(self, idx):
         # When switching to first level tab, refresh its directory list
@@ -145,8 +148,8 @@ class MainWindow(QMainWindow):
                 self.analysis_list_widget.blockSignals(True)
                 self.analysis_list_widget.clear()
                 
-                from PyQt6.QtWidgets import QListWidgetItem
-                for full_path, display_name in self.dir_manager.get_display_names():
+                from PyQt6.QtWidgets import QListWidgetItem
+                for full_path, display_name in self.dir_manager.get_display_names(sort_by_time=True):
                     item = QListWidgetItem(display_name)
                     item.setToolTip(full_path)
                     item.setData(Qt.ItemDataRole.UserRole, full_path)
@@ -258,11 +261,82 @@ class MainWindow(QMainWindow):
             del self._reg_worker
             del self._reg_thread
 
-        self._reg_worker.finished.connect(_on_finished)
-        self._reg_worker.error.connect(lambda e: self.reg_log.append(f"ERROR: {e}"))
-        self._reg_thread.start()
-
-def main():
+        self._reg_worker.finished.connect(_on_finished)
+        self._reg_worker.error.connect(lambda e: self.reg_log.append(f"ERROR: {e}"))
+        self._reg_thread.start()
+
+    def run_convert_and_register(self):
+        """Run conversion followed by registration on all directories in one step."""
+        if not self.selected_dirs:
+            QMessageBox.warning(self, "No Directories",
+                                "Please add at least one directory to the list before running.")
+            return
+
+        mode = self.mode_combo.currentText().lower()
+
+        # Gather registration parameters from the Registration tab
+        reg_params = {}
+        if hasattr(self, 'param_names') and hasattr(self, 'param_edits'):
+            for name, edit in zip(self.param_names, self.param_edits):
+                value = edit.text().strip()
+                if value:
+                    reg_params[name] = value
+
+        combine = True
+        if hasattr(self, 'combine_checkbox'):
+            combine = self.combine_checkbox.isChecked()
+
+        # Disable the button while running
+        run_btn = None
+        for w in self.findChildren(QPushButton):
+            if w.text().startswith("Convert + Register"):
+                run_btn = w
+                break
+        if run_btn:
+            run_btn.setEnabled(False)
+
+        self.conv_log.clear()
+        if hasattr(self, 'reg_log'):
+            self.reg_log.clear()
+
+        # Create thread and worker
+        self._cr_thread = QThread()
+        self._cr_worker = ConvertRegisterWorker(
+            self.selected_dirs.copy(), mode, reg_params, combine)
+        self._cr_worker.moveToThread(self._cr_thread)
+
+        # Connect signals
+        self._cr_thread.started.connect(self._cr_worker.run)
+        def _cr_log(s):
+            self.conv_log.append(s)
+            if hasattr(self, 'reg_log'):
+                self.reg_log.append(s)
+            QApplication.processEvents()
+        self._cr_worker.log.connect(_cr_log)
+
+        def _on_finished():
+            if run_btn:
+                run_btn.setEnabled(True)
+            self._cr_thread.quit()
+            self._cr_thread.wait()
+            self._cr_worker.deleteLater()
+            del self._cr_worker
+            del self._cr_thread
+
+        def _on_error(err_msg):
+            self.conv_log.append(f"[ERROR] {err_msg}")
+            if hasattr(self, 'reg_log'):
+                self.reg_log.append(f"[ERROR] {err_msg}")
+            QMessageBox.critical(self, "Convert+Register Error",
+                                 f"An error occurred:\n{err_msg}")
+
+        self._cr_worker.finished.connect(_on_finished)
+        self._cr_worker.error.connect(_on_error)
+
+        # Start the thread
+        self._cr_thread.start()
+
+def main():
     app = QApplication(sys.argv)
     try:
         qdarktheme.setup_theme()  # or your own apply_dark_theme()