melage 0.0.68__py3-none-any.whl → 1.0.0__py3-none-any.whl

melage/widgets/{dockWidgets.py → DockWidgets.py}

@@ -1,6 +1,6 @@
 __AUTHOR__ = 'Bahram Jafrasteh'
 
-
+from pathlib import Path
 import sys
 sys.path.append("../")
 from PyQt5 import QtWidgets, QtCore, QtGui
@@ -16,7 +16,10 @@ colorNames =("#FFCC08","darkRed","red", "darkOrange", "orange", "#8b8b00","yello
 
 
 from melage.utils.utils import read_txt_color, set_new_color_scheme, addTreeRoot, update_color_scheme, addLastColor, update_image_sch
-from melage.utils.source_folder import source_folder
+from melage.config import settings
+
+
+
 
 
 class dockWidgets():
@@ -26,6 +29,34 @@ class dockWidgets():
     def __init__(self):
         pass
 
+    # This function should be a method in your main class
+    def style_row_by_checkstate(self, item):
+        """
+        Styles the entire row based on the check state of the item in the first column.
+        """
+        # Get the model from self, not from an argument
+        model = self.tree_colors.model().sourceModel()
+        if not model:
+            return
+
+        row = item.row()
+        # Get the item in the first column to read the consistent check state for the row
+        check_item = model.item(row, 0)
+
+        if check_item and check_item.checkState() == QtCore.Qt.Checked:
+            brush = QtGui.QBrush(QtGui.QColor(212, 237, 218, 60))  # Light green
+        else:
+            brush = QtGui.QBrush(QtCore.Qt.transparent)  # Default/transparent
+
+        # Loop through all columns in the row and apply the style
+        for col in range(model.columnCount()):
+            item_in_row = model.item(row, col)
+            if item_in_row:
+                item_in_row.setBackground(brush)
+
+
+
+
     def createDockWidget(self, Main):
         """
         Creating main attributes for the main widgets
@@ -197,6 +228,12 @@ class dockWidgets():
         self.tree_colors.setRootIsDecorated(True)
         self.tree_colors.setUniformRowHeights(True)
         self.tree_colors.setModel(self.tags_model)
+        self.tree_colors.setStyleSheet("""
+            QTreeView::item {
+                padding-top: 5px;      /* 5px space above the content */
+                padding-bottom: 5px;   /* 5px space below the content */
+            }
+        """)
 
         # layout
         main_layout = QtWidgets.QVBoxLayout()
@@ -945,10 +982,10 @@ class dockWidgets():
 
         #size = self.dw2_cb.style().pixelMetric(QtWidgets.QStyle.PM_SmallIconSize)
         #pixmp = QtGui.QPixmap(size, size)
-        #color_name, color_index_rgb, _ = read_txt_color(source_folder+"/color/LUT_albert.txt", from_one=True)
+        #color_name, color_index_rgb, _ = read_txt_color(settings.RESOURCE_DIR+"/color/LUT_albert.txt", from_one=True)
         #set_new_color_scheme(self, color_name, color_index_rgb)
 
-        self.color_name, self.color_index_rgb, _ = read_txt_color(source_folder+"/color/Simple.txt", mode= '', from_one=True)
+        self.color_name, self.color_index_rgb, _ = read_txt_color(settings.RESOURCE_DIR+"/color/Simple.txt", mode= '', from_one=True)
         #update_color_scheme(self, None, dialog=False, update_widget=False)
         from collections import defaultdict
         self.colorsCombinations = defaultdict(list)
@@ -966,8 +1003,23 @@ class dockWidgets():
         set_new_color_scheme(self)
 
 
-        self.tree_colors.model().sourceModel().itemChanged.connect(self.changeColorPen)
 
+        #self.tree_colors.model().sourceModel().itemChanged.connect(self.Upper_changeColorPen)
+        self.tree_colors.clicked.connect(self.on_row_clicked)
+        # In your setup method, after populating the model...
+
+        # This connection is correct, assuming the function signature is fixed
+        #self.tree_colors.model().sourceModel().itemChanged.connect(self.style_row_by_checkstate)
+
+        # This loop must be corrected
+        model = self.tree_colors.model().sourceModel()
+        root = model.invisibleRootItem()
+        for row in range(root.rowCount()):
+            # Get the item in the first column (where the checkbox is)
+            item = root.child(row, 0)
+            if item:
+                # Call the function with only the item
+                self.style_row_by_checkstate(item)
         #####
 
 
@@ -1378,7 +1430,13 @@ class dockWidgets():
         self.tree_images.setRootIsDecorated(True)
         self.tree_images.setUniformRowHeights(True)
         self.tree_images.setModel(self.tags_model_image)
-
+        self.tree_images.setStyleSheet("""
+            QTreeView::item {
+                padding-top: 5px;      /* 5px space above the content */
+                padding-bottom: 5px;   /* 5px space below the content */
+            }
+        """)
+        #self.tree_images.clicked.connect(self.on_row_clicked)
         # layout
         #main_layout = QtWidgets.QVBoxLayout()
 
@@ -1399,7 +1457,8 @@ class dockWidgets():
         self.imported_images = []
 
 
-        self.tree_images.model().sourceModel().itemChanged.connect(self.changeImage)
+        #self.tree_images.model().sourceModel().itemChanged.connect(self.changeImage)
+        self.tree_images.clicked.connect(self.on_row_clicked_image)
 
         #self.gridLayout_color.addWidget(self.tree_colors, 1, 0, 1, 1)
 
@@ -1536,7 +1595,7 @@ class dockWidgets():
         :return:
         """
         def dialog():
-            from melage.widgets.fileDialog_widget import QFileDialogPreview
+            from melage.widgets.helpers.fileDialog_widget import QFileDialogPreview
             opts = QtWidgets.QFileDialog.DontUseNativeDialog
             dialg = QFileDialogPreview(self, "Open File", self.source_dir, self._filters, options=opts,
                                        index=self._last_index_select_image_mri,
@@ -1573,14 +1632,14 @@ class dockWidgets():
         menu_import.setTitle(_translate('Main', "Import"))
         import_image_action_1 = QtWidgets.QAction(self)
         icon_mri = QtGui.QIcon()
-        icon_mri.addPixmap(QtGui.QPixmap(source_folder+"/mri.png"), QtGui.QIcon.Normal, QtGui.QIcon.On)
+        icon_mri.addPixmap(QtGui.QPixmap(settings.RESOURCE_DIR+"/mri.png"), QtGui.QIcon.Normal, QtGui.QIcon.On)
         icon_mriS = QtGui.QIcon()
-        icon_mriS.addPixmap(QtGui.QPixmap(source_folder+"/mri_seg.png"), QtGui.QIcon.Normal, QtGui.QIcon.On)
+        icon_mriS.addPixmap(QtGui.QPixmap(settings.RESOURCE_DIR+"/mri_seg.png"), QtGui.QIcon.Normal, QtGui.QIcon.On)
 
         icon_eco = QtGui.QIcon()
-        icon_eco.addPixmap(QtGui.QPixmap(source_folder+"/eco.png"), QtGui.QIcon.Normal, QtGui.QIcon.On)
+        icon_eco.addPixmap(QtGui.QPixmap(settings.RESOURCE_DIR+"/eco.png"), QtGui.QIcon.Normal, QtGui.QIcon.On)
         icon_ecoS = QtGui.QIcon()
-        icon_ecoS.addPixmap(QtGui.QPixmap(source_folder+"/eco_seg.png"), QtGui.QIcon.Normal, QtGui.QIcon.On)
+        icon_ecoS.addPixmap(QtGui.QPixmap(settings.RESOURCE_DIR+"/eco_seg.png"), QtGui.QIcon.Normal, QtGui.QIcon.On)
 
         import_image_action_1.setIcon(icon_eco)
         import_image_action_1.setIconText('Images (view 1)')
@@ -1715,42 +1774,36 @@ class dockWidgets():
         remove_action = menu.addAction("&Remove")
         import_action = menu.addAction("&Import")
         export_action = menu.addAction("&Export")
-        menu_color = QtWidgets.QMenu(menu)
-        menu_color.setObjectName('Color')
-        menu_color.setWindowIconText('CCC')
-        _translate = QtCore.QCoreApplication.translate
-        menu_color.setTitle(_translate('Main', "Scheme"))
-        action_albert = QtWidgets.QAction(self)
-        action_albert.setIconText('Albert')
-        menu_color.addAction(action_albert)
 
-        action_tissue = QtWidgets.QAction(self)
-        action_tissue.setIconText('Tissue')
-        menu_color.addAction(action_tissue)
+        # --- Dynamic Submenu Creation ---
+        menu_color = QtWidgets.QMenu("Scheme", menu)
+
+        scheme_action_group = QtWidgets.QActionGroup(self)
+        scheme_action_group.setExclusive(True)
 
-        action_tissue12 = QtWidgets.QAction(self)
-        action_tissue12.setIconText('Tissue12')
-        menu_color.addAction(action_tissue12)
+        # 1. Define the directory to scan
+        color_dir = Path(settings.RESOURCE_DIR) / 'color'
 
-        action_mcrib = QtWidgets.QAction(self)
-        action_mcrib.setIconText('MCrib')
-        menu_color.addAction(action_mcrib)
+        # 2. Loop through each .txt file and create an action for it
+        if color_dir.is_dir():
+            # Sort files alphabetically for a consistent menu order
+            for file_path in sorted(color_dir.glob('*.txt')):
+                # Create an action for this file
+                action = QtWidgets.QAction(self)
 
-        action_pediatrics1 = QtWidgets.QAction(self)
-        action_pediatrics1.setIconText('Pediatric1')
-        menu_color.addAction(action_pediatrics1)
+                # Use the filename without extension as the action's text (e.g., "Simple")
+                action.setText(file_path.stem)
 
-        action_pediatrics2 = QtWidgets.QAction(self)
-        action_pediatrics2.setIconText('Pediatric2')
-        menu_color.addAction(action_pediatrics2)
+                action.setCheckable(True)
+                scheme_action_group.addAction(action)
 
-        action_simple = QtWidgets.QAction(self)
-        action_simple.setIconText('Simple')
-        menu_color.addAction(action_simple)
+                # Store the full file path in the action's data field. This is key!
+                action.setData(str(file_path))
 
+                menu_color.addAction(action)
 
-        menu.addMenu(menu_color)
-        #menu_color.addAction(import_action)
+        if not menu_color.isEmpty():
+            menu.addMenu(menu_color)
 
         action = menu.exec_(self.tree_colors.viewport().mapToGlobal(pos))
         if action == edit_action:
@@ -1770,6 +1823,8 @@ class dockWidgets():
             root = self.tree_colors.model().sourceModel().invisibleRootItem()
             root.removeRow(index.row())
         else:
+            if action is None:
+                return
             if action==import_action:
                 from PyQt5.QtWidgets import QFileDialog
                 filters = "TXT(*.txt)"
@@ -1778,8 +1833,6 @@ class dockWidgets():
                 filen = fileObj[0]
                 if filen=='':
                     return
-            elif action == action_simple:
-                filen = source_folder+"/color/Simple.txt"
             elif action == export_action:
                 filters = "TXT (*.txt)"
                 opts = QtWidgets.QFileDialog.DontUseNativeDialog
@@ -1809,18 +1862,10 @@ class dockWidgets():
                     print(e)
 
 
-            elif action == action_pediatrics1:
-                filen = source_folder+"/color/pediatric1.txt"
-            elif action == action_pediatrics2:
-                filen = source_folder+"/color/pediatric2.txt"
-            elif action == action_albert:
-                filen = source_folder + "/color/albert_LUT.txt"
-            elif action == action_mcrib:
-                filen = source_folder + "/color/mcrib_LUT.txt"
-            elif action == action_tissue:
-                filen = source_folder + "/color/Tissue.txt"
-            elif action == action_tissue12:
-                filen = source_folder + "/color/Tissue12.txt"
+            # 3. Handle ALL dynamically created scheme actions with one check
+            elif action.data():
+                filen = action.data()
+
             else:
                 return
             try: #TODO : Sep 11 2024
@@ -1828,6 +1873,21 @@ class dockWidgets():
             except:
                 return
             #if not (hasattr(self, 'readImECO') and hasattr(self, 'readImMRI')):
+
+            ind_avail = [9876]
+            try:
+                ind_avail += list(np.unique(self.readImECO.npSeg))
+            except:
+                pass
+            try:
+                ind_avail += list(np.unique(self.readImMRI.npSeg))
+            except:
+                pass
+            color_vec = possible_color_index_rgb[:, 0].astype('int')
+            list_avail = list(set(color_vec) & set(ind_avail))
+            mask_color = np.isin(color_vec, list_avail)
+            possible_color_index_rgb = possible_color_index_rgb[mask_color, :]
+            possible_color_name = list(np.array(possible_color_name)[mask_color])
             uq = []
             set_not_in_new_list = set(uq) - (set(possible_color_index_rgb[:, 0].astype('int')))
             set_kept_new_list = set_not_in_new_list - (
@@ -1856,9 +1916,14 @@ class dockWidgets():
                 possible_color_name.append(new_colr_name)
                 possible_color_index_rgb = np.vstack((possible_color_index_rgb, np.array(new_color_rgb)))
 
+
+
+
             # self.color_index_rgb, self.color_name, self.colorsCombinations = combinedIndex(self.colorsCombinations, possible_color_index_rgb, possible_color_name, np.unique(data), uq1)
             self.color_index_rgb, self.color_name, self.colorsCombinations = generate_color_scheme_info(
-                possible_color_index_rgb, possible_color_name)
+                self, possible_color_index_rgb, possible_color_name)
+
+
             try:
                 # self.dw2_cb.currentTextChanged.disconnect(self.changeColorPen)
                 self.tree_colors.itemChanged.disconnect(self.changeColorPen)
@@ -1877,11 +1942,14 @@ class dockWidgets():
                 widget = getattr(self, name)
                 if hasattr(widget, 'colorsCombinations'):
                     widget.colorsCombinations = self.colorsCombinations
+                if hasattr(widget, 'color_name'):
+                    widget.color_name = self.color_name
                 if not widget.isVisible():
                     continue
                 if hasattr(widget, 'makeObject'):
                     widget.makeObject()
 
+
                 if num in [13]:
                     try:
                         widget.paint(self.readImECO.npSeg,

melage/widgets/SettingsWidget.py

@@ -0,0 +1,98 @@
+from PyQt5 import QtWidgets, QtCore
+from PyQt5.QtWidgets import QDialog, QFileDialog, QLineEdit, QPushButton
+from pathlib import Path
+
+# Import the global settings instance
+from melage.config import settings
+
+
+class SettingsDialog(QDialog):
+    """
+    A dialog for editing application settings.
+    It reads from and saves to the global SettingsManager.
+    """
+
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.setWindowTitle("MELAGE Settings")
+        self.setModal(True)  # Block other windows while open
+        self.setupUi()
+        self.load_settings()
+
+    def setupUi(self):
+        self.main_layout = QtWidgets.QVBoxLayout(self)
+
+        # --- Create a form layout ---
+        form_layout = QtWidgets.QFormLayout()
+
+        # --- Auto-save setting ---
+        self.auto_save_spinbox = QtWidgets.QDoubleSpinBox()
+        self.auto_save_spinbox.setSuffix(" minutes")
+        form_layout.addRow("Auto-save interval:", self.auto_save_spinbox)
+
+        # --- Default Save Directory ---
+        self.save_dir_edit = QLineEdit()
+        self.save_dir_button = QPushButton("Browse...")
+        self.save_dir_button.clicked.connect(self.browse_save_dir)
+        save_dir_layout = QtWidgets.QHBoxLayout()
+        save_dir_layout.addWidget(self.save_dir_edit)
+        save_dir_layout.addWidget(self.save_dir_button)
+        form_layout.addRow("Default Save Directory:", save_dir_layout)
+
+        # --- Models Directory ---
+        self.models_dir_edit = QLineEdit()
+        self.models_dir_button = QPushButton("Browse...")
+        self.models_dir_button.clicked.connect(self.browse_models_dir)
+        models_dir_layout = QtWidgets.QHBoxLayout()
+        models_dir_layout.addWidget(self.models_dir_edit)
+        models_dir_layout.addWidget(self.models_dir_button)
+        form_layout.addRow("Models Directory:", models_dir_layout)
+
+        self.main_layout.addLayout(form_layout)
+
+        # --- OK / Cancel Buttons ---
+        button_box = QtWidgets.QDialogButtonBox(
+            QtWidgets.QDialogButtonBox.Ok | QtWidgets.QDialogButtonBox.Cancel
+        )
+        button_box.accepted.connect(self.accept)  # Calls our save_settings method
+        button_box.rejected.connect(self.reject)
+
+        self.main_layout.addWidget(button_box)
+
+    def browse_save_dir(self):
+        """Lets user pick a default save directory."""
+        directory = QFileDialog.getExistingDirectory(
+            self, "Select Default Save Directory", self.save_dir_edit.text()
+        )
+        if directory:
+            self.save_dir_edit.setText(directory)
+
+    def browse_models_dir(self):
+        """Lets user pick a models directory."""
+        directory = QFileDialog.getExistingDirectory(
+            self, "Select Models Directory", self.models_dir_edit.text()
+        )
+        if directory:
+            self.models_dir_edit.setText(directory)
+
+    def load_settings(self):
+        """Load current settings from the manager into the UI."""
+        self.auto_save_spinbox.setValue(settings.auto_save_interval)
+        self.save_dir_edit.setText(str(settings.DEFAULT_USE_DIR))
+        self.models_dir_edit.setText(str(settings.DEFAULT_MODELS_DIR))
+
+    def update_use_dir(self, new_dir):
+        settings.DEFAULT_USE_DIR = str(Path(new_dir))
+
+    def save_settings(self):
+        """Save UI values back to the settings manager and persist."""
+        settings.auto_save_interval = self.auto_save_spinbox.value()
+        settings.DEFAULT_USE_DIR = str(Path(self.save_dir_edit.text()))
+        settings.DEFAULT_MODELS_DIR = str(Path(self.models_dir_edit.text()))
+
+        settings.save()  # This saves to the JSON file
+
+    def accept(self):
+        """Called when OK is clicked."""
+        self.save_settings()
+        super().accept()  # Closes the dialog

melage/widgets/__init__.py

@@ -0,0 +1,49 @@
+from PyQt5.QtWidgets import QWidget
+import nibabel as nib
+
+class MelagePlugin:
+    """
+    The base class "contract" for all MELAGE plugins.
+
+    A plugin must provide its name and a method to create its main widget.
+    """
+
+    def __init__(self):
+        pass
+
+    @property
+    def name(self) -> str:
+        """The name of the plugin to be shown in the menu."""
+        raise NotImplementedError("Plugin must have a name.")
+
+    @property
+    def description(self) -> str:
+        """A short description for tooltips."""
+        return ""  # Optional
+
+    @property
+    def reference(self) -> str:
+        """
+        Returns a citation, DOI, or URL for the algorithm.
+        Supports HTML (e.g., <a href='...'>Link</a>).
+        """
+        return ""
+
+    @property
+    def category(self) -> str:
+        """Category to group plugins in (e.g., "Segmentation", "Registration")."""
+        return "General"  # Default category
+
+    def get_widget(self, parent=None) -> QWidget:
+        """
+        The main function. This method must create and return
+        the plugin's main QWidget (or QDialog).
+        """
+        raise NotImplementedError("Plugin must provide a widget.")
+
+
+from .DockWidgets import dockWidgets
+from .EnhanceImageWidget import enhanceIm
+from .SettingsWidget import SettingsDialog
+from .openglWidgets import openglWidgets
+from .plugin_manager import PluginManager