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

melage/utils/utils.py

@@ -4,6 +4,7 @@ __AUTHOR__ = 'Bahram Jafrasteh'
 
 import sys
 from operator import index
+from pathlib import Path
 
 sys.path.append("../../")
 import numpy as np
@@ -28,7 +29,7 @@ try:
 except:
     None
 try:
-    from melage.utils.source_folder import source_folder
+    from melage.config import settings
 except:
     pass
 # Direction of medical image Left, Right, Posterior Anterior, Inferior, Superior
@@ -43,6 +44,50 @@ class Item:
     size: bytes
 
 
+
+
+
+def get_filter_for_file(filename, all_filters):
+    """
+    Returns the specific filter string (e.g., 'Nifti (*.nii)') that matches
+    the given filename.
+    """
+    # 1. Split the massive filter string into individual categories
+    # "Nifti(...);;Vol(...)" -> ["Nifti(...)", "Vol(...)"]
+    categories = all_filters.split(';;')
+
+    # We compare in lowercase to handle extensions robustly (e.g., .NII vs .nii)
+    filename_lower = filename.lower()
+
+    for category in categories:
+        # 2. Extract the part inside parentheses: "*.nii *.nii.gz"
+        start = category.find('(')
+        end = category.find(')')
+
+        if start != -1 and end != -1:
+            # Get the content inside ()
+            pattern_str = category[start + 1:end]
+
+            # Split into individual extensions: ["*.nii", "*.nii.gz"]
+            patterns = pattern_str.split()
+
+            for pattern in patterns:
+                # Clean the pattern to get the suffix
+                # "*.nii.gz" -> ".nii.gz"
+                # "**" -> skip
+                clean_ext = pattern.replace('*', '').lower()
+
+                if not clean_ext:
+                    continue  # Skip empty or pure wildcards
+
+                # 3. Check if the filename ends with this extension
+                # "mri.nii.gz" ends with ".nii.gz" -> Match!
+                if filename_lower.endswith(clean_ext):
+                    return category
+
+    # Fallback: If no specific match found, return "All Files" or the first one
+    return "All Files (*)"
+
 def guess_num_image_index(nifti_input):
     """
     Guess which axis of the image shape represents the 'num_images' (volume/time/channel) dimension.
@@ -56,7 +101,7 @@ def guess_num_image_index(nifti_input):
     if isinstance(nifti_input, nib.Nifti1Image):
         hdr = nifti_input.header
     else:
-        return None, 1
+        return np.argmin(nifti_input.shape), 1
 
     ndim = hdr['dim'][0]
     shape = hdr['dim'][1:4]
@@ -380,7 +425,10 @@ def resample_to_spacing(im, newSpacing, method='spline'):
 
 
         # Define the new spacing (voxel size) for resampling
-        new_spacing = (newSpacing, newSpacing, newSpacing)
+        if type(newSpacing)==list or type(newSpacing)==tuple:
+            new_spacing = newSpacing
+        else:
+            new_spacing = (newSpacing, newSpacing, newSpacing)
 
         # Calculate the new size based on the original size and spacing
         new_size = [int(sz * spc / new_spc + 0.5) for sz, spc, new_spc in
@@ -403,7 +451,7 @@ def resample_to_spacing(im, newSpacing, method='spline'):
         return read_sitk_as_nib(resampled_image)
     except:
         from nibabel.processing import resample_to_output
-        return resample_to_output(im, [newSpacing, newSpacing, newSpacing])
+        return resample_to_output(im, new_spacing)
 
 
 ###################### Help dialogue to open new image ######################
@@ -468,174 +516,6 @@ def calculate_snr(image_array):
 
 ###################### A class to  resize image######################
 
-class resize_window(QtWidgets.QDialog):
-    from PyQt5.QtCore import pyqtSignal
-    closeSig = pyqtSignal()
-    resizeim = pyqtSignal(object)
-    comboboxCh = pyqtSignal(object, object)
-    """
-    A dialog for combo box created for reading 4d images
-    """
-    def __init__(self, parent=None, use_combobox=False):
-        QtWidgets.QDialog.__init__(self, parent)
-        self.setWindowTitle("Child Window!")
-        Dialog = self.window()
-        self.use_combobox = use_combobox
-        self.setupUi(Dialog)
-        self.check_box.setCheckState(Qt.Checked)
-        self._status = False
-
-    def setupUi(self, Dialog):
-
-        Dialog.setObjectName("Dialog")
-        Dialog.resize(500, 112)
-        self.grid_main = QtWidgets.QGridLayout(self)
-        self.grid_main.setContentsMargins(10,10,10,10)
-        self.grid_main.setObjectName("gridLayout")
-
-        self.hbox_0 = QtWidgets.QHBoxLayout()
-        self.label_warning = QtWidgets.QLabel()
-        self.label_warning.setText('The pixels are not isotropic. Do you want to resize image (isotropic)?')
-
-
-        self.hbox_0.addWidget(self.label_warning)
-
-        _translate = QtCore.QCoreApplication.translate
-        self.pushbutton = QtWidgets.QDialogButtonBox()
-        self.pushbutton_cancel = QtWidgets.QPushButton()
-        self.pushbutton.setStandardButtons(QtWidgets.QDialogButtonBox.Ok | QtWidgets.QDialogButtonBox.Cancel)
-        self.pushbutton.accepted.connect(self.accept_it)
-        self.pushbutton.rejected.connect(self.reject_it)
-
-        #self.hbox_0.addWidget(self.pushbutton)
-
-        if self.use_combobox:
-            self.comboBox_image = QtWidgets.QComboBox()
-            self.comboBox_image.setObjectName("comboBox_image")
-            self.comboBox_image.addItem("")
-            self.comboBox_image.addItem("")
-            self.comboBox_image.currentIndexChanged.connect(self.comboBOX_changed)
-            #
-            self.hbox_0.addWidget(self.comboBox_image)
-            self.grid_main.addLayout(self.hbox_0, 0, 0, 1, 1)
-        else:
-            self.grid_main.addLayout(self.hbox_0, 0, 0, 1, 1)
-
-        self.grid_main.addWidget(self.pushbutton, 3, 0, 1, 1)
-        self.check_box = QtWidgets.QCheckBox()
-
-        self.check_box.stateChanged.connect(self.changeAllSpacing)
-
-
-        self.label_current_spc0 = QtWidgets.QLabel()
-        self.label_current_spc0.setText('Current Spacing')
-
-        self.label_current_spc = QtWidgets.QLabel()
-        #self.label_current_spc.setReadOnly(True)
-        self.label_current_spc.setText('0,0,0')
-
-
-        self.radioButton_1 = QtWidgets.QCheckBox()
-
-        self.radioButton_1.setObjectName("radioButton_1")
-        self.radioButton_1.setChecked(False)
-
-        self.hbox = QtWidgets.QHBoxLayout()
-        self.hbox.addWidget(self.check_box)
-        self.hbox.addWidget(self.radioButton_1)
-        self.hbox.addWidget(self.label_current_spc0)
-        self.hbox.addWidget(self.label_current_spc)
-
-
-        self.hbox2 = QtWidgets.QHBoxLayout()
-        self.label_new_spc0 = QtWidgets.QLabel()
-        self.label_new_spc0.setText('New Spacing')
-        self.label_new_spc0.setStyleSheet('color: Red')
-
-        self.label_new_spc = QtWidgets.QDoubleSpinBox(self)
-        self.label_new_spc_y = QtWidgets.QDoubleSpinBox(self)
-        self.label_new_spc_z = QtWidgets.QDoubleSpinBox(self)
-
-        for spin_box in (self.label_new_spc, self.label_new_spc_y, self.label_new_spc_z):
-            spin_box.setMinimum(0.01)
-            spin_box.setMaximum(20)
-            spin_box.setSingleStep(0.1)
-            spin_box.setValue(1.0)
-            spin_box.setDecimals(2)
-
-        self.hbox2.addWidget(self.label_new_spc0)
-        self.hbox2.addWidget(self.label_new_spc)
-        self.hbox2.addWidget(self.label_new_spc_y)
-        self.hbox2.addWidget(self.label_new_spc_z)
-
-
-        #self.pushbutton.setText(_translate("Dialog", "OK"))
-        #self.grid_main.addWidget(self.label_warning, 0,0,1,1)
-        self.grid_main.addLayout(self.hbox, 1,0,1,1)
-        self.grid_main.addLayout(self.hbox2,2,0,1,1)
-
-        #self.hbox3 = QtWidgets.QHBoxLayout()
-
-
-        #self.grid_main.addLayout(self.hbox_0, 3, 0, 1, 1)
-
-
-        self.retranslateUi(Dialog)
-
-        QtCore.QMetaObject.connectSlotsByName(Dialog)
-
-    def changeAllSpacing(self, state):
-        if state == QtCore.Qt.Checked:
-            # Connect the change signal to synchronize function
-            self.label_new_spc.valueChanged.connect(self.synchronizeSpacings)
-            self.label_new_spc_y.valueChanged.connect(self.synchronizeSpacings)
-            self.label_new_spc_z.valueChanged.connect(self.synchronizeSpacings)
-        else:
-            # Disconnect the synchronize function to allow independent changes
-            self.label_new_spc.valueChanged.disconnect(self.synchronizeSpacings)
-            self.label_new_spc_y.valueChanged.disconnect(self.synchronizeSpacings)
-            self.label_new_spc_z.valueChanged.disconnect(self.synchronizeSpacings)
-
-    def synchronizeSpacings(self, value):
-        # Set the value of all spin boxes to the changed value
-        self.label_new_spc.blockSignals(True)
-        self.label_new_spc_y.blockSignals(True)
-        self.label_new_spc_z.blockSignals(True)
-        self.label_new_spc.setValue(value)
-        self.label_new_spc_y.setValue(value)
-        self.label_new_spc_z.setValue(value)
-        self.label_new_spc.blockSignals(False)
-        self.label_new_spc_y.blockSignals(False)
-        self.label_new_spc_z.blockSignals(False)
-
-    def comboBOX_changed(self):
-        ind = self.comboBox_image.currentIndex()
-        self.comboboxCh.emit(None, ind)
-
-    def retranslateUi(self, Dialog):
-        _translate = QtCore.QCoreApplication.translate
-        Dialog.setWindowTitle(_translate("Dialog", "Resize..."))
-
-        _translate = QtCore.QCoreApplication.translate
-        self.radioButton_1.setText(_translate("Main", "Linear"))
-        self.check_box.setText(_translate("Main", "Isotropic"))
-        if self.use_combobox:
-            self.comboBox_image.setItemText(0, _translate("Form", "        Top Image        "))
-            self.comboBox_image.setItemText(1, _translate("Form", "      Bottom Image      "))
-    def closeEvent(self, a0: QtGui.QCloseEvent) -> None:
-        self.closeSig.emit()
-        super(resize_window, self).closeEvent(a0)
-    def accept_it(self):
-        self._status = True
-        if self.use_combobox:
-            index = self.comboBox_image.currentIndex()
-            self.resizeim.emit(index)
-        self.accept()
-
-    def reject_it(self):
-        self._status = False
-        self.reject()
-
 ########### COMBO BOX To read 4D images #####################
 class ComboBox_Dialog(QtWidgets.QDialog):
     """
@@ -920,9 +800,199 @@ def manually_check_tree_item(self, txt='9876'):
     for l in ls:
         root.child(l).setCheckState(Qt.Checked)
     return ls
+####################### Discover all scheme files #####################
+def discover_color_files(base_folder):
+    """
+    Dynamically finds all .txt files in the 'color' subdirectory.
+
+    Args:
+        base_folder (str): The root folder containing the 'color' directory.
 
+    Returns:
+        dict: A dictionary where keys are filenames (without extension)
+              and values are the relative paths to the .txt files.
+              Returns an empty dictionary if the folder doesn't exist.
+    """
+    color_dir = Path(base_folder) / 'color'
+    if not color_dir.is_dir():
+        print(f"Warning: Color directory not found at '{color_dir}'")
+        return {}
+
+    # Create a dictionary mapping the filename (e.g., 'Simple')
+    # to its relative path (e.g., 'color/Simple.txt')
+    # The .lower() makes the key consistent for lookups.
+    return {
+        path.stem: f"/color/{path.name}"
+        for path in color_dir.glob('*.txt')
+    }
 ###################### Updating current color scheme ##################
-def update_color_scheme(self, data, data_add=None, dialog=True, update_widget=True):
+
+MAX_COLORS = 255
+COMBINED_COLOR_ID = 9876
+DEFAULT_COLOR_FILES = {
+    'simple': '/color/Simple.txt',
+    'tissue': '/color/Tissue.txt',
+    'albert': '/color/albert_LUT.txt',
+    'mcrib': '/color/mcrib_LUT.txt',
+}
+from PyQt5.QtWidgets import QFileDialog
+
+# --- Helper Functions (These perform the specific, isolated tasks) ---
+
+def _get_required_indices(data, data_add=None):
+    """Extracts unique positive integer indices from data arrays."""
+
+    indices = set([l for l in np.unique(data).astype('int') if l > 0])
+    if data_add is not None:
+        indices.update([l for l in np.unique(data_add).astype('int') if l > 0])
+    return {idx for idx in indices if idx > 0}
+
+
+def _get_color_filepath(app_instance, show_dialog, unique_count):
+
+    """Gets color file path via dialog or automatic selection."""
+    if show_dialog:
+        filters = "Text files (*.txt)"
+        opts = QFileDialog.DontUseNativeDialog
+        file_path, _ = QFileDialog.getOpenFileName(app_instance, "Open Color File", settings.DEFAULT_USE_DIR, filters,
+                                                   options=opts)
+        if file_path!='':
+            return file_path
+    available_files = discover_color_files(settings.RESOURCE_DIR)
+    if not available_files:
+        print("Error: No color files found.")
+        return None # No files to choose from
+    # Automatic selection logic
+    # This example selects a file based on name, similar to before.
+    if unique_count <= 2 and 'Simple' in available_files:
+        filepath = available_files['Simple']
+    elif unique_count <= 9 and 'Tissue' in available_files:
+        filepath = available_files['Tissue']
+    elif unique_count < 90 and 'albert_LUT' in available_files:
+        filepath = available_files['albert_LUT']
+    elif 'mcrib_LUT' in available_files: # Fallback for larger counts
+        filepath = available_files['mcrib_LUT']
+    else:
+        # If no specific logic matches, just pick the first available file
+        filepath = next(iter(available_files.values()))
+    filepath = available_files["FreeSurferColorLUT"]
+    return settings.RESOURCE_DIR + filepath
+
+
+def _load_color_definitions(file_path):
+    """Loads color definitions from a text file, trying multiple formats."""
+    try:
+        names, rgb_data, _ = read_txt_color(file_path, from_one=False, mode='albert')
+        return {'names': names, 'rgb': rgb_data}
+    except Exception as e1:
+        print(f"Could not read '{file_path}' in primary format. Trying fallback. Error: {e1}")
+        try:
+            names, rgb_data, _ = read_txt_color(file_path, from_one=False)
+            return {'names': names, 'rgb': rgb_data}
+        except Exception as e2:
+            print(f"Error: Failed to read color file '{file_path}'. Error: {e2}")
+            return None
+
+
+def _update_ui_widgets(app_instance):
+    """Safely disconnects, updates, and reconnects UI signals and widgets."""
+    try:
+        #self.dw2_cb.currentTextChanged.disconnect(self.changeColorPen)
+        app_instance.tree_colors.itemChanged.disconnect(app_instance.changeColorPen)
+    except:
+        pass
+
+    set_new_color_scheme(app_instance)
+    try:
+        #self.dw2_cb.currentTextChanged.connect(self.changeColorPen)
+        app_instance.tree_colors.itemChanged.connect(app_instance.changeColorPen)
+    except:
+        pass
+
+
+# --- Main Function ---
+
+def update_color_scheme(app_instance, data, data_add=None, dialog=True, update_widget=True):
+    """
+    Updates the application's color scheme based on indices present in the data.
+
+    Args:
+        app_instance: The instance of the application class (what was 'self').
+        data (np.ndarray): The primary data array with color indices.
+        data_add (np.ndarray, optional): Additional data array with color indices.
+        dialog (bool): If True, shows a file dialog to select a color file.
+        update_widget (bool): If True, updates the UI widgets after the scheme is changed.
+
+    Returns:
+        tuple[np.ndarray, bool]: The original data array and a success flag.
+    """
+    if data is None:
+        data = np.array([0, 1])
+
+    # 1. Determine which color indices are required
+    required_indices = _get_required_indices(data, data_add)
+    if len(required_indices) > MAX_COLORS:
+        print(f"Error: Number of unique colors exceeds the limit of {MAX_COLORS}.")
+        return data, False
+
+    current_indices = set(app_instance.color_index_rgb[:, 0].astype(int))
+    new_indices_needed = required_indices - current_indices
+
+    if not new_indices_needed:
+        return data, True  # Success, no update was needed
+
+    # 2. Get the color file and load the color definitions
+    color_file_path = _get_color_filepath(app_instance, dialog, len(required_indices))
+    #if not color_file_path:
+    #    return data, False  # User cancelled or no file found
+
+    loaded_colors = _load_color_definitions(color_file_path)
+    #if loaded_colors is None:
+    #    return data, False  # Failed to load file
+
+    # 3. Merge new colors with the existing scheme and update the app's state
+    loaded_rgb_map = {int(row[0]): row for row in loaded_colors['rgb']}
+    loaded_name_map = {int(name.split('_')[0]): name for name in loaded_colors['names']}
+
+    final_rgb = list(app_instance.color_index_rgb)
+    final_names = list(app_instance.color_name)
+
+    for ii, index in enumerate(new_indices_needed):
+        if index in loaded_rgb_map:
+            final_rgb.append(loaded_rgb_map[index])
+            final_names.append(loaded_name_map.get(index, f"{index}_unknown"))
+        else:
+            new_rgb_row = [index, np.random.rand(), np.random.rand(), np.random.rand(), 1]
+            final_rgb.append(new_rgb_row)
+            final_names.append(f"{index}_structure_unknown")
+
+    # Ensure the special "Combined" color exists
+    if COMBINED_COLOR_ID not in {int(row[0]) for row in final_rgb}:
+        final_rgb.append([COMBINED_COLOR_ID, 1, 0, 0, 1])
+        final_names.append(f"{COMBINED_COLOR_ID}_Combined")
+
+
+    # Update the application state directly on the passed instance
+    app_instance.color_index_rgb, app_instance.color_name, app_instance.colorsCombinations = \
+        generate_color_scheme_info(app_instance,np.array(final_rgb), final_names)
+
+    widgets_num = [0, 1, 2, 3, 4, 5, 10, 11, 13, 23]
+    for num in widgets_num:
+        name = 'openGLWidget_' + str(num + 1)
+        widget = getattr(app_instance, name)
+        if hasattr(widget, 'colorsCombinations'):
+            widget.colorsCombinations = app_instance.colorsCombinations
+        if hasattr(widget, 'color_name'):
+            widget.color_name = app_instance.color_name
+
+    # 4. Update the UI components
+    if update_widget:
+        _update_ui_widgets(app_instance)
+
+    return data, True
+
+
+def update_color_scheme0(self, data, data_add=None, dialog=True, update_widget=True):
     """
     Updating current color scheme
     Args:
@@ -935,7 +1005,7 @@ def update_color_scheme(self, data, data_add=None, dialog=True, update_widget=Tr
 
     """
     if data_add is not None:
-        uq1 = [l for l in np.unique(data_add) if l > 0]
+        uq1 = [l for l in np.unique(data_add).astype('int') if l > 0]
     else:
         uq1 = []
     if data is None:
@@ -963,13 +1033,13 @@ def update_color_scheme(self, data, data_add=None, dialog=True, update_widget=Tr
             print('automatic files')
             len_u = len(np.unique(data))
             if len_u<=2:
-                filen = source_folder + '/color/Simple.txt'
+                filen = settings.RESOURCE_DIR + '/color/Simple.txt'
             elif len_u<=9:
-                filen = source_folder + '/color/Tissue.txt'
+                filen = settings.RESOURCE_DIR + '/color/Tissue.txt'
             elif len_u <90:
-                filen = source_folder + '/color/albert_LUT.txt'
+                filen = settings.RESOURCE_DIR + '/color/albert_LUT.txt'
             else:
-                filen = source_folder + '/color/mcrib_LUT.txt'
+                filen = settings.RESOURCE_DIR + '/color/mcrib_LUT.txt'
             from_one = False
         try:
             possible_color_name, possible_color_index_rgb, _ = read_txt_color(filen, from_one=from_one, mode='albert')
@@ -1007,7 +1077,7 @@ def update_color_scheme(self, data, data_add=None, dialog=True, update_widget=Tr
             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.color_index_rgb, self.color_name, self.colorsCombinations = generate_color_scheme_info(self, possible_color_index_rgb, possible_color_name)
         try:
             #self.dw2_cb.currentTextChanged.disconnect(self.changeColorPen)
             self.tree_colors.itemChanged.disconnect(self.changeColorPen)
@@ -1193,7 +1263,7 @@ def getUnique(mat):
     return np.unique(mat)
 
 ###################### Generate info for color schemes ##################
-def generate_color_scheme_info(color_index_rgb, color_name):
+def generate_color_scheme_info(reader, color_index_rgb, color_name):
     """
     Generate color scheme information
     Args:
@@ -1258,7 +1328,77 @@ def set_new_color_scheme(self):
         addTreeRoot(parent, '9876', 'Combined', colr)
 
 ################# SET IMAGE SCHEME ###########################
-def update_image_sch(self, info=None, color = [1,1,0],loaded = False):
+from PyQt5 import QtGui, QtCore
+import os
+import numpy as np
+
+# Place this helper method inside your main class
+def _is_image_already_added(self, file_path, view_index):
+    """Checks if an image has already been added to a specific view."""
+    for item_data in self.imported_images:
+        existing_file = item_data[0][0][0]
+        existing_view_index = item_data[0][0][2]
+        if file_path == existing_file and view_index == existing_view_index:
+            return True
+    return False
+
+# Your updated function
+def update_image_sch(self, info=None, color=[1, 1, 0], loaded=False):
+    """
+    Sets a new color scheme and adds items for multiple images.
+    """
+    # SUGGESTION: Add a guard clause for safety
+    if info is None:
+        return
+
+    if hasattr(self, 'tree_images'):
+        parent = self.tree_images.model().sourceModel().invisibleRootItem()
+        fileObj, index, index_view = info
+
+        # Determine the description string for the view
+        if index >= 3:
+            indc = f'View {index_view + 1} (seg)'
+        else:
+            indc = f'View {index_view + 1}'
+
+        color_255 = [int(c * 255) for c in color]
+
+        for file in fileObj[0]:
+            if '*' in file:
+                continue
+
+            # SUGGESTION: Use the clearer helper function
+            if not _is_image_already_added(self, file, index_view):
+                self.imported_images.append([[[file, fileObj[1], index_view], index], color, loaded, indc])
+            else:
+                # If it already exists, skip adding it to the tree
+                continue
+
+            # --- Create Tree Items ---
+            node1 = QtGui.QStandardItem(indc)
+            node1.setForeground(QtGui.QBrush(QtGui.QColor(*color_255)))
+            node1.setData(index_view)
+
+            # SUGGESTION: Set flags correctly to prevent the double-toggle bug
+            # DO NOT include ItemIsUserCheckable
+            node1.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsTristate)
+            node1.setCheckable(True)
+            node1.setFlags(node1.flags() & QtCore.Qt.ItemIsUserCheckable)
+
+            # Set initial check state
+            node1.setCheckState(QtCore.Qt.Checked if loaded else QtCore.Qt.Unchecked)
+
+            descp = os.path.basename(file)
+            node2 = QtGui.QStandardItem(descp)
+            node2.setForeground(QtGui.QBrush(QtGui.QColor(*color_255)))
+            # SUGGESTION: No need for flags on a non-checkable item
+            # node2.setFlags(...)
+            #node2.setFlags(node2.flags() | QtCore.Qt.ItemIsTristate)
+
+            parent.appendRow([node1, node2])
+
+
+def update_image_sch_to_remove(self, info=None, color = [1,1,0],loaded = False):
     """
     SET new color scheme to read multiple images
     Args:
@@ -1395,7 +1535,8 @@ def clean_parent_image2(self, filename, indc,index_view):
         if signal.checkState() == Qt.Checked:
             if signal.text() in indc:
                 try:
-                    self.tree_images.model().sourceModel().itemChanged.disconnect(self.changeImage)
+                    #self.tree_images.model().sourceModel().itemChanged.disconnect(self.changeImage)
+                    self.tree_images.clicked.disconnect(self.on_row_clicked_image)
                 except:
                     pass
                 signal.setCheckState(Qt.Unchecked)
@@ -1403,7 +1544,8 @@ def clean_parent_image2(self, filename, indc,index_view):
                 #if indc in info[0][1]:
                 indices.append(i)
                 try:
-                    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)
                 except:
                     pass
     for ind in indices:
@@ -1426,12 +1568,14 @@ def clean_parent_image(self, index_row, indc,index_view):
         if signal.checkState() == Qt.Checked:
             if signal.text() in indc:
                 try:
-                    self.tree_images.model().sourceModel().itemChanged.disconnect(self.changeImage)
+                    #self.tree_images.model().sourceModel().itemChanged.disconnect(self.changeImage)
+                    self.tree_images.clicked.disconnect(self.on_row_clicked_image)
                 except:
                     pass
                 signal.setCheckState(Qt.Unchecked)
                 try:
-                    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)
                 except:
                     pass
 
@@ -1533,6 +1677,8 @@ def read_txt_color(file, mode ='lut', from_one= False):
 
             #color_name = [l.split('\t')[0]+"_"+l.split('\t')[-1][1:-2] for l in lines[id:]]
             #color_name = [[r for r in re.sub(r'\s+', ' ', l).split() if r != '' and r!='\n'][0] + "_"+' '.join([r.replace('"', '') for r in re.sub(r'\s+', ' ', l[:-1]).split() if r != '' and r!='\n'][indices_non_numeric]) for l in lines[id:] if l[0]!='#']
+            lines = [l for l in lines if l.strip() and not l.strip().startswith('#')]
+            id = 0
             color_name = [[r for r in re.sub(r'\s+', ' ', l).split() if r != '' and r!='\n'][0] + "_"+"".join([r.replace('"', '') for r in re.sub(r'\s+', ' ', l[:-1]).split() if r != '' and r!='\n'][indices_non_numeric]) for l in lines[id:] if l[0]!='#']
             indices_el = [int([r for r in re.sub(r'\s+', ' ', l).split() if r != '' and r != '\n'][0])  for l in lines[id:] if l[0] != '#']
             color_index_rgb = np.array([[int(float(s)) for s in [r for r in re.sub(r'\s+', ' ', l).split() if r != '' and r != '\n'][index_colr_start:index_colr_end]] for l in
@@ -1675,29 +1821,29 @@ def vox2ref(affine, ref):
 ###################### Cursors ######################
 
 def cursorOpenHand():
-    bitmap = QtGui.QPixmap(source_folder+"/Hand.png")
+    bitmap = QtGui.QPixmap(settings.RESOURCE_DIR+"/Hand.png")
     return QtGui.QCursor(bitmap)
 
 def cursorClosedHand():
-    bitmap = QtGui.QPixmap(source_folder+"/Handsqueezed.png")
+    bitmap = QtGui.QPixmap(settings.RESOURCE_DIR+"/Handsqueezed.png")
     return QtGui.QCursor(bitmap)
 def cursorZoomIn():
-    bitmap = QtGui.QPixmap(source_folder+"/zoom_in.png")
+    bitmap = QtGui.QPixmap(settings.RESOURCE_DIR+"/zoom_in.png")
     return QtGui.QCursor(bitmap)
 def cursorZoomOut():
-    bitmap = QtGui.QPixmap(source_folder+"/zoom_out.png")
+    bitmap = QtGui.QPixmap(settings.RESOURCE_DIR+"/zoom_out.png")
     return QtGui.QCursor(bitmap)
 def cursorRotate():
-    bitmap = QtGui.QPixmap(source_folder+"/rotate.png")
+    bitmap = QtGui.QPixmap(settings.RESOURCE_DIR+"/rotate.png")
     return QtGui.QCursor(bitmap)
 def cursorArrow():
-    #bitmap = QtGui.QPixmap(source_folder+"/arrow.png")
+    #bitmap = QtGui.QPixmap(settings.RESOURCE_DIR+"/arrow.png")
     return QtGui.QCursor(Qt.ArrowCursor)
 def cursorPaint():
-    bitmap = QtGui.QPixmap(source_folder+"/HandwritingPlus.png")
+    bitmap = QtGui.QPixmap(settings.RESOURCE_DIR+"/HandwritingPlus.png")
     return QtGui.QCursor(bitmap)
 def cursorPaintX():
-    bitmap = QtGui.QPixmap(source_folder+"/HandwritingPlusX.png")
+    bitmap = QtGui.QPixmap(settings.RESOURCE_DIR+"/HandwritingPlusX.png")
     return QtGui.QCursor(bitmap)
 def cursorCircle(size = 50):
 
@@ -1731,10 +1877,10 @@ def cursorCircle(size = 50):
     return QtGui.QCursor(pil_image_to_qpixmap(image))
 
 def cursorErase():
-    bitmap = QtGui.QPixmap(source_folder+"/HandwritingMinus.png")
+    bitmap = QtGui.QPixmap(settings.RESOURCE_DIR+"/HandwritingMinus.png")
     return QtGui.QCursor(bitmap)
 def cursorEraseX():
-    bitmap = QtGui.QPixmap(source_folder+"/HandwritingMinusX.png")
+    bitmap = QtGui.QPixmap(settings.RESOURCE_DIR+"/HandwritingMinusX.png")
     return QtGui.QCursor(bitmap)
 
 ###################### locate proper widgets ######################
@@ -3785,8 +3931,9 @@ def histogram_equalization(source):
         import cv2
         # Reshape the 3D image into a 2D array with shape (num_slices, height * width)
         num_slices, height, width = image.shape
+        image = normalize_mri(image)
         flattened_image = image.reshape((num_slices, height * width))
-        flattened_image = normalize_mri(flattened_image)
+        #flattened_image = normalize_mri(flattened_image)
         # Apply histogram equalization to the flattened image
         if method=='ehist':
             alg = cv2.equalizeHist