melage 0.0.65__py3-none-any.whl → 1.0.0__py3-none-any.whl

melage/plugins/N4_bias/N4.py

@@ -0,0 +1,115 @@
+import numpy as np
+from PyQt5.QtWidgets import QMessageBox
+from melage.widgets import MelagePlugin
+from melage.dialogs.dynamic_gui import DynamicDialog
+from .N4_schema import get_schema
+from PyQt5.QtCore import Qt
+from PyQt5.QtCore import pyqtSignal
+import SimpleITK as sitk
+from .main.utils import N4_bias_correction
+
+
+#from .main.utils import changeCoordSystem
+# --- THE LOGIC CLASS ---
+class MainLogic(DynamicDialog):
+    """
+    This class handles the BRAIN of the WarpSeg tool.
+    The LOOKS are handled automatically by DynamicDialog + Schema.
+    """
+    completed = pyqtSignal(object)
+
+
+    def __init__(self, data_context,parent=None):
+        # 1. Initialize DynamicDialog with the Schema
+        # This single line builds the entire window!
+
+        super().__init__(parent)
+        self.create_main_ui(schema=get_schema(), default_items=False)
+        self.setAttribute(Qt.WA_DeleteOnClose)
+        self.data_context = data_context
+
+        # 2. AUTOMATICALLY WIDGET BINDING
+        # Iterate over all widgets created by the schema and bind them to 'self'.
+        for widget_id, widget_obj in self.widgets.items():
+            setattr(self, widget_id, widget_obj)
+
+        # 3. GENERAL PURPOSE SIGNAL CONNECTION (Auto-Connect)
+        # Instead of a hardcoded dictionary, we iterate through every widget from the schema
+        # and look for a matching method in this class named: on_<ID>_<Signal>
+        # This works for ANY schema changes automatically.
+        supported_signals = [
+            "clicked", "toggled", "currentIndexChanged",
+            "textChanged", "valueChanged"
+        ]
+
+        for widget_id, widget_obj in self.widgets.items():
+            for signal_name in supported_signals:
+                # 1. Check if the widget has this signal (e.g., Button has 'clicked')
+                if hasattr(widget_obj, signal_name):
+                    # 2. Check if WE have a handler method (e.g., 'on_btn_apply_clicked')
+                    handler_name = f"on_{widget_id}_{signal_name}"
+                    if hasattr(self, handler_name):
+                        # 3. Connect them!
+                        signal = getattr(widget_obj, signal_name)
+                        handler = getattr(self, handler_name)
+                        # Disconnect first to be safe (idempotent), then connect
+                        try:
+                            signal.disconnect(handler)
+                        except TypeError:
+                            pass
+                        signal.connect(handler)
+                        # print(f"Auto-connected: {widget_id}.{signal_name} -> {handler_name}")
+
+
+    @property
+    def ui_schema(self):
+        # We call the function to get the dictionary
+        return get_schema()
+
+
+    # Renamed from 'run_process' to match the schema ID 'btn_apply'
+    def on_btn_apply_clicked(self):
+        view = self.combo_view.currentText()
+        data_view = self.data_context[view]
+        if  data_view is None:
+            QMessageBox.information(self, "Error", "No image data available for the selected view.")
+            return
+
+        try:
+            """The main execution function."""
+            self.progress_bar.setValue(0)
+            max_iters = int(self.iteration.value())
+            numberFittingLevels = int((self.fit_lvl.value()))
+            shrinkFactor = int((self.shrink_fct.value()))
+            status_otsu = self.check_otsu.isChecked()
+            im = N4_bias_correction(data_view, use_otsu=status_otsu, shrinkFactor=shrinkFactor,
+                       numberFittingLevels=numberFittingLevels, max_iter=max_iters)
+            result_package = {
+                "image": im.get_fdata(),
+                "affine": im.affine,
+                "label": np.zeros_like(im.get_fdata()),
+                "view": view
+            }
+            self.completed.emit(result_package)
+            self.progress_bar.setValue(100)
+            #QMessageBox.information(self, "Done", "Segmentation Complete")
+
+        except Exception as e:
+            QMessageBox.information(self, "Error", f"{e}")
+            self.progress_bar.setValue(0)
+
+
+
+
+# --- THE PLUGIN WRAPPER ---
+class AuxPlugin(MelagePlugin):
+    @property
+    def name(self) -> str: return "N4 Bias"
+
+    @property
+    def category(self) -> str: return "Basic"
+
+
+    def get_widget(self, data_context =None,parent=None):
+        logic = MainLogic(data_context, parent)
+        return logic

melage/plugins/N4_bias/N4_schema.py

@@ -0,0 +1,40 @@
+
+from ..ui_helpers import Label, Combo, Check, Radio, Group, Button, Progress, HBox, FilePicker, SpinBox, Reference
+
+# The simplified schema using helper functions.
+# The main layout defaults to 'vbox', so items stack automatically.
+def get_schema():
+
+
+    UI_SCHEMA = {
+        "title": "N4 Bias Field Correction",
+        "min_width": 310,
+        "layout": "vbox",
+        "items": [
+
+            HBox(children=[
+                Label(text="Iteration:"),
+                SpinBox(id="iteration", value=50, min_val=1, max_val=10000, decimals=0),
+                Check(id="check_otsu", text="Otsu", checked=True),
+            ]),
+
+            HBox(children=[
+                Label(text="Fitting Level:"),
+                SpinBox(id="fit_lvl", value=1, min_val=1, max_val=12, decimals=0)
+            ]),
+            HBox(children=[
+                Label(text="Shrink Factor:"),
+                SpinBox(id="shrink_fct", value=1, min_val=1, max_val=4, decimals=0)
+            ]),
+
+
+
+
+            # --- Bottom Row: Progress + Apply ---
+            HBox(children=[
+                Progress(id="progress_bar"),
+                Button(id="btn_apply", text="Apply", default=True)
+            ])
+        ]
+    }
+    return UI_SCHEMA

melage/plugins/N4_bias/main/utils.py

@@ -0,0 +1,46 @@
+from melage.utils.utils import read_nib_as_sitk, sitk, Threshold_MultiOtsu, make_image_using_affine, nib, make_affine
+
+def N4_bias_correction(image_nib, use_otsu=True, shrinkFactor=1,
+                       numberFittingLevels=6, max_iter=5):
+    inputImage = read_nib_as_sitk(image_nib)
+    inputImage = sitk.Cast(inputImage, sitk.sitkFloat32)
+    if use_otsu:
+        #maskImage = sitk.OtsuThreshold(inputImage, 0, 1, 200)
+        threshold_val = Threshold_MultiOtsu(image_nib.get_fdata(), 1)[0]
+        a = image_nib.get_fdata().copy()
+        a[a <= threshold_val] = 0
+        a[a > threshold_val] = 1
+        mask_image = make_image_using_affine(a, image_nib.affine)
+        maskImage = read_nib_as_sitk(mask_image)
+        maskImage = sitk.Cast(maskImage, sitk.sitkUInt8)
+
+    else:
+
+        mask_image = nib.Nifti1Image((image_nib.get_fdata()>0).astype(np.int8), image_nib.affine, header=image_nib.header)
+        #maskImage = sitk.Cast(sitk.GetImageFromArray((image.get_fdata()>0).astype('int'), sitk.sitkInt8), sitk.sitkUInt8)
+        maskImage = read_nib_as_sitk(mask_image)
+        maskImage = sitk.Cast(maskImage, sitk.sitkUInt8)
+
+
+    if shrinkFactor > 1:
+        inputImage = sitk.Shrink(
+            inputImage, [shrinkFactor] * inputImage.GetDimension()
+        )
+        maskImage = sitk.Shrink(
+            maskImage, [shrinkFactor] * inputImage.GetDimension()
+        )
+
+
+    corrector = sitk.N4BiasFieldCorrectionImageFilter()
+
+
+
+    if max_iter > 5:
+        corrector.SetMaximumNumberOfIterations(
+            [max_iter] * numberFittingLevels
+        )
+
+    corrected_image = corrector.Execute(inputImage, maskImage)
+    affine = make_affine(corrected_image)
+    nib_im = nib.Nifti1Image(sitk.GetArrayFromImage(corrected_image).transpose(), affine)
+    return nib_im

melage/plugins/__init__.py

@@ -0,0 +1,2 @@
+
+

melage/plugins/bet/bet.py

@@ -0,0 +1,176 @@
+import numpy as np
+from PyQt5.QtWidgets import QMessageBox
+from melage.widgets import MelagePlugin
+from melage.dialogs.dynamic_gui import DynamicDialog
+from .bet_schema import get_schema
+from PyQt5.QtCore import Qt
+from PyQt5.QtCore import pyqtSignal
+from .main.BET import BET
+#from .main.utils import changeCoordSystem
+# --- THE LOGIC CLASS ---
+class BETLogic(DynamicDialog):
+    """
+    This class handles the BRAIN of the WarpSeg tool.
+    The LOOKS are handled automatically by DynamicDialog + Schema.
+    """
+    completed = pyqtSignal(object)
+
+
+    def __init__(self, data_context,parent=None):
+        # 1. Initialize DynamicDialog with the Schema
+        # This single line builds the entire window!
+
+        super().__init__(parent)
+        self.create_main_ui(schema=get_schema(), default_items=False)
+        self.setAttribute(Qt.WA_DeleteOnClose)
+        self.data_context = data_context
+
+        # 2. AUTOMATICALLY WIDGET BINDING
+        # Iterate over all widgets created by the schema and bind them to 'self'.
+        for widget_id, widget_obj in self.widgets.items():
+            setattr(self, widget_id, widget_obj)
+
+        # 3. GENERAL PURPOSE SIGNAL CONNECTION (Auto-Connect)
+        # Instead of a hardcoded dictionary, we iterate through every widget from the schema
+        # and look for a matching method in this class named: on_<ID>_<Signal>
+        # This works for ANY schema changes automatically.
+        supported_signals = [
+            "clicked", "toggled", "currentIndexChanged",
+            "textChanged", "valueChanged"
+        ]
+
+        for widget_id, widget_obj in self.widgets.items():
+            for signal_name in supported_signals:
+                # 1. Check if the widget has this signal (e.g., Button has 'clicked')
+                if hasattr(widget_obj, signal_name):
+                    # 2. Check if WE have a handler method (e.g., 'on_btn_apply_clicked')
+                    handler_name = f"on_{widget_id}_{signal_name}"
+                    if hasattr(self, handler_name):
+                        # 3. Connect them!
+                        signal = getattr(widget_obj, signal_name)
+                        handler = getattr(self, handler_name)
+                        # Disconnect first to be safe (idempotent), then connect
+                        try:
+                            signal.disconnect(handler)
+                        except TypeError:
+                            pass
+                        signal.connect(handler)
+                        # print(f"Auto-connected: {widget_id}.{signal_name} -> {handler_name}")
+        self.check_advanced.stateChanged.connect(self.activate_advanced)
+        self.check_thresholding.stateChanged.connect(self.change_hist_threshold)
+
+    @property
+    def ui_schema(self):
+        # We call the function to get the dictionary
+        return get_schema()
+
+    def change_hist_threshold(self, val):
+        value = not val
+        if not val:
+            self.hist_thresh_max.setEnabled(value)
+            self.hist_thresh_min.setMaximum(100)
+            self.hist_thresh_min.setMinimum(0)
+            self.hist_thresh_min.setValue(2)
+        else:
+            self.hist_thresh_max.setEnabled(value)
+            vl = self.hist_thresh_min.value()
+            if vl>10:
+                self.hist_thresh_min.setValue(10)
+            elif vl<4:
+                self.hist_thresh_min.setValue(6)
+            self.hist_thresh_min.setMaximum(10)
+            self.hist_thresh_min.setMinimum(4)
+
+
+    def get_params(self, img):
+        state = self.check_thresholding.isChecked()
+        if state:
+            from melage.utils.utils import Threshold_MultiOtsu
+            numc = int(self.hist_thresh_min.value())
+            thresholds = Threshold_MultiOtsu(img, numc)
+            t02t = thresholds[0]
+            t98t = thresholds[-1]
+        else:
+            t02t = self.hist_thresh_min.value()/100
+            t98t = self.hist_thresh_max.value()/100
+
+
+        bt = self.fractional_threshold.value()/100
+        d1 = self.search_dist_max.value()
+        d2 = self.search_dist_min.value()
+        rmin = self.rad_curv_min.value()
+        rmax = self.rad_curv_max.value()
+        n_iter = np.int64(self.iteration.value())
+        return [t02t, t98t, bt, d1, d2, rmin, rmax,n_iter]
+
+
+
+    def activate_advanced(self, value):
+        self.group_advanced.setEnabled(value)
+
+
+    # Renamed from 'run_process' to match the schema ID 'btn_apply'
+    def on_btn_apply_clicked(self):
+        view = self.combo_view.currentText()
+        data_view = self.data_context[view]
+        if  data_view is None:
+            QMessageBox.information(self, "Error", "No image data available for the selected view.")
+            return
+
+        try:
+            """The main execution function."""
+            self.lbl_status.setVisible(True)
+            self.lbl_status.setText('Initialization...')
+            self.progress_bar.setValue(0)
+            state = self.check_thresholding.isChecked()
+            data = data_view.get_fdata().copy()
+            try:
+                spacing = data_view.header['pixdim'][1:4]
+                spacing = np.max(spacing)
+            except (KeyError, TypeError, AttributeError):
+                # Fallback value
+                spacing = 1  # or simply spacing = 1
+
+            bet = BET(data, spacing)
+            info = self.get_params(data)
+            bet.update_params(info, state)
+            self.progress_bar.setValue(5)
+            self._progress = 5
+            bet.initialization(self.progress_bar, self.lbl_status)
+            self.lbl_status.setText('preparation...')
+            bet.run(self.progress_bar, self.lbl_status)
+            self.progress_bar.setValue(98)
+            self.lbl_status.setText('Computing mask...')
+            mask = bet.compute_mask()
+            self.lbl_status.setVisible(False)
+            self._progress = 100
+            self.progress_bar.setValue(self._progress)
+            self._progress =0
+            result_package = {
+                "image": None,
+                "label": mask,
+                "view": view
+            }
+            self.completed.emit(result_package)
+            self.progress_bar.setValue(100)
+            #QMessageBox.information(self, "Done", "Segmentation Complete")
+
+        except Exception as e:
+            QMessageBox.information(self, "Error", f"{e}")
+            self.progress_bar.setValue(0)
+
+
+
+
+# --- THE PLUGIN WRAPPER ---
+class BETPlugin(MelagePlugin):
+    @property
+    def name(self) -> str: return "BET"
+
+    @property
+    def category(self) -> str: return "UnSupervised Segmentation"
+
+
+    def get_widget(self, data_context =None,parent=None):
+        logic = BETLogic(data_context, parent)
+        return logic

melage/plugins/bet/bet_schema.py

@@ -0,0 +1,73 @@
+
+from ..ui_helpers import Label, Combo, Check, Radio, Group, Button, Progress, HBox, FilePicker, SpinBox, Reference
+
+# The simplified schema using helper functions.
+# The main layout defaults to 'vbox', so items stack automatically.
+def get_schema():
+
+
+    UI_SCHEMA = {
+        "title": "Brain Extaction Tools (BET)",
+        "min_width": 310,
+        "layout": "vbox",
+        "items": [
+
+            # --- Top Row: Checkbox (Advanced) + Image Selector ---
+            HBox(children=[
+                Check(id="check_advanced", text="Advanced Settings", checked=False),  # Connected to activate_advanced
+            ]),
+
+            # --- Advanced Settings Widget (Disabled by default) ---
+            # We group all the advanced settings here.
+            # The ID 'group_advanced' corresponds to 'self.widget' in your code.
+            Group(id="group_advanced", title="Advanced Parameters", enabled=False, children=[
+
+                # 1. Iteration (Splitter 3)
+                HBox(children=[
+                    Label(text="Iteration:"),
+                    SpinBox(id="iteration", value=50, min_val=1, max_val=10000, decimals=0)
+                ]),
+
+                # 2. Thresholding (Splitter)
+                # This logic is tricky: checked=True enables min, disables max.
+                # We map this behavior using 'enable_targets' logic.
+                HBox(children=[
+                    Check(id="check_thresholding", text="Auto Threshold", checked=True),
+
+                    # These two spinboxes behave differently based on the check
+                    SpinBox(id="hist_thresh_min", value=2.0, min_val=0.0, max_val=10.0),
+                    SpinBox(id="hist_thresh_max", value=98.0, min_val=0.0, max_val=100.0, enabled=False)
+                ]),
+
+                # 3. Fractional Threshold (Splitter 2)
+                HBox(children=[
+                    Label(text="Fractional Thresh(%):"),
+                    SpinBox(id="fractional_threshold", value=1.0, min_val=0.0, max_val=100.0)
+                ]),
+
+                # 4. Search Distance (Splitter 4)
+                HBox(children=[
+                    Label(text="Search Dist (Min/Max):"),
+                    SpinBox(id="search_dist_min", value=10.0, max_val=10000),
+                    SpinBox(id="search_dist_max", value=25.0, max_val=10000)
+                ]),
+
+                # 5. Radius Curvature (Splitter 5)
+                HBox(children=[
+                    Label(text="Rad Curvature (Min/Max):"),
+                    SpinBox(id="rad_curv_min", value=3.3, max_val=10000),
+                    SpinBox(id="rad_curv_max", value=10.0, max_val=10000)
+                ])
+            ]),
+
+            # --- Hidden Status Label ---
+            Label(id="lbl_status", text="", visible=False),
+
+            # --- Bottom Row: Progress + Apply ---
+            HBox(children=[
+                Progress(id="progress_bar"),
+                Button(id="btn_apply", text="Apply", default=True)
+            ])
+        ]
+    }
+    return UI_SCHEMA