Fix rebase deletions

Author: C-Achard

napari_cellseg3d/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.1rc4"
+__version__ = "0.0.2rc1"

napari_cellseg3d/code_models/model_workers.py

@@ -138,25 +138,23 @@ def show_progress(count, block_size, total_size):
             )
             with tarfile.open(filename, mode="r:gz") as tar:
                 def is_within_directory(directory, target):
-                    
-                    abs_directory = os.path.abspath(directory)
-                    abs_target = os.path.abspath(target)
-                
-                    prefix = os.path.commonprefix([abs_directory, abs_target])
-                    
-                    return prefix == abs_directory
-                
+
+                    abs_directory = Path(directory).resolve()
+                    abs_target = Path(target).resolve()
+                    # prefix = os.path.commonprefix([abs_directory, abs_target])
+                    return abs_target in abs_directory.parents
+
                 def safe_extract(tar, path=".", members=None, *, numeric_owner=False):
-                
+
                     for member in tar.getmembers():
-                        member_path = os.path.join(path, member.name)
+                        member_path = str(Path(path) / member.name)
                         if not is_within_directory(path, member_path):
                             raise Exception("Attempted Path Traversal in Tar File")
-                
-                    tar.extractall(path, members, numeric_owner=numeric_owner) 
-                    
-                
+
+                    tar.extractall(path, members, numeric_owner=numeric_owner)
+
                 safe_extract(tar, pretrained_folder_path)
+                # tar.extractall(pretrained_folder_path)
         else:
             raise ValueError(
                 f"Unknown model: {model_name}. Should be one of {', '.join(neturls)}"

napari_cellseg3d/code_plugins/plugin_crop.py

@@ -423,15 +423,16 @@ def _add_crop_sliders(
         dims = [self._x, self._y, self._z]
         [logger.debug(f"{dim}") for dim in dims]
         logger.debug("SET DIMS ATTEMPT")
-        if not self.create_new_layer.isChecked():
-            self._x = x
-            self._y = y
-            self._z = z
-            [logger.debug(f"{dim}") for dim in dims]
-        else:
-            [self._reset_dim(dim) for dim in dims]
-            [logger.debug(f"{dim}") for dim in dims]
+        # if not self.create_new_layer.isChecked():
+        #     self._x = x
+        #     self._y = y
+        #     self._z = z
+        #     [logger.debug(f"{dim}") for dim in dims]
+        # else:
+        #     [self._reset_dim(dim) for dim in dims]
+        #     [logger.debug(f"{dim}") for dim in dims]
         #############
+
         # logger.debug(f"Crop variables")
         # logger.debug(im1_stack.shape)
 
@@ -502,9 +503,9 @@ def set_slice(
             highres_crop_layer.translate = scale * izyx
             highres_crop_layer.refresh()
 
-            self._check_for_empty_layer(
-                highres_crop_layer, highres_crop_layer.data
-            )
+            # self._check_for_empty_layer(
+            #     highres_crop_layer, highres_crop_layer.data
+            # )
 
             if crop_lbls and labels_crop_layer is not None:
                 labels_crop_layer.data = im2_stack[

napari_cellseg3d/code_plugins/plugin_helper.py

@@ -37,7 +37,7 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         self.logo_label.setToolTip("Open Github page")
 
         self.info_label = ui.make_label(
-            f"You are using napari-cellseg3d v.{'0.0.1rc4'}\n\n"
+            f"You are using napari-cellseg3d v.{'0.0.2rc1'}\n\n"
             f"Plugin for cell segmentation developed\n"
             f"by the Mathis Lab of Adaptive Motor Control\n\n"
             f"Code by :\nCyril Achard\nMaxime Vidal\nJessy Lauer\nMackenzie Mathis\n"

napari_cellseg3d/code_plugins/plugin_model_inference.py

@@ -144,8 +144,7 @@ def __init__(self, viewer: "napari.viewer.Viewer", parent=None):
         )
 
         self.window_infer_box = ui.CheckBox("Use window inference")
-
-        self.window_infer_box.clicked.connect(self.toggle_display_window_size)
+        self.window_infer_box.clicked.connect(self._toggle_display_window_size)
 
         sizes_window = ["8", "16", "32", "64", "128", "256", "512"]
         # (
@@ -169,6 +168,7 @@ def __init__(self, viewer: "napari.viewer.Viewer", parent=None):
             parent=self,
             text_label="Overlap %",
         )
+
         self.keep_data_on_cpu_box = ui.CheckBox("Keep data on CPU")
 
         window_size_widgets = ui.combine_blocks(
@@ -238,19 +238,9 @@ def _set_tooltips(self):
             "DO NOT CHANGE if you are using the provided pre-trained weights"
         )
 
-        self.thresholding_checkbox.setToolTip(thresh_desc)
-        self.thresholding_count.setToolTip(thresh_desc)
-        self.window_infer_box.setToolTip(
-            "Sliding window inference runs the model on parts of the image"
-            "\nrather than the whole image, to reduce memory requirements."
-            "\nUse this if you have large images."
-        )
-        self.window_size_choice.setToolTip(
-            "Size of the window to run inference with (in pixels)"
-        )
-
-        self.window_overlap_counter.set_all_tooltips(
-            "Percentage of overlap between windows to use when using sliding window"
+        thresh_desc = (
+            "Thresholding : all values in the image below the chosen probability"
+            " threshold will be set to 0, and all others to 1."
         )
 
         self.thresholding_checkbox.setToolTip(thresh_desc)

napari_cellseg3d/interface.py

@@ -317,18 +317,33 @@ def add_label(widget, label, label_before=True, horizontal=True):
         return combine_blocks(label, widget, horizontal=horizontal)
 
 
-def add_label(widget, label, label_before=True, horizontal=True):
-    if label_before:
-        return combine_blocks(widget, label, horizontal=horizontal)
-    else:
-        return combine_blocks(label, widget, horizontal=horizontal)
+class ContainerWidget(QWidget):
+    def __init__(
+        self, l=0, t=0, r=1, b=11, vertical=True, parent=None, fixed=True
+    ):
+        """
+        Creates a container widget that can contain other widgets
+        Args:
+            l: left margin in pixels
+            t: top margin in pixels
+            r: right margin in pixels
+            b: bottom margin in pixels
+            vertical: if True, renders vertically. Horizontal otherwise
+            parent: parent QWidget
+            fixed: uses QLayout.SetFixedSize if True
+        """
 
+        super().__init__(parent)
+        self.layout = None
 
-def add_label(widget, label, label_before=True, horizontal=True):
-    if label_before:
-        return combine_blocks(widget, label, horizontal=horizontal)
-    else:
-        return combine_blocks(label, widget, horizontal=horizontal)
+        if vertical:
+            self.layout = QVBoxLayout(self)
+        else:
+            self.layout = QHBoxLayout(self)
+
+        self.layout.setContentsMargins(l, t, r, b)
+        if fixed:
+            self.layout.setSizeConstraint(QLayout.SetFixedSize)
 
 
 class RadioButton(QRadioButton):
@@ -1244,49 +1259,6 @@ def create_single_widget_group(
         layout.addWidget(group)
 
 
-
-class GroupedWidget(QGroupBox):
-    """Subclass of QGroupBox designed to easily group widgets belonging to a same category"""
-
-    def __init__(self, title, l=7, t=20, r=7, b=11, parent=None):
-        super().__init__(title, parent)
-
-        self.setSizePolicy(QSizePolicy.Fixed)
-
-        self.layout = QVBoxLayout()
-        self.layout.setContentsMargins(l, t, r, b)
-        self.layout.setSizeConstraint(QLayout.SetFixedSize)
-
-    @property
-    def layout(self) -> "QLayout":
-        return self.layout
-
-    @classmethod
-    def create_single_widget_group(
-        cls, title, widget, layout, l=7, t=20, r=7, b=11
-    ):
-        group, group_layout = cls(title, l, t, r, b)
-        group_layout.addWidget(widget)
-        group.setLayout(group_layout)
-        layout.addWidget(group)
-
-
-class ContainerWidget(QWidget):  # TODO convert calls
-    def __init__(self, l=0, t=0, r=1, b=11, vertical=True, parent=None):
-
-        super().__init__(parent)
-        self.layout = None
-
-        if vertical:
-            self.layout = QVBoxLayout(self)
-        else:
-            self.layout = QHBoxLayout(self)
-
-        self.layout.setContentsMargins(l, t, r, b)
-        if fixed:
-            self.layout.setSizeConstraint(QLayout.SetFixedSize)
-
-
 def add_widgets(layout, widgets, alignment=LEFT_AL):
     """Adds all widgets in the list to layout, with the specified alignment.
     If alignment is None, no alignment is set.

setup.cfg

@@ -52,7 +52,6 @@ install_requires =
     torch>=1.11
     monai[nibabel,scikit-image,itk,einops]>=0.9.0
     tqdm
-    monai==0.9.0
     nibabel
     scikit-image
     pillow