UI overhaul + overlap parameter

- Added overlap parameter for window
- Improved UI code slightly

Author: C-Achard

napari_cellseg3d/interface.py

@@ -1,5 +1,4 @@
 from typing import Optional
-from typing import Union
 from typing import List
 
 
@@ -61,6 +60,13 @@ def toggle_visibility(checkbox, widget):
     widget.setVisible(checkbox.isChecked())
 
 
+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 Button(QPushButton):
     """Class for a button with a title and connected to a function when clicked. Inherits from QPushButton.
 
@@ -492,20 +498,33 @@ def __init__(
         step=1,
         parent: Optional[QWidget] = None,
         fixed: Optional[bool] = True,
+        label: Optional[str] = None,
     ):
         """Args:
         min (Optional[int]): minimum value, defaults to 0
         max (Optional[int]): maximum value, defaults to 10
         default (Optional[int]): default value, defaults to 0
         step (Optional[int]): step value, defaults to 1
         parent: parent widget, defaults to None
-        fixed (bool): if True, sets the QSizePolicy of the spinbox to Fixed"""
+        fixed (bool): if True, sets the QSizePolicy of the spinbox to Fixed
+        label (Optional[str]): if provided, creates a label with the chosen title to use with the counter"""
 
         super().__init__(parent)
         set_spinbox(self, min, max, default, step, fixed)
 
+        if label is not None:
+            self.label = make_label(name=label)
+
+    # def setToolTip(self, a0: str) -> None:
+    #     self.setToolTip(a0)
+    #     if self.label is not None:
+    #         self.label.setToolTip(a0)
+
+    def get_with_label(self, horizontal=True):
+        return add_label(self, self.label, horizontal=horizontal)
+
     def set_precision(self, decimals):
-        """Sets the precision of the box to the speicifed number of decimals"""
+        """Sets the precision of the box to the specified number of decimals"""
         self.setDecimals(decimals)
 
     @classmethod
@@ -533,6 +552,7 @@ def __init__(
         step=1,
         parent: Optional[QWidget] = None,
         fixed: Optional[bool] = True,
+        label: Optional[str] = None,
     ):
         """Args:
         min (Optional[int]): minimum value, defaults to 0
@@ -544,6 +564,9 @@ def __init__(
 
         super().__init__(parent)
         set_spinbox(self, min, max, default, step, fixed)
+        self.label = None
+        if label is not None:
+            self.label = make_label(label, self)
 
     @classmethod
     def make_n(

napari_cellseg3d/model_framework.py

@@ -14,6 +14,7 @@
 from napari_cellseg3d.log_utility import Log
 from napari_cellseg3d.models import model_SegResNet as SegResNet
 from napari_cellseg3d.models import model_SwinUNetR as SwinUNetR
+
 # from napari_cellseg3d.models import model_TRAILMAP as TRAILMAP
 from napari_cellseg3d.models import model_VNet as VNet
 from napari_cellseg3d.models import model_TRAILMAP_MS as TRAILMAP_MS

napari_cellseg3d/model_workers.py

@@ -162,6 +162,9 @@ def __init__(self):
         super().__init__()
 
 
+# TODO : use dataclass for config instead ?
+
+
 class InferenceWorker(GeneratorWorker):
     """A custom worker to run inference jobs in.
     Inherits from :py:class:`napari.qt.threading.GeneratorWorker`"""
@@ -178,6 +181,7 @@ def __init__(
         instance,
         use_window,
         window_infer_size,
+        window_overlap,
         keep_on_cpu,
         stats_csv,
     ):
@@ -227,7 +231,7 @@ def __init__(
         self.instance_params = instance
         self.use_window = use_window
         self.window_infer_size = window_infer_size
-        self.window_overlap_percentage = 0.8
+        self.window_overlap_percentage = window_overlap
         self.keep_on_cpu = keep_on_cpu
         self.stats_to_csv = stats_csv
         """These attributes are all arguments of :py:func:~inference, please see that for reference"""
@@ -346,7 +350,6 @@ def inference(self):
 
         dims = self.model_dict["model_input_size"]
 
-
         if self.model_dict["name"] == "SegResNet":
             model = self.model_dict["class"].get_net(
                 input_image_size=[
@@ -445,7 +448,7 @@ def inference(self):
                 # print(inputs.shape)
 
                 inputs = inputs.to("cpu")
-                print(inputs.shape)
+                # print(inputs.shape)
 
                 # self.log("output")
                 model_output = lambda inputs: post_process_transforms(
@@ -477,7 +480,7 @@ def inference(self):
                 out = outputs.detach().cpu()
                 # del outputs # TODO fix memory ?
                 # outputs = None
-                print(out.shape)
+                # print(out.shape)
                 if self.transforms["zoom"][0]:
                     zoom = self.transforms["zoom"][1]
                     anisotropic_transform = Zoom(
@@ -489,9 +492,9 @@ def inference(self):
 
                 # out = post_process_transforms(out)
                 out = np.array(out).astype(np.float32)
-                print(out.shape)
+                # print(out.shape)
                 out = np.squeeze(out)
-                print(out.shape)
+                # print(out.shape)
                 to_instance = out  # avoid post processing since thresholding is done there anyway
 
                 # batch_len = out.shape[1]

napari_cellseg3d/plugin_model_inference.py

@@ -76,6 +76,7 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         self.keep_on_cpu = False
         self.use_window_inference = False
         self.window_inference_size = None
+        self.window_overlap = 0.25
 
         ###########################
         # interface
@@ -130,7 +131,7 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
             T=7, parent=self
         )
 
-        self.window_infer_box = ui.make_checkbox("Use window inference")
+        self.window_infer_box = ui.CheckBox(title="Use window inference")
         self.window_infer_box.clicked.connect(self.toggle_display_window_size)
 
         sizes_window = ["8", "16", "32", "64", "128", "256", "512"]
@@ -140,14 +141,29 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         )
         self.lbl_window_size_choice = self.window_size_choice.label
 
-        self.keep_data_on_cpu_box = ui.make_checkbox("Keep data on CPU")
+        self.window_overlap_counter = ui.DoubleIncrementCounter(
+            min=0,
+            max=1,
+            default=0.25,
+            step=0.05,
+            parent=self,
+            label="Overlap %",
+        )
 
-        self.window_infer_params = ui.combine_blocks(
+        self.keep_data_on_cpu_box = ui.CheckBox(title="Keep data on CPU")
+
+        window_size_widgets = ui.combine_blocks(
             self.window_size_choice,
             self.lbl_window_size_choice,
             horizontal=False,
         )
 
+        self.window_infer_params = ui.combine_blocks(
+            window_size_widgets,
+            self.window_overlap_counter.get_with_label(horizontal=False),
+            horizontal=False,
+        )
+
         ##################
         ##################
         # instance segmentation widgets
@@ -228,6 +244,10 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
             "Size of the window to run inference with (in pixels)"
         )
 
+        self.window_overlap_counter.setToolTip(
+            "Percentage of overlap between windows to use when using sliding window"
+        )
+
         self.keep_data_on_cpu_box.setToolTip(
             "If enabled, data will be kept on the RAM rather than the VRAM.\nCan avoid out of memory issues with CUDA"
         )
@@ -582,6 +602,7 @@ def start(self):
             self.window_inference_size = int(
                 self.window_size_choice.currentText()
             )
+            self.window_overlap = self.window_overlap_counter.value()
 
             self.worker = InferenceWorker(
                 device=device,
@@ -594,6 +615,7 @@ def start(self):
                 instance=self.instance_params,
                 use_window=self.use_window_inference,
                 window_infer_size=self.window_inference_size,
+                window_overlap=self.window_overlap,
                 keep_on_cpu=self.keep_on_cpu,
                 stats_csv=self.stats_to_csv,
             )