rm lfs + updated widget size + docs url

Author: C-Achard

.gitattributes

@@ -14,11 +14,13 @@ class Helper(QWidget):
     def __init__(self, viewer: "napari.viewer.Viewer"):
         super().__init__()
 
-        # TODO change url after renaming, moving and redeploying docs
-        self.help_url = "https://c-achard.github.io/cellseg-annotator-test/"  # "https://github.com/C-Achard/cellseg-annotator-test/tree/main"
+        self.help_url = "https://adaptivemotorcontrollab.github.io/cellseg3d-docs/"
 
         self.about_url = "https://wysscenter.ch/advances/3d-computer-vision-for-brain-analysis"
         self._viewer = viewer
+
+        self.info_label = ui.make_label(f"napari-cellseg3d v.{0.01}", self)
+
         self.btn1 = ui.make_button(
             "Help...", lambda: ui.open_url(self.help_url)
         )
@@ -27,26 +29,6 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         )
         self.btnc = ui.make_button("Close", self.remove_from_viewer)
 
-        ###################
-        ###################
-        ###################
-        ###################
-        # TODO test remove later
-        self.test = False  # utils.ENABLE_TEST_MODE()
-
-        if self.test:
-            self.dock = None
-
-            self.epoch = ui.make_n_spinboxes(1, 0, 1000, step=2)
-            self.epoch.setValue(0)
-            self.epoch.setRange(0, 1000)
-            self.epoch.setSingleStep(2)
-            self.epoch.valueChanged.connect(self.update_loss_plot)
-        ###################
-        ###################
-        ###################
-        ###################
-
         self.build()
 
     def build(self):
@@ -57,130 +39,14 @@ def build(self):
             self.btn2,
             self.btnc,
         ]
+        #################
         if self.test:
             widgets.append(self.epoch)
+        #################
         ui.add_widgets(vbox, widgets)
         self.setLayout(vbox)
         # self.show()
         # self._viewer.window.add_dock_widget(self, name="Help/About...", area="right")
 
     def remove_from_viewer(self):
-        if self.test and self.dock is not None:  # TODO remove
-            self._viewer.window.remove_dock_widget(self.dock)
         self._viewer.window.remove_dock_widget(self)
-
-    ################
-    ################
-    ################
-    ################ TESTING
-    def update_loss_plot(self):
-        if not self.test:
-            return
-        import matplotlib.pyplot as plt
-        import numpy as np
-
-        epoch = self.epoch.value()
-        length = epoch
-        loss = np.random.rand(length)
-        dice_metric = np.random.rand(int(length / 2))
-
-        # print("plot upd")
-        # print(epoch)
-        # print(loss)
-        # print(dice_metric)
-        if epoch < 4:
-            return
-        elif epoch == 4:
-
-            import matplotlib.pyplot as plt
-            import numpy as np
-            from matplotlib.backends.backend_qt5agg import (
-                FigureCanvasQTAgg as FigureCanvas,
-            )
-            from matplotlib.figure import Figure
-
-            bckgrd_color = (0, 0, 0, 0)  # '#262930'
-            with plt.style.context("dark_background"):
-
-                self.canvas = FigureCanvas(Figure(figsize=(7, 2.5)))
-                # loss plot
-                self.train_loss_plot = self.canvas.figure.add_subplot(1, 2, 1)
-                # dice metric validation plot
-                self.dice_metric_plot = self.canvas.figure.add_subplot(1, 2, 2)
-
-                self.canvas.figure.set_facecolor(bckgrd_color)
-                self.dice_metric_plot.set_facecolor(bckgrd_color)
-                self.train_loss_plot.set_facecolor(bckgrd_color)
-
-                self.canvas.figure.tight_layout()
-
-                self.canvas.figure.subplots_adjust(
-                    left=0.1,
-                    bottom=0.2,
-                    right=0.95,
-                    top=0.9,
-                    wspace=0.2,
-                    hspace=0,
-                )
-
-            self.canvas.setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum)
-
-            # tab_index = self.addTab(self.canvas, "Loss plot")
-            # self.setCurrentIndex(tab_index)
-            self.dock = self._viewer.window.add_dock_widget(
-                self.canvas, area="bottom"
-            )
-            self.plot_loss(loss, dice_metric)
-        else:
-            with plt.style.context("dark_background"):
-
-                self.train_loss_plot.cla()
-                self.dice_metric_plot.cla()
-
-                self.plot_loss(loss, dice_metric)
-
-    def plot_loss(self, loss, dice_metric):
-        import matplotlib.pyplot as plt
-        import numpy as np
-
-        if not self.test:
-            return
-        self.val_interval = 2
-
-        # update loss
-        with plt.style.context("dark_background"):
-            self.train_loss_plot.set_title("Epoch average loss")
-            self.train_loss_plot.set_xlabel("Epoch")
-            self.train_loss_plot.set_ylabel("Loss")
-            x = [i + 1 for i in range(len(loss))]
-            y = loss
-            self.train_loss_plot.plot(x, y)
-            # update metrics
-            x = [self.val_interval * (i + 1) for i in range(len(dice_metric))]
-            y = dice_metric
-
-            epoch_min = (np.argmax(y) + 1) * self.val_interval
-            dice_min = np.max(y)
-
-            self.dice_metric_plot.plot(x, y, zorder=1)
-            self.dice_metric_plot.set_title(
-                "Validation metric : Mean Dice coefficient"
-            )
-            self.dice_metric_plot.set_xlabel("Epoch")
-            self.dice_metric_plot.set_ylabel("Dice")
-
-            self.dice_metric_plot.scatter(
-                epoch_min,
-                dice_min,
-                c="r",
-                label="Maximum Dice coeff.",
-                zorder=5,
-            )
-            self.dice_metric_plot.legend(
-                facecolor="#262930", loc="lower right"
-            )
-            self.canvas.draw_idle()
-            ##########################
-            ##########################
-            ##########################
-            ########################## END of testing

napari_cellseg3d/plugin_helper.py

@@ -453,10 +453,12 @@ def build(self):
         ui.make_scrollable(
             containing_widget=tab,
             contained_layout=tab_layout,
-            min_wh=[200, 300],
+            min_wh=[200, 100],
         )
         self.addTab(tab, "Inference")
 
+        self.setMinimumSize(180, 100)
+
     def start(self):  # TODO update
         """Start the inference process, enables :py:attr:`~self.worker` and does the following:
 

napari_cellseg3d/plugin_model_inference.py

@@ -697,7 +697,7 @@ def build(self):
         self.addTab(data_tab, "Data")
         self.addTab(augment_tab_w, "Augmentation")
         self.addTab(train_tab, "Training")
-        self.setMinimumSize(220, 200)
+        self.setMinimumSize(220, 100)
 
     def show_dialog_lab(self):
         """Shows the  dialog to load label files in a path, loads them (see :doc:model_framework) and changes the widget

napari_cellseg3d/plugin_model_training.py

@@ -139,6 +139,8 @@ def build(self):
         )
 
         self.addTab(tab, "Review")
+
+        self.setMinimumSize(180,100)
         # self.show()
         # self._viewer.window.add_dock_widget(self, name="Reviewer", area="right")
 

napari_cellseg3d/plugin_review.py

@@ -35,7 +35,7 @@ def build(self):
         self.convert_tab.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
 
         self.setBaseSize(230, 550)
-        self.setMinimumSize(230, 500)
+        self.setMinimumSize(230, 100)
 
     def remove_from_viewer(self):
         self._viewer.window.remove_dock_widget(self)