added utilities for labels + refactored crop + remove_from_viewer methods

+ lint

Author: C-Achard

.github/workflows/build_docs.yml

@@ -0,0 +1,25 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+    # Standard drop-in approach that should work for most people.
+    - uses: ammaraskar/sphinx-action@master
+      with:
+        pre-build-command: "pip install -r dev.requirements.txt"
+        docs-folder: "docs/"
+
+    - name: GitHub Pages action
+      uses: peaceiris/[email protected]
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./docs/_build/html

src/napari_cellseg_annotator/model_framework.py

@@ -107,22 +107,6 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         self.btn_save_log.setVisible(False)
         #####################################################
 
-    def make_close_button(self):
-        btn = ui.make_button("Close", self.close)
-        return btn
-
-    def make_prev_button(self):
-        btn = ui.make_button(
-            "Previous", lambda: self.setCurrentIndex(self.currentIndex() - 1)
-        )
-        return btn
-
-    def make_next_button(self):
-        btn = ui.make_button(
-            "Next", lambda: self.setCurrentIndex(self.currentIndex() + 1)
-        )
-        return btn
-
     def send_log(self, text):
         self.log.print_and_log(text)
 

src/napari_cellseg_annotator/model_instance_seg.py

@@ -102,11 +102,12 @@ def to_instance(image, is_file_path=True):
 
     return result
 
+
 def to_semantic(image, is_file_path=True):
     if is_file_path:
         image = imread(image)
         image = image.compute()
 
     image[image >= 1] = 1
     result = image.astype(np.uint16)
-    return result
+    return result

src/napari_cellseg_annotator/napari.yaml

@@ -12,9 +12,9 @@ contributions:
     title: Create Help
     python_name: napari_cellseg_annotator.plugins:Helper
 
-  - id: napari-cellseg-annotator.crop
-    title: Crop utility
-    python_name: napari_cellseg_annotator.plugins:Cropping
+  - id: napari-cellseg-annotator.utils
+    title:  Create utilities
+    python_name: napari_cellseg_annotator.plugins:Utilities
 
   - id: napari-cellseg-annotator.infer
     title: Create Inferer
@@ -35,8 +35,8 @@ contributions:
   - command: napari-cellseg-annotator.train
     display_name: Training
 
-  - command: napari-cellseg-annotator.crop
-    display_name: Crop utility
+  - command: napari-cellseg-annotator.utils
+    display_name: Utilities
 
   - command: napari-cellseg-annotator.help
     display_name: Help/About...

src/napari_cellseg_annotator/plugin_base.py

@@ -12,7 +12,7 @@
 class BasePluginSingleImage(QTabWidget):
     """A basic plugin template for working with **single images**"""
 
-    def __init__(self, viewer: "napari.viewer.Viewer"):
+    def __init__(self, viewer: "napari.viewer.Viewer", parent=None):
         """Creates a Base plugin with several buttons pre-defined but not added to a layout :
 
         * Open file prompt to select images directory
@@ -29,10 +29,13 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
 
         super().__init__()
 
-        # self.master = parent
+        self.parent = parent
+        """Parent widget"""
         self._viewer = viewer
         """napari.viewer.Viewer: viewer in which the widget is displayed"""
 
+        self.docked_widgets = []
+
         self.image_path = ""
         """str: path to image folder"""
 
@@ -67,7 +70,7 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
             QSizePolicy.Fixed, QSizePolicy.Fixed
         )
 
-        self.btn_close = ui.make_button("Close", self.close, self)
+        self.btn_close = ui.make_button("Close", self.remove_from_viewer, self)
 
         # self.lbl_ft = QLabel("Filetype :", self)
         # self.lbl_ft2 = QLabel("(Folders of .png or single .tif files)", self)
@@ -126,13 +129,23 @@ def update_default(self):
     def remove_from_viewer(self):
         """Removes the widget from the napari window.
         Can be re-implemented in children classes if needed"""
+        if len(self.docked_widgets) != 0:
+            [
+                self._viewer.window.remove_dock_widget(w)
+                for w in self.docked_widgets
+                if w is not None
+            ]
+
+        if self.parent is not None:
+            self.parent.remove_from_viewer()
+            return
         self._viewer.window.remove_dock_widget(self)
 
 
 class BasePluginFolder(QTabWidget):
     """A basic plugin template for working with **folders of images**"""
 
-    def __init__(self, viewer: "napari.viewer.Viewer"):
+    def __init__(self, viewer: "napari.viewer.Viewer", parent=None):
         """Creates a plugin template with the following widgets defined but not added in a layout :
 
         * A button to load a folder of images
@@ -143,7 +156,7 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
 
         * A dropdown menu to select the file extension to be loaded from the folders"""
         super().__init__()
-
+        self.parent = parent
         self._viewer = viewer
 
         self.images_filepaths = [""]
@@ -188,6 +201,22 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         self.lbl_result_path.setReadOnly(True)
         #######################################################
 
+    def make_close_button(self):
+        btn = ui.make_button("Close", self.remove_from_viewer)
+        return btn
+
+    def make_prev_button(self):
+        btn = ui.make_button(
+            "Previous", lambda: self.setCurrentIndex(self.currentIndex() - 1)
+        )
+        return btn
+
+    def make_next_button(self):
+        btn = ui.make_button(
+            "Next", lambda: self.setCurrentIndex(self.currentIndex() + 1)
+        )
+        return btn
+
     def load_dataset_paths(self):
         """Loads all image paths (as str) in a given folder for which the extension matches the set filetype
 
@@ -251,11 +280,15 @@ def remove_docked_widgets(self):
             [
                 self._viewer.window.remove_dock_widget(w)
                 for w in self.docked_widgets
+                if w is not None
             ]
             self.docked_widgets = []
             self.container_docked = False
 
     def remove_from_viewer(self):
         """Close the widget and the docked widgets, if any"""
         self.remove_docked_widgets()
+        if self.parent is not None:
+            self.parent.remove_from_viewer()
+            return
         self._viewer.window.remove_dock_widget(self)

src/napari_cellseg_annotator/plugin_convert.py

@@ -4,14 +4,17 @@
 
 import napari_cellseg_annotator.interface as ui
 from napari_cellseg_annotator import utils
-from napari_cellseg_annotator.model_instance_seg import to_semantic, to_instance
+from napari_cellseg_annotator.model_instance_seg import (
+    to_semantic,
+    to_instance,
+)
 from napari_cellseg_annotator.plugin_base import BasePluginFolder
 
 
 class ConvertUtils(BasePluginFolder):
     """Utility widget that allows to convert labels from instance to semantic and the reverse."""
 
-    def __init__(self, viewer: "napari.viewer.Viewer"):
+    def __init__(self, viewer: "napari.viewer.Viewer", parent):
         """Builds a ConvertUtils widget with the following buttons:
 
         * A button to convert a folder of labels to semantic labels
@@ -23,7 +26,7 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         * A button to convert a currently selected layer to instance labels
         """
 
-        super().__init__(viewer)
+        super().__init__(viewer, parent)
 
         self._viewer = viewer
 
@@ -119,11 +122,13 @@ def build(self):
         layer_group_w.setLayout(layer_group_l)
         layout.addWidget(layer_group_w)
 
-        ui.make_scrollable(layout, self, min_wh=[110, 100], base_wh=[110, 150])
+        ui.add_blank(layout=layout, widget=self)
+        layout.addWidget(self.make_close_button())
 
+        ui.make_scrollable(layout, self, min_wh=[120, 100], base_wh=[120, 150])
 
     def folder_to_semantic(self):
-
+        """Converts folder of labels to semantic labels"""
         for file in self.labels_filepaths:
 
             image = to_semantic(file)

src/napari_cellseg_annotator/plugin_crop.py

@@ -22,7 +22,7 @@
 class Cropping(BasePluginSingleImage):
     """A utility plugin for cropping 3D volumes."""
 
-    def __init__(self, viewer: "napari.viewer.Viewer"):
+    def __init__(self, viewer: "napari.viewer.Viewer", parent):
         """Creates a Cropping plugin with several buttons :
 
         * Open file prompt to select volumes directory
@@ -38,7 +38,7 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         * A button to close the widget
         """
 
-        super().__init__(viewer)
+        super().__init__(viewer, parent)
 
         self.btn_start = ui.make_button("Start", self.start, self)
 
@@ -48,10 +48,6 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         self.lbl_label.setVisible(False)
         self.btn_label.setVisible(False)
 
-        self.docked_widgets = (
-            []
-        )  # container of docked widgets for removal on close
-
         self.box_widgets = ui.make_n_spinboxes(3, 1, 1000, DEFAULT_CROP_SIZE)
         self.box_lbl = [
             QLabel("Size in " + axis + " of cropped volume :")
@@ -87,7 +83,7 @@ def toggle_label_path(self):
     def build(self):
         """Build buttons in a layout and add them to the napari Viewer"""
 
-        tab, layout = ui.make_container_widget(0, 0, 1, 11)
+        w, layout = ui.make_container_widget(0, 0, 1, 11)
 
         data_group_w, data_group_l = ui.make_group("Data")
         data_group_l.addWidget(
@@ -128,15 +124,7 @@ def build(self):
         layout.addWidget(self.btn_start, alignment=ui.LEFT_AL)
         layout.addWidget(self.btn_close, alignment=ui.LEFT_AL)
 
-        ui.make_scrollable(layout, tab, min_wh=[180, 100])
-
-        self.addTab(tab, "Crop")
-
-        from napari_cellseg_annotator.plugin_convert import ConvertUtils
-
-        convert = ConvertUtils(self._viewer)
-        self.addTab(convert, "Convert")
-        self.setMaximumSize(230, 800)
+        ui.make_scrollable(layout, self, min_wh=[180, 100])
 
     def quicksave(self):
         """Quicksaves the cropped volume in the folder from which they originate, with their original file extension.
@@ -265,16 +253,6 @@ def save_widget():
 
         self.add_crop_sliders()
 
-    def remove_from_viewer(self):
-        """Can be re-implemented in children classes"""
-        if len(self.docked_widgets) != 0:
-            [
-                self._viewer.window.remove_dock_widget(w)
-                for w in self.docked_widgets
-            ]
-
-        self._viewer.window.remove_dock_widget(self)
-
     def add_crop_sliders(
         self,
     ):  # TODO fix OOB behaviour (check if <0 or >max_size ?)

src/napari_cellseg_annotator/plugin_helper.py

@@ -6,17 +6,14 @@
 
 # local
 from napari_cellseg_annotator import interface as ui
-from napari_cellseg_annotator import utils
 
 
 class Helper(QWidget):
     # widget testing
     def __init__(self, viewer: "napari.viewer.Viewer"):
         super().__init__()
         # self.master = parent
-        self.help_url = (
-            "https://github.com/C-Achard/cellseg-annotator-test/tree/main"
-        )
+        self.help_url = "https://c-achard.github.io/cellseg-annotator-test/"  # "https://github.com/C-Achard/cellseg-annotator-test/tree/main"
 
         self.about_url = "https://wysscenter.ch/advances/3d-computer-vision-for-brain-analysis"
         self._viewer = viewer
@@ -26,14 +23,14 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         self.btn2 = ui.make_button(
             "About...", lambda: ui.open_url(self.about_url)
         )
-        self.btnc = ui.make_button("Close", self.close)
+        self.btnc = ui.make_button("Close", self.remove_from_viewer)
 
         ###################
         ###################
         ###################
         ###################
         # TODO test remove later
-        self.test = utils.ENABLE_TEST_MODE()
+        self.test = False  # utils.ENABLE_TEST_MODE()
 
         if self.test:
             self.dock = None

src/napari_cellseg_annotator/plugin_metrics.py

@@ -2,9 +2,9 @@
 
 
 class MetricsUtils(BasePluginFolder):
-    def __init__(self, viewer: "napari.viewer.Viewer"):
+    def __init__(self, viewer: "napari.viewer.Viewer", parent):
 
-        super().__init__(viewer)
+        super().__init__(viewer, parent)
 
         self._viewer = viewer
 

src/napari_cellseg_annotator/plugin_utilities.py

@@ -11,18 +11,24 @@
 class Utilities(QTabWidget):
     def __init__(self, viewer: "napari.viewer.Viewer"):
 
-        super().__init__(viewer)
+        super().__init__()
 
         self._viewer = viewer
 
-        self.cropping_tab = Cropping(viewer)
-        self.metrics_tab = MetricsUtils(viewer)
-        self.convert_tab = ConvertUtils(viewer)
+        self.cropping_tab = Cropping(viewer, parent=self)
+        self.metrics_tab = MetricsUtils(viewer, parent=self)
+        self.convert_tab = ConvertUtils(viewer, parent=self)
 
         self.build()
 
     def build(self):
 
-        self.addTab(self.cropping_tab, "Crop")
-        self.addTab(self.metrics_tab, "Metrics")
         self.addTab(self.convert_tab, "Convert")
+        # self.addTab(self.metrics_tab, "Metrics")
+        self.addTab(self.cropping_tab, "Crop")
+
+        self.setBaseSize(220, 150)
+        self.setMinimumSize(220, 100)
+
+    def remove_from_viewer(self):
+        self._viewer.window.remove_dock_widget(self)