Merge pull request #140 from AllenCell/creation-ui-functionality

curation demo ready

src/allencell_ml_segmenter/curation/curation_data_class.py

@@ -0,0 +1,9 @@
+from dataclasses import dataclass
+from pathlib import Path
+
+
+@dataclass
+class CurationRecord:
+    raw_file: Path
+    seg1: Path
+    to_use: bool

src/allencell_ml_segmenter/curation/curation_widget.py

@@ -12,6 +12,7 @@
 from allencell_ml_segmenter.curation.main_view import CurationMainView
 
 import napari
+from napari.utils.notifications import show_info
 
 from allencell_ml_segmenter.main.main_model import MainModel
 
@@ -41,16 +42,30 @@ def __init__(self, viewer: napari.Viewer, main_model: MainModel):
         self.curation_input_view = CurationInputView(self.curation_model)
         self.initialize_view(self.curation_input_view)
 
-        self.curation_main_view = CurationMainView()
+        self.curation_main_view = CurationMainView(
+            self.viewer, self.curation_model
+        )
         self.initialize_view(self.curation_main_view)
 
         self.set_view(self.curation_input_view)
         self.curation_model.subscribe(
             Event.PROCESS_CURATION_INPUT_STARTED,
             self,
-            lambda x: self.set_view(self.curation_main_view),
+            lambda x: self.go_to_main_view(self.curation_main_view),
         )
 
+    def go_to_main_view(self, view: View) -> None:
+        if (
+            self.curation_model.get_raw_directory() is not None
+            and self.curation_model.get_raw_channel() is not None
+            and self.curation_model.get_seg1_directory() is not None
+            and self.curation_model.get_seg1_channel() is not None
+        ):
+            self.set_view(view)
+            self.curation_main_view.curation_setup()
+        else:
+            _ = show_info("Please select all required fields")
+
     def set_view(self, view: View) -> None:
         """
         Set the current views, must be initialized first

src/allencell_ml_segmenter/curation/input_view.py

@@ -71,6 +71,9 @@ def __init__(self, curation_model: CurationModel):
             QLabel("Image channel"), 1, 1, alignment=Qt.AlignRight
         )
         self._raw_image_channel_combo: QComboBox = QComboBox()
+        self._raw_image_channel_combo.activated.connect(
+            self.raw_channel_selected
+        )
         raw_grid_layout.addWidget(
             self._raw_image_channel_combo, 1, 2, alignment=Qt.AlignLeft
         )
@@ -91,7 +94,7 @@ def __init__(self, curation_model: CurationModel):
         # TODO update model accordingly
         self._seg1_directory_select: InputButton = InputButton(
             self._curation_model,
-            lambda dir: self._curation_model.set_raw_directory(dir),
+            lambda dir: self._curation_model.set_seg1_directory(dir),
             "Select directory...",
             FileInputMode.DIRECTORY,
         )
@@ -102,6 +105,9 @@ def __init__(self, curation_model: CurationModel):
             QLabel("Image channel"), 1, 1, alignment=Qt.AlignRight
         )
         self._seg1_image_channel_combo: QComboBox = QComboBox()
+        self._seg1_image_channel_combo.activated.connect(
+            self.seg1_channel_selected
+        )
         seg1_grid_layout.addWidget(
             self._seg1_image_channel_combo, 1, 2, alignment=Qt.AlignLeft
         )
@@ -122,7 +128,7 @@ def __init__(self, curation_model: CurationModel):
         # TODO update model accordingly
         self._seg2_directory_select: InputButton = InputButton(
             self._curation_model,
-            lambda dir: self._curation_model.set_raw_directory(dir),
+            lambda dir: self._curation_model.set_seg2_directory(dir),
             "Select directory...",
             FileInputMode.DIRECTORY,
         )
@@ -133,6 +139,9 @@ def __init__(self, curation_model: CurationModel):
             QLabel("Image channel"), 1, 1, alignment=Qt.AlignRight
         )
         self._seg2_image_channel_combo: QComboBox = QComboBox()
+        self._seg2_image_channel_combo.activated.connect(
+            self.seg2_channel_selected
+        )
         seg2_grid_layout.addWidget(
             self._seg2_image_channel_combo, 1, 2, alignment=Qt.AlignLeft
         )
@@ -178,7 +187,9 @@ def update_raw_channels(self, event):
                 )
             ]
         )
+        # default first index
         self._raw_image_channel_combo.setCurrentIndex(0)
+        self._curation_model.set_raw_channel(0)
 
     def update_seg1_channels(self, event):
         self._seg1_image_channel_combo.clear()
@@ -191,6 +202,7 @@ def update_seg1_channels(self, event):
             ]
         )
         self._seg1_image_channel_combo.setCurrentIndex(0)
+        self._curation_model.set_seg1_channel(0)
 
     def update_seg2_channels(self, event):
         self._seg2_image_channel_combo.clear()
@@ -203,3 +215,13 @@ def update_seg2_channels(self, event):
             ]
         )
         self._seg2_image_channel_combo.setCurrentIndex(0)
+        self._curation_model.set_seg2_channel(0)
+
+    def raw_channel_selected(self, index):
+        self._curation_model.set_raw_channel(index)
+
+    def seg1_channel_selected(self, index):
+        self._curation_model.set_seg1_channel(index)
+
+    def seg2_channel_selected(self, index):
+        self._curation_model.set_seg2_channel(index)

src/allencell_ml_segmenter/curation/main_view.py

@@ -1,3 +1,5 @@
+from typing import List
+import napari
 from qtpy.QtCore import Qt
 from qtpy.QtWidgets import (
     QVBoxLayout,
@@ -8,20 +10,31 @@
     QPushButton,
     QProgressBar,
     QRadioButton,
+    QGridLayout,
 )
+from aicsimageio import AICSImage
 
 from allencell_ml_segmenter._style import Style
 from allencell_ml_segmenter.core.view import View
+from allencell_ml_segmenter.curation.curation_data_class import CurationRecord
+from allencell_ml_segmenter.curation.curation_model import CurationModel
+from allencell_ml_segmenter.main.main_model import MainModel
 from allencell_ml_segmenter.widgets.label_with_hint_widget import LabelWithHint
 
+from napari.utils.notifications import show_info
+
 
 class CurationMainView(View):
     """
     View for Curation UI
     """
 
-    def __init__(self):
+    def __init__(self, viewer: napari.Viewer, curation_model: CurationModel):
         super().__init__()
+        self.viewer = viewer
+        self._curation_model = curation_model
+        self.curation_index = 0
+        self.curation_record: List[CurationRecord] = list()
 
         self.setLayout(QVBoxLayout())
         self.layout().setContentsMargins(0, 10, 0, 10)
@@ -65,6 +78,7 @@ def __init__(self):
         progress_bar_layout.addWidget(inner_progress_frame)
         self.next_button: QPushButton = QPushButton("Next ►")
         self.next_button.setObjectName("big_blue_btn")
+        self.next_button.clicked.connect(self.next_image)
         progress_bar_layout.addWidget(
             self.next_button, alignment=Qt.AlignRight
         )
@@ -80,6 +94,7 @@ def __init__(self):
             QLabel("Use this image for training")
         )
         self.yes_radio: QRadioButton = QRadioButton("Yes")
+        self.yes_radio.setChecked(True)
         use_image_frame.layout().addWidget(self.yes_radio)
         self.no_radio: QRadioButton = QRadioButton("No")
         use_image_frame.layout().addWidget(self.no_radio)
@@ -93,10 +108,12 @@ def __init__(self):
             QLabel("File name..."), alignment=Qt.AlignLeft
         )
         self.layout().addLayout(excluding_mask_labels)
+
         # buttons for excluding mask
         excluding_mask_buttons = QHBoxLayout()
         excluding_create_button = QPushButton("+ Create")
         excluding_create_button.setObjectName("small_blue_btn")
+        excluding_create_button.clicked.connect(self.add_points_in_viewer)
         excluding_propagate_button = QPushButton("Propagate in 3D")
         excluding_delete_button = QPushButton("Delete")
         excluding_save_button = QPushButton("Save")
@@ -133,3 +150,79 @@ def getTypeOfWork(self):
 
     def showResults(self):
         print("show result")
+
+    def remove_all_images(self):
+        self.viewer.layers.clear()
+
+    def curation_setup(self):
+        _ = show_info("Loading curation images")
+        self.raw_images = [
+            f for f in self._curation_model.get_raw_directory().iterdir()
+        ]
+        self.seg1_images = [
+            f for f in self._curation_model.get_seg1_directory().iterdir()
+        ]
+
+        # set progress bar
+        self.progress_bar.setMaximum(len(self.raw_images))
+        self.progress_bar.setValue(1)
+        # set progress bar hint
+        self.progress_bar_image_count.setText(
+            f"{self.curation_index + 1}/{len(self.raw_images)}"
+        )
+        self.remove_all_images()
+
+        first_raw = self.raw_images[0]
+        self.viewer.add_image(
+            AICSImage(str(first_raw)).data, name=f"[raw] {first_raw.name}"
+        )
+        first_seg1 = self.seg1_images[0]
+        self.viewer.add_image(
+            AICSImage(str(first_seg1)).data, name=f"[seg] {first_seg1.name}"
+        )
+
+    def next_image(self):
+        _ = show_info("Loading the next image...")
+        self.curation_index = self.curation_index + 1
+        if self.curation_index < len(self.raw_images):
+            self.remove_all_images()
+
+            raw_to_view = self.raw_images[self.curation_index]
+            self.viewer.add_image(
+                AICSImage(str(raw_to_view)).data,
+                name=f"[raw] {raw_to_view.name}",
+            )
+            seg1_to_view = self.seg1_images[self.curation_index]
+            self.viewer.add_image(
+                AICSImage(str(seg1_to_view)).data,
+                name=f"[seg] {seg1_to_view.name}",
+            )
+            self._update_progress_bar()
+        else:
+            _ = show_info("No more image to load")
+
+    def _update_progress_bar(self):
+        # update progress bar
+        self.progress_bar.setValue(self.progress_bar.value() + 1)
+        # set progress bar hint
+        self.progress_bar_image_count.setText(
+            f"{self.curation_index + 1}/{len(self.raw_images)}"
+        )
+
+    def _update_curation_record(self):
+        use_this_image = True
+        if self.no_radio.isChecked():
+            use_this_image = False
+        if self._curation_model.get_seg2_directory() is not None:
+            self.curation_record.append(
+                CurationRecord(
+                    self.raw_images[self.curation_index],
+                    self.seg1_images[self.curation_index],
+                    use_this_image,
+                )
+            )
+
+    def add_points_in_viewer(self):
+        _ = show_info("Draw excluding area")
+        points_layer = self.viewer.add_shapes(None)
+        points_layer.mode = "add_polygon"