Merge pull request #142 from AllenCell/home-directory-curation

Home directory curation

src/allencell_ml_segmenter/constants.py

@@ -1,9 +1,9 @@
-CYTO_DL_HOME_PATH = "/Users/chrishu/dev/code/test2/cyto-dl"
-USER_EXPERIMENTS_PATH = (
-    "/Users/chrishu/dev/code/test2/allencell-ml-segmenter/logs/train/runs"
-)
-
-# CYTO_DL_HOME_PATH = "/Users/brian.kim/Desktop/work/cyto-dl"
+# CYTO_DL_HOME_PATH = "/Users/chrishu/dev/code/test2/cyto-dl"
 # USER_EXPERIMENTS_PATH = (
-#     "/Users/brian.kim/Desktop/work/cyto-dl/cyto_dl/logs/train/runs"
+#     "/Users/chrishu/dev/code/test2/allencell-ml-segmenter/logs/train/runs"
 # )
+
+CYTO_DL_HOME_PATH = "/Users/brian.kim/Desktop/work/cyto-dl"
+USER_EXPERIMENTS_PATH = (
+    "/Users/brian.kim/Desktop/work/allencell-ml-segmenter/logs/train/runs"
+)

src/allencell_ml_segmenter/core/event.py

@@ -19,7 +19,9 @@ class Event(Enum):
     # Action events. This signals a change in the UI. These are a direct result of a user action
     ACTIOIN_REFRESH = "refresh"
     ACTION_CHANGE_VIEW = "change_view"
+    # Training
     ACTION_START_TRAINING = "start_training"
+    # Prediction
     ACTION_PREDICTION_MODEL_FILE = "model_file"
     ACTION_PREDICTION_PREPROCESSING_METHOD = "preprocessing_method"
     ACTION_PREDICTION_POSTPROCESSING_METHOD = "postprocessing_method"
@@ -29,9 +31,12 @@ class Event(Enum):
     ACTION_PREDICTION_POSTPROCESSING_AUTO_THRESHOLD = (
         "postprocessing_auto_threshold"
     )
+    # Curation
     ACTION_CURATION_RAW_SELECTED = "curation_raw_selected"
     ACTION_CURATION_SEG1_SELECTED = "curation_seg1_selected"
     ACTION_CURATION_SEG2_SELECTED = "curation_seg2_selected"
+    # Experiment related
+    ACTION_EXPERIMENT_SELECTED = "experiment_selected"
 
     # View selection events. These can stem from a user action, or from a process (i.e. prediction process ends, and a new view is shown automatically).
     VIEW_SELECTION_TRAINING = "training_selected"

src/allencell_ml_segmenter/curation/curation_model.py

@@ -11,7 +11,7 @@ class CurationModel(Publisher):
     Stores state relevant to prediction processes.
     """
 
-    def __init__(self):
+    def __init__(self) -> None:
         super().__init__()
         self.current_view = None
 
@@ -29,73 +29,127 @@ def __init__(self):
         self._seg1_image_channel_count: int = None
         self._seg2_image_channel_count: int = None
 
-    def set_raw_directory(self, dir: Path):
+    def set_raw_directory(self, dir: Path) -> None:
+        """
+        Set the raw image directory path
+        """
         self._raw_directory = dir
         self._raw_image_channel_count = self.get_total_num_channels(
             self._raw_directory
         )
         self.dispatch(Event.ACTION_CURATION_RAW_SELECTED)
 
     def get_raw_directory(self) -> Path:
+        """
+        Get the raw image directory path
+        """
         return self._raw_directory
 
-    def set_seg1_directory(self, dir: Path):
+    def set_seg1_directory(self, dir: Path) -> None:
+        """
+        Set the seg1 image directory path
+        """
         self._seg1_directory = dir
         self._seg1_image_channel_count = self.get_total_num_channels(
             self._seg1_directory
         )
         self.dispatch(Event.ACTION_CURATION_SEG1_SELECTED)
 
     def get_seg1_directory(self) -> Path:
+        """
+        Get the seg1 image directory path
+        """
         return self._seg1_directory
 
-    def set_seg2_directory(self, dir: Path):
+    def set_seg2_directory(self, dir: Path) -> None:
+        """
+        Set the seg2 image directory path
+        """
         self._seg2_directory = dir
         self._seg2_image_channel_count = self.get_total_num_channels(
             self._seg2_directory
         )
         self.dispatch(Event.ACTION_CURATION_SEG2_SELECTED)
 
     def get_seg2_directory(self) -> Path:
+        """
+        Get the seg2 image directory path
+        """
         return self._seg2_directory
 
-    def set_raw_channel(self, channel: int):
+    def set_raw_channel(self, channel: int) -> None:
+        """
+        Set the raw image channel
+        """
         self._raw_image_channel = channel
 
     def get_raw_channel(self) -> int:
+        """
+        Get the raw image channel
+        """
         return self._raw_image_channel
 
-    def set_seg1_channel(self, channel: int):
+    def set_seg1_channel(self, channel: int) -> None:
+        """
+        Set the seg1 image channel
+        """
         self._seg1_image_channel = channel
 
     def get_seg1_channel(self) -> int:
+        """
+        get the seg1 image channel
+        """
         return self._seg1_image_channel
 
-    def set_seg2_channel(self, channel: int):
+    def set_seg2_channel(self, channel: int) -> None:
+        """
+        Set the seg2 image channel
+        """
         self._seg2_image_channel = channel
 
     def get_seg2_channel(self) -> int:
+        """
+        Get the seg2 image channel
+        """
         return self._seg2_image_channel
 
-    def set_view(self):
+    def set_view(self) -> None:
+        """
+        Set current curation view
+        """
         self.dispatch(Event.PROCESS_CURATION_INPUT_STARTED)
 
-    def get_view(self):
+    def get_view(self) -> str:
+        """
+        Get current curation view
+        """
         return self.current_view
 
-    def get_total_num_channels_raw(self):
+    def get_total_num_channels_raw(self) -> int:
+        """
+        Get total number of raw channels
+        """
         return self._raw_image_channel_count
 
-    def get_total_num_channels_seg1(self):
+    def get_total_num_channels_seg1(self) -> int:
+        """
+        Get total number of seg1 channels
+        """
         return self._seg1_image_channel_count
 
-    def get_total_num_channels_seg2(self):
+    def get_total_num_channels_seg2(self) -> int:
+        """
+        Get total number of seg2 channels
+        """
         return self._seg2_image_channel_count
 
-    def get_total_num_channels(self, path) -> int:
+    def get_total_num_channels(self, path: Path) -> int:
+        """
+        Determine total number of channels for image in a set folder
+        """
         # we expect user to have the same number of channels for all images in their folders
         # and that only images are stored in those folders
-        first_image = path.iterdir().__next__()
-        img = AICSImage(str(first_image.resolve()))
+        first_image: Path = path.iterdir().__next__()
+        img: AICSImage = AICSImage(str(first_image.resolve()))
         # return num channel
         return img.dims.C

src/allencell_ml_segmenter/curation/curation_widget.py

@@ -1,3 +1,5 @@
+from typing import Dict
+
 from qtpy.QtWidgets import (
     QVBoxLayout,
     QSizePolicy,
@@ -14,6 +16,7 @@
 import napari
 from napari.utils.notifications import show_info
 
+from allencell_ml_segmenter.main.experiments_model import ExperimentsModel
 from allencell_ml_segmenter.main.main_model import MainModel
 
 
@@ -27,23 +30,31 @@ class CurationUiMeta(type(QStackedWidget), type(Subscriber)):
 
 
 class CurationWidget(QStackedWidget, Subscriber, metaclass=CurationUiMeta):
-    def __init__(self, viewer: napari.Viewer, main_model: MainModel):
+    def __init__(
+        self,
+        viewer: napari.Viewer,
+        main_model: MainModel,
+        experiments_model: ExperimentsModel,
+    ) -> None:
         super().__init__()
-        self.main_model = main_model
+        self.main_model: MainModel = main_model
         self.viewer: napari.Viewer = viewer
-        self.view_to_index = dict()
-        self.curation_model = CurationModel()
+        self.experiments_model: ExperimentsModel = experiments_model
+        self.view_to_index: Dict[View, int] = dict()
+        self.curation_model: CurationModel = CurationModel()
 
         # basic styling
         self.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.MinimumExpanding)
         self.setLayout(QVBoxLayout())
         self.layout().setContentsMargins(0, 0, 0, 0)
 
-        self.curation_input_view = CurationInputView(self.curation_model)
+        self.curation_input_view: CurationInputView = CurationInputView(
+            self.curation_model
+        )
         self.initialize_view(self.curation_input_view)
 
-        self.curation_main_view = CurationMainView(
-            self.viewer, self.curation_model
+        self.curation_main_view: CurationMainView = CurationMainView(
+            self.viewer, self.curation_model, self.experiments_model
         )
         self.initialize_view(self.curation_main_view)
 
@@ -55,6 +66,9 @@ def __init__(self, viewer: napari.Viewer, main_model: MainModel):
         )
 
     def go_to_main_view(self, view: View) -> None:
+        """
+        Switch to main curation view
+        """
         if (
             self.curation_model.get_raw_directory() is not None
             and self.curation_model.get_raw_channel() is not None
@@ -73,6 +87,9 @@ def set_view(self, view: View) -> None:
         self.setCurrentIndex(self.view_to_index[view])
 
     def initialize_view(self, view: View) -> None:
+        """
+        Initialize views. This is necessary because QStackedWidget requires all child widgets to be added
+        """
         # QStackedWidget count method keeps track of how many child widgets have been added
         self.view_to_index[view] = self.count()
         self.addWidget(view)