working on utils + fixes

Author: C-Achard

docs/res/model_instance_seg.rst

@@ -12,3 +12,11 @@ binary_connected
 binary_watershed
 **************************************
 .. autofunction:: napari_cellseg_annotator.model_instance_seg::binary_watershed
+
+to_instance
+**************************************
+.. autofunction:: napari_cellseg_annotator.model_instance_seg::to_instance
+
+to_semantic
+**************************************
+.. autofunction:: napari_cellseg_annotator.model_instance_seg::to_semantic

docs/res/utils.rst

@@ -13,6 +13,10 @@ get_time
 **************************************
 .. autofunction:: napari_cellseg_annotator.utils::get_time
 
+get_time_filepath
+**************************************
+.. autofunction:: napari_cellseg_annotator.utils::get_time_filepath
+
 save_stack
 **************************************
 .. autofunction:: napari_cellseg_annotator.utils::save_stack
@@ -21,6 +25,10 @@ get_padding_dim
 **************************************
 .. autofunction:: napari_cellseg_annotator.utils::get_padding_dim
 
+dice_coeff
+**************************************
+.. autofunction:: napari_cellseg_annotator.utils::dice_coeff
+
 normalize_x
 **************************************
 .. autofunction:: napari_cellseg_annotator.utils::normalize_x

src/napari_cellseg_annotator/model_framework.py

@@ -3,6 +3,7 @@
 
 import napari
 import torch
+
 # Qt
 from qtpy.QtWidgets import QLineEdit
 from qtpy.QtWidgets import QProgressBar

src/napari_cellseg_annotator/model_instance_seg.py

@@ -92,21 +92,39 @@ def binary_watershed(
 
 
 def to_instance(image, is_file_path=True):
+    """Converts a **ground-truth** label to instance (unique id per object) labels. Does not remove small objects.
+
+    Args:
+        image: image or path to image
+        is_file_path: if True, will consider ``image`` to be a string containing a path to a file, if not treats it as an image data array.
+
+    Returns: resulting converted labels
+
+    """
     if is_file_path:
-        image = imread(image)
-        image = image.compute()
+        image = [imread(image)]
+        # image = image.compute()
 
     result = binary_watershed(
-        image, thres_small=1, thres_seeding=0.3, rem_seed_thres=1
+        image, thres_small=0, thres_seeding=0.3, rem_seed_thres=0
     )  # TODO add params ?
 
     return result
 
 
 def to_semantic(image, is_file_path=True):
+    """Converts a **ground-truth** label to semantic (binary 0/1) labels.
+
+    Args:
+        image: image or path to image
+        is_file_path: if True, will consider ``image`` to be a string containing a path to a file, if not treats it as an image data array.
+
+    Returns: resulting converted labels
+
+    """
     if is_file_path:
         image = imread(image)
-        image = image.compute()
+        # image = image.compute()
 
     image[image >= 1] = 1
     result = image.astype(np.uint16)

src/napari_cellseg_annotator/model_workers.py

@@ -4,6 +4,7 @@
 
 import numpy as np
 import torch
+
 # MONAI
 from monai.data import CacheDataset
 from monai.data import DataLoader
@@ -30,6 +31,7 @@
 from monai.transforms import Zoom
 from napari.qt.threading import GeneratorWorker
 from napari.qt.threading import WorkerBaseSignals
+
 # Qt
 from qtpy.QtCore import Signal
 from tifffile import imwrite
@@ -305,7 +307,7 @@ def inference(self):
                 file_path = (
                     self.results_path
                     + "/"
-                    + f"Prediction_{image_id}"
+                    + f"Prediction_{image_id}_"
                     + original_filename
                     + "_"
                     + self.model_dict["name"]

src/napari_cellseg_annotator/plugin_base.py

@@ -42,6 +42,9 @@ def __init__(self, viewer: "napari.viewer.Viewer", parent=None):
         self.label_path = ""
         """str: path to label folder"""
 
+        self.results_path = ""
+        """str: path to results folder"""
+
         self.filetype = ""
         """str: filetype, .tif or .png"""
         self.as_folder = False
@@ -124,6 +127,7 @@ def load_results_path(self):
             self.update_default()
 
     def update_default(self):
+        """Updates default path for smoother navigation when opening file dialogs"""
         self._default_path = [self.image_path, self.label_path]
 
     def remove_from_viewer(self):
@@ -245,7 +249,7 @@ def load_image_dataset(self):
     def load_label_dataset(self):
         """Show file dialog to set :py:attr:`~labels_filepaths`"""
         filenames = self.load_dataset_paths()
-        if filenames != "" and filenames != [""]:
+        if filenames != "" and filenames != [""] and filenames != []:
             self.labels_filepaths = filenames
             path = os.path.dirname(filenames[0])
             self.lbl_label_files.setText(path)

src/napari_cellseg_annotator/plugin_convert.py

@@ -129,47 +129,72 @@ def build(self):
 
     def folder_to_semantic(self):
         """Converts folder of labels to semantic labels"""
+
+        results_folder = (
+            self.results_path
+            + f"/converted_to_semantic_labels_{utils.get_date_time()}"
+        )
+
+        os.makedirs(results_folder, exist_ok=False)
+
         for file in self.labels_filepaths:
 
             image = to_semantic(file)
 
             imwrite(
-                self.results_path
-                + f"/converted_to_semantic_labels_{utils.get_date_time()}/"
-                + os.path.basename(file),
+                results_folder + "/" + os.path.basename(file),
                 image,
             )
 
     def layer_to_semantic(self):
         """Converts selected layer to semantic labels"""
 
         im = self._viewer.layers.selection.active.data
+        name = self._viewer.layers.selection.active.name
         semantic_labels = to_semantic(im, is_file_path=False)
 
-        self._viewer.add_labels(
-            semantic_labels, name=f"Converted to semantic_{utils.get_time()}"
-        )
+        if self.results_path != "":
+            imwrite(
+                self.results_path
+                + f"/{name}_semantic_{utils.get_time_filepath()}"
+                + self.filetype_choice.currentText(),
+                semantic_labels,
+            )
+
+        self._viewer.add_labels(semantic_labels, name=f"converted_semantic")
 
     def folder_to_instance(self):
         """Converts the chosen folder to instance labels"""
 
+        results_folder = (
+            self.results_path
+            + f"/converted_to_instance_labels_{utils.get_date_time()}"
+        )
+
+        os.makedirs(results_folder, exist_ok=False)
+
         for file in self.labels_filepaths:
 
             image = to_instance(file)
 
             imwrite(
-                self.results_path
-                + f"/converted_to_instance_labels_{utils.get_date_time()}/"
-                + os.path.basename(file),
+                results_folder + "/" + os.path.basename(file),
                 image,
             )
 
     def layer_to_instance(self):
         """Converts the selected layer to instance labels"""
 
         im = [self._viewer.layers.selection.active.data]
+        name = self._viewer.layers.selection.active.name
         instance_labels = to_instance(im, is_file_path=False)
 
-        self._viewer.add_labels(
-            instance_labels, name=f"Converted to instance_{utils.get_time()}"
-        )
+        if self.results_path != "":
+            imwrite(
+                self.results_path
+                + f"/{name}_instance_{utils.get_time_filepath()}"
+                + self.filetype_choice.currentText(),
+                instance_labels,
+            )
+
+        self._viewer.add_labels(instance_labels, name=f"converted_instance")

src/napari_cellseg_annotator/plugin_crop.py

@@ -6,6 +6,7 @@
 from magicgui import magicgui
 from magicgui.widgets import Container
 from magicgui.widgets import Slider
+
 # Qt
 from qtpy.QtWidgets import QLabel
 from qtpy.QtWidgets import QSizePolicy

src/napari_cellseg_annotator/plugin_dock.py

@@ -1,9 +1,11 @@
 import os
 import warnings
+
 # import shutil
 from pathlib import Path
 
 import pandas as pd
+
 # Qt
 from qtpy.QtWidgets import QVBoxLayout
 from qtpy.QtWidgets import QWidget

src/napari_cellseg_annotator/plugin_helper.py

@@ -1,4 +1,5 @@
 import napari
+
 # Qt
 from qtpy.QtWidgets import QSizePolicy
 from qtpy.QtWidgets import QVBoxLayout