tau-fibrils-yolo 0.1.0__tar.gz → 0.1.1__tar.gz

{tau_fibrils_yolo-0.1.0 → tau_fibrils_yolo-0.1.1}/.gitignore

@@ -27,7 +27,8 @@ venv/
 
 push.sh
 todo.txt
-*.pt
+trained_models/
+pretrained_models/
 qupath/
 output/
 notebooks/

{tau_fibrils_yolo-0.1.0 → tau_fibrils_yolo-0.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tau-fibrils-yolo
-Version: 0.1.0
+Version: 0.1.1
 Summary: YoloV8 model for the detection of Tau fibrils in EM images.
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License:                     GNU AFFERO GENERAL PUBLIC LICENSE
@@ -686,13 +686,12 @@ Requires-Dist: numpy
 Requires-Dist: pandas
 Requires-Dist: tifffile
 Requires-Dist: matplotlib
-Requires-Dist: pooch==1.8.0
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
 Requires-Dist: ultralytics
 Requires-Dist: opencv-contrib-python-headless
-Requires-Dist: imaging-server-kit>=0.1.3
-Requires-Dist: napari-serverkit>=0.0.9
+Requires-Dist: imaging-server-kit==0.1.3
+Requires-Dist: napari-serverkit==0.0.9
 Dynamic: license-file
 
 ![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)

{tau_fibrils_yolo-0.1.0 → tau_fibrils_yolo-0.1.1}/pyproject.toml

@@ -27,13 +27,12 @@ dependencies = [
     "pandas",
     "tifffile",
     "matplotlib",
-    "pooch==1.8.0",
     "scikit-image",
     "scikit-learn",
     "ultralytics",
     "opencv-contrib-python-headless",
-    "imaging-server-kit>=0.1.3",
-    "napari-serverkit>=0.0.9",
+    "imaging-server-kit==0.1.3",
+    "napari-serverkit==0.0.9",
 ]
 
 [project.entry-points."napari.manifest"]

{tau_fibrils_yolo-0.1.0 → tau_fibrils_yolo-0.1.1}/src/tau_fibrils_yolo/__init__.py

@@ -10,13 +10,13 @@ import imaging_server_kit as sk
 
 
 class YoloDetectorWidget(QWidget):
-    def __init__(self, viewer):
+    def __init__(self, napari_viewer):
         super().__init__()
         multi = sk.combine(
             [detect_fibrils, max_iou_boxes, min_distance_boxes, boxes_kernel_density],
             name="Tau fibrils analysis",
         )
-        widget = sk.to_qwidget(multi, viewer)
+        widget = sk.to_qwidget(multi, napari_viewer)
         self.setLayout(widget.layout())
 
 

{tau_fibrils_yolo-0.1.0 → tau_fibrils_yolo-0.1.1}/src/tau_fibrils_yolo/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.1.0'
-__version_tuple__ = version_tuple = (0, 1, 0)
+__version__ = version = '0.1.1'
+__version_tuple__ = version_tuple = (0, 1, 1)
 
-__commit_id__ = commit_id = 'g53b41a1b4'
+__commit_id__ = commit_id = 'g697cbb526'

{tau_fibrils_yolo-0.1.0 → tau_fibrils_yolo-0.1.1}/src/tau_fibrils_yolo/widget.py

@@ -4,7 +4,6 @@ from pathlib import Path
 
 import imaging_server_kit as sk
 import numpy as np
-import pooch
 from skimage.color import gray2rgb
 from ultralytics import YOLO
 
@@ -18,25 +17,10 @@ _MODEL = None
 MODEL_DIR = Path(os.getenv("XDG_DATA_HOME", Path.home())) / ".yolo"
 WEIGHTS_PATH = MODEL_DIR / "yolo_fibrils_100ep.pt"
 
-
-def retrieve_model():
-    MODEL_DIR.mkdir(parents=True, exist_ok=True)
-    if WEIGHTS_PATH.exists():
-        return str(WEIGHTS_PATH)
-
-    return pooch.retrieve(
-        url="https://sandbox.zenodo.org/records/99113/files/100ep.pt",
-        known_hash="md5:2fc4be1e4feae93f75e335856be3083d",
-        path=str(MODEL_DIR),
-        fname=WEIGHTS_PATH.name,
-        progressbar=True,
-    )
-
-
 def get_model() -> YOLO:
     global _MODEL
     if _MODEL is None:
-        weights = retrieve_model()
+        weights = resources.files("tau_fibrils_yolo").joinpath("model/100ep.pt")
         _MODEL = YOLO(weights)
     return _MODEL
 
@@ -50,9 +34,7 @@ def cast_to_rgb(image: np.ndarray) -> np.ndarray:
     return image
 
 
-@sk.algorithm(
-    # parameters={"image": sk.Image(rgb=True)}
-)
+@sk.algorithm
 def _detect_fibrils_tile(image: np.ndarray, imgsz: int, iou: float, conf: float):
     """Runs the model on a tile corresponding to the model's imgsz that it was trained on."""
 

{tau_fibrils_yolo-0.1.0 → tau_fibrils_yolo-0.1.1}/src/tau_fibrils_yolo.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tau-fibrils-yolo
-Version: 0.1.0
+Version: 0.1.1
 Summary: YoloV8 model for the detection of Tau fibrils in EM images.
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License:                     GNU AFFERO GENERAL PUBLIC LICENSE
@@ -686,13 +686,12 @@ Requires-Dist: numpy
 Requires-Dist: pandas
 Requires-Dist: tifffile
 Requires-Dist: matplotlib
-Requires-Dist: pooch==1.8.0
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
 Requires-Dist: ultralytics
 Requires-Dist: opencv-contrib-python-headless
-Requires-Dist: imaging-server-kit>=0.1.3
-Requires-Dist: napari-serverkit>=0.0.9
+Requires-Dist: imaging-server-kit==0.1.3
+Requires-Dist: napari-serverkit==0.0.9
 Dynamic: license-file
 
 ![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)

{tau_fibrils_yolo-0.1.0 → tau_fibrils_yolo-0.1.1}/src/tau_fibrils_yolo.egg-info/SOURCES.txt

@@ -24,4 +24,5 @@ src/tau_fibrils_yolo.egg-info/dependency_links.txt
 src/tau_fibrils_yolo.egg-info/entry_points.txt
 src/tau_fibrils_yolo.egg-info/requires.txt
 src/tau_fibrils_yolo.egg-info/top_level.txt
+src/tau_fibrils_yolo/model/100ep.pt
 src/tau_fibrils_yolo/sample/sample.tif

{tau_fibrils_yolo-0.1.0 → tau_fibrils_yolo-0.1.1}/src/tau_fibrils_yolo.egg-info/requires.txt

@@ -5,10 +5,9 @@ numpy
 pandas
 tifffile
 matplotlib
-pooch==1.8.0
 scikit-image
 scikit-learn
 ultralytics
 opencv-contrib-python-headless
-imaging-server-kit>=0.1.3
-napari-serverkit>=0.0.9
+imaging-server-kit==0.1.3
+napari-serverkit==0.0.9