Merge pull request #101 from Kitware/main

Bring master changes

.github/workflows/ci.yml

@@ -66,3 +66,25 @@ jobs:
         pip install -e '.[dev]'
     - name: Invoke PyTest
       run: pytest -v .
+
+  semantic_release:
+    runs-on: ubuntu-latest
+    name: Semantic release noop
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel "build<0.10.0" python-semantic-release
+
+      - name: Python Semantic Release
+        id: release
+        uses: python-semantic-release/[email protected]
+        with:
+          root_options: -vv --noop

examples/conda-env-cuda.yml

@@ -0,0 +1,13 @@
+name: nrtk-explorer-cuda
+channels:
+  - nvidia
+  - pytorch
+  - conda-forge
+dependencies:
+  - pytorch::pytorch
+  - pytorch::torchvision
+  - pytorch::torchaudio
+  - pytorch::pytorch-cuda=11.8
+  - nrtk-explorer
+variables:
+    channel_priority: flexible

pyproject.toml

@@ -28,10 +28,10 @@ classifiers = [
 
 dependencies = [
     "accelerate",
-    "kwcoco",
     "nrtk>=0.4.2",
     "numpy",
     "Pillow",
+    "pybsm>=0.6",
     "scikit-learn==1.5.1",
     "smqtk_image_io",
     "tabulate",
@@ -47,6 +47,10 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
+kwcoco= [
+  "kwcoco",
+]
+
 dev = [
   "black",
   "flake8",

src/nrtk_explorer/app/core.py

@@ -6,7 +6,7 @@
 from trame_server.utils.namespace import Translator
 from nrtk_explorer.library import images_manager
 from nrtk_explorer.library.filtering import FilterProtocol
-from nrtk_explorer.library.dataset import get_dataset
+from nrtk_explorer.library.dataset import get_dataset, get_image_fpath
 
 from nrtk_explorer.app.embeddings import EmbeddingsApp
 from nrtk_explorer.app.transforms import TransformsApp
@@ -54,6 +54,8 @@ def __init__(self, server=None):
         self.input_paths = known_args.dataset
         self.state.current_dataset = str(Path(self.input_paths[0]).resolve())
 
+        self.ctrl.get_image_fpath = lambda i: get_image_fpath(i, self.state.current_dataset)
+
         self.context["image_objects"] = {}
         self.context["images_manager"] = images_manager.ImagesManager()
 

src/nrtk_explorer/app/image_server.py

@@ -2,7 +2,6 @@
 from PIL import Image
 import io
 from trame.app import get_server
-from nrtk_explorer.library.dataset import get_image_path
 
 
 ORIGINAL_IMAGE_ENDPOINT = "original-image"
@@ -25,7 +24,7 @@ def make_response(image, format):
 
 async def original_image_endpoint(request: web.Request):
     id = request.match_info["id"]
-    image_path = get_image_path(id)
+    image_path = server.controller.get_image_fpath(int(id))
 
     if image_path in server.context.images_manager.images:
         image = server.context.images_manager.images[image_path]

src/nrtk_explorer/app/transforms.py

@@ -37,7 +37,7 @@
     dataset_id_to_image_id,
     dataset_id_to_transformed_image_id,
 )
-from nrtk_explorer.library.dataset import get_dataset, get_image_path
+from nrtk_explorer.library.dataset import get_dataset
 import nrtk_explorer.app.image_server
 
 
@@ -121,6 +121,10 @@ def tranformed_became_visible(old, new):
         self.server.controller.add("on_server_ready")(self.on_server_ready)
         self._on_hover_fn = None
 
+    @property
+    def get_image_fpath(self):
+        return self.server.controller.get_image_fpath
+
     def on_server_ready(self, *args, **kwargs):
         # Bind instance methods to state change
         self.state.change("current_dataset")(self.on_current_dataset_change)
@@ -295,7 +299,7 @@ async def _update_images(self):
             self.state.hovered_id = ""
 
         for selected_id in selected_ids:
-            filename = get_image_path(selected_id)
+            filename = self.get_image_fpath(int(selected_id))
             img = self.context.images_manager.load_image(filename)
             image_id = dataset_id_to_image_id(selected_id)
             self.context.image_objects[image_id] = img

src/nrtk_explorer/library/dataset.py

@@ -1,24 +1,59 @@
-import kwcoco
+"""
+Module to load the dataset and get the image file path given an image id.
+
+Example:
+    dataset = get_dataset("path/to/dataset.json")
+    image_fpath = dataset.get_image_fpath(image_id)
+"""
+
+from functools import lru_cache
 from pathlib import Path
 
+import json
+
+
+class DefaultDataset:
+    """Default dataset class to load the dataset and get the image file path given an image id."""
+
+    def __init__(self, path: str):
+        with open(path) as f:
+            self.data = json.load(f)
+            self.fpath = path
+            self.cats = {cat["id"]: cat for cat in self.data["categories"]}
+            self.anns = {ann["id"]: ann for ann in self.data["annotations"]}
+            self.imgs = {img["id"]: img for img in self.data["images"]}
+
+    def get_image_fpath(self, selected_id: int):
+        """Get the image file path given an image id."""
+        dataset_dir = Path(self.fpath).parent
+        file_name = self.imgs[selected_id]["file_name"]
+        return str(dataset_dir / file_name)
 
-def load_dataset(path: str):
-    return kwcoco.CocoDataset(path)
 
+@lru_cache
+def __load_dataset(path: str):
+    """Load the dataset given the path to the dataset file."""
+    try:
+        import kwcoco
 
-dataset: kwcoco.CocoDataset = kwcoco.CocoDataset()
-dataset_path: str = ""
+        return kwcoco.CocoDataset(path)
+    except ImportError:
+        return DefaultDataset(path)
 
 
-def get_dataset(path: str, force_reload=False):
-    global dataset, dataset_path
-    if dataset_path != path or force_reload:
-        dataset_path = path
-        dataset = load_dataset(dataset_path)
-    return dataset
+def get_dataset(path: str, force_reload: bool = False):
+    """Get the dataset object given the path to the dataset file.
+    Args:
+        path (str): Path to the dataset file.
+        force_reload (bool): Whether to force reload the dataset. Default: False.
+    Return:
+        dataset: Dataset object.
+    """
+    if force_reload:
+        __load_dataset.cache_clear()
+    return __load_dataset(path)
 
 
-def get_image_path(id: str):
-    dataset_dir = Path(dataset_path).parent
-    file_name = dataset.imgs[int(id)]["file_name"]
-    return str(dataset_dir / file_name)
+def get_image_fpath(selected_id: int, path: str):
+    """Get the image file path given an image id."""
+    return get_dataset(path).get_image_fpath(selected_id)

src/nrtk_explorer/library/nrtk_transforms.py

@@ -12,7 +12,7 @@
 logger.setLevel(logging.INFO)
 
 try:
-    from pybsm.otf import darkCurrentFromDensity
+    from pybsm.otf import dark_current_from_density
     from nrtk.impls.perturb_image.generic.cv2.blur import GaussianBlurPerturber
     from nrtk.impls.perturb_image.pybsm.perturber import PybsmPerturber, PybsmSensor, PybsmScenario
 except ImportError:
@@ -99,7 +99,7 @@ def createSampleSensorAndScenario():
     intTime = 30.0e-3
 
     # dark current density of 1 nA/cm2 guess, guess mid range for a silicon camera
-    darkCurrent = darkCurrentFromDensity(1e-5, wx, wy)
+    darkCurrent = dark_current_from_density(1e-5, wx, wy)
 
     # rms read noise (rms electrons)
     readNoise = 25.0

tests/test_dataset.py

@@ -0,0 +1,40 @@
+from nrtk_explorer.library.dataset import get_dataset, DefaultDataset
+import nrtk_explorer.test_data
+
+from unittest import mock
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture
+def dataset_path():
+    dir_name = Path(nrtk_explorer.test_data.__file__).parent
+    return f"{dir_name}/coco-od-2017/test_val2017.json"
+
+
+def test_get_dataset(dataset_path):
+    ds1 = get_dataset(dataset_path)
+    assert ds1 is not None
+
+    ds1 = get_dataset(dataset_path)
+    ds2 = get_dataset(dataset_path)
+    assert ds1 is ds2
+
+    ds1 = get_dataset(dataset_path)
+    ds2 = get_dataset(dataset_path, force_reload=True)
+    assert ds1 is not ds2
+
+
+@mock.patch("nrtk_explorer.library.dataset.__load_dataset", lambda path: DefaultDataset(path))
+def test_get_dataset_empty():
+    with pytest.raises(FileNotFoundError):
+        get_dataset("nonexisting")
+
+
+def test_DefaultDataset(dataset_path):
+    ds = DefaultDataset(dataset_path)
+    assert len(ds.imgs) > 0
+    assert len(ds.cats) > 0
+    assert len(ds.anns) > 0
+    assert Path(ds.get_image_fpath(491497)).name == "000000491497.jpg"