fix some typing issues

bioimage-io · Jun 8, 2024 · d936a56 · d936a56
1 parent 0134584
commit d936a56
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Showing 2 changed files with 22 additions and 16 deletions.
diff --git a/bioimageio/spec/partner_utils/imjoy/_plugin_parser.py b/bioimageio/spec/partner_utils/imjoy/_plugin_parser.py
@@ -196,7 +196,6 @@ def enrich_partial_rdf_with_imjoy_plugin(
 ) -> Dict[str, Any]:
     """
     a (partial) rdf may have 'rdf_source' or 'source' which resolve to rdf data that may be overwritten.
-    Due to resolving imjoy plugins this is not done in bioimageio.spec.collection atm
     """
 
     enriched_rdf: Dict[str, Any] = {}

diff --git a/example/load_model_and_create_your_own.ipynb b/example/load_model_and_create_your_own.ipynb
@@ -202,11 +202,17 @@
     "from typing import Any\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
-    "from imageio.v3 import imread\n",
+    "import imageio.v3\n",
     "from numpy.typing import NDArray\n",
     "\n",
+    "from bioimageio.spec._internal.io import FileSource\n",
     "from bioimageio.spec.utils import download\n",
     "\n",
+    "def imread(src: FileSource) -> NDArray[Any]:\n",
+    "    \"\"\"typed `imageio.v3.imread`\"\"\"\n",
+    "    img: NDArray[Any] = imageio.v3.imread(download(src).path)\n",
+    "    return img\n",
+    "\n",
     "print(f\"The model is named '{model.name}'\")\n",
     "print(f\"Description:\\n{model.description}\")\n",
     "print(f\"License: {model.license}\")"
@@ -250,11 +256,11 @@
     "for i, cover in enumerate(model.covers):\n",
     "    downloaded_cover = download(cover)\n",
     "    cover_data: NDArray[Any] = imread(downloaded_cover.path)\n",
-    "    plt.figure(figsize=(10, 10))\n",
-    "    plt.imshow(cover_data)\n",
-    "    plt.xticks([])\n",
-    "    plt.yticks([])\n",
-    "    plt.title(f\"cover image {downloaded_cover.original_file_name}\")\n",
+    "    _ = plt.figure(figsize=(10, 10))\n",
+    "    plt.imshow(cover_data)  # type: ignore\n",
+    "    plt.xticks([])  # type: ignore\n",
+    "    plt.yticks([])  # type: ignore\n",
+    "    plt.title(f\"cover image {downloaded_cover.original_file_name}\")  # type: ignore\n",
     "    plt.show()"
    ]
   },
@@ -276,7 +282,7 @@
     "        continue\n",
     "\n",
     "    print(w.weights_format_name)\n",
-    "    print(f\"weights are available at {w.source.absolute}\")\n",
+    "    print(f\"weights are available at {w.source.absolute()}\")\n",
     "    print(f\"and have a SHA-256 value of {w.sha256}\")\n",
     "    details = {k: v for k, v in w.model_dump(mode=\"json\", exclude_none=True).items() if k not in (\"source\", \"sha256\")}\n",
     "    if details:\n",
@@ -304,9 +310,9 @@
     "    print(f\"\\ninput '{ipt.id}' with axes:\")\n",
     "    pprint(ipt.axes)\n",
     "    print(f\"Data description: {ipt.data}\")\n",
-    "    print(f\"Test tensor available at:  {ipt.test_tensor.source.absolute}\")\n",
+    "    print(f\"Test tensor available at:  {ipt.test_tensor.source.absolute()}\")\n",
     "    if len(ipt.preprocessing) > 1:\n",
-    "        print(f\"This input is preprocessed with: \")\n",
+    "        print(\"This input is preprocessed with: \")\n",
     "        for p in ipt.preprocessing:\n",
     "            print(p)\n",
     "\n",
@@ -317,9 +323,9 @@
     "    print(f\"\\noutput '{out.id}' with axes:\")\n",
     "    pprint(out.axes)\n",
     "    print(f\"Data description: {out.data}\")\n",
-    "    print(f\"Test tensor available at:  {out.test_tensor.source.absolute}\")\n",
+    "    print(f\"Test tensor available at:  {out.test_tensor.source.absolute()}\")\n",
     "    if len(out.postprocessing) > 1:\n",
-    "        print(f\"This output is postprocessed with: \")\n",
+    "        print(\"This output is postprocessed with: \")\n",
     "        for p in out.postprocessing:\n",
     "            print(p)"
    ]
@@ -348,7 +354,7 @@
     "    arch = w.architecture\n",
     "    print(f\"callable: {arch.callable}\")\n",
     "    if isinstance(arch, ArchitectureFromFileDescr):\n",
-    "        print(f\"import from file: {arch.source.absolute}\")\n",
+    "        print(f\"import from file: {arch.source.absolute()}\")\n",
     "        if arch.sha256 is not None:\n",
     "            print(f\"SHA-256: {arch.sha256}\")\n",
     "    elif isinstance(arch, ArchitectureFromLibraryDescr):\n",
@@ -610,9 +616,10 @@
    "outputs": [],
    "source": [
     "for cover in my_model_descr.covers:\n",
-    "    plt.imshow(imread(cover))\n",
-    "    plt.xticks([])\n",
-    "    plt.yticks([])\n",
+    "    img: NDArray[Any] = imread(download(cover).path)\n",
+    "    _ = plt.imshow(img)\n",
+    "    plt.xticks([])  # type: ignore\n",
+    "    plt.yticks([])  # type: ignore\n",
     "    plt.show()"
    ]
   },