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update load_model_and_create_your_own
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‎example/load_model_and_create_your_own.ipynb‎

Lines changed: 71 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -79,7 +79,7 @@
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"from loguru import logger\n",
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"from numpy.typing import NDArray\n",
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"\n",
82-
"from bioimageio.spec.utils import download\n",
82+
"from bioimageio.spec.utils import get_reader\n",
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"\n",
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"# redirect stderr to stdout for better output comparison across runs with 'pytest --nbval'\n",
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"sys.stderr = sys.stdout\n",
@@ -388,13 +388,13 @@
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],
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"source": [
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"for i, cover in enumerate(model.covers):\n",
391-
" downloaded_cover = download(cover)\n",
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" cover_data: NDArray[Any] = imread(downloaded_cover.read()) # type: ignore\n",
391+
" cover_reader = get_reader(cover)\n",
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" cover_data: NDArray[Any] = imread(cover_reader.read())\n",
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" _ = plt.figure(figsize=(10, 10))\n",
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" plt.imshow(cover_data) # type: ignore\n",
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" plt.xticks([]) # type: ignore\n",
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" plt.yticks([]) # type: ignore\n",
397-
" plt.title(f\"cover image {downloaded_cover.original_file_name}\") # type: ignore\n",
397+
" plt.title(f\"cover image {cover_reader.original_file_name}\") # type: ignore\n",
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" plt.show()"
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]
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},
@@ -713,6 +713,55 @@
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" assert_never(arch)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"### Invalid Resource Descriptions\n",
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"\n",
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"To inspect invalid (or other non-model) resource description, use `load_description`, which always returns a description object (unlike `load_model_description`, which will throw an exception if the loaded resource is not a valid model).\n",
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"\n",
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"`load_description` may return:\n",
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"- A valid description of a known resource type (`ModelDescr`, `DatasetDescr`, `NotebeookDescr`, or `ApplicationDescr`).\n",
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"- A valid description of a generic resource: `GenericDescr` with a `type` other than `'model'`, `'dataset'`, `'notebook'`, or `'application'`.\n",
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"- An invalid description if there were any validation errors (`InvalidDescr`).\\\n",
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" This can also occur with valid models when using an older version of the bioimageio.spec library. \\\n",
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" In these cases the validation summary includes a warning like `\"future format_version '0.5.3' treated as '0.4.10'\"`, see example below"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Description class name: InvalidDescr\n",
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"Type and format version attributes are always accessible (may return 'unknown'): model 0.4.10\n",
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"Validation status: failed\n",
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"Validation errors: ['Input should be a valid dictionary or instance of AttachmentsDescr', '...']\n",
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"Validation warnings: [\"future format_version '0.5.3' treated as '0.4.10'\"]\n"
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]
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}
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],
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"source": [
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"from bioimageio.spec import load_description\n",
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"\n",
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"# load the model with an older format version to force an error\n",
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"# (backward conversion is not supported)\n",
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"descr = load_description(model_source, format_version=\"0.4\")\n",
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"\n",
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"# Print a few attributes instead of rendering the full validation summary with lots of errors...\n",
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"# descr.validation_summary.display()\n",
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"print(f\"Description class name: {descr.__class__.__name__}\")\n",
759+
"print(f\"Type and format version attributes are always accessible (may return 'unknown'): {descr.type} {descr.format_version}\")\n",
760+
"print(f\"Validation status: {descr.validation_summary.status}\")\n",
761+
"print(f\"Validation errors: {[descr.validation_summary.errors[0].msg, '...']}\")\n",
762+
"print(f\"Validation warnings: {[w.msg for w in descr.validation_summary.warnings]}\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
@@ -727,7 +776,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"execution_count": 12,
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-09-25T15:14:17.617583Z",
@@ -759,7 +808,7 @@
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"traceback": [
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"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[1;31mValidationError\u001b[0m Traceback (most recent call last)",
762-
"Cell \u001b[1;32mIn[11], line 3\u001b[0m\n\u001b[0;32m 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01mbioimageio\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmodel\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mv0_5\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m ModelDescr\n\u001b[1;32m----> 3\u001b[0m _ \u001b[38;5;241m=\u001b[39m \u001b[43mModelDescr\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;66;03m# pyright: ignore[reportCallIssue]\u001b[39;00m\n",
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"Cell \u001b[1;32mIn[12], line 3\u001b[0m\n\u001b[0;32m 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01mbioimageio\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmodel\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mv0_5\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m ModelDescr\n\u001b[1;32m----> 3\u001b[0m _ \u001b[38;5;241m=\u001b[39m \u001b[43mModelDescr\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;66;03m# pyright: ignore[reportCallIssue]\u001b[39;00m\n",
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"\u001b[1;31mValidationError\u001b[0m: 4 validation errors for ModelDescr:\nname\n Field required [input={'format_version': '0.5.5', 'type': 'model'}]\ninputs\n Field required [input={'format_version': '0.5.5', 'type': 'model'}]\noutputs\n Field required [input={'format_version': '0.5.5', 'type': 'model'}]\nweights\n Field required [input={'format_version': '0.5.5', 'type': 'model'}]"
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]
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}
@@ -788,7 +837,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"execution_count": 13,
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-09-25T15:14:17.688095Z",
@@ -816,7 +865,7 @@
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"traceback": [
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"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[1;31mValidationError\u001b[0m Traceback (most recent call last)",
819-
"Cell \u001b[1;32mIn[12], line 3\u001b[0m\n\u001b[0;32m 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01mbioimageio\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmodel\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mv0_5\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m InputTensorDescr\n\u001b[1;32m----> 3\u001b[0m _ \u001b[38;5;241m=\u001b[39m \u001b[43mInputTensorDescr\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;66;03m# pyright: ignore[reportCallIssue]\u001b[39;00m\n",
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"Cell \u001b[1;32mIn[13], line 3\u001b[0m\n\u001b[0;32m 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01mbioimageio\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmodel\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mv0_5\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m InputTensorDescr\n\u001b[1;32m----> 3\u001b[0m _ \u001b[38;5;241m=\u001b[39m \u001b[43mInputTensorDescr\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;66;03m# pyright: ignore[reportCallIssue]\u001b[39;00m\n",
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"\u001b[1;31mValidationError\u001b[0m: 1 validation errors for InputTensorDescr:\naxes\n Field required [input={}]"
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]
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}
@@ -829,7 +878,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 13,
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"execution_count": 14,
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-09-25T15:14:17.770073Z",
@@ -883,7 +932,7 @@
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{
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"cell_type": "code",
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"execution_count": 15,
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-09-25T15:14:19.851930Z",
@@ -911,7 +960,7 @@
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"traceback": [
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"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[1;31mValidationError\u001b[0m Traceback (most recent call last)",
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"Cell \u001b[1;32mIn[14], line 3\u001b[0m\n\u001b[0;32m 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01mbioimageio\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmodel\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mv0_5\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m OutputTensorDescr\n\u001b[1;32m----> 3\u001b[0m _ \u001b[38;5;241m=\u001b[39m \u001b[43mOutputTensorDescr\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;66;03m# pyright: ignore[reportCallIssue]\u001b[39;00m\n",
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"Cell \u001b[1;32mIn[15], line 3\u001b[0m\n\u001b[0;32m 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01mbioimageio\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmodel\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mv0_5\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m OutputTensorDescr\n\u001b[1;32m----> 3\u001b[0m _ \u001b[38;5;241m=\u001b[39m \u001b[43mOutputTensorDescr\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;66;03m# pyright: ignore[reportCallIssue]\u001b[39;00m\n",
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"\u001b[1;31mValidationError\u001b[0m: 1 validation errors for OutputTensorDescr:\naxes\n Field required [input={}]"
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]
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}
@@ -924,7 +973,7 @@
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},
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{
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"cell_type": "code",
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"metadata": {
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"execution": {
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-09-25T15:14:22.239956Z",
@@ -1005,7 +1054,7 @@
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"traceback": [
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"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[1;31mValidationError\u001b[0m Traceback (most recent call last)",
1008-
"Cell \u001b[1;32mIn[16], line 3\u001b[0m\n\u001b[0;32m 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01mbioimageio\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmodel\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mv0_5\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m PytorchStateDictWeightsDescr\n\u001b[1;32m----> 3\u001b[0m _ \u001b[38;5;241m=\u001b[39m \u001b[43mPytorchStateDictWeightsDescr\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;66;03m# pyright: ignore[reportCallIssue]\u001b[39;00m\n",
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"Cell \u001b[1;32mIn[17], line 3\u001b[0m\n\u001b[0;32m 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01mbioimageio\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmodel\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mv0_5\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m PytorchStateDictWeightsDescr\n\u001b[1;32m----> 3\u001b[0m _ \u001b[38;5;241m=\u001b[39m \u001b[43mPytorchStateDictWeightsDescr\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;66;03m# pyright: ignore[reportCallIssue]\u001b[39;00m\n",
10091058
"\u001b[1;31mValidationError\u001b[0m: 3 validation errors for PytorchStateDictWeightsDescr:\nsource\n Field required [input={}]\narchitecture\n Field required [input={}]\npytorch_version\n Field required [input={}]"
10101059
]
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}
@@ -1032,7 +1081,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 18,
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-09-25T15:14:22.306568Z",
@@ -1077,7 +1126,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 19,
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-09-25T15:14:27.148305Z",
@@ -1107,7 +1156,7 @@
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},
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{
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"cell_type": "code",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-09-25T15:14:28.098738Z",
@@ -1137,7 +1186,7 @@
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-09-25T15:14:28.858588Z",
@@ -1182,7 +1231,7 @@
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-09-25T15:14:29.687571Z",
@@ -1261,7 +1310,7 @@
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{
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-09-25T15:14:32.351633Z",
@@ -1329,7 +1378,7 @@
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},
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{
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"cell_type": "code",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-09-25T15:14:32.521339Z",
@@ -1564,7 +1613,7 @@
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},
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{
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"execution_count": 25,
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"metadata": {
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"execution": {
15701619
"iopub.execute_input": "2025-09-25T15:15:03.940263Z",

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