def test_dataset_rdf_round_trip():
from bioimageio.spec import load_raw_resource_description, serialize_raw_resource_description_to_dict
data = dict(
id="platynereis_em_training_data",
authors=[{
"name": "Constantin Pape"
}],
cite=[{
"doi": "https://doi.org/10.1016/j.cell.2021.07.017",
"text": "Vergara, Pape, Meechan et al."
}],
covers=[
"https://raw.githubusercontent.com/ilastik/bioimage-io-models/main/dataset_src/platy-cover0.png"
],
description=
"Training data for EM segmentation of cellular membranes, nuclei, cuticle and cilia in Platynereis.",
documentation=
"https://raw.githubusercontent.com/ilastik/bioimage-io-models/main/dataset_src/platy.md",
format_version="0.2.2",
license="CC-BY-4.0",
name="Platynereis EM Traning Data",
source="https://doi.org/10.5281/zenodo.3675220",
tags=[
"electron-microscopy", "platynereis", "cells", "cilia", "nuclei",
"instance-segmentation", "3D"
],
type="dataset",
)
raw = load_raw_resource_description(data)
serialized = serialize_raw_resource_description_to_dict(raw)
assert data == serialized
def test_spec_round_trip(unet2d_nuclei_broad_any_minor):
from bioimageio.spec import load_raw_resource_description, serialize_raw_resource_description_to_dict
data = unet2d_nuclei_broad_any_minor
# monkeypatch: yaml.load already converts timestamp to datetime.datetime, while we serialize it to ISO 8601
if "timestamp" in data:
data["timestamp"] = data["timestamp"].isoformat()
raw_model = load_raw_resource_description(unet2d_nuclei_broad_any_minor)
serialized = serialize_raw_resource_description_to_dict(raw_model)
assert isinstance(serialized, dict)
assert serialized == data
raw_model_from_serialized = load_raw_resource_description(serialized)
assert raw_model_from_serialized == raw_model
def test_update_format(unet2d_nuclei_broad_before_latest, tmp_path):
from bioimageio.spec.commands import update_format
path = tmp_path / "rdf_new.yaml"
update_format(unet2d_nuclei_broad_before_latest, path)
assert path.exists()
model = load_raw_resource_description(path)
assert model.format_version == format_version
def test_load_raw_model_unet2d_keras_tf(unet2d_keras_tf):
from bioimageio.spec import load_raw_resource_description
raw_model = load_raw_resource_description(unet2d_keras_tf,
update_to_format="latest")
assert isinstance(raw_model, raw_nodes.Model)
# test attachments
assert len(raw_model.attachments.files) == 1
assert (raw_model.root_path / raw_model.attachments.files[0]).exists()
def test_update_rdf_using_rd(unet2d_nuclei_broad_latest):
from bioimageio.spec.commands import update_rdf
source = load_raw_resource_description(unet2d_nuclei_broad_latest)
update = dict(name="updated",
outputs=[{
"name": "updated",
"halo": ["KEEP", "DROP", 0, 9, 9]
}])
actual = update_rdf(source, update)
assert isinstance(actual, raw_nodes.Model)
assert actual.name == "updated"
assert actual.outputs[0].name == "updated"
assert actual.outputs[0].halo == [0, 0, 9, 9]
def test_spec_round_trip_w_attachments(unet2d_nuclei_broad_latest):
from bioimageio.spec import load_raw_resource_description, serialize_raw_resource_description_to_dict
data = unet2d_nuclei_broad_latest
# monkeypatch: yaml.load already converts timestamp to datetime.datetime, while we serialize it to ISO 8601
if "timestamp" in data:
data["timestamp"] = data["timestamp"].isoformat()
data["attachments"] = {
"files": ["some_file.ext"],
"another_unknown_attachment": ["sub", "whatever", {
"weird": 10
}]
}
raw_model = load_raw_resource_description(data)
serialized = serialize_raw_resource_description_to_dict(raw_model)
assert isinstance(serialized, dict)
assert serialized == data
raw_model_from_serialized = load_raw_resource_description(serialized)
assert raw_model_from_serialized == raw_model
def test_load_raw_model_to_format(unet2d_nuclei_broad_before_latest):
from bioimageio.spec import load_raw_resource_description
format_targets = [(0, 3), (0, 4)]
format_version = tuple(
map(int, unet2d_nuclei_broad_before_latest["format_version"].split(".")
[:2]))
for target in format_targets:
if format_version <= target:
to_format = ".".join(map(str, target))
raw_model = load_raw_resource_description(
unet2d_nuclei_broad_before_latest, update_to_format=to_format)
assert raw_model.format_version[:raw_model.format_version.
rfind(".")] == to_format
def test_load_raw_model_stardist(stardist_model):
from bioimageio.spec import load_raw_resource_description
raw_model = load_raw_resource_description(stardist_model)
assert raw_model
def test_load_raw_model_hpa(hpa_model):
from bioimageio.spec import load_raw_resource_description
raw_model = load_raw_resource_description(hpa_model)
assert raw_model
def test_load_raw_model_multi_tensor(unet2d_multi_tensor):
from bioimageio.spec import load_raw_resource_description
raw_model = load_raw_resource_description(unet2d_multi_tensor)
assert raw_model
def test_load_raw_model(unet2d_nuclei_broad_any):
from bioimageio.spec import load_raw_resource_description
raw_model = load_raw_resource_description(unet2d_nuclei_broad_any)
assert raw_model
def test_load_raw_model_diff_output_shape(unet2d_diff_output_shape):
from bioimageio.spec import load_raw_resource_description
raw_model = load_raw_resource_description(unet2d_diff_output_shape)
assert raw_model
def test_loaded_remote_raw_model_is_valid(unet2d_nuclei_broad_url):
from bioimageio.spec import load_raw_resource_description
raw_model = load_raw_resource_description(unet2d_nuclei_broad_url)
raw_model = load_raw_resource_description(raw_model)
assert raw_model
