Merge pull request #406 from bioimage-io/predict_cmd

add predict command

bioimageio/core/VERSION

@@ -1,3 +1,3 @@
 {
-    "version": "0.6.8"
+    "version": "0.6.9"
 }

bioimageio/core/__init__.py

@@ -4,17 +4,20 @@
 
 from bioimageio.spec import build_description as build_description
 from bioimageio.spec import dump_description as dump_description
+from bioimageio.spec import load_dataset_description as load_dataset_description
 from bioimageio.spec import load_description as load_description
 from bioimageio.spec import (
     load_description_and_validate_format_only as load_description_and_validate_format_only,
 )
+from bioimageio.spec import load_model_description as load_model_description
 from bioimageio.spec import save_bioimageio_package as save_bioimageio_package
 from bioimageio.spec import (
     save_bioimageio_package_as_folder as save_bioimageio_package_as_folder,
 )
 from bioimageio.spec import save_bioimageio_yaml_only as save_bioimageio_yaml_only
 from bioimageio.spec import validate_format as validate_format
 
+from . import digest_spec as digest_spec
 from ._prediction_pipeline import PredictionPipeline as PredictionPipeline
 from ._prediction_pipeline import (
     create_prediction_pipeline as create_prediction_pipeline,
@@ -38,4 +41,4 @@
 # aliases
 test_resource = test_description
 load_resource = load_description
-load_model = load_description
+load_model = load_model_description

bioimageio/core/__main__.py

@@ -1,4 +1,10 @@
-from bioimageio.core.commands import main
+from bioimageio.core.cli import Bioimageio
+
+
+def main():
+    cli = Bioimageio()  # pyright: ignore[reportCallIssue]
+    cli.run()
+
 
 if __name__ == "__main__":
     main()

bioimageio/core/_prediction_pipeline.py

@@ -55,8 +55,8 @@ def __init__(
         postprocessing: List[Processing],
         model_adapter: ModelAdapter,
         default_ns: Union[
-            v0_5.ParameterizedSize.N,
-            Mapping[Tuple[MemberId, AxisId], v0_5.ParameterizedSize.N],
+            v0_5.ParameterizedSize_N,
+            Mapping[Tuple[MemberId, AxisId], v0_5.ParameterizedSize_N],
         ] = 10,
         default_batch_size: int = 1,
     ) -> None:
@@ -179,40 +179,17 @@ def get_output_sample_id(self, input_sample_id: SampleId):
                 self.model_description.id or self.model_description.name
             )
 
-    def predict_sample_with_blocking(
+    def predict_sample_with_fixed_blocking(
         self,
         sample: Sample,
+        input_block_shape: Mapping[MemberId, Mapping[AxisId, int]],
+        *,
         skip_preprocessing: bool = False,
         skip_postprocessing: bool = False,
-        ns: Optional[
-            Union[
-                v0_5.ParameterizedSize.N,
-                Mapping[Tuple[MemberId, AxisId], v0_5.ParameterizedSize.N],
-            ]
-        ] = None,
-        batch_size: Optional[int] = None,
     ) -> Sample:
-        """predict a sample by splitting it into blocks according to the model and the `ns` parameter"""
         if not skip_preprocessing:
             self.apply_preprocessing(sample)
 
-        if isinstance(self.model_description, v0_4.ModelDescr):
-            raise NotImplementedError(
-                "predict with blocking not implemented for v0_4.ModelDescr {self.model_description.name}"
-            )
-
-        ns = ns or self._default_ns
-        if isinstance(ns, int):
-            ns = {
-                (ipt.id, a.id): ns
-                for ipt in self.model_description.inputs
-                for a in ipt.axes
-                if isinstance(a.size, v0_5.ParameterizedSize)
-            }
-        input_block_shape = self.model_description.get_tensor_sizes(
-            ns, batch_size or self._default_batch_size
-        ).inputs
-
         n_blocks, input_blocks = sample.split_into_blocks(
             input_block_shape,
             halo=self._default_input_halo,
@@ -239,6 +216,47 @@ def predict_sample_with_blocking(
 
         return predicted_sample
 
+    def predict_sample_with_blocking(
+        self,
+        sample: Sample,
+        skip_preprocessing: bool = False,
+        skip_postprocessing: bool = False,
+        ns: Optional[
+            Union[
+                v0_5.ParameterizedSize_N,
+                Mapping[Tuple[MemberId, AxisId], v0_5.ParameterizedSize_N],
+            ]
+        ] = None,
+        batch_size: Optional[int] = None,
+    ) -> Sample:
+        """predict a sample by splitting it into blocks according to the model and the `ns` parameter"""
+
+        if isinstance(self.model_description, v0_4.ModelDescr):
+            raise NotImplementedError(
+                "`predict_sample_with_blocking` not implemented for v0_4.ModelDescr"
+                + f" {self.model_description.name}."
+                + " Consider using `predict_sample_with_fixed_blocking`"
+            )
+
+        ns = ns or self._default_ns
+        if isinstance(ns, int):
+            ns = {
+                (ipt.id, a.id): ns
+                for ipt in self.model_description.inputs
+                for a in ipt.axes
+                if isinstance(a.size, v0_5.ParameterizedSize)
+            }
+        input_block_shape = self.model_description.get_tensor_sizes(
+            ns, batch_size or self._default_batch_size
+        ).inputs
+
+        return self.predict_sample_with_fixed_blocking(
+            sample,
+            input_block_shape=input_block_shape,
+            skip_preprocessing=skip_preprocessing,
+            skip_postprocessing=skip_postprocessing,
+        )
+
     # def predict(
     #     self,
     #     inputs: Predict_IO,
@@ -310,8 +328,8 @@ def create_prediction_pipeline(
     ),
     model_adapter: Optional[ModelAdapter] = None,
     ns: Union[
-        v0_5.ParameterizedSize.N,
-        Mapping[Tuple[MemberId, AxisId], v0_5.ParameterizedSize.N],
+        v0_5.ParameterizedSize_N,
+        Mapping[Tuple[MemberId, AxisId], v0_5.ParameterizedSize_N],
     ] = 10,
     **deprecated_kwargs: Any,
 ) -> PredictionPipeline:

bioimageio/core/_resource_tests.py

@@ -1,7 +1,7 @@
 import traceback
 import warnings
 from itertools import product
-from typing import Dict, Hashable, List, Literal, Optional, Set, Tuple, Union
+from typing import Dict, Hashable, List, Literal, Optional, Sequence, Set, Tuple, Union
 
 import numpy as np
 from loguru import logger
@@ -57,7 +57,7 @@ def test_description(
     *,
     format_version: Union[Literal["discover", "latest"], str] = "discover",
     weight_format: Optional[WeightsFormat] = None,
-    devices: Optional[List[str]] = None,
+    devices: Optional[Sequence[str]] = None,
     absolute_tolerance: float = 1.5e-4,
     relative_tolerance: float = 1e-4,
     decimal: Optional[int] = None,
@@ -83,7 +83,7 @@ def load_description_and_test(
     *,
     format_version: Union[Literal["discover", "latest"], str] = "discover",
     weight_format: Optional[WeightsFormat] = None,
-    devices: Optional[List[str]] = None,
+    devices: Optional[Sequence[str]] = None,
     absolute_tolerance: float = 1.5e-4,
     relative_tolerance: float = 1e-4,
     decimal: Optional[int] = None,
@@ -138,12 +138,12 @@ def load_description_and_test(
 def _test_model_inference(
     model: Union[v0_4.ModelDescr, v0_5.ModelDescr],
     weight_format: WeightsFormat,
-    devices: Optional[List[str]],
+    devices: Optional[Sequence[str]],
     absolute_tolerance: float,
     relative_tolerance: float,
     decimal: Optional[int],
 ) -> None:
-    test_name = "Reproduce test outputs from test inputs"
+    test_name = f"Reproduce test outputs from test inputs ({weight_format})"
     logger.info("starting '{}'", test_name)
     error: Optional[str] = None
     tb: List[str] = []
@@ -209,15 +209,15 @@ def _test_model_inference(
 def _test_model_inference_parametrized(
     model: v0_5.ModelDescr,
     weight_format: WeightsFormat,
-    devices: Optional[List[str]],
+    devices: Optional[Sequence[str]],
 ) -> None:
     if not any(
         isinstance(a.size, v0_5.ParameterizedSize)
         for ipt in model.inputs
         for a in ipt.axes
     ):
         # no parameterized sizes => set n=0
-        ns: Set[v0_5.ParameterizedSize.N] = {0}
+        ns: Set[v0_5.ParameterizedSize_N] = {0}
     else:
         ns = {0, 1, 2}
 
@@ -236,7 +236,7 @@ def _test_model_inference_parametrized(
         # no batch axis
         batch_sizes = {1}
 
-    test_cases: Set[Tuple[v0_5.ParameterizedSize.N, BatchSize]] = {
+    test_cases: Set[Tuple[v0_5.ParameterizedSize_N, BatchSize]] = {
         (n, b) for n, b in product(sorted(ns), sorted(batch_sizes))
     }
     logger.info(

bioimageio/core/axis.py

@@ -26,19 +26,6 @@ def _get_axis_type(a: Literal["b", "t", "i", "c", "x", "y", "z"]):
 S = TypeVar("S", bound=str)
 
 
-def _get_axis_id(a: Union[Literal["b", "t", "i", "c"], S]):
-    if a == "b":
-        return AxisId("batch")
-    elif a == "t":
-        return AxisId("time")
-    elif a == "i":
-        return AxisId("index")
-    elif a == "c":
-        return AxisId("channel")
-    else:
-        return AxisId(a)
-
-
 AxisId = v0_5.AxisId
 
 T = TypeVar("T")
@@ -47,7 +34,7 @@ def _get_axis_id(a: Union[Literal["b", "t", "i", "c"], S]):
 BatchSize = int
 
 AxisLetter = Literal["b", "i", "t", "c", "z", "y", "x"]
-AxisLike = Union[AxisLetter, v0_5.AnyAxis, "Axis"]
+AxisLike = Union[AxisId, AxisLetter, v0_5.AnyAxis, "Axis"]
 
 
 @dataclass
@@ -62,7 +49,7 @@ def create(cls, axis: AxisLike) -> Axis:
         elif isinstance(axis, Axis):
             return Axis(id=axis.id, type=axis.type)
         elif isinstance(axis, str):
-            return Axis(id=_get_axis_id(axis), type=_get_axis_type(axis))
+            return Axis(id=AxisId(axis), type=_get_axis_type(axis))
         elif isinstance(axis, v0_5.AxisBase):
             return Axis(id=AxisId(axis.id), type=axis.type)
         else:
@@ -71,7 +58,7 @@ def create(cls, axis: AxisLike) -> Axis:
 
 @dataclass
 class AxisInfo(Axis):
-    maybe_singleton: bool
+    maybe_singleton: bool  # TODO: replace 'maybe_singleton' with size min/max for better axis guessing
 
     @classmethod
     def create(cls, axis: AxisLike, maybe_singleton: Optional[bool] = None) -> AxisInfo:
@@ -80,18 +67,16 @@ def create(cls, axis: AxisLike, maybe_singleton: Optional[bool] = None) -> AxisI
 
         axis_base = super().create(axis)
         if maybe_singleton is None:
-            if isinstance(axis, Axis):
-                maybe_singleton = False
-            elif isinstance(axis, str):
-                maybe_singleton = axis == "b"
+            if isinstance(axis, (Axis, str)):
+                maybe_singleton = True
             else:
                 if axis.size is None:
                     maybe_singleton = True
                 elif isinstance(axis.size, int):
                     maybe_singleton = axis.size == 1
                 elif isinstance(axis.size, v0_5.SizeReference):
                     maybe_singleton = (
-                        False  # TODO: check if singleton is ok for a `SizeReference`
+                        True  # TODO: check if singleton is ok for a `SizeReference`
                     )
                 elif isinstance(
                     axis.size, (v0_5.ParameterizedSize, v0_5.DataDependentSize)