Recipe runner CLI entry point

starfish/__init__.py

@@ -20,6 +20,7 @@
 from .experiment.experiment import Experiment, FieldOfView
 from .imagestack.imagestack import ImageStack
 from .intensity_table.intensity_table import IntensityTable
+from .recipe import cli
 from .starfish import starfish
 
 

starfish/recipe/cli.py

@@ -0,0 +1,28 @@
+from slicedimage.io import resolve_path_or_url
+
+from starfish.config import StarfishConfig
+from starfish.starfish import starfish
+from starfish.util import click
+from .recipe import Recipe
+
+
+@starfish.command("recipe")
+@click.option("--recipe", required=True, type=str, metavar="RECIPE_PATH_OR_URL")
+@click.option(
+    "--input", type=str, multiple=True, metavar="INPUT_FILE_PATH_OR_URL",
+    help="input file paths or urls to map to the recipe input parameters")
+@click.option(
+    "--output", type=str, multiple=True, metavar="OUTPUT_FILE_PATH",
+    help="output file paths to write recipe outputs to")
+@click.pass_context
+def run_recipe(ctx, recipe, input, output):
+    """Runs a recipe with a given set of inputs and outputs."""
+    config = StarfishConfig()
+
+    backend, relativeurl, _ = resolve_path_or_url(
+        recipe, backend_config=config.slicedimage)
+    with backend.read_contextmanager(relativeurl) as fh:
+        recipe_str = fh.read()
+
+    recipe_obj = Recipe(recipe_str, input, output)
+    recipe_obj.run_and_save()

starfish/test/full_pipelines/recipe/_base_recipe_test.py

@@ -0,0 +1,45 @@
+import os
+import shutil
+from pathlib import Path
+from typing import Iterable, Optional
+
+from starfish.util import exec
+
+
+class RecipeTest:
+    """This is a base class for testing recipes.  Each recipe test should define its recipe file,
+    the input files, the output files, and a test method that verifies the correctness of the
+    results.
+    """
+    @property
+    def recipe(self) -> Path:
+        raise NotImplementedError()
+
+    @property
+    def input_url_or_paths(self) -> Iterable[str]:
+        raise NotImplementedError()
+
+    @property
+    def output_paths(self) -> Iterable[Path]:
+        raise NotImplementedError()
+
+    def verify_results(self, tempdir: Path):
+        raise NotImplementedError()
+
+    def test_run_recipe(self):
+        cmdline = ["starfish", "recipe", "--recipe", self.recipe]
+        for input_url_or_path in self.input_url_or_paths:
+            cmdline.extend(["--input", input_url_or_path])
+        for output_path in self.output_paths:
+            cmdline.extend([
+                "--output",
+                lambda tempdir, *args, **kwargs: os.path.join(tempdir, os.fspath(output_path))])
+
+        tempdir: Optional[str] = None
+        try:
+            tempdir = exec.stages([cmdline], keep_data=True)
+
+            self.verify_results(Path(tempdir))
+        finally:
+            if tempdir is not None and os.getenv("TEST_KEEP_DATA") is None:
+                shutil.rmtree(tempdir)

starfish/test/full_pipelines/recipe/iss_recipe.txt

@@ -0,0 +1,55 @@
+primary_image = file_inputs[0]
+dots = file_inputs[1]
+nuclei = file_inputs[2]
+codebook = file_inputs[3]
+
+max_proj = compute(
+    Filter.MaxProject,
+    primary_image,
+    dims=['c', 'z'])
+
+transformation_list = compute(
+    LearnTransform.Translation,
+    max_proj,
+    reference_stack=dots, upsampling=1000, axes=Axes.ROUND)
+
+transformed = compute(
+    ApplyTransform.Warp,
+    primary_image,
+    transformation_list)
+
+filtered_primary = compute(
+    Filter.WhiteTophat,
+    transformed,
+    masking_radius=15)
+
+filtered_nuclei = compute(
+    Filter.WhiteTophat,
+    nuclei,
+    masking_radius=15)
+
+filtered_dots = compute(
+    Filter.WhiteTophat,
+    dots,
+    masking_radius=15)
+
+spots = compute(
+    DetectSpots.BlobDetector,
+    filtered_primary, filtered_dots, {Axes.ROUND, Axes.CH},
+    min_sigma=4, max_sigma=6, num_sigma=20, threshold=0.01)
+
+segmentation = compute(
+    Segment.Watershed,
+    filtered_primary, filtered_nuclei,
+    nuclei_threshold=.16, input_threshold=.22, min_distance=57)
+
+target_assignment = compute(
+    AssignTargets.Label,
+    segmentation, spots)
+
+decoded = compute(
+    Decode.PerRoundMaxChannel,
+    target_assignment,
+    codebook=codebook)
+
+file_outputs[0] = decoded

starfish/test/full_pipelines/recipe/test_iss.py

@@ -0,0 +1,53 @@
+"""
+Notes
+-----
+This test and docs/source/usage/iss/iss_cli.sh test the same code paths and should be updated
+together
+"""
+import os
+import unittest
+from pathlib import Path
+from typing import Iterable
+
+import numpy as np
+import pandas as pd
+import pytest
+
+from starfish.intensity_table.intensity_table import IntensityTable
+from starfish.types import Features
+from ._base_recipe_test import RecipeTest
+
+
+URL = "https://d2nhj9g34unfro.cloudfront.net/20181005/ISS-TEST/experiment.json"
+
+
+@pytest.mark.slow
+class TestWithIssData(RecipeTest, unittest.TestCase):
+    @property
+    def recipe(self) -> Path:
+        test_file_path = Path(__file__)
+        recipe = test_file_path.parent / "iss_recipe.txt"
+        return recipe
+
+    @property
+    def input_url_or_paths(self) -> Iterable[str]:
+        return [
+            f"@{URL}[fov_001][primary]",  # primary image
+            f"@{URL}[fov_001][dots]",     # dots image
+            f"@{URL}[fov_001][nuclei]",   # nuclei image
+            f"@{URL}",                    # codebook
+        ]
+
+    @property
+    def output_paths(self) -> Iterable[Path]:
+        return [
+            Path("decoded_spots.nc")
+        ]
+
+    def verify_results(self, tempdir: Path):
+        intensities = IntensityTable.open_netcdf(os.fspath(tempdir / "decoded_spots.nc"))
+        genes, counts = np.unique(
+            intensities.coords[Features.TARGET], return_counts=True)
+        gene_counts = pd.Series(counts, genes)
+        assert gene_counts['ACTB'] == 9
+        assert gene_counts['GAPDH'] == 9