debugging task converter

Author: tclose

conftest.py

@@ -1,15 +1,25 @@
 import os
 from pathlib import Path
+import traceback
+import tempfile
 import pytest
 from click.testing import CliRunner
 
 
-PKG_DIR = Path(__file__).parent
+@pytest.fixture(scope="session")
+def pkg_dir():
+    return Path(__file__).parent
 
 
 @pytest.fixture(scope="session")
-def pkg_dir():
-    return PKG_DIR
+def example_specs_dir(pkg_dir):
+    return pkg_dir / "example-specs"
+
+
+@pytest.fixture
+def work_dir():
+    work_dir = tempfile.mkdtemp()
+    return Path(work_dir)
 
 
 @pytest.fixture
@@ -42,3 +52,8 @@ def pytest_internalerror(excinfo):
 @pytest.fixture
 def catch_cli_exceptions():
     return CATCH_CLI_EXCEPTIONS
+
+
+def show_cli_trace(result):
+    "Used in testing to show traceback of CLI output"
+    return "".join(traceback.format_exception(*result.exc_info))

example-specs/ants_registration.yml

@@ -0,0 +1,16 @@
+task_name: Registration
+nipype_module: nipype.interfaces.ants.registration
+output_requirements:
+    output_warped_image: ["fixed_image", "moving_image", "output_transform_prefix"]
+output_templates:
+    output_warped_image: "{output_transform_prefix}warped"
+doctest:
+    fixed_image: test.nii.gz
+    moving_image: test.nii.gz
+    cmdline: >- 
+        antsRegistration --output [ output_, output_warped_image.nii.gz ]
+        --metric Mattes[ test.nii, test.nii, 1, 32, Random, 0.05 ]
+    tests_inputs: []
+    tests_outputs:
+    - AttributeError
+  

example-specs/ants_registration_param.yml

@@ -0,0 +1,14 @@
+module: nipype.interfaces.ants.segmentation
+tasks:
+    N4BiasFieldCorrection:
+        output_requirements:
+            output_image: []
+            bias_image: ["save_bias"]
+        output_templates:
+            output_image: ""
+        doctest:
+            input_image: test.nii.gz
+            cmdline:
+        tests_inputs: []
+        tests_outputs:
+        - AttributeError

example-specs/ants_segmentation.yml

@@ -0,0 +1,11 @@
+module: nipype.interfaces..freesurfer.preprocess
+tasks:
+    ApplyVolTransform:
+        output_requirements: []
+        output_templates:
+            transformed_file: "{source_file}_warped"
+        doctest:
+            source_file: test.nii.gz
+            cmdline: mri_vol2vol
+        tests_inputs: []
+        tests_outputs: []

example-specs/ants_segmentation_param.yml

@@ -1,37 +1,40 @@
-function: smriprep.workflows.base:init_single_subject_wf
-splits:
-    - func_name: registration
-      first_node: ds_surfs
-    - func_name: segmentation
-      first_node: lta2itk_fwd
-ignore_tasks:
-    - smriprep.interfaces.DerivativesDataSink
-    - nipype.interfaces.utility.base.IdentityInterface
-args:
-    debug: false
-    freesurfer: true
-    fast_track: false
-    hires: true
-    layout:
-        type: bids:BIDSLayout
-        args:
-            root: test-data/bids-data/ds000113
-    longitudinal: false
-    low_mem: false
-    name: single_subject_wf
-    omp_nthreads: 1
-    output_dir: .
-    skull_strip_fixed_seed: false
-    skull_strip_mode: force
-    skull_strip_template:
-        type: niworkflows.utils.spaces:Reference
-        args:
-            space: OASIS30ANTs
-    spaces:
-        type: niworkflows.utils.spaces:SpatialReferences
+module: smriprep.workflows.base
+workflows:
+    init_single_subject_wf:
         args:
+            debug: false
+            freesurfer: true
+            fast_track: false
+            hires: true
+            layout:
+                type: bids:BIDSLayout
+                args:
+                    root: test-data/bids-data/ds000113
+            longitudinal: false
+            low_mem: false
+            name: single_subject_wf
+            omp_nthreads: 1
+            output_dir: .
+            skull_strip_fixed_seed: false
+            skull_strip_mode: force
+            skull_strip_template:
+                type: niworkflows.utils.spaces:Reference
+                args:
+                    space: OASIS30ANTs
             spaces:
-              - MNI152NLin2009cAsym
-              - fsaverage5
-    subject_id: test
-    bids_filters: null
+                type: niworkflows.utils.spaces:SpatialReferences
+                args:
+                    spaces:
+                    - MNI152NLin2009cAsym
+                    - fsaverage5
+            subject_id: test
+            bids_filters: null
+    splits:
+        - func_name: registration
+            first_node: ds_surfs
+        - func_name: segmentation
+            first_node: lta2itk_fwd
+    ignore_tasks:
+        - smriprep.interfaces.DerivativesDataSink
+        - nipype.interfaces.utility.base.IdentityInterface
+

example-specs/freesurfer_preprocess.yml

@@ -1,3 +1,4 @@
+from pathlib import Path
 import click
 import yaml
 from nipype2pydra import __version__
@@ -15,50 +16,36 @@ def cli():
 @cli.command(
     help="""Port Nipype task interface code to Pydra
 
-SPEC_FILE is a YAML file which defines the manually specified aspects of the conversion
-see https://github.com/nipype/nipype2pydra/tree/main/example-specs for examples
+YAML_SPEC is a YAML file which defines interfaces to be imported along with an
+manually specified aspects of the conversion see
+https://github.com/nipype/nipype2pydra/tree/main/example-specs for examples
 
-OUT_FILE is where the converted code will be generated
+OUTPUT_BASE_DIR is the path of generated module file
 """
 )
-@click.argument("spec-file", type=click.File())
-@click.argument("out-file", type=click.File(mode="w"))
+@click.argument("yaml-spec", type=click.File())
+@click.argument("output-file", type=Path)
 @click.option(
     "-c",
     "--callables",
     type=click.File(),
     default=None,
     help="a Python file containing callable functions required in the command interface",
 )
-@click.option(
-    "-i",
-    "--interface_name",
-    multiple=True,
-    default=[],
-    help=(
-        "name of the interfaces (name used in Nipype, e.g. BET) to be converted. If not"
-        "provided all interfaces defined in the spec are converted"
-    ),
-)
-def task(spec_file, out_file, interface_name, callables):
-
-    spec = yaml.safe_load(spec_file)
+def task(yaml_spec, output_file, callables):
 
-    if interface_name:
-        spec = {n: v for n, v in spec.items() if n in interface_name}
+    spec = yaml.safe_load(yaml_spec)
 
-    converter = TaskConverter(spec, callables)
-    code = converter.generate()
-    out_file.write(code)
+    converter = TaskConverter(callables_module=callables, **spec)
+    converter.generate(output_file)
 
 
 @cli.command(help="Port Nipype workflow creation functions to Pydra")
-@click.argument("spec-file", type=click.File())
-@click.argument("out-file", type=click.File(mode="w"))
-def workflow(spec_file, out_file):
+@click.argument("yaml-spec", type=click.File())
+@click.argument("output-module-file", type=click.File(mode="w"))
+def workflow(yaml_spec, output_module_file):
 
-    spec = yaml.safe_load(spec_file)
+    spec = yaml.safe_load(yaml_spec)
 
     converter = WorkflowConverter(spec)
-    code = converter.generate()
-    out_file.write(code)
+    converter.generate(output_module_file)