handle Optional[sitk.Image]

Author: dyollb

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -23,20 +23,20 @@ repos:
       - id: detect-private-key
 
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.3.0
     hooks:
       - id: black
         name: format code
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
         name: format imports
         args: ["--profile", "black"]
 
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.14
+    rev: 0.7.16
     hooks:
       - id: mdformat
         name: format markdown
@@ -46,28 +46,28 @@ repos:
         exclude: CHANGELOG.md
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 6.0.0
     hooks:
       - id: flake8
         name: check PEP8
         args: ["--ignore=E501,W503,E203"]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.34.0
+    rev: v3.7.0
     hooks:
       - id: pyupgrade
         name: upgrade code
         args: ["--py37-plus"]
 
   - repo: https://github.com/hadialqattan/pycln
-    rev: v1.2.5
+    rev: v2.1.5
     hooks:
       - id: pycln
         name: prune imports
         args: [--expand-stars]
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.3.1
+    rev: 1.7.0
     hooks:
       - id: nbqa-black
         additional_dependencies: [black]

examples/pre_processing.py

@@ -1,4 +1,4 @@
-from typing import Optional
+from typing import Optional, Union
 
 import SimpleITK as sitk
 import typer
@@ -9,7 +9,16 @@
 
 
 @register_command(app)
-def median_filter(input: sitk.Image, radius: int) -> sitk.Image:
+def add(input1: sitk.Image, input2: Union[sitk.Image, None] = None) -> sitk.Image:
+    """Perform foo filtering"""
+    if input2:
+        sum: sitk.Image = input1 + input2
+        return sum
+    return input1
+
+
+@register_command(app)
+def median_filter(input: sitk.Image, radius: int = 2) -> sitk.Image:
     """Perform median filtering"""
     image: sitk.Image = sitk.Median(input, [radius] * input.GetDimension())
     return image

setup.cfg

@@ -1,6 +1,7 @@
 [metadata]
 name = sitk-cli
-version = 0.4.0
+version = 0.5.0
+requires-python = ">=3.8"
 url = https://github.com/dyollb/sitk-cli
 description = Wrap SimpleITK functions as command lines
 long_description = file: README.md

src/sitk_cli/lib.py

@@ -1,6 +1,6 @@
 from inspect import Parameter, isclass, signature
 from pathlib import Path
-from typing import Optional
+from typing import Optional, Union, get_args, get_origin
 
 import SimpleITK as sitk
 import typer
@@ -14,10 +14,15 @@ def make_cli(func, output_arg_name="output"):
 
     def _translate_param(p: Parameter):
         annotation, default = p.annotation, p.default
-        if isclass(p.annotation) and issubclass(
-            p.annotation, (sitk.Image, sitk.Transform)
-        ):
-            if issubclass(p.annotation, sitk.Image):
+
+        # handle Optional[A] and Union[A, None]
+        origin = get_origin(annotation)
+        args = get_args(annotation)
+        if origin is Union and args and not isinstance(args[0], type(None)):
+            annotation = get_args(annotation)[0]
+
+        if isclass(annotation) and issubclass(annotation, (sitk.Image, sitk.Transform)):
+            if issubclass(annotation, sitk.Image):
                 image_args.append(p.name)
             else:
                 transform_args.append(p.name)