fix: pattern resolver update (#116)

`PatternResolver` in `med-imagetools` updated the input argument from
`pattern_parser` to `pattern_matcher`, updated this to match here.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **Chores**
- Updated parameter naming in the `PatternResolver` class for improved
clarity and consistency.
- Modified the `roiNames` parameter format in segmentation loading tests
for better structure and clarity.
- Adjusted expected output labels in segmentation tests to reflect new
naming conventions.
- Reorganized import statements to source functions from a new module,
maintaining accessibility.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

src/readii/io/utils/pattern_resolver.py

@@ -3,7 +3,7 @@
 from typing import Any, ClassVar, Dict, Tuple
 
 from imgtools.dicom.sort.exceptions import InvalidPatternError  # type: ignore
-from imgtools.dicom.sort.parser import PatternParser  # type: ignore
+from imgtools.pattern_parser.parser import PatternParser  # type: ignore
 
 from readii.utils import logger
 
@@ -58,7 +58,7 @@ def __init__(self, filename_format: str) -> None:
 
 		try:
 			self.pattern_parser = PatternParser(
-				self.filename_format, pattern_parser=self.DEFAULT_PATTERN
+				self.filename_format, pattern_matcher=self.DEFAULT_PATTERN
 			)
 			self.formatted_pattern, self.keys = self.parse()  # Validate the pattern by parsing it
 		except InvalidPatternError as e:

src/readii/process/__init__.py

@@ -9,15 +9,15 @@
     survivalStatusToNumericMapping,
     timeOutcomeColumnSetup,
 )
-from .select import (
-    dropUpToFeature,
-    getOnlyPyradiomicsFeatures,
-    selectByColumnValue,
-)
 from .split import (
     replaceColumnValues,
     splitDataByColumnValue,
 )
+from .subset import (
+    dropUpToFeature,
+    getOnlyPyradiomicsFeatures,
+    selectByColumnValue,
+)
 
 __all__ = [
     "addOutcomeLabels",

tests/test_feature_extraction.py

@@ -37,8 +37,8 @@ def lung4DRTSTRUCTImage():
     lung4DRTSTRUCTPath = "tests/4D-Lung/113_HM10395/11-26-1999-NA-p4-13296/1.000000-P4P113S303I10349 Gated 40.0B-47.35/1-1.dcm"
     lung4DCTPath = "tests/4D-Lung/113_HM10395/11-26-1999-NA-p4-13296/1.000000-P4P113S303I10349 Gated 40.0B-29543"
     segDictionary = loadSegmentation(lung4DRTSTRUCTPath, modality = 'RTSTRUCT',
-                                     baseImageDirPath = lung4DCTPath, roiNames = 'Tumor_c.*')
-    return segDictionary['Tumor_c40']
+                                     baseImageDirPath = lung4DCTPath, roiNames = {'GTV':'Tumor_c.*'})
+    return segDictionary['GTV']
 
 @pytest.fixture
 def pyradiomicsParamFilePath():

tests/test_image_processing.py

@@ -18,8 +18,8 @@ def lung4DRTSTRUCTImage():
     lung4DRTSTRUCTPath = "tests/4D-Lung/113_HM10395/11-26-1999-NA-p4-13296/1.000000-P4P113S303I10349 Gated 40.0B-47.35/1-1.dcm"
     lung4DCTPath = "tests/4D-Lung/113_HM10395/11-26-1999-NA-p4-13296/1.000000-P4P113S303I10349 Gated 40.0B-29543"
     segDictionary = loadSegmentation(lung4DRTSTRUCTPath, modality = 'RTSTRUCT',
-                                     baseImageDirPath = lung4DCTPath, roiNames = 'Tumor_c.*')
-    return segDictionary['Tumor_c40']
+                                     baseImageDirPath = lung4DCTPath, roiNames = {'GTV':'Tumor_c.*'})
+    return segDictionary['GTV']
 
 
 def test_flattenImage(nsclcSEGImage):

tests/test_loaders.py

@@ -53,19 +53,28 @@ def test_loadSegmentationSEG(nsclcSEGPath):
         "Wrong origin"
 
 
-def test_loadSegmentationRTSTRUCT(lung4DRTSTRUCTPath, lung4DCTPath):
+
+@pytest.mark.parametrize(
+    "roiNames, expected",
+    [
+        ({"GTV":'Tumor_c.*'}, "GTV"),
+        ('Tumor_c.*', "Tumor_c40"),
+        (["Tumor_c40"], "Tumor_c40"),
+    ]
+)
+def test_loadSegmentationRTSTRUCT(lung4DRTSTRUCTPath, lung4DCTPath, roiNames, expected):
     """Test loading a RTSTRUCT file"""
     actual = loadSegmentation(segImagePath = lung4DRTSTRUCTPath,
                               modality = 'RTSTRUCT',
                               baseImageDirPath = lung4DCTPath,
-                              roiNames = 'Tumor_c.*')
+                              roiNames = roiNames)
 
     assert isinstance(actual, dict), \
         "Wrong object type, should be dictionary"
-    assert list(actual.keys()) == ['Tumor_c40'], \
-        "Segmentation label is wrong, should be Heart"
+    assert list(actual.keys()) == [expected], \
+        f"Segmentation label is wrong, should be GTV, getting {list(actual.keys())}"
 
-    actualImage = actual['Tumor_c40']
+    actualImage = actual[expected]
 
     assert isinstance(actualImage, sitk.Image), \
         "Wrong object type"