Skip to content

fix: pattern resolver update #116

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 14 commits into from
Jan 30, 2025
Merged

fix: pattern resolver update #116

Show file tree
Hide file tree
Changes from 13 commits
Commits
Show all changes
14 commits
Select commit Hold shift + click to select a range
53a2c3f
fix: updated PatternParser instantiation to match updated inputs from…
strixy16 Jan 30, 2025
78b071d
build: updated pixi dependencies
strixy16 Jan 30, 2025
e8749a4
build: updated pixi lock file
strixy16 Jan 30, 2025
5ba51ff
Merge remote-tracking branch 'origin/main' into katys/fix/pattern_res…
strixy16 Jan 30, 2025
fc258ab
build: latest pixi lock from main
strixy16 Jan 30, 2025
261ce2d
test: use dictionary input for roiNames
strixy16 Jan 30, 2025
70e5098
test: updated roiNames in lung4D RT fixture
strixy16 Jan 30, 2025
abaac85
tests: updated RTSTRUCT fixture
strixy16 Jan 30, 2025
53d9ac4
refactor: rename select to subset.py in process for ruff check
strixy16 Jan 30, 2025
02e1c74
fix: correct error message in for rtstruct loading
strixy16 Jan 30, 2025
d578309
style: sort imports for ruff
strixy16 Jan 30, 2025
dd188a9
build: update for med-imagetools
strixy16 Jan 30, 2025
6377f26
test: set up different roiNames input types for rtstruct loading
strixy16 Jan 30, 2025
e5517ce
fix: PatternParser moved in med-imagetools
strixy16 Jan 30, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4,122 changes: 2,221 additions & 1,901 deletions pixi.lock
View file
Open in desktop

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion src/readii/io/utils/pattern_resolver.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down
10 changes: 5 additions & 5 deletions src/readii/process/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down
0 src/readii/process/select.py → src/readii/process/subset.py
View file
Open in desktop
File renamed without changes.
4 changes: 2 additions & 2 deletions tests/test_feature_extraction.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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():
Expand Down
4 changes: 2 additions & 2 deletions tests/test_image_processing.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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):
Expand Down
19 changes: 14 additions & 5 deletions tests/test_loaders.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down
Loading