Fix features selection (#16)

* Fixed features_selection * Remove unsupported * Bump version
TechnionComputationalMRILab · Mar 25, 2024 · d683953 · d683953 · github-actions · Mar 25, 2024
1 parent 928c21c
commit d683953
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Showing 12 changed files with 12 additions and 14 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pd-dwi"
-version = "1.0.4"
+version = "1.0.5"
 description = "Physiologically-Decomposed Diffusion-Weighted MRI machine-learning model for predicting response to neoadjuvant chemotherapy in invasive breast cancer"
 authors = [
     "Maya Gilad <[email protected]>"
@@ -14,8 +14,6 @@ classifiers = [
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
     "Development Status :: 3 - Alpha"
 ]
 readme = "README.md"

diff --git a/src/pd_dwi/config/config.py b/src/pd_dwi/config/config.py
@@ -63,7 +63,7 @@ class Classifier(BaseModel):
 
 class Pipeline(BaseModel):
     features_transformer: FeatureTransformer
-    feature_selection: FeatureSelection
+    features_selection: FeatureSelection
     classifier: Classifier
 
 

diff --git a/src/pd_dwi/config/samples/F.yaml b/src/pd_dwi/config/samples/F.yaml
@@ -29,7 +29,7 @@ pipeline:
           Original: { }
         setting:
           resampledPixelSpacing: [ 1.27,1.27,4.0 ]
-  feature_selection:
+  features_selection:
     k: 100
   classifier:
     module: xgboost.XGBClassifier

diff --git a/src/pd_dwi/config/samples/adc0100.yaml b/src/pd_dwi/config/samples/adc0100.yaml
@@ -29,7 +29,7 @@ pipeline:
           Original: {}
         setting:
           resampledPixelSpacing:  [1.27,1.27,4.0]
-  feature_selection:
+  features_selection:
     k: 100
   classifier:
     module: xgboost.XGBClassifier

diff --git a/src/pd_dwi/config/samples/adc0100600800.yaml b/src/pd_dwi/config/samples/adc0100600800.yaml
@@ -29,7 +29,7 @@ pipeline:
           Original: {}
         setting:
           resampledPixelSpacing:  [1.27,1.27,4.0]
-  feature_selection:
+  features_selection:
     k: 100
   classifier:
     module: xgboost.XGBClassifier

diff --git a/src/pd_dwi/config/samples/adc0100_F.yaml b/src/pd_dwi/config/samples/adc0100_F.yaml
@@ -36,7 +36,7 @@ pipeline:
           Original: { }
         setting:
           resampledPixelSpacing: [ 1.27,1.27,4.0 ]
-  feature_selection:
+  features_selection:
     k: 100
   classifier:
     module: xgboost.XGBClassifier

diff --git a/src/pd_dwi/config/samples/adc100600800.yaml b/src/pd_dwi/config/samples/adc100600800.yaml
@@ -29,7 +29,7 @@ pipeline:
           Original: {}
         setting:
           resampledPixelSpacing:  [1.27,1.27,4.0]
-  feature_selection:
+  features_selection:
     k: 100
   classifier:
     module: xgboost.XGBClassifier

diff --git a/src/pd_dwi/training_utils.py b/src/pd_dwi/training_utils.py
@@ -55,7 +55,7 @@ def create_pipeline_from_config(cfg: ModelConfig) -> Pipeline:
         remainder='drop'
     )
 
-    cfg_feature_selection = cfg.pipeline.feature_selection
+    cfg_feature_selection = cfg.pipeline.features_selection
     if cfg_feature_selection is None:
         features_selection = SelectKBest(f_classif)
     else:

diff --git a/tests/data/invalid_encoders_bad_modality.yaml b/tests/data/invalid_encoders_bad_modality.yaml
@@ -35,7 +35,7 @@ pipeline:
           Original: { }
         setting:
           resampledPixelSpacing: [ 1.27,1.27,4.0 ]
-  feature_selection:
+  features_selection:
     k: 100
   classifier:
     module: xgboost.XGBClassifier

diff --git a/tests/data/invalid_encoders_bad_time_points.yaml b/tests/data/invalid_encoders_bad_time_points.yaml
@@ -34,7 +34,7 @@ pipeline:
           Original: { }
         setting:
           resampledPixelSpacing: [ 1.27,1.27,4.0 ]
-  feature_selection:
+  features_selection:
     k: 100
   classifier:
     module: xgboost.XGBClassifier

diff --git a/tests/data/invalid_no_modalities.yaml b/tests/data/invalid_no_modalities.yaml
@@ -32,7 +32,7 @@ pipeline:
           Original: { }
         setting:
           resampledPixelSpacing: [ 1.27,1.27,4.0 ]
-  feature_selection:
+  features_selection:
     k: 100
   classifier:
     module: xgboost.XGBClassifier

diff --git a/tests/data/valid.yaml b/tests/data/valid.yaml
@@ -36,7 +36,7 @@ pipeline:
           Original: { }
         setting:
           resampledPixelSpacing: [ 1.27,1.27,4.0 ]
-  feature_selection:
+  features_selection:
     k: 100
   classifier:
     module: xgboost.XGBClassifier
File	Stmts	Miss	Cover	Missing
pd_dwi
__init__.py	2	0	100%
dataset.py	46	32	30%	12, 15–18, 20–22, 24, 26–27, 29, 31–32, 34–37, 39–43, 45, 47–49, 56, 59, 62, 66, 69
model.py	80	37	53%	56, 58–60, 62–63, 66, 68–70, 72–73, 77–78, 80–82, 84–85, 87–88, 90, 92–94, 100–111
training_utils.py	53	4	92%	27–28, 60, 84
pd_dwi/config
__init__.py	0	0	100%
config.py	71	1	98%	100
utils.py	11	1	90%	15
pd_dwi/feature_selection
__init__.py	0	0	100%
select_k_best.py	6	0	100%
pd_dwi/models
__init__.py	12	4	66%	14–16, 18
pd_dwi/preprocessing
__init__.py	0	0	100%
column_transformer.py	10	4	60%	14–15, 18, 20
pd_dwi/preprocessing/transformers
__init__.py	0	0	100%
hormone_receptor_encoder.py	19	9	52%	16–17, 19, 22–24, 26, 29, 32
radiomics_encoder.py	69	28	59%	40, 43, 55–56, 58, 61, 63–64, 66, 68, 71, 74, 77–82, 84–85, 87, 90, 93–98
sbr_grade_encoder.py	21	9	57%	18–19, 22, 24, 27–28, 30, 33, 36
pd_dwi/scripts
__init__.py	0	0	100%
cli.py	17	1	94%	24
list_command.py	9	0	100%
predict_command.py	25	14	44%	9–10, 12–13, 15, 17–19, 21, 23–24, 26–27, 29
score_command.py	8	2	75%	5–6
train_command.py	10	3	70%	5–7
TOTAL	469	149	68%