Commit 49658726 authored by Alessia Marcolini's avatar Alessia Marcolini
Browse files

Update features configuration file

parent ebe27862
...@@ -33,7 +33,7 @@ OUTFILE = f'radiomics_features_{BBOX}.csv' # output file name ...@@ -33,7 +33,7 @@ OUTFILE = f'radiomics_features_{BBOX}.csv' # output file name
clinical = pd.read_csv(Path('data') / DATASET / 'processed' / f'clinical_{DATASET}.csv') clinical = pd.read_csv(Path('data') / DATASET / 'processed' / f'clinical_{DATASET}.csv')
#%% #%%
params_shape = '02_radiomics_features_extraction/shape_new.yaml' # param file to use to create the extractor params_shape = '02_radiomics_features_extraction/shape.yaml' # param file to use to create the extractor
extractor_shape = RadiomicsFeatureExtractor(params_shape) extractor_shape = RadiomicsFeatureExtractor(params_shape)
params_intensity_CT = '02_radiomics_features_extraction/intensity_CT.yaml' # param file to use to create the extractor params_intensity_CT = '02_radiomics_features_extraction/intensity_CT.yaml' # param file to use to create the extractor
...@@ -42,7 +42,7 @@ extractor_intensity_CT = RadiomicsFeatureExtractor(params_intensity_CT) ...@@ -42,7 +42,7 @@ extractor_intensity_CT = RadiomicsFeatureExtractor(params_intensity_CT)
params_intensity_PET = '02_radiomics_features_extraction/intensity_PET.yaml' # param file to use to create the extractor params_intensity_PET = '02_radiomics_features_extraction/intensity_PET.yaml' # param file to use to create the extractor
extractor_intensity_PET = RadiomicsFeatureExtractor(params_intensity_PET) extractor_intensity_PET = RadiomicsFeatureExtractor(params_intensity_PET)
params_texture = '02_radiomics_features_extraction/texture_new.yaml' # param file to use to create the extractor params_texture = '02_radiomics_features_extraction/texture.yaml' # param file to use to create the extractor
extractor_texture = RadiomicsFeatureExtractor(params_texture) extractor_texture = RadiomicsFeatureExtractor(params_texture)
filenames = [f for f in os.listdir(DATADIR) if f.endswith('.npy')] filenames = [f for f in os.listdir(DATADIR) if f.endswith('.npy')]
......
#
# Damiana
#
setting:
label: 1
interpolator: 'sitkBSpline' # This is an enumerated value, here None is not allowed
weightingNorm: 'euclidean'
normalize: False
# Image types to use: "Original" for unfiltered image, for possible filters, see documentation.
imageType:
Original: {}
# Featureclasses, from which features must be calculated. If a featureclass is not mentioned, no features are calculated
# for that class. Otherwise, the specified features are calculated, or, if none are specified, all are calculated (excluding redundant/deprecated features).
featureClass:
firstorder:
- 'Variance'
- 'Skewness'
- 'Kurtosis'
#
# Damiana
#
setting:
label: 1
interpolator: 'sitkBSpline' # This is an enumerated value, here None is not allowed
weightingNorm: 'euclidean'
normalize: False
# Image types to use: "Original" for unfiltered image, for possible filters, see documentation.
imageType:
Original: {}
# Featureclasses, from which features must be calculated. If a featureclass is not mentioned, no features are calculated
# for that class. Otherwise, the specified features are calculated, or, if none are specified, all are calculated (excluding redundant/deprecated features).
featureClass:
firstorder:
- 'Variance'
- 'Skewness'
- 'Kurtosis'
myfirstorder:
- 'SuvMax'
- 'SuvPeak'
- 'SuvMean'
- 'AUCCSH'
- 'TLG'
- 'InactiveVolume' #TBC
- 'gETU'
\ No newline at end of file
...@@ -14,4 +14,10 @@ imageType: ...@@ -14,4 +14,10 @@ imageType:
# Featureclasses, from which features must be calculated. If a featureclass is not mentioned, no features are calculated # Featureclasses, from which features must be calculated. If a featureclass is not mentioned, no features are calculated
# for that class. Otherwise, the specified features are calculated, or, if none are specified, all are calculated (excluding redundant/deprecated features). # for that class. Otherwise, the specified features are calculated, or, if none are specified, all are calculated (excluding redundant/deprecated features).
featureClass: featureClass:
myshape:
- 'Compactness2' # 1. Compactness
- 'Eccentricity' # 4. Eccentricity
- 'Solidity' # 5. Solidity
shape: shape:
- 'Volume' # 2. Volume
- 'Maximum3DDiameter' # 3. Size
...@@ -14,7 +14,7 @@ imageType: ...@@ -14,7 +14,7 @@ imageType:
# Featureclasses, from which features must be calculated. If a featureclass is not mentioned, no features are calculated # Featureclasses, from which features must be calculated. If a featureclass is not mentioned, no features are calculated
# for that class. Otherwise, the specified features are calculated, or, if none are specified, all are calculated (excluding redundant/deprecated features). # for that class. Otherwise, the specified features are calculated, or, if none are specified, all are calculated (excluding redundant/deprecated features).
featureClass: featureClass:
glcm: myglcm:
- 'JointEnergy' - 'JointEnergy'
- 'Contrast' - 'Contrast'
- 'Correlation' - 'Correlation'
...@@ -23,7 +23,7 @@ featureClass: ...@@ -23,7 +23,7 @@ featureClass:
- 'JointAverage' - 'JointAverage'
- 'DifferenceVariance' - 'DifferenceVariance'
- 'Autocorrelation' - 'Autocorrelation'
glrlm: myglrlm:
- 'ShortRunEmphasis' - 'ShortRunEmphasis'
- 'LongRunEmphasis' - 'LongRunEmphasis'
- 'GrayLevelNonUniformity' - 'GrayLevelNonUniformity'
...@@ -37,7 +37,7 @@ featureClass: ...@@ -37,7 +37,7 @@ featureClass:
- 'LongRunHighGrayLevelEmphasis' - 'LongRunHighGrayLevelEmphasis'
- 'GrayLevelVariance' - 'GrayLevelVariance'
- 'RunVariance' - 'RunVariance'
glszm: myglszm:
- 'SmallAreaEmphasis' - 'SmallAreaEmphasis'
- 'LargeAreaEmphasis' - 'LargeAreaEmphasis'
- 'GrayLevelNonUniformity' - 'GrayLevelNonUniformity'
...@@ -52,7 +52,7 @@ featureClass: ...@@ -52,7 +52,7 @@ featureClass:
- 'LargeAreaHighGrayLevelEmphasis' - 'LargeAreaHighGrayLevelEmphasis'
- 'GrayLevelVariance' - 'GrayLevelVariance'
- 'ZoneVariance' - 'ZoneVariance'
ngtdm: myngtdm:
- 'Coarseness' - 'Coarseness'
- 'Contrast' - 'Contrast'
- 'Busyness' - 'Busyness'
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment