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Mesh volume and diameters #427

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merged 5 commits into from Sep 28, 2018
Merged

Mesh volume and diameters #427

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8451138
TEST: Add explicit install of numpy in install step
JoostJM Sep 28, 2018
00e18bf
ENH: Calculate Volume based on triangle mesh
JoostJM Sep 18, 2018
7fd96f2
ENH: Calculate Maximum diameters based upon mesh
JoostJM Sep 21, 2018
1642170
TEST: Update baseline
JoostJM Sep 21, 2018
263e8b3
STYL: Update shape documentation and feature names
JoostJM Sep 27, 2018
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32 changes: 17 additions & 15 deletions data/baseline/baseline_shape.csv
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@@ -1,27 +1,29 @@
featureName,brain1,brain2,breast1,lung1,lung2
general_info_TestCase,brain1,brain2,breast1,lung1,lung2
general_info_PythonVersion,2.7.11,2.7.11,2.7.11,2.7.11,2.7.11
general_info_BoundingBox,"(162, 84, 11, 47, 70, 7)","(205, 155, 8, 20, 15, 3)","(21, 64, 8, 9, 12, 3)","(206, 347, 32, 24, 26, 3)","(318, 333, 15, 87, 66, 11)"
general_info_EnabledImageTypes,{'Original': {}},{'Original': {}},{'Original': {}},{'Original': {}},{'Original': {}}
general_info_GeneralSettings,"{'distances': [1], 'voxelArrayShift': 2000, 'additionalInfo': True, 'enableCExtensions': True, 'force2D': False, 'interpolator': None, 'resampledPixelSpacing': None, 'gldm_a': 0, 'weightingNorm': None, 'normalizeScale': 1, 'normalize': False, 'force2Ddimension': 0, 'removeOutliers': None, 'minimumROISize': None, 'binWidth': 25, 'label': 1, 'minimumROIDimensions': 1, 'preCrop': False, 'resegmentRange': None, 'padDistance': 5}","{'distances': [1], 'voxelArrayShift': 2000, 'additionalInfo': True, 'enableCExtensions': True, 'force2D': False, 'interpolator': None, 'resampledPixelSpacing': None, 'gldm_a': 0, 'weightingNorm': None, 'normalizeScale': 1, 'normalize': False, 'force2Ddimension': 0, 'removeOutliers': None, 'minimumROISize': None, 'binWidth': 25, 'label': 1, 'minimumROIDimensions': 1, 'preCrop': False, 'resegmentRange': None, 'padDistance': 5}","{'distances': [1], 'voxelArrayShift': 2000, 'additionalInfo': True, 'enableCExtensions': True, 'force2D': False, 'interpolator': None, 'resampledPixelSpacing': None, 'gldm_a': 0, 'weightingNorm': None, 'normalizeScale': 1, 'normalize': False, 'force2Ddimension': 0, 'removeOutliers': None, 'minimumROISize': None, 'binWidth': 25, 'label': 1, 'minimumROIDimensions': 1, 'preCrop': False, 'resegmentRange': None, 'padDistance': 5}","{'distances': [1], 'voxelArrayShift': 2000, 'additionalInfo': True, 'enableCExtensions': True, 'force2D': False, 'interpolator': None, 'resampledPixelSpacing': None, 'gldm_a': 0, 'weightingNorm': None, 'normalizeScale': 1, 'normalize': False, 'force2Ddimension': 0, 'removeOutliers': None, 'minimumROISize': None, 'binWidth': 25, 'label': 1, 'minimumROIDimensions': 1, 'preCrop': False, 'resegmentRange': None, 'padDistance': 5}","{'distances': [1], 'voxelArrayShift': 2000, 'additionalInfo': True, 'enableCExtensions': True, 'force2D': False, 'interpolator': None, 'resampledPixelSpacing': None, 'gldm_a': 0, 'weightingNorm': None, 'normalizeScale': 1, 'normalize': False, 'force2Ddimension': 0, 'removeOutliers': None, 'minimumROISize': None, 'binWidth': 25, 'label': 1, 'minimumROIDimensions': 1, 'preCrop': False, 'resegmentRange': None, 'padDistance': 5}"
general_info_ImageHash,5c9ce3ca174f0f8324aa4d277e0fef82dc5ac566,f2b8fbc4d5d1da08a1a70e79a301f8a830139438,016951a8f9e8e5de21092d9d62b77262f92e04a5,34dca4200809a5e76c702d6b9503d958093057a3,14f57fd04838eb8c9cca2a0dd871d29971585975
general_info_ImageSpacing,"(0.7812499999999999, 0.7812499999999999, 6.499999999999998)","(0.7812499999999999, 0.7812499999999999, 6.499999999999998)","(0.664062, 0.664062, 2.1)","(0.5703125, 0.5703125, 5.0)","(0.6269531, 0.6269531, 5.0)"
general_info_MaskHash,9dc2c3137b31fd872997d92c9a92d5178126d9d3,b41049c71633e194bee4891750392b72eabd8800,5aa7d57fd57e83125b605c036c40f4a0d0cfd3e4,054d887740012177bd1f9031ddac2b67170af0f3,e284ff05593bc6cb2747261882e452d4efbccb3a
general_info_NumpyVersion,1.14.0,1.14.0,1.14.0,1.14.0,1.14.0
general_info_NumpyVersion,1.14.1,1.14.1,1.14.1,1.14.1,1.14.1
general_info_PyWaveletVersion,0.5.2,0.5.2,0.5.2,0.5.2,0.5.2
general_info_SimpleITKVersion,0.9.1,0.9.1,0.9.1,0.9.1,0.9.1
general_info_Version,1.3.0.post61.dev0+gec8ca3f,1.3.0.post61.dev0+gec8ca3f,1.3.0.post61.dev0+gec8ca3f,1.3.0.post61.dev0+gec8ca3f,1.3.0.post61.dev0+gec8ca3f
general_info_Version,2.0.1b1.post11+g127d134,2.0.1b1.post11+g127d134,2.0.1b1.post11+g127d134,2.0.1b1.post11+g127d134,2.0.1b1.post11+g127d134
general_info_VolumeNum,2,1,1,1,1
general_info_VoxelNum,4137,453,143,837,24644
original_shape_Maximum3DDiameter,65.53661458728622,19.654138400092734,7.772702166226878,18.182594712754316,65.4490741679312
original_shape_Maximum2DDiameterSlice,47.218791363317415,15.566295972790057,7.772646432112296,15.978930906357792,55.24662905771692
original_shape_Sphericity,0.48506174422170256,0.7688488022971132,0.7267247983585284,0.7593187496870597,0.6737235654781801
original_shape_MinorAxis,34.849701666854735,13.383589687312327,5.4115477584202845,12.4886227814091,41.459751886690256
original_shape_Elongation,0.5621171627174115,0.7407691177548195,0.699983810275405,0.7187910312752436,0.7433464635239118
original_shape_SurfaceVolumeRatio,0.39230826186319245,0.5173438720250226,1.3055392937755952,0.5746714029458282,0.19691793910543032
original_shape_Volume,16412.658691406243,1797.180175781249,132.42579545515324,1361.1978149414062,48434.108762463955
original_shape_MajorAxis,61.997220469808774,18.067153943831176,7.730961315078329,17.37448331715047,55.77446577218644
original_shape_SurfaceArea,6438.821603779402,929.7601508652822,172.88707947619218,782.2414579991738,9537.544879912666
original_shape_Flatness,0.46105975346582545,0.6188162226844605,0.6842246761542062,0.5143357681770736,0.5692892353827333
original_shape_LeastAxis,28.584423185376462,11.180247958180262,5.289714502170166,8.936318223606337,31.751802973328452
original_shape_Maximum2DDiameterColumn,44.54879040515578,18.584714191036134,5.353919918723103,16.04444054074884,61.55885055061254
original_shape_Maximum2DDiameterRow,61.58017671347248,14.779664291265208,7.304682000000001,13.537563480922259,57.72119646362829
original_shape_Maximum3DDiameter,69.6009903059,24.4445322363,9.08101860833,21.3449467202,68.9824710303
original_shape_Maximum2DDiameterSlice,53.5939777692,16.3129789202,8.39979371027,16.6273237626,55.8023479973
original_shape_Sphericity,0.480242186182,0.75130449808,0.695903713518,0.748037658194,0.672409930059
original_shape_MinorAxisLength,34.849701666854706,13.383589687312323,5.4115477584202925,12.488622781409092,41.45975188669023
original_shape_Elongation,0.5621171627174109,0.7407691177548188,0.6999838102754056,0.7187910312752432,0.7433464635239126
original_shape_SurfaceVolumeRatio,0.398386088279,0.535570612898,1.39322476873,0.587720147764,0.197495275935
original_shape_MeshVolume,16149.4954427,1736.01786296,124.091304832,1330.97607931,48292.5216046
original_shape_MajorAxisLength,61.99722046980879,18.067153943831187,7.730961315078334,17.374483317150464,55.77446577218634
original_shape_SurfaceArea,6433.7343171,929.760150865,172.887079476,782.241457999,9537.54487991
original_shape_Flatness,0.46105975346582634,0.6188162226844603,0.6842246761542068,0.5143357681770733,0.569289235382734
original_shape_LeastAxisLength,28.584423185376522,11.180247958180265,5.289714502170174,8.93631822360633,31.75180297332843
original_shape_Maximum2DDiameterColumn,49.4908549791,23.593253306,7.12140846294,19.5556659888,65.3030786496
original_shape_Maximum2DDiameterRow,65.8890595172,20.7289284953,8.24091097816,17.5574948384,62.1026289395
original_shape_VoxelVolume,16412.658691406243,1797.180175781249,132.42579545515324,1361.1978149414062,48434.108762463955
33 changes: 17 additions & 16 deletions ...es/exampleSettings/Full_shape_params.yaml → ...les/exampleSettings/example_allShape.yaml
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Expand Up @@ -14,19 +14,20 @@ setting:
# for that class. Otherwise, the specified features are calculated, or, if none are specified, all are calculated (excluding redundant/deprecated features).
featureClass:
shape: # disable redundant Compactness 1 and Compactness 2 features by specifying all other shape features
- 'Volume'
- 'SurfaceArea'
- 'SurfaceVolumeRatio'
- 'Compactness1'
- 'Compactness2'
- 'Sphericity'
- 'SphericalDisproportion'
- 'Maximum3DDiameter'
- 'Maximum2DDiameterSlice'
- 'Maximum2DDiameterColumn'
- 'Maximum2DDiameterRow'
- 'MajorAxis'
- 'MinorAxis'
- 'LeastAxis'
- 'Elongation'
- 'Flatness'
- VoxelVolume
- MeshVolume
- SurfaceArea
- SurfaceVolumeRatio
- Compactness1
- Compactness2
- Sphericity
- SphericalDisproportion
- Maximum3DDiameter
- Maximum2DDiameterSlice
- Maximum2DDiameterColumn
- Maximum2DDiameterRow
- MajorAxisLength
- MinorAxisLength
- LeastAxisLength
- Elongation
- Flatness