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Update testing #353

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merged 5 commits into from
Mar 13, 2018
Merged

Update testing #353

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ca94c9e
ENH: Update the getTestCase() function
JoostJM Mar 6, 2018
617ddcc
ENH: Reconfigure tests
JoostJM Mar 6, 2018
b447fa4
BUG: Update test_cmatrices to new interface
JoostJM Mar 7, 2018
61e82ca
STYL: Fix Flake8 errors
JoostJM Mar 7, 2018
d7447de
ENH: Further update getTestCase() function
JoostJM Mar 8, 2018
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57 changes: 16 additions & 41 deletions bin/addClassToBaseline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,41 +5,26 @@
import csv
import os

import six
from radiomics import featureextractor, getTestCase

from radiomics import featureextractor, imageoperations
TEST_CASES = ('brain1', 'brain2', 'breast1', 'lung1', 'lung2')


def main():
global TEST_CASES
dataDir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "data")
baselineDir = os.path.join(dataDir, "baseline")

testCases = []

kwargs = {'binWidth': 25,
'interpolator': None,
'resampledPixelSpacing': None,
'padDistance': 5,
'voxelArrayShift': 2000,
'symmetricalGLCM': False,
'weightingNorm': None,
'gldm_a': 0}

extractor = featureextractor.RadiomicsFeaturesExtractor(**kwargs)

for cls in extractor.getFeatureClassNames():
if os.path.exists(os.path.join(baselineDir, 'baseline_%s.csv' % (cls))):
with open(os.path.join(baselineDir, 'baseline_%s.csv' % (cls)), 'rb') as baselineFile:
csvReader = csv.reader(baselineFile)
six.next(csvReader) # Skip header row
for testRow in csvReader:
testCases += [testRow[0]]
if len(testCases) > 0: break

if len(testCases) == 0:
print("No baselinefiles containing testcases found, exiting...")
exit(-1)

newClasses = [cls for cls in extractor.getFeatureClassNames() if
not os.path.exists(os.path.join(baselineDir, 'baseline_%s.csv' % (cls)))]

Expand All @@ -51,9 +36,6 @@ def main():

newBaseline = {}

# When C matrices is merged, force baseline to be build using the Python implementation of the functions.
# radiomics.pythonMatrixCalculation(True)

extractor.disableAllFeatures()
extractor.disableAllImageTypes()

Expand All @@ -63,42 +45,35 @@ def main():
newBaseline[cls] = {}

print("Computing new baseline")
for testCase in testCases:
for testCase in TEST_CASES:
print("\tCalculating test case", testCase)
imagePath = os.path.join(dataDir, testCase + '_image.nrrd')
maskPath = os.path.join(dataDir, testCase + '_label.nrrd')
imagePath, maskPath = getTestCase(testCase)
image, mask = extractor.loadImage(imagePath, maskPath)
if image is None or mask is None:
print("Error during loading of image/mask, testcase:", testCase)
continue # testImage or mask not found / error during loading

provenance = extractor.getProvenance(imagePath, maskPath, mask)

bb, correctedMask = imageoperations.checkMask(image, mask)
if correctedMask is not None:
mask = correctedMask
image, mask = imageoperations.cropToTumorMask(image, mask, bb)
for cls in newClasses:
print("\t\tCalculating class", cls)
extractor.disableAllFeatures()
extractor.enableFeatureClassByName(cls)
newBaseline[cls][testCase] = collections.OrderedDict()
newBaseline[cls][testCase]["Patient ID"] = testCase
newBaseline[cls][testCase].update(provenance)
featureClass = extractor.featureClasses[cls](image, mask, **extractor.settings)
featureClass.enableAllFeatures()
featureClass.calculateFeatures()
newBaseline[cls][testCase].update(featureClass.featureValues)
newBaseline[cls][testCase]['general_info_TestCase'] = testCase
newBaseline[cls][testCase].update(extractor.execute(image, mask))

print("Writing new baseline")
for cls in newClasses:
baselineFile = os.path.join(baselineDir, 'baseline_%s.csv' % (cls))
with open(baselineFile, 'wb') as baseline:
csvWriter = csv.writer(baseline)
header = newBaseline[cls][testCases[0]].keys()
header = ['featureName'] + list(TEST_CASES)
csvWriter.writerow(header)
for testCase in testCases:
row = []
for h in header:
row += [newBaseline[cls][testCase][h]]

features = newBaseline[cls][TEST_CASES[0]].keys()
for f in features:
row = [f]
for testCase in TEST_CASES:
row.append(newBaseline[cls][testCase].get(f, ''))
csvWriter.writerow(row)
baseline.close()

Expand Down
38 changes: 32 additions & 6 deletions data/baseline/baseline_firstorder.csv
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Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,32 @@
Patient ID,general_info_BoundingBox,general_info_GeneralSettings,general_info_ImageHash,general_info_ImageSpacing,general_info_InputImages,general_info_MaskHash,general_info_Version,general_info_VolumeNum,general_info_VoxelNum,InterquartileRange,Skewness,Uniformity,MeanAbsoluteDeviation,Energy,RobustMeanAbsoluteDeviation,Median,TotalEnergy,Maximum,RootMeanSquared,90Percentile,Minimum,Entropy,StandardDeviation,Range,Variance,10Percentile,Kurtosis,Mean
brain1,"(162, 84, 11, 47, 70, 7)","{'verbose': False, 'voxelArrayShift': 2000, 'binWidth': 25, 'label': 1, 'interpolator': None, 'symmetricalGLCM': False, 'resampledPixelSpacing': None, 'gldm_a': 0, 'weightingNorm': None, 'padDistance': 5}",5c9ce3ca174f0f8324aa4d277e0fef82dc5ac566,"(0.7812499999999999, 0.7812499999999999, 6.499999999999998)",{'original': {}},9dc2c3137b31fd872997d92c9a92d5178126d9d3,0.post403.dev0+gd611f07,2,4137,253.0,0.27565085908587594,0.045156963555862184,133.44726195252767,33122817481.0,103.00138343026681,812.0,131407662125.54922,1266.0,2829.5728210757125,1044.4000000000001,468.0,4.6019355539037967,156.61123589440385,798.0,24527.079208372608,632.0,2.1807729393860265,825.23543630650227
brain2,"(205, 155, 8, 20, 15, 3)","{'verbose': False, 'voxelArrayShift': 2000, 'binWidth': 25, 'label': 1, 'interpolator': None, 'symmetricalGLCM': False, 'resampledPixelSpacing': None, 'gldm_a': 0, 'weightingNorm': None, 'padDistance': 5}",f2b8fbc4d5d1da08a1a70e79a301f8a830139438,"(0.7812499999999999, 0.7812499999999999, 6.499999999999998)",{'original': {}},b41049c71633e194bee4891750392b72eabd8800,0.post403.dev0+gd611f07,1,453,97.0,0.4386372506317367,0.095965576558533008,73.554269062273107,2594007770.0,44.018676959200739,375.0,10291168521.118156,729.0,2392.9660398741912,532.60000000000002,8.0,3.8206001230555682,102.1243477592642,721.0,10429.38240525513,305.20000000000005,4.6747161961935264,390.78587196467993
breast1,"(21, 64, 8, 9, 12, 3)","{'verbose': False, 'voxelArrayShift': 2000, 'binWidth': 25, 'label': 1, 'interpolator': None, 'symmetricalGLCM': False, 'resampledPixelSpacing': None, 'gldm_a': 0, 'weightingNorm': None, 'padDistance': 5}",016951a8f9e8e5de21092d9d62b77262f92e04a5,"(0.664062, 0.664062, 2.1)",{'original': {}},5aa7d57fd57e83125b605c036c40f4a0d0cfd3e4,0.post403.dev0+gd611f07,1,143,30.0,0.041827973131320723,0.38901657782776666,13.93975255513717,649499543.0,11.083091863105961,130.0,601471983.42331111,162.0,2131.1862532762934,151.80000000000001,102.0,1.4490921348002006,16.042281168059137,60.0,257.35478507506485,110.2,1.8044408150083193,131.12587412587413
lung1,"(206, 347, 32, 24, 26, 3)","{'verbose': False, 'voxelArrayShift': 2000, 'binWidth': 25, 'label': 1, 'interpolator': None, 'symmetricalGLCM': False, 'resampledPixelSpacing': None, 'gldm_a': 0, 'weightingNorm': None, 'padDistance': 5}",34dca4200809a5e76c702d6b9503d958093057a3,"(0.5703125, 0.5703125, 5.0)",{'original': {}},054d887740012177bd1f9031ddac2b67170af0f3,0.post403.dev0+gd611f07,1,837,198.0,-0.73366595360417897,0.07442664462743856,105.09444751337841,3150327991.0,81.580905349794236,-31.0,5123320881.3595581,106.0,1940.0599797967793,71.0,-506.0,4.0208349271393855,124.01818919070283,612.0,15380.51125014096,-245.40000000000001,2.6959270958193589,-63.908004778972519
lung2,"(318, 333, 15, 87, 66, 11)","{'verbose': False, 'voxelArrayShift': 2000, 'binWidth': 25, 'label': 1, 'interpolator': None, 'symmetricalGLCM': False, 'resampledPixelSpacing': None, 'gldm_a': 0, 'weightingNorm': None, 'padDistance': 5}",14f57fd04838eb8c9cca2a0dd871d29971585975,"(0.6269531, 0.6269531, 5.0)",{'original': {}},e284ff05593bc6cb2747261882e452d4efbccb3a,0.post403.dev0+gd611f07,1,24644,30.0,-3.0222132456965567,0.28153721195636616,59.581897780966464,99558480758.0,19.669786252104565,41.0,195667354538.98093,297.0,2009.9420229154007,60.700000000000728,-840.0,2.6529019354413741,96.957559721307049,1137.0,9400.7683871108238,-102.0,12.884706923906494,7.6020938159389706
featureName,brain1,brain2,breast1,lung1,lung2
general_info_TestCase,brain1,brain2,breast1,lung1,lung2
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_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_VolumeNum,2,1,1,1,1
general_info_VoxelNum,4137,453,143,837,24644
original_firstorder_InterquartileRange,253.0,97.0,30.0,198.0,30.0
original_firstorder_Skewness,0.27565085908587594,0.4386372506317367,0.04182797313132072,-0.733665953604179,-3.0222132456965567
original_firstorder_Uniformity,0.045156963555862184,0.09596557655853301,0.38901657782776666,0.07442664462743856,0.28153721195636616
original_firstorder_Median,812.0,375.0,130.0,-31.0,41.0
original_firstorder_Energy,33122817481.0,2594007770.0,649499543.0,3150327991.0,99558480758.0
original_firstorder_RobustMeanAbsoluteDeviation,103.00138343026681,44.01867695920074,11.083091863105961,81.58090534979424,19.669786252104565
original_firstorder_MeanAbsoluteDeviation,133.44726195252767,73.55426906227311,13.93975255513717,105.09444751337841,59.581897780966464
original_firstorder_TotalEnergy,131407662125.54922,10291168521.118156,601471983.4233111,5123320881.359558,195667354538.98093
original_firstorder_Maximum,1266.0,729.0,162.0,106.0,297.0
original_firstorder_RootMeanSquared,2829.5728210757125,2392.966039874191,2131.1862532762934,1940.0599797967793,2009.9420229154007
original_firstorder_90Percentile,1044.4,532.6,151.8,71.0,60.70000000000073
original_firstorder_Minimum,468.0,8.0,102.0,-506.0,-840.0
original_firstorder_Entropy,4.601935553903797,3.820600123055568,1.4490921348002006,4.0208349271393855,2.652901935441374
original_firstorder_Range,798.0,721.0,60.0,612.0,1137.0
original_firstorder_Variance,24527.07920837261,10429.38240525513,257.35478507506485,15380.51125014096,9400.768387110824
original_firstorder_10Percentile,632.0,305.20000000000005,110.2,-245.4,-102.0
original_firstorder_Kurtosis,2.1807729393860265,4.674716196193526,1.8044408150083193,2.695927095819359,12.884706923906494
original_firstorder_Mean,825.2354363065023,390.7858719646799,131.12587412587413,-63.90800477897252,7.602093815938971
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