def make_workspace(self,
mdict,
controls_measurement,
dose_measurements=[]):
'''Make a workspace and module for running CalculateStatistics
mdict - a two-level dictionary that mimics the measurements structure
for instance:
mdict = { cpmeas.Image: { "M1": [ 1,2,3] }}
for the measurement M1 with values for 3 image sets
controls_measurement - the name of the controls measurement
'''
module = C.CalculateStatistics()
module.module_num = 1
module.grouping_values.value = controls_measurement
pipeline = cpp.Pipeline()
pipeline.add_module(module)
m = cpmeas.Measurements()
nimages = None
for object_name in mdict.keys():
odict = mdict[object_name]
for feature in odict.keys():
m.add_all_measurements(object_name, feature, odict[feature])
if nimages is None:
nimages = len(odict[feature])
else:
self.assertEqual(nimages, len(odict[feature]))
if object_name == cpmeas.IMAGE and feature in dose_measurements:
if len(module.dose_values) > 1:
module.add_dose_value()
dv = module.dose_values[-1]
dv.measurement.value = feature
m.image_set_number = nimages
image_set_list = cpi.ImageSetList()
for i in range(nimages):
image_set = image_set_list.get_image_set(i)
workspace = cpw.Workspace(pipeline, module, image_set, cpo.ObjectSet(),
m, image_set_list)
return workspace, module
def test_02_01_compare_to_matlab(self):
expected = {
'EC50_DistCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':
3.982812,
'EC50_DistCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':
4.139827,
'EC50_DistCytoplasm_Intensity_MedianIntensity_CorrGreen':
4.178600,
'EC50_DistCytoplasm_Intensity_MinIntensityEdge_CorrGreen':
4.059770,
'EC50_DistCytoplasm_Intensity_MinIntensity_CorrGreen':
4.066357,
'EC50_DistCytoplasm_Math_Ratio1':
4.491367,
'EC50_DistCytoplasm_Math_Ratio2':
3.848722,
'EC50_DistCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':
4.948056,
'EC50_DistCytoplasm_Texture_Entropy_CorrGreen_1':
4.687104,
'EC50_DistCytoplasm_Texture_InfoMeas2_CorrGreen_1':
5.0285,
'EC50_DistCytoplasm_Texture_InverseDifferenceMoment_CorrGreen_1':
4.319017,
'EC50_DistCytoplasm_Texture_SumAverage_CorrGreen_1':
4.548876,
'EC50_DistCytoplasm_Texture_SumEntropy_CorrGreen_1':
4.779139,
'EC50_DistCytoplasm_Texture_Variance_CorrGreen_1':
4.218379,
'EC50_DistanceCells_Correlation_Correlation_CorrGreenCorrBlue':
3.708711,
'EC50_DistanceCells_Intensity_IntegratedIntensityEdge_CorrGreen':
4.135146,
'EC50_DistanceCells_Intensity_LowerQuartileIntensity_CorrGreen':
4.5372,
'EC50_DistanceCells_Intensity_MeanIntensityEdge_CorrGreen':
4.1371,
'EC50_DistanceCells_Intensity_MinIntensityEdge_CorrGreen':
4.033999,
'EC50_DistanceCells_Intensity_MinIntensity_CorrGreen':
4.079470,
'EC50_DistanceCells_Texture_AngularSecondMoment_CorrGreen_1':
5.118689,
'EC50_DistanceCells_Texture_Correlation_CorrGreen_1':
4.002074,
'EC50_DistanceCells_Texture_Entropy_CorrGreen_1':
5.008000,
'EC50_DistanceCells_Texture_InfoMeas1_CorrGreen_1':
3.883586,
'EC50_DistanceCells_Texture_InverseDifferenceMoment_CorrGreen_1':
3.977216,
'EC50_DistanceCells_Texture_SumAverage_CorrGreen_1':
4.9741,
'EC50_DistanceCells_Texture_SumEntropy_CorrGreen_1':
5.1455,
'EC50_DistanceCells_Texture_SumVariance_CorrGreen_1':
4.593041,
'EC50_DistanceCells_Texture_Variance_CorrGreen_1':
4.619517,
'EC50_Nuclei_Correlation_Correlation_CorrGreenCorrBlue':
3.751133,
'EC50_Nuclei_Math_Ratio1':
4.491367,
'EC50_Nuclei_Math_Ratio2':
3.848722,
'EC50_Nuclei_Texture_SumAverage_CorrGreen_1':
3.765297,
'EC50_PropCells_AreaShape_Area':
4.740853,
'EC50_PropCells_AreaShape_MajorAxisLength':
5.064460,
'EC50_PropCells_AreaShape_MinorAxisLength':
4.751471,
'EC50_PropCells_AreaShape_Perimeter':
4.949292,
'EC50_PropCells_Correlation_Correlation_CorrGreenCorrBlue':
3.772565,
'EC50_PropCells_Texture_GaborX_CorrGreen_1':
5.007167,
'EC50_PropCells_Texture_InfoMeas2_CorrBlue_1':
4.341353,
'EC50_PropCells_Texture_SumVariance_CorrBlue_1':
4.298359,
'EC50_PropCells_Texture_SumVariance_CorrGreen_1':
4.610826,
'EC50_PropCells_Texture_Variance_CorrBlue_1':
4.396352,
'EC50_PropCells_Texture_Variance_CorrGreen_1':
4.632468,
'EC50_PropCytoplasm_AreaShape_Area':
4.669679,
'EC50_PropCytoplasm_AreaShape_MinorAxisLength':
4.754476,
'EC50_PropCytoplasm_AreaShape_Perimeter':
4.949292,
'EC50_PropCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':
4.072830,
'EC50_PropCytoplasm_Intensity_IntegratedIntensity_CorrGreen':
4.0934,
'EC50_PropCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':
3.925800,
'EC50_PropCytoplasm_Intensity_MedianIntensity_CorrGreen':
3.9252,
'EC50_PropCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':
4.777481,
'EC50_PropCytoplasm_Texture_Entropy_CorrGreen_1':
4.4432,
'EC50_PropCytoplasm_Texture_GaborX_CorrGreen_1':
5.163371,
'EC50_PropCytoplasm_Texture_InfoMeas2_CorrGreen_1':
4.701046,
'EC50_PropCytoplasm_Texture_SumEntropy_CorrGreen_1':
4.510543,
'EC50_ThresholdedCells_Texture_AngularSecondMoment_CorrBlue_1':
4.560315,
'EC50_ThresholdedCells_Texture_AngularSecondMoment_CorrGreen_1':
4.966674,
'EC50_ThresholdedCells_Texture_Entropy_CorrBlue_1':
4.457866,
'EC50_ThresholdedCells_Texture_InfoMeas2_CorrBlue_1':
4.624049,
'EC50_ThresholdedCells_Texture_SumAverage_CorrBlue_1':
4.686706,
'EC50_ThresholdedCells_Texture_SumEntropy_CorrBlue_1':
4.537378,
'EC50_ThresholdedCells_Texture_SumVariance_CorrBlue_1':
4.322820,
'EC50_ThresholdedCells_Texture_SumVariance_CorrGreen_1':
4.742158,
'EC50_ThresholdedCells_Texture_Variance_CorrBlue_1':
4.265549,
'EC50_ThresholdedCells_Texture_Variance_CorrGreen_1':
4.860020,
'OneTailedZfactor_DistCytoplasm_Intensity_MedianIntensity_CorrGreen':
-4.322503,
'OneTailedZfactor_DistCytoplasm_Intensity_MinIntensityEdge_CorrGreen':
-4.322503,
'OneTailedZfactor_DistCytoplasm_Intensity_MinIntensity_CorrGreen':
-4.322503,
'OneTailedZfactor_DistCytoplasm_Math_Ratio1':
0.622059,
'OneTailedZfactor_DistCytoplasm_Math_Ratio2':
-4.508284,
'OneTailedZfactor_DistCytoplasm_Texture_Entropy_CorrGreen_1':
-4.645887,
'OneTailedZfactor_DistCytoplasm_Texture_InfoMeas2_CorrGreen_1':
-4.279118,
'OneTailedZfactor_DistCytoplasm_Texture_SumAverage_CorrGreen_1':
-4.765570,
'OneTailedZfactor_DistCytoplasm_Texture_SumEntropy_CorrGreen_1':
-4.682335,
'OneTailedZfactor_DistCytoplasm_Texture_Variance_CorrGreen_1':
-4.415607,
'OneTailedZfactor_DistanceCells_Intensity_MeanIntensityEdge_CorrGreen':
-4.200105,
'OneTailedZfactor_DistanceCells_Intensity_MinIntensityEdge_CorrGreen':
-4.316452,
'OneTailedZfactor_DistanceCells_Intensity_MinIntensity_CorrGreen':
-4.316452,
'OneTailedZfactor_DistanceCells_Texture_Correlation_CorrGreen_1':
0.202500,
'OneTailedZfactor_DistanceCells_Texture_Entropy_CorrGreen_1':
-4.404815,
'OneTailedZfactor_DistanceCells_Texture_InfoMeas1_CorrGreen_1':
-4.508513,
'OneTailedZfactor_DistanceCells_Texture_SumAverage_CorrGreen_1':
-4.225356,
'OneTailedZfactor_DistanceCells_Texture_SumEntropy_CorrGreen_1':
-4.382768,
'OneTailedZfactor_DistanceCells_Texture_SumVariance_CorrGreen_1':
0.492125,
'OneTailedZfactor_DistanceCells_Texture_Variance_CorrGreen_1':
0.477360,
'OneTailedZfactor_Nuclei_Correlation_Correlation_CorrGreenCorrBlue':
0.563780,
'OneTailedZfactor_Nuclei_Math_Ratio1':
0.622059,
'OneTailedZfactor_Nuclei_Math_Ratio2':
-4.508284,
'OneTailedZfactor_Nuclei_Texture_SumAverage_CorrGreen_1':
0.426178,
'OneTailedZfactor_PropCells_AreaShape_Area':
-4.216674,
'OneTailedZfactor_PropCells_AreaShape_MajorAxisLength':
-4.119131,
'OneTailedZfactor_PropCells_AreaShape_MinorAxisLength':
-4.109793,
'OneTailedZfactor_PropCells_AreaShape_Perimeter':
-4.068050,
'OneTailedZfactor_PropCells_Correlation_Correlation_CorrGreenCorrBlue':
0.765440,
'OneTailedZfactor_PropCells_Texture_GaborX_CorrGreen_1':
0.114982,
'OneTailedZfactor_PropCells_Texture_InfoMeas2_CorrBlue_1':
0.108409,
'OneTailedZfactor_PropCells_Texture_SumVariance_CorrBlue_1':
0.191251,
'OneTailedZfactor_PropCells_Texture_SumVariance_CorrGreen_1':
0.559865,
'OneTailedZfactor_PropCells_Texture_Variance_CorrBlue_1':
0.254078,
'OneTailedZfactor_PropCells_Texture_Variance_CorrGreen_1':
0.556108,
'OneTailedZfactor_PropCytoplasm_AreaShape_Area':
-4.223021,
'OneTailedZfactor_PropCytoplasm_AreaShape_MinorAxisLength':
-4.095632,
'OneTailedZfactor_PropCytoplasm_AreaShape_Perimeter':
-4.068050,
'OneTailedZfactor_PropCytoplasm_Intensity_MedianIntensity_CorrGreen':
-4.194663,
'OneTailedZfactor_PropCytoplasm_Texture_Entropy_CorrGreen_1':
-4.443338,
'OneTailedZfactor_PropCytoplasm_Texture_GaborX_CorrGreen_1':
0.207265,
'OneTailedZfactor_PropCytoplasm_Texture_InfoMeas2_CorrGreen_1':
-4.297250,
'OneTailedZfactor_PropCytoplasm_Texture_SumEntropy_CorrGreen_1':
-4.525324,
'OneTailedZfactor_ThresholdedCells_Texture_Entropy_CorrBlue_1':
0.167795,
'OneTailedZfactor_ThresholdedCells_Texture_InfoMeas2_CorrBlue_1':
0.067560,
'OneTailedZfactor_ThresholdedCells_Texture_SumAverage_CorrBlue_1':
0.478527,
'OneTailedZfactor_ThresholdedCells_Texture_SumEntropy_CorrBlue_1':
0.155119,
'OneTailedZfactor_ThresholdedCells_Texture_SumVariance_CorrBlue_1':
0.535907,
'OneTailedZfactor_ThresholdedCells_Texture_SumVariance_CorrGreen_1':
0.572801,
'OneTailedZfactor_ThresholdedCells_Texture_Variance_CorrBlue_1':
0.423454,
'OneTailedZfactor_ThresholdedCells_Texture_Variance_CorrGreen_1':
0.440500,
'Vfactor_DistCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':
0.500429,
'Vfactor_DistCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':
0.325675,
'Vfactor_DistCytoplasm_Intensity_MedianIntensity_CorrGreen':
0.323524,
'Vfactor_DistCytoplasm_Intensity_MinIntensityEdge_CorrGreen':
0.138487,
'Vfactor_DistCytoplasm_Intensity_MinIntensity_CorrGreen':
0.128157,
'Vfactor_DistCytoplasm_Math_Ratio1':
0.503610,
'Vfactor_DistCytoplasm_Math_Ratio2':
0.319610,
'Vfactor_DistCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':
0.522880,
'Vfactor_DistCytoplasm_Texture_Entropy_CorrGreen_1':
0.504303,
'Vfactor_DistCytoplasm_Texture_InfoMeas2_CorrGreen_1':
0.289432,
'Vfactor_DistCytoplasm_Texture_InverseDifferenceMoment_CorrGreen_1':
0.234123,
'Vfactor_DistCytoplasm_Texture_SumAverage_CorrGreen_1':
0.591687,
'Vfactor_DistCytoplasm_Texture_SumEntropy_CorrGreen_1':
0.520356,
'Vfactor_DistCytoplasm_Texture_Variance_CorrGreen_1':
-0.007649,
'Vfactor_DistanceCells_Correlation_Correlation_CorrGreenCorrBlue':
0.761198,
'Vfactor_DistanceCells_Intensity_IntegratedIntensityEdge_CorrGreen':
0.234655,
'Vfactor_DistanceCells_Intensity_LowerQuartileIntensity_CorrGreen':
0.252240,
'Vfactor_DistanceCells_Intensity_MeanIntensityEdge_CorrGreen':
0.195125,
'Vfactor_DistanceCells_Intensity_MinIntensityEdge_CorrGreen':
0.138299,
'Vfactor_DistanceCells_Intensity_MinIntensity_CorrGreen':
0.126784,
'Vfactor_DistanceCells_Texture_AngularSecondMoment_CorrGreen_1':
0.342691,
'Vfactor_DistanceCells_Texture_Correlation_CorrGreen_1':
0.314396,
'Vfactor_DistanceCells_Texture_Entropy_CorrGreen_1':
0.311771,
'Vfactor_DistanceCells_Texture_InfoMeas1_CorrGreen_1':
0.410631,
'Vfactor_DistanceCells_Texture_InverseDifferenceMoment_CorrGreen_1':
0.170576,
'Vfactor_DistanceCells_Texture_SumAverage_CorrGreen_1':
0.223147,
'Vfactor_DistanceCells_Texture_SumEntropy_CorrGreen_1':
0.269519,
'Vfactor_DistanceCells_Texture_SumVariance_CorrGreen_1':
0.571528,
'Vfactor_DistanceCells_Texture_Variance_CorrGreen_1':
0.566272,
'Vfactor_Nuclei_Correlation_Correlation_CorrGreenCorrBlue':
0.705051,
'Vfactor_Nuclei_Math_Ratio1':
0.503610,
'Vfactor_Nuclei_Math_Ratio2':
0.319610,
'Vfactor_Nuclei_Texture_SumAverage_CorrGreen_1':
0.553708,
'Vfactor_PropCells_AreaShape_Area':
0.340093,
'Vfactor_PropCells_AreaShape_MajorAxisLength':
0.243838,
'Vfactor_PropCells_AreaShape_MinorAxisLength':
0.320691,
'Vfactor_PropCells_AreaShape_Perimeter':
0.238915,
'Vfactor_PropCells_Correlation_Correlation_CorrGreenCorrBlue':
0.723520,
'Vfactor_PropCells_Texture_GaborX_CorrGreen_1':
0.213161,
'Vfactor_PropCells_Texture_InfoMeas2_CorrBlue_1':
0.199791,
'Vfactor_PropCells_Texture_SumVariance_CorrBlue_1':
0.078959,
'Vfactor_PropCells_Texture_SumVariance_CorrGreen_1':
0.642844,
'Vfactor_PropCells_Texture_Variance_CorrBlue_1':
0.199105,
'Vfactor_PropCells_Texture_Variance_CorrGreen_1':
0.640818,
'Vfactor_PropCytoplasm_AreaShape_Area':
0.325845,
'Vfactor_PropCytoplasm_AreaShape_MinorAxisLength':
0.312258,
'Vfactor_PropCytoplasm_AreaShape_Perimeter':
0.238915,
'Vfactor_PropCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':
0.337565,
'Vfactor_PropCytoplasm_Intensity_IntegratedIntensity_CorrGreen':
0.292900,
'Vfactor_PropCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':
0.175528,
'Vfactor_PropCytoplasm_Intensity_MedianIntensity_CorrGreen':
0.193308,
'Vfactor_PropCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':
0.276152,
'Vfactor_PropCytoplasm_Texture_Entropy_CorrGreen_1':
0.239567,
'Vfactor_PropCytoplasm_Texture_GaborX_CorrGreen_1':
0.332380,
'Vfactor_PropCytoplasm_Texture_InfoMeas2_CorrGreen_1':
0.379141,
'Vfactor_PropCytoplasm_Texture_SumEntropy_CorrGreen_1':
0.337740,
'Vfactor_ThresholdedCells_Texture_AngularSecondMoment_CorrBlue_1':
0.334520,
'Vfactor_ThresholdedCells_Texture_AngularSecondMoment_CorrGreen_1':
0.192882,
'Vfactor_ThresholdedCells_Texture_Entropy_CorrBlue_1':
0.276245,
'Vfactor_ThresholdedCells_Texture_InfoMeas2_CorrBlue_1':
0.139166,
'Vfactor_ThresholdedCells_Texture_SumAverage_CorrBlue_1':
0.465237,
'Vfactor_ThresholdedCells_Texture_SumEntropy_CorrBlue_1':
0.355399,
'Vfactor_ThresholdedCells_Texture_SumVariance_CorrBlue_1':
0.453937,
'Vfactor_ThresholdedCells_Texture_SumVariance_CorrGreen_1':
0.564371,
'Vfactor_ThresholdedCells_Texture_Variance_CorrBlue_1':
0.360566,
'Vfactor_ThresholdedCells_Texture_Variance_CorrGreen_1':
0.548770,
'Zfactor_DistCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':
0.531914,
'Zfactor_DistCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':
0.265558,
'Zfactor_DistCytoplasm_Intensity_MedianIntensity_CorrGreen':
0.178586,
'Zfactor_DistCytoplasm_Intensity_MinIntensityEdge_CorrGreen':
0.084566,
'Zfactor_DistCytoplasm_Intensity_MinIntensity_CorrGreen':
0.086476,
'Zfactor_DistCytoplasm_Math_Ratio1':
0.623284,
'Zfactor_DistCytoplasm_Math_Ratio2':
0.358916,
'Zfactor_DistCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':
0.429510,
'Zfactor_DistCytoplasm_Texture_Entropy_CorrGreen_1':
0.508275,
'Zfactor_DistCytoplasm_Texture_InfoMeas2_CorrGreen_1':
0.068695,
'Zfactor_DistCytoplasm_Texture_InverseDifferenceMoment_CorrGreen_1':
0.347949,
'Zfactor_DistCytoplasm_Texture_SumAverage_CorrGreen_1':
0.646576,
'Zfactor_DistCytoplasm_Texture_SumEntropy_CorrGreen_1':
0.494276,
'Zfactor_DistCytoplasm_Texture_Variance_CorrGreen_1':
0.179011,
'Zfactor_DistanceCells_Correlation_Correlation_CorrGreenCorrBlue':
0.824686,
'Zfactor_DistanceCells_Intensity_IntegratedIntensityEdge_CorrGreen':
0.027644,
'Zfactor_DistanceCells_Intensity_LowerQuartileIntensity_CorrGreen':
0.088491,
'Zfactor_DistanceCells_Intensity_MeanIntensityEdge_CorrGreen':
0.065056,
'Zfactor_DistanceCells_Intensity_MinIntensityEdge_CorrGreen':
0.089658,
'Zfactor_DistanceCells_Intensity_MinIntensity_CorrGreen':
0.078017,
'Zfactor_DistanceCells_Texture_AngularSecondMoment_CorrGreen_1':
0.238131,
'Zfactor_DistanceCells_Texture_Correlation_CorrGreen_1':
0.301107,
'Zfactor_DistanceCells_Texture_Entropy_CorrGreen_1':
0.251143,
'Zfactor_DistanceCells_Texture_InfoMeas1_CorrGreen_1':
0.564957,
'Zfactor_DistanceCells_Texture_InverseDifferenceMoment_CorrGreen_1':
0.302767,
'Zfactor_DistanceCells_Texture_SumAverage_CorrGreen_1':
0.036459,
'Zfactor_DistanceCells_Texture_SumEntropy_CorrGreen_1':
0.159798,
'Zfactor_DistanceCells_Texture_SumVariance_CorrGreen_1':
0.516938,
'Zfactor_DistanceCells_Texture_Variance_CorrGreen_1':
0.501186,
'Zfactor_Nuclei_Correlation_Correlation_CorrGreenCorrBlue':
0.691408,
'Zfactor_Nuclei_Math_Ratio1':
0.623284,
'Zfactor_Nuclei_Math_Ratio2':
0.358916,
'Zfactor_Nuclei_Texture_SumAverage_CorrGreen_1':
0.587347,
'Zfactor_PropCells_AreaShape_Area':
0.132425,
'Zfactor_PropCells_AreaShape_MajorAxisLength':
0.034809,
'Zfactor_PropCells_AreaShape_MinorAxisLength':
0.113864,
'Zfactor_PropCells_AreaShape_Perimeter':
0.005984,
'Zfactor_PropCells_Correlation_Correlation_CorrGreenCorrBlue':
0.717632,
'Zfactor_PropCells_Texture_GaborX_CorrGreen_1':
0.251023,
'Zfactor_PropCells_Texture_InfoMeas2_CorrBlue_1':
0.149719,
'Zfactor_PropCells_Texture_SumVariance_CorrBlue_1':
0.102050,
'Zfactor_PropCells_Texture_SumVariance_CorrGreen_1':
0.611960,
'Zfactor_PropCells_Texture_Variance_CorrBlue_1':
0.197090,
'Zfactor_PropCells_Texture_Variance_CorrGreen_1':
0.614879,
'Zfactor_PropCytoplasm_AreaShape_Area':
0.205042,
'Zfactor_PropCytoplasm_AreaShape_MinorAxisLength':
0.072682,
'Zfactor_PropCytoplasm_AreaShape_Perimeter':
0.005984,
'Zfactor_PropCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':
0.272017,
'Zfactor_PropCytoplasm_Intensity_IntegratedIntensity_CorrGreen':
0.115327,
'Zfactor_PropCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':
0.141850,
'Zfactor_PropCytoplasm_Intensity_MedianIntensity_CorrGreen':
0.105803,
'Zfactor_PropCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':
0.107640,
'Zfactor_PropCytoplasm_Texture_Entropy_CorrGreen_1':
0.067896,
'Zfactor_PropCytoplasm_Texture_GaborX_CorrGreen_1':
0.136688,
'Zfactor_PropCytoplasm_Texture_InfoMeas2_CorrGreen_1':
0.334749,
'Zfactor_PropCytoplasm_Texture_SumEntropy_CorrGreen_1':
0.208829,
'Zfactor_ThresholdedCells_Texture_AngularSecondMoment_CorrBlue_1':
0.263467,
'Zfactor_ThresholdedCells_Texture_AngularSecondMoment_CorrGreen_1':
0.124355,
'Zfactor_ThresholdedCells_Texture_Entropy_CorrBlue_1':
0.236433,
'Zfactor_ThresholdedCells_Texture_InfoMeas2_CorrBlue_1':
0.125845,
'Zfactor_ThresholdedCells_Texture_SumAverage_CorrBlue_1':
0.449333,
'Zfactor_ThresholdedCells_Texture_SumEntropy_CorrBlue_1':
0.323243,
'Zfactor_ThresholdedCells_Texture_SumVariance_CorrBlue_1':
0.507477,
'Zfactor_ThresholdedCells_Texture_SumVariance_CorrGreen_1':
0.599000,
'Zfactor_ThresholdedCells_Texture_Variance_CorrBlue_1':
0.361424,
'Zfactor_ThresholdedCells_Texture_Variance_CorrGreen_1':
0.481393
}
temp_dir = tempfile.mkdtemp()
try:
cpprefs.set_headless()
cpprefs.set_default_output_directory(temp_dir)
print "Writing output to %s" % temp_dir
path = os.path.split(__file__)[0]
measurements = loadmat(os.path.join(path,
'calculatestatistics.mat'),
struct_as_record=True)
measurements = measurements['m']
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
m = cpmeas.Measurements()
doses = [
0, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 0, 0, 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 0, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 0, 0, 1, 2, 3,
4, 5, 6, 7, 8, 9, 10, 10, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 10,
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 10, 0, 1, 2, 3, 4, 5, 6, 7, 8,
9, 0, 10, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0
]
for i, dose in enumerate(doses):
m.add_image_measurement("Dose", dose)
for object_name in measurements.dtype.fields:
omeasurements = measurements[object_name][0, 0]
for feature_name in omeasurements.dtype.fields:
data = omeasurements[feature_name][0, 0][0, i]
m.add_measurement(object_name, feature_name, data)
if i < len(doses) - 1:
m.next_image_set()
pipeline = cpp.Pipeline()
module = C.CalculateStatistics()
module.grouping_values.value = "Dose"
module.dose_values[0].log_transform.value = False
module.dose_values[0].measurement.value = "Dose"
module.dose_values[0].wants_save_figure.value = True
module.dose_values[0].figure_name.value = "EC49_"
module.module_num = 1
pipeline.add_module(module)
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
workspace = cpw.Workspace(pipeline, module, image_set,
cpo.ObjectSet(), m, image_set_list)
module.post_run(workspace)
for feature_name in m.get_feature_names(cpmeas.EXPERIMENT):
if not expected.has_key(feature_name):
print "Missing measurement: %s" % feature_name
continue
value = m.get_experiment_measurement(feature_name)
e_value = expected[feature_name]
diff = abs(value - e_value) * 2 / abs(value + e_value)
self.assertTrue(
diff < .05, "%s: Matlab: %f, Python: %f diff: %f" %
(feature_name, e_value, value, diff))
if diff > .01:
print(
"Warning: > 1%% difference for %s: Matlab: %f, Python: %f diff: %f"
% (feature_name, e_value, value, diff))
if feature_name.startswith("EC50"):
filename = "EC49_" + feature_name[5:] + ".pdf"
self.assertTrue(
os.path.isfile(os.path.join(temp_dir, filename)))
finally:
try:
workspace.measurements.hdf5_dict.hdf5_file.close()
except:
pass
for filename in os.listdir(temp_dir):
path = os.path.join(temp_dir, filename)
os.remove(path)
os.rmdir(temp_dir)
