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In [83]:



    


%matplotlib inline
import pandas as pd
import numpy as np
import scipy.stats as stats
import matplotlib.pyplot as plt
import mia



    


















    






Warning: Cannot change to a different GUI toolkit: qt. Using osx instead.

Loading and Preprocessing

Loading the hologic and synthetic datasets.





In [42]:



    


hologic = pd.DataFrame.from_csv("real_intensity_lines.csv")
hologic.drop(hologic.columns[:2], axis=1, inplace=True)
hologic.drop('breast_area', axis=1, inplace=True)

phantom = pd.DataFrame.from_csv("synthetic_intensity_lines.csv")
phantom.drop(phantom.columns[:2], axis=1, inplace=True)
phantom.drop('breast_area', axis=1, inplace=True)

Loading the meta data for the real and synthetic datasets.





In [43]:



    


hologic_meta = mia.analysis.create_hologic_meta_data(hologic, "meta_data/real_meta.csv")
phantom_meta = mia.analysis.create_synthetic_meta_data(phantom, 
                                                       "meta_data/synthetic_meta.csv")
phantom_meta.index.name = 'img_name'

Prepare the BI-RADS/VBD labels for both datasets.





In [44]:



    


hologic_labels = hologic_meta.drop_duplicates().BIRADS
phantom_labels = phantom_meta['VBD.1']

class_labels = pd.concat([hologic_labels, phantom_labels])
class_labels.index.name = "img_name"
labels = mia.analysis.remove_duplicate_index(class_labels)[0]

Creating Features

Create blob features from distribution of blobs





In [45]:



    


hologic_intensity_features = hologic[hologic.columns[4:]]
hologic_intensity_features = hologic_intensity_features.groupby(hologic.index).agg(np.mean)
phantom_intensity_features = phantom[phantom.columns[4:]]
phantom_intensity_features = phantom_intensity_features.groupby(phantom.index).agg(np.mean)

Take a random subset of the real mammograms. This is important so that each patient is not over represented.





In [46]:



    


hologic_intensity_features['patient_id'] = hologic_meta.drop_duplicates()['patient_id']
hologic_intensity_features_subset = mia.analysis.create_random_subset(hologic_intensity_features, 
                                                                      'patient_id')

Take a random subset of the phantom mammograms. This is important so that each case is not over represented.





In [47]:



    


syn_feature_meta = mia.analysis.remove_duplicate_index(phantom_meta)
phantom_intensity_features['phantom_name'] = syn_feature_meta.phantom_name.tolist()
phantom_intensity_features_subset \
    = mia.analysis.create_random_subset(phantom_intensity_features, 'phantom_name')

Combine the features from both datasets.





In [48]:



    


features = pd.concat([hologic_intensity_features_subset, phantom_intensity_features_subset])
assert features.shape[0] == 96
features.head()



    


















    
Out[48]:










  
    

      
      mean
      std
      min
      25%
      50%
      75%
      max
      skew
      kurtosis
    

  
  
    

      p214-010-60001-cl.png
       0.362584
       0.099563
       0.176311
       0.290825
       0.350695
       0.425325
       0.651941
       0.554375
       0.564813
    

    

      p214-010-60005-cr.png
       0.390749
       0.115338
       0.178942
       0.308598
       0.382695
       0.464941
       0.671299
       0.285397
      -0.168101
    

    

      p214-010-60008-mr.png
       0.380682
       0.068131
       0.252233
       0.335284
       0.374149
       0.418809
       0.586883
       0.533288
       0.537177
    

    

      p214-010-60012-cr.png
       0.310309
       0.084479
       0.157582
       0.252724
       0.301992
       0.359711
       0.574846
       0.591287
       0.876965
    

    

      p214-010-60013-cl.png
       0.328995
       0.077626
       0.185815
       0.275454
       0.321237
       0.373890
       0.553304
       0.527032
       0.352804

Filter some features, such as the min, to remove noise.





In [49]:



    


selected_features = features.copy()

Compare Real and Synthetic Features

Compare the distributions of features detected from the real mammograms and the phantoms using the Kolmogorov-Smirnov two sample test.





In [50]:



    


ks_stats = [list(stats.ks_2samp(hologic_intensity_features[col], 
                                phantom_intensity_features[col]))
                                for col in selected_features.columns]

ks_test = pd.DataFrame(ks_stats, columns=['KS', 'p-value'], index=selected_features.columns)
ks_test.to_latex("tables/line_intensity_features_ks.tex")
ks_test



    


















    
Out[50]:










  
    

      
      KS
      p-value
    

  
  
    

      mean
       1.000000
       3.587622e-59
    

    

      std
       0.966667
       2.546525e-55
    

    

      min
       1.000000
       3.587622e-59
    

    

      25%
       1.000000
       3.587622e-59
    

    

      50%
       1.000000
       3.587622e-59
    

    

      75%
       1.000000
       3.587622e-59
    

    

      max
       1.000000
       3.587622e-59
    

    

      skew
       1.000000
       3.587622e-59
    

    

      kurtosis
       0.213889
       4.106586e-03

Dimensionality Reduction

t-SNE

Running t-SNE to obtain a two dimensional representation.





In [51]:



    


real_index = hologic_intensity_features_subset.index
phantom_index = phantom_intensity_features_subset.index



    











In [52]:



    


kwargs = {
    'learning_rate': 200,
    'perplexity': 20,
    'verbose': 1
}



    











In [53]:



    


SNE_mapping_2d = mia.analysis.tSNE(selected_features, n_components=2, **kwargs)



    


















    






[t-SNE] Computing pairwise distances...
[t-SNE] Computed conditional probabilities for sample 96 / 96
[t-SNE] Mean sigma: 0.714076
[t-SNE] Error after 65 iterations with early exaggeration: 12.750609
[t-SNE] Error after 130 iterations: 0.743695

















In [54]:



    


mia.plotting.plot_mapping_2d(SNE_mapping_2d, real_index, phantom_index, labels)
plt.savefig('figures/mappings/line_intensity_SNE_mapping_2d.png', dpi=300)

Running t-SNE to obtain a 3 dimensional mapping





In [55]:



    


SNE_mapping_3d = mia.analysis.tSNE(selected_features, n_components=3, **kwargs)



    


















    






[t-SNE] Computing pairwise distances...
[t-SNE] Computed conditional probabilities for sample 96 / 96
[t-SNE] Mean sigma: 0.714076
[t-SNE] Error after 100 iterations with early exaggeration: 16.315305
[t-SNE] Error after 297 iterations: 2.612050

















In [84]:



    


mia.plotting.plot_mapping_3d(SNE_mapping_3d, real_index, phantom_index, labels)



    


















    
Out[84]:








<matplotlib.axes._subplots.Axes3DSubplot at 0x115f941d0>

Isomap

Running Isomap to obtain a 2 dimensional mapping





In [57]:



    


iso_kwargs = {
    'n_neighbors': 4,
}



    











In [58]:



    


iso_mapping_2d = mia.analysis.isomap(selected_features, n_components=2, **iso_kwargs)



    











In [59]:



    


mia.plotting.plot_mapping_2d(iso_mapping_2d, real_index, phantom_index, labels)
plt.savefig('figures/mappings/line_intensity_iso_mapping_2d.png', dpi=300)



    


















    
























In [60]:



    


iso_mapping_3d = mia.analysis.isomap(selected_features, n_components=3, **iso_kwargs)



    











In [86]:



    


mia.plotting.plot_mapping_3d(iso_mapping_3d, real_index, phantom_index, labels)



    


















    
Out[86]:








<matplotlib.axes._subplots.Axes3DSubplot at 0x117134a90>

Locally Linear Embedding

Running locally linear embedding to obtain 2d mapping





In [62]:



    


lle_kwargs = {
    'n_neighbors': 4,
}



    











In [63]:



    


lle_mapping_2d = mia.analysis.lle(selected_features, n_components=2, **lle_kwargs)



    











In [64]:



    


mia.plotting.plot_mapping_2d(lle_mapping_2d, real_index, phantom_index, labels)
plt.savefig('figures/mappings/line_intensity_lle_mapping_2d.png', dpi=300)



    


















    
























In [65]:



    


lle_mapping_3d = mia.analysis.lle(selected_features, n_components=3, **lle_kwargs)



    











In [87]:



    


mia.plotting.plot_mapping_3d(lle_mapping_3d, real_index, phantom_index, labels)



    


















    
Out[87]:








<matplotlib.axes._subplots.Axes3DSubplot at 0x115c09d90>

Quality Assessment of Dimensionality Reduction

Assess the quality of the DR against measurements from the co-ranking matrices. First create co-ranking matrices for each of the dimensionality reduction mappings





In [67]:



    


max_k = 50



    











In [68]:



    


SNE_mapping_2d_cm = mia.coranking.coranking_matrix(selected_features, 
                                                   SNE_mapping_2d)
iso_mapping_2d_cm = mia.coranking.coranking_matrix(selected_features, 
                                                   iso_mapping_2d)
lle_mapping_2d_cm = mia.coranking.coranking_matrix(selected_features, 
                                                   lle_mapping_2d)

SNE_mapping_3d_cm = mia.coranking.coranking_matrix(selected_features, 
                                                   SNE_mapping_3d)
iso_mapping_3d_cm = mia.coranking.coranking_matrix(selected_features, 
                                                   iso_mapping_3d)
lle_mapping_3d_cm = mia.coranking.coranking_matrix(selected_features, 
                                                   lle_mapping_3d)

2D Mappings





In [69]:



    


SNE_trustworthiness_2d = [mia.coranking.trustworthiness(SNE_mapping_2d_cm, k) 
                          for k in range(1, max_k)]
iso_trustworthiness_2d = [mia.coranking.trustworthiness(iso_mapping_2d_cm, k) 
                          for k in range(1, max_k)]
lle_trustworthiness_2d = [mia.coranking.trustworthiness(lle_mapping_2d_cm, k) 
                          for k in range(1, max_k)]



    











In [70]:



    


trustworthiness_df = pd.DataFrame([SNE_trustworthiness_2d,
                                   iso_trustworthiness_2d,
                                   lle_trustworthiness_2d], 
                                   index=['SNE', 'Isomap', 'LLE']).T
trustworthiness_df.plot()
plt.savefig('figures/quality_measures/line_intensity_trustworthiness_2d.png', dpi=300)



    


















    
























In [71]:



    


SNE_continuity_2d = [mia.coranking.continuity(SNE_mapping_2d_cm, k) 
                     for k in range(1, max_k)]
iso_continuity_2d = [mia.coranking.continuity(iso_mapping_2d_cm, k) 
                     for k in range(1, max_k)]
lle_continuity_2d = [mia.coranking.continuity(lle_mapping_2d_cm, k) 
                     for k in range(1, max_k)]



    











In [72]:



    


continuity_df = pd.DataFrame([SNE_continuity_2d,
                              iso_continuity_2d,
                              lle_continuity_2d], 
                              index=['SNE', 'Isomap', 'LLE']).T
continuity_df.plot()
plt.savefig('figures/quality_measures/line_intensity_continuity_2d.png', dpi=300)



    


















    
























In [73]:



    


SNE_lcmc_2d = [mia.coranking.LCMC(SNE_mapping_2d_cm, k) 
               for k in range(2, max_k)]
iso_lcmc_2d = [mia.coranking.LCMC(iso_mapping_2d_cm, k) 
               for k in range(2, max_k)]
lle_lcmc_2d = [mia.coranking.LCMC(lle_mapping_2d_cm, k) 
               for k in range(2, max_k)]



    











In [74]:



    


lcmc_df = pd.DataFrame([SNE_lcmc_2d,
                        iso_lcmc_2d,
                        lle_lcmc_2d], 
                        index=['SNE', 'Isomap', 'LLE']).T
lcmc_df.plot()
plt.savefig('figures/quality_measures/line_intensity_lcmc_2d.png', dpi=300)

3D Mappings





In [75]:



    


SNE_trustworthiness_3d = [mia.coranking.trustworthiness(SNE_mapping_3d_cm, k) 
                          for k in range(1, max_k)]
iso_trustworthiness_3d = [mia.coranking.trustworthiness(iso_mapping_3d_cm, k) 
                          for k in range(1, max_k)]
lle_trustworthiness_3d = [mia.coranking.trustworthiness(lle_mapping_3d_cm, k) 
                          for k in range(1, max_k)]



    











In [76]:



    


trustworthiness3d_df = pd.DataFrame([SNE_trustworthiness_3d,
                                   iso_trustworthiness_3d,
                                   lle_trustworthiness_3d], 
                                   index=['SNE', 'Isomap', 'LLE']).T
trustworthiness3d_df.plot()
plt.savefig('figures/quality_measures/line_intensity_trustworthiness_3d.png', dpi=300)



    


















    
























In [77]:



    


SNE_continuity_3d = [mia.coranking.continuity(SNE_mapping_3d_cm, k) 
                     for k in range(1, max_k)]
iso_continuity_3d = [mia.coranking.continuity(iso_mapping_3d_cm, k) 
                     for k in range(1, max_k)]
lle_continuity_3d = [mia.coranking.continuity(lle_mapping_3d_cm, k) 
                     for k in range(1, max_k)]



    











In [78]:



    


continuity3d_df = pd.DataFrame([SNE_continuity_3d,
                              iso_continuity_3d,
                              lle_continuity_3d], 
                              index=['SNE', 'Isomap', 'LLE']).T
continuity3d_df.plot()
plt.savefig('figures/quality_measures/line_intensity_continuity_3d.png', dpi=300)



    


















    
























In [79]:



    


SNE_lcmc_3d = [mia.coranking.LCMC(SNE_mapping_3d_cm, k) 
               for k in range(2, max_k)]
iso_lcmc_3d = [mia.coranking.LCMC(iso_mapping_3d_cm, k) 
               for k in range(2, max_k)]
lle_lcmc_3d = [mia.coranking.LCMC(lle_mapping_3d_cm, k) 
               for k in range(2, max_k)]



    











In [80]:



    


lcmc3d_df = pd.DataFrame([SNE_lcmc_3d,
                        iso_lcmc_3d,
                        lle_lcmc_3d], 
                        index=['SNE', 'Isomap', 'LLE']).T
lcmc3d_df.plot()
plt.savefig('figures/quality_measures/line_intensity_lcmc_3d.png', dpi=300)

Content source: samueljackson92/major-project

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