Exemple #1
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def malis_f1_score(gt_lbl, pred_lbl):
    if (np.max(gt_lbl) == 0):
        gt_lbl += 1
    ret = rand_index(gt_lbl, pred_lbl)[1]
    ret = float(ret)
    return ret
Exemple #2
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def malis_rand_index(gt_lbl, pred_lbl):
    ret = rand_index(gt_lbl, pred_lbl)[0]
    ret = float(ret)
    return ret
Exemple #3
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#hdf5_raw_file = 'zebrafish_friedrich/raw.hdf5'
#hdf5_gt_file = 'zebrafish_friedrich/labels_2.hdf5'

# hdf5_raw = h5py.File(hdf5_raw_file, 'r')
h5seg = h5py.File(hdf5_gt_file, 'r')
# hdf5_aff = h5py.File(hdf5_aff_file, 'r')

seg = np.asarray(h5seg['main']).astype(np.int32)
aff = m.seg_to_affgraph(seg, nhood)
cc, ccSizes = m.connected_components_affgraph(aff, nhood)
aff2 = m.seg_to_affgraph(cc, nhood)
cc2, ccSizes2 = m.connected_components_affgraph(aff2, nhood)

print "Comparing 'seg' and 'cc':"
frac_disagree = np.mean(seg.ravel() != cc.ravel())
ri, fscore, prec, rec = m.rand_index(seg, cc)
V_rand, V_rand_split, V_rand_merge = m.compute_V_rand_N2(seg, cc)
print "Connected components disagree at %f%% locations" % (frac_disagree * 100)
print "\tRand index: %f, fscore: %f, prec: %f, rec: %f" % (ri, fscore, prec,
                                                           rec)
print "\tV_rand: %f, V_rand_split: %f, V_rand_merge: %f" % (
    V_rand, V_rand_split, V_rand_merge)

print "Comparing 'cc' and 'cc2':"
frac_disagree = np.mean(cc.ravel() != cc2.ravel())
ri, fscore, prec, rec = m.rand_index(cc, cc2)
V_rand, V_rand_split, V_rand_merge = m.compute_V_rand_N2(cc, cc2)
print "Connected components disagree at %f%% locations" % (frac_disagree * 100)
print "\tRand index: %f, fscore: %f, prec: %f, rec: %f" % (ri, fscore, prec,
                                                           rec)
print "\tV_rand: %f, V_rand_split: %f, V_rand_merge: %f" % (
Exemple #4
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def malis_f1_score (gt_lbl, pred_lbl):
    ret = rand_index (gt_lbl, pred_lbl) [1]
    ret = float (ret)
    return ret
#hdf5_raw_file = 'zebrafish_friedrich/raw.hdf5'
#hdf5_gt_file = 'zebrafish_friedrich/labels_2.hdf5'


# hdf5_raw = h5py.File(hdf5_raw_file, 'r')
h5seg = h5py.File(hdf5_gt_file, 'r')
# hdf5_aff = h5py.File(hdf5_aff_file, 'r')

seg = np.asarray(h5seg['main']).astype(np.int32)
aff = m.seg_to_affgraph(seg,nhood)
cc,ccSizes = m.connected_components_affgraph(aff,nhood)
aff2 = m.seg_to_affgraph(cc,nhood)
cc2,ccSizes2 = m.connected_components_affgraph(aff2,nhood)

print "Comparing 'seg' and 'cc':"
frac_disagree = np.mean(seg.ravel()!=cc.ravel())
ri,fscore,prec,rec = m.rand_index(seg,cc)
V_rand,V_rand_split,V_rand_merge = m.compute_V_rand_N2(seg,cc)
print "Connected components disagree at %f%% locations" % (frac_disagree*100)
print "\tRand index: %f, fscore: %f, prec: %f, rec: %f" % (ri,fscore,prec,rec)
print "\tV_rand: %f, V_rand_split: %f, V_rand_merge: %f" % (V_rand,V_rand_split,V_rand_merge)

print "Comparing 'cc' and 'cc2':"
frac_disagree = np.mean(cc.ravel()!=cc2.ravel())
ri,fscore,prec,rec = m.rand_index(cc,cc2)
V_rand,V_rand_split,V_rand_merge = m.compute_V_rand_N2(cc,cc2)
print "Connected components disagree at %f%% locations" % (frac_disagree*100)
print "\tRand index: %f, fscore: %f, prec: %f, rec: %f" % (ri,fscore,prec,rec)
print "\tV_rand: %f, V_rand_split: %f, V_rand_merge: %f" % (V_rand,V_rand_split,V_rand_merge)