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a small python script which generates some test data in which I want to run pairwise comparisons on. There is an unresolved error that comes up when running the `get_hd()` function
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import numpy as np | |
import tables as tb | |
class Iris(tb.IsDescription): | |
subject_id = tb.IntCol() | |
iris_id = tb.IntCol() | |
database = tb.StringCol(5) | |
is_left = tb.BoolCol() | |
is_flipped = tb.BoolCol() | |
templates = tb.BoolCol(shape=(17, 20*480)) | |
masks1 = tb.BoolCol(shape=(17, 20*480)) | |
phasors = tb.ComplexCol(itemsize=8, shape=(17, 20*240)) | |
masks2 = tb.BoolCol(shape=(17, 20*240)) | |
def create_hdf5(): | |
""" | |
""" | |
with tb.openFile('test.h5', 'w') as f: | |
# Create and fill the table of irises | |
irises = f.createTable(f.root, 'irises', Iris, 'Irises', filters=tb.Filters(1)) | |
for ii in range(4620): | |
r = irises.row | |
r['subject_id'] = ii | |
r['iris_id'] = 0 | |
r['database'] = 'test' | |
r['is_left'] = True | |
r['is_flipped'] = False | |
r['templates'] = np.empty((17, 20*480), np.bool8) | |
r['masks1'] = np.empty((17, 20*480), np.bool8) | |
r['phasors'] = np.empty((17, 20*240), np.complex) | |
r['masks2'] = np.empty((17, 20*240), np.bool8) | |
r.append() | |
irises.flush() | |
def get_hd(): | |
""" | |
""" | |
from itertools import combinations, izip | |
with tb.openFile('test.h5') as f: | |
irises = f.root.irises | |
templates = f.root.irises.cols.templates | |
masks = f.root.irises.cols.masks1 | |
N_irises = len(irises) | |
print '%i Comparisons' % (N_irises*(N_irises - 1)/2) | |
D = np.empty((N_irises, N_irises)) | |
for (t1, m1, ii), (t2, m2, jj) in combinations(izip(templates, masks, range(N_irises)), 2): | |
D[ii, jj] = ii*jj | |
np.save('test', D) |
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