def test_with_poly(self):
T = time.time()
ass1 = Assignment1()
mean_err = 0
d = 30
index = 0
for i in tqdm(range(100)):
a = np.random.randn(d)
f = np.poly1d(a)
ff = ass1.interpolate(f, -10, 10, 100)
xs = np.random.random(200) * 20 - 10
err = 0
for x in xs:
yy = ff(x)
y = f(x)
err += abs(y - yy)
err = err / 200
mean_err += err
index = i
mean_err = mean_err / 100
print(index)
T = time.time() - T
print(T)
print(mean_err)
def tfunc(self, function_name, f, s, to, number_of_dots, draw=False):
assignment1 = Assignment1()
interpolated = assignment1.interpolate(f, s, to, number_of_dots)
print(function_name)
xs = (np.random.random(20)) * ((to - s)) - (to - s) / 2
xs = np.concatenate((np.array([s, to]), xs))
ys = []
y2s = []
r_err = 0
for x in xs:
if (x < s):
x = s + 1
y2 = interpolated(x)
y2s.append(y2)
y = f(x)
ys.append(y)
#print(x)
#print(f"{x} {y} {y2} {abs((y - y2) / y)}")
r_err = r_err + abs((y - y2) / y)
if (draw):
#x2s = [number for number in np.linspace(s * 1.0, to * 1.0)]
#y2s = [f(number) for number in x2s]
plt.plot(xs, y2s, "bo")
plt.plot(xs, ys, "ro")
plt.show()
print(r_err / 20)
def test_with_poly_restrict(self):
ass1 = Assignment1()
a = np.random.randn(5)
f = RESTRICT_INVOCATIONS(10)(np.poly1d(a))
ff = ass1.interpolate(f, -10, 10, 10)
xs = np.random.random(20)
for x in xs:
yy = ff(x)
def process_video(video_file, output_file, max_frames=None):
a1 = Assignment1()
a1.encode_features(False)
a1.train(False)
writer = skvideo.io.FFmpegWriter(output_file)
reader = skvideo.io.FFmpegReader(video_file, inputdict={}, outputdict={})
for i, frame in enumerate(reader.nextFrame()):
if max_frames and i > max_frames:
break
print('Processing frame {:d}/{:d}'.format(i + 1, reader.inputframenum))
mosaic = a1.mosaic_fast(frame / 255)
writer.writeFrame(mosaic * 255)
def test_get_region_of_gene():
a1 = Assignment1()
assert a1.get_region_of_gene() == "chr21:43659559-43696079"
def test_calculate_average_genome_coverage_of_file():
a1 = Assignment1()
x = 47.15
assert x - 1 <= a1.get_average_genome_coverage_of_file() <= x + 1
def test_gene_symbol():
a1 = Assignment1()
assert a1.get_gene_symbol() == "RRP1B"
def test_get_number_of_properly_paired_reads_of_gene():
a1 = Assignment1()
assert a1.get_number_of_properly_paired_reads_of_gene() == 11624
def test_get_aligner_from_sam_header():
a1 = Assignment1()
assert a1.get_aligner_from_sam_header() == "novoalign"
def test_get_number_mapped_reads():
a1 = Assignment1()
assert a1.get_number_mapped_reads_of_gene() == 11821
def test_get_number_of_exons():
a1 = Assignment1()
assert a1.get_number_of_exons() == 16
plt.subplot(num_rows, num_cols, i)
plt.title(str(patch_idx))
plt.imshow(patch)
else:
plt.subplot(num_rows, num_cols, i)
# plt.title(str(patch_idx))
plt.imshow(neighbors[col])
fig = plt.gcf()
plt.show()
fname = utils.datetime_filename('output/A1_test/neighbors/grid.png')
fig.savefig(fname, format='png', dpi=300)
if __name__ == '__main__':
main = Assignment1()
main.encode_features(False)
main.train(False)
make_folders()
print('Test Grid')
test_grid()
print('\nTest Feature')
test_feature()
print('\nTest Distance')
test_distance()
print('\nTest Neighbors')
test_neighbors()