def showNodule(series_uid, batch_ndx=None):
ds = LunaDataset(series_uid=series_uid)
malignant_list = [i for i, x in enumerate(ds.noduleInfo_list) if x[0]]
if batch_ndx is None:
if malignant_list:
batch_ndx = malignant_list[0]
else:
print(
"Warning: no malignant samples found; using first non-malignant sample."
)
batch_ndx = 0
ct = Ct(series_uid)
ct_tensor, malignant_tensor, series_uid, center_irc = ds[batch_ndx]
ct_ary = ct_tensor[0].numpy()
fig = plt.figure(figsize=(15, 25))
group_list = [
[9, 11, 13],
[15, 16, 17],
[19, 21, 23],
]
subplot = fig.add_subplot(len(group_list) + 2, 3, 1)
subplot.set_title('index {}'.format(int(center_irc.index)))
plt.imshow(ct.ary[int(center_irc.index)], clim=clim, cmap='gray')
subplot = fig.add_subplot(len(group_list) + 2, 3, 2)
subplot.set_title('row {}'.format(int(center_irc.row)))
plt.imshow(ct.ary[:, int(center_irc.row)], clim=clim, cmap='gray')
subplot = fig.add_subplot(len(group_list) + 2, 3, 3)
subplot.set_title('col {}'.format(int(center_irc.col)))
plt.imshow(ct.ary[:, :, int(center_irc.col)], clim=clim, cmap='gray')
subplot = fig.add_subplot(len(group_list) + 2, 3, 4)
subplot.set_title('index {}'.format(int(center_irc.index)))
plt.imshow(ct_ary[ct_ary.shape[0] // 2], clim=clim, cmap='gray')
subplot = fig.add_subplot(len(group_list) + 2, 3, 5)
subplot.set_title('row {}'.format(int(center_irc.row)))
plt.imshow(ct_ary[:, ct_ary.shape[1] // 2], clim=clim, cmap='gray')
subplot = fig.add_subplot(len(group_list) + 2, 3, 6)
subplot.set_title('col {}'.format(int(center_irc.col)))
plt.imshow(ct_ary[:, :, ct_ary.shape[2] // 2], clim=clim, cmap='gray')
for row, index_list in enumerate(group_list):
for col, index in enumerate(index_list):
subplot = fig.add_subplot(
len(group_list) + 2, 3, row * 3 + col + 7)
subplot.set_title('slice {}'.format(index))
plt.imshow(ct_ary[index], clim=clim, cmap='gray')
print(series_uid, batch_ndx, bool(malignant_tensor[0]), malignant_list)
def findMalignantSamples(start_ndx=0, limit=100):
ds = LunaDataset()
malignantSample_list = []
for sample_tup in ds.noduleInfo_list:
if sample_tup[0]:
malignantSample_list.append(sample_tup)
if len(malignantSample_list) >= limit:
break
return malignantSample_list