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- import matplotlib
- matplotlib.use('nbagg')
- import numpy as np
- import matplotlib.pyplot as plt
- from p2ch12.dsets import Ct, LunaDataset
- clim=(0.0, 1.3)
- def findMalignantSamples(start_ndx=0, limit=10):
- ds = LunaDataset()
- malignantSample_list = []
- for sample_tup in ds.sample_list:
- if sample_tup[2]:
- print(len(malignantSample_list), sample_tup)
- malignantSample_list.append(sample_tup)
- if len(malignantSample_list) >= limit:
- break
- return malignantSample_list
- def showNodule(series_uid, batch_ndx=None, **kwargs):
- ds = LunaDataset(series_uid=series_uid, **kwargs)
- malignant_list = [i for i, x in enumerate(ds.sample_list) if x[2]]
- 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]
- malignant_tensor, diameter_mm, series_uid, center_irc, nodule_tensor = ds[batch_ndx]
- ct_ary = nodule_tensor[1].numpy()
- fig = plt.figure(figsize=(15, 25))
- group_list = [
- #[0,1,2],
- [9,11,13],
- [15, 16, 17],
- [19,21,23],
- #[12,13,14],
- #[15]
- ]
- 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*2], clim=clim, cmap='gray')
- print(series_uid, batch_ndx, bool(malignant_tensor[0]), malignant_list, ct.vxSize_xyz)
- return ct_ary
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