def generate(self):
while True:
rand_idxs = np.arange(len(self.oc_gt_paths))
if self.random:
self.rng.shuffle(rand_idxs)
for pos in xrange(0, len(rand_idxs), self.batch_size):
idxs_batch = rand_idxs[pos:pos + self.batch_size]
nb = len(idxs_batch)
# allocate batches
x_batch = np.zeros((nb,) + self.p_transform['patch_size'], dtype='float32')
y_batch = np.zeros((nb,) + self.p_transform['patch_size'], dtype='float32')
z_batch = np.zeros((nb,) + self.p_transform['patch_size'], dtype='float32')
batch_ids = []
for i, idx in enumerate(idxs_batch):
oc_gt_path = self.oc_gt_paths[idx]
cid = contour.get_contour_id(oc_gt_path)
did = contour.get_dicom_id(oc_gt_path)
sid = str(contour.get_slice_id(oc_gt_path))
ic_gt_path = contour.get_icontour_path(oc_gt_path)
sample_id = cid + '_' + did + '_' + sid
batch_ids.append(sample_id)
try:
x, pixel_spacing = scan.read_dicom_slice(did, sid)
except Exception:
print 'cannot open dicom, dicom id: ', did, ', slice id:', sid
try:
ic_contour_lst = contour.parse_contour_file(ic_gt_path)
except Exception:
print 'cannot open i-contour', ic_gt_path
try:
oc_contour_lst = contour.parse_contour_file(oc_gt_path)
except Exception:
print 'cannot open o-contour', oc_gt_path
y = contour.poly_to_mask(ic_contour_lst,x.shape[0],x.shape[1])
z = contour.poly_to_mask(oc_contour_lst,x.shape[0],x.shape[1])
x_batch[i] = self.data_prep_fun(x, pixel_spacing)
y_batch[i] = self.mask_prep_fun(y)
z_batch[i] = self.mask_prep_fun(z)
if self.full_batch:
if nb == self.batch_size:
yield x_batch, y_batch, z_batch, batch_ids
else:
yield x_batch, y_batch, z_batch, batch_ids
if not self.infinite:
break
def generate_polygon_mask_plot(icp):
did = contour.get_dicom_id(icp)
sid = contour.get_slice_id(icp)
c_lst = contour.parse_contour_file(icp)
mask = contour.poly_to_mask(c_lst,256,256)
outfile = 'plots/pm_'+contour.get_contour_id(icp)+'_' \
+did+'_' \
+str(sid)+'.jpg'
print 'plotting polygones and masks to file', outfile
utils_plots.plot_polygone_on_mask(c_lst, mask, outfile, resolution=100)
def generate_ocontours_icontours_border_plots(lst_ocontours, pixel_spacing_normalization=False):
for idx, ocp in enumerate(lst_ocontours):
icp = contour.get_icontour_path(ocp)
did = contour.get_dicom_id(ocp)
sid = contour.get_slice_id(ocp)
slice, pixel_spacing = scan.read_dicom_slice(did, sid)
oc_lst = contour.parse_contour_file(ocp)
ic_lst = contour.parse_contour_file(icp)
outfile = 'plots/'+contour.get_contour_id(ocp)+'_' \
+did+'_' \
+str(sid)+'.jpg'
print pixel_spacing, 'plotting mask to file', outfile
if pixel_spacing_normalization:
assert pixel_spacing[0]==pixel_spacing[1]
slice = scipy.ndimage.zoom(slice, pixel_spacing[0], order=0)
masko = contour.poly_to_mask(oc_lst,slice.shape[0],slice.shape[1])
maski = contour.poly_to_mask(ic_lst,slice.shape[0],slice.shape[1])
utils_plots.plot_borders_on_slice(slice, masko, maski, outfile, figsize=(20, 20))#, x_bs=[75,175], y_bs=[75,175])
def generate_polygon_mask_plots():
for idx, icp in enumerate(contour.get_list_available_icontours()):
did = contour.get_dicom_id(icp)
sid = contour.get_slice_id(icp)
c_lst = contour.parse_contour_file(icp)
mask = contour.poly_to_mask(c_lst,256,256)
outfile = 'plots/bp_oc_ic_'+contour.get_contour_id(icp)+'_' \
+did+'_' \
+str(sid)+'.jpg'
print 'plotting polygones and masks to file', outfile
utils_plots.plot_polygone_on_mask(c_lst, mask, outfile)
def generate_masked_scan_plots(lst_ocontours):
for idx, ocp in enumerate(lst_ocontours):
did = contour.get_dicom_id(ocp)
sid = contour.get_slice_id(ocp)
slice, pixel_spacing = scan.read_dicom_slice(did, sid)
oc_lst = contour.parse_contour_file(ocp)
outfile = 'plots/masked_scan_'+contour.get_contour_id(ocp)+'_' \
+did+'_' \
+str(sid)+'.jpg'
print pixel_spacing, 'plotting masked slice to file', outfile
mask = contour.poly_to_mask(oc_lst,slice.shape[0],slice.shape[1])
masked_slice = mask*slice
utils_plots.plot_slice(masked_slice, outfile, figsize=(20, 20), x_bs=[75,175], y_bs=[75,175])
def generate_histograms_masked_scan(lst_ocontours):
for idx, ocp in enumerate(lst_ocontours):
did = contour.get_dicom_id(ocp)
sid = contour.get_slice_id(ocp)
slice, pixel_spacing = scan.read_dicom_slice(did, sid)
oc_lst = contour.parse_contour_file(ocp)
outfile = 'plots/hist_masked_sc_'+contour.get_contour_id(ocp)+'_' \
+did+'_' \
+str(sid)+'.jpg'
print pixel_spacing, 'plotting masked slice to file', outfile
mask = contour.poly_to_mask(oc_lst,slice.shape[0],slice.shape[1])
masked_slice = mask*slice
print np.amin(masked_slice), np.amax(masked_slice)
bins = np.arange(0,550,10)
hist,bins = np.histogram(masked_slice, bins=bins)
print hist
th_mslice = masked_slice > 150
utils_plots.plot_slice_hist(masked_slice, th_mslice, bins[1:], outfile, figsize=(10, 5), x_bs=[75,175], y_bs=[75,175])