def read_from_dir(data_dir, phasename='PV'):
mhd_path = glob(os.path.join(data_dir, phasename + '_Image*.mhd'))[0]
mhd_image = read_mhd_image(mhd_path)
mask_path = os.path.join(data_dir, phasename + '_Registration.mhd')
mask_image = read_mhd_image(mask_path)
mhd_image = np.squeeze(mhd_image)
mask_image = np.squeeze(mask_image)
return mask_image, mhd_image
def load_patch(patch_path, return_roi=False, parent_dir=None):
if not return_roi:
if patch_path.endswith('.jpg'):
return Image.open(patch_path)
if patch_path.endswith('.npy'):
return np.load(patch_path)
else:
phasenames = ['NC', 'ART', 'PV']
if patch_path.endswith('.jpg'):
basename = os.path.basename(patch_path)
basename = basename[: basename.rfind('_')]
mask_images = []
mhd_images = []
for phasename in phasenames:
image_path = glob(os.path.join(parent_dir, basename, phasename + '_Image*.mhd'))[0]
mask_path = os.path.join(parent_dir, basename, phasename + '_Registration.mhd')
mhd_image = read_mhd_image(image_path, rejust=True)
mhd_image = np.squeeze(mhd_image)
# show_image(mhd_image)
mask_image = read_mhd_image(mask_path)
mask_image = np.squeeze(mask_image)
[xmin, xmax, ymin, ymax] = get_boundingbox(mask_image)
# xmin -= 15
# xmax += 15
# ymin -= 15
# ymax += 15
mask_image = mask_image[xmin: xmax, ymin: ymax]
mhd_image = mhd_image[xmin: xmax, ymin: ymax]
mhd_image[mask_image != 1] = 0
mask_images.append(mask_image)
mhd_images.append(mhd_image)
mhd_images = convert2depthlaster(mhd_images)
return mhd_images
if patch_path.endswith('.npy'):
basename = os.path.basename(patch_path)
basename = basename[: basename.rfind('_')]
mask_images = []
mhd_images = []
for phasename in phasenames:
image_path = glob(os.path.join(parent_dir, basename, phasename + '_Image*.mhd'))[0]
mask_path = os.path.join(parent_dir, basename, phasename + '_Registration.mhd')
mhd_image = read_mhd_image(image_path, rejust=False) # 因为存储的是ｎｐｙ格式，所以不进行窗宽窗位的调整
mhd_image = np.squeeze(mhd_image)
# show_image(mhd_image)
mask_image = read_mhd_image(mask_path)
mask_image = np.squeeze(mask_image)
[xmin, xmax, ymin, ymax] = get_boundingbox(mask_image)
# xmin -= 15
# xmax += 15
# ymin -= 15
# ymax += 15
mask_image = mask_image[xmin: xmax, ymin: ymax]
mhd_image = mhd_image[xmin: xmax, ymin: ymax]
mhd_image[mask_image != 1] = 0
mask_images.append(mask_image)
mhd_images.append(mhd_image)
mhd_images = convert2depthlaster(mhd_images)
return mhd_images
def extract_patch_npy(dir_name, suffix_name, save_dir, patch_size, patch_step=1):
'''
提取指定类型病灶的ｐａｔｃｈ 保存原始像素值，存成ｎｐｙ的格式
:param patch_size: 提取ｐａｔｃｈ的大小
:param dir_name: 目前所有病例的存储路径
:param suffix_name: 指定的病灶类型的后缀，比如说cyst 就是０
:param save_dir: 提取得到的ｐａｔｃｈ的存储路径
:param patch_step: 提取ｐａｔｃｈ的步长
:return: None
'''
count = 0
names = os.listdir(dir_name)
for name in names:
if name.endswith(suffix_name):
# 只提取指定类型病灶的ｐａｔｃｈ
mask_images = []
mhd_images = []
for phasename in phasenames:
image_path = glob(os.path.join(dir_name, name, phasename + '_Image*.mhd'))[0]
mask_path = os.path.join(dir_name, name, phasename + '_Registration.mhd')
mhd_image = read_mhd_image(image_path)
mhd_image = np.squeeze(mhd_image)
# show_image(mhd_image)
mask_image = read_mhd_image(mask_path)
mask_image = np.squeeze(mask_image)
[xmin, xmax, ymin, ymax] = get_boundingbox(mask_image)
mask_image = mask_image[xmin: xmax, ymin: ymax]
mhd_image = mhd_image[xmin: xmax, ymin: ymax]
mhd_image[mask_image != 1] = 0
mask_images.append(mask_image)
mhd_images.append(mhd_image)
# show_image(mhd_image)
mask_images = convert2depthlaster(mask_images)
mhd_images = convert2depthlaster(mhd_images)
count += 1
[width, height, depth] = list(np.shape(mhd_images))
patch_count = 1
if width * height >= 900:
patch_step = int(math.sqrt(width * height / 160))
for i in range(patch_size / 2, width - patch_size / 2, patch_step):
for j in range(patch_size / 2, height - patch_size / 2, patch_step):
cur_patch = mhd_images[i - patch_size / 2:i + patch_size / 2,
j - patch_size / 2: j + patch_size / 2, :]
if (np.sum(mask_images[i - patch_size / 2:i + patch_size / 2,
j - patch_size / 2: j + patch_size / 2, :]) / (
(patch_size - 1) * (patch_size - 1) * 3)) < 0.9:
continue
save_path = os.path.join(save_dir, name + '_' + str(patch_count) + '.npy')
# print save_path
np.save(save_path, np.array(cur_patch))
patch_count += 1
if patch_count == 1:
continue
# save_path = os.path.join(save_dir, name + '_' + str(patch_count) + '.png')
# roi_image = Image.fromarray(np.asarray(mhd_images, np.uint8))
# roi_image.save(save_path)
print count
def extract_liver_density(dir_name, suffix_name, save_dir, subclass, type):
'''
提取肝脏的平均密度
:param dir_name: 目前所有病例的存储路径
:param suffix_name: 指定的病灶类型的后缀，比如说cyst 就是０
:param save_dir: 提取得到的ｐａｔｃｈ的存储路径
:return: None
'''
count = 0
names = os.listdir(dir_name)
liver_density_dict = {}
for name in names:
if name.endswith(suffix_name):
# 只提取指定类型病灶的ｐａｔｃｈ
liver_density = []
for phasename in phasenames:
image_path = glob(
os.path.join(dir_name, name,
phasename + '_Image*.mhd'))[0]
liver_mask_path = glob(
os.path.join(dir_name, name,
phasename + '*Liver*.mhd'))[0]
mask_path = os.path.join(dir_name, name,
phasename + '_Registration.mhd')
mhd_image = read_mhd_image(image_path, rejust=False)
mhd_image = np.squeeze(mhd_image)
# show_image(mhd_image)
mask_image = read_mhd_image(mask_path)
mask_image = np.squeeze(mask_image)
liver_mask_image = read_mhd_image(liver_mask_path)
liver_mask_image = np.squeeze(liver_mask_image)
# 计算肝脏的平均密度
value_sum = np.sum(mhd_image[liver_mask_image != 0])
pixel_num = np.sum(liver_mask_image != 0)
average_value = (1.0 * value_sum) / (1.0 * pixel_num)
liver_density.append(average_value)
print name, liver_density
liver_density_dict[name] = liver_density
scio.savemat(
os.path.join(
save_dir, 'raw_liver_density_' + str(subclass) + '_' +
str(type) + '.mat'), liver_density_dict)
return liver_density_dict
def load_ROI(dir_name):
phasenames = ['NC', 'ART', 'PV']
mask_images = []
mhd_images = []
for phasename in phasenames:
image_path = glob(os.path.join(dir_name, phasename + '_Image*.mhd'))[0]
mask_path = os.path.join(dir_name, phasename + '_Registration.mhd')
mhd_image = read_mhd_image(image_path, rejust=True)
mhd_image = np.squeeze(mhd_image)
# show_image(mhd_image)
mask_image = read_mhd_image(mask_path)
mask_image = np.squeeze(mask_image)
[xmin, xmax, ymin, ymax] = get_boundingbox(mask_image)
# xmin -= 15
# xmax += 15
# ymin -= 15
# ymax += 15
mask_image = mask_image[xmin:xmax, ymin:ymax]
mhd_image = mhd_image[xmin:xmax, ymin:ymax]
mhd_image[mask_image != 1] = 0
mask_images.append(mask_image)
mhd_images.append(mhd_image)
mhd_images = convert2depthlaster(mhd_images)
return mhd_images
def extract_patch_npy_for_JI(dir_name, suffix_name, save_path, patch_size, patch_step=1, erode_size=1):
'''
提取指定类型病灶的ｐａｔｃｈ 保存原始像素值，存成ｎｐｙ的格式
:param patch_size: 提取ｐａｔｃｈ的大小
:param dir_name: 目前所有病例的存储路径
:param suffix_name: 指定的病灶类型的后缀，比如说cyst 就是０
:param save_path: 提取得到的ｐａｔｃｈ的存储路径
:param patch_step: 提取ｐａｔｃｈ的步长
:param erode_size: 向内缩的距离，因为我们需要确定内部区域,所以为了得到内部区域，我们就将原区域向内缩以得到内部区域
:return: None
'''
count = 0
names = os.listdir(dir_name)
patches = []
for name in names:
if name.endswith(suffix_name):
# 只提取指定类型病灶的ｐａｔｃｈ
mask_images = []
mhd_images = []
flag = True
for phasename in phasenames:
image_path = glob(os.path.join(dir_name, name, phasename + '_Image*.mhd'))[0]
mask_path = os.path.join(dir_name, name, phasename + '_Registration.mhd')
mhd_image = read_mhd_image(image_path)
mhd_image = np.squeeze(mhd_image)
# show_image(mhd_image)
mask_image = read_mhd_image(mask_path)
mask_image = np.squeeze(mask_image)
[xmin, xmax, ymin, ymax] = get_boundingbox(mask_image)
if (xmax - xmin) <= erode_size or (ymax - ymin) <= erode_size:
flag = False
continue
mask_image = image_erode(mask_image, erode_size)
[xmin, xmax, ymin, ymax] = get_boundingbox(mask_image)
mask_image = mask_image[xmin: xmax, ymin: ymax]
mhd_image = mhd_image[xmin: xmax, ymin: ymax]
# mhd_image[mask_image != 1] = 0
mask_images.append(mask_image)
mhd_images.append(mhd_image)
# show_image(mhd_image)
if not flag:
continue
mask_images = convert2depthlaster(mask_images)
mhd_images = convert2depthlaster(mhd_images)
count += 1
[width, height, depth] = list(np.shape(mhd_images))
patch_count = 1
# if width * height >= 900:
# patch_step = int(math.sqrt(width * height / 100))
for i in range(patch_size / 2, width - patch_size / 2, patch_step):
for j in range(patch_size / 2, height - patch_size / 2, patch_step):
cur_patch = mhd_images[i - patch_size / 2:i + patch_size / 2 + 1,
j - patch_size / 2: j + patch_size / 2 + 1, :]
if (np.sum(mask_images[i - patch_size / 2:i + patch_size / 2,
j - patch_size / 2: j + patch_size / 2, :]) / (
(patch_size - 1) * (patch_size - 1) * 3)) < 0.5:
continue
# save_path = os.path.join(save_dir, name + '_' + str(patch_count) + '.npy')
# print save_path
# np.save(save_path, np.array(cur_patch))
cur_patch = np.reshape(cur_patch, [patch_size*patch_size*3])
patches.append(cur_patch)
patch_count += 1
if patch_count == 1:
continue
print np.shape(patches)
patches = np.concatenate([patches, np.expand_dims([int(suffix_name)] * len(patches), axis=1)], axis=1)
print np.shape(patches)
np.save(save_path, patches)
print count
def extract_patches_multifiles(data_dir, names, target_label, patch_size, patch_step, save_dir):
patches = []
labeles = []
coding_labeles = []
for name in names:
if name is not None and not name.endswith(target_label):
continue
cur_data_dir = os.path.join(data_dir, name)
patches_save_path = os.path.join(cur_data_dir, 'patches.npy')
coding_labeles_path = os.path.join(cur_data_dir, 'coding_labeles.npy')
labeles_path = os.path.join(cur_data_dir, 'labeles.npy')
mask_images = []
mhd_images = []
if not os.path.exists(patches_save_path):
for phasename in ['NC', 'ART', 'PV']:
image_path = glob(os.path.join(data_dir, name, phasename + '_Image*.mhd'))[0]
mask_path = os.path.join(data_dir, name, phasename + '_Registration.mhd')
mhd_image = read_mhd_image(image_path, rejust=True)
mhd_image = np.squeeze(mhd_image)
# show_image(mhd_image)
mask_image = read_mhd_image(mask_path)
mask_image = np.squeeze(mask_image)
[xmin, xmax, ymin, ymax] = get_boundingbox(mask_image)
mask_image = mask_image[xmin: xmax, ymin: ymax]
mhd_image = mhd_image[xmin: xmax, ymin: ymax]
mhd_image[mask_image != 1] = 0
mask_images.append(mask_image)
mhd_images.append(mhd_image)
# show_image(mhd_image)
cur_patches = []
cur_coding_labeles = []
mask_images = convert2depthlaster(mask_images)
coding_image = convert_coding(cur_data_dir)
mhd_images = convert2depthlaster(mhd_images)
[width, height, _] = list(np.shape(mhd_images))
print 'extract patches from ', cur_data_dir, ' at ', str(
os.getpid()), ' corresponding size is [', width, height, ']'
for i in range(patch_size / 2, width - patch_size / 2, patch_step):
for j in range(patch_size / 2, height - patch_size / 2, patch_step):
cur_patch = mhd_images[i - patch_size / 2:i + patch_size / 2 + 1, j - patch_size / 2: j + patch_size / 2 + 1, :]
cur_label = target_label
cur_coding_label = coding_image[i, j]
if save_dir is not None:
save_path_dir = os.path.join(save_dir, str(cur_coding_label), str(cur_label))
if os.path.exists(save_path_dir):
cur_id = len(os.listdir(save_path_dir))
else:
cur_id = 0
save_path = os.path.join(save_dir, str(cur_coding_label), str(cur_label), str(cur_id) + '.npy')
check_save_path(save_path)
np.save(save_path, cur_patch)
else:
cur_patches.append(flatten_multiphase(np.array(cur_patch)))
cur_coding_labeles.append(cur_coding_label)
if save_dir is None:
if len(cur_patches) == 0:
continue
patches.append(cur_patches)
coding_labeles.append(cur_coding_labeles)
labeles.append(int(target_label))
np.save(patches_save_path, cur_patches)
np.save(coding_labeles_path, cur_coding_labeles)
else:
cur_patches = np.load(patches_save_path)
cur_coding_labeles = np.load(coding_labeles_path)
coding_labeles.append(cur_coding_labeles)
patches.append(cur_patches)
labeles.append(int(target_label))
print len(patches), len(coding_labeles), len(labeles)
return patches, coding_labeles, labeles
def extract_patch(dir_name, suffix_name, patch_size, patch_step=1):
'''
提取指定类型病灶的ｐａｔｃｈ
:param patch_size: 提取ｐａｔｃｈ的大小
:param dir_name: 目前所有病例的存储路径
:param suffix_name: 指定的病灶类型的后缀，比如说cyst 就是０
:param patch_step: 提取ｐａｔｃｈ的步长
:return: patch_arr (图像的个数, patch的个数)
'''
count = 0
names = os.listdir(dir_name)
patches_arr = []
paths = []
return_mhd_images = []
for name in names:
if name.endswith(suffix_name):
# 只提取指定类型病灶的ｐａｔｃｈ
mask_images = []
mhd_images = []
paths.append(os.path.join(dir_name, name))
for phasename in phasenames:
image_path = glob(
os.path.join(dir_name, name, phasename + '_Image*.mhd'))[0]
mask_path = os.path.join(dir_name, name,
phasename + '_Registration.mhd')
mhd_image = read_mhd_image(image_path, rejust=mhd_adjust)
mhd_image = np.squeeze(mhd_image)
# show_image(mhd_image)
mask_image = read_mhd_image(mask_path)
mask_image = np.squeeze(mask_image)
[xmin, xmax, ymin, ymax] = get_boundingbox(mask_image)
# xmin -= 15
# xmax += 15
# ymin -= 15
# ymax += 15
mask_image = mask_image[xmin:xmax, ymin:ymax]
mhd_image = mhd_image[xmin:xmax, ymin:ymax]
mhd_image[mask_image != 1] = 0
mask_images.append(mask_image)
mhd_images.append(mhd_image)
# show_image(mhd_image)
mask_images = convert2depthlaster(mask_images)
mhd_images = convert2depthlaster(mhd_images)
return_mhd_images.append(mhd_images)
# show_image(mhd_images)
count += 1
[width, height, depth] = list(np.shape(mhd_images))
patch_count = 1
# if width * height >= 400:
# patch_step = int(math.sqrt(width * height / 100))
patches = []
for i in range(patch_size / 2, width - patch_size / 2, patch_step):
for j in range(patch_size / 2, height - patch_size / 2,
patch_step):
cur_patch = mhd_images[i - patch_size / 2:i +
patch_size / 2,
j - patch_size / 2:j +
patch_size / 2, :]
if (np.sum(mask_images[i - patch_size / 2:i + patch_size /
2, j - patch_size / 2:j +
patch_size / 2, :]) /
((patch_size - 1) * (patch_size - 1) * 3)) < 0.9:
continue
patches.append(cur_patch)
patches_arr.append(patches)
if patch_count == 1:
continue
print len(patches_arr)
return patches_arr, paths, return_mhd_images
def generate_heatmap_version2(data_path, pointed_phase_index, patch_size,
save_path):
'''
生成label map，生成的label map严格按照ROI的边界来生成
:param data_path:
:param pointed_phase_index:
:param patch_size:
:param save_path:
:return:
'''
start_time = time.time()
mhd_images = []
mask_images = []
for phase_name in ['NC', 'ART', 'PV']:
image_path = glob(os.path.join(data_path,
phase_name + '_Image*.mhd'))[0]
mask_path = os.path.join(data_path, phase_name + '_Registration.mhd')
mhd_image = read_mhd_image(image_path)
mask_image = read_mhd_image(mask_path)
mhd_image = np.squeeze(mhd_image)
mask_image = np.squeeze(mask_image)
mhd_images.append(mhd_image)
mask_images.append(mask_image)
mask_images = convert2depthlaster(mask_images)
mhd_images = convert2depthlaster(mhd_images)
print np.shape(mask_images)
new_mask_image = np.zeros([512, 512], np.uint8)
[xmin, xmax, ymin,
ymax] = get_boundingbox(mask_images[:, :, pointed_phase_index])
roi_image = mask_images[xmin:xmax, ymin:ymax, :]
patches = []
for i in range(xmin, xmax):
for j in range(ymin, ymax):
if mask_images[i, j, pointed_phase_index] == 0:
continue
cur_patch = mhd_images[i - patch_size / 2:i + patch_size / 2,
j - patch_size / 2:j + patch_size / 2, :]
patches.append(cur_patch)
start_index = 0
end_index = 0
predicted_labels = []
while True:
end_index = start_index + net_config.BATCH_SIZE
print end_index, '/', len(patches)
if end_index >= len(patches):
end_index = len(patches)
cur_patches = patches[start_index:end_index]
# expand_patches = patches[start_index: end_index]
expand_patches = [roi_image] * len(
cur_patches) # 使用完整的ＲＯＩ作为ｅｘｐａｎｄ 的ｐａｔｃｈ
roi_images_values = resize_images(cur_patches,
net_config.ROI_SIZE_W,
rescale=(not divided_liver))
expand_roi_images_values = resize_images(expand_patches,
net_config.EXPAND_SIZE_W,
rescale=(not divided_liver))
predicted_label_value = sess.run(predicted_label_tensor,
feed_dict={
roi_images:
roi_images_values,
expand_roi_images:
expand_roi_images_values,
batch_size_tensor:
len(roi_images_values),
is_training_tensor:
False
})
predicted_labels.extend(predicted_label_value)
if end_index == len(patches):
break
start_index = end_index
start_index = 0
statics = [0, 0, 0, 0]
for i in range(xmin, xmax):
for j in range(ymin, ymax):
if mask_images[i, j, pointed_phase_index] == 0:
continue
print(i - xmin) * (xmax - xmin) + (j - ymin)
new_mask_image[i, j] = predicted_labels[start_index] + 2
statics[predicted_labels[start_index]] += 1
start_index += 1
print statics
end_time = time.time()
print 'cost time is ', (end_time - start_time)
save_mhd_image(new_mask_image, save_path)
def extract_interior_patch_npy(dir_name,
suffix_name,
save_dir,
patch_size,
patch_step=1,
erode_size=1):
'''
提取指定类型病灶的ｐａｔｃｈ 保存原始像素值，存成ｎｐｙ的格式
:param patch_size: 提取ｐａｔｃｈ的大小
:param dir_name: 目前所有病例的存储路径
:param suffix_name: 指定的病灶类型的后缀，比如说cyst 就是０
:param save_dir: 提取得到的ｐａｔｃｈ的存储路径
:param patch_step: 提取ｐａｔｃｈ的步长
:param erode_size: 向内缩的距离，因为我们需要确定内部区域,所以为了得到内部区域，我们就将原区域向内缩以得到内部区域
:return: None
'''
count = 0
names = os.listdir(dir_name)
patches = []
for name in names:
if name.endswith(suffix_name):
# 只提取指定类型病灶的ｐａｔｃｈ
mask_images = []
mhd_images = []
flag = True
for phasename in phasenames:
image_path = glob(
os.path.join(dir_name, name, phasename + '_Image*.mhd'))[0]
mask_path = os.path.join(dir_name, name,
phasename + '_Registration.mhd')
mhd_image = read_mhd_image(image_path)
mhd_image = np.squeeze(mhd_image)
# show_image(mhd_image)
mask_image = read_mhd_image(mask_path)
mask_image = np.squeeze(mask_image)
[xmin, xmax, ymin, ymax] = get_boundingbox(mask_image)
if (xmax - xmin) <= 5 or (ymax - ymin) <= 5:
flag = False
continue
mask_image = image_erode(mask_image, erode_size)
[xmin, xmax, ymin, ymax] = get_boundingbox(mask_image)
mask_image = mask_image[xmin:xmax, ymin:ymax]
mhd_image = mhd_image[xmin:xmax, ymin:ymax]
# mhd_image[mask_image != 1] = 0
mask_images.append(mask_image)
mhd_images.append(mhd_image)
# show_image(mhd_image)
if not flag:
continue
mask_images = convert2depthlaster(mask_images)
mhd_images = convert2depthlaster(mhd_images)
count += 1
[width, height, depth] = list(np.shape(mhd_images))
patch_count = 1
cur_patches = []
# if width * height >= 900:
# patch_step = int(math.sqrt(width * height / 100))
for i in range(patch_size / 2, width - patch_size / 2, patch_step):
for j in range(patch_size / 2, height - patch_size / 2,
patch_step):
cur_patch = mhd_images[i - patch_size / 2:i +
patch_size / 2,
j - patch_size / 2:j +
patch_size / 2, :]
if (np.sum(mask_images[i - patch_size / 2:i + patch_size /
2, j - patch_size / 2:j +
patch_size / 2, :]) /
((patch_size - 1) * (patch_size - 1) * 3)) < 0.5:
continue
if save_dir is not None:
save_path = os.path.join(
save_dir, name + '_' + str(patch_count) + '.npy')
np.save(save_path, np.array(cur_patch))
else:
cur_patches.append(flatten_arr(np.asarray(cur_patch)))
patch_count += 1
if save_dir is None:
if len(cur_patches) == 0:
continue
patches.append(cur_patches)
if patch_count == 1:
continue
# save_path = os.path.join(save_dir, name + '_' + str(patch_count) + '.png')
# roi_image = Image.fromarray(np.asarray(mhd_images, np.uint8))
# roi_image.save(save_path)
print count
if save_dir is None:
return patches