def view_tomo(self,sigma=2,R=10):
# d = {v_siz:(32,32,32), vs:{uuid0:{center, v, id}, uuid1:{center, v, id} ... }}
subvols_loc = os.path.join(self.dump_path,"demo_single_particle_subvolumes.pickle")
d = io_file.pickle_load(subvols_loc)
a = io_file.read_mrc_data(self.path)
if 'self.centers' not in dir():
centers = []
uuids = []
for k,v in d['vs'].items():
if v['v'] is not None:
centers.append(v['center'])
uuids.append(k)
self.centers = centers
self.uuids = uuids
# denoise
a_smooth = smooth(a,sigma)
for slice_num in range(a_smooth.shape[2]):
centers = np.array(centers)
slice_centers = centers[(centers[:,2]-slice_num)**2<R**2]
img = a_smooth[:,:,slice_num]
plt.rcParams['figure.figsize'] = (15.0, 12.0)
fig = plt.figure()
ax = fig.add_subplot(111)
plt.axis('off')
for center_num in range(len(slice_centers)):
y, x = slice_centers[center_num][0:2]
r = np.sqrt(R**2 - (slice_centers[center_num][2]-slice_num)**2)
circle = plt.Circle((x, y), r, color='b', fill=False)
plt.gcf().gca().add_artist(circle)
ax_u = ax.imshow(img, cmap = 'gray')
def view_subtom(self,subvol_num,sigma=2,R=10):
subvols_loc = os.path.join(self.dump_path,"demo_single_particle_subvolumes.pickle")
d = io_file.pickle_load(subvols_loc)
a = io_file.read_mrc_data(self.path)
# denoise
a_smooth = smooth(a,sigma)
if 'self.centers' not in dir():
centers = []
uuids = []
for k,v in d['vs'].items():
if v['v'] is not None:
centers.append(v['center'])
uuids.append(k)
self.centers = centers
self.uuids = uuids
y, x, z = self.centers[subvol_num]
img = a_smooth[:,:,z]
plt.rcParams['figure.figsize'] = (10.0, 8.0)
fig = plt.figure()
ax = fig.add_subplot(111)
circle = plt.Circle((x, y), R, color='b', fill=False)
plt.gcf().gca().add_artist(circle)
plt.axis('off')
output_str = '%d of %d, uuid = %s' % (
subvol_num, len(centers), self.uuids[subvol_num])
plt.title(output_str)
ax_u = ax.imshow(img, cmap = 'gray')
save_path = 'tmp_sub.png'
# plt.imsave(save_path, img, cmap='gray')
plt.savefig(save_path)
return save_path
def g_denoising(G_type, a, name, gaussian_sigma, save_flag=False):
b_time = time.time()
if G_type == 1:
a = G.smooth(a, gaussian_sigma)
elif G_type == 2:
a = G.dog_smooth(a, gaussian_sigma)
elif G_type == 3:
a = G.dog_smooth__large_map(a, gaussian_sigma)
end_time = time.time()
print('Gaussian de-noise takes', end_time - b_time, 's', ' sigma=',
gaussian_sigma)
if save_flag:
img = (a[:, :, int(a.shape[2] / 2)]).copy()
# TODO: Change the image and tomogram saving path
img_path = '/Users/apple/Desktop/Lab/Zach_Project/Denoising_Result/Gaussian/' + str(name) + '_G=' + \
str(gaussian_sigma) + '_type=' + str(G_type) + '.png'
plt.imsave(img_path, img, cmap='gray')
mrc_path = '/Users/apple/Desktop/Lab/Zach_Project/Denoising_Result/Gaussian/' + str(name) + '_G=' + \
str(gaussian_sigma) + '_type=' + str(G_type) + '.mrc'
io_file.put_mrc_data(a, mrc_path)
return img
def plot_slice(self,
z,
z_lower,
z_upper,
NewBox,
FinishCurrentBox,
label,
sigma=2,
R=10):
time1 = time.time()
a = self.volume
# Smooth
if sigma == 0:
a_smooth = a
else:
a_smooth = smooth(a, sigma)
# Get image
img = a_smooth[:, :, z]
plt.rcParams['figure.figsize'] = self.figsize
self.current_ax.imshow(img, cmap=self.cmap)
# Change box color based on lower and upper bound of z
box_c = 'green'
if z <= z_lower or z >= z_upper:
box_c = 'red'
# Store label and bounding box info when done with the current box
if FinishCurrentBox:
coordinates = toggle_selector.RS.extents # Return (xmin, xmax, ymin, ymax)
coordinates = coordinates * 5
xmin = coordinates[0]
xmax = coordinates[1]
ymin = coordinates[2]
ymax = coordinates[3]
boxInfo = [
xmin, ymin, z_lower, xmax - xmin, ymax - ymin,
z_upper - z_lower
]
self.annotations[label] = boxInfo
# Adding a new bounding box
if NewBox:
toggle_selector.RS = RectangleSelector(
self.current_ax,
self.line_select_callback,
drawtype='box',
useblit=True,
button=[1, 3], # don't use middle button
minspanx=5,
minspany=5,
spancoords='pixels',
interactive=True,
rectprops=dict(edgecolor=box_c, alpha=1, fill=False))
plt.connect('key_press_event', toggle_selector)
print('plot_slice time', time.time() - time1)
def active_contour_slice(v, sigma=3.5, membrane_thickness=5, display_slice=-1, out_dir = './output', save_flag=True):
if os.path.exists(out_dir):
shutil.rmtree(out_dir)
os.makedirs(out_dir)
mask_v = np.zeros(v.shape)
print(v.shape)
vg = FG.smooth(v, sigma)
for slice_num in range(mask_v.shape[2]):
save_flag_slice = False
if slice_num == display_slice and save_flag:
save_flag_slice = True
print('processing slice ', slice_num)
ori_img = (v[:, :, slice_num]).copy()
if save_flag_slice: plt.imsave(os.path.join(out_dir, 'original.png'), ori_img, cmap='gray')
img = (vg[:, :, slice_num]).copy()
if save_flag_slice: plt.imsave(os.path.join(out_dir, 'original_smooth.png'), img, cmap='gray')
# generate init circle
s = np.linspace(0, 2*np.pi, 400)
x = 80 + 60*np.sin(s)
y = 80 + 60*np.cos(s)
init = np.array([x, y]).T
# init = create_sphere(20,20,20,10) # sphere for 3d active contour
snake = active_contour(img, init, alpha=0.015, beta=10, gamma=0.001)
# Note: The default format of the returned coordinates is (x,y) instead of (row,col) in skimage 0.15.x - 0.17.x
snake[:,[0,1]]= snake[:, [1,0]]
r = snake[:,0].astype(int)
c = snake[:,1].astype(int)
img2 = img.copy()
colour = np.min(img2)
img2[r,c] = colour
if save_flag_slice: plt.imsave(os.path.join(out_dir, 'contour.png'), img2, cmap='gray')
mask = np.zeros(ori_img.shape)
rr,cc = polygon(r, c)
mask[rr,cc] = 2
mask[r,c] = 1
for i in range(membrane_thickness):
mask = contour_shrink(mask)
mask[mask==0] = 3
if save_flag_slice: plt.imsave(os.path.join(out_dir, 'mask.png'), mask, cmap='gray')
mask_v [:,:,slice_num] = mask
mask_im = AIVU.cub_img(mask_v)['im']
# better visualize the results
for i in range(0,mask_im.shape[0],mask_v.shape[0]):
mask_im[i,:]=0
for i in range(0,mask_im.shape[1],mask_v.shape[1]):
mask_im[:,i]=0
if save_flag: plt.imsave(os.path.join(out_dir, 'result.png'), mask_im, cmap='gray')
return mask_v
se = N.array(op['debug']['start_end'])
v = v[se[0, 0]:se[0, 1], se[1, 0]:se[1, 1], se[2, 0]:se[2, 1]]
v = v.astype(N.float)
v -= v.mean()
IF.put_mrc(v, '/tmp/v.mrc', overwrite=True)
if op['inverse_intensity']:
v = -v
print('intensity distribution of v', 'max', v.max(), 'min', v.min(),
'mean', v.mean())
print('# gaussian smoothing')
vg = FG.smooth(v, sigma=float(op['sigma']) / voxel_spacing)
print('intensity distribution of vg', 'max', vg.max(), 'min', vg.min(),
'mean', vg.mean())
IF.put_mrc(vg, '/tmp/vg.mrc', overwrite=True)
R = feature(vg)
IF.put_mrc(R, op['out_file'], overwrite=True)
'''
IF.put_mrc(R, '/tmp/r.mrc', overwrite=True)
S = FD.gradient_magnitude_square(dif)
print '# calculate directional dirvative along thee gradient'
Rdd = FD.directional_derivative_along_gradient(R, d=dif)
Sdd = FD.directional_derivative_along_gradient(S, d=dif)
def sphere_seg(v,
sigma,
init_level_set=None,
out_dir='./output',
save_flag=False):
"""
sphere_seg: membrane segmentation by sphere fitting
@params:
v: volume data sigma: gaussian sigma for denoising
init_level_set: initial level set for morphsnake
@return:
[x, y, z, R]: coordinates and radius of the sphere
"""
np.random.seed(12345)
if save_flag:
if os.path.exists(out_dir):
shutil.rmtree(out_dir)
os.makedirs(out_dir)
# morphsnake
if init_level_set:
init = init_level_set
else:
circle_set = circle_level_set(v.shape[:2], (80, 80), 60)
init_mask = np.zeros(v.shape)
for i in range(init_mask.shape[2]):
init_mask[:, :, i] = circle_set
init = checkerboard_level_set(v.shape)
init = np.multiply(init, init_mask)
v_im = AIVU.cub_img(v)['im']
if save_flag:
plt.imsave(os.path.join(out_dir, 'original.png'), v_im, cmap='gray')
vg = FG.smooth(v, sigma)
mask_v = ACWE(image=vg, iterations=25, init_level_set=init)
mask_im = AIVU.cub_img(mask_v)['im']
if save_flag:
plt.imsave(os.path.join(out_dir, 'morphsnake_result.png'),
mask_im,
cmap='gray')
# RANSC
coords = np.array(np.where(mask_v == 1))
coords = coords.T # (N,3)
# robustly fit line only using inlier data with RANSAC algorithm
xyz = coords
model_robust, inliers = ransac(xyz,
CircleModel3D,
min_samples=20,
residual_threshold=3,
max_trials=50)
outliers = inliers == False
# print('inliers_num = ', sum(inliers), 'inliers_num = ', sum(outliers))
x, y, z, R = model_robust.params
v_RANSC = np.zeros(mask_v.shape)
assert len(inliers) == coords.shape[0]
if save_flag:
for i in range(len(inliers)):
if inliers[i]:
v_RANSC[coords[i][0]][coords[i][1]][coords[i][2]] = 2
else:
v_RANSC[coords[i][0]][coords[i][1]][coords[i][2]] = 1
vim_RANSC = AIVU.cub_img(v_RANSC)['im']
plt.imsave(os.path.join(out_dir, 'RANSC_result.png'),
vim_RANSC,
cmap='gray')
a = FG.smooth(v, sigma)
a.flags.writeable = True
color = np.min(a)
thickness = 1
center = (x, y, z)
grid = np.mgrid[[slice(i) for i in a.shape]]
grid = (grid.T - center).T
phi1 = R - np.sqrt(np.sum((grid)**2, 0))
phi2 = np.max(R - thickness, 0) - np.sqrt(np.sum((grid)**2, 0))
res = np.int8(phi1 > 0) - np.int8(phi2 > 0)
a[res == 1] = color
vim = AIVU.cub_img(a)['im']
plt.imsave(os.path.join(out_dir, 'result.png'), vim, cmap='gray')
return model_robust.params
def encoder_simple_conv_test(d, pose, img_org_file, out_dir, clus_num):
if pose:
assert img_org_file is not None
tom0 = auto.read_mrc_numpy_vol(img_org_file)
tom = AFG.smooth(tom0, 2.0)
x_keys = [_ for _ in d['vs'] if d['vs'][_]['v'] is not None]
x_train_no_pose = [N.expand_dims(d['vs'][_]['v'], -1) for _ in x_keys]
x_train_no_pose = N.array(x_train_no_pose)
x_center = [d['vs'][_]['center'] for _ in x_keys]
x_train = []
default_val = tom.mean()
x_train_no_pose -= x_train_no_pose.max()
x_train_no_pose = N.abs(x_train_no_pose)
print('pose normalizing')
for i in range(len(x_train_no_pose)):
center = x_center[i]
v = x_train_no_pose[i][:, :, :, 0]
c = auto.center_mass(v)
# calculate principal directions
rm = auto.pca(v=v, c=c)['v']
mid_co = (N.array(v.shape) - 1) / 2.0
loc_r__pn = rm.T.dot(mid_co - c)
# pose normalize so that the major axis is along x-axis
vr = auto.rotate_retrieve(v,
tom=tom,
rm=rm,
center=center,
loc_r=loc_r__pn,
default_val=default_val)
x_train.append(vr)
x_train = N.array(x_train)
x_train = N.expand_dims(x_train, axis=4)
print('pose normalization finished')
else:
x_keys = [_ for _ in d['vs'] if d['vs'][_]['v'] is not None]
x_train = [N.expand_dims(d['vs'][_]['v'], -1) for _ in x_keys]
x_train = N.array(x_train)
if False:
# warning, if you normalize here, you need also to normalize when decoding.
# so it is better not normalize. Use batch normalization in the network instead
if True:
x_train -= x_train.mean()
x_train /= x_train.std()
else:
x_train -= x_train.min()
x_train /= x_train.max()
x_train -= 0.5
x_train *= 2
# print('x_train.shape', x_train.shape)
model_dir = op_join(out_dir, 'model')
if not os.path.isdir(model_dir):
os.makedirs(model_dir)
model_autoencoder_checkpoint_file = op_join(
model_dir, 'model-autoencoder--weights--best.h5')
model_autoencoder_file = op_join(model_dir, 'model-autoencoder.h5')
model_encoder_file = op_join(model_dir, 'model-encoder.h5')
model_decoder_file = op_join(model_dir, 'model-decoder.h5')
if not os.path.isfile(model_autoencoder_file):
enc = encoder_simple_conv(img_shape=d['v_siz'])
autoencoder = enc['autoencoder']
autoencoder_p = autoencoder
from keras.optimizers import Adam
# choose a proper lr to control convergance speed, and val_loss
adam = Adam(lr=0.001, beta_1=0.9, decay=0.001 / 500)
# sgd = SGD(lr=0.01, decay=1e-6, momentum=0.9, nesterov=True)
autoencoder_p.compile(optimizer=adam, loss='mean_squared_error')
if os.path.isfile(model_autoencoder_checkpoint_file):
print('loading previous best weights',
model_autoencoder_checkpoint_file)
autoencoder_p.load_weights(model_autoencoder_checkpoint_file)
from keras.callbacks import EarlyStopping, ModelCheckpoint
earlyStopping = EarlyStopping(monitor='val_loss',
patience=20,
verbose=0,
mode='auto')
checkpoint = ModelCheckpoint(model_autoencoder_checkpoint_file,
monitor='val_loss',
verbose=1,
save_best_only=True,
mode='auto')
# use a large batch size when batch normalization is used
autoencoder_p.fit(x_train,
x_train,
nb_epoch=100,
batch_size=128,
shuffle=True,
validation_split=0.1,
callbacks=[checkpoint, earlyStopping])
# we use the best weights for subsequent analysis
autoencoder_p.load_weights(model_autoencoder_checkpoint_file)
enc['autoencoder'].save(model_autoencoder_file)
enc['encoder'].save(model_encoder_file)
enc['decoder'].save(model_decoder_file)
else:
import keras.models as KM
enc = dict()
enc['autoencoder'] = KM.load_model(model_autoencoder_file)
enc['encoder'] = KM.load_model(model_encoder_file)
enc['decoder'] = KM.load_model(model_decoder_file)
x_enc = enc['encoder'].predict(x_train)
# use kmeans to seperate x_enc into a specific number of clusters,
# then decode cluster centers, and patch the decoded cluster centers back to the image,
# can use mayavi???
import multiprocessing
from sklearn.cluster import KMeans
kmeans_n_init = multiprocessing.cpu_count()
kmeans = KMeans(n_clusters=clus_num, n_jobs=-1, n_init=100).fit(x_enc)
x_km_cent = N.array(
[_.reshape(x_enc[0].shape) for _ in kmeans.cluster_centers_])
x_km_cent_pred = enc['decoder'].predict(x_km_cent)
# save cluster info and cluster centers
clus_center_dir = op_join(out_dir, 'clus-center')
if not os.path.isdir(clus_center_dir): os.makedirs(clus_center_dir)
kmeans_clus = defaultdict(list)
for i, l in enumerate(kmeans.labels_):
kmeans_clus[l].append(x_keys[i])
AIF.pickle_dump(kmeans_clus, op_join(clus_center_dir, 'kmeans.pickle'))
ccents = {}
for i in range(len(x_km_cent_pred)):
ccents[i] = x_km_cent_pred[i].reshape(d['v_siz'])
AIF.pickle_dump(ccents, op_join(clus_center_dir, 'ccents.pickle'))
AIF.pickle_dump(x_km_cent, op_join(clus_center_dir, 'ccents_d.pickle'))
Load Volume and Display image¶
change to parent directory to use aitom library
"""
import os
os.chdir("..")
# load mrc file using io module
# example data:
# http://ftp.ebi.ac.uk/pub/databases/empiar/archive/10045/data/ribosomes/AnticipatedResults/Particles/Tomograms/05/IS002_291013_005_subtomo000001.mrc
import aitom.io.file as IF
a = IF.read_mrc_data("data/IS002_291013_005_subtomo000001.mrc")
# denoising using gaussian filter for visualization
from aitom.filter.gaussian import smooth
a = smooth(a, sigma=8)
# display image using image module
import aitom.image.vol.util as IVU
'''
a_im is a dict:
'im': image data, type of numpy.ndarray, elements in [0, 1]
'vt': volume data
'''
a_im = IVU.cub_img(a)
print(type(a_im['im']))
print(a_im['im'].shape)
print(a_im['im'][1][1])
import matplotlib.pyplot as plt
plt.imshow(a_im['im'], cmap='gray')