def pick(self, mrc_filename):
"""Do the picking job through tensorflow.
This function read the micrograph data information based on the given filename of micrograph.
Then do the auto picking based on pre-trained CNN model.
Args:
mrc_filename: string, it is the filename of the target micrograph.
Returns:
return list_coordinate
list_coordinate: a list, the length of this list stands for the number of picked particles.
Each element in the list is also a list, the length is 4, the first one is y-axis,
the second one is x-axis, the third one is the predicted score, the fourth is the micrograph filename.
"""
# read the micrograph image data
print(mrc_filename)
header, body = DataLoader.readMrcFile(mrc_filename)
num_col = header[0]
num_row = header[1]
body_2d = np.array(body, dtype = np.float32).reshape(num_row, num_col)
# do process to micrograph
body_2d, bin_size = DataLoader.preprocess_micrograph(body_2d)
# Edge detection to get the ice noise mask
# a binary matrix, 1 stands for the ice noise site
# mask = edge_detection_ice(body_2d)
step_size = 4
candidate_patches = None
candidate_patches_exist = False
num_total_patch = 0
patch_size = int(self.particle_size/bin_size)
# the size to do peak detection
local_window_size = int(0.6*patch_size/step_size)
#print("image_col:", body_2d.shape[0])
#print("particle_size:", patch_size)
#print("step_size:", step_size)
map_col = int((body_2d.shape[0]-patch_size)/step_size)
map_row = int((body_2d.shape[1]-patch_size)/step_size)
#prediction = np.zeros((map_col, map_row), dtype = float)
time1 = time.time()
particle_candidate_all = []
map_index_col = 0
for col in range(0, body_2d.shape[0]-patch_size+1, step_size):
for row in range(0, body_2d.shape[1]-patch_size+1, step_size):
# extract the particle patch
patch = np.copy(body_2d[col:(col+patch_size), row:(row+patch_size)])
# do preprocess to the particle
patch = DataLoader.preprocess_particle(patch, self.model_input_size)
particle_candidate_all.append(patch)
num_total_patch = num_total_patch + 1
map_index_col = map_index_col + 1
map_index_row = map_index_col-map_col+map_row
#print("map_col:",map_col)
#print("map_row:",map_row)
#print(len(particle_candidate_all))
#print("map_index_col:",map_index_col)
#print("map_index_row:",map_index_row)
#print("col*row:",map_index_col*map_index_row)
# reshape it to fit the input format of the model
particle_candidate_all = np.array(particle_candidate_all).reshape(num_total_patch, self.model_input_size[1], self.model_input_size[2], 1)
# predict
predictions = self.deepModel.evaluation(particle_candidate_all, self.sess)
predictions = predictions[:, 1:2]
predictions = predictions.reshape(map_index_col, map_index_row)
time_cost = time.time() - time1
print("time cost: %d s"%time_cost)
#display.save_image(prediction, "prediction.png")
# get the prediction value to be a positive sample, it is a value between 0~1
# the following code not tested
# do a connected component analysis
# prediction = detete_large_component(prediction)
# do a local peak detection to get the best coordinate
# list_coordinate is a 2D list of shape (number_particle, 3)
# element in list_coordinate is [x_coordinate, y_coordinate, prediction_value]
list_coordinate = self.peak_detection(predictions, local_window_size)
# add the mrc filename to the list of each coordinate
for i in range(len(list_coordinate)):
list_coordinate[i].append(mrc_filename)
# transform the coordinates to the original size
list_coordinate[i][0] = (list_coordinate[i][0]*step_size+patch_size/2)*bin_size
list_coordinate[i][1] = (list_coordinate[i][1]*step_size+patch_size/2)*bin_size
return list_coordinate
def pick(self, mrc_filename):
if mrc_filename.endswith('.rec'):
header, body = DataLoader.readRecFile(mrc_filename)
else:
header, body = DataLoader.readMrcFile(mrc_filename)
if header == None or body == None:
return []
num_col = header[0]
num_row = header[1]
body_2d = np.array(body, dtype=np.float32).reshape(num_row, num_col)
body_2d_ori = body_2d
body_2d, bin_size = DataLoader.preprocess_micrograph(body_2d)
step_size = 4
candidate_patches = None
candidate_patches_exist = False
num_total_patch = 0
patch_size = int(self.particle_size / bin_size)
local_window_size = int(patch_size / step_size)
#local_window_size = int(0.6*patch_size)
map_col = int((body_2d.shape[0] - patch_size + 1) / step_size)
map_row = int((body_2d.shape[1] - patch_size + 1) / step_size)
time1 = time.time()
particle_candidate_all = []
map_index_col = 0
for col in range(0, body_2d.shape[0] - patch_size, step_size):
for row in range(0, body_2d.shape[1] - patch_size, step_size):
patch = np.copy(body_2d[col:(col + patch_size),
row:(row + patch_size)])
#patch = DataLoader.preprocess_particle(patch, self.model_input_size)
particle_candidate_all.append(patch)
num_total_patch = num_total_patch + 1
map_index_col = map_index_col + 1
map_index_row = map_index_col - map_col + map_row
#particle_candidate_all = np.array(particle_candidate_all).reshape(
# num_total_patch, self.model_input_size[1], self.model_input_size[2], 1)
particle_candidate_all = np.array(particle_candidate_all).reshape(
num_total_patch, patch_size, patch_size, 1)
predictions = self.deepModel.evaluation(particle_candidate_all,
self.sess)
predictions = predictions[:, 1:2]
predictions = predictions.reshape(map_index_col, map_index_row)
time_cost = time.time() - time1
if self.verbose:
print("gpu time: %.1f s" % time_cost)
list_coordinate = self.peak_detection(predictions, local_window_size)
for i in range(len(list_coordinate)):
list_coordinate[i].append(mrc_filename)
list_coordinate[i][0] = (list_coordinate[i][0] * step_size +
patch_size / 2) * bin_size
list_coordinate[i][1] = (list_coordinate[i][1] * step_size +
patch_size / 2) * bin_size
#return all coordinate
list_coordinate_all = [i for i in list_coordinate if i[2] > 0.0]
list_coordinate_all = sorted(list_coordinate_all,
key=lambda x: x[2],
reverse=True)
#print ("size = ", len(list_coordinate))
list_coordinate = [i for i in list_coordinate if i[2] > self.threshold]
list_coordinate = sorted(list_coordinate,
key=lambda x: x[2],
reverse=True)
#print ("filtered size = ", len(list_coordinate))
#list_coordinate = list_coordinate[:100]
print("#candidate:%d, #picked:%d" %
(num_total_patch, len(list_coordinate)))
plot_list_coordinate = copy.deepcopy(list_coordinate)
for i in range(len(plot_list_coordinate)):
plot_list_coordinate[i][0] = plot_list_coordinate[i][0] / bin_size
plot_list_coordinate[i][1] = plot_list_coordinate[i][1] / bin_size
if self.plot_picking_result:
#print ">>>>>>>>>>>>>>>", body_2d.shape
reference_coordinate_file = mrc_filename.replace(
'.mrc', '_DW_recentered.star')
reference_coordinate_file = os.path.join(
'/data00/Data/piezo/train', reference_coordinate_file)
#print(reference_coordinate_file)
if os.path.isfile(reference_coordinate_file):
reference_coordinate = DataLoader.read_coordinate_from_star(
reference_coordinate_file)
for i in range(len(reference_coordinate)):
reference_coordinate[i][
0] = reference_coordinate[i][0] / bin_size
reference_coordinate[i][
1] = reference_coordinate[i][1] / bin_size
#display.plot_circle_in_micrograph(body_2d, reference_coordinate, plot_list_coordinate, patch_size, "plot/micro_circle_%s.png" % (os.path.basename(mrc_filename)))
#plot_dir = os.path.basename(self.output_dir)
plot_dir = os.path.join(os.path.abspath(self.output_dir), "plot")
#pos = plot_dir.rfind('/')
#plot_dir = os.path.join(plot_dir[:pos], 'plot')
if self.verbose:
print "plot_dir >>>>>>>>>> ", plot_dir
if self.plot_picking_result and os.path.exists(plot_dir) == False:
os.makedirs(plot_dir)
display.plot_circle_in_micrograph(
body_2d, plot_list_coordinate, patch_size, plot_dir +
"/micro_circle_%s.png" % (os.path.basename(mrc_filename)))
#display.plot_circle_in_micrograph(body_2d_ori, list_coordinate, self.particle_size, "plot/micro_circle_%s.png" % (os.path.basename(mrc_filename)))
return list_coordinate, list_coordinate_all
unique_name = 'stack_2406_2x_SumCorr_movie_DW'
#unique_name = 'stack_3025_2x_SumCorr_movie_DW'
coordinates = []
class_number = []
starfile = os.path.join(basepath, unique_name + new + '.star')
with open(starfile) as fin:
idx = 0
for l in fin:
idx += 1
if idx <= 5 or l.strip() == '':
continue
t = map(float, l.strip().split())
coordinates.append([int(t[0]), int(t[1])])
class_number.append(int(t[2]))
plot = 'test_plot_%d' % peek_cls + new + '.png'
filename = os.path.join(mrcpath, unique_name + '.mrc')
header, body = DataLoader.readMrcFile(filename)
n_col = header[0]
n_row = header[1]
print n_col, n_row
body_2d = np.array(body, dtype=np.float32).reshape(n_row, n_col, 1)
body_2d, bin_size = DataLoader.preprocess_micrograph(body_2d)
coordinates = np.array(coordinates)
coordinates = coordinates / bin_size
plot_circle_in_micrograph(body_2d,
coordinates,
class_number,
180 / bin_size,
plot,
color='white')
def pick(self, mrc_filename):
"""Do the picking job through tensorflow.
This function read the micrograph data information based on the given filename of micrograph.
Then do the auto picking based on pre-trained CNN model.
Args:
mrc_filename: string, it is the filename of the target micrograph.
Returns:
return list_coordinate
list_coordinate: a list, the length of this list stands for the number of picked particles.
Each element in the list is also a list, the length is 4, the first one is y-axis,
the second one is x-axis, the third one is the predicted score, the fourth is the micrograph filename.
"""
# read the micrograph image data
print(mrc_filename)
header, body = DataLoader.readMrcFile(mrc_filename)
num_col = header[0]
num_row = header[1]
body_2d = np.array(body, dtype=np.float32).reshape(num_row, num_col)
# do process to micrograph
body_2d, bin_size = DataLoader.preprocess_micrograph(body_2d)
# Edge detection to get the ice noise mask
# a binary matrix, 1 stands for the ice noise site
# mask = edge_detection_ice(body_2d)
step_size = 4
candidate_patches = None
candidate_patches_exist = False
num_total_patch = 0
patch_size = int(self.particle_size / bin_size)
# the size to do peak detection
local_window_size = int(0.6 * patch_size / step_size)
#print("image_col:", body_2d.shape[0])
#print("particle_size:", patch_size)
#print("step_size:", step_size)
map_col = int((body_2d.shape[0] - patch_size) / step_size)
map_row = int((body_2d.shape[1] - patch_size) / step_size)
#prediction = np.zeros((map_col, map_row), dtype = float)
time1 = time.time()
particle_candidate_all = []
map_index_col = 0
for col in range(0, body_2d.shape[0] - patch_size + 1, step_size):
for row in range(0, body_2d.shape[1] - patch_size + 1, step_size):
# extract the particle patch
patch = np.copy(body_2d[col:(col + patch_size),
row:(row + patch_size)])
# do preprocess to the particle
patch = DataLoader.preprocess_particle(patch,
self.model_input_size)
particle_candidate_all.append(patch)
num_total_patch = num_total_patch + 1
map_index_col = map_index_col + 1
map_index_row = map_index_col - map_col + map_row
#print("map_col:",map_col)
#print("map_row:",map_row)
#print(len(particle_candidate_all))
#print("map_index_col:",map_index_col)
#print("map_index_row:",map_index_row)
#print("col*row:",map_index_col*map_index_row)
# reshape it to fit the input format of the model
particle_candidate_all = np.array(particle_candidate_all).reshape(
num_total_patch, self.model_input_size[1],
self.model_input_size[2], 1)
# predict
predictions = self.deepModel.evaluation(particle_candidate_all,
self.sess)
predictions = predictions[:, 1:2]
predictions = predictions.reshape(map_index_col, map_index_row)
time_cost = time.time() - time1
print("time cost: %d s" % time_cost)
#display.save_image(prediction, "prediction.png")
# get the prediction value to be a positive sample, it is a value between 0~1
# the following code not tested
# do a connected component analysis
# prediction = detete_large_component(prediction)
# do a local peak detection to get the best coordinate
# list_coordinate is a 2D list of shape (number_particle, 3)
# element in list_coordinate is [x_coordinate, y_coordinate, prediction_value]
list_coordinate = self.peak_detection(predictions, local_window_size)
# add the mrc filename to the list of each coordinate
for i in range(len(list_coordinate)):
list_coordinate[i].append(mrc_filename)
# transform the coordinates to the original size
list_coordinate[i][0] = (list_coordinate[i][0] * step_size +
patch_size / 2) * bin_size
list_coordinate[i][1] = (list_coordinate[i][1] * step_size +
patch_size / 2) * bin_size
return list_coordinate