Пример #1
0
    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
Пример #2
0
    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
Пример #3
0
    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')
Пример #4
0
    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