celldetective 1.4.2__py3-none-any.whl → 1.5.0b1__py3-none-any.whl

celldetective/gui/processes/segment_cells.py

@@ -1,499 +0,0 @@
-from multiprocessing import Process
-import time
-import datetime
-import os
-import json
-import numpy as np
-from celldetective.io import (
-    extract_position_name,
-    locate_segmentation_model,
-    auto_load_number_of_frames,
-    load_frames,
-    _check_label_dims,
-    _load_frames_to_segment,
-)
-from celldetective.utils import (
-    _rescale_labels,
-    _segment_image_with_stardist_model,
-    _segment_image_with_cellpose_model,
-    _prep_stardist_model,
-    _prep_cellpose_model,
-    _get_normalize_kwargs_from_config,
-    extract_experiment_channels,
-    _estimate_scale_factor,
-    _extract_channel_indices_from_config,
-    config_section_to_dict,
-    _extract_nbr_channels_from_config,
-    _get_img_num_per_channel,
-)
-
-from pathlib import Path, PurePath
-from glob import glob
-from shutil import rmtree
-from tqdm import tqdm
-import numpy as np
-from csbdeep.io import save_tiff_imagej_compatible
-from celldetective.segmentation import (
-    segment_frame_from_thresholds,
-    merge_instance_segmentation,
-)
-import gc
-from art import tprint
-
-import concurrent.futures
-
-
-class BaseSegmentProcess(Process):
-
-    def __init__(self, queue=None, process_args=None, *args, **kwargs):
-
-        super().__init__(*args, **kwargs)
-
-        self.queue = queue
-
-        if process_args is not None:
-            for key, value in process_args.items():
-                setattr(self, key, value)
-
-        tprint("Segment")
-
-        # Experiment
-        self.locate_experiment_config()
-
-        print(f"Position: {extract_position_name(self.pos)}...")
-        print("Configuration file: ", self.config)
-        print(f"Population: {self.mode}...")
-        self.instruction_file = os.sep.join(
-            ["configs", f"segmentation_instructions_{self.mode}.json"]
-        )
-
-        self.read_instructions()
-        self.extract_experiment_parameters()
-        self.detect_movie_length()
-        self.write_folders()
-
-    def read_instructions(self):
-        print("Looking for instruction file...")
-        instr_path = PurePath(self.exp_dir, Path(f"{self.instruction_file}"))
-        if os.path.exists(instr_path):
-            with open(instr_path, "r") as f:
-                _instructions = json.load(f)
-                print(f"Measurement instruction file successfully loaded...")
-                print(f"Instructions: {_instructions}...")
-            self.flip = _instructions.get("flip", False)
-        else:
-            self.flip = False
-
-    def write_folders(self):
-
-        self.mode = self.mode.lower()
-        self.label_folder = f"labels_{self.mode}"
-
-        if os.path.exists(self.pos + self.label_folder):
-            print("Erasing the previous labels folder...")
-            rmtree(self.pos + self.label_folder)
-        os.mkdir(self.pos + self.label_folder)
-        print(f"Labels folder successfully generated...")
-
-    def extract_experiment_parameters(self):
-
-        self.spatial_calibration = float(
-            config_section_to_dict(self.config, "MovieSettings")["pxtoum"]
-        )
-        self.len_movie = float(
-            config_section_to_dict(self.config, "MovieSettings")["len_movie"]
-        )
-        self.movie_prefix = config_section_to_dict(self.config, "MovieSettings")[
-            "movie_prefix"
-        ]
-        self.nbr_channels = _extract_nbr_channels_from_config(self.config)
-        self.channel_names, self.channel_indices = extract_experiment_channels(
-            self.exp_dir
-        )
-
-    def locate_experiment_config(self):
-
-        parent1 = Path(self.pos).parent
-        self.exp_dir = parent1.parent
-        self.config = PurePath(self.exp_dir, Path("config.ini"))
-
-        if not os.path.exists(self.config):
-            print(
-                "The configuration file for the experiment could not be located. Abort."
-            )
-            self.abort_process()
-
-    def detect_movie_length(self):
-
-        try:
-            self.file = glob(self.pos + f"movie/{self.movie_prefix}*.tif")[0]
-        except Exception as e:
-            print(f"Error {e}.\nMovie could not be found. Check the prefix.")
-            self.abort_process()
-
-        len_movie_auto = auto_load_number_of_frames(self.file)
-        if len_movie_auto is not None:
-            self.len_movie = len_movie_auto
-
-    def end_process(self):
-
-        self.terminate()
-        self.queue.put("finished")
-
-    def abort_process(self):
-
-        self.terminate()
-        self.queue.put("error")
-
-
-class SegmentCellDLProcess(BaseSegmentProcess):
-
-    def __init__(self, *args, **kwargs):
-
-        super().__init__(*args, **kwargs)
-
-        self.check_gpu()
-
-        # Model
-        self.locate_model_path()
-        self.extract_model_input_parameters()
-        self.detect_channels()
-        self.detect_rescaling()
-
-        self.write_log()
-
-        self.sum_done = 0
-        self.t0 = time.time()
-
-    def extract_model_input_parameters(self):
-
-        self.required_channels = self.input_config["channels"]
-        if "selected_channels" in self.input_config:
-            self.required_channels = self.input_config["selected_channels"]
-
-        self.target_cell_size = None
-        if (
-            "target_cell_size_um" in self.input_config
-            and "cell_size_um" in self.input_config
-        ):
-            self.target_cell_size = self.input_config["target_cell_size_um"]
-            self.cell_size = self.input_config["cell_size_um"]
-
-        self.normalize_kwargs = _get_normalize_kwargs_from_config(self.input_config)
-
-        self.model_type = self.input_config["model_type"]
-        self.required_spatial_calibration = self.input_config["spatial_calibration"]
-        print(
-            f"Spatial calibration expected by the model: {self.required_spatial_calibration}..."
-        )
-
-        if self.model_type == "cellpose":
-            self.diameter = self.input_config["diameter"]
-            self.cellprob_threshold = self.input_config["cellprob_threshold"]
-            self.flow_threshold = self.input_config["flow_threshold"]
-
-    def write_log(self):
-
-        log = f"segmentation model: {self.model_name}\n"
-        with open(self.pos + f"log_{self.mode}.txt", "a") as f:
-            f.write(f"{datetime.datetime.now()} SEGMENT \n")
-            f.write(log)
-
-    def detect_channels(self):
-
-        self.channel_indices = _extract_channel_indices_from_config(
-            self.config, self.required_channels
-        )
-        print(
-            f"Required channels: {self.required_channels} located at channel indices {self.channel_indices}."
-        )
-        self.img_num_channels = _get_img_num_per_channel(
-            self.channel_indices, int(self.len_movie), self.nbr_channels
-        )
-
-    def detect_rescaling(self):
-
-        self.scale = _estimate_scale_factor(
-            self.spatial_calibration, self.required_spatial_calibration
-        )
-        print(f"Scale: {self.scale}...")
-
-        if self.target_cell_size is not None and self.scale is not None:
-            self.scale *= self.cell_size / self.target_cell_size
-        elif self.target_cell_size is not None:
-            if self.target_cell_size != self.cell_size:
-                self.scale = self.cell_size / self.target_cell_size
-
-        print(f"Scale accounting for expected cell size: {self.scale}...")
-
-    def locate_model_path(self):
-
-        self.model_complete_path = locate_segmentation_model(self.model_name)
-        if self.model_complete_path is None:
-            print("Model could not be found. Abort.")
-            self.abort_process()
-        else:
-            print(f"Model path: {self.model_complete_path}...")
-
-        if not os.path.exists(self.model_complete_path + "config_input.json"):
-            print(
-                "The configuration for the inputs to the model could not be located. Abort."
-            )
-            self.abort_process()
-
-        with open(self.model_complete_path + "config_input.json") as config_file:
-            self.input_config = json.load(config_file)
-
-    def check_gpu(self):
-
-        if not self.use_gpu:
-            os.environ["CUDA_VISIBLE_DEVICES"] = "-1"
-
-    def run(self):
-
-        try:
-
-            if self.model_type == "stardist":
-                model, scale_model = _prep_stardist_model(
-                    self.model_name,
-                    Path(self.model_complete_path).parent,
-                    use_gpu=self.use_gpu,
-                    scale=self.scale,
-                )
-
-            elif self.model_type == "cellpose":
-                model, scale_model = _prep_cellpose_model(
-                    self.model_name,
-                    self.model_complete_path,
-                    use_gpu=self.use_gpu,
-                    n_channels=len(self.required_channels),
-                    scale=self.scale,
-                )
-
-            list_indices = range(self.len_movie)
-            if self.flip:
-                list_indices = reversed(list_indices)
-
-            for i, t in enumerate(tqdm(list_indices, desc="frame")):
-
-                f = _load_frames_to_segment(
-                    self.file,
-                    self.img_num_channels[:, t],
-                    scale_model=scale_model,
-                    normalize_kwargs=self.normalize_kwargs,
-                )
-
-                if self.model_type == "stardist":
-                    Y_pred = _segment_image_with_stardist_model(
-                        f, model=model, return_details=False
-                    )
-
-                elif self.model_type == "cellpose":
-                    Y_pred = _segment_image_with_cellpose_model(
-                        f,
-                        model=model,
-                        diameter=self.diameter,
-                        cellprob_threshold=self.cellprob_threshold,
-                        flow_threshold=self.flow_threshold,
-                    )
-
-                if self.scale is not None:
-                    Y_pred = _rescale_labels(Y_pred, scale_model=scale_model)
-
-                Y_pred = _check_label_dims(Y_pred, file=self.file)
-
-                save_tiff_imagej_compatible(
-                    self.pos
-                    + os.sep.join([self.label_folder, f"{str(t).zfill(4)}.tif"]),
-                    Y_pred,
-                    axes="YX",
-                )
-
-                del f
-                del Y_pred
-                gc.collect()
-
-                # Send signal for progress bar
-                self.sum_done += 1 / self.len_movie * 100
-                mean_exec_per_step = (time.time() - self.t0) / (i + 1)
-                pred_time = (self.len_movie - (i + 1)) * mean_exec_per_step
-                self.queue.put([self.sum_done, pred_time])
-
-        except Exception as e:
-            print(e)
-
-        try:
-            del model
-        except:
-            pass
-
-        gc.collect()
-        print("Done.")
-
-        # Send end signal
-        self.queue.put("finished")
-        self.queue.close()
-
-
-class SegmentCellThresholdProcess(BaseSegmentProcess):
-
-    def __init__(self, *args, **kwargs):
-
-        super().__init__(*args, **kwargs)
-
-        self.equalize = False
-
-        # Model
-
-        self.load_threshold_config()
-        self.extract_threshold_parameters()
-        self.detect_channels()
-        self.prepare_equalize()
-
-        self.write_log()
-
-        self.sum_done = 0
-        self.t0 = time.time()
-
-    def prepare_equalize(self):
-
-        for i in range(len(self.instructions)):
-
-            if self.equalize[i]:
-                f_reference = load_frames(
-                    self.img_num_channels[:, self.equalize_time[i]],
-                    self.file,
-                    scale=None,
-                    normalize_input=False,
-                )
-                f_reference = f_reference[:, :, self.instructions[i]["target_channel"]]
-            else:
-                f_reference = None
-
-            self.instructions[i].update({"equalize_reference": f_reference})
-
-    def load_threshold_config(self):
-
-        self.instructions = []
-        for inst in self.threshold_instructions:
-            if os.path.exists(inst):
-                with open(inst, "r") as f:
-                    self.instructions.append(json.load(f))
-            else:
-                print("The configuration path is not valid. Abort.")
-                self.abort_process()
-
-    def extract_threshold_parameters(self):
-
-        self.required_channels = []
-        self.equalize = []
-        self.equalize_time = []
-
-        for i in range(len(self.instructions)):
-            ch = [self.instructions[i]["target_channel"]]
-            self.required_channels.append(ch)
-
-            if "equalize_reference" in self.instructions[i]:
-                equalize, equalize_time = self.instructions[i]["equalize_reference"]
-                self.equalize.append(equalize)
-                self.equalize_time.append(equalize_time)
-
-    def write_log(self):
-
-        log = f"Threshold segmentation: {self.threshold_instructions}\n"
-        with open(self.pos + f"log_{self.mode}.txt", "a") as f:
-            f.write(f"{datetime.datetime.now()} SEGMENT \n")
-            f.write(log)
-
-    def detect_channels(self):
-
-        for i in range(len(self.instructions)):
-
-            self.channel_indices = _extract_channel_indices_from_config(
-                self.config, self.required_channels[i]
-            )
-            print(
-                f"Required channels: {self.required_channels[i]} located at channel indices {self.channel_indices}."
-            )
-            self.instructions[i].update({"target_channel": self.channel_indices[0]})
-            self.instructions[i].update({"channel_names": self.channel_names})
-
-        self.img_num_channels = _get_img_num_per_channel(
-            np.arange(self.nbr_channels), self.len_movie, self.nbr_channels
-        )
-
-    def parallel_job(self, indices):
-
-        try:
-
-            for t in tqdm(
-                indices, desc="frame"
-            ):  # for t in tqdm(range(self.len_movie),desc="frame"):
-
-                # Load channels at time t
-                masks = []
-                for i in range(len(self.instructions)):
-                    f = load_frames(
-                        self.img_num_channels[:, t],
-                        self.file,
-                        scale=None,
-                        normalize_input=False,
-                    )
-                    mask = segment_frame_from_thresholds(f, **self.instructions[i])
-                    # print(f'Frame {t}; segment with {self.instructions[i]=}...')
-                    masks.append(mask)
-
-                if len(self.instructions) > 1:
-                    mask = merge_instance_segmentation(masks, mode="OR")
-
-                save_tiff_imagej_compatible(
-                    os.sep.join(
-                        [self.pos, self.label_folder, f"{str(t).zfill(4)}.tif"]
-                    ),
-                    mask.astype(np.uint16),
-                    axes="YX",
-                )
-
-                del f
-                del mask
-                gc.collect()
-
-                # Send signal for progress bar
-                self.sum_done += 1 / self.len_movie * 100
-                mean_exec_per_step = (time.time() - self.t0) / (
-                    self.sum_done * self.len_movie / 100 + 1
-                )
-                pred_time = (
-                    self.len_movie - (self.sum_done * self.len_movie / 100 + 1)
-                ) * mean_exec_per_step
-                self.queue.put([self.sum_done, pred_time])
-
-        except Exception as e:
-            print(e)
-
-        return
-
-    def run(self):
-
-        self.indices = list(range(self.img_num_channels.shape[1]))
-        if self.flip:
-            self.indices = np.array(list(reversed(self.indices)))
-
-        chunks = np.array_split(self.indices, self.n_threads)
-
-        with concurrent.futures.ThreadPoolExecutor(
-            max_workers=self.n_threads
-        ) as executor:
-            results = results = executor.map(
-                self.parallel_job, chunks
-            )  # list(map(lambda x: executor.submit(self.parallel_job, x), chunks))
-            try:
-                for i, return_value in enumerate(results):
-                    print(f"Thread {i} output check: ", return_value)
-            except Exception as e:
-                print("Exception: ", e)
-
-        print("Done.")
-        # Send end signal
-        self.queue.put("finished")
-        self.queue.close()