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

celldetective/scripts/measure_cells.py

@@ -5,10 +5,34 @@ Copright © 2022 Laboratoire Adhesion et Inflammation, Authored by Remy Torro.
 import argparse
 import os
 import json
-from celldetective.io import auto_load_number_of_frames, load_frames, fix_missing_labels, locate_labels, extract_position_name
-from celldetective.utils import extract_experiment_channels, config_section_to_dict, _get_img_num_per_channel, extract_experiment_channels
-from celldetective.utils import _remove_invalid_cols, remove_redundant_features, remove_trajectory_measurements, _extract_coordinates_from_features
-from celldetective.measure import drop_tonal_features, measure_features, measure_isotropic_intensity, center_of_mass_to_abs_coordinates, measure_radial_distance_to_center
+from celldetective.utils.image_loaders import (
+    locate_labels,
+    auto_load_number_of_frames,
+    load_frames,
+    fix_missing_labels,
+    _get_img_num_per_channel,
+)
+from celldetective.utils.experiment import (
+    extract_position_name,
+    extract_experiment_channels,
+)
+from celldetective import (
+    extract_experiment_channels,
+)
+from celldetective.utils.parsing import config_section_to_dict
+from celldetective.utils.data_cleaning import (
+    _remove_invalid_cols,
+    _extract_coordinates_from_features,
+    remove_redundant_features,
+    remove_trajectory_measurements,
+)
+from celldetective.measure import (
+    drop_tonal_features,
+    measure_features,
+    measure_isotropic_intensity,
+    center_of_mass_to_abs_coordinates,
+    measure_radial_distance_to_center,
+)
 from pathlib import Path, PurePath
 from glob import glob
 from tqdm import tqdm
@@ -20,38 +44,54 @@ import datetime
 
 tprint("Measure")
 
-parser = argparse.ArgumentParser(description="Measure features and intensities in a multichannel timeseries.",
-								formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-parser.add_argument('-p',"--position", required=True, help="Path to the position")
-parser.add_argument("--mode", default="target", choices=["target","effector","targets","effectors"],help="Cell population of interest")
+parser = argparse.ArgumentParser(
+    description="Measure features and intensities in a multichannel timeseries.",
+    formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+)
+parser.add_argument("-p", "--position", required=True, help="Path to the position")
+parser.add_argument(
+    "--mode",
+    default="target",
+    choices=["target", "effector", "targets", "effectors"],
+    help="Cell population of interest",
+)
 parser.add_argument("--threads", default="1", help="Number of parallel threads")
 
 args = parser.parse_args()
 process_arguments = vars(args)
-pos = str(process_arguments['position'])
-mode = str(process_arguments['mode'])
-n_threads = int(process_arguments['threads'])
-
-column_labels = {'track': "TRACK_ID", 'time': 'FRAME', 'x': 'POSITION_X', 'y': 'POSITION_Y'}
-
-if mode.lower()=="target" or mode.lower()=="targets":
-	label_folder = "labels_targets"
-	table_name = "trajectories_targets.csv"
-	instruction_file = os.sep.join(["configs","measurement_instructions_targets.json"])
-
-elif mode.lower()=="effector" or mode.lower()=="effectors":
-	label_folder = "labels_effectors"
-	table_name = "trajectories_effectors.csv"
-	instruction_file = os.sep.join(["configs","measurement_instructions_effectors.json"])
+pos = str(process_arguments["position"])
+mode = str(process_arguments["mode"])
+n_threads = int(process_arguments["threads"])
+
+column_labels = {
+    "track": "TRACK_ID",
+    "time": "FRAME",
+    "x": "POSITION_X",
+    "y": "POSITION_Y",
+}
+
+if mode.lower() == "target" or mode.lower() == "targets":
+    label_folder = "labels_targets"
+    table_name = "trajectories_targets.csv"
+    instruction_file = os.sep.join(["configs", "measurement_instructions_targets.json"])
+
+elif mode.lower() == "effector" or mode.lower() == "effectors":
+    label_folder = "labels_effectors"
+    table_name = "trajectories_effectors.csv"
+    instruction_file = os.sep.join(
+        ["configs", "measurement_instructions_effectors.json"]
+    )
 
 # Locate experiment config
 parent1 = Path(pos).parent
 expfolder = parent1.parent
-config = PurePath(expfolder,Path("config.ini"))
-assert os.path.exists(config),'The configuration file for the experiment could not be located. Abort.'
+config = PurePath(expfolder, Path("config.ini"))
+assert os.path.exists(
+    config
+), "The configuration file for the experiment could not be located. Abort."
 
 print(f"Position: {extract_position_name(pos)}...")
-print("Configuration file: ",config)
+print("Configuration file: ", config)
 print(f"Population: {mode}...")
 
 # from exp config fetch spatial calib, channel names
@@ -63,139 +103,147 @@ channel_names, channel_indices = extract_experiment_channels(expfolder)
 nbr_channels = len(channel_names)
 
 # from tracking instructions, fetch btrack config, features, haralick, clean_traj, idea: fetch custom timeline?
-instr_path = PurePath(expfolder,Path(f"{instruction_file}"))
-print('Looking for measurement instruction file...')
+instr_path = PurePath(expfolder, Path(f"{instruction_file}"))
+print("Looking for measurement 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}...")
-
-	if 'background_correction' in instructions:
-		background_correction = instructions['background_correction']
-	else:
-		background_correction = None
-
-	if 'features' in instructions:
-		features = instructions['features']
-	else:
-		features = None
-
-	if 'border_distances' in instructions:
-		border_distances = instructions['border_distances']
-	else:
-		border_distances = None
-
-	if 'spot_detection' in instructions:
-		spot_detection = instructions['spot_detection']
-	else:
-		spot_detection = None
-
-	if 'haralick_options' in instructions:
-		haralick_options = instructions['haralick_options']
-	else:
-		haralick_options = None
-
-	if 'intensity_measurement_radii' in instructions:
-		intensity_measurement_radii = instructions['intensity_measurement_radii']
-	else:
-		intensity_measurement_radii = None
-
-	if 'isotropic_operations' in instructions:
-		isotropic_operations = instructions['isotropic_operations']
-	else:
-		isotropic_operations = None
-
-	if 'clear_previous' in instructions:
-		clear_previous = instructions['clear_previous']
-	else:
-		clear_previous = True
+    with open(instr_path, "r") as f:
+        instructions = json.load(f)
+        print(f"Measurement instruction file successfully loaded...")
+        print(f"Instructions: {instructions}...")
+
+    if "background_correction" in instructions:
+        background_correction = instructions["background_correction"]
+    else:
+        background_correction = None
+
+    if "features" in instructions:
+        features = instructions["features"]
+    else:
+        features = None
+
+    if "border_distances" in instructions:
+        border_distances = instructions["border_distances"]
+    else:
+        border_distances = None
+
+    if "spot_detection" in instructions:
+        spot_detection = instructions["spot_detection"]
+    else:
+        spot_detection = None
+
+    if "haralick_options" in instructions:
+        haralick_options = instructions["haralick_options"]
+    else:
+        haralick_options = None
+
+    if "intensity_measurement_radii" in instructions:
+        intensity_measurement_radii = instructions["intensity_measurement_radii"]
+    else:
+        intensity_measurement_radii = None
+
+    if "isotropic_operations" in instructions:
+        isotropic_operations = instructions["isotropic_operations"]
+    else:
+        isotropic_operations = None
+
+    if "clear_previous" in instructions:
+        clear_previous = instructions["clear_previous"]
+    else:
+        clear_previous = True
 
 else:
-	print('No measurement instructions found. Use default measurements.')
-	features = ['area', 'intensity_mean']
-	border_distances = None
-	haralick_options = None
-	clear_previous = False
-	background_correction = None
-	spot_detection = None
-	intensity_measurement_radii = 10
-	isotropic_operations = ['mean']
+    print("No measurement instructions found. Use default measurements.")
+    features = ["area", "intensity_mean"]
+    border_distances = None
+    haralick_options = None
+    clear_previous = False
+    background_correction = None
+    spot_detection = None
+    intensity_measurement_radii = 10
+    isotropic_operations = ["mean"]
 
 if features is None:
-	features = []
+    features = []
 
 # from pos fetch labels
-label_path = natsorted(glob(os.sep.join([pos, label_folder, '*.tif'])))
-if len(label_path)>0:
-	print(f"Found {len(label_path)} segmented frames...")
+label_path = natsorted(glob(os.sep.join([pos, label_folder, "*.tif"])))
+if len(label_path) > 0:
+    print(f"Found {len(label_path)} segmented frames...")
 else:
-	print(f"No segmented frames have been found. Please run segmentation first, skipping... Features cannot be computed.")
-	features = None
-	haralick_options = None
-	border_distances = None
-	label_path = None
+    print(
+        f"No segmented frames have been found. Please run segmentation first, skipping... Features cannot be computed."
+    )
+    features = None
+    haralick_options = None
+    border_distances = None
+    label_path = None
 
 # Do this if features or Haralick is not None, else don't need stack
 try:
-	file = glob(pos+os.sep.join(["movie", f"{movie_prefix}*.tif"]))[0]
+    file = glob(pos + os.sep.join(["movie", f"{movie_prefix}*.tif"]))[0]
 except IndexError:
-	print('Movie could not be found. Check the prefix. If you intended to measure texture or tone, this will not be performed.')
-	file = None
-	haralick_option = None
-	features = drop_tonal_features(features)
+    print(
+        "Movie could not be found. Check the prefix. If you intended to measure texture or tone, this will not be performed."
+    )
+    file = None
+    haralick_option = None
+    features = drop_tonal_features(features)
 
 # Load trajectories, add centroid if not in trajectory
-trajectories = pos+os.sep.join(['output','tables', table_name])
+trajectories = pos + os.sep.join(["output", "tables", table_name])
 if os.path.exists(trajectories):
-	print('A trajectory table was found...')
-	trajectories = pd.read_csv(trajectories)
-	if 'TRACK_ID' not in list(trajectories.columns):
-		do_iso_intensities = False
-		intensity_measurement_radii = None
-		if clear_previous:
-			print('No TRACK_ID... Clear previous measurements...')
-			trajectories = None #remove_trajectory_measurements(trajectories, column_labels)
-			do_features = True
-			features += ['centroid']
-	else:
-		if clear_previous:
-			print('TRACK_ID found... Clear previous measurements...')
-			trajectories = remove_trajectory_measurements(trajectories, column_labels)
+    print("A trajectory table was found...")
+    trajectories = pd.read_csv(trajectories)
+    if "TRACK_ID" not in list(trajectories.columns):
+        do_iso_intensities = False
+        intensity_measurement_radii = None
+        if clear_previous:
+            print("No TRACK_ID... Clear previous measurements...")
+            trajectories = (
+                None  # remove_trajectory_measurements(trajectories, column_labels)
+            )
+            do_features = True
+            features += ["centroid"]
+    else:
+        if clear_previous:
+            print("TRACK_ID found... Clear previous measurements...")
+            trajectories = remove_trajectory_measurements(trajectories, column_labels)
 else:
-	trajectories = None
-	do_features = True
-	features += ['centroid']
-	do_iso_intensities = False
+    trajectories = None
+    do_features = True
+    features += ["centroid"]
+    do_iso_intensities = False
 
 
 len_movie_auto = auto_load_number_of_frames(file)
 if len_movie_auto is not None:
-	len_movie = len_movie_auto
+    len_movie = len_movie_auto
 
 if label_path is not None and file is not None:
-	test = len(label_path)==len_movie
-	if not test:
-		fix_missing_labels(pos, population=mode, prefix=movie_prefix)
-		label_path = natsorted(glob(os.sep.join([pos, label_folder, '*.tif'])))
+    test = len(label_path) == len_movie
+    if not test:
+        fix_missing_labels(pos, population=mode, prefix=movie_prefix)
+        label_path = natsorted(glob(os.sep.join([pos, label_folder, "*.tif"])))
 
 img_num_channels = _get_img_num_per_channel(channel_indices, len_movie, nbr_channels)
 
 
 # Test what to do
 if (file is None) or (intensity_measurement_radii is None):
-	do_iso_intensities = False
-	print('Either no image, no positions or no radii were provided... Isotropic intensities will not be computed...')
+    do_iso_intensities = False
+    print(
+        "Either no image, no positions or no radii were provided... Isotropic intensities will not be computed..."
+    )
 else:
-	do_iso_intensities = True
+    do_iso_intensities = True
 
 if label_path is None:
-	do_features = False
-	print('No labels were provided... Features will not be computed...')
+    do_features = False
+    print("No labels were provided... Features will not be computed...")
 else:
-	do_features = True
+    do_features = True
 
 
 #######################################
@@ -204,76 +252,127 @@ else:
 
 timestep_dataframes = []
 if trajectories is None:
-	print('Use features as a substitute for the trajectory table.')
-	if 'label' not in features:
-		features.append('label')
+    print("Use features as a substitute for the trajectory table.")
+    if "label" not in features:
+        features.append("label")
 
 if label_path is not None:
-	label_names = [os.path.split(lbl)[-1] for lbl in label_path]
-
-
-features_log=f'features: {features}'
-border_distances_log=f'border_distances: {border_distances}'
-haralick_options_log=f'haralick_options: {haralick_options}'
-background_correction_log=f'background_correction: {background_correction}'
-spot_detection_log=f'spot_detection: {spot_detection}'
-intensity_measurement_radii_log=f'intensity_measurement_radii: {intensity_measurement_radii}'
-isotropic_options_log=f'isotropic_operations: {isotropic_operations} \n'
-log='\n'.join([features_log,border_distances_log,haralick_options_log,background_correction_log,spot_detection_log,intensity_measurement_radii_log,isotropic_options_log])
-with open(pos + f'log_{mode}.json', 'a') as f:
-	f.write(f'{datetime.datetime.now()} MEASURE \n')
-	f.write(log+'\n')
+    label_names = [os.path.split(lbl)[-1] for lbl in label_path]
+
+
+features_log = f"features: {features}"
+border_distances_log = f"border_distances: {border_distances}"
+haralick_options_log = f"haralick_options: {haralick_options}"
+background_correction_log = f"background_correction: {background_correction}"
+spot_detection_log = f"spot_detection: {spot_detection}"
+intensity_measurement_radii_log = (
+    f"intensity_measurement_radii: {intensity_measurement_radii}"
+)
+isotropic_options_log = f"isotropic_operations: {isotropic_operations} \n"
+log = "\n".join(
+    [
+        features_log,
+        border_distances_log,
+        haralick_options_log,
+        background_correction_log,
+        spot_detection_log,
+        intensity_measurement_radii_log,
+        isotropic_options_log,
+    ]
+)
+with open(pos + f"log_{mode}.json", "a") as f:
+    f.write(f"{datetime.datetime.now()} MEASURE \n")
+    f.write(log + "\n")
 
 
 def measure_index(indices):
 
-	#global column_labels
-
-	for t in tqdm(indices,desc="frame"):
-
-		if file is not None:
-			img = load_frames(img_num_channels[:,t], file, scale=None, normalize_input=False)
-
-		if label_path is not None:
-			
-			lbl = locate_labels(pos, population=mode, frames=t)
-			if lbl is None:
-				continue
-
-		if trajectories is not None:
-
-			positions_at_t = trajectories.loc[trajectories[column_labels['time']]==t].copy()
-
-		if do_features:
-			feature_table = measure_features(img, lbl, features=features, border_dist=border_distances,
-											 channels=channel_names, haralick_options=haralick_options, verbose=False,
-											 normalisation_list=background_correction, spot_detection=spot_detection)
-			if trajectories is None:
-				positions_at_t = _extract_coordinates_from_features(feature_table, timepoint=t)
-				column_labels = {'track': "ID", 'time': column_labels['time'], 'x': column_labels['x'],
-								 'y': column_labels['y']}
-			feature_table.rename(columns={'centroid-1': 'POSITION_X', 'centroid-0': 'POSITION_Y'}, inplace=True)
-		
-		if do_iso_intensities and not trajectories is None:
-			iso_table = measure_isotropic_intensity(positions_at_t, img, channels=channel_names, intensity_measurement_radii=intensity_measurement_radii, column_labels=column_labels, operations=isotropic_operations, verbose=False)
-
-		if do_iso_intensities and do_features and not trajectories is None:
-			measurements_at_t = iso_table.merge(feature_table, how='outer', on='class_id',suffixes=('_delme', ''))
-			measurements_at_t = measurements_at_t[[c for c in measurements_at_t.columns if not c.endswith('_delme')]]
-		elif do_iso_intensities * (not do_features) * (not trajectories is None):
-			measurements_at_t = iso_table
-		elif do_features:
-			measurements_at_t = positions_at_t.merge(feature_table, how='outer', on='class_id',suffixes=('_delme', ''))
-			measurements_at_t = measurements_at_t[[c for c in measurements_at_t.columns if not c.endswith('_delme')]]
-
-		measurements_at_t = center_of_mass_to_abs_coordinates(measurements_at_t)
-		measurements_at_t = measure_radial_distance_to_center(measurements_at_t, volume=img.shape, column_labels=column_labels)
-
-		if measurements_at_t is not None:
-			measurements_at_t[column_labels['time']] = t
-			timestep_dataframes.append(measurements_at_t)
-
-	return
+    # global column_labels
+
+    for t in tqdm(indices, desc="frame"):
+
+        if file is not None:
+            img = load_frames(
+                img_num_channels[:, t], file, scale=None, normalize_input=False
+            )
+
+        if label_path is not None:
+
+            lbl = locate_labels(pos, population=mode, frames=t)
+            if lbl is None:
+                continue
+
+        if trajectories is not None:
+
+            positions_at_t = trajectories.loc[
+                trajectories[column_labels["time"]] == t
+            ].copy()
+
+        if do_features:
+            feature_table = measure_features(
+                img,
+                lbl,
+                features=features,
+                border_dist=border_distances,
+                channels=channel_names,
+                haralick_options=haralick_options,
+                verbose=False,
+                normalisation_list=background_correction,
+                spot_detection=spot_detection,
+            )
+            if trajectories is None:
+                positions_at_t = _extract_coordinates_from_features(
+                    feature_table, timepoint=t
+                )
+                column_labels = {
+                    "track": "ID",
+                    "time": column_labels["time"],
+                    "x": column_labels["x"],
+                    "y": column_labels["y"],
+                }
+            feature_table.rename(
+                columns={"centroid-1": "POSITION_X", "centroid-0": "POSITION_Y"},
+                inplace=True,
+            )
+
+        if do_iso_intensities and not trajectories is None:
+            iso_table = measure_isotropic_intensity(
+                positions_at_t,
+                img,
+                channels=channel_names,
+                intensity_measurement_radii=intensity_measurement_radii,
+                column_labels=column_labels,
+                operations=isotropic_operations,
+                verbose=False,
+            )
+
+        if do_iso_intensities and do_features and not trajectories is None:
+            measurements_at_t = iso_table.merge(
+                feature_table, how="outer", on="class_id", suffixes=("_delme", "")
+            )
+            measurements_at_t = measurements_at_t[
+                [c for c in measurements_at_t.columns if not c.endswith("_delme")]
+            ]
+        elif do_iso_intensities * (not do_features) * (not trajectories is None):
+            measurements_at_t = iso_table
+        elif do_features:
+            measurements_at_t = positions_at_t.merge(
+                feature_table, how="outer", on="class_id", suffixes=("_delme", "")
+            )
+            measurements_at_t = measurements_at_t[
+                [c for c in measurements_at_t.columns if not c.endswith("_delme")]
+            ]
+
+        measurements_at_t = center_of_mass_to_abs_coordinates(measurements_at_t)
+        measurements_at_t = measure_radial_distance_to_center(
+            measurements_at_t, volume=img.shape, column_labels=column_labels
+        )
+
+        if measurements_at_t is not None:
+            measurements_at_t[column_labels["time"]] = t
+            timestep_dataframes.append(measurements_at_t)
+
+    return
 
 
 print(f"Starting the measurements with {n_threads} thread(s)...")
@@ -285,33 +384,35 @@ indices = list(range(img_num_channels.shape[1]))
 chunks = np.array_split(indices, n_threads)
 
 with concurrent.futures.ThreadPoolExecutor() as executor:
-	results = executor.map(measure_index, chunks)
-	try:
-		for i,return_value in enumerate(results):
-			print(f"Thread {i} output check: ",return_value)
-	except Exception as e:
-		print("Exception: ", e)
+    results = executor.map(measure_index, 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.")
 
-print('Done.')
 
+if len(timestep_dataframes) > 0:
 
-if len(timestep_dataframes)>0:
-	
-	df = pd.concat(timestep_dataframes)	
+    df = pd.concat(timestep_dataframes)
 
-	if trajectories is not None:
-		df = df.sort_values(by=[column_labels['track'],column_labels['time']])
-		df = df.dropna(subset=[column_labels['track']])
-	else:
-		df['ID'] = np.arange(len(df))
-		df = df.sort_values(by=[column_labels['time'], 'ID'])
+    if trajectories is not None:
+        df = df.sort_values(by=[column_labels["track"], column_labels["time"]])
+        df = df.dropna(subset=[column_labels["track"]])
+    else:
+        df["ID"] = np.arange(len(df))
+        df = df.sort_values(by=[column_labels["time"], "ID"])
 
-	df = df.reset_index(drop=True)
-	df = _remove_invalid_cols(df)
+    df = df.reset_index(drop=True)
+    df = _remove_invalid_cols(df)
 
-	df.to_csv(pos+os.sep.join(["output", "tables", table_name]), index=False)
-	print(f'Measurement table successfully exported in  {os.sep.join(["output", "tables"])}...')
-	print('Done.')
+    df.to_csv(pos + os.sep.join(["output", "tables", table_name]), index=False)
+    print(
+        f'Measurement table successfully exported in  {os.sep.join(["output", "tables"])}...'
+    )
+    print("Done.")
 else:
-	print('No measurement could be performed. Check your inputs.')
-	print('Done.')
+    print("No measurement could be performed. Check your inputs.")
+    print("Done.")