celldetective 1.2.1__py3-none-any.whl → 1.2.2.post1__py3-none-any.whl

celldetective/scripts/track_cells.py

@@ -7,12 +7,11 @@ import datetime
 import os
 import json
 from celldetective.io import auto_load_number_of_frames, load_frames, interpret_tracking_configuration
-from celldetective.utils import extract_experiment_channels, _extract_channel_indices_from_config, _extract_channel_indices, ConfigSectionMap, _extract_nbr_channels_from_config, _get_img_num_per_channel, extract_experiment_channels
+from celldetective.utils import extract_experiment_channels, ConfigSectionMap, _get_img_num_per_channel, extract_experiment_channels
 from celldetective.measure import drop_tonal_features, measure_features
 from celldetective.tracking import track
 from pathlib import Path, PurePath
 from glob import glob
-from shutil import rmtree
 from tqdm import tqdm
 import numpy as np
 import pandas as pd
@@ -21,7 +20,6 @@ import os
 from natsort import natsorted
 from art import tprint
 from tifffile import imread
-import threading
 
 tprint("Track")
 
@@ -60,7 +58,6 @@ 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.'
-print("Configuration file: ",config)
 
 # from exp config fetch spatial calib, channel names
 movie_prefix = ConfigSectionMap(config,"MovieSettings")["movie_prefix"]
@@ -76,10 +73,9 @@ 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}"))
 if os.path.exists(instr_path):
-	print(f"Tracking instructions for the {mode} population has been successfully located.")
+	print(f"Tracking instructions for the {mode} population have been successfully loaded...")
 	with open(instr_path, 'r') as f:
 		instructions = json.load(f)
-		print("Reading the following instructions: ",instructions)
 	btrack_config = interpret_tracking_configuration(instructions['btrack_config_path'])
 
 	if 'features' in instructions:
@@ -102,7 +98,7 @@ if os.path.exists(instr_path):
 	else:
 		post_processing_options = None
 else:
-	print('No tracking instructions found. Use standard bTrack motion model.')
+	print('Tracking instructions could not be located... Using a standard bTrack motion model instead...')
 	btrack_config = interpret_tracking_configuration(None)
 	features = None
 	mask_channels = None
@@ -117,7 +113,7 @@ label_path = natsorted(glob(pos+f"{label_folder}"+os.sep+"*.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...")
+	print(f"No segmented frames have been found. Please run segmentation first. Abort...")
 	os.abort()
 
 # Do this if features or Haralick is not None, else don't need stack
@@ -168,14 +164,20 @@ def measure_index(indices):
 # Multithreading
 indices = list(range(img_num_channels.shape[1]))
 chunks = np.array_split(indices, n_threads)
-threads = []
-for i in range(n_threads):
-	thread_i = threading.Thread(target=measure_index, args=[chunks[i]])
-	threads.append(thread_i)
-for th in threads:
-	th.start()
-for th in threads:
-	th.join()
+
+import concurrent.futures
+
+with concurrent.futures.ThreadPoolExecutor() as executor:
+	executor.map(measure_index, chunks)
+
+# threads = []
+# for i in range(n_threads):
+# 	thread_i = threading.Thread(target=measure_index, args=[chunks[i]])
+# 	threads.append(thread_i)
+# for th in threads:
+# 	th.start()
+# for th in threads:
+# 	th.join()
 
 df = pd.concat(timestep_dataframes)	
 df.reset_index(inplace=True, drop=True)
@@ -202,8 +204,6 @@ trajectories, napari_data = track(None,
 		  			clean_trajectories_kwargs=post_processing_options, 
 		  			volume=(shape_x, shape_y),
 		  			)
-print(trajectories)
-print(trajectories.columns)
 
 # out trajectory table, create POSITION_X_um, POSITION_Y_um, TIME_min (new ones)
 # Save napari data

celldetective/scripts/train_segmentation_model.py

@@ -11,11 +11,10 @@ from tqdm import tqdm
 import numpy as np
 import random
 
-from celldetective.utils import load_image_dataset, normalize_per_channel, augmenter, interpolate_nan
+from celldetective.utils import load_image_dataset, augmenter, interpolate_nan
 from celldetective.io import normalize_multichannel
 from stardist import fill_label_holes
 from art import tprint
-import matplotlib.pyplot as plt
 from distutils.dir_util import copy_tree
 from csbdeep.utils import save_json
 

celldetective/scripts/train_signal_model.py

@@ -5,11 +5,8 @@ Copright © 2023 Laboratoire Adhesion et Inflammation, Authored by Remy Torro.
 import argparse
 import os
 import json
-from pathlib import Path, PurePath
 from glob import glob
-from tqdm import tqdm
 import numpy as np
-import gc
 from art import tprint
 from celldetective.signals import SignalDetectionModel
 from celldetective.io import locate_signal_model

celldetective/segmentation.py

@@ -3,7 +3,7 @@ Segmentation module
 """
 import json
 import os
-from .io import locate_segmentation_model, get_stack_normalization_values, normalize_multichannel
+from .io import locate_segmentation_model, normalize_multichannel
 from .utils import _estimate_scale_factor, _extract_channel_indices
 from pathlib import Path
 from tqdm import tqdm

celldetective/signals.py

@@ -9,7 +9,7 @@ from tensorflow.keras.losses import CategoricalCrossentropy, MeanSquaredError, M
 from tensorflow.keras.metrics import Precision, Recall, MeanIoU
 from tensorflow.keras.models import load_model,clone_model
 from tensorflow.config.experimental import list_physical_devices, set_memory_growth
-from tensorflow.keras.utils import to_categorical, plot_model
+from tensorflow.keras.utils import to_categorical
 from tensorflow.keras import Input, Model
 from tensorflow.keras.layers import Conv1D, BatchNormalization, Dense, Activation, Add, MaxPooling1D, Dropout, GlobalAveragePooling1D, Concatenate, ZeroPadding1D, Flatten
 from tensorflow.keras.callbacks import Callback
@@ -18,13 +18,12 @@ from sklearn.metrics import jaccard_score, balanced_accuracy_score, precision_sc
 from scipy.interpolate import interp1d
 from scipy.ndimage import shift
 
-from celldetective.io import get_signal_models_list, locate_signal_model, get_position_pickle, get_position_table
+from celldetective.io import locate_signal_model, get_position_pickle, get_position_table
 from celldetective.tracking import clean_trajectories, interpolate_nan_properties
 from celldetective.utils import regression_plot, train_test_split, compute_weights
 import matplotlib.pyplot as plt
 from natsort import natsorted
 from glob import glob
-import shutil
 import random
 from celldetective.utils import color_from_status, color_from_class
 from math import floor, ceil
@@ -3074,7 +3073,7 @@ def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], retu
 	3. Tracks with missing or NaN values in the specified signal are ignored during calculation.
 	4. Tracks are aligned based on their 'FRAME' values and the specified `time_col` (if provided).
 	"""
-	
+
 	assert signal_name in list(df.columns),"The signal you want to plot is not one of the measured features."
 	if isinstance(class_value,int):
 		class_value = [class_value]
@@ -3083,6 +3082,11 @@ def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], retu
 		max_duration = ceil(np.amax(df.groupby(['position','TRACK_ID']).size().values))
 	else:
 		max_duration = forced_max_duration
+	
+	abs_time = False
+	if isinstance(time_col, (int,float)):
+		abs_time = True
+
 	n_tracks = len(df.groupby(['position','TRACK_ID']))
 	signal_matrix = np.zeros((n_tracks,int(max_duration)*2 + 1))
 	signal_matrix[:,:] = np.nan
@@ -3094,11 +3098,16 @@ def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], retu
 		cclass = track_group[class_col].to_numpy()[0]
 		if cclass != 0:
 			ref_time = 0
+			if abs_time:
+				ref_time = time_col
 		else:
-			try:
-				ref_time = floor(track_group[time_col].to_numpy()[0])
-			except:
-				continue
+			if not abs_time:
+				try:
+					ref_time = floor(track_group[time_col].to_numpy()[0])
+				except:
+					continue
+			else:
+				ref_time = time_col
 		if conflict_mode=='mean':
 			signal = track_group.groupby('FRAME')[signal_name].mean().to_numpy()
 		elif conflict_mode=='first':

celldetective/tracking.py

@@ -10,7 +10,6 @@ from celldetective.measure import measure_features
 from celldetective.utils import rename_intensity_column, velocity_per_track
 from celldetective.io import view_on_napari_btrack, interpret_tracking_configuration
 
-from btrack.datasets import cell_config
 import os
 import subprocess
 
@@ -153,6 +152,8 @@ def track(labels, configuration=None, stack=None, spatial_calibration=1, feature
 		df_temp = pd.DataFrame(x_scaled, columns=columns, index = df.index)
 		df[columns] = df_temp
 
+	# set dummy features to NaN
+	df.loc[df['dummy'],['class_id']+columns] = np.nan 
 	df = df.sort_values(by=[column_labels['track'],column_labels['time']])
 	df = velocity_per_track(df, window_size=3, mode='bi')
 

celldetective/utils.py

@@ -17,7 +17,6 @@ import json
 from csbdeep.utils import normalize_mi_ma
 from glob import glob
 from urllib.request import urlopen
-from urllib.parse import urlparse
 import zipfile
 from tqdm import tqdm
 import shutil
@@ -2435,4 +2434,45 @@ def collapse_trajectories_by_status(df, status=None, projection='mean', populati
 	group_table = group_table.sort_values(by=groupby_columns + [status],ignore_index=True)
 	group_table = group_table.reset_index(drop=True)
 
-	return group_table
+	return group_table
+
+def step_function(t, t_shift, dt):
+
+	"""
+	Computes a step function using the logistic sigmoid function.
+
+	This function calculates the value of a sigmoid function, which is often used to model
+	a step change or transition. The sigmoid function is defined as:
+	
+	.. math::
+		f(t) = \\frac{1}{1 + \\exp{\\left( -\\frac{t - t_{shift}}{dt} \\right)}}
+	
+	where `t` is the input variable, `t_shift` is the point of the transition, and `dt` controls
+	the steepness of the transition.
+
+	Parameters
+	----------
+	t : array_like
+		The input values for which the step function will be computed.
+	t_shift : float
+		The point in the `t` domain where the transition occurs.
+	dt : float
+		The parameter that controls the steepness of the transition. Smaller values make the
+		transition steeper, while larger values make it smoother.
+
+	Returns
+	-------
+	array_like
+		The computed values of the step function for each value in `t`.
+
+	Examples
+	--------
+	>>> import numpy as np
+	>>> t = np.array([0, 1, 2, 3, 4, 5])
+	>>> t_shift = 2
+	>>> dt = 1
+	>>> step_function(t, t_shift, dt)
+	array([0.26894142, 0.37754067, 0.5       , 0.62245933, 0.73105858, 0.81757448])
+	"""
+
+	return 1/(1+np.exp(-(t-t_shift)/dt))

{celldetective-1.2.1.dist-info → celldetective-1.2.2.post1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.2.1
+Version: 1.2.2.post1
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -12,14 +12,14 @@ Requires-Dist: wheel
 Requires-Dist: nbsphinx
 Requires-Dist: nbsphinx-link
 Requires-Dist: sphinx-rtd-theme
-Requires-Dist: sphinx==5.0.2
-Requires-Dist: jinja2<3.1
+Requires-Dist: sphinx
+Requires-Dist: jinja2
 Requires-Dist: ipykernel
 Requires-Dist: stardist
 Requires-Dist: cellpose<3
 Requires-Dist: scikit-learn
 Requires-Dist: btrack
-Requires-Dist: tensorflow<=2.12.1
+Requires-Dist: tensorflow~=2.15.0
 Requires-Dist: napari
 Requires-Dist: tqdm
 Requires-Dist: mahotas
@@ -32,9 +32,10 @@ Requires-Dist: seaborn
 Requires-Dist: opencv-python-headless==4.7.0.72
 Requires-Dist: liblapack
 Requires-Dist: gputools
-Requires-Dist: lmfit~=1.2.2
-Requires-Dist: superqt[cmap]>=0.6.1
+Requires-Dist: lmfit
+Requires-Dist: superqt[cmap]
 Requires-Dist: matplotlib-scalebar
+Requires-Dist: numpy==1.26.4
 
 # Celldetective
 
@@ -165,23 +166,25 @@ steps.
 
 To use the software, you must install python, *e.g.* through
 [Anaconda](https://www.anaconda.com/download). We developed and tested
-the software in Python 3.9.18.
+the software in Python 3.9 and more recently 3.11.
 
 # Installation
 
 ## Stable release
 
-Celldetective can be installed with `pip`:
+Celldetective requires a version of Python between 3.9 and 3.11 (included). If your Python version is older or more recent, consider using `conda` to create an environment as described below.
+
+With the proper Python version, Celldetective can be directly installed with `pip`:
 
 ``` bash
 pip install celldetective
 ```
 
-We recommend that you create an environment to use Celldetective, *e.g.*
+We recommend that you create an environment to use Celldetective, to protect your package versions and fix the Python version *e.g.*
 with `conda`:
 
 ``` bash
-conda create -n celldetective python=3.9.18 pyqt
+conda create -n celldetective python=3.11 pyqt
 conda activate celldetective
 pip install celldetective
 ```
@@ -207,6 +210,10 @@ will be immediately available in the python environment:
 git clone git://github.com/remyeltorro/celldetective.git
 cd celldetective
 
+# optional: create an environment
+conda create -n celldetective python=3.11 pyqt
+conda activate celldetective
+
 # install the celldetective package in editable/development mode
 pip install -r requirements.txt
 pip install -e .
@@ -229,10 +236,10 @@ with package requirements for other projects. Run the following lines to
 create an environment named \"celldetective\":
 
 ``` bash
-conda create -n celldetective python=3.9.18 pyqt
+conda create -n celldetective python=3.11 pyqt
 conda activate celldetective
 pip install -r requirements.txt
-pip install .
+pip install -e .
 ```
 
 The installation of the dependencies will take a few minutes (up to half

celldetective-1.2.2.post1.dist-info/RECORD

@@ -0,0 +1,86 @@
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{celldetective-1.2.1.dist-info → celldetective-1.2.2.post1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (73.0.1)
+Generator: setuptools (75.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

celldetective/models/segmentation_effectors/primNK_cfse/config_input.json

@@ -1,29 +0,0 @@
-{
-    "channels": [
-        "effector_fluo_channel",
-        "None"
-    ],
-    "diameter": 30.0,
-    "cellprob_threshold": 0.0,
-    "flow_threshold": 0.4,
-    "normalization_percentile": [
-        true,
-        true
-    ],
-    "normalization_clip": [
-        true,
-        true
-    ],
-    "normalization_values": [
-        [
-            0.5,
-            99.0
-        ],
-        [
-            1.0,
-            99.0
-        ]
-    ],
-    "model_type": "cellpose",
-    "spatial_calibration": 0.21783999999999998
-}

celldetective/models/segmentation_effectors/primNK_cfse/training_instructions.json

@@ -1,37 +0,0 @@
-{
-    "model_name": "cp-cfse-transfer",
-    "model_type": "cellpose",
-    "pretrained": "/home/limozin/Documents/GitHub/celldetective/celldetective/models/segmentation_generic/CP_cyto2",
-    "spatial_calibration": 0.21783999999999998,
-    "channel_option": [
-        "effector_fluo_channel",
-        "None"
-    ],
-    "normalization_percentile": [
-        true,
-        true
-    ],
-    "normalization_clip": [
-        true,
-        true
-    ],
-    "normalization_values": [
-        [
-            0.5,
-            99.0
-        ],
-        [
-            1.0,
-            99.0
-        ]
-    ],
-    "ds": [
-        "/home/limozin/Desktop/primNK_w_MCF7/dataset"
-    ],
-    "augmentation_factor": 1.5,
-    "validation_split": 0.2,
-    "learning_rate": 0.001,
-    "batch_size": 8,
-    "epochs": 3000,
-    "target_directory": "/home/limozin/Documents/GitHub/celldetective/celldetective/models/segmentation_effectors"
-}