celldetective 1.4.0__py3-none-any.whl → 1.4.1__py3-none-any.whl

celldetective/utils.py

@@ -1,8 +1,6 @@
-
 import numpy as np
 import pandas as pd
 import matplotlib.pyplot as plt
-import re
 import os
 from scipy.ndimage import shift, zoom
 os.environ['TF_CPP_MIN_VLOG_LEVEL'] = '3'
@@ -31,11 +29,11 @@ from scipy.stats import ks_2samp
 from cliffs_delta import cliffs_delta
 from stardist.models import StarDist2D
 from cellpose.models import CellposeModel
-from pathlib import PosixPath, PurePosixPath, WindowsPath
+from pathlib import PosixPath, PurePath, PurePosixPath, WindowsPath, Path
 from prettytable import PrettyTable
+from typing import List, Dict, Union, Optional
 
-
-def is_integer_array(arr):
+def is_integer_array(arr: np.ndarray) -> bool:
 
 	# Mask out NaNs
 	non_nan_values = arr[arr==arr].flatten()
@@ -46,7 +44,7 @@ def is_integer_array(arr):
 	else:
 		return False
 
-def get_config(experiment):
+def get_config(experiment: Union[str,Path]) -> str:
 
 	"""
 	Retrieves the path to the configuration file for a given experiment.
@@ -94,7 +92,7 @@ def get_config(experiment):
 	return config
 
 
-def _remove_invalid_cols(df):
+def _remove_invalid_cols(df: pd.DataFrame) -> pd.DataFrame:
 
 	"""
 	Removes invalid columns from a DataFrame.
@@ -120,7 +118,7 @@ def _remove_invalid_cols(df):
 	df = df.dropna(axis=1, how='all')
 	return df
 
-def _extract_coordinates_from_features(df, timepoint):
+def _extract_coordinates_from_features(df: pd.DataFrame, timepoint: int) -> pd.DataFrame:
 
 	"""
 	Re-format coordinates from a regionprops table to tracking/measurement table format. 
@@ -161,7 +159,7 @@ def _extract_coordinates_from_features(df, timepoint):
 
 	return coords
 
-def _mask_intensity_measurements(df, mask_channels):
+def _mask_intensity_measurements(df: pd.DataFrame, mask_channels: Optional[List[str]]):
 
 	"""
 	Removes columns from a DataFrame that match specific channel name patterns.
@@ -210,7 +208,7 @@ def _mask_intensity_measurements(df, mask_channels):
 			df = df.drop(cols_to_drop, axis=1)
 	return df
 
-def _rearrange_multichannel_frame(frame, n_channels=None):
+def _rearrange_multichannel_frame(frame: np.ndarray, n_channels: Optional[int] = None) -> np.ndarray:
 
 	"""
 	Rearranges the axes of a multi-channel frame to ensure the channel axis is at the end.
@@ -271,7 +269,7 @@ def _rearrange_multichannel_frame(frame, n_channels=None):
 
 	return frame
 
-def _fix_no_contrast(frames, value=1):
+def _fix_no_contrast(frames: np.ndarray, value: Union[float,int] = 1):
 
 	"""
 	Ensures that frames with no contrast (i.e., containing only a single unique value) are adjusted.
@@ -310,7 +308,7 @@ def _fix_no_contrast(frames, value=1):
 			frames[0,0,k] += value
 	return frames
 
-def zoom_multiframes(frames, zoom_factor):
+def zoom_multiframes(frames: np.ndarray, zoom_factor: float) -> np.ndarray:
 
 	"""
 	Applies zooming to each frame (channel) in a multi-frame image.
@@ -1153,27 +1151,24 @@ def demangle_column_name(name):
 
 def extract_cols_from_query(query: str):
 	
-	# Track variables in a dictionary to be used as a dictionary of globals. From: https://stackoverflow.com/questions/64576913/extract-pandas-dataframe-column-names-from-query-string
-	
-	variables = {}
+	backtick_pattern = r'`([^`]+)`'
+	backticked = set(re.findall(backtick_pattern, query))
 
-	while True:
-		try:
-			# Try creating a Expr object with the query string and dictionary of globals.
-			# This will raise an error as long as the dictionary of globals is incomplete.
-			env = pd.core.computation.scope.ensure_scope(level=0, global_dict=variables)
-			pd.core.computation.eval.Expr(query, env=env)
+	# 2. Remove backtick sections so they don't get double-counted
+	cleaned_query = re.sub(backtick_pattern, "", query)
 
-			# Exit the loop when evaluation is successful.
-			break
-		except pd.errors.UndefinedVariableError as e:
-			# This relies on the format defined here: https://github.com/pandas-dev/pandas/blob/965ceca9fd796940050d6fc817707bba1c4f9bff/pandas/errors/__init__.py#L401
-			name = re.findall("name '(.+?)' is not defined", str(e))[0]
+	# 3. Extract bare identifiers from the remaining string
+	identifier_pattern = r'\b([A-Za-z_]\w*)\b'
+	bare = set(re.findall(identifier_pattern, cleaned_query))
 
-			# Add the name to the globals dictionary with a dummy value.
-			variables[name] = None
+	# 4. Remove Python keywords, operators, and pandas builtins
+	blacklist = set(dir(pd)) | set(dir(__builtins__)) | {
+		"and", "or", "not", "in", "True", "False"
+	}
+	bare = {c for c in bare if c not in blacklist}
+	cols = backticked | bare
 
-	return [demangle_column_name(name) for name in variables.keys()]
+	return list([demangle_column_name(c) for c in cols])
 
 def create_patch_mask(h, w, center=None, radius=None):
 
@@ -1280,7 +1275,7 @@ def rename_intensity_column(df, channels):
 		sections = np.array(re.split('-|_', intensity_cols[k]))
 		test_digit = np.array([False for s in sections])
 		for j,s in enumerate(sections):
-			if s.isdigit():
+			if str(s).isdigit():
 				if int(s)<len(channel_names):
 					test_digit[j] = True
 			
@@ -1813,8 +1808,8 @@ def _extract_channel_indices(channels, required_channels):
 
 	return channel_indices
 
-def ConfigSectionMap(path,section):
-
+def config_section_to_dict(path: Union[str,PurePath,Path], section: str) -> Union[Dict,None]:
+	
 	"""
 	Parse the config file to extract experiment parameters
 	following https://wiki.python.org/moin/ConfigParserExamples
@@ -1837,7 +1832,7 @@ def ConfigSectionMap(path,section):
 	--------
 	>>> config = "path/to/config_file.ini"
 	>>> section = "Channels"
-	>>> channel_dictionary = ConfigSectionMap(config,section)
+	>>> channel_dictionary = config_section_to_dict(config,section)
 	>>> print(channel_dictionary)
 	# {'brightfield_channel': '0',
 	#  'live_nuclei_channel': 'nan',
@@ -1861,7 +1856,7 @@ def ConfigSectionMap(path,section):
 		try:
 			dict1[option] = Config.get(section, option)
 			if dict1[option] == -1:
-				DebugPrint("skip: %s" % option)
+				print("skip: %s" % option)
 		except:
 			print("exception on %s!" % option)
 			dict1[option] = None
@@ -1915,7 +1910,7 @@ def _extract_channel_indices_from_config(config, channels_to_extract):
 	channels = []
 	for c in channels_to_extract:
 		try:
-			c1 = int(ConfigSectionMap(config,"Channels")[c])
+			c1 = int(config_section_to_dict(config, "Channels")[c])
 			channels.append(c1)
 		except Exception as e:
 			print(f"Warning: The channel {c} required by the model is not available in your data...")
@@ -1941,10 +1936,10 @@ def _extract_nbr_channels_from_config(config, return_names=False):
 	nbr_channels = 0
 	channels = []
 	try:
-		fields = ConfigSectionMap(config,"Channels")
+		fields = config_section_to_dict(config, "Channels")
 		for c in fields:
 			try:
-				channel = int(ConfigSectionMap(config, "Channels")[c])
+				channel = int(config_section_to_dict(config, "Channels")[c])
 				nbr_channels += 1
 				channels.append(c)
 			except:
@@ -1958,49 +1953,49 @@ def _extract_nbr_channels_from_config(config, return_names=False):
 		nbr_channels = 0
 		channels = []
 		try:
-			brightfield_channel = int(ConfigSectionMap(config,"MovieSettings")["brightfield_channel"])
+			brightfield_channel = int(config_section_to_dict(config, "MovieSettings")["brightfield_channel"])
 			nbr_channels += 1
 			channels.append('brightfield_channel')
 		except:
 			brightfield_channel = None
 
 		try:
-			live_nuclei_channel = int(ConfigSectionMap(config,"MovieSettings")["live_nuclei_channel"])
+			live_nuclei_channel = int(config_section_to_dict(config, "MovieSettings")["live_nuclei_channel"])
 			nbr_channels += 1
 			channels.append('live_nuclei_channel')
 		except:
 			live_nuclei_channel = None
 
 		try:
-			dead_nuclei_channel = int(ConfigSectionMap(config,"MovieSettings")["dead_nuclei_channel"])
+			dead_nuclei_channel = int(config_section_to_dict(config, "MovieSettings")["dead_nuclei_channel"])
 			nbr_channels +=1
 			channels.append('dead_nuclei_channel')
 		except:
 			dead_nuclei_channel = None
 
 		try:
-			effector_fluo_channel = int(ConfigSectionMap(config,"MovieSettings")["effector_fluo_channel"])
+			effector_fluo_channel = int(config_section_to_dict(config, "MovieSettings")["effector_fluo_channel"])
 			nbr_channels +=1
 			channels.append('effector_fluo_channel')
 		except:
 			effector_fluo_channel = None
 
 		try:
-			adhesion_channel = int(ConfigSectionMap(config,"MovieSettings")["adhesion_channel"])
+			adhesion_channel = int(config_section_to_dict(config, "MovieSettings")["adhesion_channel"])
 			nbr_channels += 1
 			channels.append('adhesion_channel')
 		except:
 			adhesion_channel = None
 
 		try:
-			fluo_channel_1 = int(ConfigSectionMap(config,"MovieSettings")["fluo_channel_1"])
+			fluo_channel_1 = int(config_section_to_dict(config, "MovieSettings")["fluo_channel_1"])
 			nbr_channels += 1
 			channels.append('fluo_channel_1')
 		except:
 			fluo_channel_1 = None	
 
 		try:
-			fluo_channel_2 = int(ConfigSectionMap(config,"MovieSettings")["fluo_channel_2"])
+			fluo_channel_2 = int(config_section_to_dict(config, "MovieSettings")["fluo_channel_2"])
 			nbr_channels += 1
 			channels.append('fluo_channel_2')
 		except:
@@ -2106,10 +2101,10 @@ def _extract_labels_from_config(config,number_of_wells):
 
 	
 	try:
-		concentrations = ConfigSectionMap(config,"Labels")["concentrations"].split(",")
-		cell_types = ConfigSectionMap(config,"Labels")["cell_types"].split(",")
-		antibodies = ConfigSectionMap(config,"Labels")["antibodies"].split(",")
-		pharmaceutical_agents = ConfigSectionMap(config,"Labels")["pharmaceutical_agents"].split(",")
+		concentrations = config_section_to_dict(config, "Labels")["concentrations"].split(",")
+		cell_types = config_section_to_dict(config, "Labels")["cell_types"].split(",")
+		antibodies = config_section_to_dict(config, "Labels")["antibodies"].split(",")
+		pharmaceutical_agents = config_section_to_dict(config, "Labels")["pharmaceutical_agents"].split(",")
 		index = np.arange(len(concentrations)).astype(int) + 1
 		if not np.all(pharmaceutical_agents=="None"):
 			labels = [f"W{idx}: [CT] "+a+"; [Ab] "+b+" @ "+c+" pM "+d for idx,a,b,c,d in zip(index,cell_types,antibodies,concentrations,pharmaceutical_agents)]
@@ -2155,10 +2150,10 @@ def _extract_channels_from_config(config):
 	channel_names = []
 	channel_indices = []
 	try:
-		fields = ConfigSectionMap(config,"Channels")
+		fields = config_section_to_dict(config, "Channels")
 		for c in fields:
 			try:
-				idx = int(ConfigSectionMap(config, "Channels")[c])
+				idx = int(config_section_to_dict(config, "Channels")[c])
 				channel_names.append(c)
 				channel_indices.append(idx)
 			except:
@@ -2207,7 +2202,7 @@ def extract_experiment_channels(experiment):
 	return _extract_channels_from_config(config)
 
 
-def get_software_location():
+def get_software_location() -> str:
 
 	"""
 	Get the installation folder of celldetective.
@@ -2260,7 +2255,7 @@ def remove_trajectory_measurements(trajectories, column_labels={'track': "TRACK_
 	tracks = trajectories.copy()
 
 	columns_to_keep = [column_labels['track'], column_labels['time'], column_labels['x'], column_labels['y'],column_labels['x']+'_um', column_labels['y']+'_um', 'class_id', 
-					  't', 'state', 'generation', 'root', 'parent', 'ID', 't0', 'class', 'status', 'class_color', 'status_color', 'class_firstdetection', 't_firstdetection', 'velocity']
+					  't', 'state', 'generation', 'root', 'parent', 'ID', 't0', 'class', 'status', 'class_color', 'status_color', 'class_firstdetection', 't_firstdetection', 'status_firstdetection','velocity']
 	cols = list(tracks.columns)
 	for c in columns_to_keep:
 		if c not in cols:
@@ -2852,8 +2847,7 @@ def download_url_to_file(url, dst, progress=True):
 		shutil.move(f.name, dst)
 	finally:
 		f.close()
-		if os.path.exists(f.name):
-			os.remove(f.name)
+		remove_file_if_exists(f.name)
 
 def get_zenodo_files(cat=None):
 
@@ -2985,7 +2979,7 @@ def collapse_trajectories_by_status(df, status=None, projection='mean', populati
 
 	return group_table
 
-def step_function(t, t_shift, dt):
+def step_function(t: Union[np.ndarray,List], t_shift: float, dt: float) -> np.ndarray:
 
 	"""
 	Computes a step function using the logistic sigmoid function.
@@ -3027,7 +3021,7 @@ def step_function(t, t_shift, dt):
 	return 1/(1+np.exp(-(t-t_shift)/dt))
 
 
-def test_2samp_generic(data, feature=None, groupby_cols=None, method="ks_2samp", *args, **kwargs):
+def test_2samp_generic(data: pd.DataFrame, feature: Optional[str] = None, groupby_cols: Optional[Union[str,List[str]]] = None, method="ks_2samp", *args, **kwargs) -> pd.DataFrame:
 
 	"""
 	Performs pairwise statistical tests between groups of data, comparing a specified feature using a chosen method.
@@ -3099,9 +3093,16 @@ def test_2samp_generic(data, feature=None, groupby_cols=None, method="ks_2samp",
 
 	return pivot
 
-def pretty_table(dct):
+def pretty_table(dct: dict):
 	table = PrettyTable()
 	for c in dct.keys():
 		table.add_column(str(c), [])
 	table.add_row([dct.get(c, "") for c in dct.keys()])
-	print(table)
+	print(table)
+
+def remove_file_if_exists(file: Union[str,Path]):
+	if os.path.exists(file):
+		try:
+			os.remove(file)
+		except Exception as e:
+			print(e)

{celldetective-1.4.0.dist-info → celldetective-1.4.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: celldetective
-Version: 1.4.0
+Version: 1.4.1
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

celldetective-1.4.1.dist-info/RECORD

@@ -0,0 +1,123 @@
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