celldetective 1.4.2__py3-none-any.whl → 1.5.0b0__py3-none-any.whl

celldetective/utils/stats.py

@@ -0,0 +1,90 @@
+from typing import Optional, Union, List
+
+import pandas as pd
+from cliffs_delta import cliffs_delta
+from scipy.stats import ks_2samp
+
+
+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.
+
+    The function applies two-sample statistical tests, such as the Kolmogorov-Smirnov (KS) test or Cliff's Delta,
+    to compare distributions of a given feature across groups defined by `groupby_cols`. It returns the test results
+    in a pivot table format with each group's pairwise comparison.
+
+    Parameters
+    ----------
+    data : pandas.DataFrame
+            The input dataset containing the feature to be tested.
+    feature : str
+            The name of the column representing the feature to compare between groups.
+    groupby_cols : list or str
+            The column(s) used to group the data. These columns define the groups that will be compared pairwise.
+    method : str, optional, default="ks_2samp"
+            The statistical test to use. Options:
+            - "ks_2samp": Two-sample Kolmogorov-Smirnov test (default).
+            - "cliffs_delta": Cliff's Delta for effect size between two distributions.
+    *args, **kwargs :
+            Additional arguments and keyword arguments for the selected test method.
+
+    Returns
+    -------
+    pivot : pandas.DataFrame
+            A pivot table containing the pairwise test results (p-values or effect sizes).
+            The rows and columns represent the unique groups defined by `groupby_cols`,
+            and the values represent the test result (e.g., p-values or effect sizes) between each group.
+
+    Notes
+    -----
+    - The function compares all unique pairwise combinations of the groups based on `groupby_cols`.
+    - For the "ks_2samp" method, the test compares the distributions using the Kolmogorov-Smirnov test.
+    - For the "cliffs_delta" method, the function calculates the effect size between two distributions.
+    - The results are returned in a symmetric pivot table where each cell represents the test result for the corresponding group pair.
+
+    """
+
+    assert groupby_cols is not None, "Please set a valid groupby_cols..."
+    assert feature is not None, "Please set a feature to test..."
+
+    results = []
+
+    for lbl1, group1 in data.dropna(subset=feature).groupby(groupby_cols):
+        for lbl2, group2 in data.dropna(subset=feature).groupby(groupby_cols):
+
+            dist1 = group1[feature].values
+            dist2 = group2[feature].values
+            if method == "ks_2samp":
+                test = ks_2samp(
+                    list(dist1),
+                    list(dist2),
+                    alternative="less",
+                    mode="auto",
+                    *args,
+                    **kwargs,
+                )
+                val = test.pvalue
+            elif method == "cliffs_delta":
+                test = cliffs_delta(list(dist1), list(dist2), *args, **kwargs)
+                val = test[0]
+
+            results.append({"cdt1": lbl1, "cdt2": lbl2, "value": val})
+
+    results = pd.DataFrame(results)
+    results["cdt1"] = results["cdt1"].astype(str)
+    results["cdt2"] = results["cdt2"].astype(str)
+
+    pivot = results.pivot(index="cdt1", columns="cdt2", values="value")
+    pivot.reset_index(inplace=True)
+    pivot.columns.name = None
+    pivot.set_index("cdt1", drop=True, inplace=True)
+    pivot.index.name = None
+
+    return pivot

celldetective/utils/types.py

@@ -0,0 +1,21 @@
+import numpy
+import numpy as np
+
+
+def is_integer_array(arr: np.ndarray) -> bool:
+
+    # Mask out NaNs
+    non_nan_values = arr[arr == arr].flatten()
+    test = np.all(np.mod(non_nan_values, 1) == 0)
+
+    if test:
+        return True
+    else:
+        return False
+
+
+def test_bool_array(array):
+    if array.dtype == "bool":
+        return np.array(array, dtype=int)
+    else:
+        return array

{celldetective-1.4.2.dist-info → celldetective-1.5.0b0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: celldetective
-Version: 1.4.2
+Version: 1.5.0b0
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

celldetective-1.5.0b0.dist-info/RECORD

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+celldetective/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+celldetective/utils/color_mappings.py,sha256=yarqOTSrTsnOPPiPrrN_vLoPCbgWqF3wjqFwpbp-KsU,1007
+celldetective/utils/data_cleaning.py,sha256=K-2gScxLreX7QkrM0h3dZdP0IsmvCzcxNh2-M9PALZY,22025
+celldetective/utils/data_loaders.py,sha256=tExtC_7gX16VYmYFz8BU7jRKLDug2egVghU1YIcGRh0,16292
+celldetective/utils/dataset_helpers.py,sha256=3ezpHO6nytw2Mx0D3maP_4535V2ohOTQn6Qpfk8gnms,6898
+celldetective/utils/downloaders.py,sha256=Cf7K-f_Bm4M6HIfgiSoIoph0O1NS6LZIaYvgWKauXes,6595
+celldetective/utils/experiment.py,sha256=bgADS70QuW4KGbzDJbVpVM-tw4qmZKMWtDT1cSxugrY,58342
+celldetective/utils/image_augmenters.py,sha256=USYd8z6dVn5z1x96IYJ4mG0smN9I_S21QMGU0wyHmjc,11654
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+celldetective/utils/image_loaders.py,sha256=nsyneHM67R9r-mmWKI7Z6xpe5MQCLOFsaYKFhxw2R-c,34032
+celldetective/utils/image_transforms.py,sha256=cgaHuEUArWWHgxlBlcQLf--zQa-4VphPJ2s2EyPN29o,11213
+celldetective/utils/io.py,sha256=WQH6B27iS722eVV8HHRaSvxMRZ217LoiEIPOqNGtqJk,1632
+celldetective/utils/mask_cleaning.py,sha256=n1Q2RfyhX0W3AcLO0U6ucSyDGRCofj6bPLSO_xeVZPI,12545
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+celldetective/utils/masks.py,sha256=wz47NrCsLD_9WX2Goswl_ThgnxyLJokIN6cj8KH7ZjI,7075
+celldetective/utils/maths.py,sha256=cYdIqSgpaDO1JZOpmgGFPPikEvu66absC64op_6kw0o,12003
+celldetective/utils/model_getters.py,sha256=jVq9FhAF-xUmFOETWP6hByhoWgapmJGlNmSK11fQ69g,11370
+celldetective/utils/model_loaders.py,sha256=CjScJBGtnenb8qRMZkEozdj1-ULYHvsDFS4AVgYbB5s,10576
+celldetective/utils/normalization.py,sha256=SN-nrycZtmtqv8v1S9bAKvDTGiN6cQKfryitwNtH1bA,15635
+celldetective/utils/parsing.py,sha256=1zpIH9tyULCRmO5Kwzy6yA01fqm5uE_mZKYtondy-VA,14443
+celldetective/utils/resources.py,sha256=3Fz_W0NYWl_Ixc2AjEmkOv5f7ejXerCLJ2z1iWhGWUI,1153
+celldetective/utils/stats.py,sha256=4TVHRqi38Y0sed-izaMI51sMP0fd5tC5M68EYyfJjkE,3636
+celldetective/utils/types.py,sha256=lRfWSMVzTkxgoctGGp0NqD551akuxu0ygna7zVGonTg,397
+celldetective/utils/cellpose_utils/__init__.py,sha256=grsglxR29vj42tlgsBoXnVnjrIJWsBXqbtkjFjzqH7A,4898
+celldetective/utils/event_detection/__init__.py,sha256=KX20PwPTevdbZ-25otDy_QTmealcDx5xNCfH2SOVIZM,323
+celldetective/utils/plots/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+celldetective/utils/plots/regression.py,sha256=oUCn29-hp7PxMqC-R0yoL60KMw5ZWpZAIoCDh2ErlcY,1764
+celldetective/utils/stardist_utils/__init__.py,sha256=e9s3DEaTKCUOGZb5k_DgShBTl4B0U-Jmg3Ioo8D5PyE,3978
+celldetective-1.5.0b0.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tests/test_events.py,sha256=eLFwwEEJfQAdwhews3-fn1HSvzozcNNFN_Qn0gOvQkE,685
+tests/test_filters.py,sha256=uj4NVyUnKXa18EpTSiWCetGKI1VFopDyNSJSUxX44wA,1689
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+tests/test_measure.py,sha256=FEUAs1rVHylvIvubCb0bJDNGZLVmkgXNgI3NaGQ1dA8,4542
+tests/test_neighborhood.py,sha256=gk5FmoI7ANEczUtNXYRxc48KzkfYzemwS_eYaLq4_NI,2093
+tests/test_notebooks.py,sha256=WP5TJM1HV1oN8Hp38MLyE2YuLXjUoMvMJBa343vp1Dg,299
+tests/test_preprocessing.py,sha256=c0rKS9d5h37uDcV7fVOTnn5GMVbEB84b8ZTCTdRmvFs,1422
+tests/test_segmentation.py,sha256=k1b_zIZdlytEdJcHjAUQEO3gTBAHtv5WvrwQN2xD4kc,3470
+tests/test_signals.py,sha256=No4cah6KxplhDcKXnU8RrA7eDla4hWw6ccf7xGnBokU,3599
+tests/test_tracking.py,sha256=_YLjwQ3EChQssoHDfEnUJ7fI1yC5KEcJsFnAVR64L70,18909
+tests/test_utils.py,sha256=aSB_eMw9fzTsnxxdYoNmdQQRrXkWqBXB7Uv4TGU6kYE,4778
+tests/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tests/gui/test_new_project.py,sha256=wRjW2vEaZb0LWT-f8G8-Ptk8CW9z8-FDPLpV5uqj6ck,8778
+tests/gui/test_project.py,sha256=KzAnodIc0Ovta0ARL5Kr5PkOR5euA6qczT_GhEZpyE4,4710
+celldetective-1.5.0b0.dist-info/METADATA,sha256=btAint9Y6sB0i_XItoVQqUHMsn1KtXNm0JSeavdXH48,10947
+celldetective-1.5.0b0.dist-info/WHEEL,sha256=qELbo2s1Yzl39ZmrAibXA2jjPLUYfnVhUNTlyF1rq0Y,92
+celldetective-1.5.0b0.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
+celldetective-1.5.0b0.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
+celldetective-1.5.0b0.dist-info/RECORD,,

{celldetective-1.4.2.dist-info → celldetective-1.5.0b0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.10.2)
+Generator: setuptools (80.10.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

tests/gui/test_new_project.py

@@ -2,7 +2,7 @@ import pytest
 from PyQt5 import QtCore
 from PyQt5.QtWidgets import QApplication
 from celldetective.gui.InitWindow import AppInitWindow
-from celldetective.utils import get_software_location
+from celldetective import get_software_location
 import os
 from unittest.mock import patch
 import shutil
@@ -11,126 +11,138 @@ from pathlib import Path
 abs_path = os.sep.join([os.path.split(os.path.dirname(os.path.realpath(__file__)))[0]])
 print(abs_path)
 
+
 @pytest.fixture
 def app(qtbot):
-	software_location = get_software_location()
-	test_app = AppInitWindow(software_location=software_location)
-	qtbot.addWidget(test_app)
-	return test_app
+    software_location = get_software_location()
+    test_app = AppInitWindow(software_location=software_location)
+    qtbot.addWidget(test_app)
+    return test_app
+
 
 def test_new_project(app, qtbot):
-	# app.newExpAction.trigger()
-	# qtbot.wait(1000)
-	interaction_time = 500
-	test_directory = os.path.dirname(os.path.abspath(__file__))
-	parent_directory = str(Path(test_directory).parent)
-
-	# Patch QFileDialog.getExistingDirectory to return test_directory
-	with patch('PyQt5.QtWidgets.QFileDialog.getExistingDirectory', return_value=parent_directory):
-		
-		if os.path.exists(os.sep.join([parent_directory, "ExperimentTest"])):
-			shutil.rmtree(os.sep.join([parent_directory, "ExperimentTest"]))
-		
-		app.newExpAction.trigger()
-		qtbot.wait(interaction_time*3)
-
-		app.new_exp_window.expName.setText('ExperimentTest')
-		qtbot.wait(interaction_time)
-
-		app.new_exp_window.SliderWells.setValue(10)
-		qtbot.wait(interaction_time)
-
-		app.new_exp_window.SliderPos.setValue(3)
-		qtbot.wait(interaction_time)
-
-		app.new_exp_window.MovieLengthSlider.setValue(1)
-		qtbot.wait(interaction_time)
-
-		app.new_exp_window.PxToUm_field.setText("0,3112")
-		qtbot.wait(interaction_time)
-
-		app.new_exp_window.shape_x_field.setText("660")
-		qtbot.wait(interaction_time)
-
-		app.new_exp_window.shape_y_field.setText('682')
-		qtbot.wait(interaction_time)
-
-		# set first channel
-		app.new_exp_window.checkBoxes[0].setChecked(True)
-		qtbot.wait(interaction_time)
-
-		app.new_exp_window.sliders[0].setValue(0)
-		qtbot.wait(interaction_time)
-
-		# set second with channel index of 1
-		app.new_exp_window.checkBoxes[1].setChecked(True)
-		qtbot.wait(interaction_time)
-
-		app.new_exp_window.sliders[1].setValue(3)
-		qtbot.wait(interaction_time)
-
-		app.new_exp_window.checkBoxes[2].setChecked(True)
-		qtbot.wait(interaction_time)
-
-		app.new_exp_window.sliders[2].setValue(1)
-		qtbot.wait(interaction_time)
-
-		# add extra custom channel
-		qtbot.mouseClick(app.new_exp_window.addChannelBtn, QtCore.Qt.LeftButton)
-		qtbot.wait(interaction_time)
-
-		app.new_exp_window.name_le.setText('empty_channel')
-		qtbot.wait(interaction_time)
-		
-		qtbot.mouseClick(app.new_exp_window.createBtn, QtCore.Qt.LeftButton)
-		qtbot.wait(interaction_time)
-
-		app.new_exp_window.checkBoxes[-1].setChecked(True)
-		qtbot.wait(interaction_time)
-
-		app.new_exp_window.sliders[-1].setValue(2)
-		qtbot.wait(interaction_time)
-
-		# Untick populations and create new one
-		for box in app.new_exp_window.population_checkboxes:
-			if box.text() == 'targets':
-				box.setChecked(True)
-			else:
-				box.setChecked(False)
-		
-		qtbot.mouseClick(app.new_exp_window.addPopBtn, QtCore.Qt.LeftButton)
-		qtbot.wait(interaction_time)
-
-		app.new_exp_window.name_le.setText('more_cells')
-		qtbot.wait(interaction_time)
-		
-		qtbot.mouseClick(app.new_exp_window.addPopBtn, QtCore.Qt.LeftButton)
-		qtbot.wait(interaction_time)
-		
-		qtbot.mouseClick(app.new_exp_window.validate_button, QtCore.Qt.LeftButton)
-		qtbot.wait(interaction_time)
-		
-		qtbot.mouseClick(app.new_exp_window.w.submit_btn, QtCore.Qt.LeftButton)
-		qtbot.wait(interaction_time)
-		
-		shutil.copy(os.sep.join([parent_directory, "assets", "sample.tif"]), os.sep.join([parent_directory, "ExperimentTest", "W1", "100", "movie", "sample.tif"]))
-		qtbot.wait(interaction_time)
-
-		qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
-		qtbot.mouseClick(app.control_panel.view_stack_btn, QtCore.Qt.LeftButton)
-		qtbot.wait(interaction_time)
-		
-		app.control_panel.viewer.channels_cb.setCurrentIndex(1)
-		qtbot.wait(interaction_time*2)
-		
-		app.control_panel.viewer.contrast_slider.setValue([200,300])
-		qtbot.wait(interaction_time*2)
-	
-	# QApplication.closeAllWindows()
-	# try:
-	# 	shutil.rmtree(os.sep.join([parent_directory, "ExperimentTest"]))
-	# except:
-	# 	pass
+    # app.newExpAction.trigger()
+    # qtbot.wait(1000)
+    interaction_time = 500
+    test_directory = os.path.dirname(os.path.abspath(__file__))
+    parent_directory = str(Path(test_directory).parent)
+
+    # Patch QFileDialog.getExistingDirectory to return test_directory
+    with patch(
+        "PyQt5.QtWidgets.QFileDialog.getExistingDirectory",
+        return_value=parent_directory,
+    ):
+
+        if os.path.exists(os.sep.join([parent_directory, "ExperimentTest"])):
+            shutil.rmtree(os.sep.join([parent_directory, "ExperimentTest"]))
+
+        app.new_exp_action.trigger()
+        qtbot.wait(interaction_time * 3)
+
+        app.new_exp_window.expName.setText("ExperimentTest")
+        qtbot.wait(interaction_time)
+
+        app.new_exp_window.SliderWells.setValue(10)
+        qtbot.wait(interaction_time)
+
+        app.new_exp_window.SliderPos.setValue(3)
+        qtbot.wait(interaction_time)
+
+        app.new_exp_window.MovieLengthSlider.setValue(1)
+        qtbot.wait(interaction_time)
+
+        app.new_exp_window.PxToUm_field.setText("0,3112")
+        qtbot.wait(interaction_time)
+
+        app.new_exp_window.shape_x_field.setText("660")
+        qtbot.wait(interaction_time)
+
+        app.new_exp_window.shape_y_field.setText("682")
+        qtbot.wait(interaction_time)
+
+        # set first channel
+        app.new_exp_window.checkBoxes[0].setChecked(True)
+        qtbot.wait(interaction_time)
+
+        app.new_exp_window.sliders[0].setValue(0)
+        qtbot.wait(interaction_time)
+
+        # set second with channel index of 1
+        app.new_exp_window.checkBoxes[1].setChecked(True)
+        qtbot.wait(interaction_time)
+
+        app.new_exp_window.sliders[1].setValue(3)
+        qtbot.wait(interaction_time)
+
+        app.new_exp_window.checkBoxes[2].setChecked(True)
+        qtbot.wait(interaction_time)
+
+        app.new_exp_window.sliders[2].setValue(1)
+        qtbot.wait(interaction_time)
+
+        # add extra custom channel
+        qtbot.mouseClick(app.new_exp_window.addChannelBtn, QtCore.Qt.LeftButton)
+        qtbot.wait(interaction_time)
+
+        app.new_exp_window.name_le.setText("empty_channel")
+        qtbot.wait(interaction_time)
+
+        qtbot.mouseClick(app.new_exp_window.createBtn, QtCore.Qt.LeftButton)
+        qtbot.wait(interaction_time)
+
+        app.new_exp_window.checkBoxes[-1].setChecked(True)
+        qtbot.wait(interaction_time)
+
+        app.new_exp_window.sliders[-1].setValue(2)
+        qtbot.wait(interaction_time)
+
+        # Untick populations and create new one
+        for box in app.new_exp_window.population_checkboxes:
+            if box.text() == "targets":
+                box.setChecked(True)
+            else:
+                box.setChecked(False)
+
+        qtbot.mouseClick(app.new_exp_window.addPopBtn, QtCore.Qt.LeftButton)
+        qtbot.wait(interaction_time)
+
+        app.new_exp_window.name_le.setText("more_cells")
+        qtbot.wait(interaction_time)
+
+        qtbot.mouseClick(app.new_exp_window.addPopBtn, QtCore.Qt.LeftButton)
+        qtbot.wait(interaction_time)
+
+        qtbot.mouseClick(app.new_exp_window.validate_button, QtCore.Qt.LeftButton)
+        qtbot.wait(interaction_time)
+
+        qtbot.mouseClick(app.new_exp_window.w.submit_btn, QtCore.Qt.LeftButton)
+        qtbot.wait(interaction_time)
+
+        shutil.copy(
+            os.sep.join([parent_directory, "assets", "sample.tif"]),
+            os.sep.join(
+                [parent_directory, "ExperimentTest", "W1", "100", "movie", "sample.tif"]
+            ),
+        )
+        qtbot.wait(interaction_time)
+
+        qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+        qtbot.mouseClick(app.control_panel.view_stack_btn, QtCore.Qt.LeftButton)
+        qtbot.wait(interaction_time)
+
+        app.control_panel.viewer.channel_cb.setCurrentIndex(1)
+        qtbot.wait(interaction_time * 2)
+
+        app.control_panel.viewer.contrast_slider.setValue([200, 300])
+        qtbot.wait(interaction_time * 2)
+
+    # QApplication.closeAllWindows()
+    # try:
+    # 	shutil.rmtree(os.sep.join([parent_directory, "ExperimentTest"]))
+    # except:
+    # 	pass
+
+
 # def test_lauch_app(app, qtbot):
 # 	app.show()
 # 	qtbot.wait(1000)