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

tests/test_utils.py

@@ -2,117 +2,163 @@ import unittest
 import matplotlib.pyplot as plt
 import numpy as np
 import os
-from celldetective.utils import create_patch_mask, remove_redundant_features, _extract_channel_indices, _get_img_num_per_channel, split_by_ratio,extract_experiment_channels, estimate_unreliable_edge, unpad, mask_edges
+from celldetective.utils.dataset_helpers import split_by_ratio
+from celldetective.utils.masks import create_patch_mask
+from celldetective.utils.image_transforms import (
+    estimate_unreliable_edge,
+    unpad,
+    mask_edges,
+)
+from celldetective.utils.image_loaders import (
+    _get_img_num_per_channel,
+    _extract_channel_indices,
+)
+from celldetective.utils.data_cleaning import remove_redundant_features
+from celldetective.utils.experiment import extract_experiment_channels
+
 
 class TestPatchMask(unittest.TestCase):
 
-	@classmethod
-	def setUpClass(self):
-		self.radius = 3
+    @classmethod
+    def setUpClass(self):
+        self.radius = 3
+
+    def test_correct_shape(self):
+        self.patch = create_patch_mask(self.radius, self.radius)
+        self.assertEqual(self.patch.shape, (3, 3))
 
-	def test_correct_shape(self):
-		self.patch = create_patch_mask(self.radius, self.radius)
-		self.assertEqual(self.patch.shape,(3,3))
+    def test_correct_ring(self):
+        self.patch = create_patch_mask(5, 5, radius=[1, 2])
+        self.assertFalse(self.patch[2, 2])
 
-	def test_correct_ring(self):
-		self.patch = create_patch_mask(5, 5,radius=[1,2])
-		self.assertFalse(self.patch[2,2])
 
 class TestRemoveRedundantFeatures(unittest.TestCase):
 
-	@classmethod
-	def setUpClass(self):
-		self.list_a = ['feat1','feat2','feat3','feat4','intensity_mean']
-		self.list_b = ['feat5','feat2','feat1','feat6','test_channel_mean']
-		self.expected = ['feat3','feat4']
+    @classmethod
+    def setUpClass(self):
+        self.list_a = ["feat1", "feat2", "feat3", "feat4", "intensity_mean"]
+        self.list_b = ["feat5", "feat2", "feat1", "feat6", "test_channel_mean"]
+        self.expected = ["feat3", "feat4"]
 
-	def test_remove_red_features(self):
-		self.assertEqual(remove_redundant_features(self.list_a, self.list_b, channel_names=['test_channel']), self.expected)
+    def test_remove_red_features(self):
+        self.assertEqual(
+            remove_redundant_features(
+                self.list_a, self.list_b, channel_names=["test_channel"]
+            ),
+            self.expected,
+        )
 
 
 class TestExtractChannelIndices(unittest.TestCase):
 
-	@classmethod
-	def setUpClass(self):
-		self.channels = ['ch1','ch2','ch3','ch4']
-		self.required_channels = ['ch4','ch2']
-		self.expected_indices = [3,1]
+    @classmethod
+    def setUpClass(self):
+        self.channels = ["ch1", "ch2", "ch3", "ch4"]
+        self.required_channels = ["ch4", "ch2"]
+        self.expected_indices = [3, 1]
 
-	def test_extracted_channels_are_correct(self):
-		self.assertEqual(list(_extract_channel_indices(self.channels, self.required_channels)), self.expected_indices)
+    def test_extracted_channels_are_correct(self):
+        self.assertEqual(
+            list(_extract_channel_indices(self.channels, self.required_channels)),
+            self.expected_indices,
+        )
 
 
 class TestImgIndexPerChannel(unittest.TestCase):
 
-	@classmethod
-	def setUpClass(self):
-		self.channels_indices = [1]
-		self.len_movie = 5
-		self.nbr_channels = 3
-		self.expected_indices = [1,4,7,10,13]
+    @classmethod
+    def setUpClass(self):
+        self.channels_indices = [1]
+        self.len_movie = 5
+        self.nbr_channels = 3
+        self.expected_indices = [1, 4, 7, 10, 13]
 
-	def test_index_sequence_is_correct(self):
-		self.assertEqual(list(_get_img_num_per_channel(self.channels_indices, self.len_movie, self.nbr_channels)[0]), self.expected_indices)
+    def test_index_sequence_is_correct(self):
+        self.assertEqual(
+            list(
+                _get_img_num_per_channel(
+                    self.channels_indices, self.len_movie, self.nbr_channels
+                )[0]
+            ),
+            self.expected_indices,
+        )
 
 
 class TestSplitArrayByRatio(unittest.TestCase):
 
-	@classmethod
-	def setUpClass(self):
-		self.array_length = 100
-		self.array = np.ones(self.array_length)
+    @classmethod
+    def setUpClass(self):
+        self.array_length = 100
+        self.array = np.ones(self.array_length)
+
+    def test_ratio_split_is_correct(self):
+        split_array = split_by_ratio(self.array, 0.5, 0.25, 0.1)
+        self.assertTrue(
+            np.all(
+                [
+                    len(split_array[0]) == 50,
+                    len(split_array[1]) == 25,
+                    len(split_array[2]) == 10,
+                ]
+            )
+        )
 
-	def test_ratio_split_is_correct(self):
-		split_array = split_by_ratio(self.array,0.5,0.25,0.1)
-		self.assertTrue(np.all([len(split_array[0])==50, len(split_array[1])==25, len(split_array[2])==10]))
 
 class TestUnpad(unittest.TestCase):
 
-	@classmethod
-	def setUpClass(self):
-		self.array = np.array([[0,0,0],
-							  [0,1,0],
-							  [0,0,0]])
+    @classmethod
+    def setUpClass(self):
+        self.array = np.array([[0, 0, 0], [0, 1, 0], [0, 0, 0]])
+
+    def test_unpad(self):
+        expected_unpad_array = np.array([[1]])
+        test_array = unpad(self.array, 1)
+        self.assertTrue(np.array_equal(test_array, expected_unpad_array))
 
-	def test_unpad(self):
-		expected_unpad_array = np.array([[1]])
-		test_array = unpad(self.array, 1)
-		self.assertTrue(np.array_equal(test_array, expected_unpad_array))
 
 class TestMaskEdge(unittest.TestCase):
 
-	@classmethod
-	def setUpClass(self):
-		self.binary_mask = np.array([[1, 1, 1, 1, 1],
-									 [1, 1, 1, 1, 1],
-									 [1, 1, 1, 1, 1],
-									 [1, 1, 1, 1, 1],
-									 [1, 1, 1, 1, 1]])
-
-	def test_mask_edge_properly(self):
-		expected_output = np.array([[False, False, False, False, False],
-									[False, True, True, True, False],
-									[False, True, True, True, False],
-									[False, True, True, True, False],
-									[False, False, False, False, False]])
-		actual_output = mask_edges(self.binary_mask, 1)
-		self.assertTrue(np.array_equal(actual_output, expected_output))
+    @classmethod
+    def setUpClass(self):
+        self.binary_mask = np.array(
+            [
+                [1, 1, 1, 1, 1],
+                [1, 1, 1, 1, 1],
+                [1, 1, 1, 1, 1],
+                [1, 1, 1, 1, 1],
+                [1, 1, 1, 1, 1],
+            ]
+        )
+
+    def test_mask_edge_properly(self):
+        expected_output = np.array(
+            [
+                [False, False, False, False, False],
+                [False, True, True, True, False],
+                [False, True, True, True, False],
+                [False, True, True, True, False],
+                [False, False, False, False, False],
+            ]
+        )
+        actual_output = mask_edges(self.binary_mask, 1)
+        self.assertTrue(np.array_equal(actual_output, expected_output))
+
 
 class TestEstimateFilterEdge(unittest.TestCase):
 
-	@classmethod
-	def setUpClass(self):
-		self.protocol1 = [['gauss',2],['std',4]]
-		self.expected1 = 6
-		self.protocol2 = [['gauss',4],['variance','string_arg']]
-		self.expected2 = 4
+    @classmethod
+    def setUpClass(self):
+        self.protocol1 = [["gauss", 2], ["std", 4]]
+        self.expected1 = 6
+        self.protocol2 = [["gauss", 4], ["variance", "string_arg"]]
+        self.expected2 = 4
+
+    def test_edge_is_estimated_properly_with_only_number_arguments(self):
+        self.assertEqual(self.expected1, estimate_unreliable_edge(self.protocol1))
 
-	def test_edge_is_estimated_properly_with_only_number_arguments(self):
-		self.assertEqual(self.expected1, estimate_unreliable_edge(self.protocol1))
-	
-	def test_edge_is_estimated_properly_with_mixed_arguments(self):
-		self.assertEqual(self.expected2, estimate_unreliable_edge(self.protocol2))
+    def test_edge_is_estimated_properly_with_mixed_arguments(self):
+        self.assertEqual(self.expected2, estimate_unreliable_edge(self.protocol2))
 
 
-if __name__=="__main__":
-	unittest.main()
+if __name__ == "__main__":
+    unittest.main()

celldetective/gui/base_components.py

@@ -1,23 +0,0 @@
-from PyQt5.QtWidgets import QMainWindow, QWidget, QDialog
-from PyQt5.QtCore import Qt
-from celldetective.gui import Styles
-
-
-class CelldetectiveWidget(QWidget, Styles):
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.setWindowIcon(self.celldetective_icon)
-        self.setAttribute(Qt.WA_DeleteOnClose)
-
-
-class CelldetectiveMainWindow(QMainWindow, Styles):
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.setWindowIcon(self.celldetective_icon)
-        self.setAttribute(Qt.WA_DeleteOnClose)
-
-
-class CelldetectiveDialog(QDialog, Styles):
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.setWindowIcon(self.celldetective_icon)