fix unit-test segmentation and utils

qim3d/operations/_common_operations_methods.py

 import numpy as np
 import qim3d.filters as filters
-from qim3d.utils._logger import log
+from qim3d.utils import log
 
 __all__ = ["remove_background", "fade_mask", "overlay_rgb_images"]
 

qim3d/tests/utils/test_augmentations.py

@@ -5,13 +5,13 @@ import pytest
 
 # unit tests for Augmentation()
 def test_augmentation():
-    augment_class = qim3d.models.Augmentation()
+    augment_class = qim3d.ml.Augmentation()
 
     assert augment_class.resize == "crop"
 
 
 def test_augment():
-    augment_class = qim3d.models.Augmentation()
+    augment_class = qim3d.ml.Augmentation()
 
     album_augment = augment_class.augment(256, 256)
 
@@ -26,11 +26,11 @@ def test_resize():
         ValueError,
         match=f"Invalid resize type: {resize_str}. Use either 'crop', 'resize' or 'padding'.",
     ):
-        augment_class = qim3d.models.Augmentation(resize=resize_str)
+        augment_class = qim3d.ml.Augmentation(resize=resize_str)
 
 
 def test_levels():
-    augment_class = qim3d.models.Augmentation()
+    augment_class = qim3d.ml.Augmentation()
 
     level = "Not a valid level"
 

qim3d/tests/utils/test_data.py

@@ -10,7 +10,7 @@ def test_dataset():
     folder = 'folder_data'
     temp_data(folder, img_shape = img_shape)
     
-    images = qim3d.models.Dataset(folder)
+    images = qim3d.ml.Dataset(folder)
 
     assert images[0][0].shape == img_shape
 
@@ -19,19 +19,19 @@ def test_dataset():
 
 # unit tests for check_resize()
 def test_check_resize():
-    h_adjust,w_adjust = qim3d.models.data.check_resize(240,240,resize = 'crop',n_channels = 6)
+    h_adjust,w_adjust = qim3d.ml._data.check_resize(240,240,resize = 'crop',n_channels = 6)
 
     assert (h_adjust,w_adjust) == (192,192)
 
 def test_check_resize_pad():
-    h_adjust,w_adjust = qim3d.models.data.check_resize(16,16,resize = 'padding',n_channels = 6)
+    h_adjust,w_adjust = qim3d.ml._data.check_resize(16,16,resize = 'padding',n_channels = 6)
 
     assert (h_adjust,w_adjust) == (64,64)
 
 def test_check_resize_fail():
 
     with pytest.raises(ValueError,match="The size of the image is too small compared to the depth of the UNet. Choose a different 'resize' and/or a smaller model."):
-        h_adjust,w_adjust = qim3d.models.data.check_resize(16,16,resize = 'crop',n_channels = 6)
+        h_adjust,w_adjust = qim3d.ml._data.check_resize(16,16,resize = 'crop',n_channels = 6)
 
 
 # unit tests for prepare_datasets()
@@ -42,9 +42,9 @@ def test_prepare_datasets():
     folder = 'folder_data'
     img = temp_data(folder,n = n)
 
-    my_model = qim3d.models.UNet()
-    my_augmentation = qim3d.models.Augmentation(transform_test='light')
-    train_set, val_set, test_set = qim3d.models.prepare_datasets(folder,validation,my_model,my_augmentation)
+    my_model = qim3d.ml.models.UNet()
+    my_augmentation = qim3d.ml.Augmentation(transform_test='light')
+    train_set, val_set, test_set = qim3d.ml.prepare_datasets(folder,validation,my_model,my_augmentation)
 
     assert (len(train_set),len(val_set),len(test_set)) == (int((1-validation)*n), int(n*validation), n)
 
@@ -56,7 +56,7 @@ def test_validation():
     validation = 10
     
     with pytest.raises(ValueError,match = "The validation fraction must be a float between 0 and 1."):
-        augment_class = qim3d.models.prepare_datasets('folder',validation,'my_model','my_augmentation')
+        augment_class = qim3d.ml.prepare_datasets('folder',validation,'my_model','my_augmentation')
 
 
 # unit test for prepare_dataloaders()
@@ -65,11 +65,11 @@ def test_prepare_dataloaders():
     temp_data(folder)
 
     batch_size = 1
-    my_model = qim3d.models.UNet()
-    my_augmentation = qim3d.models.Augmentation()
-    train_set, val_set, test_set = qim3d.models.prepare_datasets(folder,1/3,my_model,my_augmentation)
+    my_model = qim3d.ml.models.UNet()
+    my_augmentation = qim3d.ml.Augmentation()
+    train_set, val_set, test_set = qim3d.ml.prepare_datasets(folder,1/3,my_model,my_augmentation)
 
-    _,val_loader,_ = qim3d.models.prepare_dataloaders(train_set,val_set,test_set,
+    _,val_loader,_ = qim3d.ml.prepare_dataloaders(train_set,val_set,test_set,
                                                                            batch_size,num_workers = 1,
                                                                            pin_memory = False)
     

qim3d/tests/utils/test_doi.py

@@ -4,12 +4,12 @@ doi = "https://doi.org/10.1007/s10851-021-01041-3"
 
 
 def test_get_bibtex():
-    bibtext = qim3d.utils.doi.get_bibtex(doi)
+    bibtext = qim3d.utils._doi.get_bibtex(doi)
 
     assert "Measuring Shape Relations Using r-Parallel Sets" in bibtext
 
 
 def test_get_reference():
-    reference = qim3d.utils.doi.get_reference(doi)
+    reference = qim3d.utils._doi.get_reference(doi)
 
     assert "Stephensen" in reference

qim3d/tests/utils/test_helpers.py

@@ -33,7 +33,7 @@ def test_get_local_ip():
         else:
             return False
 
-    local_ip = qim3d.utils.misc.get_local_ip()
+    local_ip = qim3d.utils._misc.get_local_ip()
 
     assert validate_ip(local_ip) == True
 
@@ -42,7 +42,7 @@ def test_stringify_path1():
     """Test that the function converts os.PathLike objects to strings"""
     blobs_path = Path(qim3d.__file__).parents[0] / "img_examples" / "blobs_256x256.tif"
 
-    assert str(blobs_path) == qim3d.utils.misc.stringify_path(blobs_path)
+    assert str(blobs_path) == qim3d.utils._misc.stringify_path(blobs_path)
 
 
 def test_stringify_path2():
@@ -50,4 +50,4 @@ def test_stringify_path2():
     # Create test_path
     test_path = os.path.join("this", "path", "doesnt", "exist.tif")
 
-    assert test_path == qim3d.utils.misc.stringify_path(test_path)
+    assert test_path == qim3d.utils._misc.stringify_path(test_path)