WIP refactoring testing in progress

Author: SebastianoF

tests/__init__.py

@@ -0,0 +1,326 @@
+import collections
+import os
+from os.path import join as jph
+
+from nose.tools import assert_raises
+
+from nilabels.tools.aux_methods.label_descriptor_manager import LabelsDescriptorManager, \
+    generate_dummy_label_descriptor
+
+
+# PATH MANAGER
+
+test_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+pfo_tmp_test = jph(test_dir, 'z_tmp_test')
+
+
+
+# AUXILIARY
+
+
+def check_list_equal(l1, l2):
+    return len(l1) == len(l2) and sorted(l1) == sorted(l2)
+
+
+# DECORATORS
+
+
+def write_and_erase_temporary_folder(test_func):
+    def wrap(*args, **kwargs):
+        # 1) Before: create folder
+        os.system('mkdir {}'.format(pfo_tmp_test))
+        # 2) Run test
+        test_func(*args, **kwargs)
+        # 3) After: delete folder and its content
+        os.system('rm -r {}'.format(pfo_tmp_test))
+
+    return wrap
+
+
+def write_and_erase_temporary_folder_with_simple_image(test_func):
+    def wrap(*args, **kwargs):
+
+        # 1) Before: create folder
+        os.system('mkdir {}'.format(pfo_tmp_test))
+        # 1bis) Then, generate image in the generated folder
+        # TODO
+        # 2) Run test
+        test_func(*args, **kwargs)
+        # 3) After: delete folder and its content
+        os.system('rm -r {}'.format(pfo_tmp_test))
+
+    return wrap
+
+
+# TESTING:
+
+# --- > Testing generate dummy descriptor
+
+@write_and_erase_temporary_folder
+def test_generate_dummy_labels_descriptor_wrong_input1():
+    with assert_raises(IOError):
+        generate_dummy_label_descriptor(jph(pfo_tmp_test, 'label_descriptor.txt'), list_labels=range(5),
+                                        list_roi_names=['1', '2'])
+
+
+@write_and_erase_temporary_folder
+def test_generate_dummy_labels_descriptor_wrong_input2():
+    with assert_raises(IOError):
+        generate_dummy_label_descriptor(jph(pfo_tmp_test, 'label_descriptor.txt'), list_labels=range(5),
+                                        list_roi_names=['1', '2', '3', '4', '5'],
+                                        list_colors_triplets=[[0, 0, 0], [1, 1, 1]])
+
+
+@write_and_erase_temporary_folder
+def test_generate_labels_descriptor_list_roi_names_None():
+    d = generate_dummy_label_descriptor(jph(pfo_tmp_test, 'dummy_label_descriptor.txt'), list_labels=range(5),
+                                        list_roi_names=None, list_colors_triplets=[[1, 1, 1], ] * 5)
+
+    for k in d.keys():
+        assert d[k][-1] == 'label {}'.format(k)
+
+
+@write_and_erase_temporary_folder
+def test_generate_labels_descriptor_list_colors_triplets_None():
+    d = generate_dummy_label_descriptor(jph(pfo_tmp_test, 'dummy_label_descriptor.txt'), list_labels=range(5),
+                                        list_roi_names=None, list_colors_triplets=[[1, 1, 1], ] * 5)
+    for k in d.keys():
+        assert len(d[k][1]) == 3
+
+
+@write_and_erase_temporary_folder
+def test_generate_labels_descriptor_general():
+    list_labels         = [1, 2, 3, 4, 5]
+    list_color_triplets = [[1, 1, 1], [2, 2, 2], [3, 3, 3], [4, 4, 4], [5, 5, 5]]
+    list_roi_names      = ['one', 'two', 'three', 'four', 'five']
+
+    d = generate_dummy_label_descriptor(jph(pfo_tmp_test, 'dummy_label_descriptor.txt'), list_labels=list_labels,
+                                        list_roi_names=list_roi_names, list_colors_triplets=list_color_triplets)
+    for k_num, k in enumerate(d.keys()):
+        assert int(k) == list_labels[k_num]
+        assert d[k][0]  == list_color_triplets[k_num]
+        assert d[k][-1] == list_roi_names[k_num]
+
+# --- > Testing basics methods labels descriptor class manager
+
+
+@write_and_erase_temporary_folder
+def test_basics_methods_labels_descriptor_manager_wrong_input_path():
+
+    pfi_unexisting_label_descriptor_manager = 'zzz_path_to_spam'
+    with assert_raises(IOError):
+        LabelsDescriptorManager(pfi_unexisting_label_descriptor_manager)
+
+
+if __name__ == '__main__':
+    test_generate_dummy_labels_descriptor_wrong_input1()
+    test_generate_dummy_labels_descriptor_wrong_input2()
+    test_generate_labels_descriptor_list_roi_names_None()
+    test_generate_labels_descriptor_list_colors_triplets_None()
+    test_generate_labels_descriptor_general()
+    test_basics_methods_labels_descriptor_manager_wrong_input_path()
+
+
+
+#
+#
+# def test_basics_methods_labels_descriptor_manager_wrong_input_convention():
+#
+#     not_allowed_convention_name = 'just_spam'
+#     with assert_raises(IOError):
+#         LabelsDescriptorManager(jph(ldg.pfo_target_atlas, 'label_descriptor.txt'), not_allowed_convention_name)
+#
+#
+# def test_basic_dict_input():
+#     _create_data_set_for_tests()
+#
+#     dict_ld = collections.OrderedDict()
+#     dict_ld.update({0: [[0, 0, 0],   [1.0, 1.0, 1.0], 'Bkg']})
+#     dict_ld.update({1: [[255, 0, 0], [1.0, 1.0, 1.0], 'Skull']})
+#     dict_ld.update({2: [[0, 255, 0], [1.0, 1.0, 1.0], 'WM']})
+#     dict_ld.update({3: [[0, 0, 255], [1.0, 1.0, 1.0], 'GM']})
+#     dict_ld.update({4: [[255, 0, 255], [1.0, 1.0, 1.0], 'CSF']})
+#
+#     ldm = LabelsDescriptorManager(jph(ldg.pfo_target_atlas, 'label_descriptor.txt'))
+#
+#     check_list_equal(ldm.dict_label_descriptor.keys(), dict_ld.keys())
+#     for k in ldm.dict_label_descriptor.keys():
+#         check_list_equal(ldm.dict_label_descriptor[k], dict_ld[k])
+#
+#
+# def test_save_in_itk_snap_convention():
+#     _create_data_set_for_tests()
+#
+#     ldm = LabelsDescriptorManager(jph(ldg.pfo_target_atlas, 'label_descriptor.txt'))
+#     ldm.save_label_descriptor(jph(ldg.pfo_target_atlas, 'label_descriptor2.txt'))
+#
+#     f1 = open(jph(ldg.pfo_target_atlas, 'label_descriptor.txt'), 'r')
+#     f2 = open(jph(ldg.pfo_target_atlas, 'label_descriptor2.txt'), 'r')
+#
+#     for l1, l2 in zip(f1.readlines(), f2.readlines()):
+#         assert l1 == l2
+#
+#     os.system('rm {}'.format(jph(ldg.pfo_target_atlas, 'label_descriptor2.txt')))
+#
+#
+# def test_save_in_fsl_convention_reload_as_dict_and_compare():
+#     _create_data_set_for_tests()
+#
+#     ldm_itk = LabelsDescriptorManager(jph(ldg.pfo_target_atlas, 'label_descriptor.txt'))
+#     # change convention
+#     ldm_itk.convention = 'fsl'
+#     ldm_itk.save_label_descriptor(jph(ldg.pfo_target_atlas, 'label_descriptor_fsl.txt'))
+#
+#     ldm_fsl = LabelsDescriptorManager(jph(ldg.pfo_target_atlas, 'label_descriptor_fsl.txt'), labels_descriptor_convention='fsl')
+#
+#     # NOTE: test works only with default 1.0 values - fsl convention is less informative than itk-snap..
+#     check_list_equal(ldm_itk.dict_label_descriptor.keys(), ldm_fsl.dict_label_descriptor.keys())
+#     for k in ldm_itk.dict_label_descriptor.keys():
+#         check_list_equal(ldm_itk.dict_label_descriptor[k], ldm_fsl.dict_label_descriptor[k])
+#
+#     os.system('rm {}'.format(jph(ldg.pfo_target_atlas, 'label_descriptor_fsl.txt')))
+#
+#
+# # TESTING: labels permutations - permute_labels_in_descriptor
+#
+#
+# def test_relabel_labels_descriptor():
+#     _create_data_set_for_tests()
+#
+#     dict_expected = collections.OrderedDict()
+#     dict_expected.update({0: [[0, 0, 0], [1.0, 1.0, 1.0], 'Bkg']})
+#     dict_expected.update({10: [[255, 0, 0], [1.0, 1.0, 1.0], 'Skull']})
+#     dict_expected.update({11: [[0, 255, 0], [1.0, 1.0, 1.0], 'WM']})
+#     dict_expected.update({12: [[0, 0, 255], [1.0, 1.0, 1.0], 'GM']})
+#     dict_expected.update({4: [[255, 0, 255], [1.0, 1.0, 1.0], 'CSF']})
+#
+#     ldm_original = LabelsDescriptorManager(jph(ldg.pfo_target_atlas, 'label_descriptor.txt'))
+#
+#     old_labels = [1, 2, 3]
+#     new_labels = [10, 11, 12]
+#
+#     ldm_relabelled = ldm_original.relabel(old_labels, new_labels, sort=True)
+#
+#     check_list_equal(dict_expected.keys(), ldm_relabelled.dict_label_descriptor.keys())
+#     for k in dict_expected.keys():
+#         check_list_equal(dict_expected[k], ldm_relabelled.dict_label_descriptor[k])
+#
+#
+# def test_relabel_labels_descriptor_with_merging():
+#     _create_data_set_for_tests()
+#
+#     dict_expected = collections.OrderedDict()
+#     dict_expected.update({0: [[0, 0, 0], [1.0, 1.0, 1.0], 'Bkg']})
+#     # dict_expected.update({1: [[255, 0, 0], [1.0, 1.0, 1.0], 'Skull']})
+#     dict_expected.update({1: [[0, 255, 0], [1.0, 1.0, 1.0], 'WM']})
+#     dict_expected.update({5: [[0, 0, 255], [1.0, 1.0, 1.0], 'GM']})
+#     dict_expected.update({4: [[255, 0, 255], [1.0, 1.0, 1.0], 'CSF']})
+#
+#     ldm_original = LabelsDescriptorManager(jph(ldg.pfo_target_atlas, 'label_descriptor.txt'))
+#
+#     old_labels = [1, 2, 3]
+#     new_labels = [1, 1, 5]
+#
+#     ldm_relabelled = ldm_original.relabel(old_labels, new_labels, sort=True)
+#
+#     check_list_equal(dict_expected.keys(), ldm_relabelled.dict_label_descriptor.keys())
+#     for k in dict_expected.keys():
+#         check_list_equal(dict_expected[k], ldm_relabelled.dict_label_descriptor[k])
+#
+#
+#
+# def test_permute_labels_from_descriptor_wrong_input_permutation():
+#     _create_data_set_for_tests()
+#
+#     ldm = LabelsDescriptorManager(jph(ldg.pfo_target_atlas, 'label_descriptor.txt'))
+#     perm = [[1, 2, 3], [1, 1]]
+#
+#     with assert_raises(IOError):
+#         ldm.permute_labels(perm)
+#
+#
+# def test_permute_labels_from_descriptor_check():
+#     _create_data_set_for_tests()
+#
+#     dict_expected = collections.OrderedDict()
+#     dict_expected.update({0: [[0, 0, 0], [1.0, 1.0, 1.0], 'Bkg']})
+#     dict_expected.update({1: [[255, 0, 0], [1.0, 1.0, 1.0], 'Skull']})
+#     dict_expected.update({3: [[0, 255, 0], [1.0, 1.0, 1.0], 'WM']})
+#     dict_expected.update({2: [[0, 0, 255], [1.0, 1.0, 1.0], 'GM']})
+#     dict_expected.update({4: [[255, 0, 255], [1.0, 1.0, 1.0], 'CSF']})
+#
+#     ldm_original = LabelsDescriptorManager(jph(ldg.pfo_target_atlas, 'label_descriptor.txt'))
+#     perm = [[1, 2, 3], [1, 3, 2]]
+#     ldm_relabelled = ldm_original.permute_labels(perm)
+#
+#     check_list_equal(dict_expected.keys(), ldm_relabelled.dict_label_descriptor.keys())
+#     for k in dict_expected.keys():
+#         check_list_equal(dict_expected[k], ldm_relabelled.dict_label_descriptor[k])
+#
+#
+# def test_erase_labels():
+#     _create_data_set_for_tests()
+#
+#     dict_expected = collections.OrderedDict()
+#     dict_expected.update({0: [[0, 0, 0], [1.0, 1.0, 1.0], 'Bkg']})
+#     dict_expected.update({1: [[255, 0, 0], [1.0, 1.0, 1.0], 'Skull']})
+#     dict_expected.update({4: [[255, 0, 255], [1.0, 1.0, 1.0], 'CSF']})
+#
+#     ldm_original = LabelsDescriptorManager(jph(ldg.pfo_target_atlas, 'label_descriptor.txt'))
+#     labels_to_erase = [2, 3]
+#     ldm_relabelled = ldm_original.erase_labels(labels_to_erase)
+#
+#     check_list_equal(dict_expected.keys(), ldm_relabelled.dict_label_descriptor.keys())
+#     for k in dict_expected.keys():
+#         check_list_equal(dict_expected[k], ldm_relabelled.dict_label_descriptor[k])
+#
+#
+# def test_erase_labels_unexisting_labels():
+#     _create_data_set_for_tests()
+#
+#     dict_expected = collections.OrderedDict()
+#     dict_expected.update({0: [[0, 0, 0], [1.0, 1.0, 1.0], 'Bkg']})
+#     dict_expected.update({1: [[255, 0, 0], [1.0, 1.0, 1.0], 'Skull']})
+#     dict_expected.update({3: [[0, 0, 255], [1.0, 1.0, 1.0], 'GM']})
+#
+#     ldm_original = LabelsDescriptorManager(jph(ldg.pfo_target_atlas, 'label_descriptor.txt'))
+#     labels_to_erase = [2, 4, 16, 32]
+#     ldm_relabelled = ldm_original.erase_labels(labels_to_erase)
+#
+#     check_list_equal(dict_expected.keys(), ldm_relabelled.dict_label_descriptor.keys())
+#     for k in dict_expected.keys():
+#         check_list_equal(dict_expected[k], ldm_relabelled.dict_label_descriptor[k])
+#
+#
+# def test_assign_all_other_labels_the_same_value():
+#     _create_data_set_for_tests()
+#
+#     dict_expected = collections.OrderedDict()
+#     dict_expected.update({0: [[0, 0, 0], [1.0, 1.0, 1.0], 'Bkg']})
+#     dict_expected.update({1: [[255, 0, 0], [1.0, 1.0, 1.0], 'Skull']})
+#     dict_expected.update({4: [[255, 0, 255], [1.0, 1.0, 1.0], 'CSF']})
+#
+#     ldm_original = LabelsDescriptorManager(jph(ldg.pfo_target_atlas, 'label_descriptor.txt'))
+#     labels_to_keep = [1, 4]
+#     other_value = 0
+#     ldm_relabelled = ldm_original.assign_all_other_labels_the_same_value(labels_to_keep, other_value)
+#
+#     check_list_equal(dict_expected.keys(), ldm_relabelled.dict_label_descriptor.keys())
+#     for k in dict_expected.keys():
+#         check_list_equal(dict_expected[k], ldm_relabelled.dict_label_descriptor[k])
+#
+#
+# def test_keep_one_label():
+#     _create_data_set_for_tests()
+#
+#     dict_expected = collections.OrderedDict()
+#     dict_expected.update({0: [[0, 0, 0], [1.0, 1.0, 1.0], 'Bkg']})
+#     dict_expected.update({3: [[0, 0, 255], [1.0, 1.0, 1.0], 'GM']})
+#
+#     ldm_original = LabelsDescriptorManager(jph(ldg.pfo_target_atlas, 'label_descriptor.txt'))
+#     label_to_keep = 3
+#     ldm_relabelled = ldm_original.keep_one_label(label_to_keep)
+#
+#     check_list_equal(dict_expected.keys(), ldm_relabelled.dict_label_descriptor.keys())
+#     for k in dict_expected.keys():
+#         check_list_equal(dict_expected[k], ldm_relabelled.dict_label_descriptor[k])