{"action":"created","comment":{"url":"https://api.github.com/repos/nilearn/nilearn/pulls/comments/45718177","id":45718177,"diff_hunk":"@@ -0,0 +1,115 @@\n+\"\"\" Test Region Extractor and its functions \"\"\"\n+\n+import numpy as np\n+import nibabel\n+\n+from nose.tools import assert_raises, assert_equal\n+\n+from nilearn.regions.region_extractor import (connected_regions,\n+                                              RegionExtractor)\n+from nilearn.regions.region_extractor import _threshold_maps\n+from nilearn.image import iter_img\n+\n+from nilearn._utils.testing import assert_raises_regex, generate_maps\n+\n+\n+def _make_random_data(shape):\n+    affine = np.eye(4)\n+    rng = np.random.RandomState(0)\n+    data_rng = rng.normal(size=shape)\n+    img = nibabel.Nifti1Image(data_rng, affine)\n+    data = img.get_data()\n+    return img, data\n+\n+\n+def test_invalid_thresholds_in_threshold_maps():\n+    shape = (91, 109, 91)\n+    maps = generate_maps(shape, n_regions=2)\n+    map_0 = maps[0]\n+\n+    for invalid_threshold in [10, '80%', 'auto']:\n+        assert_raises_regex(ValueError,\n+                            \"Threshold must be float value\",\n+                            _threshold_maps,\n+                            map_0, threshold=invalid_threshold)\n+\n+\n+def test_passing_threshold_maps():\n+    # smoke test for function _threshold_maps with randomly\n+    # generated maps\n+    shape = (6, 8, 10)\n+    maps = generate_maps(shape, n_regions=3)\n+    map_0 = maps[0]\n+    for map_img, threshold in zip(iter_img(map_0), [0.0, 0.5, 1.0]):\n+        thr_maps = _threshold_maps(map_img, threshold=threshold)\n+\n+\n+def test_invalids_extract_types_in_connected_regions():\n+    shape = (91, 109, 91)\n+    n_regions = 2\n+    maps = generate_maps(shape, n_regions)\n+    map_0 = maps[0]\n+    valid_names = ['connected_components', 'local_regions']\n+\n+    # test whether same error raises as expected when given invalid inputs to\n+    # extract_type of regions extraction\n+    message = (\"'extract_type' should be {0}\").format(valid_names)\n+    for img in iter_img(map_0):\n+        assert_raises_regex(ValueError,\n+                            message,\n+                            connected_regions,\n+                            img, min_size=40,\n+                            extract_type='connect_regions')\n+\n+    # test whether error raises when there is an invalid inputs to extract\n+    invalid_extract_type = ['local', 'asdf', 10]\n+    for type_ in invalid_extract_type:\n+        assert_raises(ValueError, connected_regions,\n+                      img, extract_type=type_)\n+\n+\n+def test_passing_connected_regions():\n+    shape = (91, 109, 91)\n+    n_regions = 4\n+    maps = generate_maps(shape, n_regions)\n+    map_0 = maps[0]\n+\n+    valid_extract_types = ['connected_components', 'local_regions']\n+    # smoke test for function connected_regions","path":"nilearn/regions/tests/test_region_extractor.py","position":78,"original_position":78,"commit_id":"a1f1a7230b829fbf3830b05f9c9b9aae6ca08d00","original_commit_id":"a1f1a7230b829fbf3830b05f9c9b9aae6ca08d00","user":{"login":"lesteve","id":1680079,"avatar_url":"https://avatars.githubusercontent.com/u/1680079?v=3","gravatar_id":"","url":"https://api.github.com/users/lesteve","html_url":"https://github.com/lesteve","followers_url":"https://api.github.com/users/lesteve/followers","following_url":"https://api.github.com/users/lesteve/following{/other_user}","gists_url":"https://api.github.com/users/lesteve/gists{/gist_id}","starred_url":"https://api.github.com/users/lesteve/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lesteve/subscriptions","organizations_url":"https://api.github.com/users/lesteve/orgs","repos_url":"https://api.github.com/users/lesteve/repos","events_url":"https://api.github.com/users/lesteve/events{/privacy}","received_events_url":"https://api.github.com/users/lesteve/received_events","type":"User","site_admin":false},"body":"Can we not do better than a smoke test, e.g. generate a few regions with gaussian + noise and make sure that we find the regions as we expect?","created_at":"2015-11-24T10:28:40Z","updated_at":"2015-11-24T10:28:40Z","html_url":"https://github.com/nilearn/nilearn/pull/651#discussion_r45718177","pull_request_url":"https://api.github.com/repos/nilearn/nilearn/pulls/651","_links":{"self":{"href":"https://api.github.com/repos/nilearn/nilearn/pulls/comments/45718177"},"html":{"href":"https://github.com/nilearn/nilearn/pull/651#discussion_r45718177"},"pull_request":{"href":"https://api.github.com/repos/nilearn/nilearn/pulls/651"}}},"pull_request":{"url":"https://api.github.com/repos/nilearn/nilearn/pulls/651","id":39828251,"html_url":"https://github.com/nilearn/nilearn/pull/651","diff_url":"https://github.com/nilearn/nilearn/pull/651.diff","patch_url":"https://github.com/nilearn/nilearn/pull/651.patch","issue_url":"https://api.github.com/repos/nilearn/nilearn/issues/651","number":651,"state":"open","locked":false,"title":"[MRG] Region Extractor","user":{"login":"KamalakerDadi","id":11410385,"avatar_url":"https://avatars.githubusercontent.com/u/11410385?v=3","gravatar_id":"","url":"https://api.github.com/users/KamalakerDadi","html_url":"https://github.com/KamalakerDadi","followers_url":"https://api.github.com/users/KamalakerDadi/followers","following_url":"https://api.github.com/users/KamalakerDadi/following{/other_user}","gists_url":"https://api.github.com/users/KamalakerDadi/gists{/gist_id}","starred_url":"https://api.github.com/users/KamalakerDadi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/KamalakerDadi/subscriptions","organizations_url":"https://api.github.com/users/KamalakerDadi/orgs","repos_url":"https://api.github.com/users/KamalakerDadi/repos","events_url":"https://api.github.com/users/KamalakerDadi/events{/privacy}","received_events_url":"https://api.github.com/users/KamalakerDadi/received_events","type":"User","site_admin":false},"body":"Fix #633 \r\nTo Do List:\r\n- [x] Code\r\n- [x] Documentation\r\n- [x] Tests\r\n- [x] Example\r\n\r\n* Code design\r\n   * ```class``` named as ```RegionExtractor``` - to *extract regions* from the maps and also extracts *subjects timeseries signals* from those extracted regions by inheriting ```NiftiMapsMasker```.\r\n         * function named as ```threshold_img``` to keep meaningful voxels for region extraction.\r\n         * function named as ```connected_regions``` to extract regions from thresholded images.\r\n\r\n*  ``` RegionExtractor ```\r\n      * ```fit()``` extract regions.\r\n      * ```transform()``` regions to signals.\r\n         * example: ```plot_extract_regions_canica_maps.py``` \r\n         * example: ```plot_extract_regions_smith_atlas_networks.py```\r\n\r\n*  ```threshold_img``` - two different ways of thresholding. (integrated in ```nilearn.image.image```)\r\n      1. ```percentile``` - ```scoreatpercentile```.\r\n      2. ```img_value``` - based on voxel intensity value.\r\n          * example: ```plot_extract_regions_statistical_maps.py```\r\n\r\n*  ```connected_regions``` - two different ways of extracting regions.\r\n      1. ```local_regions``` uses random walker method.\r\n      2. ```connected_components``` uses only labelling which labels based on unique features. \r\n           * example: ```plot_extract_regions_statistical_maps.py```\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n","created_at":"2015-07-13T16:08:17Z","updated_at":"2015-11-24T10:28:40Z","closed_at":null,"merged_at":null,"merge_commit_sha":"bbd2d4f82e8baf7cd19910db67140f1535f6a6b9","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/nilearn/nilearn/pulls/651/commits","review_comments_url":"https://api.github.com/repos/nilearn/nilearn/pulls/651/comments","review_comment_url":"https://api.github.com/repos/nilearn/nilearn/pulls/comments{/number}","comments_url":"https://api.github.com/repos/nilearn/nilearn/issues/651/comments","statuses_url":"https://api.github.com/repos/nilearn/nilearn/statuses/a1f1a7230b829fbf3830b05f9c9b9aae6ca08d00","head":{"label":"KamalakerDadi:AutoExtractor","ref":"AutoExtractor","sha":"a1f1a7230b829fbf3830b05f9c9b9aae6ca08d00","user":{"login":"KamalakerDadi","id":11410385,"avatar_url":"https://avatars.githubusercontent.com/u/11410385?v=3","gravatar_id":"","url":"https://api.github.com/users/KamalakerDadi","html_url":"https://github.com/KamalakerDadi","followers_url":"https://api.github.com/users/KamalakerDadi/followers","following_url":"https://api.github.com/users/KamalakerDadi/following{/other_user}","gists_url":"https://api.github.com/users/KamalakerDadi/gists{/gist_id}","starred_url":"https://api.github.com/users/KamalakerDadi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/KamalakerDadi/subscriptions","organizations_url":"https://api.github.com/users/KamalakerDadi/orgs","repos_url":"https://api.github.com/users/KamalakerDadi/repos","events_url":"https://api.github.com/users/KamalakerDadi/events{/privacy}","received_events_url":"https://api.github.com/users/KamalakerDadi/received_events","type":"User","site_admin":false},"repo":{"id":32379132,"name":"nilearn","full_name":"KamalakerDadi/nilearn","owner":{"login":"KamalakerDadi","id":11410385,"avatar_url":"https://avatars.githubusercontent.com/u/11410385?v=3","gravatar_id":"","url":"https://api.github.com/users/KamalakerDadi","html_url":"https://github.com/KamalakerDadi","followers_url":"https://api.github.com/users/KamalakerDadi/followers","following_url":"https://api.github.com/users/KamalakerDadi/following{/other_user}","gists_url":"https://api.github.com/users/KamalakerDadi/gists{/gist_id}","starred_url":"https://api.github.com/users/KamalakerDadi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/KamalakerDadi/subscriptions","organizations_url":"https://api.github.com/users/KamalakerDadi/orgs","repos_url":"https://api.github.com/users/KamalakerDadi/repos","events_url":"https://api.github.com/users/KamalakerDadi/events{/privacy}","received_events_url":"https://api.github.com/users/KamalakerDadi/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/KamalakerDadi/nilearn","description":"Machine 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