{"action":"created","comment":{"url":"https://api.github.com/repos/nilearn/nilearn/pulls/comments/46311538","id":46311538,"diff_hunk":"@@ -75,3 +79,61 @@ def is_spd(M, decimal=15, verbose=1):\n     if not ispd and verbose > 0:\n         print(\"matrix has a negative eigenvalue: %.3f\" % eigvalsh.min())\n     return ispd\n+\n+\n+def check_threshold(threshold, data, percentile_calculate, name='threshold'):\n+    \"\"\" Checks if the given threshold is in correct format and within the limit\n+    and also if necessary, this function also returns score of the data\n+    calculated based upon the given specific percentile function.\n+\n+    Parameters\n+    ----------\n+    threshold: a float value or a real number or a percentage in string.\n+        If threshold is a float value, it should be within the range of the\n+        maximum intensity value of the data.\n+        If threshold is a percentage expressed in a string it must finish with a\n+        percent sign like \"99.7%\" or just a real number as 99.\n+    data: ndarray\n+        an array of the input masked data.\n+    percentile_calculate: a percentile function {scoreatpercentile, fastabspercentile}\n+        define the name of a specific percentile function to use it to\n+        calculate the score on the data.\n+    name: string, optional\n+        A string just used for representing the name of the threshold for a precise\n+        error message.\n+\n+    Returns\n+    -------\n+    threshold: a number\n+        returns the score of the percentile on the data or\n+        returns threshold as it is if given threshold is not a string percentile.\n+    \"\"\"\n+    if isinstance(threshold, float):\n+        # checks whether the given float value exceeds the maximum\n+        # value of the image data\n+        value_check = abs(data).max()\n+        if abs(threshold) > value_check:\n+            warnings.warn(\"The given float value must not exceed %d. \"\n+                          \"But, you have given threshold=%s \" % (value_check,\n+                                                                 threshold))\n+    elif isinstance(threshold, _basestring):\n+        message = ('If \"{0}\" is given as string it '\n+                   'should be a number followed by the percent '\n+                   'sign, e.g. \"25.3%\"').format(name)\n+        if not threshold.endswith('%'):\n+            raise ValueError(message)\n+\n+        try:\n+            percentile = float(threshold[:-1])\n+        except ValueError as exc:\n+            exc.args += (message, )\n+            raise\n+\n+        threshold = percentile_calculate(data, percentile)\n+\n+    elif isinstance(threshold, numbers.Real):","path":"nilearn/_utils/extmath.py","position":69,"original_position":69,"commit_id":"2d4daa7bff59d0d1995fe8480134ae45410847e4","original_commit_id":"2d4daa7bff59d0d1995fe8480134ae45410847e4","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":"What was wrong with the old check_threshold code?","created_at":"2015-12-01T17:46:02Z","updated_at":"2015-12-01T17:46:02Z","html_url":"https://github.com/nilearn/nilearn/pull/651#discussion_r46311538","pull_request_url":"https://api.github.com/repos/nilearn/nilearn/pulls/651","_links":{"self":{"href":"https://api.github.com/repos/nilearn/nilearn/pulls/comments/46311538"},"html":{"href":"https://github.com/nilearn/nilearn/pull/651#discussion_r46311538"},"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":"2015-12-01T17:46:02Z","closed_at":null,"merged_at":null,"merge_commit_sha":"f8ff092de1d74150a60e5e3cfacfcbf1bc07b654","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/2d4daa7bff59d0d1995fe8480134ae45410847e4","head":{"label":"KamalakerDadi:AutoExtractor","ref":"AutoExtractor","sha":"2d4daa7bff59d0d1995fe8480134ae45410847e4","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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