{"action":"created","comment":{"url":"https://api.github.com/repos/mne-tools/mne-python/pulls/comments/26724785","id":26724785,"diff_hunk":"@@ -167,43 +167,57 @@ def mne_analyze_colormap(limits=[5, 10, 15], format='mayavi'):\n         brain.scale_data_colormap(fmin=-15, fmid=0, fmax=15, transparent=False)\n \n     \"\"\"\n-    l = np.asarray(limits, dtype='float')\n-    if len(l) != 3:\n-        raise ValueError('limits must have 3 elements')\n-    if any(l < 0):\n-        raise ValueError('limits must all be positive')\n-    if any(np.diff(l) <= 0):\n+    # Ensure limits is an array\n+    limits = np.asarray(limits, dtype='float')\n+\n+    if len(limits) != 3 and len(limits) != 6:\n+        raise ValueError('limits must have 3 or 6 elements')\n+    if len(limits) == 3 and any(limits < 0.):\n+        raise ValueError('if 3 elements, limits must all be non-negative')\n+    if any(np.diff(limits) <= 0):\n         raise ValueError('limits must be monotonically increasing')\n     if format == 'matplotlib':\n         from matplotlib import colors\n-        l = (np.concatenate((-np.flipud(l), l)) + l[-1]) / (2 * l[-1])\n-        cdict = {'red': ((l[0], 0.0, 0.0),\n-                         (l[1], 0.0, 0.0),\n-                         (l[2], 0.5, 0.5),\n-                         (l[3], 0.5, 0.5),\n-                         (l[4], 1.0, 1.0),\n-                         (l[5], 1.0, 1.0)),\n-                 'green': ((l[0], 1.0, 1.0),\n-                           (l[1], 0.0, 0.0),\n-                           (l[2], 0.5, 0.5),\n-                           (l[3], 0.5, 0.5),\n-                           (l[4], 0.0, 0.0),\n-                           (l[5], 1.0, 1.0)),\n-                 'blue': ((l[0], 1.0, 1.0),\n-                          (l[1], 1.0, 1.0),\n-                          (l[2], 0.5, 0.5),\n-                          (l[3], 0.5, 0.5),\n-                          (l[4], 0.0, 0.0),\n-                          (l[5], 0.0, 0.0))}\n+        if len(limits) == 3:\n+            limits = (np.concatenate((-np.flipud(limits), limits)) +\n+                      limits[-1]) / (2 * limits[-1])\n+        else:\n+            limits = (limits - np.min(limits)) / np.max(limits -\n+                                                        np.min(limits))\n+\n+        cdict = {'red': ((limits[0], 0.0, 0.0),\n+                         (limits[1], 0.0, 0.0),\n+                         (limits[2], 0.5, 0.5),\n+                         (limits[3], 0.5, 0.5),\n+                         (limits[4], 1.0, 1.0),\n+                         (limits[5], 1.0, 1.0)),\n+                 'green': ((limits[0], 1.0, 1.0),\n+                           (limits[1], 0.0, 0.0),\n+                           (limits[2], 0.5, 0.5),\n+                           (limits[3], 0.5, 0.5),\n+                           (limits[4], 0.0, 0.0),\n+                           (limits[5], 1.0, 1.0)),\n+                 'blue': ((limits[0], 1.0, 1.0),\n+                          (limits[1], 1.0, 1.0),\n+                          (limits[2], 0.5, 0.5),\n+                          (limits[3], 0.5, 0.5),\n+                          (limits[4], 0.0, 0.0),\n+                          (limits[5], 0.0, 0.0))}\n         return colors.LinearSegmentedColormap('mne_analyze', cdict)\n     elif format == 'mayavi':\n-        l = np.concatenate((-np.flipud(l), [0], l)) / l[-1]\n+        if len(limits) == 3:\n+            limits = np.concatenate((-np.flipud(limits), [0], limits)) /\\\n+                limits[-1]\n+        else:\n+            limits = [limits[:3], [0], limits[3:]]","path":"mne/viz/utils.py","position":72,"original_position":72,"commit_id":"d8350b5ebc09a63d71e0883c6271ed3a8908ec65","original_commit_id":"d8350b5ebc09a63d71e0883c6271ed3a8908ec65","user":{"login":"wronk","id":5296721,"avatar_url":"https://avatars.githubusercontent.com/u/5296721?v=3","gravatar_id":"","url":"https://api.github.com/users/wronk","html_url":"https://github.com/wronk","followers_url":"https://api.github.com/users/wronk/followers","following_url":"https://api.github.com/users/wronk/following{/other_user}","gists_url":"https://api.github.com/users/wronk/gists{/gist_id}","starred_url":"https://api.github.com/users/wronk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wronk/subscriptions","organizations_url":"https://api.github.com/users/wronk/orgs","repos_url":"https://api.github.com/users/wronk/repos","events_url":"https://api.github.com/users/wronk/events{/privacy}","received_events_url":"https://api.github.com/users/wronk/received_events","type":"User","site_admin":false},"body":"Thanks. Needs to be on length 7 list, updating it.","created_at":"2015-03-19T01:55:31Z","updated_at":"2015-03-19T01:55:31Z","html_url":"https://github.com/mne-tools/mne-python/pull/1782#discussion_r26724785","pull_request_url":"https://api.github.com/repos/mne-tools/mne-python/pulls/1782","_links":{"self":{"href":"https://api.github.com/repos/mne-tools/mne-python/pulls/comments/26724785"},"html":{"href":"https://github.com/mne-tools/mne-python/pull/1782#discussion_r26724785"},"pull_request":{"href":"https://api.github.com/repos/mne-tools/mne-python/pulls/1782"}}},"pull_request":{"url":"https://api.github.com/repos/mne-tools/mne-python/pulls/1782","id":28847496,"html_url":"https://github.com/mne-tools/mne-python/pull/1782","diff_url":"https://github.com/mne-tools/mne-python/pull/1782.diff","patch_url":"https://github.com/mne-tools/mne-python/pull/1782.patch","issue_url":"https://api.github.com/repos/mne-tools/mne-python/issues/1782","number":1782,"state":"open","locked":false,"title":"Cmap enh","user":{"login":"wronk","id":5296721,"avatar_url":"https://avatars.githubusercontent.com/u/5296721?v=3","gravatar_id":"","url":"https://api.github.com/users/wronk","html_url":"https://github.com/wronk","followers_url":"https://api.github.com/users/wronk/followers","following_url":"https://api.github.com/users/wronk/following{/other_user}","gists_url":"https://api.github.com/users/wronk/gists{/gist_id}","starred_url":"https://api.github.com/users/wronk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wronk/subscriptions","organizations_url":"https://api.github.com/users/wronk/orgs","repos_url":"https://api.github.com/users/wronk/repos","events_url":"https://api.github.com/users/wronk/events{/privacy}","received_events_url":"https://api.github.com/users/wronk/received_events","type":"User","site_admin":false},"body":"Here's my WIP for updating the way a user specifies the colormap (as per #1754). I also made a clarification in the plot_source_estimate docstring. @dengemann, I left my modifications to mne_analyze_colormap so that anyone can potentially pass it all 6 control points (3 neg, 3 pos) and create an asymmetric cmap. However, I took that out of the default options in the source estimate plotting functions to make the API simpler.\r\n\r\n## Current API\r\nCurrently, user must know the appropriate float values for the cmap control points or use the 5, 10, 15 flim defaults.\r\n`colormap = mne.viz.mne_analyze_colormap(limits=[5, 10, 15])`\r\n`brain = stc.plot('fsaverage', 'inflated', 'rh', colormap)`\r\n`brain.scale_data_colormap(fmin=-15, fmid=0, fmax=15, transparent=False)`\r\n\r\n## WIP API\r\nUser can now use percentiles (in addition to hard values as before) to set the cmap control points. The old API can still be used. User can also specify to have the cmap control points set automatically based on default percentiles.\r\n\r\n#### Replicating old behavior: fmin/fmid/fmax input with mne_analyze cmap\r\n`fmin, fmid, fmax = 3, 4, 5`\r\n`colormap = mne.viz.mne_analyze_colormap(limits=[fmin, fmid, fmax])`\r\n`p = stc.plot(colormap=colormap, fmin=-1 * fmax, fmid=0, fmax=fmax, transparent=False)`\r\n![retrotest](https://cloud.githubusercontent.com/assets/5296721/6086767/27fc493c-adf9-11e4-89b7-169e1694bc6c.jpg)\r\n\r\n\r\n#### New behavior: Automatic limits using mne_analyze cmap\r\n`limits = 'auto'`\r\n`colormap = 'mne_analyze'`\r\n`p = stc.plot(colormap=colormap, limits=limits)`\r\n![autolimits](https://cloud.githubusercontent.com/assets/5296721/6086996/21ecd7d0-adfb-11e4-9a57-a1ee79e8b2b8.jpg)\r\n\r\n\r\n#### New behavior: f limits with tuple and mne_analyze cmap\r\n`colormap='mne_analyze'`\r\n`fmin, fmid, fmax = 3, 4, 5`\r\n`limits = (fmin, fmid, fmax)`\r\n`p = stc.plot(colormap=colormap, limits=limits)`\r\n\r\n#### New behavior: using f limits  with dict (specifying hard values) and mne_analyze cmap\r\nNote the the limits are specified with keyword `pos_lims` so the user knows these will be mirrored across zero to create the negative counterparts to each limit.\r\n`colormap='mne_analyze'`\r\n`fmin, fmid, fmax = 3, 4, 5`\r\n`limits = dict(kind='value', pos_lims=[fmin, fmid, fmax])`\r\n`p = stc.plot(colormap=colormap, limits=limits)`\r\n\r\n#### New behavior: using f limits but with dict (specifying percentiles) and mne_analyze cmap\r\n`colormap='mne_analyze'`\r\n`limits = dict(kind='percent', pos_lims=[90., 95., 99.])`\r\n`p = stc.plot(colormap=colormap, limits=limits)`\r\n\r\n#### New behavior: using f limits but with dict (specifying percentiles) and hot cmap\r\nNote that the `lims` keyword specifies the limits here (instead of `pos_lims`) because we aren't using the mirrored mne_analyze cmap\r\n`colormap='hot'`\r\n`limits = dict(kind='percent', lims=[90., 95., 99.])`\r\n`p = stc.plot(colormap=colormap, limits=limits)`\r\n![hotlimpercent](https://cloud.githubusercontent.com/assets/5296721/6087499/0e1eee4a-ae01-11e4-8cfe-f64807af3a49.jpg)","created_at":"2015-02-06T22:26:51Z","updated_at":"2015-03-19T01:55:31Z","closed_at":null,"merged_at":null,"merge_commit_sha":"f98e97d7705e9d88a645f752966fcb3a64de8a33","assignee":null,"milestone":{"url":"https://api.github.com/repos/mne-tools/mne-python/milestones/5","html_url":"https://github.com/mne-tools/mne-python/milestones/0.9","labels_url":"https://api.github.com/repos/mne-tools/mne-python/milestones/5/labels","id":1011721,"number":5,"title":"0.9","description":null,"creator":{"login":"Eric89GXL","id":2365790,"avatar_url":"https://avatars.githubusercontent.com/u/2365790?v=3","gravatar_id":"","url":"https://api.github.com/users/Eric89GXL","html_url":"https://github.com/Eric89GXL","followers_url":"https://api.github.com/users/Eric89GXL/followers","following_url":"https://api.github.com/users/Eric89GXL/following{/other_user}","gists_url":"https://api.github.com/users/Eric89GXL/gists{/gist_id}","starred_url":"https://api.github.com/users/Eric89GXL/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Eric89GXL/subscriptions","organizations_url":"https://api.github.com/users/Eric89GXL/orgs","repos_url":"https://api.github.com/users/Eric89GXL/repos","events_url":"https://api.github.com/users/Eric89GXL/events{/privacy}","received_events_url":"https://api.github.com/users/Eric89GXL/received_events","type":"User","site_admin":false},"open_issues":26,"closed_issues":26,"state":"open","created_at":"2015-03-09T03:10:39Z","updated_at":"2015-03-18T06:50:30Z","due_on":null,"closed_at":null},"commits_url":"https://api.github.com/repos/mne-tools/mne-python/pulls/1782/commits","review_comments_url":"https://api.github.com/repos/mne-tools/mne-python/pulls/1782/comments","review_comment_url":"https://api.github.com/repos/mne-tools/mne-python/pulls/comments{/number}","comments_url":"https://api.github.com/repos/mne-tools/mne-python/issues/1782/comments","statuses_url":"https://api.github.com/repos/mne-tools/mne-python/statuses/d8350b5ebc09a63d71e0883c6271ed3a8908ec65","head":{"label":"wronk:cmap_enh","ref":"cmap_enh","sha":"d8350b5ebc09a63d71e0883c6271ed3a8908ec65","user":{"login":"wronk","id":5296721,"avatar_url":"https://avatars.githubusercontent.com/u/5296721?v=3","gravatar_id":"","url":"https://api.github.com/users/wronk","html_url":"https://github.com/wronk","followers_url":"https://api.github.com/users/wronk/followers","following_url":"https://api.github.com/users/wronk/following{/other_user}","gists_url":"https://api.github.com/users/wronk/gists{/gist_id}","starred_url":"https://api.github.com/users/wronk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wronk/subscriptions","organizations_url":"https://api.github.com/users/wronk/orgs","repos_url":"https://api.github.com/users/wronk/repos","events_url":"https://api.github.com/users/wronk/events{/privacy}","received_events_url":"https://api.github.com/users/wronk/received_events","type":"User","site_admin":false},"repo":{"id":12385398,"name":"mne-python","full_name":"wronk/mne-python","owner":{"login":"wronk","id":5296721,"avatar_url":"https://avatars.githubusercontent.com/u/5296721?v=3","gravatar_id":"","url":"https://api.github.com/users/wronk","html_url":"https://github.com/wronk","followers_url":"https://api.github.com/users/wronk/followers","following_url":"https://api.github.com/users/wronk/following{/other_user}","gists_url":"https://api.github.com/users/wronk/gists{/gist_id}","starred_url":"https://api.github.com/users/wronk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wronk/subscriptions","organizations_url":"https://api.github.com/users/wronk/orgs","repos_url":"https://api.github.com/users/wronk/repos","events_url":"https://api.github.com/users/wronk/events{/privacy}","received_events_url":"https://api.github.com/users/wronk/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/wronk/mne-python","description":"MNE 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