{"action":"created","comment":{"url":"https://api.github.com/repos/mne-tools/mne-python/pulls/comments/48457301","id":48457301,"diff_hunk":"@@ -0,0 +1,58 @@\n+\"\"\"\n+==============================================================\n+PSD estimation for MEG sensors\n+==============================================================\n+\n+PSD calculation with both multitaper and welch's method are displayed\n+\"\"\"\n+# Authors: Chris Holdgraf <choldgraf@gmail.com>\n+#          Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>\n+#          Denis Engemann <denis.engemann@gmail.com>\n+#\n+# License: BSD (3-clause)\n+\n+import matplotlib.pyplot as plt\n+\n+import mne\n+from mne import io\n+from mne.time_frequency import psd_welch, psd_multitaper\n+from mne.datasets import somato\n+\n+print(__doc__)\n+\n+###############################################################################\n+# Set parameters\n+data_path = somato.data_path()\n+raw_fname = data_path + '/MEG/somato/sef_raw_sss.fif'\n+event_id, tmin, tmax = 1, -1., 3.\n+fmin, fmax = 2, 40\n+n_fft = 256\n+\n+# Setup for reading the raw data\n+raw = io.Raw(raw_fname)\n+baseline = (None, 0)\n+events = mne.find_events(raw, stim_channel='STI 014')\n+\n+# picks MEG gradiometers\n+picks = mne.pick_types(raw.info, meg='grad', eeg=False, eog=True, stim=False)\n+\n+epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,\n+                    baseline=baseline, reject=dict(grad=4000e-13, eog=350e-6))\n+picks_psd = picks[:5]\n+\n+###############################################################################\n+# Calculate power spectral density\n+psds_we, freqs_we = psd_welch(epochs, tmin=tmin, tmax=tmax, fmin=fmin,\n+                              fmax=fmax, n_fft=n_fft, proj=False,\n+                              picks=picks_psd)\n+psds_mt, freqs_mt = psd_multitaper(epochs, tmin=tmin, tmax=tmax, fmin=fmin,","path":"examples/time_frequency/plot_psd_sensors.py","position":48,"original_position":48,"commit_id":"928df54b13c27d09c9216c92335271692eb29a38","original_commit_id":"928df54b13c27d09c9216c92335271692eb29a38","user":{"login":"choldgraf","id":1839645,"avatar_url":"https://avatars.githubusercontent.com/u/1839645?v=3","gravatar_id":"","url":"https://api.github.com/users/choldgraf","html_url":"https://github.com/choldgraf","followers_url":"https://api.github.com/users/choldgraf/followers","following_url":"https://api.github.com/users/choldgraf/following{/other_user}","gists_url":"https://api.github.com/users/choldgraf/gists{/gist_id}","starred_url":"https://api.github.com/users/choldgraf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/choldgraf/subscriptions","organizations_url":"https://api.github.com/users/choldgraf/orgs","repos_url":"https://api.github.com/users/choldgraf/repos","events_url":"https://api.github.com/users/choldgraf/events{/privacy}","received_events_url":"https://api.github.com/users/choldgraf/received_events","type":"User","site_admin":false},"body":"I didn't see anything that used compute_raw/compute_epochs_psd in the examples, everything else called a method associated with Raw or Epochs, or a function that calculates a PSD using their own non-deprecated code.\r\n\r\nThough I now notice that a few objects use the soon-to-be-deprecated functions (such as plot_epochs_psd). I assume those should be changed to use the psd_welch function instead?  In that case, I can update the code and then just add code for the `psd_` functions to the existing examples, rather than adding a new example.","created_at":"2015-12-27T18:58:14Z","updated_at":"2015-12-27T18:58:14Z","html_url":"https://github.com/mne-tools/mne-python/pull/2710#discussion_r48457301","pull_request_url":"https://api.github.com/repos/mne-tools/mne-python/pulls/2710","_links":{"self":{"href":"https://api.github.com/repos/mne-tools/mne-python/pulls/comments/48457301"},"html":{"href":"https://github.com/mne-tools/mne-python/pull/2710#discussion_r48457301"},"pull_request":{"href":"https://api.github.com/repos/mne-tools/mne-python/pulls/2710"}}},"pull_request":{"url":"https://api.github.com/repos/mne-tools/mne-python/pulls/2710","id":53761037,"html_url":"https://github.com/mne-tools/mne-python/pull/2710","diff_url":"https://github.com/mne-tools/mne-python/pull/2710.diff","patch_url":"https://github.com/mne-tools/mne-python/pull/2710.patch","issue_url":"https://api.github.com/repos/mne-tools/mne-python/issues/2710","number":2710,"state":"open","locked":false,"title":"ENH: refactor PSD functions","user":{"login":"choldgraf","id":1839645,"avatar_url":"https://avatars.githubusercontent.com/u/1839645?v=3","gravatar_id":"","url":"https://api.github.com/users/choldgraf","html_url":"https://github.com/choldgraf","followers_url":"https://api.github.com/users/choldgraf/followers","following_url":"https://api.github.com/users/choldgraf/following{/other_user}","gists_url":"https://api.github.com/users/choldgraf/gists{/gist_id}","starred_url":"https://api.github.com/users/choldgraf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/choldgraf/subscriptions","organizations_url":"https://api.github.com/users/choldgraf/orgs","repos_url":"https://api.github.com/users/choldgraf/repos","events_url":"https://api.github.com/users/choldgraf/events{/privacy}","received_events_url":"https://api.github.com/users/choldgraf/received_events","type":"User","site_admin":false},"body":"This is a quick update that adds information to docstring so people know where to look for the under-the-hood PSD estimation. It also adds code to keep the estimated psd/frequencies with the object after the transform method is called.","created_at":"2015-12-15T20:58:30Z","updated_at":"2015-12-27T18:58:14Z","closed_at":null,"merged_at":null,"merge_commit_sha":"11778083dabba164c69890bc847bfc439979c4e6","assignee":null,"milestone":{"url":"https://api.github.com/repos/mne-tools/mne-python/milestones/8","html_url":"https://github.com/mne-tools/mne-python/milestones/0.12","labels_url":"https://api.github.com/repos/mne-tools/mne-python/milestones/8/labels","id":1429321,"number":8,"title":"0.12","description":"","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":30,"closed_issues":8,"state":"open","created_at":"2015-11-25T13:36:18Z","updated_at":"2015-12-27T10:20:57Z","due_on":"2016-04-29T04:00:00Z","closed_at":null},"commits_url":"https://api.github.com/repos/mne-tools/mne-python/pulls/2710/commits","review_comments_url":"https://api.github.com/repos/mne-tools/mne-python/pulls/2710/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/2710/comments","statuses_url":"https://api.github.com/repos/mne-tools/mne-python/statuses/928df54b13c27d09c9216c92335271692eb29a38","head":{"label":"choldgraf:update_psdestimator_doc","ref":"update_psdestimator_doc","sha":"928df54b13c27d09c9216c92335271692eb29a38","user":{"login":"choldgraf","id":1839645,"avatar_url":"https://avatars.githubusercontent.com/u/1839645?v=3","gravatar_id":"","url":"https://api.github.com/users/choldgraf","html_url":"https://github.com/choldgraf","followers_url":"https://api.github.com/users/choldgraf/followers","following_url":"https://api.github.com/users/choldgraf/following{/other_user}","gists_url":"https://api.github.com/users/choldgraf/gists{/gist_id}","starred_url":"https://api.github.com/users/choldgraf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/choldgraf/subscriptions","organizations_url":"https://api.github.com/users/choldgraf/orgs","repos_url":"https://api.github.com/users/choldgraf/repos","events_url":"https://api.github.com/users/choldgraf/events{/privacy}","received_events_url":"https://api.github.com/users/choldgraf/received_events","type":"User","site_admin":false},"repo":{"id":29602471,"name":"mne-python","full_name":"choldgraf/mne-python","owner":{"login":"choldgraf","id":1839645,"avatar_url":"https://avatars.githubusercontent.com/u/1839645?v=3","gravatar_id":"","url":"https://api.github.com/users/choldgraf","html_url":"https://github.com/choldgraf","followers_url":"https://api.github.com/users/choldgraf/followers","following_url":"https://api.github.com/users/choldgraf/following{/other_user}","gists_url":"https://api.github.com/users/choldgraf/gists{/gist_id}","starred_url":"https://api.github.com/users/choldgraf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/choldgraf/subscriptions","organizations_url":"https://api.github.com/users/choldgraf/orgs","repos_url":"https://api.github.com/users/choldgraf/repos","events_url":"https://api.github.com/users/choldgraf/events{/privacy}","received_events_url":"https://api.github.com/users/choldgraf/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/choldgraf/mne-python","description":"MNE 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