{"action":"created","comment":{"url":"https://api.github.com/repos/snoplusuk/echidna/pulls/comments/25882785","id":25882785,"diff_hunk":"@@ -23,56 +23,80 @@\n import echidna.limit.limit_config as limit_config\n import echidna.limit.limit_setting as limit_setting\n import echidna.limit.chi_squared as chi_squared\n+import echidna.output.plot_chi_squared as plot_chi_squared\n \n \n if __name__ == \"__main__\":\n+    import argparse\n+    \n+\n+    parser = argparse.ArgumentParser(description=\"Example limit setting script\")\n+    parser.add_argument(\"-v\", \"--verbose\", action=\"store_true\",\n+                        help=\"Print progress and timing information\")\n+    args = parser.parse_args()\n+\n     # Create signal spectrum\n     Te130_0n2b = store.load(echidna.__echidna_home__ +\n-                            \"data/TeLoadedTe130_0n2b.ntuple_reco.hdf5\")\n+                            \"/data/Te130_0n2b_mc_smeared.hdf5\")\n+    print Te130_0n2b._name\n \n     # Create background spectra\n     Te130_2n2b = store.load(echidna.__echidna_home__ +\n-                            \"data/TeLoadedTe130_2n2b.ntuple_reco.hdf5\")\n-    B8 = store.load(echidna.__echidna_home__ +\n-                    \"data/TeLoadedB8.ntuple_reco.hdf5\")\n+                            \"/data/Te130_2n2b_mc_smeared.hdf5\")\n+    print Te130_2n2b._name\n+    B8_Solar = store.load(echidna.__echidna_home__ +\n+                          \"/data/B8_Solar_mc_smeared.hdf5\")\n+    print B8_Solar._name\n \n     # Shrink spectra to 5 years - livetime used by Andy\n     # And make 3.5m fiducial volume cut\n+    # Temporary fix to _num_decays and _raw_events\n+    Te130_0n2b._num_decays = Te130_0n2b.sum()\n+    Te130_0n2b._raw_events = 200034","path":"echidna/scripts/zero_nu_limit.py","position":37,"original_position":37,"commit_id":"0b4862608889f3c491ef93b3c92cdbca141bcbcf","original_commit_id":"0b4862608889f3c491ef93b3c92cdbca141bcbcf","user":{"login":"jwaterfield","id":1927874,"avatar_url":"https://avatars.githubusercontent.com/u/1927874?v=3","gravatar_id":"","url":"https://api.github.com/users/jwaterfield","html_url":"https://github.com/jwaterfield","followers_url":"https://api.github.com/users/jwaterfield/followers","following_url":"https://api.github.com/users/jwaterfield/following{/other_user}","gists_url":"https://api.github.com/users/jwaterfield/gists{/gist_id}","starred_url":"https://api.github.com/users/jwaterfield/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jwaterfield/subscriptions","organizations_url":"https://api.github.com/users/jwaterfield/orgs","repos_url":"https://api.github.com/users/jwaterfield/repos","events_url":"https://api.github.com/users/jwaterfield/events{/privacy}","received_events_url":"https://api.github.com/users/jwaterfield/received_events","type":"User","site_admin":false},"body":"Do you still have access to feynman I can point you too where we are storing the data so you have access to everything if you'd like","created_at":"2015-03-05T17:27:59Z","updated_at":"2015-03-05T17:27:59Z","html_url":"https://github.com/snoplusuk/echidna/pull/49#discussion_r25882785","pull_request_url":"https://api.github.com/repos/snoplusuk/echidna/pulls/49","_links":{"self":{"href":"https://api.github.com/repos/snoplusuk/echidna/pulls/comments/25882785"},"html":{"href":"https://github.com/snoplusuk/echidna/pull/49#discussion_r25882785"},"pull_request":{"href":"https://api.github.com/repos/snoplusuk/echidna/pulls/49"}}},"pull_request":{"url":"https://api.github.com/repos/snoplusuk/echidna/pulls/49","id":30567508,"html_url":"https://github.com/snoplusuk/echidna/pull/49","diff_url":"https://github.com/snoplusuk/echidna/pull/49.diff","patch_url":"https://github.com/snoplusuk/echidna/pull/49.patch","issue_url":"https://api.github.com/repos/snoplusuk/echidna/issues/49","number":49,"state":"open","locked":false,"title":"Updates limit setting code","user":{"login":"ashleyrback","id":1931666,"avatar_url":"https://avatars.githubusercontent.com/u/1931666?v=3","gravatar_id":"","url":"https://api.github.com/users/ashleyrback","html_url":"https://github.com/ashleyrback","followers_url":"https://api.github.com/users/ashleyrback/followers","following_url":"https://api.github.com/users/ashleyrback/following{/other_user}","gists_url":"https://api.github.com/users/ashleyrback/gists{/gist_id}","starred_url":"https://api.github.com/users/ashleyrback/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ashleyrback/subscriptions","organizations_url":"https://api.github.com/users/ashleyrback/orgs","repos_url":"https://api.github.com/users/ashleyrback/repos","events_url":"https://api.github.com/users/ashleyrback/events{/privacy}","received_events_url":"https://api.github.com/users/ashleyrback/received_events","type":"User","site_admin":false},"body":"Includes:\r\n\r\nBug fixes/updates:\r\n\r\n  * Updates to `limit_config` class. Limit setting code was returning scaled\r\n    counts at limit rather than `spectra.sum()` counts. Changes `_chi_squareds`\r\n    to have 3 columns: chi squared, current count and sum. Changed other\r\n    class methods accordingly.\r\n  * Updates `zero_nu_limit` script:\r\n    * Now uses smeared hdf5s\r\n    * Decreases granularity in loops --> was too slow\r\n    * Updated count values, priors\r\n    * Saves systematic analysers (see below)\r\n    * Plots signal vs chi squared\r\n    * Adds verbosity option\r\n\r\nNew:\r\n\r\n  * Adds `SystAnalyser` class to `limit_setting`. A class for analysing the\r\n    effect of systematics. Creates instances via\r\n    `LimitSetting.configure_background`.\r\n  * Adds `utilities` module and timing utility\r\n  * Adds `plot_chi_squared` module with `chi_squared_vs_signal` method. More to\r\n    follow.\r\n  * Adds `dump_ndarray` and `load_ndarray` functions to `store` module. These\r\n    allow you to dump/load any class instance that is mainly numpy arrays, e.g.\r\n    `SystAnalyser` class.","created_at":"2015-03-05T15:45:49Z","updated_at":"2015-03-05T17:27:59Z","closed_at":null,"merged_at":null,"merge_commit_sha":"c59a2362b8ba59ec5dccf1f6ddf5dfdc31032ed8","assignee":{"login":"jwaterfield","id":1927874,"avatar_url":"https://avatars.githubusercontent.com/u/1927874?v=3","gravatar_id":"","url":"https://api.github.com/users/jwaterfield","html_url":"https://github.com/jwaterfield","followers_url":"https://api.github.com/users/jwaterfield/followers","following_url":"https://api.github.com/users/jwaterfield/following{/other_user}","gists_url":"https://api.github.com/users/jwaterfield/gists{/gist_id}","starred_url":"https://api.github.com/users/jwaterfield/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jwaterfield/subscriptions","organizations_url":"https://api.github.com/users/jwaterfield/orgs","repos_url":"https://api.github.com/users/jwaterfield/repos","events_url":"https://api.github.com/users/jwaterfield/events{/privacy}","received_events_url":"https://api.github.com/users/jwaterfield/received_events","type":"User","site_admin":false},"milestone":null,"commits_url":"https://api.github.com/repos/snoplusuk/echidna/pulls/49/commits","review_comments_url":"https://api.github.com/repos/snoplusuk/echidna/pulls/49/comments","review_comment_url":"https://api.github.com/repos/snoplusuk/echidna/pulls/comments{/number}","comments_url":"https://api.github.com/repos/snoplusuk/echidna/issues/49/comments","statuses_url":"https://api.github.com/repos/snoplusuk/echidna/statuses/0b4862608889f3c491ef93b3c92cdbca141bcbcf","head":{"label":"ashleyrback:limit_setting_update","ref":"limit_setting_update","sha":"0b4862608889f3c491ef93b3c92cdbca141bcbcf","user":{"login":"ashleyrback","id":1931666,"avatar_url":"https://avatars.githubusercontent.com/u/1931666?v=3","gravatar_id":"","url":"https://api.github.com/users/ashleyrback","html_url":"https://github.com/ashleyrback","followers_url":"https://api.github.com/users/ashleyrback/followers","following_url":"https://api.github.com/users/ashleyrback/following{/other_user}","gists_url":"https://api.github.com/users/ashleyrback/gists{/gist_id}","starred_url":"https://api.github.com/users/ashleyrback/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ashleyrback/subscriptions","organizations_url":"https://api.github.com/users/ashleyrback/orgs","repos_url":"https://api.github.com/users/ashleyrback/repos","events_url":"https://api.github.com/users/ashleyrback/events{/privacy}","received_events_url":"https://api.github.com/users/ashleyrback/received_events","type":"User","site_admin":false},"repo":{"id":26441505,"name":"echidna","full_name":"ashleyrback/echidna","owner":{"login":"ashleyrback","id":1931666,"avatar_url":"https://avatars.githubusercontent.com/u/1931666?v=3","gravatar_id":"","url":"https://api.github.com/users/ashleyrback","html_url":"https://github.com/ashleyrback","followers_url":"https://api.github.com/users/ashleyrback/followers","following_url":"https://api.github.com/users/ashleyrback/following{/other_user}","gists_url":"https://api.github.com/users/ashleyrback/gists{/gist_id}","starred_url":"https://api.github.com/users/ashleyrback/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ashleyrback/subscriptions","organizations_url":"https://api.github.com/users/ashleyrback/orgs","repos_url":"https://api.github.com/users/ashleyrback/repos","events_url":"https://api.github.com/users/ashleyrback/events{/privacy}","received_events_url":"https://api.github.com/users/ashleyrback/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/ashleyrback/echidna","description":"","fork":true,"url":"https://api.github.com/repos/ashleyrback/echidna","forks_url":"https://api.github.com/repos/ashleyrback/echidna/forks","keys_url":"https://api.github.com/repos/ashleyrback/echidna/keys{/key_id}","collaborators_url":"https://api.github.com/repos/ashleyrback/echidna/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/ashleyrback/echidna/teams","hooks_url":"https://api.github.com/repos/ashleyrback/echidna/hooks","issue_events_url":"https://api.github.com/repos/ashleyrback/echidna/issues/events{/number}","events_url":"https://api.github.com/repos/ashleyrback/echidna/events","assignees_url":"https://api.github.com/repos/ashleyrback/echidna/assignees{/user}","branches_url":"https://api.github.com/repos/ashleyrback/echidna/branches{/branch}","tags_url":"https://api.github.com/repos/ashleyrback/echidna/tags","blobs_url":"https://api.github.com/repos/ashleyrback/echidna/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/ashleyrback/echidna/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/ashleyrback/echidna/git/refs{/sha}","trees_url":"https://api.github.com/repos/ashleyrback/echidna/git/trees{/sha}","statuses_url":"https://api.github.com/repos/ashleyrback/echidna/statuses/{sha}","languages_url":"https://api.github.com/repos/ashleyrba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