{"action":"created","comment":{"url":"https://api.github.com/repos/ligo-cbc/pycbc/pulls/comments/92182201","pull_request_review_id":12691956,"id":92182201,"diff_hunk":"@@ -19,112 +22,216 @@ class fw(object):\n         self.attrs = self.f.attrs\n \n     def __setitem__(self, name, data):\n-        self.f.create_dataset(name, data=data, compression='gzip',\n-                              compression_opts=9, shuffle=True)\n+        # Make a new item if isn't in the hdf file\n+        if not name in self.f:\n+            self.f.create_dataset(name, data=data, compression=\"gzip\",\n+                                  compression_opts=9, shuffle=True,\n+                                  maxshape=data.shape)\n+        # Else re-size that section and reassign values\n+        else:\n+            self.f[name].resize(data.shape)\n+            self.f[name][:] = data\n+\n+    def __getitem__(self, *args):\n+        return self.f.__getitem__(*args)\n+\n+    def close(self):\n+        self.f.close()\n \n parser = argparse.ArgumentParser()\n # General required options\n parser.add_argument('--version', action='version', \n-         version=pycbc.version.git_verbose_msg)\n+                    version=pycbc.version.git_verbose_msg)\n parser.add_argument('--coinc-files', nargs='+', \n-         help='List of coincidence files used to calculate the FAP, FAR, etc.')\n+                    help='List of coincidence files used to calculate the '\n+                         'FAP, FAR, etc.')\n parser.add_argument('--verbose', action='count')\n parser.add_argument('--cluster-window', type=float, default=10,\n-         help='Length of time window in seconds to cluster coinc events, [default=10s]')\n+                    help='Length of time window in seconds to cluster coinc '\n+                         'events, [default=10s]')\n parser.add_argument('--veto-window', type=float, default=.1,\n-         help='Time around each zerolag trigger to window out, [default=.1s]')\n+                    help='Time around each zerolag trigger to window out, '\n+                         '[default=.1s]')\n+parser.add_argument('--veto-window-hierarch', type=float, default=1.0,\n+                    help='Time around each trigger to window out for a very '\n+                         'louder trigger in the hierarchical removal '\n+                         'procedure. [default=1.0s]')\n+parser.add_argument('--cont-hier-removal', action='store_true',\n+                    default='store_false', \n+                    help='Use this option to do continuous hierarchical '\n+                         'removal without any cutoff number of hierarchical '\n+                         'removals to stop at. [default=false]')\n+parser.add_argument('--max-hier-removal', type=int, default=0,\n+                    help='Maximum amount of hierarchical removals to carry '\n+                         'out when hierarchical removal is desired. Choose '\n+                         '0 for no hierarchical removal. Choose 1 to do at '\n+                         'most 1 hierarchical removal, and so on. The code '\n+                         'will write the triggers out for whichever comes '\n+                         'first: that there are no more hierarchical removals '\n+                         'to do, or the max allowed amount of hierarchical '\n+                         'removals has been reached. [default=0]')\n+parser.add_argument('--store-last-h-rm-background', action='store_true',","path":"bin/hdfcoinc/pycbc_coinc_statmap","position":79,"original_position":79,"commit_id":"adaf1d40e3bc8559d1c023c774b982675cfd49dc","original_commit_id":"adaf1d40e3bc8559d1c023c774b982675cfd49dc","user":{"login":"stevereyes01","id":12528399,"avatar_url":"https://avatars.githubusercontent.com/u/12528399?v=3","gravatar_id":"","url":"https://api.github.com/users/stevereyes01","html_url":"https://github.com/stevereyes01","followers_url":"https://api.github.com/users/stevereyes01/followers","following_url":"https://api.github.com/users/stevereyes01/following{/other_user}","gists_url":"https://api.github.com/users/stevereyes01/gists{/gist_id}","starred_url":"https://api.github.com/users/stevereyes01/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stevereyes01/subscriptions","organizations_url":"https://api.github.com/users/stevereyes01/orgs","repos_url":"https://api.github.com/users/stevereyes01/repos","events_url":"https://api.github.com/users/stevereyes01/events{/privacy}","received_events_url":"https://api.github.com/users/stevereyes01/received_events","type":"User","site_admin":false},"body":"If you see @ahnitz 's 3rd request from above he states:\r\n3. What is stored in the 'background' and 'background_exc' columns should not be changed.\r\n\r\nWhat I decided to do in the code is store every stage of the hierarchical removed inclusive background but write out to f['background/'] either the background from 0 hierarchical removals, or the background after N hierarchical removals. This is to maintain compatibility with codes downstream.","created_at":"2016-12-13T14:45:52Z","updated_at":"2016-12-13T14:45:52Z","html_url":"https://github.com/ligo-cbc/pycbc/pull/1328#discussion_r92182201","pull_request_url":"https://api.github.com/repos/ligo-cbc/pycbc/pulls/1328","_links":{"self":{"href":"https://api.github.com/repos/ligo-cbc/pycbc/pulls/comments/92182201"},"html":{"href":"https://github.com/ligo-cbc/pycbc/pull/1328#discussion_r92182201"},"pull_request":{"href":"https://api.github.com/repos/ligo-cbc/pycbc/pulls/1328"}}},"pull_request":{"url":"https://api.github.com/repos/ligo-cbc/pycbc/pulls/1328","id":96959002,"html_url":"https://github.com/ligo-cbc/pycbc/pull/1328","diff_url":"https://github.com/ligo-cbc/pycbc/pull/1328.diff","patch_url":"https://github.com/ligo-cbc/pycbc/pull/1328.patch","issue_url":"https://api.github.com/repos/ligo-cbc/pycbc/issues/1328","number":1328,"state":"open","locked":false,"title":"Stat map code with hierarchical removal","user":{"login":"stevereyes01","id":12528399,"avatar_url":"https://avatars.githubusercontent.com/u/12528399?v=3","gravatar_id":"","url":"https://api.github.com/users/stevereyes01","html_url":"https://github.com/stevereyes01","followers_url":"https://api.github.com/users/stevereyes01/followers","following_url":"https://api.github.com/users/stevereyes01/following{/other_user}","gists_url":"https://api.github.com/users/stevereyes01/gists{/gist_id}","starred_url":"https://api.github.com/users/stevereyes01/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stevereyes01/subscriptions","organizations_url":"https://api.github.com/users/stevereyes01/orgs","repos_url":"https://api.github.com/users/stevereyes01/repos","events_url":"https://api.github.com/users/stevereyes01/events{/privacy}","received_events_url":"https://api.github.com/users/stevereyes01/received_events","type":"User","site_admin":false},"body":"This is basically all of the work on hierarchical removal that I've got. I'm fairly convinced that it's working correctly, but I'd like to have a fresh pair of eyes look over it very closely. It's also not a very Pythonic code, but I think it works.\r\n\r\nSee https://sugwg-jobs.phy.syr.edu/~steven.reyes/ER10/hierarchical_removal_plots/\r\n\r\n\"No hierarchical removal\" plot:\r\n![image](https://cloud.githubusercontent.com/assets/12528399/20976645/23bdf8ba-bc71-11e6-86f4-6865f6a0c865.png)\r\n\r\n\"1 hierarchical removal\" plot:\r\n![image](https://cloud.githubusercontent.com/assets/12528399/20976419/7c2863ba-bc70-11e6-9fe5-f566682748a7.png)\r\n\r\n\"2 hierarchical removals\" plot:\r\n![image](https://cloud.githubusercontent.com/assets/12528399/20976426/8295a6cc-bc70-11e6-9b1a-3fbd1bfd2af8.png)\r\n\r\nI'd like to make the pycbc_page_foreground tables too for all of these. I'd also like to write up a short document or something about how I wrote this code, and what I think I'm doing in the code.\r\n\r\nThe way you run this code is basically:\r\n```\r\npython pycbc_coinc_statmap_copy \\\r\n--coinc-files H1L1-DISTRIBUTE_BACKGROUND_BINS_MBIN-2-1126051217-11203200.hdf \\\r\n--verbose \\\r\n--cluster-window 10 \\\r\n--veto-window 0.1 \\\r\n--veto-window-hierarch 1.0 \\\r\n--max-hier-removal 0 \\\r\n--output-file clustered_copy_no_removal.hdf\r\n```\r\n\r\nTo run with no hierarchical removal. But if you want to try and do more hierarchical removals you can change the option `--max-hier-removal` to any other integer. The code will write out the results of the **last** hierarchical removal that it could do. So if you set `--max-hier-removal 5`, and you are only justified in removing 2 foreground triggers, the code will do 2 hierarchical removals and write the hdf file after removing 2 foreground triggers, it won't write any of the intermediate steps. If you want the intermediate steps you could just run this code using `--max-hier-removal 0`, then `--max-hier-removal 1`, then `--max-hier-removal 2`, etc.\r\n\r\n","created_at":"2016-12-07T16:34:10Z","updated_at":"2016-12-13T14:45:52Z","closed_at":null,"merged_at":null,"merge_commit_sha":"f1a9691d187160c01212ee67664471c08c5a4883","assignee":{"login":"ahnitz","id":2206534,"avatar_url":"https://avatars.githubusercontent.com/u/2206534?v=3","gravatar_id":"","url":"https://api.github.com/users/ahnitz","html_url":"https://github.com/ahnitz","followers_url":"https://api.github.com/users/ahnitz/followers","following_url":"https://api.github.com/users/ahnitz/following{/other_user}","gists_url":"https://api.github.com/users/ahnitz/gists{/gist_id}","starred_url":"https://api.github.com/users/ahnitz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ahnitz/subscriptions","organizations_url":"https://api.github.com/users/ahnitz/orgs","repos_url":"https://api.github.com/users/ahnitz/repos","events_url":"https://api.github.com/users/ahnitz/events{/privacy}","received_events_url":"https://api.github.com/users/ahnitz/received_events","type":"User","site_admin":false},"assignees":[{"login":"ahnitz","id":2206534,"avatar_url":"https://avatars.githubusercontent.com/u/2206534?v=3","gravatar_id":"","url":"https://api.github.com/users/ahnitz","html_url":"https://github.com/ahnitz","followers_url":"https://api.github.com/users/ahnitz/followers","following_url":"https://api.github.com/users/ahnitz/following{/other_user}","gists_url":"https://api.github.com/users/ahnitz/gists{/gist_id}","starred_url":"https://api.github.com/users/ahnitz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ahnitz/subscriptions","organizations_url":"https://api.github.com/users/ahnitz/orgs","repos_url":"https://api.github.com/users/ahnitz/repos","events_url":"https://api.github.com/users/ahnitz/events{/privacy}","received_events_url":"https://api.github.com/users/ahnitz/received_events","type":"User","site_admin":false},{"login":"duncan-brown","id":11262902,"avatar_url":"https://avatars.githubusercontent.com/u/11262902?v=3","gravatar_id":"","url":"https://api.github.com/users/duncan-brown","html_url":"https://github.com/duncan-brown","followers_url":"https://api.github.com/users/duncan-brown/followers","following_url":"https://api.github.com/users/duncan-brown/following{/other_user}","gists_url":"https://api.github.com/users/duncan-brown/gists{/gist_id}","starred_url":"https://api.github.com/users/duncan-brown/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/duncan-brown/subscriptions","organizations_url":"https://api.github.com/users/duncan-brown/orgs","repos_url":"https://api.github.com/users/duncan-brown/repos","events_url":"https://api.github.com/users/duncan-brown/events{/privacy}","received_events_url":"https://api.github.com/users/duncan-brown/received_events","type":"User","site_admin":false}],"milestone":null,"commits_url":"https://api.github.com/repos/ligo-cbc/pycbc/pulls/1328/commits","review_comments_url":"https://api.github.com/repos/ligo-cbc/pycbc/pulls/1328/comments","review_comment_url":"https://api.github.com/repos/ligo-cbc/pycbc/pulls/comments{/number}","comments_url":"https://api.github.com/repos/ligo-cbc/pycbc/issues/1328/comments","statuses_url":"https://api.github.com/repos/ligo-cbc/pycbc/statuses/adaf1d40e3bc8559d1c023c774b982675cfd49dc","head":{"label":"stevereyes01:statMapPlayground","ref":"statMapPlayground","sha":"adaf1d40e3bc8559d1c023c774b982675cfd49dc","user":{"login":"stevereyes01","id":12528399,"avatar_url":"https://avatars.githubusercontent.com/u/12528399?v=3","gravatar_id":"","url":"https://api.github.com/users/stevereyes01","html_url":"https://github.com/stevereyes01","followers_url":"https://api.github.com/users/stevereyes01/followers","following_url":"https://api.github.com/users/stevereyes01/following{/other_user}","gists_url":"https://api.github.com/users/stevereyes01/gists{/gist_id}","starred_url":"https://api.github.com/users/stevereyes01/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stevereyes01/subscriptions","organizations_url":"https://api.github.com/users/stevereyes01/orgs","repos_url":"https://api.github.com/users/stevereyes01/repos","events_url":"https://api.github.com/users/stevereyes01/events{/privacy}","received_events_url":"https://api.github.com/users/stevereyes01/received_events","type":"User","site_admin":false},"repo":{"id":36811056,"name":"pycbc","full_name":"stevereyes01/pycbc","owner":{"login":"stevereyes01","id":12528399,"avatar_url":"https://avatars.githubusercontent.com/u/12528399?v=3","gravatar_id":"","url":"https://api.github.com/users/stevereyes01","html_url":"https://github.com/stevereyes01","followers_url":"https://api.github.com/users/stevereyes01/followers","following_url":"https://api.github.com/users/stevereyes01/following{/other_user}","gists_url":"https://api.github.com/users/stevereyes01/gists{/gist_id}","starred_url":"https://api.github.com/users/stevereyes01/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/user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