{"action":"created","comment":{"url":"https://api.github.com/repos/gammapy/gammapy/pulls/comments/59209531","id":59209531,"diff_hunk":"@@ -2,56 +2,180 @@\n from __future__ import (absolute_import, division, print_function,\n                         unicode_literals)\n import logging\n+import numpy as np\n+from astropy.coordinates import Angle\n+from astropy.units import Quantity\n+from astropy.io import fits\n from ..utils.scripts import get_parser\n+from ..background import fill_acceptance_image\n+from ..image import SkyMap, SkyMapCollection, disk_correlate\n+from ..stats import significance\n \n __all__ = ['ImageAnalysis']\n \n log = logging.getLogger(__name__)\n \n \n-def image_pipe_main(args=None):\n-    parser = get_parser(ImageAnalysis)\n-    parser.add_argument('config_file', type=str,\n-                        help='Config file in YAML format')\n-    # TODO: add option to dump the default config file\n-    args = parser.parse_args(args)\n-    analysis = ImageAnalysis.from_yaml(args.config_file)\n-    analysis.run()\n-\n-\n class ImageAnalysis(object):\n     \"\"\"Gammapy 2D image based analysis.\n+\n+    Parameters\n+    ----------\n+    empty_image : `~gammapy.image.SkyMap`\n+            ref to an empty image\n+    energy_band : `~gammapy.utils.energy.Energy\n+        Energy band for which we want to compute the image\n+    offset_band :`astropy.coordinates.Angle`\n+        Offset Band where you compute the image\n+    data_store : `~gammapy.data.DataStore`\n+        `DataStore` where are situated the events\n+    counts_image : ~gammapy.image.SkyMap`\n+            count image\n+    bkg_image : ~gammapy.image.SkyMap`\n+            bkg image\n     \"\"\"\n \n-    def __init__(self, config):\n-        self.config = config\n-\n-    @classmethod\n-    def from_yaml(cls, filename):\n-        \"\"\"Read config from YAML file.\"\"\"\n-        import yaml\n-        log.info('Reading {}'.format(filename))\n-        with open(filename) as fh:\n-            config = yaml.safe_load(fh)\n-        return cls(config)\n-\n-    def run(self):\n-        \"\"\"Run analysis chain.\"\"\"\n-        log.info('Running analysis ...')\n-        print(self.config['general']['outdir'])\n-        print(self.config)\n-\n-    def make_counts(self):\n+    def __init__(self, empty_image=None,\n+                 energy_band=None, offset_band=None,\n+                 data_store=None, counts_image=None, bkg_image=None):\n+        self.maps = SkyMapCollection()\n+        if counts_image:\n+            self.maps[\"total_counts\"] = counts_image\n+        else:\n+            self.data_store = data_store\n+            self.energy_band = energy_band\n+            self.offset_band = offset_band\n+\n+            self.empty_image = empty_image\n+            self.header = self.empty_image.to_image_hdu().header\n+        if bkg_image:\n+            self.maps[\"total_bkg\"] = bkg_image\n+\n+    def make_counts(self, obs_id):\n+        \"\"\"Fill the counts image for the events of one observation.\n+\n+        Parameters\n+        ----------\n+        obs_id : int\n+            Number of the observation\n+\n+        \"\"\"\n+        self.maps[\"counts\"] = SkyMap.empty_like(self.empty_image)\n+        obs = self.data_store.obs(obs_id=obs_id)\n+        events = obs.events.select_energy(self.energy_band)\n+        events = events.select_offset(self.offset_band)\n+        self.maps[\"counts\"].fill(events=events)\n+        self.maps[\"counts\"].data = self.maps[\"counts\"].data.value\n         log.info('Making counts image ...')\n \n-    def make_exposure(self):\n-        log.info('Making exposure image ...')\n+    def make_total_counts(self):\n+        \"\"\"Stack the total count from the observation in the 'DataStore'\n+\n+        \"\"\"\n+        self.maps[\"total_counts\"] = SkyMap.empty_like(self.empty_image)\n+        for obs_id in self.data_store.obs_table['OBS_ID']:\n+            self.make_counts(obs_id)\n+            self.maps[\"total_counts\"].data += self.maps[\"counts\"].data\n+\n+    def make_background(self, obs_id):\n+        \"\"\"Make the background map for one observation from a bkg model\n+\n+        Parameters\n+        ----------\n+        obs_id : int\n+            Number of the observation\n+\n+        \"\"\"\n+        self.maps[\"bkg\"] = SkyMap.empty_like(self.empty_image)\n+        obs = self.data_store.obs(obs_id=obs_id)\n+        table = obs.bkg.acceptance_curve_in_energy_band(energy_band=self.energy_band)\n+        center = obs.pointing_radec.galactic\n+        bkg_hdu = fill_acceptance_image(self.header, center, table[\"offset\"], table[\"Acceptance\"], self.offset_band[1])\n+        livetime = obs.observation_live_time_duration\n+        self.maps[\"bkg\"].data = Quantity(bkg_hdu.data, table[\"Acceptance\"].unit) * self.maps[\n+            \"bkg\"].solid_angle() * livetime\n+        self.maps[\"bkg\"].data = self.maps[\"bkg\"].data.decompose()\n+        self.maps[\"bkg\"].data = self.maps[\"bkg\"].data.value\n \n-    def make_background(self):\n         log.info('Making background image ...')\n \n+    def make_background_normalized_offcounts(self, obs_id, exclusion_mask):\n+        \"\"\"Normalized the background compare to te events in the counts maps outside the exclusion maps\n+\n+        Parameters\n+        ----------\n+        exclusion_mask : `~gammapy.image.ExclusionMask`\n+            Exclusion regions\n+\n+\n+        \"\"\"\n+        self.make_counts(obs_id)\n+        self.make_background(obs_id)\n+        counts_sum = np.sum(self.maps[\"counts\"].data * exclusion_mask.data)\n+        bkg_sum = np.sum(self.maps[\"bkg\"].data * exclusion_mask.data)\n+        scale = counts_sum / bkg_sum\n+        self.maps[\"bkg\"].data = scale * self.maps[\"bkg\"].data\n+        self.maps['exclusion'] = exclusion_mask\n+\n+    def make_total_bkg(self, exclusion_mask):","path":"gammapy/scripts/image_pipe.py","position":152,"original_position":151,"commit_id":"5973d6a20d0b98cbacda5e1a28b34fa00d52c900","original_commit_id":"9bfc3aab26a3036a4fb7ed91d0f61b6180e828ff","user":{"login":"adonath","id":3715928,"avatar_url":"https://avatars.githubusercontent.com/u/3715928?v=3","gravatar_id":"","url":"https://api.github.com/users/adonath","html_url":"https://github.com/adonath","followers_url":"https://api.github.com/users/adonath/followers","following_url":"https://api.github.com/users/adonath/following{/other_user}","gists_url":"https://api.github.com/users/adonath/gists{/gist_id}","starred_url":"https://api.github.com/users/adonath/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adonath/subscriptions","organizations_url":"https://api.github.com/users/adonath/orgs","repos_url":"https://api.github.com/users/adonath/repos","events_url":"https://api.github.com/users/adonath/events{/privacy}","received_events_url":"https://api.github.com/users/adonath/received_events","type":"User","site_admin":false},"body":"Does  'make_background_normalized_offcounts' actually have to be visible to the user?\r\nBecause right now `make_total_bkg` only does the a loop over observation IDs. But if a list of obs IDs is passed, it can still contain only one value.\r\n","created_at":"2016-04-11T14:08:26Z","updated_at":"2016-04-11T14:08:26Z","html_url":"https://github.com/gammapy/gammapy/pull/503#discussion_r59209531","pull_request_url":"https://api.github.com/repos/gammapy/gammapy/pulls/503","_links":{"self":{"href":"https://api.github.com/repos/gammapy/gammapy/pulls/comments/59209531"},"html":{"href":"https://github.com/gammapy/gammapy/pull/503#discussion_r59209531"},"pull_request":{"href":"https://api.github.com/repos/gammapy/gammapy/pulls/503"}}},"pull_request":{"url":"https://api.github.com/repos/gammapy/gammapy/pulls/503","id":65486008,"html_url":"https://github.com/gammapy/gammapy/pull/503","diff_url":"https://github.com/gammapy/gammapy/pull/503.diff","patch_url":"https://github.com/gammapy/gammapy/pull/503.patch","issue_url":"https://api.github.com/repos/gammapy/gammapy/issues/503","number":503,"state":"open","locked":false,"title":"Some changes to the OFFBkgMaker class","user":{"login":"JouvinLea","id":14295716,"avatar_url":"https://avatars.githubusercontent.com/u/14295716?v=3","gravatar_id":"","url":"https://api.github.com/users/JouvinLea","html_url":"https://github.com/JouvinLea","followers_url":"https://api.github.com/users/JouvinLea/followers","following_url":"https://api.github.com/users/JouvinLea/following{/other_user}","gists_url":"https://api.github.com/users/JouvinLea/gists{/gist_id}","starred_url":"https://api.github.com/users/JouvinLea/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JouvinLea/subscriptions","organizations_url":"https://api.github.com/users/JouvinLea/orgs","repos_url":"https://api.github.com/users/JouvinLea/repos","events_url":"https://api.github.com/users/JouvinLea/events{/privacy}","received_events_url":"https://api.github.com/users/JouvinLea/received_events","type":"User","site_admin":false},"body":"This pull request contains:\r\n* improvements to the off data background maker class\r\n* a new image analysis class to compute stacked counts and background images for multiple observations","created_at":"2016-04-06T15:26:10Z","updated_at":"2016-04-11T14:08:26Z","closed_at":null,"merged_at":null,"merge_commit_sha":"f63ab991ce72c531b7b58e9d266097ea0d92aa09","assignee":{"login":"adonath","id":3715928,"avatar_url":"https://avatars.githubusercontent.com/u/3715928?v=3","gravatar_id":"","url":"https://api.github.com/users/adonath","html_url":"https://github.com/adonath","followers_url":"https://api.github.com/users/adonath/followers","following_url":"https://api.github.com/users/adonath/following{/other_user}","gists_url":"https://api.github.com/users/adonath/gists{/gist_id}","starred_url":"https://api.github.com/users/adonath/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adonath/subscriptions","organizations_url":"https://api.github.com/users/adonath/orgs","repos_url":"https://api.github.com/users/adonath/repos","events_url":"https://api.github.com/users/adonath/events{/privacy}","received_events_url":"https://api.github.com/users/adonath/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/gammapy/gammapy/milestones/5","html_url":"https://github.com/gammapy/gammapy/milestones/0.4","labels_url":"https://api.github.com/repos/gammapy/gammapy/milestones/5/labels","id":1058090,"number":5,"title":"0.4","description":"","creator":{"login":"cdeil","id":852409,"avatar_url":"https://avatars.githubusercontent.com/u/852409?v=3","gravatar_id":"","url":"https://api.github.com/users/cdeil","html_url":"https://github.com/cdeil","followers_url":"https://api.github.com/users/cdeil/followers","following_url":"https://api.github.com/users/cdeil/following{/other_user}","gists_url":"https://api.github.com/users/cdeil/gists{/gist_id}","starred_url":"https://api.github.com/users/cdeil/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cdeil/subscriptions","organizations_url":"https://api.github.com/users/cdeil/orgs","repos_url":"https://api.github.com/users/cdeil/repos","events_url":"https://api.github.com/users/cdeil/events{/privacy}","received_events_url":"https://api.github.com/users/cdeil/received_events","type":"User","site_admin":false},"open_issues":10,"closed_issues":123,"state":"open","created_at":"2015-04-08T11:51:53Z","updated_at":"2016-04-11T13:15:57Z","due_on":"2016-02-28T23:00:00Z","closed_at":null},"commits_url":"https://api.github.com/repos/gammapy/gammapy/pulls/503/commits","review_comments_url":"https://api.github.com/repos/gammapy/gammapy/pulls/503/comments","review_comment_url":"https://api.github.com/repos/gammapy/gammapy/pulls/comments{/number}","comments_url":"https://api.github.com/repos/gammapy/gammapy/issues/503/comments","statuses_url":"https://api.github.com/repos/gammapy/gammapy/statuses/5973d6a20d0b98cbacda5e1a28b34fa00d52c900","head":{"label":"JouvinLea:MakeImages","ref":"MakeImages","sha":"5973d6a20d0b98cbacda5e1a28b34fa00d52c900","user":{"login":"JouvinLea","id":14295716,"avatar_url":"https://avatars.githubusercontent.com/u/14295716?v=3","gravatar_id":"","url":"https://api.github.com/users/JouvinLea","html_url":"https://github.com/JouvinLea","followers_url":"https://api.github.com/users/JouvinLea/followers","following_url":"https://api.github.com/users/JouvinLea/following{/other_user}","gists_url":"https://api.github.com/users/JouvinLea/gists{/gist_id}","starred_url":"https://api.github.com/users/JouvinLea/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JouvinLea/subscriptions","organizations_url":"https://api.github.com/users/JouvinLea/orgs","repos_url":"https://api.github.com/users/JouvinLea/repos","events_url":"https://api.github.com/users/JouvinLea/events{/privacy}","received_events_url":"https://api.github.com/users/JouvinLea/received_events","type":"User","site_admin":false},"repo":{"id":46556710,"name":"gammapy","full_name":"JouvinLea/gammapy","owner":{"login":"JouvinLea","id":14295716,"avatar_url":"https://avatars.githubusercontent.com/u/14295716?v=3","gravatar_id":"","url":"https://api.github.com/users/JouvinLea","html_url":"https://github.com/JouvinLea","followers_url":"https://api.github.com/users/JouvinLea/followers","following_url":"https://api.github.com/users/JouvinLea/following{/other_user}","gists_url":"https://api.github.com/users/JouvinLea/gists{/gist_id}","starred_url":"https://api.github.com/users/JouvinLea/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JouvinLea/subscriptions","organizations_url":"https://api.github.com/users/JouvinLea/orgs","repos_url":"https://api.github.com/users/JouvinLea/repos","events_url":"https://api.github.com/users/JouvinLea/events{/privacy}","received_events_url":"https://api.github.com/users/JouvinLea/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/JouvinLea/gammapy","description":"A 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