{"action":"created","comment":{"url":"https://api.github.com/repos/LSSTScienceCollaborations/StackClub/pulls/comments/209111153","pull_request_review_id":145063607,"id":209111153,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIwOTExMTE1Mw==","diff_hunk":"@@ -0,0 +1,271 @@\n+{\n+ \"cells\": [\n+  {\n+   \"cell_type\": \"markdown\",\n+   \"metadata\": {},\n+   \"source\": [\n+    \"# HSC Re-Run: Making Forced Photometry Light Curves from Scratch\\n\",\n+    \"\\n\",\n+    \"<br>Owner: **Justin Myles** ([@jtmyles](https://github.com/LSSTScienceCollaborations/StackClub/issues/new?body=@jtmyles))\\n\",\n+    \"<br>Last Verified to Run: **N/A -- in development**\\n\",\n+    \"\\n\",\n+    \"This project addresses issue [#63: HSC Re-run](https://github.com/LSSTScienceCollaborations/StackClub/issues/63)\\n\",\n+    \"\\n\",\n+    \"This notebook demonstrates the [LSST Science Piplines data processing tutorial](https://pipelines.lsst.io/) with emphasis on how a given [obs package](https://github.com/lsst/obs_base) works under the hood of the command line tasks. It makes use of the [obs_subaru](https://github.com/lsst/obs_subaru) package to measure a forced photometry light curve for a small patch in the HSC sky in the [ci_hsc](https://github.com/lsst/ci_hsc/) repository. \\n\",\n+    \"\\n\",\n+    \"### Learning Objectives:\\n\",\n+    \"After working through and studying this notebook you should be able to understand how to use the DRP pipeline from image visualization through to a forced photometry light curve. Specific learning objectives include: \\n\",\n+    \"   1. [configure command-line tasks](https://pipelines.lsst.io/v/w-2018-12/modules/lsst.pipe.base/command-line-task-config-howto.html) for your science case\\n\",\n+    \"   2. TODO\\n\",\n+    \"   \\n\",\n+    \"Other techniques that are demonstrated, but not empasized, in this notebook are\\n\",\n+    \"   1. Use the `butler` to fetch data\\n\",\n+    \"   2. Visualize data with the LSST Stack\\n\",\n+    \"   3. TODO\\n\",\n+    \"\\n\",\n+    \"### Logistics\\n\",\n+    \"This notebook is intended to be runnable on `lsst-lspdev.ncsa.illinois.edu` from a local git clone of https://github.com/LSSTScienceCollaborations/StackClub.\\n\",\n+    \"\\n\",\n+    \"\\n\",\n+    \"## Set Up\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"code\",\n+   \"execution_count\": null,\n+   \"metadata\": {},\n+   \"outputs\": [],\n+   \"source\": [\n+    \"import os\\n\",\n+    \"import sys\\n\",\n+    \"import eups.setupcmd\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"markdown\",\n+   \"metadata\": {},\n+   \"source\": [\n+    \"## Part I: Interacting with data. Introduction to the Butler\\n\",\n+    \"https://pipelines.lsst.io/getting-started/data-setup.html\\n\",\n+    \"\\n\",\n+    \"Part I runs the following command-line tasks\\n\",\n+    \"```\\n\",\n+    \"eups list lsst_distrib\\n\",\n+    \"setup -j -r /home/jmyles/repositories/ci_hsc\\n\",\n+    \"echo \\\"lsst.obs.hsc.HscMapper\\\" > /home/jmyles/DATA/_mapper\\n\",\n+    \"ingestImages.py /home/jmyles/DATA /home/jmyles/repositories/ci_hsc/raw/*.fits --mode=link\\n\",\n+    \"ln -s /home/jmyles/repositories/ci_hsc/CALIB/ /home/jmyles/DATA/CALIB\\n\",\n+    \"installTransmissionCurves.py /home/jmyles/DATA\\n\",\n+    \"mkdir -p /home/jmyles/DATA/ref_cats\\n\",\n+    \"ln -s /home/jmyles/repositories/ci_hsc/ps1_pv3_3pi_20170110 /home/jmyles/DATA/ref_cats/ps1_pv3_3pi_20170110\\n\",\n+    \"```\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"code\",\n+   \"execution_count\": null,\n+   \"metadata\": {},\n+   \"outputs\": [],\n+   \"source\": [\n+    \"!eups list lsst_distrib\\n\",\n+    \"datarepo = \\\"/home/jmyles/repositories/ci_hsc/\\\"\\n\",\n+    \"datadir = \\\"/home/jmyles/DATA/\\\"\\n\",\n+    \"os.system(\\\"mkdir -p {}\\\".format(datadir))\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"code\",\n+   \"execution_count\": null,\n+   \"metadata\": {},\n+   \"outputs\": [],\n+   \"source\": [\n+    \"#!setup -j -r /home/jmyles/repositories/ci_hsc\\n\",\n+    \"\\n\",\n+    \"setup = eups.setupcmd.EupsSetup([\\\"-j\\\",\\\"-r\\\", datarepo])\\n\",\n+    \"status = setup.run()\\n\",\n+    \"print('setup exited with status {}'.format(status))\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"markdown\",\n+   \"metadata\": {},\n+   \"source\": [\n+    \"A Butler needs a *mapper* file \\\"to find and organize data in a format specific to each camera.\\\" We write this file to the data repository so that any instantiated Butler object knows which mapper to use.\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"code\",\n+   \"execution_count\": null,\n+   \"metadata\": {},\n+   \"outputs\": [],\n+   \"source\": [\n+    \"with open(datadir + \\\"_mapper\\\", \\\"w\\\") as f:\\n\",","path":"ImageProcessing/Re-RunHSC.ipynb","position":102,"original_position":102,"commit_id":"fe3e08ac33ba82c1d267799c23280495595c2d56","original_commit_id":"fe3e08ac33ba82c1d267799c23280495595c2d56","user":{"login":"drphilmarshall","id":710903,"node_id":"MDQ6VXNlcjcxMDkwMw==","avatar_url":"https://avatars2.githubusercontent.com/u/710903?v=4","gravatar_id":"","url":"https://api.github.com/users/drphilmarshall","html_url":"https://github.com/drphilmarshall","followers_url":"https://api.github.com/users/drphilmarshall/followers","following_url":"https://api.github.com/users/drphilmarshall/following{/other_user}","gists_url":"https://api.github.com/users/drphilmarshall/gists{/gist_id}","starred_url":"https://api.github.com/users/drphilmarshall/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drphilmarshall/subscriptions","organizations_url":"https://api.github.com/users/drphilmarshall/orgs","repos_url":"https://api.github.com/users/drphilmarshall/repos","events_url":"https://api.github.com/users/drphilmarshall/events{/privacy}","received_events_url":"https://api.github.com/users/drphilmarshall/received_events","type":"User","site_admin":false},"body":"I'd set the mapper file name in a variable here, and then call `open` separately - that way we'll know what file to look for in teh folder. ","created_at":"2018-08-09T23:44:10Z","updated_at":"2018-08-09T23:52:27Z","html_url":"https://github.com/LSSTScienceCollaborations/StackClub/pull/86#discussion_r209111153","pull_request_url":"https://api.github.com/repos/LSSTScienceCollaborations/StackClub/pulls/86","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/LSSTScienceCollaborations/StackClub/pulls/comments/209111153"},"html":{"href":"https://github.com/LSSTScienceCollaborations/StackClub/pull/86#discussion_r209111153"},"pull_request":{"href":"https://api.github.com/repos/LSSTScienceCollaborations/StackClub/pulls/86"}}},"pull_request":{"url":"https://api.github.com/repos/LSSTScienceCollaborations/StackClub/pulls/86","id":207471086,"node_id":"MDExOlB1bGxSZXF1ZXN0MjA3NDcxMDg2","html_url":"https://github.com/LSSTScienceCollaborations/StackClub/pull/86","diff_url":"https://github.com/LSSTScienceCollaborations/StackClub/pull/86.diff","patch_url":"https://github.com/LSSTScienceCollaborations/StackClub/pull/86.patch","issue_url":"https://api.github.com/repos/LSSTScienceCollaborations/StackClub/issues/86","number":86,"state":"open","locked":false,"title":"Project/hsc re run","user":{"login":"jtmyles","id":11759110,"node_id":"MDQ6VXNlcjExNzU5MTEw","avatar_url":"https://avatars3.githubusercontent.com/u/11759110?v=4","gravatar_id":"","url":"https://api.github.com/users/jtmyles","html_url":"https://github.com/jtmyles","followers_url":"https://api.github.com/users/jtmyles/followers","following_url":"https://api.github.com/users/jtmyles/following{/other_user}","gists_url":"https://api.github.com/users/jtmyles/gists{/gist_id}","starred_url":"https://api.github.com/users/jtmyles/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jtmyles/subscriptions","organizations_url":"https://api.github.com/users/jtmyles/orgs","repos_url":"https://api.github.com/users/jtmyles/repos","events_url":"https://api.github.com/users/jtmyles/events{/privacy}","received_events_url":"https://api.github.com/users/jtmyles/received_events","type":"User","site_admin":false},"body":"This preliminary commit includes some code directly from the source of the command-line routines for part I (using the butler). @drphilmarshall could you review this preliminary commit? One question that I think we should address at this stage is whether the code from the command-line routines used here gives the right level of insight into how the stack instantiates a butler. For example, I'm unsure of whether users will want to see more of how the ingest script works. I'd appreciate all comments anyone has -- 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