{"action":"created","comment":{"url":"https://api.github.com/repos/spacetelescope/jwst/pulls/comments/219839876","pull_request_review_id":158108465,"id":219839876,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIxOTgzOTg3Ng==","diff_hunk":"@@ -390,159 +423,210 @@ def create_grism_bbox(input_model, reference_files,\n \n     Notes\n     -----\n-    The wavelengthrange reference file is used to govern the extent of the\n-    bounding box for each object. The name of the catalog has been stored\n-    in the input models meta information under the source_catalog key.\n+    The wavelengthrange reference file is used to govern\n+    the extent of the bounding box for each object. The name of the\n+    catalog has been stored in the input models meta information under\n+    the source_catalog key.\n \n-    It's left to the calling routine to cut the bounding boxes at the extent\n-    of the detector (for example, extract 2d would only extract the on-detector\n-    portion of the bounding box)\n+    It's left to the calling routine to cut the bounding boxes at the\n+    extent of the detector (for example, extract 2d would only extract\n+    the on-detector portion of the bounding box)\n \n-    Bounding box dispersion direction is dependent on the filter and module for\n-    NIRCAM and changes for GRISMR, but is consistent for GRISMC, see\n-    https://jwst-docs.stsci.edu/display/JTI/NIRCam+Wide+Field+Slitless+Spectroscopy\n+    Bounding box dispersion direction is dependent on the filter and\n+    module for NIRCAM and changes for GRISMR, but is consistent for\n+    GRISMC, see https://jwst-\n+    docs.stsci.edu/display/JTI/NIRCam+Wide+Field+Slitless+Spectroscopy\n \n-    NIRISS only has one detector, but GRISMC disperses along rows and GRISMR disperses\n-    along columns.\n+    NIRISS only has one detector, but GRISMC disperses along rows and\n+    GRISMR disperses along columns.\n+\n+    photutils is used to create the source catalog in the pipeline,\n+    it's currently using the fits wcs for it's sky translation, it\n+    grabs the fits wcs from the data model using get_fits_wcs(). Until\n+    GWCS is fully implemented, this translation may be off in the\n+    pipeline.\n \n     \"\"\"\n-    # figure out the dispersion direction, shouldn't this be in the polynomials already?\n-    disperse_row_right = True  # disperse to increasing x\n-    disperse_column = False  # column always disperses to increasing y\n+    if use_fits_wcs:\n+        log.info(\"Using fits_wcs object for sky->detector translations\")\n+\n+    if not isinstance(mmag_extract, (int, float)):\n+        raise TypeError(\"Expected mmag_extract to be an int or float\")\n+    log.info(\"Extracting objects < abmag = {0}\".format(mmag_extract))\n+\n+    if extract_orders is not None:\n+        if isinstance(extract_orders, list):\n+            if not all(isinstance(item, int) for item in extract_orders):\n+                raise TypeError(\"Expected extract_orders to be a list of ints\")\n+        else:\n+            raise TypeError(\"Expected extract_orders to be a list of ints\")","path":"jwst/assign_wcs/util.py","position":164,"original_position":164,"commit_id":"7f9c73df38d663b3644d8c6b442c1145f272b610","original_commit_id":"7f9c73df38d663b3644d8c6b442c1145f272b610","user":{"login":"sosey","id":503615,"node_id":"MDQ6VXNlcjUwMzYxNQ==","avatar_url":"https://avatars3.githubusercontent.com/u/503615?v=4","gravatar_id":"","url":"https://api.github.com/users/sosey","html_url":"https://github.com/sosey","followers_url":"https://api.github.com/users/sosey/followers","following_url":"https://api.github.com/users/sosey/following{/other_user}","gists_url":"https://api.github.com/users/sosey/gists{/gist_id}","starred_url":"https://api.github.com/users/sosey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sosey/subscriptions","organizations_url":"https://api.github.com/users/sosey/orgs","repos_url":"https://api.github.com/users/sosey/repos","events_url":"https://api.github.com/users/sosey/events{/privacy}","received_events_url":"https://api.github.com/users/sosey/received_events","type":"User","site_admin":false},"body":"ah, yah, that was also from the bad merge, thanks for catching :) ","created_at":"2018-09-24T13:43:52Z","updated_at":"2018-09-24T13:43:52Z","html_url":"https://github.com/spacetelescope/jwst/pull/1801#discussion_r219839876","pull_request_url":"https://api.github.com/repos/spacetelescope/jwst/pulls/1801","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/spacetelescope/jwst/pulls/comments/219839876"},"html":{"href":"https://github.com/spacetelescope/jwst/pull/1801#discussion_r219839876"},"pull_request":{"href":"https://api.github.com/repos/spacetelescope/jwst/pulls/1801"}},"in_reply_to_id":219834916},"pull_request":{"url":"https://api.github.com/repos/spacetelescope/jwst/pulls/1801","id":174393108,"node_id":"MDExOlB1bGxSZXF1ZXN0MTc0MzkzMTA4","html_url":"https://github.com/spacetelescope/jwst/pull/1801","diff_url":"https://github.com/spacetelescope/jwst/pull/1801.diff","patch_url":"https://github.com/spacetelescope/jwst/pull/1801.patch","issue_url":"https://api.github.com/repos/spacetelescope/jwst/issues/1801","number":1801,"state":"open","locked":false,"title":"WIP: extract specific grism orders only","user":{"login":"sosey","id":503615,"node_id":"MDQ6VXNlcjUwMzYxNQ==","avatar_url":"https://avatars3.githubusercontent.com/u/503615?v=4","gravatar_id":"","url":"https://api.github.com/users/sosey","html_url":"https://github.com/sosey","followers_url":"https://api.github.com/users/sosey/followers","following_url":"https://api.github.com/users/sosey/following{/other_user}","gists_url":"https://api.github.com/users/sosey/gists{/gist_id}","starred_url":"https://api.github.com/users/sosey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sosey/subscriptions","organizations_url":"https://api.github.com/users/sosey/orgs","repos_url":"https://api.github.com/users/sosey/repos","events_url":"https://api.github.com/users/sosey/events{/privacy}","received_events_url":"https://api.github.com/users/sosey/received_events","type":"User","site_admin":false},"body":"This closes #1756 \r\n\r\nAfter looking through the code in more detail and thinking some more .....`specwcs` is only used in `assign_wcs`, during which the grism methods read the reference file, create models, and return the model pipeline back to the calling method that creates the WCS and attaches it to the output model. In order to pass the information about what orders should be extracted by default, I'd have to add them to the grism transform models as a data member to carry around.  But it really doesn't make sense, in my head at least, to have that information in those models since they cover everything that's available. It makes the transform models more confusing to grok.  \r\n\r\nI'd like to go the other way, add the `extract_orders` to the `wavelengthrange` reference file. There is a single `wavelengthrange` file  for each instrument, it has a list of orders, a list of filters, and the list of wavelength min and max values that are used to create the extraction boxes for each order. I think it's reasonable to add the default orders to extract here, and the reference file is already passed to `extract_2d`.  I will also add a new parameter to the extraction method so that users can override the default order extractions.\r\n\r\nI think this will make the reference files the most clear,  and their use and application in the pipeline methods the most clear. \r\n\r\nI've also added an  `extract_orders` parameter to `assign_wcs.util.create_grism_bbox`. This is the routine that does the heavy lifting. It currently lives in `assign_wcs.util`, however, there's no reason it has to. It uses the wcs, and creates bounding boxes, but performs no extractions. It might make more sense to move this to the general lib directory under jwst. If so, I'll do that with a separate PR. \r\n\r\nThings that still need to be done before PR merged:\r\n\r\n- [x]  finish testing that the code works as expected\r\n- [ ]  add documentation\r\n- [x]  let RedCat know about the reference file changes\r\n- [x]  deliver the updated wavelengthrange reference files for both nircam and niriss","created_at":"2018-03-12T14:54:56Z","updated_at":"2018-09-24T13:43:52Z","closed_at":null,"merged_at":null,"merge_commit_sha":"1b80de1d9a74e5e62261d2c2953ec42220671d90","assignee":{"login":"sosey","id":503615,"node_id":"MDQ6VXNlcjUwMzYxNQ==","avatar_url":"https://avatars3.githubusercontent.com/u/503615?v=4","gravatar_id":"","url":"https://api.github.com/users/sosey","html_url":"https://github.com/sosey","followers_url":"https://api.github.com/users/sosey/followers","following_url":"https://api.github.com/users/sosey/following{/other_user}","gists_url":"https://api.github.com/users/sosey/gists{/gist_id}","starred_url":"https://api.github.com/users/sosey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sosey/subscriptions","organizations_url":"https://api.github.com/users/sosey/orgs","repos_url":"https://api.github.com/users/sosey/repos","events_url":"https://api.github.com/users/sosey/events{/privacy}","received_events_url":"https://api.github.com/users/sosey/received_events","type":"User","site_admin":false},"assignees":[{"login":"sosey","id":503615,"node_id":"MDQ6VXNlcjUwMzYxNQ==","avatar_url":"https://avatars3.githubusercontent.com/u/503615?v=4","gravatar_id":"","url":"https://api.github.com/users/sosey","html_url":"https://github.com/sosey","followers_url":"https://api.github.com/users/sosey/followers","following_url":"https://api.github.com/users/sosey/following{/other_user}","gists_url":"https://api.github.com/users/sosey/gists{/gist_id}","starred_url":"https://api.github.com/users/sosey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sosey/subscriptions","organizations_url":"https://api.github.com/users/sosey/orgs","repos_url":"https://api.github.com/users/sosey/repos","events_url":"https://api.github.com/users/sosey/events{/privacy}","received_events_url":"https://api.github.com/users/sosey/received_events","type":"User","site_admin":false}],"requested_reviewers":[],"requested_teams":[],"labels":[{"id":397006407,"node_id":"MDU6TGFiZWwzOTcwMDY0MDc=","url":"https://api.github.com/repos/spacetelescope/jwst/labels/NIRCAM","name":"NIRCAM","color":"c2e0c6","default":false},{"id":397006293,"node_id":"MDU6TGFiZWwzOTcwMDYyOTM=","url":"https://api.github.com/repos/spacetelescope/jwst/labels/NIRISS","name":"NIRISS","color":"0e8a16","default":false},{"id":443310881,"node_id":"MDU6TGFiZWw0NDMzMTA4ODE=","url":"https://api.github.com/repos/spacetelescope/jwst/labels/Wide%20Field%20Slitless%20Spec%20(WFSS)","name":"Wide 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