payload: {"action":"created","comment":{"url":"https://api.github.com/repos/spacetelescope/jwst/pulls/comments/301205079","pull_request_review_id":258996125,"id":301205079,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDMwMTIwNTA3OQ==","diff_hunk":"@@ -0,0 +1,374 @@\n+Description\n+===========\n+ \n+Steps in the pipelines calculate arrays for variances, or modify variance arrays \n+from <previous steps> in the pipeline.  In some cases these arrays are only used \n+internally to the current step.  For several steps, these arrays must be propagated to\n+subsequent steps in the pipeline, or included in the cumulate error array.\n+\n+Stage 1 pipelines \n+-----------------\n+Stage 1 pipelines perform detector-level corrections and ramp fitting for\n+individual exposures, for nearly all imaging and spectroscopic modes. Details \n+of the pipelines can be found at `Stage 1 Pipelines\n+<https://jwst-pipeline.readthedocs.io/en/latest/jwst/pipeline/calwebb_detector1.html>`_\n+\n+There are two unique configuration files to be used to control this pipeline, \n+depending on whether the data are to be treated as a Time Series Observation \n+(in which case some of the steps are set to be skipped by default).\n+\n+The steps to be executed differ for Near-IR and MIRI exposures. For \n+Near-IR, the steps are group_scale, dq_init, saturation, superbias, refpix, \n+linearity, persistence, dark_current, jump, ramp fitting, and gain scale.\n+For MIRI, the steps are group_scale, dq_init, saturation, firstframe, lastframe,\n+linearity, rcsd, dark_current, refpix, jump, ramp fitting, and gain scale.\n+\n+Of all of those steps, below are the particular steps that alter the ERR,\n+VAR_POISSON, or VAR_RNOISE arrays of the science ramp data and output those\n+altered arrays in the science product that is passed to the next step in the\n+pipeline.  For the steps not listed below, those arrays do not exist or are\n+propagated unchanged to the next pipeline step.\n+\n+\n+Ramp_fitting\n+++++++++++++\n+This step calculates and populates the VAR_POISSON, VAR_RNOISE arrays\n+(the variances and errors associated with ramp fitting) in the 'rate' and\n+'rateints' files, and updates the ERR arrays in those files. The details of the \n+calculations can be found at `Ramp fitting \n+<https://jwst-pipeline.readthedocs.io/en/latest/jwst/ramp_fitting/main.html>`_\n+\n+\n+\n+Group_scale\n++++++++++++\n+The group_scale step is applied after the ramp_fitting step, and applies to both the \n+rate and rateints products from ramp_fit. The correction is applied to the ERR, \n+(and will also be applied to the) VAR_POISSON, and VAR_RNOISE arrays.  The details\n+of the calculations can be found at `Group Scale\n+<https://jwst-pipeline.readthedocs.io/en/latest/jwst/group_scale/description.html>`_\n+\n+\n+Stage 2 pipelines \n+-----------------\n+Stage 2 pipelines perform additional instrument-level and observing-mode corrections and \n+calibrations to produce fully calibrated exposures. There are two Stage 2 pipelines: one \n+for `imaging \n+<https://jwst-pipeline.readthedocs.io/en/latest/jwst/pipeline/calwebb_image2.html>`_\n+and one for `spectroscopy \n+<https://jwst-pipeline.readthedocs.io/en/latest/jwst/pipeline/calwebb_spec2.html>`_\n+In these pipelines, the various steps that apply corrections and calibrations\n+apply those same corrections/calibrations to all variance arrays arrays.\n+\n+There are two unique configuration files to be used to control these pipelines, \n+depending on whether the data are to be treated as a Time Series Observation \n+(in which case some of the steps are set to be skipped by default).\n+\n+\n+Stage 2 Imaging Processing pipeline - calwebb_image2 & calwebb_tso-image2\n++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+The steps executed in this pipeline depend on whether the data are to be treated\n+as TSO.  For non-TSO exposures, the steps are background image subtraction,\n+assign_wcs, flat_field, photom, and resample.  For TSO exposures, the steps are\n+assign_wcs, flat_field, and photom.\n+\n+Of the steps listed above, below are the steps that alter the ERR or VAR arrays\n+of the science ramp data and output those altered arrays in the science product \n+that is passed to the next step in the pipeline.  For the steps not listed below,\n+those arrays do not exist or are propagated unchanged to the next pipeline step.\n+\n+Flat_field\n+~~~~~~~~~~\n+(NOTE: get from the latest online readthedocs for this step once James updates it.)\n+The SCI array from the flat-field reference file is divided into the VAR_POISSON\n+and VAR_RNOISE arrays of the science data set. The variance in the flat is\n+calculated in this step; the ERR array is then recalculated as these three \n+variances added in quadrature.  The newly created VAR_FLAT array and the updated \n+VAR_POISSON and VAR_RNOISE are output to the science products(s). For details of\n+the flat fielding correction, see `Flatfielding\n+<https://jwst-pipeline.readthedocs.io/en/latest/jwst/flatfield/index.html>`_\n+\n+\n+Photom\n+~~~~~~\n+The photom step is applied for the modes: imaging and non-IFU spectroscopy,\n+NIRSpec IFU, and MIRI MRS. The application of the step to these modes is very\n+similar - for details see `Photom\n+<https://jwst-pipeline.readthedocs.io/en/latest/jwst/photom/index.html>`_\n+\n+For these modes, the calibration information includes a scalar\n+flux conversion constant, as well as optional arrays of wavelength and\n+relative response (as a function of wavelength).  The combination of the scalar\n+conversion factor and the 2-D response values is applied to the science data,\n+including the SCI and ERR arrays, as well as the variance (VAR_POISSON,\n+VAR_RNOISE, and VAR_FLAT) arrays. The correction values are divided into the SCI \n+and ERR arrays, and the square of the correction values are divided into the \n+variance arrays.\n+\n+\n+Stage 2 Spectroscopic Processing pipeline - calwebb_spec2 & calwebb_tso-spec2\n++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n+The steps executed in this pipeline depend on whether the data are to be treated\n+as TSO.  For non-TSO exposures, the steps are assign_wcs, background image\n+subtraction, imprint, msaflagopen, extract_2d, flat_field, srctype, straylight,\n+fringe, pathloss, barshadow, photom, resample_spec, cube_build, and extract_1d.\n+For TSO exposures, some of the steps are in the list above are skipped.  The\n+paricular steps executed depend on particular instruments or instrument modes-\n+see `Calwebb_spec2\n+<https://jwst-pipeline.readthedocs.io/en/latest/jwst/pipeline/calwebb_spec2.html#calwebb-spec2>`_\n+\n+Of the steps listed above, below are the steps that alter the ERR or VAR\n+arrays of the science ramp data and output those altered arrays in the science\n+product that is passed to the next step in the pipeline.  For the steps not\n+listed below, those arrays do not exist or are propagated unchanged to the next\n+pipeline step.\n+\n+Flat_field\n+~~~~~~~~~~\n+{NOTE get from the latest online readthedocs for the step once James updates it.}\n+The SCI array from the flat-field reference file is divided into the VAR_POISSON\n+and VAR_RNOISE arrays of the science data set. The variance in the flat is\n+calculated in this step; the ERR array is then recalculated as these three\n+variances added in quadrature.  The newly created VAR_FLAT array and the updated\n+VAR_POISSON and VAR_RNOISE are output to the science products(s). For details of\n+the flat fielding correction, see `Flatfielding\n+<https://jwst-pipeline.readthedocs.io/en/latest/jwst/flatfield/index.html>`_\n+\n+\n+Fringe \n+~~~~~~\n+For MIRI MRS (IFU) mode exposures, the ERR array in the science data set is\n+divided by a fringe reference image.  For details of the fringe correction, see 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draft of error propagation document","user":{"login":"dmggh","id":3719822,"node_id":"MDQ6VXNlcjM3MTk4MjI=","avatar_url":"https://avatars3.githubusercontent.com/u/3719822?v=4","gravatar_id":"","url":"https://api.github.com/users/dmggh","html_url":"https://github.com/dmggh","followers_url":"https://api.github.com/users/dmggh/followers","following_url":"https://api.github.com/users/dmggh/following{/other_user}","gists_url":"https://api.github.com/users/dmggh/gists{/gist_id}","starred_url":"https://api.github.com/users/dmggh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dmggh/subscriptions","organizations_url":"https://api.github.com/users/dmggh/orgs","repos_url":"https://api.github.com/users/dmggh/repos","events_url":"https://api.github.com/users/dmggh/events{/privacy}","received_events_url":"https://api.github.com/users/dmggh/received_events","type":"User","site_admin":false},"body":"I haven't been able to build this locally, so this 0th draft may not build 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