From c4decc5edb35b4f0b3ab8be3155c43e7cf8e8bb9 Mon Sep 17 00:00:00 2001 From: Dave Davis Date: Wed, 4 Sep 2024 10:52:11 -0400 Subject: [PATCH 1/3] rcal-890 Update Docs for B15 --- docs/roman/pipeline/exposure_pipeline.rst | 21 +++++++++++++++++++-- docs/roman/pipeline/mosaic_pipeline.rst | 11 +++++++---- romancal/pipeline/mosaic_pipeline.py | 2 +- 3 files changed, 27 insertions(+), 7 deletions(-) diff --git a/docs/roman/pipeline/exposure_pipeline.rst b/docs/roman/pipeline/exposure_pipeline.rst index 50b354494..491d802d6 100644 --- a/docs/roman/pipeline/exposure_pipeline.rst +++ b/docs/roman/pipeline/exposure_pipeline.rst @@ -32,7 +32,7 @@ table below. :ref:`assign_wcs ` |check| |check| |check| :ref:`flatfield ` |check| :ref:`photom ` |check| - :ref:`source_detection ` |check| + :ref:`source_catalog ` |check| :ref:`tweakreg ` |check| ================================================== ========= ========= ========= @@ -87,9 +87,26 @@ Outputs :Data model: `~romancal.datamodels.ImageModel` :File suffix: _cal +Catalog file (SourceCatalog) ++++++++++++++++++++++++++++++++++++ + +The catalog data is in + +:Data model: `astropy.table.Table` +:File suffix: _cat + +Segmentation Map (SegmentationMapModel) +++++++++++++++++++++++++++++++++++++++++ + +The segmentation map is + +:Data model: `~romancal.datamodels.MosaicSegmentationMapModel` +:File suffix: _segm + Result of applying all pipeline steps up through the :ref:`tweakreg ` step is to produce calibrated data with the image WCS aligned to Gaia, and is 2D image data, which will have one less data dimensions as the input raw 3D data. In addition to being a 2-dimensional image the output from the pipeline has the :ref:`reference pixels ` -removed from the edges of the science array and saved as additional 3D arrays. +removed from the edges of the science array and saved as additional 3D arrays. The +source catalog and segmentation map from the individual exposues is also saved. diff --git a/docs/roman/pipeline/mosaic_pipeline.rst b/docs/roman/pipeline/mosaic_pipeline.rst index 63a442ac1..d0cfb6e5d 100644 --- a/docs/roman/pipeline/mosaic_pipeline.rst +++ b/docs/roman/pipeline/mosaic_pipeline.rst @@ -9,9 +9,11 @@ Mosaic Level Image Processing The ``MosaicPipeline`` applies corrections to an overlapping group of images and is setup to process only imaging observations. -This pipeline is used to determine a common background, :ref:`skymatch `, detect pixels the are -not consistent with the other datasets, :ref:`outlier_detection `, and resample the image to a -single undistorted image, :ref:`resample `. +This pipeline is used to apply the flux scale factor, :ref:`flux `, +determine a common background, :ref:`skymatch `, detect pixels the are +not consistent with the other datasets, :ref:`outlier_detection `, resample the image to a +single undistorted image, :ref:`resample `, and to run :ref:`source_catalog ` +on the resulting corrected image. The list of steps applied by the ``MosaicPipeline`` pipeline is shown in the table below. @@ -22,6 +24,7 @@ table below. ======================================================= ========= ========= ========= Step WFI-Image WFI-Prism WFI-Grism ======================================================= ========= ========= ========= + :ref:`flux ` |check| |xmark| |xmark| :ref:`skymatch ` |check| |xmark| |xmark| :ref:`outlier_detection ` |check| |xmark| |xmark| :ref:`resample ` |check| |xmark| |xmark| @@ -38,7 +41,7 @@ You can see the options for strun using: strun --help roman_mos -and this will list all the strun options all well as the step options for the roman_mos. +and this will list all the strun options as well as the step options for the roman_mos. Inputs diff --git a/romancal/pipeline/mosaic_pipeline.py b/romancal/pipeline/mosaic_pipeline.py index 099804658..f34b8c53c 100644 --- a/romancal/pipeline/mosaic_pipeline.py +++ b/romancal/pipeline/mosaic_pipeline.py @@ -34,7 +34,7 @@ class MosaicPipeline(RomanPipeline): """ MosaicPipeline: Apply all calibration steps to the roman data to produce level 3 products. Included steps are: - ``skymatch``, ``outlier_detection`` and ``resample``. + ``flux``, ``skymatch``, ``outlier_detection``, ``resample`` and ``source catalog``. """ class_alias = "roman_mos" From 29f33d927fbb98d0c75963bd3924dfd7cd05363f Mon Sep 17 00:00:00 2001 From: Dave Davis Date: Fri, 6 Sep 2024 10:12:12 -0400 Subject: [PATCH 2/3] rcal-890 Updates from review comments --- docs/roman/data_products/product_types.rst | 62 ++++++++++++---------- 1 file changed, 33 insertions(+), 29 deletions(-) diff --git a/docs/roman/data_products/product_types.rst b/docs/roman/data_products/product_types.rst index 769ae737b..faa7bb34a 100644 --- a/docs/roman/data_products/product_types.rst +++ b/docs/roman/data_products/product_types.rst @@ -24,35 +24,39 @@ The following table contains lists of all data product types for the Exposure pi are the only files that are produced in the standard processing. All the other are optional (opt) files that can be produced when the user is running the pipeline. The input for each optional step is the output of the preceding step. -+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+ -| Pipeline Step | Input | Output suffix | Data Model | Units | Description | -+================================================+=================+==========================+==================+=====================+=======================================+ -| | | uncal | ScienceRawModel | DN | 3-D uncalibrated exposure data | -+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+ -| :ref:`dq_init ` | uncal | dqinit (opt) | RampModel | DN | 3-D data quality flags applied | -+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+ -| :ref:`saturation ` | | saturation (opt) | RampModel | DN | 3-D data saturated values flagged | -+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+ -| :ref:`refpix ` | | refpix (opt) | RampModel | DN | 3-D ref pix corrected data | -+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+ -| :ref:`linearity ` | | linearity (opt) | RampModel | DN | 3-D linearity corrected data | -+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+ -| :ref:`dark_current ` | | darkcurrent (opt) | RampModel | DN | 3-D dark current subtracted data | -+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+ -| :ref:`ramp_fitting ` | | rampfit (opt) | ImageModel | DN/s | 2-D slope corrected data | -+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+ -| :ref:`assign_wcs ` | | assignwcs (opt) | ImageModel | DN/s | 2-D data with gwcs | -+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+ -| :ref:`flatfield ` | | flat (opt) | ImageModel | DN/s | 2-D QE corrected data | -+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+ -| :ref:`photom ` | | photom (opt) | ImageModel | DN/s | Add phometric data to header | -+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+ -| :ref:`source_detection `| | sourcedetectionstep (opt)| ImageModel | DN/s | Sources identified in the data | -+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+ -| :ref:`tweakreg ` | | tweakregstep (opt) | ImageModel | DN/s | WCS aligned with GAIA | -+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+ -| | | cal | ImageModel | DN/s | 2-D calibrated exposure data | -+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+ ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| Pipeline Step | Input | Output suffix | Data Model | Units | Description | ++================================================+=================+==========================+=====================+==================+=======================================+ +| | | uncal | ScienceRawModel | DN | 3-D uncalibrated exposure data | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| :ref:`dq_init ` | uncal | dqinit (opt) | RampModel | DN | 3-D data quality flags applied | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| :ref:`saturation ` | | saturation (opt) | RampModel | DN | 3-D data saturated values flagged | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| :ref:`refpix ` | | refpix (opt) | RampModel | DN | 3-D ref pix corrected data | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| :ref:`linearity ` | | linearity (opt) | RampModel | DN | 3-D linearity corrected data | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| :ref:`dark_current ` | | darkcurrent (opt) | RampModel | DN | 3-D dark current subtracted data | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| :ref:`ramp_fitting ` | | rampfit (opt) | ImageModel | DN/s | 2-D slope corrected data | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| :ref:`assign_wcs ` | | assignwcs (opt) | ImageModel | DN/s | 2-D data with gwcs | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| :ref:`flatfield ` | | flat (opt) | ImageModel | DN/s | 2-D QE corrected data | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| :ref:`photom ` | | photom (opt) | ImageModel | DN/s | Add phometric data to header | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| :ref:`source_catalog ` | | sourcecatalogstep (opt) | ImageModel | DN/s | 2-D data | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| | cat | astropy.table | Sources identified in the data | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| | segm |SegmentationMapModel | | segmentation map | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| :ref:`tweakreg ` | | tweakregstep (opt) | ImageModel | DN/s | WCS aligned with GAIA | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ +| | | cal | ImageModel | DN/s | 2-D calibrated exposure data | ++------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+ From 2e8f8c21cfba5459399211ca0d53fcaa5d78a174 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 6 Sep 2024 14:13:54 +0000 Subject: [PATCH 3/3] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/roman/pipeline/exposure_pipeline.rst | 2 +- docs/roman/pipeline/mosaic_pipeline.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/roman/pipeline/exposure_pipeline.rst b/docs/roman/pipeline/exposure_pipeline.rst index 491d802d6..dda8ee7a9 100644 --- a/docs/roman/pipeline/exposure_pipeline.rst +++ b/docs/roman/pipeline/exposure_pipeline.rst @@ -102,7 +102,7 @@ The segmentation map is :Data model: `~romancal.datamodels.MosaicSegmentationMapModel` :File suffix: _segm - + Result of applying all pipeline steps up through the :ref:`tweakreg ` step is to produce calibrated data with the image WCS aligned to Gaia, and is 2D image data, which will have one less data dimensions as the input diff --git a/docs/roman/pipeline/mosaic_pipeline.rst b/docs/roman/pipeline/mosaic_pipeline.rst index d0cfb6e5d..578556932 100644 --- a/docs/roman/pipeline/mosaic_pipeline.rst +++ b/docs/roman/pipeline/mosaic_pipeline.rst @@ -13,7 +13,7 @@ This pipeline is used to apply the flux scale factor, :ref:`flux `, determine a common background, :ref:`skymatch `, detect pixels the are not consistent with the other datasets, :ref:`outlier_detection `, resample the image to a single undistorted image, :ref:`resample `, and to run :ref:`source_catalog ` -on the resulting corrected image. +on the resulting corrected image. The list of steps applied by the ``MosaicPipeline`` pipeline is shown in the table below.