adding source detection step

CHANGES.rst

@@ -5,9 +5,15 @@ general
 -------
 - Updated datamodel maker utility imports. [#654]
 
+<<<<<<< HEAD
 - Update non-VOunits to using ``astropy.units``. [#658]
 
 - update minimum version of ``asdf`` to ``2.14.2`` and ``jsonschema`` to ``4.0.1`` and added minimum dependency checks to CI [#664]
+=======
+source_detection
+----------------
+- Added SourceDetection Step to pipeline [#608]
+>>>>>>> 05ff1e7 (adding source detection step)
 
 0.10.0 (2023-02-21)
 ===================

docs/roman/package_index.rst

@@ -13,3 +13,4 @@
    references_general/index.rst
    stpipe/index.rst
    refpix/index.rst
+   source_detection/index.rst

docs/roman/source_detection/arguments.rst

@@ -0,0 +1,57 @@
+Arguments
+=========
+The source detection fitting step has several arguments. These can be specified
+by the user by passing them to the step in a Python session, or setting them
+in a parameter file.
+
+* ``--kernel_fwhm``: A parameter for DAOStarFinder: size of Gaussian kernel in
+                     pixels. Default is 2.0.
+* ``--sharplo``: A parameter for DAOStarFinder: lower bound for sharpness.
+                 Default is 0.0.
+* ``--sharphi``: A parameter for DAOStarFinder: upper bound for sharpness.
+                 Default is 1.0.
+* ``--roundlo``: A parameter for DAOStarFinder: lower bound for roundness.
+                 Default is -1.0. A circular source will have a zero roundness.
+                 A source extended in x or y will have a negative or positive
+                 roundness, respectively.
+* ``--roundhi``: A parameter for DAOStarFinder: upper bound for roundness.
+                 Default is 1.0. A circular source will have a zero roundness.
+                 A source extended in x or y will have a negative or positive
+                 roundness, respectively.
+* ``--peakmax``: A parameter for DAOStarFinder: upper limit on brightest pixel
+                 in sources. Default is 1000.0.
+* ``--max_sources``: The maximum number of sources in the output catalog,
+                     choosing brightest. Default is None, which will return all
+                     detected sources.
+* ``--scalar_threshold``: If specified, the absolute detection threshold to be
+                          used for the entire image. Units are assumed to be the
+                          same as input data. One of `scalar_threshold`,
+                          `calc_scalar_threshold` must be chosen. Default is
+                          None.
+* ``--calc_scalar_threshold``: If specified, a single scalar threshold will be
+                               determined for the entire image. This is done by
+                               calculating a 2D background image, and using that
+                               to determine a single threshold value for the
+                               entire image. One of `scalar_threshold` or
+                               `calc_scalar_threshold` must be chosen.
+                               must be chosen. Default is True.
+* ``--snr_threshold``: If using `calc_threshold_img`, the SNR for the threshold
+                       image. Default is 3.0.
+* ``--bkg_estimator``: If using `calc_threshold_img`, choice of mean, median, or
+                        mode. Default is median.
+* ``--bkg_boxsize``: If using `calc_threshold_img` size of box in pixels for
+                     2D background / threshold images and if using
+                     calc_threshold_2d, the size of the box used when detecting
+                     sources. Default is 3.
+* ``--bkg_sigma``: If using `calc_threshold_img`, n sigma for sigma clipping
+                   for background calculation. Default is 2.0.
+* ``--bkg_filter_size``: If using `calc_threshold_img` or `calc_threshold_2d`,
+                         size of square gaussian kernel for background
+                         calculation. Default is 3.
+* ``--save_catalogs``: A True/False value that specifies whether to write
+                      the optional output catalog. Default is False.
+* ``--output_cat_filetype``: If `save_catalogs` is True, file type of output
+                             catalog from choice of asdf and escv. Catalog
+                             will be saved as a numpy array with four dimensions.
+                             In order, these represent source ID, x centroid
+                             position, y centroid position, and flux.

docs/roman/source_detection/description.rst

@@ -0,0 +1,55 @@
+Description
+============
+
+The source detection step produces catalogs of point-like sources for use by the
+Tweakreg step for image alignment. It uses DAOStarFinder to detect point sources
+in the image.
+
+
+Outputs / Returns
+=================
+
+By default, the resulting source catalog will be temporarily attached to the
+output ImageModel in the `meta.source_catalog.tweakreg_catalog` attribute as 4D
+numpy array representing, in order, source ID, x centroid position, y centroid
+positon, and flux. This catalog will then be deleted from the model in the
+Tweakreg step.
+
+Optionally, the catalog can be saved to disk in which case a
+`meta.source_catalog.tweakreg_catalog_name` attribute will be added to the file
+to point Tweakreg to the catalog on disk. To do this, set `save_catalogs` to
+True. Output catalogs will be saved in the same directory as input files, and
+are also 4D numpy arrays representing, in order, source ID, x centroid position,
+y centroid positon, and flux. Output catalogs can be in ASDF or ECSV format.
+
+NOTE: The intermediate resulting ImageModel from SourceDetectionStep can
+only be saved if it does not contain an attached catalog - to do this, use the
+`save_catalogs` option to seperate the catalog from the file and save them
+separately.
+
+Options for Thresholding
+========================
+
+The DAOStarFinder routine detects point-like sources in in image that are above
+a certain, specified floating point threshold. This step provides several options
+for calculating this threshold, either using one value for the entire image,
+or by detecting sources in segments of the image and using a different appropriate
+threshold for each (useful if background varies across the image).
+
+The first option is to set `scalar_threshold` - this will use the specified
+threshold as the detection threshold for the entire image.
+
+The second option is to use `calc_threshold` - this will calculate a single
+threshold value for the entire image based on the sigma-clipped average
+(mean, median, or mode) background level of the whole image.
+
+Other Options
+=============
+
+Limiting maximum number of sources
+----------------------------------
+
+By default, all detected sources will be returned in the final output catalog.
+If you wish to limit the number of sources, this can be done with the
+`max_sources` argument, which will sort the output catalog by flux and return
+only the N brightest.

docs/roman/source_detection/index.rst

@@ -0,0 +1,13 @@
+.. _source_detection_step:
+
+================
+Source Detection
+================
+
+.. toctree::
+   :maxdepth: 2
+
+   description.rst
+   arguments.rst
+
+.. automodapi:: romancal.source_detection

pyproject.toml

@@ -19,12 +19,19 @@ dependencies = [
     'gwcs >=0.18.1',
     'jsonschema >=4.0.1',
     'numpy >=1.20',
+    'photutils >= 1.6.0',
     'pyparsing >=2.4.7',
     'requests >=2.22',
+<<<<<<< HEAD
     # 'rad >=0.14.1',
     'rad @ git+https://github.com/spacetelescope/rad.git@main',
     #'roman_datamodels >=0.14.1',
     'roman_datamodels @ git+https://github.com/spacetelescope/roman_datamodels.git@main',
+=======
+    'rad @git+https://github.com/cshanahan1/rad.git@source_cat',
+    #'roman_datamodels >=0.14.1',
+    'roman_datamodels @git+https://github.com/cshanahan1/roman_datamodels.git@source_detection_new',
+>>>>>>> 05ff1e7 (adding source detection step)
     'stcal >=1.3.3',
     'stpipe >=0.4.2',
     'tweakwcs >=0.8.0'

romancal/lib/suffix.py

@@ -82,6 +82,7 @@
     "linearitystep",
     "dark_current",
     "jump",
+    "sourcedetectionstep",
     "tweakregstep",
 }
 

romancal/pipeline/exposure_pipeline.py

@@ -17,6 +17,7 @@
 from romancal.photom import PhotomStep
 from romancal.ramp_fitting import ramp_fit_step
 from romancal.saturation import SaturationStep
+from romancal.source_detection import SourceDetectionStep
 
 from ..stpipe import RomanPipeline
 
@@ -53,6 +54,7 @@ class ExposurePipeline(RomanPipeline):
         "assign_wcs": AssignWcsStep,
         "flatfield": FlatFieldStep,
         "photom": PhotomStep,
+        "source_detection": SourceDetectionStep,
     }
 
     # start the actual processing
@@ -110,6 +112,8 @@ def process(self, input):
             result.meta.cal_step.flat_field = "SKIPPED"
         result = self.photom(result)
 
+        result = self.source_detection(result)
+
         # setup output_file for saving
         self.setup_output(result)
         log.info("Roman exposure calibration pipeline ending...")

romancal/source_detection/__init__.py

@@ -0,0 +1,3 @@
+from .source_detection_step import SourceDetectionStep
+
+__all__ = ["SourceDetectionStep"]