incorporate findsat_mrt into acstools (#176)

* added findsat_mrt and utils_findsat_mrt

* updated __init__.py with findsat_mrt and utils_findsat_mrt

* added rst files for findsat_mrt and utils_findsat_mrt

* added MRT kernels

* fixed default kernels directory

* Revert "added MRT kernels"

This reverts commit 75f1cee.

* added kernels to data and updated path in findsat_mrt

* minor fix

* fixed error in diagnostic plot colors

* fixed bug with diagnostic plots

* added wfc_wrapper class

* added the execute command to the wfc wrapper

* added docstring for wfc_wrapper

* updated docstrings inside wfc_wrapper class

* updated docstrings for wfc_wrapper

* fixed bug in keyword inheritence for wfc_wrapper

* added gitattributes file to handle line endings

* fixed line ending character

* first round of formatting fixes

* second round of formatting fixes for findsat_mrt.py

* pep8 fixes on findsat_mrt.py

* first round of reformatting fixes on utils_findsat_mrt.py

* formatting and pep8 fixes for utils_findat_mrt.py

* fixed outdated code in streak_endpoints function

* replaced doc/source/utils_findsat_mrt.py with doc/source/utils_findsat_mrt.rst

* fixed outdated header info

* fixed additional outdated header info

* removed extraneous if statement in find_mrt_sources.py

* added info about how many sources found, or warning if none

* removed add_streak from satfinder as it was no longer used

* moved create_mrt_line_kernel function to utils_findat_mrt.py

* simplified checks for images that are None

* added check for subarray

* updated error handling for wfc_wrapper

* modified keywords to update class attributes where relevant, fixed a few missing attributes in wfc_wrapper

* findsat_mrt plots sent to output file if in non-interactive mode

* suppressed plotting of individual streaks during filtering stage

* modified plotting keyword for trail filtering stages to avoid accidentally making many plots

* additional pep8 fixes

* added photutils as requirement in setup

* updated packages in setup.cfg

* works now if matplotlib not installed

* added large truth files to lfs

* added jc8m32j5q_flc.fits for findsat_mrt testing

* added test for findsat_mrt

* fixed class name in findsat_mrt test, removed unneeded lines

* added warning to ignore that always appears during MRT calc

* fixed bug in MRT calc when only one thread used

* fix error in setup.cfg file

* closed poola after MRT calc

* added temp directory to findsat_mrt_test, removed file comparison

* fixed warning when writing out fits catalog

* removed messages from debugging

* added comparison between derived mask and truth

* removed extra print statements from utils_findsat_mrt

* fixed error in fits file comparison

* formatting fixes from flake8 test

* minor formatting fixes in __init__

* linked new packages to top level index file

* added photutils to required packages

* added ccdproc to required packages

* fixed handling when matplotlib is not present

* removed unused import of matplotlib

* removed rcparams setting from findsat_mrt.py

* fixed indentation issue raised by link_check

* added citations and citation format fixes

* updated documentation for findsat_mrt

* removed gitattributes

* flake8 formatting fixes for findsat_mrt

* removed unneeded reference in findsat_mrt

* fixed formatting errors in findsat_mrt docs

* even more formatting fixes

* fixed broken link

* updated docstrings to follow standard format, headings, and indicate Errors raised

* added more comments in findsat_mrt and utils_findsat_mrt

* adjusted which functions were hidden, I think I was using that syntax improperly sometimes

* Delete utils_findsat_mrt.py

This file is not needed

* removed warning filter from setup file and added warning filter explicitly to utils file

* put warning filter inside trailfinder instead of outside where it keeps getting overwritten

* updated docs to show findsat_mrt and utils on same page, fixed bug in class docstrings

* fixed minor formatting issues in docstrings

* fixed a few plots and error message suppresion

* added update_dq function

* a few more minor format changes to meet STScI standards

* Delete utils_findsat_mrt.rst

file no longer needed

* fixed error in test program and docstring of findsat_mrt

* pep8 fixes

* fixed another docstring format issue

* removed external package from list of required

* added checks for ccdproc and photutils

* added checks for skimage

* added check for scipy

* WIP: 2023-03-24 part 1
[ci skip]

* WIP: 2023-03-24 part 1.1
[ci skip]

* WIP: 2023-03-24 part 1.2
[ci skip]

* WIP: Still working on it [ci skip]

* WIP: Until mask_bad_pixels

* WIP: Updates 2023-03-30
[ci skip]

* Lim edits 2023-03-31

* Fix tests

* fixed some plotting in streak_endpoints

* fixed streak_endpoints for perfectly horizontal line

* fixed error in merge_tables where length returned rather than table

* fixed error in ploting to file, other minor tweaks

* fixed doc for ignore_flags keyword, additional log info in persistence check

* removed plot keywords from most functions in TrailFinder

* minor error in docstring

* minor updates before merging into findsat_mrt branch

* updated maxwidth parameter to be more appropriate for 4x4 binning

* minor formatting fixes

* pep8 and flake8 fixes

* Update acstools/findsat_mrt.py

Co-authored-by: P. L. Lim <[email protected]>

* Update acstools/tests/test_wfc_findsat_mrt.py

Co-authored-by: P. L. Lim <[email protected]>

---------

Co-authored-by: P. L. Lim <[email protected]>

acstools/__init__.py

@@ -19,3 +19,5 @@
 from . import acsphotcte  # noqa
 from . import satdet  # noqa
 from . import utils_calib  # noqa
+from . import findsat_mrt  # noqa
+from . import utils_findsat_mrt  # noqa