Create co-added images (phase 2) (#6)

* Rename refine to reprocess

* Lots of refactor of camera WCS reprocessing

* Calculate ZP for each frame

* Add PA to frame data

* Sigma-clip, fit, and calculate PA drift

* Support processing spec frames

* Add initial plotting

* Add zero point plot

* Allow to force using time range to select frames

* Use UTC and getmtime

* Fix cases when the reference WCS is empty

* Move extract_sources out of Cameras and add MF pixels

* Add placeholder columns to sources during extraction

* Add CameraSolution and GuiderSolution classes

* Missing colon

* Add data model file

* Use model to update PROC and SOURCES extensions

* Major, major refactor

* Move some code around

* Remove GAIA_CACHE

* Add MF WCS (!) and some header keywords

* Allow to load FITS file into dataclass

* Bump version to 0.3.0a0

* Change some types in SOURCES data model

* Fix update_fits()

* Add DIRNAME

* Change header comment

* Typing

* post_init -> __post_init__

* Fix a few bugs

* Fix merge issues

* Update deps

* Deal with empty dataframe when converting to Table

* Some fixes

* Some fixes

* Remove table_from_dataframe

* Use MF pixels for global solution

* Use parquet for sources files

* Close HDU list

* Reset detections index to ensure Gaia match

* Fix call to update_fits

* Various fixes to guiding. Decrease guide tolerance

* Guide in PA

* Write PACORR to header

* Minimum version to load dataclasses -> 0.4.0a0

* Prevent multiple rotation corrections

* Disable rotation correction for now

* Comment unused lines

* Pretty complete rewrite of co-add functions using dataclasses

* Rename master frame to full frame

* Deal with spec telescope

* Add camera name to log message

* Typo in get_dark_subtrcted_data

* Support dark subtraction in old files without DIRNAME

* Support reprocessing old files. Fix some bugs.

* Plots for FWHM, ZP, and PA

* Add comments and remove redundant code

* Add guider offsets plots

* Various fixes to the datamodel and type casting

* Fix corner case in populating the ap. phot DF

* Fix dtypes that were not serializable

* Save PA offset to guider solution and FITS

* Improve logic to guide in PA

* Fix repetitive message during acquisition

* Set umask so that new files inherit the parent folder permissions

* Tweaks to plotting

Dockerfile

@@ -15,4 +15,7 @@ RUN pip3 install -U pip setuptools wheel
 RUN cd lvmguider && pip3 install .
 RUN rm -Rf lvmguider
 
+# Set umask so that new files inherit the parent folder permissions.
+RUN echo "umask 0002" >> /etc/bash.bashrc
+
 ENTRYPOINT lvmguider actor start --debug

docs/sphinx/conf.py

@@ -1,7 +1,8 @@
 import os
 
 from pkg_resources import parse_version
-from trurl import __version__
+
+from lvmguider import __version__
 
 
 # Are we building in RTD?

src/lvmguider/__init__.py

@@ -3,14 +3,9 @@
 import pathlib
 import warnings
 
-from astropy.wcs import FITSFixedWarning
-
 from sdsstools import Configuration, get_logger, get_package_version
 
 
-warnings.simplefilter("ignore", category=FITSFixedWarning)
-
-
 NAME = "lvmguider"
 
 

src/lvmguider/actor/commands/guide.py

@@ -45,7 +45,7 @@ def is_stopping(command: GuiderCommand):
 @click.option(
     "--reference-pixel",
     type=click.Tuple((float, float)),
-    help="The pixel of the master frame to use as pointing reference.",
+    help="The pixel of the full frame to use as pointing reference.",
 )
 @click.option(
     "--guide-tolerance",

src/lvmguider/actor/commands/set_pixel.py

@@ -26,7 +26,7 @@
 @click.argument("PIXEL-X", type=float)
 @click.argument("PIXEL-Z", type=float)
 async def set_pixel(command: GuiderCommand, pixel_x: float, pixel_z: float):
-    """Sets the master frame pixel coordinates on which to guide.
+    """Sets the full frame pixel coordinates on which to guide.
 
     This command can be issued during active guiding to change the pointing
     of the telescope.
@@ -43,7 +43,7 @@ async def set_pixel(command: GuiderCommand, pixel_x: float, pixel_z: float):
 
 @lvmguider_parser.command()
 async def reset_pixel(command: GuiderCommand):
-    """Resets the master frame pixel on which to guide to the central pixel..
+    """Resets the full frame pixel on which to guide to the central pixel..
 
     This command can be issued during active guiding to change the pointing
     of the telescope.

src/lvmguider/astrometrynet.py

@@ -24,7 +24,8 @@
 import pandas
 from astropy.io import fits
 from astropy.table import Table
-from astropy.wcs import WCS
+from astropy.units import UnitsWarning
+from astropy.wcs import WCS, FITSFixedWarning
 
 
 PathLike = TypeVar("PathLike", pathlib.Path, str)
@@ -478,16 +479,20 @@ def astrometrynet_quick(
         else:
             return solution
 
-    warnings.simplefilter("ignore")
-    wcs = WCS(open(wcs_output).read(), relax=True)
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore", category=FITSFixedWarning)
+        wcs = WCS(open(wcs_output).read(), relax=True)
 
     solution.wcs = wcs
     solution.stdout = open(stdout).read()
     solution.stderr = open(stderr).read()
 
     if os.path.exists(corr_file):
-        stars = Table.read(corr_file).to_pandas()
-        solution.stars = stars
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", category=UnitsWarning)
+
+            stars = Table.read(corr_file).to_pandas()
+            solution.stars = stars
 
     return solution
 

src/lvmguider/cameras.py

@@ -169,7 +169,7 @@ async def expose(
         if len(sources) > 0:
             all_sources = pandas.concat(sources)
             valid = all_sources.loc[all_sources.valid == 1]
-            fwhm = numpy.median(valid["fwhm"]) if len(valid) > 0 else None
+            fwhm = float(numpy.median(valid["fwhm"])) if len(valid) > 0 else None
         else:
             valid = []
             fwhm = None