Bugfixing

CHANGES.rst

@@ -1,6 +1,10 @@
 1.2.1 (Unreleased)
 ==================
 
+- Fixed crash for ``astrometric_catalog`` for background observations
+- Fixed crash when filtering out guide stars
+- Fixed issue with background files in ``move_raw_obs_step``
+- Fixed logging, will now properly output to a log file
 - Fix crash for background observations in ``get_short_band_name``
 - For background association, strip whitespace and lowercase for more robust matching
 - Imports update - now supports numpy>2.0!

pjpipe/__init__.py

@@ -1,7 +1,9 @@
+import logging
 import os
-import re
 import sys
+from datetime import datetime
 from importlib.metadata import version
+from logging.handlers import RotatingFileHandler
 
 # Set the CRDS server URL before any imports
 os.environ["CRDS_SERVER_URL"] = "https://jwst-crds.stsci.edu"
@@ -12,6 +14,20 @@
 # Get the version
 __version__ = version(__name__)
 
+# Set up the logger
+log = logging.getLogger(__name__)
+dt = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
+log_file = f"pjpipe_{dt}.log"
+log_level = "INFO"
+log_format = "%(asctime)s - %(levelname)s - %(message)s"
+logging.basicConfig(level=logging.INFO,
+                    format=log_format,
+                    handlers=[
+                        logging.FileHandler(log_file),
+                        logging.StreamHandler(),
+                    ]
+                    )
+
 from .apply_wcs_adjust import ApplyWCSAdjustStep
 from .astrometric_align import AstrometricAlignStep
 from .astrometric_catalog import AstrometricCatalogStep

pjpipe/anchoring/anchoring_step.py

@@ -34,8 +34,7 @@
 matplotlib.rcParams['font.family'] = 'STIXGeneral'
 matplotlib.rcParams['font.size'] = 14
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 
 def line_func_curvefit(x, b, m):

pjpipe/apply_wcs_adjust/apply_wcs_adjust_step.py

@@ -18,8 +18,7 @@
 
 from ..utils import band_exts
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 
 class ApplyWCSAdjustStep:

pjpipe/astrometric_align/astrometric_align_step.py

@@ -39,8 +39,7 @@
     "exact",
 ]
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 
 def get_lv3_wcs(im):

pjpipe/astrometric_catalog/astrometric_catalog_step.py

@@ -10,12 +10,11 @@
 from astropy.wcs import WCS
 from photutils.detection import DAOStarFinder, IRAFStarFinder
 
-from ..utils import parse_parameter_dict, fwhms_pix, sigma_clip, recursive_setattr
+from ..utils import parse_parameter_dict, fwhms_pix, sigma_clip, recursive_setattr, get_short_band_name
 
 from .constrained_diffusion import constrained_diffusion
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 ALLOWED_STARFIND_METHODS = [
     "dao",
@@ -143,7 +142,9 @@ def generate_astro_cat(
         mean, median, rms = sigma_clip(data, dq_mask=mask)
         threshold = median + snr * rms
 
-        kernel_fwhm = fwhms_pix[self.band]
+        # Make sure we only have the filter here
+        short_band = get_short_band_name(self.band)
+        kernel_fwhm = fwhms_pix[short_band]
 
         if self.starfind_method == "dao":
             finder = DAOStarFinder

pjpipe/download/download_step.py

@@ -16,8 +16,7 @@
 from stdatamodels.jwst import datamodels
 from tqdm import tqdm
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 
 def download(
@@ -437,7 +436,7 @@ def get_products(
 
         # Filter out guide stars if requested
         if self.filter_gs:
-            mask = np.char.find(products["dataURI"], "_gs-") == -1
+            mask = ["_gs-" not in x for x in products["dataURI"]]
             products = products[mask]
 
         # Perform filtering if requested

pjpipe/gaia_query/gaia_query_step.py

@@ -5,8 +5,7 @@
 from astropy.coordinates import name_resolve
 from astroquery.gaia import Gaia
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 
 class GaiaQueryStep:

pjpipe/get_wcs_adjust/custom_catalogs.py

@@ -6,8 +6,7 @@
 
 from ..astrometric_catalog.constrained_diffusion import constrained_diffusion
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 
 def constrained_diffusion_catalog(datamodel,

pjpipe/get_wcs_adjust/get_wcs_adjust_step.py

@@ -26,8 +26,7 @@
 
 from .custom_catalogs import constrained_diffusion_catalog
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 RAD_TO_ARCSEC = 3600 * np.rad2deg(1)
 

pjpipe/level_match/level_match_step.py

@@ -46,8 +46,7 @@
 matplotlib.rcParams['font.family'] = 'STIXGeneral'
 matplotlib.rcParams['font.size'] = 14
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 
 def get_dithers(files,

pjpipe/lv1/lv1_step.py

@@ -15,8 +15,7 @@
 
 from ..utils import attribute_setter, save_file
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 # Set OpenCV number of threads to 1 to avoid MP issues on newer Macbooks
 cv.setNumThreads(1)

pjpipe/lv2/lv2_step.py

@@ -18,8 +18,7 @@
 
 from ..utils import get_band_type, get_obs_table, attribute_setter, save_file
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 BGR_CHECK_TYPES = [
     "parallel_off",

pjpipe/lv3/lv3_step.py

@@ -34,8 +34,7 @@ class ModelLibrary:
     get_short_band_name,
 )
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 BGR_CHECK_TYPES = [
     "parallel_off",

pjpipe/lyot_mask/lyot_mask_step.py

@@ -15,8 +15,7 @@
 
 from ..utils import get_dq_bit_mask
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 ALLOWED_METHODS = ["mask", "mask_overlap"]
 

pjpipe/lyot_separate/lyot_separate_step.py

@@ -14,8 +14,7 @@
 
 from ..utils import get_dq_bit_mask
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 # Rough lyot outline
 LYOT_I = slice(735, None)

pjpipe/mosaic_individual_fields/mosaic_individual_fields_step.py

@@ -12,8 +12,7 @@
 
 from ..utils import parse_parameter_dict, recursive_setattr
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 
 class MosaicIndividualFieldsStep:

pjpipe/move_raw_obs/move_raw_obs_step.py

@@ -10,8 +10,7 @@
 
 from ..utils import get_band_ext, get_band_type, save_file, get_short_band_name
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 
 class MoveRawObsStep:
@@ -257,7 +256,7 @@ def move_raw_files(
                             save_file(im=im, out_name=hdu_out_name, dr_version=self.dr_version)
 
                     elif self.band_type == "miri":
-                        if hdu_filter == self.band:
+                        if hdu_filter == band_short:
                             save_file(im=im, out_name=hdu_out_name, dr_version=self.dr_version)
 
                 del im

pjpipe/multi_tile_destripe/multi_tile_destripe_step.py

@@ -31,8 +31,7 @@
 matplotlib.rcParams['font.family'] = 'STIXGeneral'
 matplotlib.rcParams['font.size'] = 14
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 ALLOWED_WEIGHT_METHODS = [
     "mean",

pjpipe/pipeline.py

@@ -91,8 +91,7 @@
     "release": None,
 }
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 
 class PJPipeline:

pjpipe/psf_matching/psf_matching_step.py

@@ -13,8 +13,7 @@
 
 from ..utils import do_jwst_convolution
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 
 class PSFMatchingStep:

pjpipe/psf_model/psf_model_step.py

@@ -23,8 +23,7 @@
 from ..utils import get_dq_bit_mask, make_source_mask
 
 matplotlib.use("agg")
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 ALLOWED_METHODS = ["replace", "subtract"]
 

pjpipe/regress_against_previous/regress_against_previous_step.py

@@ -24,8 +24,7 @@
 matplotlib.rcParams['font.family'] = 'STIXGeneral'
 matplotlib.rcParams['font.size'] = 14
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 
 def get_diff_image(

pjpipe/release/release_step.py

@@ -6,8 +6,7 @@
 from astropy.io import fits
 from tqdm import tqdm
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 
 class ReleaseStep:

pjpipe/single_tile_destripe/single_tile_destripe_step.py

@@ -33,8 +33,7 @@
 matplotlib.rcParams['font.family'] = 'STIXGeneral'
 matplotlib.rcParams['font.size'] = 14
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 DESTRIPING_METHODS = [
     "row_median",

pjpipe/utils/utils.py

@@ -144,8 +144,7 @@
     "miri": "mirimage",
 }
 
-log = logging.getLogger("stpipe")
-log.addHandler(logging.NullHandler())
+log = logging.getLogger(__name__)
 
 
 def get_pixscale(hdu):