add pca_superbias to bias frame task

data/BOT_jh_glob_patterns.ini

@@ -1,7 +1,7 @@
 [BOT_acq]
 fe55 = fe55_flat_*_flat_*
 fe55_bias = fe55_flat_bias_*
-bias_frame = bias_bias_*
+bias_frame = *_bias_*
 bias_stability = *_bias_*
 read_noise = bias_bias_*
 raft_noise_correlations = bias_bias_*

harnessed_jobs/bias_frame_BOT/v0/bias_frame_jh_task.py

@@ -8,14 +8,17 @@ def bias_frame_jh_task(det_name):
     import siteUtils
     import json
     from bot_eo_analyses import glob_pattern, bias_frame_task, \
-        bias_stability_task
+        bias_stability_task, pca_corrected_superbias
 
     run = siteUtils.getRunNumber()
     acq_jobname = siteUtils.getProcessName('BOT_acq')
     bias_files \
         = siteUtils.dependency_glob(glob_pattern('bias_frame', det_name),
                                     acq_jobname=acq_jobname,
-                                    description='Bias frames:')
+                                    description='Bias frames:')[10:]
+    # Skip the first 10 bias files to avoid transient features in the
+    # imaging array from after just starting the run.
+    bias_files = sorted(bias_files, key=os.path.basename)[5:]
     if not bias_files:
         print("bias_frame_task: Needed data files are missing for detector",
               det_name)
@@ -30,7 +33,7 @@ def bias_frame_jh_task(det_name):
               det_name)
         return None
 
-    bias_frame, pca_files = bias_frame_task(run, det_name, bias_files[1:])
+    bias_frame, pca_files = bias_frame_task(run, det_name, bias_files)
     bias_stability_files = sorted(bias_stability_files)
 
     if not os.environ.get('LCATR_USE_PCA_BIAS_FIT', "True") == 'True':
@@ -39,6 +42,9 @@ def bias_frame_jh_task(det_name):
     bias_stability_task(run, det_name, bias_stability_files,
                         pca_files=pca_files)
 
+    if pca_files is not None:
+        pca_corrected_superbias(run, det_name, bias_files, pca_files)
+
     return bias_frame
 
 

python/bot_eo_analyses.py

@@ -45,6 +45,7 @@
            'get_analysis_types',
            'fe55_task',
            'bias_frame_task',
+           'pca_corrected_superbias',
            'bias_stability_task',
            'scan_mode_analysis_task',
            'get_scan_mode_files',
@@ -564,13 +565,21 @@ def bias_frame_task(run, det_name, bias_files, bias_frame=None):
 
     return bias_frame, pca_files
 
+
+def pca_corrected_superbias(run, det_name, bias_files, pca_bias_files):
+    file_prefix = make_file_prefix(run, det_name)
+    outfile = f'{file_prefix}_pca_superbias.fits'
+    sensorTest.pca_superbias(bias_files, pca_bias_files, outfile)
+
+
 def image_stats(image, nsigma=10):
     """Compute clipped mean and stdev of the image."""
     stat_ctrl = afwMath.StatisticsControl(numSigmaClip=nsigma)
     flags = afwMath.MEANCLIP | afwMath.STDEVCLIP
     stats = afwMath.makeStatistics(image, flags=flags, sctrl=stat_ctrl)
     return stats.getValue(afwMath.MEANCLIP), stats.getValue(afwMath.STDEVCLIP)
 
+
 def bias_stability_task(run, det_name, bias_files, nsigma=10,
                         pca_files=None):
     """Compute amp-wise bias stability time histories and serial profiles."""

python/bot_eo_validators.py

@@ -72,9 +72,11 @@ def validate_bias_frame(results, det_names):
         bias_frame = f'{file_prefix}_median_bias.fits'
         rolloff_mask = f'{file_prefix}_edge_rolloff_mask.fits'
         pca_bias_file = f'{file_prefix}_pca_bias.fits'
+        pca_superbias = f'{file_prefix}_pca_superbias.fits'
 
         # Add/update the metadata to the primary HDU of these files.
-        for fitsfile in (bias_frame, rolloff_mask, pca_bias_file):
+        for fitsfile in (bias_frame, rolloff_mask, pca_bias_file,
+                         pca_superbias):
             if os.path.isfile(fitsfile):
                 eotestUtils.addHeaderData(fitsfile, TESTTYPE='BIAS',
                                           DATE=eotestUtils.utc_now_isoformat())