Merge pull request #129 from lsst-camera-dh/LSSTTD-1606_superbias_sub…

…traction_w_rowcol

superbias handling

harnessed_jobs/bias_frame_BOT/v0/bias_frame_jh_task.py

@@ -33,21 +33,24 @@ def bias_frame_jh_task(det_name):
               det_name)
         return None
 
-    bias_frame, pca_files = bias_frame_task(run, det_name, bias_files)
+    superbias_file, bias_model_components \
+        = 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':
-        pca_files = None
+        bias_model_components = None
     if siteUtils.get_analysis_run('bias') == 'rowcol':
-        pca_files = 'rowcol'
-    print("pca_files:", pca_files)
+        bias_model_components = 'rowcol', superbias_file
+    print("bias_model_components:", bias_model_components)
     bias_stability_task(run, det_name, bias_stability_files,
-                        pca_files=pca_files)
+                        bias_model_components=bias_model_components)
 
-    if pca_files is not None and pca_files != 'rowcol':
-        pca_corrected_superbias(run, det_name, bias_files, pca_files)
+    if (bias_model_components is not None and
+        bias_model_components[0] != 'rowcol'):
+        pca_corrected_superbias(run, det_name, bias_files,
+                                bias_model_components)
 
-    return bias_frame
+    return superbias_file
 
 
 if __name__ == '__main__':

harnessed_jobs/raft_results_summary_BOT/v0/raft_results_task.py

@@ -114,7 +114,7 @@ def plt_savefig(filename):
     bias_run = siteUtils.get_analysis_run('bias')
     if bias_run is not None and bias_run.lower() == 'rowcol':
         for key in bias_frames:
-            bias_frames[key] = 'rowcol'
+            bias_frames[key] = ('rowcol', bias_frames[key])
 
     # Dark mosaic
     dark_files = None

python/bot_eo_analyses.py

@@ -305,9 +305,14 @@ def bias_filename(run, det_name):
     bias_run = siteUtils.get_analysis_run('bias')
     if bias_run is not None and bias_run.lower() == 'rowcol':
         # This will set the bias_frame option for all tasks to
-        # 'rowcol' and so the eotest.sensor.MaskedCCD code will use
-        # the parallel+serial overscan model for bias subtraction.
-        return 'rowcol'
+        # ('rowcol', superbias_file) and so the eotest.sensor.MaskedCCD
+        # code will use the parallel+serial overscan correction and
+        # superbias subtraction for bias correction.
+        superbias_file = make_bias_filename(run, det_name)
+        bias_frame = siteUtils.dependency_glob(
+            superbias_file, description='superbias file:')
+        bias_frame = bias_frame[0] if bias_frame else None
+        return 'rowcol', bias_frame
     elif bias_run is None:
         if use_pca_bias:
             file_prefix = make_file_prefix(run, det_name)
@@ -690,7 +695,7 @@ def image_stats(image, nsigma=10):
 
 
 def bias_stability_task(run, det_name, bias_files, nsigma=10,
-                        pca_files=None, llc_size=200):
+                        bias_model_components=None, llc_size=200):
     """Compute amp-wise bias stability time histories and serial profiles."""
     raft, slot = det_name.split('_')
     file_prefix = make_file_prefix(run, det_name)
@@ -708,7 +713,7 @@ def bias_stability_task(run, det_name, bias_files, nsigma=10,
                 key = f'TEMP{i}'
                 if key in hdus['REB_COND'].header:
                     temps[key] = hdus['REB_COND'].header[key]
-        ccd = sensorTest.MaskedCCD(bias_file, bias_frame=pca_files)
+        ccd = sensorTest.MaskedCCD(bias_file, bias_frame=bias_model_components)
         for amp in ccd:
             # Retrieve the per row overscan subtracted imaging section.
             amp_image = ccd.unbiased_and_trimmed_image(amp)

python/stage_bot_data.py

@@ -98,6 +98,9 @@ def get_isr_files(det_name, run):
         if isinstance(bias_fn, str):
             if os.path.isfile(bias_fn):
                 files.add(bias_fn)
+        elif isinstance(bias_fn, (tuple, list)) and bias_fn[0] == 'rowcol':
+            if bias_fn[1] is not None:
+                files.add(bias_fn[1])
         else:
             files = files.union(bias_fn)
     except IndexError: