Merge branch 'dev' into stf_parallelize

Keck-DataReductionPipelines · May 13, 2024 · d6008bf · d6008bf
2 parents 7782bf8 + dc2ff64
commit d6008bf
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Showing 6 changed files with 34 additions and 18 deletions.
diff --git a/kai/instruments.py b/kai/instruments.py
@@ -273,7 +273,7 @@ def get_position_angle(self, hdr):
         """
         # pa = float(hdr['ROTPOSN']) - self.get_instrument_angle(hdr)
         pa = hdr['PA_IMAG']
-        
+
         #if in PCU mode, read the PCU rotation angle instead
         if 'PCUZ' in hdr.keys():
             if hdr['PCUZ'] > 20:  
@@ -366,6 +366,10 @@ def flip_images(self, files, rootDir=''):
                     #     hdu_list[hh].data = new_data[::-1, :]
                     hdu_list[hh].data = new_data[::-1, :]
 
+            # Need to modify PA_IMAG to account for the flip. Added 2023-10-30 by J. Lu.
+            pa_orig = hdu_list[0].header['PA_IMAG']
+            hdu_list[0].header['PA_IMAG'] = 360.0 - pa_orig
+
             hdu_list.writeto(new_file, overwrite=True)
 
             # Add header values. 
@@ -415,7 +419,6 @@ def get_saturation_level(self):
         Set to the 95% saturation threshold in DN.
         """
         return 17000.0
-
 
 ##################################################
 #

diff --git a/kai/reduce/analysis.py b/kai/reduce/analysis.py
@@ -98,6 +98,7 @@ def __init__(self, epoch, rootDir='/g/lu/data/orion/', filt='kp',
 
         self.starlist = rootDir + 'source_list/psf_central.dat'
         self.labellist = rootDir+ 'source_list/label.dat'
+        self.labellist_accel = True
         self.orbitlist = rootDir+ 'source_list/orbits.dat'
         self.calFile = rootDir + 'source_list/photo_calib.dat'
 
@@ -780,11 +781,18 @@ def alignCombo(self):
 
             # Make a named/labeled version
             cmd = 'java -Xmx1024m align %s ' % (self.alignFlags)
-            #cmd += '-N %s ' % self.labellist
-            cmd += '-accel_file %s ' % self.labellist
+
+            # Support label.dat files with or without accelerations.
+            if self.labellist_accel:
+                cmd += '-accel_file %s ' % self.labellist
+            else:
+                cmd += '-N %s ' % self.labellist
+
             if (self.orbitlist != None) and (self.orbitlist != ''):
                 cmd += '-o %s ' % self.orbitlist
+
             cmd += '-r align%s%s_%3.1f_named ' % (self.imgSuffix, file_ext, self.corrMain[0])
+
             cmd += alnList2
             print(cmd)
 

diff --git a/kai/reduce/calib.py b/kai/reduce/calib.py
@@ -10,6 +10,7 @@
 from datetime import datetime
 from pkg_resources import parse_version
 import warnings
+import pdb
 
 module_dir = os.path.dirname(__file__)
 
@@ -225,14 +226,15 @@ def makeflat(
 
         warnings.warn(warning_message)
 
-    # Perform linearity correction
-    for i in range(len(lampson_copied)):
-        lin_correction.lin_correction(lampson_copied[i],
-                                      instrument=instrument)
-
-    for i in range(len(lampsoff_copied)):
-        lin_correction.lin_correction(lampsoff_copied[i],
-                                      instrument=instrument)
+    # Perform linearity correction [only NIRC2]
+    if instrument is 'NIRC2':
+        for i in range(len(lampson_copied)):
+            lin_correction.lin_correction(lampson_copied[i],
+                instrument=instrument)
+
+        for i in range(len(lampsoff_copied)):
+            lin_correction.lin_correction(lampsoff_copied[i],
+                instrument=instrument)
 
     if (len(offFiles) != 0):
         f_on = open(_onlis, 'w')

diff --git a/kai/reduce/data.py b/kai/reduce/data.py
@@ -283,7 +283,8 @@ def clean(
                 overwrite=True)
 
             # Linearity correction
-            lin_correction.lin_correction(_cp, instrument=instrument)
+            if instrument is 'NIRC2':
+                lin_correction.lin_correction(_cp, instrument=instrument)
 
             ### Sky subtract ###
             # Get the proper sky for this science frame.

diff --git a/kai/reduce/masks/osiris_img_mask.fits b/kai/reduce/masks/osiris_img_mask.fits
diff --git a/kai/reduce/sky.py b/kai/reduce/sky.py
@@ -122,8 +122,9 @@ def makesky(
 
 
     # Perform linearity correction
-    for i in range(len(skies)):
-        lin_correction.lin_correction(nn[i], instrument=instrument)
+    if instrument is 'NIRC2':
+        for i in range(len(skies)):
+            lin_correction.lin_correction(nn[i], instrument=instrument)
 
     # scale skies to common median
     if skyscale:
@@ -306,8 +307,9 @@ def makesky_lp(
         warnings.warn(warning_message)
 
     # Perform linearity correction
-    for i in range(len(skies)):
-        lin_correction.lin_correction(skies[i], instrument=instrument)
+    if instrument is 'NIRC2':
+        for i in range(len(skies)):
+            lin_correction.lin_correction(skies[i], instrument=instrument)
 
     # Read in the list of files and rotation angles
     files, angles = read_sky_rot_file(_skyRot)