updating to release

geminidr/core/primitives_register.py

@@ -492,7 +492,7 @@ def _create_wcs_from_offsets(adinput, adref, center_of_rotation=None):
 
     if center_of_rotation is None:
         if 'GNIRS' in adref.tags:
-            center_of_rotation = (629.0, 519.0)  # (x, y; 0-indexed)
+            center_of_rotation = (519.0, 629.0)  # (y, x; 0-indexed)
         else:
             try:
                 for m in adref[0].wcs.forward_transform:

geminidr/gmos/parameters_gmos.py

@@ -4,6 +4,18 @@
 from geminidr.core import parameters_visualize, parameters_ccd
 from geminidr.gemini import parameters_qa
 
+def badamps_check(value):
+    try:
+        badamps = [int(x) for x in value.split(',')]
+    except AttributeError:  # not a str, must be int
+        if value is None:
+            return True
+        return value > 0
+    except ValueError:  # items are not int-able
+        return False
+    else:
+        return len(badamps) >= 1 and min(badamps) > 0
+
 class displayConfig(parameters_visualize.displayConfig):
     remove_bias = config.Field("Remove estimated bias level before displaying?", bool, True)
 
@@ -13,6 +25,14 @@ class measureBGConfig(parameters_qa.measureBGConfig):
 class measureIQConfig(parameters_qa.measureIQConfig):
     remove_bias = config.Field("Remove estimated bias level before displaying?", bool, True)
 
+class maskFaultyAmpConfig(config.Config):
+    suffix = config.Field("Filename suffix", str, "_badAmpMasked", optional=True)
+    instrument = config.Field("Applicable instrument", str, None, optional=True)
+    bad_amps = config.Field("Amps to mask as a list", (int, str), None,
+                                optional=True, check=badamps_check)
+    valid_from = config.Field("Mask data taken after this date (YYYYMMDD)", str, None, optional=True)
+    valid_to = config.Field("Mask data taken before this date (YYYYMMDD)", str, None, optional=True)
+
 class subtractOverscanConfig(parameters_ccd.subtractOverscanConfig):
     nbiascontam = config.RangeField("Number of columns to exclude from averaging",
                                int, None, min=0, optional=True)

geminidr/gmos/primitives_gmos.py

@@ -6,6 +6,10 @@
 import os
 from importlib import import_module
 
+import numpy as np
+
+from datetime import datetime
+
 import astrodata
 import gemini_instruments
 
@@ -22,6 +26,8 @@
 from gemini_instruments.gmos.pixel_functions import get_bias_level
 
 from recipe_system.utils.decorators import parameter_override
+
+
 # ------------------------------------------------------------------------------
 @parameter_override
 class GMOS(Gemini, CCD):
@@ -37,6 +43,54 @@ def __init__(self, adinputs, **kwargs):
         self.inst_lookups = 'geminidr.gmos.lookups'
         self._param_update(parameters_gmos)
 
+    def maskFaultyAmp(self, adinputs=None, **params):
+        log = self.log
+
+        log.debug(gt.log_message("primitive", self.myself(), "starting"))
+        timestamp_key = 'MASKAMP5'
+
+        suffix = params["suffix"]
+        instrument = params["instrument"]
+        badamps = params["bad_amps"]
+        validfromstr = params["valid_from"]
+        validtostr = params["valid_to"]
+
+        if badamps is None or instrument is None:
+            return adinputs
+        elif badamps:
+            try:
+                badamplist = [int(x) for x in badamps.split(',')]
+            except AttributeError:  # not a str, must be int
+                badamplist = [badamps]
+
+        if validfromstr:
+            validfrom = datetime.strptime(validfromstr, '%Y%m%d')
+        else:
+            validfrom = datetime(1900, 1, 1)
+
+        if validtostr:
+            validto = datetime.strptime(validtostr, '%Y%m%d')
+        else:
+            validto = datetime(2200, 1, 1)
+
+        for ad in adinputs:
+            if instrument == ad.instrument() and \
+                    validfrom.date() <= ad.ut_date() <= validto.date():
+
+                ampsstr = ', '.join([str(i) for i in badamplist])
+                plural = 's' if len(ampsstr) > 1 else ''
+                log.status(f'Masking amp{plural} {ampsstr}')
+
+                for amp in badamplist:
+                    ext = amp - 1
+                    mask = np.ones(ad[ext].mask.shape, dtype=ad[ext].mask.dtype)
+                    ad[ext].mask = mask
+
+            gt.mark_history(ad, primname=self.myself(), keyword=timestamp_key)
+            ad.update_filename(suffix=suffix, strip=True)
+
+        return adinputs
+
     def standardizeInstrumentHeaders(self, adinputs=None, suffix=None):
         """
         This primitive is used to make the changes and additions to the
@@ -91,7 +145,7 @@ def standardizeInstrumentHeaders(self, adinputs=None, suffix=None):
             # Update keywords in the image extensions. The descriptors return
             # the true values on unprepared data.
             descriptors = ['pixel_scale', 'read_noise', 'gain_setting',
-                               'gain', 'saturation_level']
+                           'gain', 'saturation_level']
             for desc in descriptors:
                 keyword = ad._keyword_for(desc)
                 comment = self.keyword_comments[keyword]
@@ -180,9 +234,10 @@ def subtractOverscan(self, adinputs=None, **params):
                 dsec_list = ad.data_section()
                 osec_list = ad.overscan_section()
                 for ext, dsec, osec in zip(ad, dsec_list, osec_list):
-                    ext.hdr['BIASSEC'] = '[{}:{},{}:{}]'.format(osec.x1+1,
-                                                    osec.x2, y1+1, osec.y2)
-                    #ext.hdr['DATASEC'] = '[{}:{},{}:{}]'.format(dsec.x1+1,
+                    ext.hdr['BIASSEC'] = '[{}:{},{}:{}]'.format(osec.x1 + 1,
+                                                                osec.x2, y1 + 1,
+                                                                osec.y2)
+                    # ext.hdr['DATASEC'] = '[{}:{},{}:{}]'.format(dsec.x1+1,
                     #                                dsec.x2, y1+1, dsec.y2)
 
         adinputs = super().subtractOverscan(adinputs, **params)
@@ -210,7 +265,8 @@ def _get_bpm_filename(self, ad):
         det = ad.detector_name(pretty=True)[:3]
         amps = '{}amp'.format(3 * ad.phu['NAMPS'])
         mos = '_mosaic' if (ad.phu.get(self.timestamp_keys['mosaicDetectors'])
-            or ad.phu.get(self.timestamp_keys['tileArrays'])) else ''
+                            or ad.phu.get(
+                    self.timestamp_keys['tileArrays'])) else ''
         mode_key = '{}_{}_{}{}_{}'.format(inst, det, xbin, ybin, amps)
 
         db_matches = sorted((k, v) for k, v in maskdb.bpm_dict.items() \
@@ -224,8 +280,8 @@ def _get_bpm_filename(self, ad):
             return None
 
         # Prepend standard path if the filename doesn't start with '/'
-        return bpm if bpm.startswith(os.path.sep) else os.path.join(bpm_dir, bpm)
-
+        return bpm if bpm.startswith(os.path.sep) else os.path.join(bpm_dir,
+                                                                    bpm)
 
     def _get_illum_mask_filename(self, ad):
         """
@@ -251,7 +307,8 @@ def _get_illum_mask_filename(self, ad):
         if mode:
             mode = mode.pop()
         else:  # DARK/BIAS (only F2 K-band darks for flats should get here)
-            log.fullinfo("{} not IMAGE or SPECT: no illumination mask".format(ad.filename))
+            log.fullinfo("{} not IMAGE or SPECT: no illumination mask".format(
+                ad.filename))
             return None
 
         try:
@@ -263,7 +320,7 @@ def _get_illum_mask_filename(self, ad):
 
         # illumMask_dict is loaded.
         bpm_dir = os.path.join(os.path.dirname(masks.__file__), 'BPM')
-        key= '{}_{}_{}{}_{}'.format(inst, det, xbin, ybin, amps)
+        key = '{}_{}_{}{}_{}'.format(inst, det, xbin, ybin, amps)
 
         for illumkey in illum_dict.keys():
             if illumkey.startswith(key):
@@ -275,4 +332,5 @@ def _get_illum_mask_filename(self, ad):
 
         log.stdinfo("Retrieved mask: {}".format(mask))
         # Prepend standard path if the filename doesn't start with '/'
-        return mask if mask.startswith(os.path.sep) else os.path.join(bpm_dir, mask)
+        return mask if mask.startswith(os.path.sep) else os.path.join(bpm_dir,
+                                                                      mask)

geminidr/gmos/recipes/qa/recipes_ARC_LS_SPECT.py

@@ -9,6 +9,7 @@
 def makeProcessedArc(p):
     p.prepare()
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.ADUToElectrons()

geminidr/gmos/recipes/qa/recipes_BIAS.py

@@ -19,6 +19,7 @@ def makeProcessedBias(p):
 
     p.prepare()
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.addToList(purpose="forStack")

geminidr/gmos/recipes/qa/recipes_FLAT_IMAGE.py

@@ -20,6 +20,7 @@ def makeProcessedFlat(p):
 
     p.prepare()
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.biasCorrect()

geminidr/gmos/recipes/qa/recipes_FLAT_LS_SPECT.py

@@ -8,6 +8,7 @@
 def makeProcessedFlat(p):
     p.prepare()
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.biasCorrect()

geminidr/gmos/recipes/qa/recipes_IMAGE.py

@@ -18,6 +18,7 @@ def reduce(p):
 
     p.prepare()
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     #p.addIllumMaskToDQ()
     p.addVAR(read_noise=True)
     p.detectSources()

geminidr/gmos/recipes/qa/recipes_LS_IMAGE.py

@@ -17,6 +17,7 @@ def reduce(p):
 
     p.prepare(attach_mdf=True)
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     #p.addIllumMaskToDQ()
     p.subtractOverscan()
     p.ADUToElectrons()

geminidr/gmos/recipes/qa/recipes_LS_SPECT.py

@@ -21,6 +21,7 @@ def reduceScience(p):
     """
     p.prepare()
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.measureIQ(display=True)
@@ -73,6 +74,7 @@ def reduceStandard(p):
     """
     p.prepare()
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.measureIQ(display=True)

geminidr/gmos/recipes/qa/recipes_NS.py

@@ -23,6 +23,7 @@ def reduce(p):
     """
     p.prepare()
     p.addDQ(static_bpm=None)
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.biasCorrect()

geminidr/gmos/recipes/ql/recipes_ARC_LS_SPECT.py

@@ -10,6 +10,7 @@
 def makeProcessedArc(p):
     p.prepare()
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.ADUToElectrons()

geminidr/gmos/recipes/ql/recipes_FLAT_LS_SPECT.py

@@ -10,6 +10,7 @@
 def makeProcessedFlatNoStack(p):
     p.prepare()
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.getProcessedBias()
@@ -28,6 +29,7 @@ def makeProcessedFlatNoStack(p):
 def makeProcessedFlatStack(p):
     p.prepare()
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.getProcessedBias()

geminidr/gmos/recipes/ql/recipes_LS_SPECT.py

@@ -18,6 +18,7 @@ def reduceScience(p):
     """
     p.prepare()
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.getProcessedBias()
@@ -55,6 +56,7 @@ def reduceStandard(p):
     """
     p.prepare()
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.getProcessedBias()

geminidr/gmos/recipes/sq/recipes_BIAS.py

@@ -21,6 +21,7 @@ def makeProcessedBias(p):
 
     p.prepare()
     p.addDQ(static_bpm=None)
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.stackFrames(zero=False)

geminidr/gmos/recipes/sq/recipes_FLAT_IMAGE.py

@@ -22,6 +22,7 @@ def makeProcessedFlat(p):
     """
     p.prepare()
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.getProcessedBias()

geminidr/gmos/recipes/sq/recipes_IMAGE.py

@@ -20,6 +20,7 @@ def reduce(p):
 
     p.prepare()
     p.addDQ()
+    p.maskAmp5()
     p.addVAR(read_noise=True)
     p.overscanCorrect()
     p.getProcessedBias()
@@ -57,6 +58,7 @@ def makeProcessedFringe(p):
     """
     p.prepare()
     p.addDQ()
+    p.maskFaultyAmp(instrument='GMOS-S', bad_amps=5, valid_from='20220128')
     #p.addIllumMaskToDQ()
     p.addVAR(read_noise=True)
     p.overscanCorrect()