Merge pull request #39 from lsst/tickets/DM-41500

DM-41500: Update to Spectractor v3.0.2

config/auxtel.ini

@@ -4,32 +4,44 @@ DISPERSER_DIR = extractor/dispersers/
 # relative path to throughput directory
 THROUGHPUT_DIR = simulation/AuxTelThroughput/
 
+[pipeline]
+# method to get target centroid, choose among: guess, fit, WCS
+SPECTRACTOR_FIT_TARGET_CENTROID = fit
+# method to get image rotation angle: False, disperser, hessian
+SPECTRACTOR_COMPUTE_ROTATION_ANGLE = disperser
+# deconvolve spectrogram with simple 2D PSF analysis: False, True
+SPECTRACTOR_DECONVOLUTION_PSF2D = True
+# deconvolve spectrogram with full forward model: False, True
+SPECTRACTOR_DECONVOLUTION_FFM = True
+# value of sigma clip parameter for the spectractor deconvolution process PSF2D and FFM
+SPECTRACTOR_DECONVOLUTION_SIGMA_CLIP = 100
+# maximum time per gradient descent iteration before TimeoutError in seconds
+SPECTRACTOR_FIT_TIMEOUT_PER_ITER = 1200
+# maximum time per gradient descent before TimeoutError in seconds
+SPECTRACTOR_FIT_TIMEOUT = 7200
+
 [instrument]
 # instrument name
 OBS_NAME = AUXTEL
 # observatory altitude in km
 OBS_ALTITUDE = 2.66299616375123
 # observatory latitude
 OBS_LATITUDE = -30.2446389756252
-# diameter of the telescope in meter
-OBS_DIAMETER = 1.20
+# effective surface of the telescope in cm**2 accounting for obscuration
+OBS_SURFACE = 9636
 # observation epoch
 OBS_EPOCH = J2000.0
-# systematics on the instrument transmission
-OBS_TRANSMISSION_SYSTEMATICS = 0.005
 # observed object to choose between STAR, HG-AR, MONOCHROMATOR
 OBS_OBJECT_TYPE = STAR
-# telescope transmission file
-OBS_TELESCOPE_TRANSMISSION = calexp_2020031500162-EMPTY_ronchi90lpmm-det000_auxtel_transmission.txt
 # full instrument transmission file
-OBS_FULL_INSTRUMENT_TRANSMISSON = calexp_2020031500162-EMPTY_ronchi90lpmm-det000_auxtel_transmission.txt
-# quantum efficiency of the detector file
-OBS_QUANTUM_EFFICIENCY = calexp_2020031500162-EMPTY_ronchi90lpmm-det000_auxtel_transmission.txt
+OBS_FULL_INSTRUMENT_TRANSMISSON = multispectra_holo4_003_HD142331_AuxTel_throughput.txt
+# systematics on the instrument transmission
+OBS_TRANSMISSION_SYSTEMATICS = 0.005
 # Camera (x,y) rotation angle with respect to (north-up, east-left) system
 OBS_CAMERA_ROTATION = 0
 # Camera (x,y) flip signs with respect to (north-up, east-left) system
 OBS_CAMERA_DEC_FLIP_SIGN = 1
-OBS_CAMERA_RA_FLIP_SIGN = -1
+OBS_CAMERA_RA_FLIP_SIGN = 1
 
 [CCD]
 # size of the image in pixel  # MFL: this number is wrong, and the CCD is not square
@@ -45,23 +57,11 @@ CCD_GAIN = 1.1
 # rebinning of the image in pixel
 CCD_REBIN = 2
 
-[dispersers]
+[spectrograph]
 # distance between hologram and CCD in mm
-DISTANCE2CCD = 175
+DISTANCE2CCD = 181
 # uncertainty on distance between hologram and CCD in mm
-DISTANCE2CCD_ERR = 0.75
-# constructor wavelength to make holograms in mm
-LAMBDA_CONSTRUCTOR = 639e-6
-# approximate effective number of lines per millimeter of the hologram
-GROOVES_PER_MM = 150
-# plate center shift on x in mm in filter frame
-PLATE_CENTER_SHIFT_X = -6.
-# plate center shift on x in mm in filter frame
-PLATE_CENTER_SHIFT_Y = -8.
-# estimate uncertainty on plate center shift on x in mm in filter frame
-PLATE_CENTER_SHIFT_X_ERR = 2.
-# estimate uncertainty on plate center shift on x in mm in filter frame
-PLATE_CENTER_SHIFT_Y_ERR = 2.
+DISTANCE2CCD_ERR = 0.4
 # default value for order 2 over order 1 transmission ratio
 GRATING_ORDER_2OVER1 = 0.1
 
@@ -91,10 +91,12 @@ ROT_ANGLE_MAX = 10
 LAMBDA_MIN = 300
 # maximum wavelength for spectrum extraction (in nm)
 LAMBDA_MAX = 1100
+# spectrum order to extract
+SPEC_ORDER = 1
 
 [background subtraction parameters]
 # half transverse width of the signal rectangular window in pixels
-PIXWIDTH_SIGNAL = 40
+PIXWIDTH_SIGNAL = 20
 # distance from dispersion axis to analyse the background in pixels
 PIXDIST_BACKGROUND = 140
 # transverse width of the background rectangular window in pixels
@@ -103,16 +105,16 @@ PIXWIDTH_BACKGROUND = 40
 PIXWIDTH_BOXSIZE = 20
 
 [PSF]
-# extraction mode: PSF_1D or PSF_2D
-PSF_EXTRACTION_MODE = PSF_2D
-# the PSF model: Moffat or MoffatGauss
+# the PSF model: Gauss, Moffat or MoffatGauss
 PSF_TYPE = Moffat
 # the order of the polynomials to model wavelength dependence of the PSF shape parameters
 PSF_POLY_ORDER = 2
 # regularisation parameter for the chisq minimisation to extract the spectrum
-PSF_FIT_REG_PARAM = 1
+PSF_FIT_REG_PARAM = 0.1
 # step size in pixels for the first transverse PSF1D fit
 PSF_PIXEL_STEP_TRANSVERSE_FIT = 50
+# PSF is not evaluated outside a region larger than max(PIXWIDTH_SIGNAL, PSF_FWHM_CLIP*fwhm) pixels
+PSF_FWHM_CLIP = 2
 
 [detection line algorithm parameters]
 # order of the background polynome to fit

python/lsst/atmospec/processStar.py

@@ -191,14 +191,14 @@ class ProcessStarTaskConfig(pipeBase.PipelineTaskConfig,
         dtype=int,
         doc="Window x size to search for the target object. Ignored if targetCentroidMethod in ('exact, wcs')"
         "XWINDOW internally.",
-        default=100,
+        default=150,
     )
     yWindow = pexConfig.Field(
         dtype=int,
         doc="Window y size to search for the targeted object. Ignored if targetCentroidMethod in "
         "('exact, wcs')"
         "YWINDOW internally.",
-        default=100,
+        default=150,
     )
     xWindowRotated = pexConfig.Field(
         dtype=int,
@@ -401,6 +401,18 @@ class ProcessStarTaskConfig(pipeBase.PipelineTaskConfig,
         "CALIB_SAVGOL_ORDER internally.",
         default=2,
     )
+    transmissionSystematicError = pexConfig.Field(
+        dtype=float,
+        doc="The systematic error on the instrumental transmission. OBS_TRANSMISSION_SYSTEMATICS internally",
+        default=0.005
+    )
+    instrumentTransmissionOverride = pexConfig.Field(
+        dtype=str,
+        doc="File to use for the full instrumental transmission. Must be located in the"
+        " $SPECTRACTOR_DIR/spectractor/simulation/AuxTelThroughput/ directory."
+        " OBS_FULL_INSTRUMENT_TRANSMISSON internally.",
+        default="multispectra_holo4_003_HD142331_AuxTel_throughput.txt"
+    )
     offsetFromMainStar = pexConfig.Field(
         dtype=int,
         doc="Number of pixels from the main star's centroid to start extraction",
@@ -851,6 +863,8 @@ def run(self, *, inputExp, inputCentroid, dataIdDict):
             'CALIB_BGD_WIDTH': self.config.calibBackgroundWidth,
             'CALIB_SAVGOL_WINDOW': self.config.calibSavgolWindow,
             'CALIB_SAVGOL_ORDER': self.config.calibSavgolOrder,
+            'OBS_TRANSMISSION_SYSTEMATICS': self.config.transmissionSystematicError,
+            'OBS_FULL_INSTRUMENT_TRANSMISSON': self.config.instrumentTransmissionOverride,
 
             # Hard-coded parameters
             'OBS_NAME': 'AUXTEL',
@@ -860,11 +874,10 @@ def run(self, *, inputExp, inputCentroid, dataIdDict):
             'OBS_NAME': 'AUXTEL',
             'OBS_ALTITUDE': 2.66299616375123,  # XXX get this from / check with utils value
             'OBS_LATITUDE': -30.2446389756252,  # XXX get this from / check with utils value
-            'OBS_DIAMETER': 1.20,
             'OBS_EPOCH': "J2000.0",
             'OBS_CAMERA_DEC_FLIP_SIGN': 1,
             'OBS_CAMERA_RA_FLIP_SIGN': 1,
-            'OBS_SURFACE': np.pi * 1.2 ** 2 / 4.,
+            'OBS_SURFACE': 9636,
             'PAPER': False,
             'SAVE': False,
             'DISTANCE2CCD_ERR': 0.4,