###-Meta-Data-###:Flow=edu.caltech.ipac.sirtf.mopexUI.modules.apex.ApexFlow
###-Meta-Data-###:User-Description=Apex Processing Flow
###-Meta-Data-###:FlowActive=true


have_uncertainties = 1
compute_uncertainties_internally = 0
run_fiducial_image_frame = 1
run_mosaic_interp = 1
run_mosaic_coadder = 1
run_detect_medfilter = 1
run_pointsourceprob = 1
run_detect = 1
run_mosaic_combiner = 1
run_gaussnoise = 1
run_extract_medfilter = 1
run_fit_radius = 1
run_sourcestimate = 1
run_aperture = 1
run_select = 1
verbose = 1
delete_intermediate_files = 0
save_namelist = 1
NICE = 0

use_psp_to_detect = 1
use_background_subtracted_image_for_fitting = 1
use_background_subtracted_image_for_aperture = 0

USE_REFINED_POINTING = 0

select_conditions = "SNR > 6.0 and deblend ! NO and deblend ! PO and deblend ! AO and deblend ! PAO"
select_columns = "srcid,detid,RA,delta_RA,Dec,delta_Dec,delta_RAD,x,delta_x,y,delta_y,delta_xy,flux,delta_flux,SNR,chi2/dof,ps_chi2/dof,status,deblend,aperture1,aperture2,aperture3,bad_pix1,bad_pix2,bad_pix3"

MOSAIC_PRF_file_name = IRAC1_Short_PRF8x_apr06.fits
PRF_file_name = IRAC1_Short_PRF8x_apr06.fits

# Use 1.22 arcsecond pixels
MOSAIC_PIXEL_SIZE_X = -0.00033889
MOSAIC_PIXEL_SIZE_Y = 0.00033889

#OUTPUT_DIR = apex_I1

#IMAGE_STACK_FILE_NAME = I1_bcd.txt
#SIGMALIST_FILE_NAME = I1_bunc.txt
#DCE_STATUS_MASK_LIST = I1_bimsk.txt
# Pmask available at http://ssc.spitzer.caltech.edu/irac/products/pmask.html
#PMASK_FILE_NAME =  cal/I1_pmask.fits

# If using dmask:
#DCE_Status_Mask_Fatal_BitPattern = 32544
# If using imask:
DCE_Status_Mask_Fatal_BitPattern = 28424
PMask_Fatal_BitPattern =  18304
RMask_Fatal_BitPattern = 7

 &FIDUCIALIMAGEFRAMEIN
# Edge_Padding is given in terms of pixels,
   Edge_Padding = 100,
# Orientation used by FIF, A means choose optimum,
   CROTA2 = A,
 &END

&SNESTIMATORIN
# Approximate for 12sec,
#  Gain = 309,
#  Read_Noise = 9.4,
#  Confusion_Sigma = 8.7,
&END

&DETECT_MEDFILTER
  Window_X = 25,
  Window_Y = 25,
  N_Outliers_Per_Window = 100,
&END

&EXTRACT_MEDFILTER
  Window_X = 45,
  Window_Y = 45,
  N_Outliers_Per_Window = 50,
&END

 &GAUSSNOISE
  Window_X = 25,
  Window_Y = 25,
  N_Outliers_Per_Window = 100,
 &END

 &POINTSOURCEPROB
# the Resample Factors are the ratios of the image pixel size,
# to the PRF sampling size,
# the same as for SOURCESTIMATE,
  PRF_ResampleX_Factor      = 8,
  PRF_ResampleY_Factor      = 8,
# the size of the input image to be matched by the PRF, in input image pixels,
  PRF_Xsize        = 3,
  PRF_Ysize        = 3,
 &END

 &PSP_GAUSSNOISE
  Window_X = 25,
  Window_Y = 25,
  N_Outliers_Per_Window = 100,
 &END

&DETECT
#Input_Type: 2 options 'snr_input' and 'image_input',
  Input_Type  = 'image_input',
# the maximum number of pixels in a cluster to be declared a detection,
# for bigger clusters the program raises the detection threshold, 
# and either splits the cluster into 2 or shrinks it down to the required size,
  Detection_Max_Area         = 9,
# the minimum number of pixels in a cluster to be declared a detection,
# smaller clusters are ignored,
  Detection_Min_Area         = 2,
  Detection_Threshold        = 4.0,
# the options for Threshold_Type are 'simple', 'combo' and 'peak',
  Threshold_Type = 'peak',
  Extended_Object_Area = 500,
  &END

 &FIT_RADIUS
 &END

 &SOURCESTIMATE
# 2 options: 'image_list' and 'tile_map',
  InputType = 'tile_map',
# the size of the area in the input image to be fitted with PRF, in,
#input image pixels,
#  Fitting_Area_X = 0,
#  Fitting_Area_Y = 0,
# maximum number of point sources to use in an attempt to deblend a,
#detection,
  Max_Number_PS = 2,
# the maximum acceptable value of chi^2/degree_of_freedom,
  Chi_Threshold = 2,
# positive number excludes point sources in the edge around the input,
#image N_Edge pixels wide from fitting,
# negative number appends an edge around the input images N_Edge pixles,
#wide to include the point sources into fitting,
# default 0,
  N_Edge = 4,
# the Rescale Factors are the ratios of the image pixel size to the PRF,
#sampling size,
  PRF_ResampleX_Factor      = 8,
  PRF_ResampleY_Factor      = 8,
#the number of fitting iterations to perform after Chi_Threshold has,
#been reached, default = 0,
  Max_N_Success_Iteration = 100,
#the relative change in chi2/dof to achieve after Chi_Threshold has been,
#reached, default = 0.001,
  MinimizeFtolSuccess = 0.00001,
   DitherPixelFraction = 0.1,
   DitherFluxFraction = 0.8,
  Background_Fit = 0,
 &END

&MOSAICINTIN
&END

&MOSAICCOADDIN
  TILEMAX_X = 2000, 
  TILEMAX_Y = 2000, 
&END
  
&APERTURE
  N_Apertures = 3,
  Aperture_Radius_1 = 2.0,
  Aperture_Radius_2 = 3.0,
  Aperture_Radius_3 = 5.0,
  Use_Annulus = 1,
  Min_Number_Pixels = 10,
  Annulus_Compute_Type = 'mode',
  Inner_Radius = 12,
  Outer_Radius = 20,
&END