Introduction to MOPEX

1
Introduction to MOPEX
David Makovoz, SSC
2
What is MOPEX

• Three aspects in describing a software package
• Algorithm description
• Interpolation, outlier detection, profile
  fittting
• Software design
• Flow charts, use case diagrams, code
  optimization
• User Interface
• What to run, what is the input, how to set
  parameters, what is the output

3
What is MOPEX

• MOsaicking and Point source EXtraction
• Astronomical image processing package developed
  at the Spitzer Science Center
• SSC post-bcd automated pipelines on-line
  processing
• Off-line processing available for download
• http//ssc.spitzer.caltech.edu/postbcd/download-m
  opex.html

4
Minimal Requirements
Minimal input requirements Set of FITS
images with the following set of WCS keywords
BITPIX NAXIS NAXIS1 NAXIS2 CRVAL1 CRVAL2
CRPIX1 CRPIX2 CTYPE1 CTYPE2

• CD1_1
• CD1_2
• CD2_1
• CD2_2
• or
• CDELT1
• CDELT2
• CROTA2

Minimal user requirements

• Basic knowledge of the Unix operating system
  commands
• ls, wc, output redirect gt, etc.
• Ability to edit ASCII files
• Reasonable level of trust in yourself and MOPEX

Ph.D. in Physics or Astronomy, Master in Computer
Science with 10 years of relevant experience
5
Running MOPEX

• Download
• http//ssc.spitzer.caltech.edu/postbcd/download-
  mopex.html
• Untar
• Set MOPEX_INSTALLATION in mopex.csh

6
mopex.csh

• gt pwd
• /local/mopex_032905
• gt vi mopex.csh
• setenv MOPEX_INSTALLATION /loca/mopex_032905
• setenv SIRTF_JAVA MOPEX_INSTALLATION/java
• setenv SIRTF_BIN MOPEX_INSTALLATION/bin
• setenv WRAPPER_UTILS MOPEX_INSTALLATION/bin
• setenv SIRTF_ANC MOPEX_INSTALLATION/source
• set path ( MOPEX_INSTALLATION/bin path )
• if (?LD_LIBRARY_PATH) then
• setenv LD_LIBRARY_PATH MOPEX_INSTALLATION/lib
  LD_LIBRARY_PATH
• else
• setenv LD_LIBRARY_PATH MOPEX_INSTALLATION/lib
  
• endif
• if (?PERL_PATH) then
• else
• setenv PERL_PATH which perl sed
  "s/\(.\)perl/\1/"
• endif

7
Running MOPEX

• Download
• http//ssc.spitzer.caltech.edu/postbcd/download-
  mopex.html
• Untar
• Set MOPEX_INSTALLATION in mopex.csh
• source mopex.csh
• Ready to go
• Run on the command line
• gt overlap.pl -n overlap_IRAC3.nl
• gt mosaic.pl -n mosaic_IRAC2_outlier.nl
• gt apex.pl -n apex_IRAC1.nl
• gt apex_qa.pl -n apex_qa_IRAC1.nl
• Configuration files a.k.a. namelists
• mosaic_outleir.nl, mosaic_mask.nl
• Comes with sample data for testing and
  demonstration
• Documentation available on-line
• Spitzer_mosaic.pdf, Spitzer_apex.pdf,
  MOPEX_FAQ.pdf, etc.

8
Run on Different Levels
I Standalone programs modules. Written in
C/C.
9
Individual Modules

• add2fits fix_coverage
  mosaic_combine_mask pointingrefine
• aperture gaussnoise
  mosaic_covg pointsourceimage
• auto_detect hdr_mask
  mosaic_dual_outlier pointsourceprob
• blend hdrupd8
  mosaic_geom prf_estimate
• c2s_trans hdrupdate
  mosaic_int radhit_stat
• compute_covar imlistarith
  mosaic_int_mask repbadpix
• compute_overlap_corr level
  mosaic_outlier s2c_trans
• crop_stack mask_pointsource
  mosaic_proj sed_fif
• detect meanfilter
  mosaic_reint snestimator
• detect_instrart medfilter
  mosaic_rmask sourcestimate
• detect_mask modefilter
  mosaic_split spectrum
• detect_radhit mosaic_coadd
  outliers_hist sub2fits
• fiducial_image_frame mosaic_coadd_mask
  pixel_area tmasspsc
• fit_radius mosaic_combine
  pmasknow urlget

10
Run on Different Levels
I Standalone programs modules. Written in
C/C. Run on the command line with input on
the command line and/or in namelists. They
can also be inserted as components of user
constructed pipelines.
II Perl scripts main mode.
11
Perl Scripts

• HDR_Split.pl easymosaic.pl
  overlap.pl
• PSEutils.pl fastsortmatch.pl
  overlap_chi2.pl
• aperture.pl fastsortrealmatch.pl
  photo.pl
• apex.pl fiducial_frame.pl
  pointing_refine.pl
• apex_1frame.pl flatfield.pl
  prf_estimate.pl
• apex_qa.pl hdr_mask.pl
  read_isds.pl
• astro.pl mosaic.pl
  score.pl
• bandmerge.pl mosaic_mask.pl
  score_new.pl
• black_spot.pl mosaic_moving.pl
  simulate.pl
• cleanup_deblend.pl mosaic_sed.pl
  simulate_isds.pl
• copy_HDR_keywords.pl mosaic_tpm.pl
  swap_refined_keywords.pl
• cosmetic.pl myscore.pl
  table_1col_stat.pl
• cr_library.pl numbertable.pl
  table_stat.pl

12
Run on Different Levels
I Standalone programs modules. Written in
C/C. Run on the command line with input on
the command line and/or in namelists. They
can also be inserted as components of user
constructed pipelines.
II Perl scripts main mode. Combine individual
modules. Run on the command line with input
in namelists and on the command line. Perl
scripts take care of the interface between the
individual modules.
III Super scripts or batch files. The perl
scripts can be put together into super script for
batch processing. It is useful for multiple
AOR processing, where the same parameters are
used for a set of different data sets.
It is left to users to create such super scripts.
Simple examples included in the package are
the ones used for testing
Run_IRAC1 Run_IRAC3
Run_MIPS70_SED Run_Encke Run_IRAC1_N2403
Run_MIPS70
13
Major Tasks

• Mosaicking with Outlier Detection mosaic.pl,
  mosaic_mask.pl
• Point Source Extraction apex.pl,
  apex_1frame.pl, apex_qa.pl
• PRF (point response function) estimation
  prf_estimate.pl
• Background Matching overlap.pl
• Pointing Refinement pointing_refinement.pl
• Mosaicking and Spectral Extraction of MIPS SED
  observations mosaic_sed.pl

Mosacking with outlier rejection mosaic.pl
14
Individual Modules mosaic_int
image interpolation reprojection, distortion
correction, rotation, resampling to a different
pixel size, different coordinate system,
different projection
15
Individual Modules mosaic_int
Area Overlap Interpolation Drizzle
Interpolation Grid Interpolation Bicubic
Interpolation
gt mosaic_int -n ch4.nl -o interp -mr1 1 -mr2 1
-c covg -tp 18304 -p pmask.fits -fi
FIF.tbl -id Image.lst -iu Sigma.lst -fo fif.tbl
-g interp.tbl
ch4.nl
MOSAICINTIN INTERP_METHOD 1(default),
2(Drizzle),3(Grid),4(Bicubic) INTERP_METHOD
3, GRID_RATIO 2, END
16
Individual Modules mosaic_coadd
add the interpolated images
gt mosaic_coadd -n ch4.nl -o Icoadd -u
interp_Sigma.lst -f fif.tbl -ti
coadd_tile_bcd.txt -g interp_Image.lst -c
interp_covgmap_Image.lst -tu
coadd_Sigma_Tiles_List -to coadd_tiles.tbl
MOSAICCOADDIN TILEMAX_X 500, TILEMAX_Y
500, END
17
Mosaicking Processing Stages and Products
Input
Interpolation
Outlier Detection
Reinterpolation
Coaddition
Mosaic Image, Uncertainty Image, Coverage Map
Combining
18
Putting Modules Together
If you think running MOPEX is complicated,
consider the alternative
gt mosaic_int -n ch4.nl -o interp -mr1 1 -mr2 1
-c covg -tp 18304 -p pmask.fits -fi
FIF.tbl -id Image.lst -iu Sigma.lst -fo fif.tbl
-g interp.tbl
gt mkdir mosaic gt mkdir mosaic/Interp gt mkdir
mosaic/Outlier gt mkdir mosaic/Rmask gt mkdir
mosaic/Reinterp gt mkdir mosaic/Coadd gt mkdir
mosaic/Combine
gt mosaic_outlier -n ch4.nl -box -u
interp_Sigma.list -f fif.tbl -g nterp.tbl -l
box_outlier_Image.lst
gt mosaic_rmask -n ch4.nl -o rmask -cm
covg_map.fits -ib box_outlier_Image.lst -dd -io
outlier_Image.lst
gt mosaic_reint -fp 18304 -o interp -co covg -rm
15 -ui interp_Sigma.lst -ii interp_Image.lst
-p pmask.fits -ri rmask_Image.lst -ud Sigma.list
-id Image.lst -l interp_Image.lst
gt mosaic_coadd -n ch4.nl -o Icoadd -u
interp_Sigma.lst -f fif.tbl -ti
coadd_tile_bcd.txt -g interp_Image.lst -c
interp_covgmap_Image.lst -tu
coadd_Sigma_Tiles_List -to coadd_tiles.tbl
19
Putting Modules Together
Perl scripts put modules together, take care of
input, interface between the modules, keep track
of all the intermediate and final products.
gt mosaic.pl -n ch4.nl
mosaic.pl
20
Namelist - Configuration File - Example

• have_uncertainties 1
• compute_uncertainties_internally 0
• run_fiducial_image_frame 1
• run_mosaic_interp 1
• run_mosaic_outlier 1
• run_mosaic_rmask 1
• run_mosaic_reinterp 1
• run_mosaic_coadder 1
• run_mosaic_combiner 1
• delete_intermediate_products 1
• USE_REFINED_POINTING 0
• MOSAIC_PIXEL_RATIO_X 2
• MOSAIC_PIXEL_RATIO_Y 2
• OUTPUT_DIR output_mosaic
• INTERP_DIR Interp_grid
• COADDER_DIR Coadd_grid

FIDUCIALIMAGEFRAMEIN Edge_Padding 10,
CROTA2 0, END MOSAICINTIN INTERP_METHOD
1(default), 2(Drizzle),3(Grid),
INTERP_METHOD 3, GRID_RATIO
2, END MOSAICOUTLIERIN BOTTOM_THRESHOLD
3., TOP_THRESHOLD 2.5, MIN_PIX_NUM 1,
TILE_XSIZ 500, TILE_YSIZ 500,
END MOSAICCOADDIN TILEMAX_X 500,
TILEMAX_Y 500, END
Parameters
Actions
Output
Input
21
Namelist - Configuration File - Example

• MOSAIC_PIXEL_RATIO_X 2
• COMBINER_DIR Combine_grid
• run_fiducial_image_frame 1
• delete_intermediate_products 1
• USE_REFINED_POINTING 0
• MOSAIC_PIXEL_RATIO_Y 2
• run_mosaic_coadder 1
• SIGMALIST_FILE_NAME SigmaList.txt
• run_mosaic_combiner 1
• MOSAICOUTLIERIN
• BOTTOM_THRESHOLD 3.,
• TOP_THRESHOLD 2.5,
• MIN_PIX_NUM 1,
• TILE_XSIZ 500,
• TILE_YSIZ 500,

FIDUCIALIMAGEFRAMEIN Edge_Padding 10,
CROTA2 0, END IMAGE_STACK_FILE_NAME
IRAC1_ImageList.txt PMask_Fatal_BitPattern
8192 run_mosaic_interp 1 INTERP_DIR
Interp_grid MOSAICINTIN INTERP_METHOD
1(default), 2(Drizzle),3(Grid), INTERP_METHOD
3, GRID_RATIO 2, END DCE_STATUS_MASK_LIST
DmaskList.txt run_mosaic_outlier 1 OUTPUT_DIR
output_mosaic DCE_Status_Mask_Fatal_BitPattern
8192 have_uncertainties 1 MOSAICCOADDIN
TILEMAX_X 500, TILEMAX_Y 500,
END run_mosaic_rmask 1
Parameters
Actions
Output
Input
22
Input
Namelist (configuration file) -
required By default in the cdf/ subdirectory,
which should not be specified.
IMAGE_STACK_FILE_NAME list of input images -
requried SIGMALIST_FILE_NAME list of
uncertainty images DCE_STATUS_MASK_LIST
list of DCE status mask images PMASK_FILE_NAME
pmask image (permanently damaged
pixels)

• One uncertainty image per input image
• One DCE status mask per input image
• One pmask for all input images
• Create a list of images
• gt ls SPITZER_I1_5598208_4bcd.fits gt
  InputImage.txt
• gt ls SPITZER_I1_5598208_4bunc.fits gt
  SigmaImage.txt
• gt ls SPITZER_I1_5598208_4bdmsk.fits gt
  MaskImage.txt
• Make sure the lists have the same number of
  images
• gt wc .txt
• 53 53 1847 ImageList.txt
• 53 53 1953 MaskList.txt
• 53 53 1900 SigmaList.txt

23
Oops!!!
gt mosaic.pl -n cdf/mosaic_outlier_5504256_ch3.nl

Wrapper-script mosaic.pl, Version
5.4 mosaic.pl terminated with error - Input
file not found (cdf/cdf/mosaic_outlier_5504256_ch3
.nl) quitting... System Exit Code (
mosaic.pl) 64
The file is indeed missing gt ls
cdf/cdf/mosaic_outlier_5504256_ch3.nl cdf/cdf/mosa
ic_outlier_5504256_ch3.nl No such file or
directory
sscdev12 mosaic.pl -n mosaic_combine.nl

Wrapper-script mosaic.pl, Version 5.4 The
number of images in ImageList.txt doesn't match
the number of images in MaskList.txt
Sure enough, it does not match gt wc
ImageList.txt 52 52 1812 ImageList.txt gt
wc MaskList.txt 53 53 1953 MaskList.txt
24
Optional Input
Uncertainty Images have_uncertainties 1 user
has to provide the SIGMALIST_FILE_NAME
have_uncertainties 0 compute_uncertainty_inter
nally 1 module snestimator will be
executed have_uncertainties 0 compute_uncertain
ty_internally 0 uncertainties are not used
Mask Bad Pixels DMask http//ssc.spitzer.caltech.
edu/irac/products/bcd_dmask.html DCE_Status_Mask_F
atal_BitPattern 32544 (bits 5,8-14) 32544 25
28 29 210 211 212 213 214
PMask http//ssc.spitzer.caltech.edu/irac/produc
ts/pmask.html PMask_Fatal_BitPattern 18304
(bits 7-10,14) 18304 27 28 29 210
214
25
Data Flow and Storage

• OUTPUT_DIR mosaic
• INTERP_DIR Interp
• COADDER_DIR Coadd
• COMBINER_DIR Combine

run_mosaic_interp 1 run_mosaic_coadder
1 run_mosaic_combiner 1 IMAGE_STACK_FILE_NAME
ImageList.txt
mosaic.pl
Mosaic Image
26
Data Flow and Storage

• OUTPUT_DIR mosaic
• INTERP_DIR Interp
• COADDER_DIR Coadd
• COMBINER_DIR Combine

run_mosaic_interp 1 run_mosaic_coadder
1 run_mosaic_combiner 1 IMAGE_STACK_FILE_NAME
ImageList.txt
run_mosaic_interp 0 run_mosaic_coadder
1 run_mosaic_combiner 1 IMAGE_STACK_FILE_NAME
ImageList.txt
OUTPUT_DIR mosaic INTERP_DIR
Interp COADDER_DIR Coadd COMBINER_DIR
Combine MOSAICCOADDIN TILEMAX_X 500,
TILEMAX_Y 500, END
mosaic.pl
nmimgs 10 Error in allocating memory for Coverage
Image for Tile 0 mosaic_coadd Error Message
0x0071 MALLOC_FAILED.
Mosaic Image
27
Data Flow and Storage

• OUTPUT_DIR mosaic
• INTERP_DIR Interp_bicub
• COADDER_DIR Coadd
• COMBINER_DIR Combine_bicub
• MOSAICINTIN
• INTERP_METHOD 4,
• END

run_mosaic_interp 1 run_mosaic_coadder
1 run_mosaic_combiner 1 IMAGE_STACK_FILE_NAME
ImageList.txt
mosaic.pl
Mosaic Image
28
Basic Mosaicking
Deep Mosaic
Shallow Mosaic
29
Mosaicking
have_uncertainties 1 compute_uncertainties_inter
nally 0 run_medfilter 1 run_detect_radhit
1 run_fiducial_image_frame 1 run_mosaic_interp
1 run_detect_outlier 1 run_mosaic_proj
1 run_mosaic_dual_outlier 1 run_level
1 run_mosaic_covg 1 run_mosaic_outlier
1 run_box_outlier 1 run_mosaic_rmask
1 run_mosaic_reinterp 1 run_mosaic_coadder
1 run_mosaic_combiner 1

• have_uncertainties 1
• compute_uncertainties_internally 0
• run_fiducial_image_frame 1
• run_mosaic_interp 1
• run_mosaic_coadder 1
• run_mosaic_combiner 1

Basic mosaicking
Mosaicking with full outlier detection
30
Outlier Detection

• Four stage outlier detection
• Single Frame Spatial Filtering ( find
  spiky objects)
• Multiframe Temporal Filtering
• Dual Spatial and Temporal
  Filtering
• Box Outlier Spatial and Temporal Filtering

Create Outlier Mask - Rmask Bit 0 - single
frame radhit detection Bit 1 - multiframe
outlier detection Bit 2 - dual outlier
detection Bit 3 - box outlier detection
31
Single Frame Outlier Detection
Bright detections with small areas are classified
as radits (cosmic ray hits) Not very reliable,
run only for areas with single coverage Already
run in the pipeline, bit 9 is set in Dmask
run_medfilter 1 run_detect_radhit
1 MEDFILTER Window_X 45, Window_Y 45,
N_Outliers_Per_Window 500, END DETECT_RADHIT
Segmentation_Threshold 3, Detection_Max_Area
3, Radhit_Threshold 10, END
32
Cosmic Ray Detection
Spatial filtering based on the shape is not
effective
33
Temporal Outlier Detection
Point source Image registration is important
Background Background matching is important
Cosmic ray hits
34
Temporal Outlier Detection
Outputs outlier maps
run_mosaic_outlier 1 MOSAICOUTLIERIN
THRESH_OPTION 1, MIN_PIX_NUM 3,
TILE_XSIZ 500, TILE_YSIZ 500, END
TILE_XSIZ TILE_YSIZ lt sqrt(RAM/(34
bytesmax(Cov)) RAM is the computer memory in
bytes, 3 - input image, input uncertainty,
output outlier map, Cov is the depth of
coverage in the data set.
35
Shallow Coverage
36
Box Outlier Detection
run_mosaic_box_outlier 1 MOSAICOUTLIERIN
BOX_X 5, BOX_Y 3, BOX_MEDIAN_BIAS
1, TILE_XSIZ 500, TILE_YSIZ 500, END
Outputs box outlier maps
37
Dual Outlier Detection
Spatial Filtering
Image1
Detection Map1
Detection Map2
Image2
Interpolation
Temporal Filtering
Interpolated Detection Map1
Dual Outlier Map1
Dual Outlier Map2
Interpolated Detection Map2
Point Source
Cosmic ray hit
38
Dual Outlier Detection
DETECT Detection_Max_Area 1000,
Detection_Min_Area 0, Detection_Threshold
3, Threshold_Type simple, END MOSAICPROJI
N END MOSAICDUALOUTLIERIN MAX_OUTL_IMAGE
2, MAX_OUTL_FRAC 0.95, TILE_XSIZ 500,
TILE_YSIZ 500, END LEVEL Threshold_Ratio
0.5, END
run_medfilter 1 run_detect_outlier
1 run_mosaic_proj 1 run_mosaic_dual_outlier
1 run_level 1
The output is dual outlier maps. One dual outlier
map for each input image. This method is
especially useful for areas of shallow
coverage. It complements the temporal outlier
detection.
39
Create Rmasks
run_mosaic_rmask 1 USE_OUTLIER_FOR_RMASK
1 USE_DUAL_OUTLIER_FOR_RMASK 1 USE_BOX_OUTLIER_F
OR_RMASK 1 MOSAICRMASKIN BOTTOM_THRESHOLD
3, TOP_THRESHOLD 10, MIN_COVERAGE 3,
BOX_BOTTOM_THRESHOLD 3, BOX_TOP_THRESHOLD
10, BOX_MIN_COVERAGE 1, RM_THRESH 0.3,
MAX_COVERAGE 100, REFINE_OUTLIER 1,
REFINE_OUTLIER_THRESH 10, END
Module mosaic_rmask combines the outlier maps and
the dual outlier maps and produces the outlier
masks - Rmasks
Bit 0 - single frame radhit detection Bit 1 -
multiframe outlier detection Bit 2 - dual
outlier detection Bit 3 - box outlier detection
40
Reinterpolation
Interpolation is redone with the module
mosaic_reint using the Rmasks. Only pixels
affected by Rmasks are reinterpolated much
faster than to do it from scratch. This is
followed by mosaic_coadd and mosaic_combine to
create the final mosaic

• run_mosaic_reinterp 1
• RMask_Fatal_BitPattern 7
• MOSAICREINTIN
• no parameters required
• END

41
Oops!!!
gt mosaic.pl -n cdf/mosaic_outlier_5504256_ch3.nl

Wrapper-script mosaic.pl, Version
5.4 add comma to no parameters required at
/stage/ssc-pipe/work/set11/postbcd/davidm/mopex/bi
n/PSEutils.pl line 349.
MOSAICREINTIN no parameters required END
MOSAICREINTIN no parameters required, END
42
Cosmic Ray Removal - Example
Shallow Mosaic
43
Cosmic Ray Removal - Example
Deep Mosaic
44
Using a Subset of Images
45
Modify FIF
run_fiducial_image_frame 1 FIF Fiducial
Image Frame FIF.tbl
\char Date-Time Mar 01, 2006, 104015 \real
CRVAL1 114.202013 \real CRVAL2
65.599497 \real CRPIX1 \real CRPIX2 \real
CROTA2 74.60869 \real CDELT1
-3.39077E-04 \real CDELT2 3.39021E-04 \int
NAXIS1 \int NAXIS2 \char PROJTYPE
TAN \real EXTENT_X 0.297710 \real EXTENT_Y
0.331224
125.0 225.0
439.5 489.0
250 450
878 977
Save as FIF_center.tbl
46
Create Subset Lists
run_mosaic_geom 1 OUTPUT_DIR
./ FIF_FILE_NAME FIF_center.tbl IMAGE_STACK_FILE
_NAME ImageList.txt RMASK_IMAGE_LIST
RmaskList.txt SIGMALIST_FILE_NAME
SigmaList.txt DCE_STATUS_MASK_LIST DmaskList.txt
IMAGE_STACK_FILE_NAME geom_ImageList.txt RMASK_I
MAGE_LIST geom_RmaskList.txt SIGMALIST_FILE_NAM
E geom_SigmaList.txt DCE_STATUS_MASK_LIST
geom_DmaskList.txt
47
Using a Subset of Images
No interpolation needed
run_mosaic_coadder 1 run_mosaic_combiner
1 process_as_subset
1 IMAGE_STACK_FILE_NAME geom_ImageList.txt RMAS
K_IMAGE_LIST geom_RmaskList.txt SIGMALIST_FILE_
NAME geom_SigmaList.txt DCE_STATUS_MASK_LIST
geom_DmaskList.txt
48
Using a Subset of Images
Have to redo interpolation
run_mosaic_interp 1 run_mosaic_coadder
1 run_mosaic_combiner
1 MOSAIC_PIXEL_RATIO_X 4 MOSAIC_PIXEL_RATIO_Y
4 FIF_FILE_NAME FIF_center.tbl IMAGE_STACK_FI
LE_NAME geom_ImageList.txt
49
Benchmarking of Mosaicking

• Interpolation scales with the number of pixels
• 256x256 image without resampling
• 1 GHz Sparc 4GB RAM
• Area Overlap 1.6 sec
• Grid (GRID_RATIO 1) 0.2 sec

50
Background Matching - overlap.pl
have_uncertainties 1 compute_uncertainties_inter
nally 0 run_medfilter 1 run_detect
1 mask_bright 1 run_fiducial_image_frame
1 run_mosaic_interp 1 compute_overlap_correction
1 apply_overlap_correction
1 mosaic_corrected_images 1
Background matching is a two step process. 1 The
images are interpolated to a common grid. 2.
The cumulative pixel-by-pixel difference between
the overlapping areas of all pairs of
interpolated images is minimized with respect to
unknown constant offsets of the input images.
51
Background Matching - Example
IRAC 5.6 micron image of the M82 galaxy
52
Point Source Extraction Processing Stages and
Products
Mosaic Image, Uncertainty Image, Coverage Map
Input
Medfilter
Background Subtracted Mosaic
Non-linear Filtering
PSP Image (point source probability)
Detection
Detection List
Noise Estimation
Noise Mosaic
PRF Fitting
Aperture Photometry
Raw Extraction Table
apex.pl
apex_1frame.pl
Select Good Sources
Extraction Table
53
apex_1frame.pl vs. apex.pl
have_uncertainties 1 run_detect_medfilter
1 run_pointsourceprob 1 run_detect
1 run_gaussnoise 1 run_extract_medfilter
1 run_sourcestimate 1 run_aperture
1 run_select 1 PRF_file_name
Mosaic_PRF.fits OUTPUT_DIR apex_1frame INPUT_
FILE_NAME out/mosaic.fits SIGMA_FILE_NAME
out/mosaic_unc.fits COVERAGE_MAP
out/mosaic_cov.fits
have_uncertainties 1 run_detect_medfilter
1 run_pointsourceprob 1 run_detect
1 run_gaussnoise 1 run_extract_medfilter
1 run_sourcestimate 1 run_aperture
1 run_select 1 MOSAIC_PRF_file_name
Mosaic_PRF.fits PRF_file_name
IRAC1_PRF8x.fits OUTPUT_DIR apex IMAGE_STACK_F
ILE_NAME ImageList.txt SIGMALIST_FILE_NAME
SigmaList.txt DCE_STATUS_MASK_LIST MaskList.txt
apex.pl can create mosaics, but it is faster to
use the results of mosaic.pl
54
Two Background Subtractions
Detection aggressive filtering do not preserve
photometry smaller window Extraction preserve
photometry bigger window
run_detect_medfilter 1 run_extract_medfilter
1 DETECT_MEDFILTER Window_X 21, Window_Y
21, N_Outliers_Per_Window 100, END
EXTRACT_MEDFILTER Window_X 45, Window_Y
45, N_Outliers_Per_Window 500, END
Warning!!! The old namelists for apex.pl and
apex_1frame.pl will not work with the new version
of MOPEX 030106
55
Alternative to Background Subtraction
use_background_subtracted_image_for_fitting 0
SOURCESTIMATE Background_Fit 1, END
use_background_subtracted_image_for_aperture
0 APERTURE Use_Annulus 1, END
56
Point Extraction Table
Column Name srcid detid N_PS RA Delta_RA Dec  Del
ta_Dec Delta_RAD x delta_x y delta_y delta_xy flux
delta_flux bckgrnd
Column Name chi2/dof ps_chi2/dof status SNR PRFPor
tion N_dof FitX FitY depth deblend aperture1 bad_p
ix1 aperture2 bad_pix2 aperture3 bad_pix3
57
Point Source Extraction MIPS24 Example
apex_qa.pl
apex_1frame.pl prf_estimate.pl
58
Point Source Extraction IRAC1 Example
apex_qa.pl
apex.pl PRF images included in MOPEX
59
Pitfalls in Point Source Extraction
Residual images are not always perfect. IRAC
undersampled data, hard to estimate the
PRF. Currently channel 1 PRF is in relatively
good shape, the PRFs for the other channels are
not so good. Background is low, cannot hide the
imperfections, the Poisson noise is higher than
the background. Bright sources are in the
non-linear regime or even saturated. Plot fitted
flux vs. aperture flux. No aperture corrections.
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aperture.pdf
gt aperture n cdf/aperture.nl il
source_list.tbl\ i mosaic_minback.fits o
aperture_minback.tbl
gt aperture.pl n aperture.nl
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Batch Processing
The input to the perl scripts can be given on the
command line.
sscist20 more Run_MIPS70 apex_1frame.pl -n
apex_1frame_mosaic_MIPS70_3865856.nl
apex_qa.pl -n apex_qa_mosaic_MIPS70_3865856.nl
select from MIPS70/3865856/apex_1frame/mosaic_e
xtract.tbl \ for "SNR gt 20 and
deblend ! A and chi2/dof lt 7" \ col
srcid,RA,Dec with header\ into
MIPS70/3865856/apex_1frame/SNR20_noA_chi2.7.tbl
prf_estimate.pl -n prf_estimate_mosaic_MIP
S70_3865856.nl cp MIPS70/3865856/prf/PRF.fits
cal/MIPS70_mosaic_PRF_new.fits
apex_1frame.pl -n apex_1frame_mosaic_MIPS70_386585
6.nl \ -O MIPS70/3865856/apex_1fra
me_new \ -p MIPS70_mosaic_PRF_new.fi
ts apex_qa.pl -n apex_qa_mosaic_MIPS70_38658
56.nl \ -O MIPS70/3865856/apex_q
a_new \ -P MIPS70_mosaic_PRF_new.f
its \ -E MIPS70/3865856/apex_1fram
e_new/mosaic_extract.tbl
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Batch Processing
The input to the perl scripts can be given on the
command line. Useful for multiple AOR batch
processing gt more mosaic_batch.pl _at_aorkey
(45678,45679,45680,456810) for(i0ilt4i)
images ImageList_.aorkey..txt sigmas
SigmaList_.aorkey..txt masks
MaskList_.aorkey..txt system(mosaic.pl -n
mosaic.nl -I images -S sigmas -d masks)
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New Features in MOPEX 030106

• INTERP_METH 1 for run_mosaic_outier
• BOX OUTLIER - run_mosaic_box_outlier
• Two background subtractions in apex.pl and
  apex_1frame.pl -
• the old namelists will not work
• aperture.pdf
• Use annulus for background estimation for
  aperture photometry

64
Thank you