Aperture photometry using APT - Revision history

Rebull: /* Looking for a cookbook? */

2013-08-07T03:49:15Z

Looking for a cookbook?

Rebull at 03:47, 7 August 2013

2013-08-07T03:47:28Z

Rebull: /* Looking for a cookbook? */

2011-08-16T02:12:18Z

Looking for a cookbook?

Rebull: /* Looking for a cookbook? */

2011-06-29T15:41:07Z

Looking for a cookbook?

Rebull: /* Other Contributions */

2011-06-29T15:37:11Z

Other Contributions

Rebull: /* Other Contributions */

2011-06-29T15:36:21Z

Other Contributions

Rebull: /* Picking an object, Doing the photometry, and Exploring the options */

2011-06-16T22:49:02Z

Picking an object, Doing the photometry, and Exploring the options

Rebull: /* Downloading, Installing, and Starting the Software */

2011-06-16T22:48:32Z

Downloading, Installing, and Starting the Software

Rebull: /* Looking for a cookbook? */

2011-06-12T02:24:57Z

Looking for a cookbook?

Rebull: /* Looking for a cookbook? */

2011-06-02T03:17:15Z

Looking for a cookbook?

@@ Line 63: / Line 63: @@
 #You can put in the aperture correction in APT (under "More settings") here, but be careful to use the right number! (See below.)  If you are absolutely sure you know what you are doing, this is an easy way to get valid photometry out right away.  However, I don't think I have ever done photometry just once. If you do fewer calculations within APT, and more later in the spreadsheet, it is less likely that you will have to redo absolutely everything in the end. The labor intensive part is measuring the fluxes. It's easy to tell Excel to multiply columns of numbers. If you aren't sure if you used the I2 aperture correction when working on the I3 image, you'll have to go back and do it again. If you don't do an aperture correction in APT but instead do it in Excel later, you can easily check/redo your multiplication. Just sayin'.
 #If you want, save your user preferences for your next APT session. You can also save/restore user preferences in separate files for different images/bands, but remember that APT ONLY automatically loads user preferences from hidden file ~/.AperturePhotometryTool/APT.pref, so you will have to explicitly read in the user-preferences file you want for the image you are working on.
-#Do photometry (click on object, recenter, calculate or recalculate values).
+#Do photometry (click on object, recenter, calculate or recalculate values). (If you know the x,y position of your source, rather than struggling to find it on the image, you can type the pixel location into the pixel boxes in APT, but do NOT hit 'snap' (yet), just hit 'recalculate photometry'. Then 'snap' again, and 'recalculate photometry' again.)
 #In another Excel spreadsheet (or tab), write down "source_intensity (sky-subtracted)" because this is the sky minus the scaled background from the annulus. Check your units.  Make absolutely sure you understand what you are doing.
 #Repeat for each object of interest in each band of interest, or create a source list and pass that to APT once you are sure of your parameters.

@@ Line 64: / Line 64: @@
 #If you want, save your user preferences for your next APT session. You can also save/restore user preferences in separate files for different images/bands, but remember that APT ONLY automatically loads user preferences from hidden file ~/.AperturePhotometryTool/APT.pref, so you will have to explicitly read in the user-preferences file you want for the image you are working on.
 #Do photometry (click on object, recenter, calculate or recalculate values).
-#In another Excel spreadsheet (or tab), write down "source_intensity (sky-included)" because this is the sky minus the scaled background from the annulus. Check your units.  Make absolutely sure you understand what you are doing.
+#In another Excel spreadsheet (or tab), write down "source_intensity (sky-subtracted)" because this is the sky minus the scaled background from the annulus. Check your units.  Make absolutely sure you understand what you are doing.
 #Repeat for each object of interest in each band of interest, or create a source list and pass that to APT once you are sure of your parameters.
 #If you didn't do this within APT, in your spreadsheet, multiply measured fluxes by aperture correction (band-dependent -- see below). Be careful that it matches the band you're using!

@@ Line 71: / Line 71: @@
 '''Apertures, sky annuli, and aperture corrections.''' See [[Photometry]] pages for explanation of what this is and why you need it. The aperture corrections are intimately related to the aperture and annulus you used, compared to what the teams used to calibrate the instrument. Which choice you make (from a variety of options provided by the instrument teams) is intimately related to the kind of data you have, whether they are crowded or complex or  relatively clean (see note below).
-*'''IRAC'''. These are listed by the instrument team in terms of '''NATIVE PIXELS'''. The one that I have had the most luck with is the native pixel aperture 3 px, annulus 3-7 px combination. Note that the images from the pipeline resample to half the native pixel size, so this corresponds to 6, 6-14 px in the resampled mosaics, which is what you're using.  If you are using that combination of aperture and sky annulus, the aperture corrections for the four IRAC channels are 1.124, 1.127, 1.143, 1.234, respectively.  Operationally, this means, using IRAC-1 as an example, that the 6/6-14 combination misses 12.4% of the flux, so take the flux you measure using 6/6-14, and multiply it by 1.124.  Do the same thing for the rest of the channels accordingly.
+*'''IRAC'''. These are listed by the instrument team in terms of '''NATIVE PIXELS'''. The one that Luisa has had the most luck with is the native pixel aperture 3 px, annulus 3-7 px combination, because she works in regions with complex structure (see note below). Note that the images from the pipeline resample to half the native pixel size, so this corresponds to 6, 6-14 px in the resampled mosaics, which is what you're using.  If you are using that combination of aperture and sky annulus, the aperture corrections for the four IRAC channels are 1.124, 1.127, 1.143, 1.234, respectively.  Operationally, this means, using IRAC-1 as an example, that the 6/6-14 combination misses 12.4% of the flux, so take the flux you measure using 6/6-14, and multiply it by 1.124.  Do the same thing for the rest of the channels accordingly. For other aperture/annulus combinations, check the [http://irsa.ipac.caltech.edu/data/SPITZER/docs/irac/iracinstrumenthandbook/ IRAC Instrument Handbook] for the other options.
-*'''MIPS'''. These are listed by the instrument team in terms of '''ARCSECONDS'''. The pixel scale of the MIPS-24 pipeline mosaics is 2.45 arcsec per pixel. The instrument teams list a variety of combinations, but I suggest trying 7"/7-13" and 7"/20-32" to see what you get. That works out to be (check me!) 2.85/2.85-5.3 and 2.85/8.16-13.06 px. APT (last I checked anyway) doesn't take fractional pixels for these parameters. So round it. 3/3-5, 3/8-13. (I expect the latter to match the PSF fitting photometry [which is what I did] a little better because the values are closest to integers.) The aperture corrections for these two combinations are 2.05 and 1.61, respectively.  For 70 microns, if anyone actually gets into this, see the [http://irsa.ipac.caltech.edu/data/SPITZER/docs/mips/mipsinstrumenthandbook/50/ MIPS Data Handbook] for the real values.
+*'''MIPS'''. These are listed by the instrument team in terms of '''ARCSECONDS'''. The pixel scale of the MIPS-24 pipeline mosaics is 2.45 arcsec per pixel. The instrument teams list a variety of combinations, but I suggest trying 7"/7-13" and 7"/20-32" to see what you get. That works out to be (check me!) 2.85/2.85-5.3 and 2.85/8.16-13.06 px. APT (last I checked anyway) doesn't take fractional pixels for these parameters. So round it. 3/3-5, 3/8-13. (I expect the latter to match the PSF fitting photometry [which is what I did] a little better because the values are closest to integers.) The aperture corrections for these two combinations are 2.05 and 1.61, respectively.  For 70 microns, if anyone actually gets into this, see the [http://irsa.ipac.caltech.edu/data/SPITZER/docs/mips/mipsinstrumenthandbook/50/ MIPS Instrument Handbook] for the real values.
 [[User:Rebull|Rebull]] 12:46, 25 May 2011 (PDT) -- NOTE on this choice of aperture for IRAC (in star-forming regions like the BRCs or CG4 or other similar regions), because Russ asked last year and I gave him a weaseley answer because I'd forgotten exactly why, and then I just spent 2 days rediscovering the reason ... In this region, and star formation regions in general, there is a LOT of structure in the background and a lot of variation in the sky level. You want to sample the sky as close to your star as possible, because otherwise you end up including in your sky estimate pixels that are of different brightnesses. This results in a lot more scatter in the CMDs. To prove this to yourself, do what I just did -- Do photometry on the same suite of stars in all four bands for 3, 3-7 and 3, 12-20 (another recommended sky/annulus combination from the IRAC team). Go [http://irsa.ipac.caltech.edu/data/SPITZER/docs/irac/iracinstrumenthandbook/28/ check and use properly] the aperture corrections for these two different combinations for the 4 channels. Then, the only difference between your photometry will be the size of the annulus. Plot the  photometry obtained with one annulus ("method 1") against that from the other ("method 2") -- you will need to plot either log(flux densities) or magnitudes. Try also (meth1/meth2) vs. (log) meth1 or some other combination that highlights the differences in the photometry (hard to see if just plotting meth1 vs meth2). Can you see differences, especially at i3i4, where the sky brightness is the most variable?  Try some CMDs too. I find a LOT more scatter in the plots using the larger sky annulus.

@@ Line 70: / Line 70: @@
 #Compare with other people's results. (It may be easier to compare with other people's magnitudes rather than flux densities, because the numbers are smaller.)
-'''Apertures, sky annuli, and aperture corrections.''' See [[Photometry]] pages for explanation of what this is and why you need it. The aperture corrections are intimately related to the aperture and annulus you used, compared to what the teams used to calibrate the instrument.
+'''Apertures, sky annuli, and aperture corrections.''' See [[Photometry]] pages for explanation of what this is and why you need it. The aperture corrections are intimately related to the aperture and annulus you used, compared to what the teams used to calibrate the instrument. Which choice you make (from a variety of options provided by the instrument teams) is intimately related to the kind of data you have, whether they are crowded or complex or  relatively clean (see note below).
 *'''IRAC'''. These are listed by the instrument team in terms of '''NATIVE PIXELS'''. The one that I have had the most luck with is the native pixel aperture 3 px, annulus 3-7 px combination. Note that the images from the pipeline resample to half the native pixel size, so this corresponds to 6, 6-14 px in the resampled mosaics, which is what you're using.  If you are using that combination of aperture and sky annulus, the aperture corrections for the four IRAC channels are 1.124, 1.127, 1.143, 1.234, respectively.  Operationally, this means, using IRAC-1 as an example, that the 6/6-14 combination misses 12.4% of the flux, so take the flux you measure using 6/6-14, and multiply it by 1.124.  Do the same thing for the rest of the channels accordingly.
 *'''MIPS'''. These are listed by the instrument team in terms of '''ARCSECONDS'''. The pixel scale of the MIPS-24 pipeline mosaics is 2.45 arcsec per pixel. The instrument teams list a variety of combinations, but I suggest trying 7"/7-13" and 7"/20-32" to see what you get. That works out to be (check me!) 2.85/2.85-5.3 and 2.85/8.16-13.06 px. APT (last I checked anyway) doesn't take fractional pixels for these parameters. So round it. 3/3-5, 3/8-13. (I expect the latter to match the PSF fitting photometry [which is what I did] a little better because the values are closest to integers.) The aperture corrections for these two combinations are 2.05 and 1.61, respectively.  For 70 microns, if anyone actually gets into this, see the [http://irsa.ipac.caltech.edu/data/SPITZER/docs/mips/mipsinstrumenthandbook/50/ MIPS Data Handbook] for the real values.
-[[User:Rebull|Rebull]] 12:46, 25 May 2011 (PDT) -- NOTE on this choice of aperture for IRAC, because Russ asked last year and I gave him a weaseley answer because I'd forgotten exactly why, and then I just spent 2 days rediscovering the reason ... In this region, and star formation regions in general, there is a LOT of structure in the background and a lot of variation in the sky level. You want to sample the sky as close to your star as possible, because otherwise you end up including in your sky estimate pixels that are of different brightnesses. This results in a lot more scatter in the CMDs. To prove this to yourself, do what I just did -- Do photometry on the same suite of stars in all four bands for 3, 3-7 and 3, 12-20 (another recommended sky/annulus combination from the IRAC team). Go [http://irsa.ipac.caltech.edu/data/SPITZER/docs/irac/iracinstrumenthandbook/28/ check and use properly] the aperture corrections for these two different combinations for the 4 channels. Then, the only difference between your photometry will be the size of the annulus. Plot the  photometry obtained with one annulus ("method 1") against that from the other ("method 2") -- you will need to plot either log(flux densities) or magnitudes. Try also (meth1/meth2) vs. (log) meth1 or some other combination that highlights the differences in the photometry (hard to see if just plotting meth1 vs meth2). Can you see differences, especially at i3i4, where the sky brightness is the most variable?  Try some CMDs too. I find a LOT more scatter in the plots using the larger sky annulus.
+[[User:Rebull|Rebull]] 12:46, 25 May 2011 (PDT) -- NOTE on this choice of aperture for IRAC (in star-forming regions like the BRCs or CG4 or other similar regions), because Russ asked last year and I gave him a weaseley answer because I'd forgotten exactly why, and then I just spent 2 days rediscovering the reason ... In this region, and star formation regions in general, there is a LOT of structure in the background and a lot of variation in the sky level. You want to sample the sky as close to your star as possible, because otherwise you end up including in your sky estimate pixels that are of different brightnesses. This results in a lot more scatter in the CMDs. To prove this to yourself, do what I just did -- Do photometry on the same suite of stars in all four bands for 3, 3-7 and 3, 12-20 (another recommended sky/annulus combination from the IRAC team). Go [http://irsa.ipac.caltech.edu/data/SPITZER/docs/irac/iracinstrumenthandbook/28/ check and use properly] the aperture corrections for these two different combinations for the 4 channels. Then, the only difference between your photometry will be the size of the annulus. Plot the  photometry obtained with one annulus ("method 1") against that from the other ("method 2") -- you will need to plot either log(flux densities) or magnitudes. Try also (meth1/meth2) vs. (log) meth1 or some other combination that highlights the differences in the photometry (hard to see if just plotting meth1 vs meth2). Can you see differences, especially at i3i4, where the sky brightness is the most variable?  Try some CMDs too. I find a LOT more scatter in the plots using the larger sky annulus.
 =Other Contributions=

@@ Line 78: / Line 78: @@
 =Other Contributions=
-One of the students from a 2008 team developed [[file:APTtutorialpresentation.pdf|this very nice APT tutorial presentation]], which may be helpful.
+One of the students from a 2008 team developed [[file:APTtutorialpresentation.pdf]], which is a very nice APT tutorial presentation, which may be helpful.
 One of the 2010 teams developed [[APT Tutorial for Educational Poster]], which may be helpful.

← Older revision		Revision as of 15:36, 29 June 2011
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	=Other Contributions=		=Other Contributions=
		+
		+	One of the students from a 2008 team developed [[file:APTtutorialpresentation.pdf\|this very nice APT tutorial presentation]], which may be helpful.

	One of the 2010 teams developed [[APT Tutorial for Educational Poster]], which may be helpful.		One of the 2010 teams developed [[APT Tutorial for Educational Poster]], which may be helpful.

@@ Line 23: / Line 23: @@
 *curve of growth - how the total flux measured changes as a function of aperture
 *source scatter - range of pixel values within the aperture -- you can explore the effects of too large or small an aperture here.
-*radial profile - circularly averaged slice through the aperture.  The PSF is circularly symmetric, so this allows you to explore the placement of the annulus (is it on top of the Airy ring?) and the level of the background more easily than the aperture slice option above.  This also allows you to investigate whether the source is resolved or saturated.
+*radial profile - circularly averaged slice through the aperture.  The PSF is often roughly circularly symmetric, so this allows you to explore the placement of the annulus (is it on top of the Airy ring?) and the level of the background more easily than the aperture slice option above.  This also allows you to investigate whether the source is resolved or saturated.
 *sky scatter - range of pixel values within the sky annulus -- you can explore the effects of too large or small an annulus, or the influence of nearby sources or nebulosity, here.
 *sky histogram - histogram of pixel values within the sky annulus -- you can explore the effects of too large or small an annulus, or the influence of nearby sources or nebulosity, here.
@@ Line 45: / Line 45: @@
 #Display a FITS image AND automatically execute the source-list tool on it : APT.csh myimage.fits mysourcelist.txt
 Prior to using APT's batch mode, you MUST save user preferences in the default location for the way you want the image displayed and the source-list tool ran (there are various available options).
 =Looking for a cookbook?=

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 '''For a comprehensive introduction to APT, please see [http://www.aperturephotometry.org/aptool/documentation/features-and-functions/ this page].'''  The stuff that is here on the wiki is more skeletal, and is meant to be a quick overview with a focus on what you need as a NITARP user of APT.  As of May 2010, two papers on APT have been submitted to PASP: http://spider.ipac.caltech.edu/staff/laher/apt/paper1.pdf (overview of APT) and
-http://spider.ipac.caltech.edu/staff/laher/apt/paper2.pdf (validation using ground-based data).  You may be interested in these more detailed discussions.
+http://spider.ipac.caltech.edu/staff/laher/apt/paper2.pdf (validation using real data).  You may be interested in these more detailed discussions.
 =Loading an image=