Astroimagej Image Processing And Photometric Extraction For Ultra-Precise Astronomical Light Curves

arXiv:1701.04817v1
[astro-ph.IM]
17
Jan
2017
DRAFT VERSION JANUARY 19, 2017
Preprint typeset using L
A
TEX style emulateapj v. 5/2/11
ASTROIMAGEJ: IMAGE PROCESSING AND PHOTOMETRIC EXTRACTION FOR ULTRA-PRECISE
ASTRONOMICAL LIGHT CURVES (EXPANDED EDITION)
KAREN A. COLLINS
1,2,3
, JOHN F. KIELKOPF
3
, KEIVAN G. STASSUN
1,2
, AND FREDERIC V. HESSMAN
4
Draft version January 19, 2017
ABSTRACT
ImageJ is a graphical user interface (GUI) driven, public domain, Java-based, software package for gen-
eral image processing traditionally used mainly in life sciences fields. The image processing capabilities of
ImageJ are useful and extendable to other scientific fields. Here we present AstroImageJ (AIJ), which pro-
vides an astronomy specific image display environment and tools for astronomy specific image calibration and
data reduction. Although AIJ maintains the general purpose image processing capabilities of ImageJ, AIJ is
streamlined for time-series differential photometry, light curve detrending and fitting, and light curve plotting,
especially for applications requiring ultra-precise light curves (e.g., exoplanet transits). AIJ reads and writes
standard FITS files, as well as other common image formats, provides FITS header viewing and editing, and
is World Coordinate System (WCS) aware, including an automated interface to the astrometry.net web portal
for plate solving images. AIJ provides research grade image calibration and analysis tools with a GUI driven
approach, and easily installed cross-platform compatibility. It enables new users, even at the level of undergrad-
uate student, high school student, or amateur astronomer, to quickly start processing, modeling, and plotting
astronomical image data with one tightly integrated software package.
Subject headings: techniques: image processing, photometric, methods: data analysis
1. INTRODUCTION
In many areas of astronomy, there is a need for image pro-
cessing and analysis capabilities and light curve extraction.
One such general purpose environment is IRAF (Tody 1986,
1993)5
. However, especially for ultra-precise photometry in
fast-paced areas of research such as exoplanet transits and mi-
crolensing, there remains a need for a general, off-the-shelf
integrated analysis environment that is at once sophisticated
yet easy to use. Indeed, citizen science and professional-
amateur collaborations increasingly require robust tools that
can deliver research-grade results while enabling broad us-
ability.
Here we present AstroImageJ (AIJ), an astronomical im-
age analysis software package that is based on ImageJ (IJ;
Rasband 1997-2014), but includes customizations to the base
IJ code and a packaged set of software plugins that provide
an astronomy specific image display environment and tools
for astronomy specific data reduction, analysis, modeling, and
plotting. AIJ and IJ are public domain, open source, Java pro-
grams inspired by NIH Image for the Macintosh computer.
Some AIJ capabilities were derived from the Astronomy plu-
gins package6
. Some astronomical algorithms are based on
code from JSkyCalc written by John Thorstensen of Dart-
mouth College. Because AIJ is Java code, the package is
compatible with computers running Apple OS X, Microsoft
Windows, and the Linux operating system (OS).
AIJ is a general purpose astronomical image processing
1 Department of Physics & Astronomy, Vanderbilt University,
Nashville, TN 37235, USA, karenacollins@outlook.com
2 Department of Physics, Fisk University, Nashville, TN 37208, USA
3 Department of Physics & Astronomy, University of Louisville,
Louisville, KY 40292, USA
4 Inst. f. Astrophysik, Georg-August-Universität Göttingen
5 IRAF is distributed by the National Optical Astronomy Observatories,
which are operated by the Association of Universities for Research in As-
tronomy, Inc., under cooperative agreement with the National Science Foun-
dation.
6 http://www.astro.physik.uni-goettingen.de/∼hessman/ImageJ/Astronomy/
tool, plus it provides interfaces to streamline the interactive
processing of image sequences. The current release (version
3.2.0) includes the following features and capabilities, where
(I) indicates a feature provided by the underlying ImageJ plat-
form, (I+) indicates an ImageJ feature that has been improved,
(A+) indicates a feature based on the Astronomy plugins pack-
age, but with significant new capabilities, and (N) indicates a
new feature that is available in AIJ, but not available in ImageJ
or the Astronomy plugins package:
• (N) Interactive astronomical image display support-
ing multiple image stacks with fast image zoom-
ing and panning, high-precision contrast adjustment,
and pixel data display similar to SAOImage DS9
(Smithsonian Astrophysical Observatory 2000)7
• (N) Live mouse pointer photometer
• (N) Sky orientation of image and pixel scale display in
a non-destructive image overlay
• (A+) Reads and writes FITS images with standard
headers, as well as most other common image formats
(e.g. tiff, jpeg, png, etc.)
• (N) Data Processor facility for image calibration in-
cluding bias, dark, flat, and non-linearity correction
with an option to run in real-time during observations
• (A+) Interactive time-series multi-aperture differential
photometry with detrend parameter extraction, and an
option to run in real-time during observations
• (N) Photometric uncertainty calculations including
source and sky Poisson noise, dark current, detector
7 SAOImage DS9 has been made possible by funding from the Chan-
dra X-ray Science Center (CXC) and the High Energy Astrophysics Science
Archive Center (HEASARC).

2
readout noise, and quantization noise, with automatic
propagation of single-aperture uncertainties through
differential photometry, normalization, and magnitude
calculations
• (N) Comparison star ensemble changes without re-
running differential photometry
• (N) Interactive multi-curve plotting streamlined for dis-
play of light curves
• (N) Interactive light curve fitting with simultaneous de-
trending
• (N) Plate solving and addition of WCS headers to im-
ages seamlessly using the Astrometry.net web interface
• (N) Time and coordinate conversion with capabil-
ity to update/enhance FITS header content (airmass,
BJDTDB, etc.)
• (A+) Point and click radial profile (i.e. seeing profile)
plots
• (N) FITS header viewing and editing
• (N) Astronomical coordinate display for images with
WCS
• (N) Object identification via an embedded SIMBAD in-
terface
• (A+) Image alignment using WCS headers or apertures
to correlate stars
• (N) Non-destructive object annotations/labels using
FITS header keywords
• (I) Mathematical operations of one image on another
or an image stack, and mathematical and logical opera-
tions on single images or image stacks
• (I+) Color image creation
• (N) Optionally enter reference star apparent magnitudes
to calculate target star magnitudes automatically
• (N) Optionally create Minor Planet Center (MPC) for-
mat for direct submission of data to the MPC
AIJ is currently used by most of the ∼ 30 member
Kilo-degree Extremely Little Telescope (KELT; Pepper et al.
2003, 2007) transit survey photometric follow-up team, so
far resulting in 10 planets published (Siverd et al. 2012;
Beatty et al. 2012; Pepper et al. 2013; Collins et al. 2014;
Bieryla et al. 2015; Fulton et al. 2015; Eastman et al. 2016;
Rodriguez et al. 2016; Kuhn et al. 2016), and at least 8 more
in press or in preparation as of this writing. AIJ users on the
team include amateur astronomers, undergraduate and gradu-
ate students, and professional astronomers. AIJ is also used
by the KELT science team to optimize the precision of, and
determine the best detrending parameters for, all follow-up
light curves that are included in the analysis of new planet
discoveries. AIJ is deployed in multiple undergraduate uni-
versity teaching labs and is also used to teach exoplanet tran-
sit analysis to high school students. We and the KELT follow-
up team have verified the accuracy of AIJ against a number
of traditional scientific and commercial photometric extrac-
tion packages, including IRAF, IDL8,9
, and MaxIm DL10
. The
IRAF and IDL photometric capabilities were adapted from
DAOPHOT (Stetson 1987). We do not track the number of
AIJ downloads, but we estimate that there are several hundred
active AIJ users based on AIJ user forum11
statistics.
AIJ’s ultra-precise photometric capabilities are demon-
strated by Collins et al. (2017a), where they achieved an RMS
of 183 and 255 parts per million for the transit model residuals
of the combined and five minute binned ground-based light
curves of WASP-12b and Qatar-1b, respectively, and transit
timing residuals from a linear ephemeris of less than ∼ 30 s.
These results are enabled by a multi-star photometer that al-
lows fixed or variable radius apertures, a variety of options
to calculate sky-background, including sky-background star
rejection, and high precision centroid capabilities, including
the ability to properly centroid on defocused stars. In addi-
tion, AIJ’s interactive GUIs and tightly coupled extraction of
differential photometry and detrend parameters, light curve
plotting, comparison star ensemble manipulation, and simul-
taneous fitting of the data to a transit model and detrending
parameters, enable the user to quickly optimize detrended and
fitted light curve precision.
For example, stars can be added to or removed from the
comparison ensemble (without re-running photometry) and
detrending parameters can be changed instantly by clicking
to enable or disable each one. When a change is made, the
light curve and fitted model plots are automatically updated
and statistical values indicating the goodness of the model fit,
such as RMS and the Bayesian Information Criterion, are in-
stantly updated. These interactive features enable a user to
quickly determine the best aperture settings, comparison en-
semble, and detrend parameter set.
Finally, if AIJ is operated in “real-time” mode during time-
series observations, the images are calibrated, photometry is
extracted, and data are plotted, detrended, and model fitted
automatically as images are written to the local system’s hard
disk by any camera control software package. This capability
works independent of (and does not interfere with) an obser-
vatory’s telescope and camera control software and allows the
user to explore exposure time, defocus, aperture settings, and
comparison star ensemble to ensure high-precision photomet-
ric results in the final post-processed data.
The following sections provide detailed descriptions of the
astronomy specific capabilities of AIJ, as well as detailed de-
scriptions of the AIJ user interface. A peer reviewed abridged
version of this work is also available (Collins et al. 2017b).
The AIJ User Guide, installation packages, and installation
instructions are available for download at the AIJ website12
.
Most of the AIJ user interface panels include “tool-tip” help
messages that optionally pop up when the mouse pointer is
positioned over an item in the display for more than a second.
An AIJ user forum11
is available to facilitate shared support
for the software. AIJ inherits all of the basic image manip-
ulation and analysis functionality from IJ. The IJ website13
provides detailed user guides and descriptions of its function-
8 http://www.harrisgeospatial.com; IDL is a product of Exelis Visual In-
formation Solutions, Inc., a subsidiary of Harris Corporation.
9 http://idlastro.gsfc.nasa.gov
10 http://www.cyanogen.com
11 http://astroimagej.1065399.n5.nabble.com/
12 http://www.astro.louisville.edu/software/astroimagej
13 http://imagej.nih.gov/ij/

3
ality.
2. AIJ OVERVIEW AND BASIC CAPABILITIES
2.1. Toolbar
When AIJ is started, the AIJ Toolbar opens and presents
the eight AIJ-specific toolbar icons labeled as 1-8 in Figure 1.
Each of those icons provides direct access to an AIJ analysis
tool or function. The icon shown depressed and labeled as 1
( ) indicates that AIJ is in astronomy mode. In this mode,
all images open into the astronomical image display mode dis-
cussed in §2.2. Icon 2 ( ) starts single aperture photometry
mode as discussed in §4.1. A double-click on Icon 2 opens the
Aperture Photometry Settings panel discussed in Appendix
A.6. Icon 3 ( ) starts the Multi-Aperture differential pho-
tometry module discussed in §4.2. Icon 4 ( ) clears all la-
bels and apertures from the image display. Icon 5 ( ) starts
the Multi-Plot module discussed in §4.3. Icon 6 ( ) opens
previously saved photometry “measurements tables” (see Ap-
pendix D). Icon 7 ( ) opens the Data Processor panel dis-
cussed in §3. Icon 8 ( ) opens the Coordinate Converter
panel discussed in Appendix A.1.
The 12 icons to the left of the AIJ icons and all of the menu
options are standard IJ tools. These tools can also be used
in AIJ, but normally only the File menu options are used for
typical time-series data reductions. A single image is opened
from the AIJ Toolbar using File→Open. A time-series of im-
ages is opened into an image “stack” from the AIJ Toolbar us-
ing File→Import→Image Sequence. Alternatively, an image
or an image sequence can be opened by dropping the file or
folder, respectively, onto the bottom area of the AIJ Toolbar,
or OS options can be enabled to automatically open images
into AIJ in response to a double click on the file in an OS
window. If all images in a sequence will not fit into the com-
puter memory allocated to AIJ, the sequence can be opened
as a “virtual stack”. In this mode, the stack of images can be
processed as if all images exist in memory, but AIJ loads only
the single active/displayed image into memory. Virtual stacks
perform more slowly than standard stacks, but memory re-
quirements are minimal. All AIJ settings are persistent across
sessions. Settings for specific configurations can be saved and
reloaded later as needed.
2.2. Astronomical Image Display
Many popular image file formats are supported by AIJ,
including the Flexible Image Transport System (FITS;
Wells et al. 1981; Pence et al. 2010) file format. The astro-
nomical image display shown in Figure 2 is unique to AIJ and
offers numerous display options useful to astronomers. An
image can also be displayed in plain IJ display mode, which
has no contrast controls, analysis controls, or mouse pointer
data decorating the image, by disabling the option at Pref-
erences→Use astro-window when images are opened in the
menus above an open image. The setting will apply to any
new images that are opened. To return to astronomical image
display mode, click on the astronomy mode icon ( ) in the
AIJ toolbar. Then left-click in an open image. To make the
change permanent, re-enable the option at Preferences→Use
astro-window when images are opened.
In astronomy mode, a menu system is available at the top
of the image display window to provide access to all astron-
omy specific AIJ features. A row of quick access icons for
control of frequently used image display options and image
analysis tools is located directly above the image. Pixel and
World Coordinate System (WCS; Greisen & Calabretta 2002;
Calabretta & Greisen 2002; Greisen et al. 2006) information
describing the image location pointed to by the mouse cursor
is displayed in the three rows above the quick access icons.
Image and WCS format information is displayed in the space
under the image menus. A non-destructive image overlay op-
tionally displays active apertures (green = target, red = com-
parison), object annotations, plate scale, and image orienta-
tion on the sky.
The Scale menu above an image display offers options for
the control of image brightness and contrast (i.e. image scale).
By default, image scale is set automatically and linearly maps
the pixel values in the range mean−0.5σ through mean+2σ
to 256 shades of gray running from black through white.
The negative image icon ( ) reverses the mapping to white
through black. Several alternate mappings are available at
the AIJ Toolbar menu item Image→Lookup Tables. The auto
scale range can be customized at Scale→set auto brightness
& contrast parameters. Image scale can be manually con-
trolled using the interactive histogram and direct entry fields
under the image. The histogram region highlighted in blue
indicates the range of pixel values currently being mapped to
black through white (by default) in the image display. The
controls on the left and right of the blue highlighted region
can be dragged left and right, or the entire blue region can be
dragged, to change the image scale. The image updates in real
time. The four boxes under the histogram labeled min, black,
white, and max indicate the minimum pixel value displayed in
the histogram, the pixel value mapped to black in the image,
the pixel value mapped to white in the image, and the maxi-
mum pixel value displayed in the histogram. By default, the
min and max values are set to the minimum and maximum
pixel values in the displayed image. To provide finer control
of the image scale settings, the min and max histogram values
can be manually set by the user after enabling Scale→Use
fixed min and max histogram values. A red border indicates
which boxes are available for user input. The <Enter> key
must be pressed to activate a new user entered value. The
auto scale icon above an image ( ) restores the auto scale
settings. If Scale→auto brightness and contrast is enabled, a
change to a displayed image or a change of which image is
displayed from a stack resets the image scale to the automatic
settings. To retain manually set values of black and white, en-
able Scale→fixed brightness and contrast. To automatically
set min and black to the minimum pixel value and white and
max to the maximum pixel value, select Scale→full dynamic
range. Image scale may also be adjusted by a right-click and
drag in the image. Dragging up and down changes the bright-
ness. Dragging left and right changes the contrast.
The zoom setting of an image display is most easily
changed by rolling a mouse wheel, if available, to zoom the
image in and out at the mouse pointer. Alternatively, image
zoom changes, centered at the last clicked location in an im-
age, can be controlled using the four magnifying glass icons
on the right side of the quick access row, or by pressing the up
and down arrows on the keyboard. Zoom can also be changed
with a control-left-click or control-right-click in the image to
zoom in or out, respectively, at the clicked point. Image pan
is controlled by a left-click and drag in the image. By default,
a middle-click in an image centers the clicked location in the
image display. However, this feature can be disabled using
the menu option Preferences→Middle click centers image at
clicked position. Right-click and drag in an image reports arc-
length in place of integrated counts in the lower-right-hand

4
FIG. 1.— The AIJ Toolbar. The icon shown depressed and labeled as 1 indicates that AIJ is in astronomy mode. In this mode, all images open into the
Astronomical Image Display mode discussed in §2.2. Icon 2 starts the single aperture photometry mode discussed in §4.1. A double-click on Icon 2 opens the
Aperture Photometry Settings panel discussed in Appendix A.6. Icon 3 starts the Multi-Aperture photometer module discussed in §4.2. Icon 4 clears all labels
and apertures from the image display. Icon 5 starts the Multi-Plot module discussed in §4.3. Icon 6 opens previously saved photometry “measurements tables”
(see Appendix D). Icon 7 opens the Data Processor panel discussed in §3. Icon 8 opens the Coordinate Converter panel discussed in Appendix A.1.
box above an image. Alt-left-click near an object to produce
an azimuthally averaged radial profile (i.e. a seeing profile)
plot. See Appendix A.5 for more radial profile plot details.
The View menu above an image provides settings to invert
the display of an image in x and/or y. The View menu also
provides options to enable or disable the display of the zoom
indicator, the X, Y, N, and E directional arrows, and the image
plate scale indicators in the image overlay. If WCS header
information is available, AIJ automatically calculates the x-
and y-axis plate scales and the orientation of the image on
the sky. If no WCS information is available, the image scale
and orientation on the sky can be set manually at WCS→Set
pixel scale for images without WCS and WCS→Set north and
east arrow orientations for images without WCS, respectively.
Image scale and orientation can be extracted from an image
with WCS headers and stored in the manual settings by using
the menu option WCS→Save current pixel scale and image
rotation to preferences. This option is useful for cases where
at least one image in a time-series has been plate-solved, but
others have not.
The blue aperture shown near the center of Figure 2 moves
with the mouse pointer. As the mouse pointer is moved
around in the image, the value of the pixel at the mouse
pointer and the peak pixel value and background-subtracted
integrated counts (see §4.1) within the mouse pointer aper-
ture are updated in the right-hand column of data displayed
above the image. This interactive mouse photometer helps
to quickly assess which stars are suitable comparison stars
during differential photometry set up. When AIJ is used in
real-time data reduction mode (see §3), the mouse photome-
ter helps to quickly determine an appropriate image exposure
time and telescope defocus setting.
If a time-series of images is opened as an image stack, a
scroll bar is displayed directly under the image as shown in
Figure 2. The scroll bar can be moved left and right, or the
left and right arrow keys on the keyboard can be used to dis-
play different images from the sequence. The right-pointing
“play” icon to the left of the scroll bar will animate the image
sequence at a predefined rate. The rate is set by right-clicking
on the play icon.
The annotation feature allows objects to be labeled non-
destructively in an image overlay. New object annotations
can be added manually, or if the image has WCS information,
target names can be extracted from SIMBAD and displayed
by right-clicking on an object. Annotations can be edited or
deleted by right-clicking near the annotated object (i.e. be-
low and near the center of the annotation text). The annota-
tions can also be stored in the FITS header for display at a
later time. The Annotate menu provides annotation and re-
lated FITS header storage options. The annotate icon above
an image ( ) toggles the display of annotations in the image
overlay.
The second through fifth icons shown as depressed in Fig-
ure 2 control which components of apertures (see §4.1) are
displayed and whether an aperture is to be centroided on the
nearest star when it is placed. The delete slice icon ( ) re-
moves the currently displayed slice from a stack, but does not
remove the image from permanent storage. The clear overlay
icon ( ) clears all apertures and annotations from the image
overlay. The show apertures icon ( ) displays stored aper-
tures (see §4.2) in the image overlay. The clear measurements
icon ( ) clears all data from the measurements table (see
Appendix D). The Multi-Aperture ( ), Stack-Aligner ( ),
Astrometry ( ), and FITS header editor ( ) icons provide
access to features described in §4.2, Appendix A.4, Appendix
A.3, and Appendix A.2, respectively.
2.3. Utilities, Algorithms, and Measurements Tables
In Appendix A we describe the following integrated utili-
ties: Coordinate Converter (A.1), FITS Header Editor (A.2),
Astrometry/Plate Solving (A.3), Image Alignment (A.4), Ra-
dial Profile plotting (A.5), Photometry Settings (A.6), Data
Processor FITS Header Updates (A.7), and Save All (A.8).
In Appendix B we describe photometric uncertainty calcu-
lations. In Appendix C we describe the optional apparent
magnitude and apparent magnitude uncertainty calculations.
In Appendix D we describe the measurements table used to
store photometric results.
3. DATA PROCESSOR: IMAGE CALIBRATION AND
REDUCTION
The Data Processor (DP) module provides tools to automate
the build of master calibration images, automate calibration
of image sequences, and optionally perform differential pho-
tometry and light curve plotting. The DP module is started by
clicking the DP icon ( ) on the AIJ Toolbar (labeled 7 in Fig-
ure 1). The user interface is shown in Figure 3. DP operates
much like a script in that it processes selected calibration and
science images in a user defined manner. Fields are provided
to define the directory/folder locations and filename patterns
of data to be processed. Checkboxes are provided to enable
various tasks that can be included in the data processing ses-
sion. Disabling certain checkboxes will automatically disable
other related input fields as appropriate to help the user under-
stand which input fields are interconnected.

5
FIG. 2.— The AIJ image display. A wide range of astronomy specific image display options and image analysis tools are available from the menus, quick
access icons, and interactive histogram. See text for details.

6
The path and image filename pattern matching the raw sci-
ence images to be processed are set in the Science Image Pro-
cessing sub-panel. File paths and names can be dragged and
dropped from the OS into a field of the DP panel to minimize
typing. The number of files matching the pattern at the speci-
fied path shows in the right-hand column labeled Totals. The
science images can be further filtered based on the image se-
quence numbers in the filename by entering minimum and/or
maximum numbers in the second row of the sub-panel.
Master bias, dark, and flat images can be created by en-
abling the Build options and entering the paths and filename
patterns matching the raw calibration images on the Build
lines of the Bias Subtraction, Dark Subtraction, and Flat Divi-
sion sub-panels, respectively. The master calibration files are
saved using the path and filename specifications in the Enable
lines of the three sub-panels. As with the science images, the
number of files matching the pattern for each raw calibration
image set shows in the right-hand column labeled Totals. If
one or more of the master calibration files have been previ-
ously built, the Build option in the respective sub-panel(s) can
be disabled to skip those master build steps. In this case, the
master calibration path and filename should be specified on
the Enable line of the respective sub-panel. AIJ provides the
option to either average or median combine the raw images
when producing the master calibration files. If the dark sub-
traction scale option is enabled, the master dark pixel values
are scaled by to the ratio of the science image exposure time to
the master dark image representative exposure time. The dark
subtraction deBias option controls whether the master dark is
saved with or without the bias image subtracted, and specifies
whether the master dark image being used for dark subtrac-
tion was saved with or without the bias image subtracted. The
dark scale and deBias options are available only if bias sub-
traction is enabled.
Bias subtraction, dark subtraction, and flat-field division
can be individually selected using the Enable option in the
corresponding sub-panel. The master calibration image paths
and filenames are specified on the Enable line of each sub-
panel. When a file path has been entered correctly and
matches a stored file, a count of “1” will appear in the Totals
column.
The Image Correction sub-panel provides the option to im-
plement CCD nonlinearity correction. This option replaces
each pixel’s ADU value in the bias-subtracted dark, flat, and
science images with the corrected ADU value
ADUcorrected = c0 + c1ADU + c2ADU2
+ c3ADU3
, (1)
where the coefficients cn describe the non-linear behavior of
the detector. Bias subtraction must be enabled and a master
bias image specified to enable the use of non-linearity correc-
tion. The Remove Outliers option uses thresholded median fil-
tering to remove artifacts from science images. This option is
useful for improving the cosmetic appearance of images (e.g.
to clean cosmic ray hits and/or hot and cold pixels). How-
ever, we strongly suggest that this option not be used when
calibrating images for photometric extraction since it can un-
predictably impact the results.
The FITS Header Updates sub-panel General option en-
ables the calculation of new astronomical data (e.g. airmass,
time in BJDTDB, target altitude, etc.) and the addition of
those data to the calibrated science image’s FITS header (see
Appendix A.7 for set up details). The Plate Solve option en-
ables astrometry and the addition of the resulting WCS data
to the calibrated (and optionally to the raw) science image’s
FITS header. Click the Astrometry Settings icon ( ) in the
FITS Header Updates sub-panel to access the astrometry set
up options discussed in Appendix A.3.
The Save Calibrated Images sub-panel provides file format
and file naming options for saving calibrated images. The
16 and 32 options specify that the calibrated images be saved
in 16-bit integer or 32-bit floating point format, respectively.
The Sub-dir box allows the specification of an optional subdi-
rectory of the science image directory to be used when saving
the calibrated science images. The Suffix box allows the spec-
ification of an optional suffix to be appended to the raw sci-
ence image file name when saving calibrated science images.
The Format box allows the specification of a file format to use
when saving the calibrated science images. If this box is left
blank, the raw science image format is used. The Format box
tool-tip shows all available file formats.
The Post Processing sub-panel provides options to run
Multi-Aperture (see §4.2) and Multi-Plot (see §4.3) after each
image is calibrated to perform differential photometry and
display a light curve as the image data are processed. This
feature is particularly useful for real-time reduction of data
at the telescope. Other options allow the current light curve
plot and image display to be written to a file after each sci-
ence image is calibrated. These images can be used to update
websites to show the progress of observations.
The Control Panel sub-panel provides control over the mas-
ter calibration build and image calibration process. If the
Polling Interval is set to zero, a click on the START button
will build any specified calibration files and process all spec-
ified science images. Then DP will return to the stop state.
This mode is ideal for post-observation calibration of data.
To calibrate data in real-time, the Polling Interval is set to a
positive number of seconds t. After clicking on START in this
mode, all science images matching the file name and num-
ber filters will be processed, and then DP will search for new
files matching the pattern every t seconds. If DP is operating
in this mode while observations are underway, calibration of
a new image written from the camera will be started within
t seconds, and optionally processed by Multi-Aperture and
Multi-Plot to update the light curve plot. After START has
been clicked, processing can be suspended by clicking on the
PAUSE button. In pause mode, the START button is labeled
CONTINUE. A click on the CONTINUE button resumes pro-
cessing, or a click on the RESET button returns DP back to the
original state. Another click on the START button will begin
processing all specified data again.
A click on the Aperture Settings button ( ) in the Con-
trol Panel sub-panel opens the Aperture Photometry Settings
panel discussed in Appendix A.6. A click on the Change
Apertures button ( ) causes the Multi-Aperture Measure-
ments set up panel discussed in §4.2 to open the next time the
START button is pressed. If the Change Apertures button is
not clicked after the RESET button is clicked, the same aper-
tures and aperture locations from the previous DP run will
be used the next time the START button is clicked (i.e. the
Multi-Aperture Measurements set up panel will not open be-
fore multi-aperture photometry starts). The Clear Measure-
ments Table Data button ( ) allows the user to clear all
data from the measurements table at any time. If the Clear
Measurements Table Data button is not clicked before start-
ing a new DP run, new measurements will be appended to
any existing measurements in the table. The number of im-
ages processed and the number of images remaining to be

7
processed are displayed in the Totals column of the Control
Panel sub-panel.
A detailed log of all processing steps with timestamps is
created by default. The log function can be disabled by dese-
lecting the DP menu item View→Show log of data processing
history. The timestamps can be enabled or disabled in the
same menu.
4. ULTRA-PRECISE PHOTOMETRY AND LIGHT
CURVE CAPABILITIES
AIJ provides interactive interfaces for single aperture pho-
tometry and multi-aperture differential photometry. The dif-
ferential photometry interface is designed to automatically
process a time-series of images and measure the light curves
of exoplanet transits, eclipsing binaries, or other variable
stars, optionally in real time at the telescope.
4.1. Single Aperture Photometry
Single aperture photometry measures the flux from a source
within a predefined region of interest in an image referred to
as an aperture. AIJ currently supports circular apertures only.
A representation of an object’s flux in the aperture, referred to
as net integrated counts, is calculated by summing all of the
pixel values within the aperture after subtracting an estimate
of the background flux near the aperture. The background flux
is estimated from the pixel values in a background annulus
centered on the aperture.
Single aperture photometry can be performed by simply
placing the mouse pointer near the center of an object in an
image. The net integrated counts within the mouse pointer
aperture are shown in the Int Cnts display area above the im-
age. The aperture and background regions are set by double
clicking the single aperture icon ( ) on the toolbar, or sin-
gle clicking the set aperture icon ( ) above an image. The
mouse pointer photometer calculates net integrated counts by
summing all of the pixel values in the mouse pointer aper-
ture after subtracting the average value of the sky background
annulus from each pixel value.
The results of a single aperture measurement can be
recorded in a “measurements table” (see Appendix D) by en-
abling the single aperture icon ( ) on the toolbar and then
left-clicking near a star. Alternatively, shift-left-click near a
star (without enabling single aperture photometry mode) as a
short cut for single aperture photometry. These two methods
of performing single aperture photometry can optionally use
the more sophisticated centroid and sky background measure-
ment algorithms described in §4.2.
An azimuthally averaged radial profile of an object can be
plotted by left-clicking near the object in an image, and then
selecting Analyze→Plot seeing profile in the menus above the
image display. As a short cut, alt-left-click near an object to
produce the plot. If centroid is enabled, the radial profile will
be centered on the object. Click the Save Apertures button in
the plot to use the aperture radii determined from the radial
profile. See Appendix A.5 for more details.
AIJ calculates photometric error as described in Appendix
B. For proper error calculation, the gain, dark current, and
read out noise of the CCD detector used to collect the data
must be entered in the Aperture Photometry Settings panel
(see Appendix A.6).
4.2. Multi-Aperture Differential Photometry
Differential photometry measures the flux of a target star
relative to the combined flux of one or more comparison stars.
The differential measurement is conducted by performing sin-
gle aperture photometry on one or more target stars and one or
more comparison stars. Then a target star’s differential flux is
calculated by dividing the target star’s net integrated counts,
FT , by the sum of the net integrated counts of all compari-
son stars (i.e. the sum of FCi , where i ranges from 1 to the
number of comparison stars n). The calculation is:
rel flux T j =
FT
Pn
i=1 FCi
, (2)
where j indicates the target star aperture number and i in-
dexes all comparison star aperture numbers. A measurements
table data column labeled rel flux T j contains the differen-
tial flux measurement for target star aperture j. The terms
relative flux and differential flux are used in this work and in
AIJ interchangeably. Differential photometric error is calcu-
lated as described in Appendix B. For proper error calculation,
the gain, dark current, and read out noise of the CCD detec-
tor used to collect the data must be entered in the Aperture
Photometry Settings panel (see Appendix A.6).
AIJ also calculates differential flux for each comparison star
aperture by comparing the flux in its aperture to the sum of the
flux in all other comparison star apertures. The calculation is:
rel flux C j =
FCj
Pn
i=1 FCi , i 6= j
, (3)
where j indicates the comparison star aperture number for
which differential flux is being calculated and i indexes all
comparison star aperture numbers. A measurements table
data column labeled rel flux C j contains the differential flux
measurement for comparison star aperture j.
Multi-Aperture (MA) automates the task of performing dif-
ferential photometry on a time-series of images. Various set-
tings are presented in a set-up panel, and then the target and
comparison star apertures are placed and adjusted interac-
tively by clicking near stars directly in the image display. The
MA module is launched by clicking the MA icon ( ) above
an image or in the AIJ Toolbar. The Multi-Aperture Measure-
ments set-up panel shown in Figure 4 opens. The top two
scroll bars allow the user to set the range of images to be pro-
cessed. The three scroll bars immediately below allow the
user set the aperture radius, the inner radius of the sky back-
ground region, and the outer radius of the sky background
region, all in units of pixels.
The Use previous apertures... option allows the previously
defined set of apertures to be re-used. Aperture definitions
can also be stored and reopened from disk in the File menu
of the image display. If WCS headers are available and the
Use RA/Dec... option is selected, the saved apertures will be
placed according to RA and Dec rather than by x and y pixel
coordinates. If the Reposition aperture to object centroid op-
tion is selected, a centroid algorithm will attempt to center the
aperture on the nearest star.
The Remove stars from background option enables itera-
tive 2σ cleaning of the sky-background region. The itera-
tion continues until the mean ADU of the pixels remaining
in the background set converges or the maximum number of
allowed iterations has been reached without convergence. The
sky background pixels remaining after the cleaning operation
are used to calculate and remove the sky background at each
pixel in the aperture. If the Assume background is a plane op-
tion is selected, AIJ fits a plane to the remaining pixels in the
background region and subtracts the value of the plane at each

8
FIG. 3.— The Data Processor panel. Data Processor automates the building of master calibration files, calibration of a time series of images, and optionally
performs differential photometry and light curve plotting. See text for more details.
pixel within the aperture to remove the sky background con-
tribution. Otherwise, AIJ subtracts the mean of the remaining
pixels in the background annulus from each pixel in the aper-
ture.
If the Vary photometer aperture radius based on FWHM
option is enabled, the aperture radius used in an individual
image of a time-series is equal to the product of the user spec-
ified FWHM factor and the average full width at half maxi-
mum (FWHM) from all apertures in that image. This mode
may improve photometric precision when seeing varies sig-
nificantly or telescope focus drifts within a time-series. If the
FWHM factor is set to “0.00”, an azimuthally averaged radial
profile (see Appendix A.5), centered on the aperture, is used
to determine the aperture radius based on the Radial profile
mode normalized flux cutoff value specified. In this mode, the
aperture radius used in an image is equal to the distance from
the center of the aperture at which the radial profile value is
equal to the specified normalized flux cutoff. The variable
aperture modes should not be used in crowded fields since the
changing aperture radius will worsen the effects of variable
amounts of contaminating flux blending into the aperture as
seeing changes.
If the Prompt to enter ref star apparent magnitude option
is enabled, the apparent magnitude of target aperture sources
will be calculated from user entered apparent magnitudes of
one or more comparison aperture sources. The target aperture
apparent magnitude data can be formatted to submit to the Mi-
nor Planet Center using the Multi-plot Main panel menu item
File→Create Minor Planet Center format. See Appendix C
for details on the use of the apparent magnitude feature.
The Aperture Settings button at the bottom provides access
to two panels containing detailed settings for the photomet-
ric measurements (see Appendix A.6). When all options have
been set, the Place Apertures button causes the set-up panel
to close and the program waits for the aperture positions to
be identified by user clicks near stars in the first image of the
time-series. If the Use previous apertures... option is enabled,
the user clicks near the first star in the set (usually the primary
target star), and all other apertures are placed relative to the
first aperture. If the Use RA/Dec... option is also enabled, no
clicks are required to apply the stored apertures since they are
placed automatically at the calculated pixel locations corre-
sponding to the stored WCS coordinates. If photometry set-
tings (e.g. aperture radii) need to be refined during aperture
placement, click the set aperture icon ( ) above the image
display.
By default, a help panel opens that describes actions avail-
able at each step during aperture placement. By default, the
first left-click in an image places a target star aperture and
all other clicks place comparison star apertures. Using shift-
left-click reverses the sense of the default aperture type when
placing new apertures. A shift-left-click in an existing aper-
ture changes it from target to comparison, and vice-verse. A
left-click inside an existing aperture deletes the aperture. An
aperture can be moved by left-clicking inside it and dragging
it to a new position. Other options are available as listed in

9
FIG. 4.— The Multi-Aperture Measurements set up panel. Multi-Aperture automates the task of performing differential photometry on a time-series of images.
Various settings are available in the set-up panel, and then the apertures are placed and adjusted interactively by clicking near stars directly in the image display.
See text for more details.
the context sensitive help panel.
When all apertures have been defined as desired, a right-
click or press of the <Enter> key will start the automated
differential photometry process on all images defined in the
set-up panel. If the Use RA/Dec... option is enabled, aper-
tures will first be positioned in each image of the series ac-
cording to the WCS information in the image header. If not,
the aperture placements start on each subsequent image in the
series at the same place in x, y space as in the previous image.
In both cases, if centroid is enabled for a particular aperture,
the centroid function will attempt to center the aperture on
the nearest star. For telescopes with poor tracking/guiding or
requiring a meridian flip during the time-series, the images
should be plate solved so that the Use RA/Dec... option can
be enabled to properly find the initial aperture placements in
each image.
The centroid function can be enabled or disabled on a per
aperture basis. An alt-left-click in an existing aperture inverts
the sense of centroid for that aperture. An aperture with cen-
troid enabled has a plus sign showing at its center. If the first
aperture has the centroid function enabled, all non-centroided
apertures will move from one image to the next based on the
average movement of all centroided apertures. This allows
apertures to be placed around faint stars that are near bright
stars that would normally capture the aperture if centroid were
enabled.
The photometry data is written to a “measurements table”
(see Appendix D) and optionally plotted by the Multi-Plot
program as MA progresses through the time-series. If MA is
run a second time duing the same AIJ session, the new mea-
surements will be appended to the existing measurements in
the measurements table. To clear the measurements table be-
fore the second run, click the clear measurements icon ( )
above the image display.
4.3. Multi-Plot
Multi-Plot (MP) provides a multi-curve plotting facility that
is tightly integrated with differential photometry and light
curve fitting. MA can automatically start MP, or MP can be
manually started by clicking the MP icon ( ) on the AIJ
Toolbar. If a measurements table has been created by MA
or opened from the OS, MP will automatically create a plot
based on the last plot settings. Alternatively, plot templates
can be saved and restored to easily format commonly created
plots. Plotting controls are accessed in two main user inter-
face panels.
The Multi-plot Main panel is shown in Figure 5. Con-
trols include selection of the default x-axis dataset from a
pull-down list of all data columns in the measurements ta-
ble, the maximum number of plotted datasets and the maxi-
mum number of detrend variables displayed in the Multi-plot
Y-data panel shown in Figure 6, plot title and subtitle, leg-
end placement and options, x− and y−axis label and scaling
options, and the overall plot size in pixels. The V.Marker 1

10
and V.Marker 2 controls provide the option to plot up to two
vertical red dashed lines with labels. For example, these lines
can be set to mark the predicted ingress and egress times on
exoplanet transit light curve plots. As discussed in the last
paragraph of Appendix A.1, new astronomical data such as
AIRMASS, BJDTDB, etc. can be calculated and added to
the measurements table using the menu item at Multi-plot
Main→Table→Add new astronomical data columns to table.
The bottom row of Multi-plot Main sub-panels provide ac-
cess to other x-axis controls that define the regions used when
normalizing, detrending, and fitting y-datasets. The Meridian
Flip settings allow the time of the telescope’s meridian flip to
be specified (if applicable) and to optionally mark that time
with a light blue dashed vertical line. If meridian flip is se-
lected as a detrending parameter for a dataset in the Multi-plot
Y-data panel, the fitting routine attempts to remove any base-
line offsets from one side of the meridian flip to the other.
The Fit and Normalize Region Selection options allow the
user to specify additional x-axis values that define the nor-
malization, detrend, and fit regions. For example, the Left and
Right settings are used to mark the regions used to normalize
the data (which normally exclude the in-transit portion of the
light curve). Also, the x-axis mid-point between the Left and
Right settings is used as the model fit starting point for the
transit model parameter TC. The Left Trim and Right Trim
settings can be used to exclude leading and/or trailing data
from the normalization, detrending, and fitting processes. A
gray vertical dashed line can optionally be displayed to iden-
tify the regions on the plot. Additional options are available
in the menus at the top of the Multi-plot Main panel.
Figure 7 shows an example plot of a WASP-12b transit and
demonstrates many of MP’s plotting capabilities. The settings
shown in Figures 5 (Multi-plot Main), 6 (Multi-plot Y-data),
and 8 (Data Set 2 Fit Settings) were used to produce this plot.
The Multi-plot Y-data panel is shown in Figure 6. Each hor-
izontal row in the user interface corresponds to an individual
plotted dataset. The example shown allows up to 13 datasets
to be plotted on a single plot. The top row of controls labeled
“1” under the Dataset heading produce the raw normalized
light curve shown as solid blue dots near the top of the plot.
Note in particular the Y-data column selected (rel flux T1)
and the Norm/Mag Ref mode selected ( ). The green ar-
eas in the Norm/Mag Ref mode icon indicate the regions of
the light curve (relative to the Left and Right markers on the
Multi-plot Main panel) that are used to normalize the data. In
this case, the in-transit data are not included in the calculation
of the normalization parameter.
The second row of plot controls (Dataset 2) again plot the
rel flux T1 data, but this time after simultaneously detrending
and fitting the data as set up in the fit panel shown in Figure
8, which is discussed in §4.4. Note the reduced systematics
and scatter in the data. This row of controls uses the Fit Mode
selection ( ) to enable the fit panel. Note that the then
Shift column is set to −0.01 which shifts the transit baseline
down to y = 0.990 on the plot for clarify. The light curve
model residuals are shown as open red circles. The residuals
plot controls are available in the fit panel corresponding to the
light curve.
The plot controls on rows corresponding to Dataset 3
through Dataset 9 display the first seven comparison star dif-
ferential light curves on the plot. The Fit Mode selection
( ), being completely green, selects all data for detrend-
ing, and the flat red line indicates that no transit model is fit
(since no transit event is expected in the comparison stars).
Note that the normalize mode selected under the Norm/Mag
Ref heading is all green also, since all comparison star data
can be used for normalization. Each comparison star light
curve is shifted from the other light curves for clarity using
the then Shift setting. Note that datasets 5, 8, and 9 have been
binned by 2 data samples using the Bin Size setting to reduce
the scatter for plotting purposes. The current implementation
of binning is actually averaging of the specified number of
data points, rather than binning into fixed size x-axis bins.
Each comparison star light curve has been detrended
against airmass. In this example, MP is set to allow up to
four trend datasets to be selected for detrending. Note that the
first Trend Select button is enabled and AIRMASS is showing
in the Trend Dataset column for all comparison stars. If the
resulting comparison star light curves are relatively flat, then
they should perform well as part of the comparison ensemble.
The plot controls for datasets 10-13 create the display of
four diagnostic curves. These curves are plotted relative to
the size of the plot page by selecting the Page Rel option on
each row. In this mode, the Scale setting forces the plot of
the data to fit within a fixed percentage of the plot range. The
then Shift value in this mode is also a percent of the plot range
with 0 being in the middle of the plot. This mode makes scal-
ing of data to fit on a plot easy when the shape of a curve is
important, but the actual values of the data are not.
Many other plotting options are available, including plot-
ting of error bars (Auto Error), legend options, input and out-
put in magnitudes, data averaging/binning, and the option to
select independent x-axis datasets for each y-axis dataset (i.e.
the X-data pull-down menus in the Multi-plot Y-data panel).
Datasets displayed in a plot have typically been modified
in one or more ways (e.g. normalized, detrended, converted
to/from magnitude, scaled, shifted, binned, etc.). The dis-
played values can be added to the measurements table as new
data columns for further manipulation or permanent storage
using the New Col button ( ) on the left-hand side of the
row corresponding to the plotted data. Model residuals and
sampled versions of the model can also be saved to the mea-
surements table using this button.
The legend is shown at the top of the plot in Figure 7, with
the light curves plotted below. Legend entries for each plotted
curve can be automatically generated based on the measure-
ments table column names known to be produced by MA by
selecting the Legend Type icon ( ). A custom legend can be
displayed individually or in combination with the automatic
legend by enabling the Legend Type icon ( ), or a curve’s
legend can be disabled by selecting the ( ) option. Legend
settings that affect all legend entries are accessed by clicking
the Legend Preferences icon ( ) at the top-right of the Multi-
plot Y-data panel. By default, the model residuals RMS values
are calculated and displayed in the legend for detrended and
fitted light curves. The light curve model parameter values are
optionally shown for fitted light curves. The predicted time of
ingress and egress are shown as red dashed vertical lines. The
meridian flip time is indicated by the light blue vertical dashed
line (although no meridian flip actually occurred for the exam-
ple observations), and the Left and Right gray dashed vertical
lines show the boundaries of the normalization, detrending,
and fitting regions.
The plot can be zoomed by placing the mouse pointer inside
the plot image and rolling the mouse scroll wheel. Also, a
left-click in the plot image zooms in by one step, and a right-
click zooms out to the full plot. After zooming in, the plot
can be panned with a left-click and drag of the mouse. A

11
FIG. 5.— The AIJ Multi-plot Main panel. The Multi-plot Main panel provides access to plotting controls that affect the overall plot. Important controls include
the default x-axis dataset (usually a time dataset such as BJDTDB), the title, legend, axis labels, plot size, and axis scaling settings. The bottom row provides
several settings used for detrending, normalization, and light curve modeling. See text for more details.
FIG. 6.— The AIJ Multi-plot Y-data panel. The Multi-plot Y-data panel provides access to plotting controls that affect individual plotted datasets. Each
horizontal row provides controls for plotting the dataset selected under the Y-data heading. See text for more details.
data point can be removed from a plot and measurements table
by holding the shift key and moving the mouse over the data
point in the plot until it is highlighted. Then, while continuing
to hold shift, a left-click will remove the data point. A shift-
right-click will retrieve the deleted point. As shortcuts, the
Left, Right, Left Trim, and Right Trim vertical markers can be
set at the mouse pointer location in the plot with a control-left-
click, control-right-click, control-shift-left-click, and control-
shift-right-click, respectively.
All typical data and image products created by a photome-
try and/or plotting and fitting session can be saved with one
action using the Save All feature available in the File menu of
the Multi-plot Main panel. There are also File menu options
in Multi-plot Main and image display panels to save each data
product separately. The menu option at File→Save all (with
options) opens a Save All settings panel before saving the files.
The menu option at File→Save all runs the process using the
previous settings without opening the settings panel. See Ap-
pendix A.8 for a full description of the Save All feature.

12
FIG. 7.— Multi-Plot example plot. The plot of a WASP-12b transit under poor observing conditions is shown. The top dataset plotted with solid blue dots is
the raw normalized differential photometry. The solid red dots show the light curve after simultaneously detrending and fitting with an exoplanet transit model,
which is shown by the red line through the data. Note the reduced systematics and scatter in the detrended data. The open red dots show the model residuals with
error bars. See the text for descriptions of the other plotted data.

13
4.4. Light Curve Fitting and Detrending
Light curve fitting is enabled for a particular dataset in the
Multi-plot Y-data panel by selecting the Fit Mode icon show-
ing the red transit model on a full green background ( ).
When this mode is selected, a Fit Settings panel will be dis-
played for the dataset as shown in Figure 8. The settings in
the figure produce the light curve model fit shown in the ex-
ample plot of Figure 7. The transiting exoplanet model is de-
scribed in Mandel & Agol (2002). The transit is modeled as
an eclipse of a spherical star by an opaque planetary sphere.
The model is parametrized by six physical values, plus a base-
line flux level, F0. The six physical parameters are the plan-
etary radius in units of the stellar radius, RP /R∗, the semi-
major axis of the planetary orbit in units of the stellar radius,
a/R∗, the transit center time, TC, the impact parameter of the
transit, b, and the quadratic limb darkening parameters, u1 and
u2. The orbital inclination can be calculated from the model
parameters as
i = cos−1

b
R∗
a

. (4)
AIJ is currently limited to finding the best fit model param-
eter values and does not provide estimates of the parameter
uncertainties. The best fit model is found by minimizing χ2
of the model residuals using the downhill simplex method to
find local minima (Nelder Mead 1965).
Before making adjustments in the Fit Settings panel, refer
§4.3 and properly configure the Fit and Normalize Region Se-
lection settings and optionally the Meridian Flip settings in
the Multi-plot Main panel, and the Norm/Mag Ref mode and
other settings in the corresponding row of the Multi-plot Y-
data panel.
The parameter settings in the User Specified Parameters
sub-panel are not fitted. The period of the exoplanet’s orbit
is not well constrained by the transit model, but its value will
impact the best fit values of some of the fitted parameters, so
the Period value must be entered by the user. Normally, the
orbital period is known from RV or wide-field survey photo-
metric data. The Host Star Parameters in the same sub-panel
are only used to estimate the physical planet radius, RP , from
the fitted parameter RP /R∗. The host star parameter values
are interrelated by tables in Allen Cox (2001) for zero age
main sequence (ZAMS) stars. The only value used in the cal-
culation of RP (displayed near middle of the right-hand side
of the panel) is R∗, so that value should be entered directly
if known. Otherwise, entering any one of the other host star
parameters will produce a rough estimate of R∗ based on the
ZAMS assumption.
The Transit Parameters sub-panel has seven rows for the
seven transit model parameters. Prior Center values will need
to be set for the seven parameters to ensure the correct χ2
minimum is found. The top four parameters shown in the sub-
panel are extracted from the light curve data by default. In the
odd case that those estimated values are not correct, the values
can be entered directly by the user. In the example shown, the
Inclination prior center value has been set by the user, but no
constraints have been placed on the range of valid final fitted
values (although the upper end is limited to 90◦
by the defi-
nition of inclination). The Quad LD u1 and Quad LD u2 pa-
rameter values have been set by the user, and the fitted values
have been locked to those values by enabling the Lock option
beside each one. The fixed values of u1 and u2 were extracted
from the Claret Bloemen (2011) theoretical models using
a website tool14
. The best fit transit model parameter values
are displayed in the Best Fit column. A green box around the
fitted parameter values indicates that the minimization con-
verged to a value less than the Fit Tolerance within the Max
Allowed Steps. Both of those minimization parameters can be
set at the bottom of the fit panel in the Fit Control sub-panel,
but the default values normally work well.
The bottom row in the Transit Parameters sub-panel shows
several values that are calculated from the best fit model. The
host star’s density, ρ∗, is particularly interesting, since a good
estimate can be derived from the transit light curve data alone.
Positioning the mouse pointer over any parameter will option-
ally cause a description of the parameter to be temporarily
displayed.
The Prior Width column allows the user to optionally limit
the range of a parameter’s fitted value. Prior Width values are
not normally needed, but may be helpful in fitting an ingress-
or egress-only partial transit. The StepSize column allows the
user to set a custom initial minimization step size. However,
the default values for each parameter normally work well, so
setting custom values is not usually necessary.
The Detrend Parameters sub-panel duplicates the detrend
settings on the Multi-plot Y-data panel. However, the Fit Set-
tings panel provides direct access to all detrend parameters
and settings. Prior center values, widths, and fitting step sizes
can optionally be set for detrend parameters as well.
Light curve detrending is accomplished by including a χ2
contribution for each selected detrend parameter in the overall
light curve fit. The χ2
contribution at each step of the min-
imization represents the goodness of the linear fit of the de-
trend parameters to the light curve after subtracting the light
curve model corresponding to the current fit step. The χ2
contribution for all n detrend parameters is calculated at each
step of the fitting process as
χ2
D =
m
X
k=1

Ok −
Pn
j=1 cjDjk

− Ek
2
σ2
k
, (5)
where j indexes the detrend parameters, k indexes the sam-
ples of the light curve, m is the total number of samples in the
light curve, Ok is the observed normalized differential target
flux, cj is the fitted linear coefficient for the detrend parame-
ter values Djk
, Ek is the expected value of the flux (which is
the normalized transit model value corresponding to the time
of the kth
data sample), and σk is the error in the normalized
differential target flux for each sample.
The Fit Statistics sub-panel lists five statistical values that
allow the user to assess the quality of the data and goodness
of the model fit to the data. The values displayed from left
to right are RMS of the model residuals, χ2
per degree of
freedom (i.e. reduced χ2
), Bayesian Information Criterion
(BIC), the number of degrees of freedom, and the total χ2
.
BIC is defined as
BIC = χ2
+ p ln n, (6)
where p is the number of fitted parameters, and n is the num-
ber of fitted data points. The BIC can be used to determine
whether the addition of a new parameter to a model (in partic-
ular an optional one such as a detrend parameter) provides a
significant improvement in the fit. If the BIC value decreases
by more than 2.0 when a model parameter is added, then the
14 http://astroutils.astronomy.ohio-state.edu/exofast/limbdark.shtml

14
FIG. 8.— The Fit Settings panel. The light curve model fitting and detrending panel settings shown here produce the light curve model fit in the example plot
of Figure 7. Light curve prior center and width values can optionally be set by the user to constrain the model fit. Direct access to all detrending parameters is
also provided along with more flexible settings. Several values calculated from the model parameters are displayed, along with several statistical values useful
for assessing data quality and goodness of the model fit to the data. See text for more details.

15
FIG. 9.— The Multi-plot Reference Star Settings panel. Star apertures can
be changed from comparison to target apertures and vice-versa. After any
change, all relative photometry values are recalculated and the measurements
table and plot are updated. Target aperture IDs start with a green T prefix
and have a deselected checkbox. Comparison aperture IDs start with a red C
prefix and have a selected checkbox. The Cycle Enabled Stars Less One and
the Cycle Individual Stars buttons speed the task of finding and excluding
poor comparison stars. See text for more details.
new model is preferred over the model with fewer parame-
ters. A larger decrease in the BIC value suggests a stronger
preference for the new model.
The Plot Settings sub-panel provides options for plotting
the light curve model and the residuals. The Fit Control sub-
panel settings are not normally needed, since by default the
model fit recalculates any time a value in the panel is changed,
and since the default Fit Tolerance and Max Allowed Steps
settings work for most light curve datasets.
4.5. Comparison Ensemble Management
The Multi-Plot environment allows the user to include
or exclude comparison stars from the comparison ensem-
ble without re-running Multi-Aperture, as long as apertures
were defined for all potentially good comparison stars in the
original Multi-Aperture run. The Multi-plot Reference Star
Settings panel shown in Figure 9 provides a checkbox cor-
responding to each target and comparison star included in
the original Multi-Aperture differential photometry run. De-
selected stars are considered target stars and selected stars
are comparison stars belonging to the comparison ensemble.
When a star is added to or removed from the ensemble, the
relative flux values for each star are recalculated and the mea-
surements table and plot are updated.
The Cycle Enabled Stars Less One button allows the user
to quickly cycle through the comparison ensemble removing
one star at a time so that poor comparison stars can be quickly
identified and removed from the ensemble. The Cycle Indi-
vidual Stars button can be used to quickly assess the quality
of each comparison star individually by cycling through each
one as a single comparison star.
5. ASTROIMAGEJ UPDATER
AIJ can be easily upgraded to the latest version using the
update facility at AIJ Toolbar→Help→Update AstroImageJ.
The AstroImageJ Updater panel shown in Figure 10 opens.
The latest release notes are displayed by clicking the Release
Notes button. The default value displayed in the Upgrade To
FIG. 10.— The AstroImageJ Updater panel. AIJ updates are easily in-
stalled by selecting the desired release number in the Upgrade To field. The
latest release notes are displayed by clicking the Release Notes button. The
selected update is installed by clicking the OK button. When the installation
is finished, AIJ automatically closes. The new version is activated when AIJ
is restarted.
field is the latest version. The update is installed by clicking
the OK button. When the installation is finished, AIJ auto-
matically closes. The new version is activated when AIJ is
restarted.
K.A.C. acknowledges support from NASA Kentucky Space
Grant Consortium Graduate Fellowships. K.A.C. and K.G.S.
acknowledge support from NSF PAARE grant AST-1358862
and the Vanderbilt Initiative in Data-intensive Astrophysics.
We thank the anonymous referee for a thoughtful reading of
the manuscript and for useful suggestions. This work has
made use of the SIMBAD database operated at CDS, Stras-
bourg, France.
APPENDIX
A. AIJ UTILITIES
A.1. Coordinate Converter
The Coordinate Converter (CC) module converts astronom-
ical coordinates and times to other formats based on observa-
tory location and target coordinates, and integrates AstroIm-
ageJ with Simbad and sky-map.org web services. CC can be
operated as a module under full control of the user, and it can
be operated under the control of DP and MP to provide auto-
mated calculations within those modules. When operated by
the user, all fields are available to be set as desired. When con-
trolled by DP and MP, only a subset of fields are enabled for
user entry, while the other fields are under the control of the
program and disabled (grayed-out) to prevent user input. A
cross-platform Java based version of CC called AstroCC runs
completely independent of AIJ and is available for download
from the AIJ website. Detailed CC help is available in the
menus above the CC panel at Help→Help.
The user controlled instance of the Coordinate Converter
panel is started by clicking the CC icon ( ) on the AIJ Tool-
bar. Figure 11 shows the panel after entering WASP-12 in the
SIMBAD Object ID field, selecting the Observatory ID, and
entering the date and time as UTC 2014-04-06 01:40:49. All
other coordinate formats, time formats, solar system object
proximities and altitudes, and moon phase are automatically

16
calculated. Note that the red background of the Moon prox-
imity box indicates that the moon is less than 15◦
from the
target (12.68◦
in this case).
The active coordinate source used to calculate the other co-
ordinate formats has a green border (J2000 Equatorial in this
case). Any coordinate or time format can become the active
source by directly entering a value into the field and pressing
Enter. The two fields in the UTC-based Time sub-panel
shown in Figure 11 with a green background show the time of
PM nautical twilight (upper) and AM nautical twilight (lower)
for the date, time, and observatory location specified. If the
date and time showing in the other UTC-based Time fields
is during dark time, the two twilight field backgrounds are
green, otherwise they are gray.
The BJDTDB time format requires dynamical time as the
time-base. Dynamical time accounts for the changing ro-
tational speed of the Earth by implementing leap-seconds.
Leap-second updates are not periodic, but are announced six
months before taking effect. The U.S. Naval Observatory
website posts a list of all leap seconds along with the effective
date of each one. To ensure that conversion to BJDTDB time
format is accurate, CC’s leap second table should be updated
by clicking the Update button in the Dynamic Time sub-panel
every 6 months or so while connected to the internet.
DP creates an instance of CC (DPCC), and depending on
user settings, data can be extracted from FITS header informa-
tion or entered manually to control the settings used by DPCC
to calculate new astronomical values to add to the calibrated
image’s FITS header information. If the FITS header contains
the time of observations, the target’s SIMBAD ID or coordi-
nates, and the observatory’s ID or coordinates, DPCC calcu-
lations can be executed with no user input. If target and/or
observatory information is not available in the header, that
missing information can be entered by the user as previously
shown in Figure 11. Appendix A.7 describes how to set up
the various DP FITS header update options and modes of op-
eration.
The menu item at Multi-plot Main→Table→Add new as-
tronomical data columns to table opens the panel shown in
Figure 12. In that panel, the user sets the time format and
data column name to be used for extraction of time from each
row in the measurements table. An instance of CC referred
to as MPCC is also opened along with the Add astronomi-
cal data to table panel. With the RA/Dec Source mode set to
Manual as shown in Figure 12, the target coordinates and ob-
servatory location should be manually entered into the MPCC
panel. With the RA/Dec Source mode set to Table, the RA
and Dec coordinates must have been extracted from the FITS
header and added to the measurements table during photom-
etry (see Appendix A.6). In this case, the corresponding data
column labels should be selected in the RA Column and DEC
Column pull-down menus. Then, when the Update Table but-
ton is clicked, the settings shown in Figure 12 will cause new
data columns AIRMASS, HJD UTC, and BJD TDB to be cal-
culated and added to the measurements table. The new data
columns can now be used for plotting, detrending, etc., and
the updated measurements table can be saved to disk.
A.2. FITS Header Editor
Information contained in the header of a FITS image open
in AIJ can be displayed and optionally edited by clicking the
FITS Header Editor icon ( ) above an image display. The
FITS Header Editor panel shown in Figure 13 opens. A FITS
header is made up of keywords and associated value and com-
ment fields. FITS header keywords and values should not be
edited unless the user understands the impact the change may
have on the downstream interpretation of the image data.
A header value is edited by double-clicking in the field and
editing the value using the keyboard. The keyword values
are locked by default, but can be edited after deselecting the
Lock Keyword Values checkbox. The Value field may contain
a string (i.e. text enclosed in single quotes), integer, real num-
ber, or boolean (i.e. a T or F). AIJ checks the formatting of the
Value field to ensure that the new entry meets the FITS spec-
ification for one of the data types allowed. The Type field is
automatically set based on contents of the Value field and can-
not be directly edited. Rows with keyword values SIMPLE,
BITPIX, NAXIS, NAXIS1, and NAXIS2 can not be edited
since these values are automatically set by AIJ according to
the image’s characteristics. The END keyword must always
be present in the last row and cannot be edited.
The buttons along the bottom of the editor, from left to
right, allow the user to delete the selected row of data (which
shows as highlighted in blue) from the header, insert a new
row below the currently selected row, save the contents of the
FITS header to a text file, save the new header to the image
in memory, save the image and new header to disk (and mem-
ory) using the same filename, save the image and new header
to disk using a new filename, or cancel the changes and exit
the editor.
A.3. Astrometry/Plate Solving
The astrometry feature “plate solves” images using an
internet connection to the astrometry.net web portal at
nova.astrometry.net (Lang et al. 2010). After a successful as-
trometric solution is found, WCS headers are automatically
added to the FITS image header, and the file can option-
ally be resaved with the new headers. AIJ searches the im-
age and extracts the source locations. Only the x, y coordi-
nates for a subset of the brightest extracted sources are sent
to nova.astrometry.net. The actual image is not transferred
across the network, which limits network traffic and improves
the solve time.
A left-click on the Astrometry icon ( ) above an image
opens the Astrometry Settings panel shown in Figure 14. A
right-click on the Astrometry icon starts the plate solve pro-
cess using the previous settings panel values. A left-click on
the Astrometry icon, after the plate solve process has started,
aborts the process. DP also provides an option in the FITS
Header Updates sub-panel (see Figure 3) to plate solve each
image as part of the calibration process. A free user key
must be obtained from nova.astrometry.net and entered into
the User Key field of the Astrometry Settings panel to enable
the astrometry feature.
Images can be blindly solved with no knowledge of the sky
coordinates or plate scale of the image. The default settings
shown in Figure 14 should work for most images. Solve time
may be faster if the Plate Scale is known and entered into the
field on the set up panel. If the approximate sky coordinates
of the center of the image are known, entering the Center RA
and Center Dec values may also improve solve time. How-
ever, the search Radius must be at least as large as the field
of view in the image. If an image has been defocused to im-
prove photometric precision, the Centroid Near Peaks option
may improve the determination of the location of the center
of each source.
When the START button is clicked, the set up panel closes
and the plate solve process starts. Progress is shown in the

17
FIG. 11.— The Coordinate Converter panel. The displayed state of the panel is shown after entering WASP-12 in the SIMBAD Object ID field, selecting the
Observatory ID, and entering the date and time as UTC 2014-04-06 01:40:49. All other coordinate formats, time formats, solar system object proximities and
altitudes, and moon phase are automatically calculated. Note that the red background of the Moon proximity box indicates that the moon is less than 15◦ from
the target (12.68◦ in this case). The active coordinate source used to calculate the other coordinate formats has a green border (J2000 Equatorial in this case).
Any coordinate or time format can become the active source by directly typing a value into the field and pressing Enter. See text for more details.
lower half of the AIJ Toolbar. By default, a log file is created
to record the results of each plate solve. If a time-series of
images have been opened into an AIJ image stack, the full set
of images can be solved by selecting the Process Stack option.
The entire plate solve process takes ∼ 10 − 20 seconds per
image.
When a field is successfully solved, nova.astrometry.net re-
turns a list of sources that are in the image. The source names
can be displayed in the image by enabling Annotate and/or
saved to the FITS header by enabling Add to Header. More
set up information is provided in the tool-tip help that is avail-
able for each option in the user interface panel.
A.4. Image Alignment
The images within a stack can be aligned using the Stack
Aligner icon ( ) above an image stack. The Stack Aligner
panel shown in Figure 15 opens and provides two methods
to align images. At the time of writing, Stack Aligner only

18
FIG. 12.— The Add astronomical data to table panel. The user sets the
time format and data column name to be used for extraction of time from
each row in the measurements table. An instance of CC referred to as MPCC
is also opened along with the add data panel. In the RA/Dec Source Manual
mode shown here, the target coordinates and observatory location should be
manually entered into the MPCC panel. Then, when the Update Table button
is clicked, the settings shown here will cause new data columns AIRMASS,
HJD UTC, and BJD TDB to be calculated and added to the measurements
table.
supports image translation for alignment. Image rotation and
scaling are not currently implemented.
If all images in the stack have been plate solved, the images
can be aligned using information in the WCS headers. To use
this mode, enable the Use only WCS headers... option and
click the OK button to start the alignment process. All images
in the stack will then be aligned to the first image.
If images have not been plate solved, apertures may be used
to identify alignment stars. Aperture placement is performed
in the same way as described for Multi-Aperture in §4.2, and
images are aligned based on the average of alignment star cen-
troid offsets between consecutive images. Aperture alignment
works best when at least a few (∼ 3 − 5) isolated stars are
available in the images. Aperture alignment will fail if the
shift from one image to the next is larger than the aperture
radius. However, the aperture radius can be made arbitrarily
large as long as centroid doesn’t capture a neighboring star in-
stead of the alignment star. For cases with large image shifts,
the Use single step mode option allows the user to click on the
first alignment star in each image of the sequence, avoiding
apertures centroiding on the wrong star. However, this mode
requires the user to click in each image of the sequence, which
may become impractical for very long image sequences.
An option is available in the Process menu above an im-
age display that provides Image Stabilizer functionality that
is useful for processing images of non-stellar objects. This
tool will remove atmospheric jitter from a rapid sequence of
planetary or lucky images, or track a comet over a long dura-
tion as it moves across a star field.
A.5. Radial Profile
An azimuthally averaged radial profile of an object can be
plotted by left-clicking near an object in an image, and then
selecting Analyze→Plot seeing profile in the menus above the
image display. As a short cut, simply alt-left-click near an
object in an image to produce the plot. If centroid is en-
abled, the radial profile will be centered on the object. Fig-
ure 16 shows an example radial profile plot. The plot shows
the half-width at half-maximum (HWHM), the FWHM, and
suggested aperture radii in pixels. The aperture radius is set
to 1.7×FWHM, the inner radius of the sky-background an-
nulus is set to 1.9×FWHM, and the outer radius of the sky-
background annulus is set to 2.55×FWHM. These radii give
an equal number of pixels in the aperture and sky-background
annulus. The FWHM is also given in seconds of arc if valid
WCS headers are available. The Save Aperture button trans-
fers the suggested aperture radii to the Aperture Photometry
Settings discussed in Appendix A.6.
A.6. Photometry Settings
Settings related to photometric measurements are specified
in the Aperture Photometry Settings panel shown in Figure 17
and the More Aperture Photometry Settings panel shown in
Figure 18. The Aperture Photometry Settings panel can be
accessed by double-clicking the Single Aperture Photometry
icon ( ) on the AIJ Toolbar, by clicking the set aperture icon
( ) above an image, by clicking the Aperture Settings button
near the bottom of the Multi-Aperture Measurements set up
panel, or by clicking the set aperture icon ( ) in the DP
Control Panel sub-panel. The More Aperture Photometry Set-
tings panel is accessed by clicking the More Settings button
on the Aperture Photometry Settings panel.
The Aperture Photometry Settings panel provides access
to the aperture radii, centroid, and background settings that
are also available in the Multi-Aperture Measurements set up
panel (see §4.2). A list of FITS keywords can be entered
to specify that the corresponding numeric data in the image
headers be added to the measurements table. The CCD gain,
readout noise, and dark current should be entered for proper
photometric error calculations. Linearity and saturation warn-
ing levels should be entered so that indicators of those condi-
tions can we properly noted in the measurements table (see
Appendix D) and the Multi-plot Reference Star Settings panel
(see §4.5).
The Howell centroid method (Howell 2006) gives highly
repeatable x,y results (i.e. is not sensitive to the x,y starting
location). If the Howell option is disabled, a center-of-mass
(i.e. center-of-flux) routine is used to calculate the centroid.
This method provides better results when placing apertures
around defocused stars.
The top two sections of the More Aperture Photometry Set-
tings panel allow the selection of photometric data items to
be included in the measurements table. See Appendix D for
a description of each data item. It is highly recommended
to enable all data items since some AIJ functionality requires
certain data items to be available in the table. The maximum
number of apertures per image is set high by default, but can
be changed as needed. The aperture display options control

19
FIG. 13.— The FITS Header Editor panel. Most fields can be directly edited by double-clicking in the fields and editing the contents using the keyboard. The
DELETE button at the bottom of the display will delete the selected row. The INSERT button adds a new row under the currently selected row. The header can
be saved to a text file, back to the image header in memory, or directly to disk. See the text for more details and a list of fields that cannot be directly edited.
which parts of the aperture overlay are displayed on the im-
age. The Sky Annulus, Source Number, and Value check boxes
duplicate the same controls available above an image display.
For typical operation, Clear overlay after use should be se-
lected and Clear overlay before use should be deselected.
A.7. Data Processor FITS Header Updates
DP provides the option to calculate new astronomical data
and add it to the FITS header of a calibrated image. The op-
tion is enabled by selecting the General check box in the FITS
Header Updates sub-panel of DP. A set up panel is accessed
by clicking the General FITS Header Settings icon ( ).
The General FITS Header Settings panel shown in Figure
19 opens. The FITS Header Input Settings sub-panel defines
FITS header keywords that are preexisting in the raw science
image headers that may be used in the calculation of various
new astronomical data values specified in the FITS Header
Output Settings sub-panel. These new astronomical data are
added to the FITS header of the calibrated images using the
specified keyword names.
The astronomical calculations require the target sky coordi-
nates and observatory geographical coordinates to be supplied
to DP Coordinate Converter (DPCC; see Appendix A.1). Both
sets of coordinates can be manually entered into DPCC by set-
ting the Target Coordinate Source option to Coordinate Con-
verter manual entry and the Observatory Location Source op-
tion to Coordinate Converter manual entry. Alternatively, co-
ordinate information can be automatically supplied to DPCC
from the FITS header of the raw image by setting the corre-
sponding keyword names in the FITS header Input Settings
sub-panel and then selecting the appropriate Target Coordi-
nate Source and Observatory Location Source to match the
type of data in the header (i.e. a target or observatory name or
a set of numeric coordinates).
A.8. Save All
All typical data and image products created by AIJ can be
saved with one action using the Save All features in the File
menu of the Multi-plot Main panel. There are also File menu
options in Multi-plot Main and image display panels to save

20
FIG. 14.— The Astrometry Settings panel. The astrometry feature “plate solves” images using an internet connection to the astrometry.net web portal at
nova.astrometry.net. After a successful astrometric solution is found, WCS headers will automatically be added to the FITS image header and the file can
optionally be automatically resaved with the new headers. See text for more details.
each data product separately. The menu option at File→Save
all (with options) opens the Save All settings panel shown in
Figure 20. Individual items that can be included in the save
all process are enabled in the array of checkboxes at the top of
the panel. A base file name, filebase, is specified in a separate
file save dialog and then the suffix names specified in the Save
All panel are appended as the files are saved. The checkbox
at the bottom of the panel specifies whether images are saved
in png or jpg format. The menu option at File→Save all runs
the process using previous settings without opening the Save
All settings panel.
If the Image option is enabled, the image in the active im-
age display (i.e. the last image clicked with the mouse if more
than one is open) is saved to a file name constructed from the
filebase and the suffix specified in Science image display suffix
and with a filetype of png or jpg, depending on the format se-
lected at the bottom of the panel. For the configuration shown
in Figure 20, the file would be named “filebase field.png”.
This image will include any items currently being displayed
in the non-destructive image overlay. If no image display is
open, no file will be created. If the Plot option is enabled and
a plot is being displayed, the plot image will be saved using
the filebase and file suffix in Plot image display suffix and with
a filetype of either png or jpg.
If the Plot Config option is enabled, the current state of
all plot settings will be saved to a plot configuration file
using the filebase and file suffix in Plot config file suf-
fix and with a filetype of plotcfg. If Data Table is en-
abled, the full measurements table will be saved to a file
using the filebase and file suffix in Full data table file suf-
fix and with a filetype as specified in the AIJ Toolbar menu
item Edit→Options→Input/Output→File extension for ta-
bles. The default filetype is xls, but this can be changed to
something more unique to AIJ (e.g tbl) so that measurements
tables can be set to open into AIJ with a double-click on the
corresponding file in an OS window. Tip: If Plot config file
suffix and Full data table file suffix are the same, when a mea-
surements table is opened into AIJ by dragging it from the OS
onto a Multi-Plot panel, or by double-clicking the file in an OS
window, the plot configuration file will be loaded along with
the measurements table so that the corresponding plot will be
automatically recreated.
If the Show Data Subset Panel and Data Subset options
are enabled, the panel shown in Figure 21 opens as part of
the Save All process to allow the user to select a subset of
data columns from the measurements table to be saved as a
separate tab-delimited file. The labels of data columns that
are to be included are selected in the pull-down menus. The
top-most item appears as the first column in the saved file.
The bottom-most item appears as the last column in the table.

21
FIG. 15.— The Stack Aligner panel. Images can be aligned using infor-
mation in the WCS headers, if images have been plate solved. Otherwise,
apertures are placed around selected alignment stars, and images are aligned
based on the centroid offsets between consecutive images. See text for more
details.
FIG. 16.— Radial Profile (Seeing Profile) plot. Alt-left-click near an object
in an image to produce an azimuthally averaged radial profile plot. The plot
shows the half-width at half-maximum (HWHM), the FWHM, and suggested
aperture radii in pixels. The aperture radius is set to 1.7×FWHM, the inner
radius of the sky-background annulus is set to 1.9×FWHM, and the outer
radius of the sky-background annulus is set to 2.55×FWHM. The FWHM
is also given in seconds of arc if valid WCS headers are available. The Save
Aperture button transfers the suggested aperture radii to the Aperture Pho-
tometry Settings discussed in Appendix A.6.
Blank entries do not produce a data column. The table will be
saved using the filebase and file suffix in Data table subset file
suffix and with a filetype of dat. If the Data Subset option is
enabled, but the Show Data Subset Panel option is disabled,
a data subset file will be created using the previous settings
without opening the Save Data Subset panel.
If the Apertures option is enabled, the aperture settings used
in the most recent Multi-Aperture run are saved to a file using
the filebase and suffix in Aperture file suffix and with a filetype
of apertures. If the Fit Panels option is enabled, images of all
open Fit Settings panels are saved to files using the filebase,
the suffix in Fit panel image suffix, the Data Set number from
the Multi-Plot Y-data panel, plus the fitted data column name,
and with a filetype of either png or jpg. If the Fit Text option
is enabled, text-based representations of all open Fit Settings
panels are saved to files using the filebase, the suffix in Fit
data text file suffix, the Data Set number from the Multi-Plot
Y-data panel, plus the fitted data column name, and with a
filetype of txt. If the Log option is enabled and a log panel is
open, the log text is saved to a file using the filebase and suffix
in Log file suffix and with a filetype of log.
B. PHOTOMETRIC ERROR CALCULATION
Proper estimation of the uncertainty (i.e. error or noise) in
each photometric measurement is important for reporting the
significance of the measurement and plotting error bars in the
light curve plot, but it is also important for the proper calcula-
tion of the best fit model to the data, since the uncertainty of
each measurement, σ, is part of the χ2
calculation used in the
fitting process (e.g. see equation 5). In short, the χ2
contri-
bution from each data point is weighted by a factor of 1/σ2
,
which places more weight on data with small errors, and less
weight on data with large errors.
Mortara Fowler (1981) and Howell (1989) discuss the
noise contributions to the measurement of a point source us-
ing CCD aperture photometry and develop the “CCD equa-
tion” to estimate the signal-to-noise ratio of a measurement.
Merline Howell (1995) construct a computer model of the
same measurement and develop the more rigorous “revised
CCD equation”. The equation gives the total noise N in ADU
for a CCD aperture photometry measurement as:
N =
q
GF∗ + npix(1 +
npix
nb
)(GFS + FD + F2
R + G2σ2
f )
G
,
(B1)
where G is the gain of the CCD in electrons/ADU, F∗ is the
net (background subtracted) integrated counts in the aperture
in ADU, npix is the number of pixels in the aperture, nb is
the number of pixels in the region used to estimate sky back-
ground, FS is the number of sky background counts per pixel
in ADU, FD is the total dark counts per pixel in electrons, FR
is read noise in electrons/pixel/read, and σf is the standard
deviation of the fractional count lost to digitization in a single
pixel (σf ≃ 0.289 ADU for f uniformly distributed between
−0.5 and 0.5).
If the net integrated counts from the source, F∗, dominates
the other terms, and the gain G = 1, the total noise ap-
proaches the Poisson noise limit of
√
F∗. The noise increases
as the number of pixels in the aperture increases (due to all of
the secondary terms in the equation), but for a non-ideal CCD,
noise introduced by inter-pixel variations decreases with in-
creasing aperture size (except in the case of perfectly guided
telescope), so the aperture size needs to be selected after con-

22
FIG. 17.— The Aperture Photometry Settings panel. The panel provides access to the aperture radii, centroid, and background settings that are also available
in the Multi-Aperture Measurements set up panel. A list of FITS keywords can be entered to specify that the corresponding numeric data in the image headers
be added to the measurements table. The CCD gain, readout noise, and dark current should be entered for proper photometric error calculations. Linearity and
saturation warning levels should be entered so that indicators of those conditions can we properly noted in the measurements table (see Appendix D) and the
Multi-plot Reference Star Settings panel (see §4.5). The More Settings button provides access to the additional options shown in Figure 18.
sidering both factors. The number of background region pix-
els should be chosen to be as large as possible, but not so
large that the pixels far from the aperture are no longer repre-
sentative of the local background at the aperture. If a source
is faint relative to the local sky background, the Poisson noise
of the sky background may dominate the overall measurement
noise.
The AIJ photometer automatically performs the noise cal-
culation described by equation B1 for each aperture. For
proper noise calculation, the gain, dark current, and read out
noise of the CCD detector used to collect the data must be
entered in the Aperture Photometry Settings panel (see Ap-
pendix A.6). For differential photometry, AIJ propagates the
noise from all apertures to derive the error in differential flux
measurements. First, the noise from the apertures of each
comparison star are combined in quadrature to give the total
comparison ensemble noise:
NE =
v
u
u
t
n
X
i=1
N2
Ci
, (B2)
where i indexes the comparison stars of the ensemble, and
NCi is the noise for each comparison star as calculated by
equation B1, and n is the number of comparison stars. Error
is then propagated through the relative flux quotient to find
the relative flux error for the target star as:
σrel flux =
FT
FE
s
N2
T
F2
T
+
N2
E
F2
E
, (B3)
where FT is the net integrated counts in the target aperture,
FE is the sum of the net integrated counts in the ensemble
of comparison star apertures, NT is the noise in the target
star aperture from equation B1, and NE is the ensemble noise
from equation B2. AIJ labels the relative flux error columns
as rel flux err Tnn, and rel flux err Cnn for target and com-
parison stars, respectively, where nn is the aperture number.
AIJ estimates the uncertainty in each measurement based
only on the factors included in equation B1. Additional
sources of photometric uncertainty not accounted for by AIJ
include atmospheric scintillation, variable leakage of flux
from neighboring stars into the aperture as seeing changes
slightly from exposure to exposure, Poisson noise in the mas-
ter dark and master flat images, slight variations in CCD bias
in the time-series, cosmic ray impacts on the detector, varying
contributions of square pixels to a circular aperture, camera
shutter open/close variations, and inaccurate determination of
sky-background from exposure-to-exposure.
Atmospheric scintillation noise can dominate for short
exposures and/or telescopes with small apertures. Reiger
(1963) described the theoretical approach to estimating the
amount of scintillation noise, Young (1967) conducted obser-
vations to test the theory and formalized the equation, and

23
FIG. 18.— The More Aperture Photometry Settings panel. The top two sections allow the selection of photometric data items to be included in the measurements
table. It is highly recommended to enable all data items since some AIJ functionality requires certain data items to be available in the table. The maximum number
of apertures per image is set high by default, but can be changed as needed.
Gilliland et al. (1993) clarified a factor in the equation. The
resulting scintillation noise equation is
σscintillation = 0.09D− 2
3 χ1.75
(2tint)− 1
2 e− h
8000 , (B4)
where D is the telescope diameter in centimeters, χ is the air-
mass, tint is the exposure time in seconds, and h is the altitude
of the observatory in meters. Again, this noise source is not
included in the AIJ photometric uncertainty estimate.
C. APPARENT MAGNITUDE CALCULATION
The apparent magnitude of target aperture sources can be
calculated by entering the apparent magnitude of one or more
comparison aperture sources. The calculations can be done
at the time multi-aperture differential photometry is being
processed by enabling the Prompt to enter ref star apparent
magnitude option in the Multi-Aperture Measurements set up
panel. This option causes a Magnitude Entry dialog box to
appear when a comparison aperture is placed. The compar-
ison aperture apparent magnitude should be entered, or the
entry should be left blank if that comparison aperture is not to
be used for target aperture apparent magnitude calculations.
However, at least one comparison aperture apparent magni-
tude must be entered to enable the calculation of target aper-
ture apparent magnitude. If WCS information is available in
the FITS image header, SIMBAD information is presented by
default to assist in determining the comparison star apparent
magnitude. This option can be disabled in the Magnitude En-
try dialog box. Click OK in the dialog to continue placing
apertures.
When OK is clicked, the comparison aperture magnitude
will show by default in the aperture image overlay. The first
value is the magnitude entered by the user, and the second
value is the net integrated counts in the aperture. The dis-
play of the two values can be controlled using the two options
near the bottom of the image display View menu in combi-
nation with the Aperture Value display icon ( ). The target
apparent magnitudes are also calculated “on-the-fly” from the
comparison aperture magnitudes and displayed as part of the
target aperture image overlay. Each time a new comparison
aperture magnitude is entered, target aperture magnitudes are
recalculated from all comparison aperture magnitudes and net
integrated counts.
Comparison aperture apparent magnitude values can be ad-
justed or added in the Multi-plot Reference Star Settings panel
after differential photometry has been completed. If mag-
nitude entry boxes are not displayed in the panel, click the
Show Magnitudes button. After adding or changing a value,
the Enter key must be pressed to update the target aperture
apparent magnitudes and the measurements table entries.
SIMBAD data for a comparison aperture can be accessed
by right-clicking on the corresponding comparison aperture
magnitude box in the Multi-plot Reference Star Settings panel.
This feature requires that at least the first image used to derive
the data in the measurements table have WCS header informa-
tion, so that the RA Xnn and Dec Xnn columns produced by
Multi-Aperture will exist with valid values in the first row of
the table, where nn is the aperture number, X = T for target
apertures, and X = C for comparison apertures.
Two columns labeled Source AMag Xnn and
Source AMag Err Xnn will be included in the measurements
table for each target aperture and for each comparison aper-

24
FIG. 19.— The General FITS Header Settings panel. The keywords speci-
fied in the FITS Header Input Settings sub-panel can be used to automatically
supply the target and observatory coordinates to DPCC. The FITS Header
Output Settings sub-panel specifies new astronomical values to calculate and
keyword names to use to store those values in the FITS header of the cali-
brated image.
ture with an apparent magnitude entry, where X and nn are as
defined previously. The columns labeled Source AMag Xnn
contain the user entered apparent magnitudes for comparison
apertures and the calculated apparent magnitudes for target
apertures. The comparison aperture apparent magnitudes will
be constant in the measurements table since the comparison
sources are assumed to have constant brightness. The
columns labeled Source AMag Err Xnn contain the apparent
magnitude errors. These error values do not include the
uncertainty in the user entered comparison source apparent
magnitudes.
If the Source AMag Xnn columns are plotted using MP, en-
able the Input in Mag option on the corresponding row of the
Multi-plot Y-data panel since these are magnitude-based data
rather than flux-based data. The Source AMag Xnn column
for the target source of interest is ideal for submitting to the
Minor Planet Center using the Multi-plot Main menu option
File→Create Minor Planet Center format.
The apparent magnitude of the source in target aperture nn
FIG. 20.— The Save All panel. All typical data and image products pro-
duced by AIJ can be saved with one action using the Save All feature. Indi-
vidual items that can be included in the save all process are enabled in the
array of checkboxes at the top of the panel. A base file path is specified in a
separate file save dialog and then the suffix names specified in the Save All
panel are appended as the files are saved. The checkbox at the bottom of the
panel specifies whether images are saved in png or jpeg format.
FIG. 21.— The Save Data Subset panel. A subset of data columns from the
measurements table can be specified and saved as a tab-delimited file. The
labels of data columns that are to be included are selected in the pull-down
menus. The number of available data column selections to be shown the next
time the panel is opened can be changed. The options at the bottom of the
panel specify if column headings, column headings hash-tag, row numbers,
and/or row labels are included in the data subset file.
is calculated as
Source AMag Tnn =
− ln
P
xx 2.512−Source AMag Cxx
ln 2.512
−
2.5 log
Source-Sky Tnn
P
xx Source-Sky Cxx
, (C1)

25
where nn is the target aperture number, xx indexes all com-
parison apertures for which an apparent magnitude has been
entered by the user, Source AMag Cxx are the user en-
tered comparison source apparent magnitudes, and Source-
Sky Tnn and Source-Sky Cxx are the net integrated counts in
apertures nn and xx as defined in Appendix D and §4.
The uncertainty in the apparent magnitude of the source in
target aperture nn is calculated as
Source Amag Err Tnn = 2.5 log (1+
s
Source Error Tnn2
Source-Sky Tnn2
+
P
xx Source Error Cxx2
(
P
xx Source-Sky Cxx)
2
!
,
(C2)
where nn is the target aperture number, xx indexes all com-
parison apertures for which an apparent magnitude has been
entered by the user, Source-Sky Tnn and Source-Sky Cxx
are the net integrated counts and Source Error Tnn and
Source Error Cxx are the net integrated counts uncertainties
for apertures nn and xx as defined in Appendix D and §4. The
target aperture apparent magnitude uncertainties do not in-
clude the uncertainty in the comparison source apparent mag-
nitudes entered by the user.
The uncertainty in the apparent magnitude of the source in
comparison aperture nn is calculated as
Source Amag Err Cnn =
2.5 log

1 +
Source Error Cnn
Source-Sky Cnn

, (C3)
where nn is the comparison aperture number and Source-
Sky Cnn and Source Error Cnn are the net integrated counts
and the net integrated counts uncertainty, respectively, for
comparison aperture nn. The comparison aperture apparent
magnitude uncertainty is simply the flux-based photometric
error converted to the magnitude scale. These values do not
include the uncertainty in the comparison source apparent
magnitudes entered by the user.
D. MEASUREMENTS TABLES
The results from single aperture photometry and multi-
aperture differential photometry are stored in “measurements
tables”. For single aperture photometry, each row in a ta-
ble contains all measurements produced from a single aper-
ture. For multi-aperture differential photometry, a row con-
tains all measurements produced by all apertures in a single
image, and a row exists for each image that has been pro-
cessed. Each column contains the same measurement from all
images. Columns are labeled with unique names, and those
names are available for selection in the pull-down menus in
the Multi-plot Main and Multi-plot Y-data panels. An exam-
ple of part of a measurements table is shown in Figure 22. As
discussed in the last paragraph of Appendix A.1, new astro-
nomical data such as AIRMASS, BJDTDB, etc. can be cal-
culated and added to the measurements table using the menu
item at Multi-plot Main→Table→Add new astronomical data
columns to table.
All data in a measurements table can be cleared by click-
ing the Clear Measurements Table Data icon ( ) above an
image display or in the Data Processor panel. One or more
rows can removed from a table by selecting them using the
mouse and then selecting the menu option Edit→Clear at the
top of the measurements table. Measurements tables can be
saved using the File menu options of the measurements ta-
ble and Multi-plot Main panels. A subset of data columns
from a measurements table can be saved using the menu op-
tion Multi-plot Main→Save data subset to file as discussed
in Appendix A.8. Measurements tables can be opened using
the File menu options on the Multi-plot Main panel, the AIJ
Toolbar Read Measurements Table icon ( ), or by dragging
a measurements table file from an OS window and dropping
it onto any of the Multi-Plot control panels. Any tab, comma,
or space delimited data table can be opened as a measure-
ments table. However, we strongly suggest that the first row
of the table contain text-based labels for each column so that
the Multi-Plot data column labels will be representative of the
data in each column of the table.
The measurements and associated column labels produced
when preforming multi-aperture differential photometry are
described in the list below. A suffix “ Xnn” denotes the aper-
ture identification, where X is either T or C for target or com-
parison aperture, respectively, and nn is the aperture number.
Each measurement item can be selected for inclusion in the
measurements table in the More Aperture Photometry Settings
panel (see Appendix A.6).
• J.D.-2400000: modified Julian Date of the observation
(UTC based). Availability requires UTC time and date
information in the FITS header. If keyword EXPTIME
is also available in the header, time of mid-exposure is
indicated, otherwise start of exposure is indicated.
• JD UTC: If this keyword value is set and successfully
extracted from the FITS header, the header value is in-
dicated. Otherwise, the full Julian Date of the obser-
vation (UTC based) is indicated based on the value in
J.D.-2400000.
• Source Radius: radius of the aperture used to calculate
net integrated counts. In fixed aperture mode, this value
is the aperture radius set by the user. In variable aper-
ture mode, this value represents the actual aperture ra-
dius calculated as the product of the average FWHM in
the image and the multiplicative factor set in the Multi-
Aperture Measurements set up panel.
• FWHM mult: in variable aperture mode, this value is
the FWHM multiplier set in the Multi-Aperture Mea-
surements set up panel. In fixed aperture mode, this
column is not included in the table.
• Source Rad(base): in variable aperture mode, this
value represents the fixed aperture radius set by the user
and should be set to a number greater than 1.5 times the
maximum FWHM expected to ensure proper measure-
ment of FWHM. In fixed aperture mode, this column is
not included in the table.
• Sky Rad(min): radius of the inner edge of the annulus
used to calculate the sky background
• Sky Rad(max): radius of the outer edge of the annulus
used to calculate the sky background
• X(IJ) Xnn: the x-location in ImageJ pixel coordinates
of the center of aperture nn
• Y(IJ) Xnn: the y-location in ImageJ pixel coordinates
of the center of aperture nn

26
FIG. 22.— Part of a Measurements Table. Multi-aperture differential photometry produces a measurements table containing all photometric data from the time
series. Each row contains all measurements from an individual image. Each column contains the same measurement from all images. Columns are labeled with
unique names, and those names are available for selection in the pull-down lists in the Multi-plot Main and Multi-plot Y-data panels.
• X(FITS) Xnn: the x-location in FITS coordinates of
the center of aperture nn
• Y(FITS) Xnn: the y-location in FITS coordinates of
the center of aperture nn
• rel flux Tnn: the ratio of the net integrated counts in
target aperture nn to the total net integrated counts of
all comparison stars. Mathematically the value is calcu-
lated as Source-Sky Tnn /
P
(Source-Sky Cxx ), where
xx indexes all comparison star apertures.
• rel flux Cnn: the ratio of the net integrated counts
in comparison aperture nn to the total net integrated
counts of all other comparison stars. Mathematically
the value is calculated as Source-Sky Cnn /
P
(Source-
Sky Cxx), where xx indexes all comparison star aper-
tures and xx 6= nn.
• rel flux err Xnn: the error in the relative flux for ob-
ject nn. The error is calculated by propagating all
Source Error Xnn values through the equations defined
for rel flux Xnn as described in Appendix B.
• rel flux SNR Xnn: signal-to-noise ratio for
rel flux Xnn. This value is simply rel flux Xnn /
rel flux err Xnn.
• Source-Sky Xnn: net integrated counts within aperture
nn. Net integrated counts is defined as the sum of all
pixel values less sky background for all pixels having a
center that falls within the aperture radius.
• Source Error Xnn: error in the net integrated counts
for aperture nn. See Appendix B for a description of
how the photometric error is calculated.
• Source SNR Xnn: signal-to-noise ratio aperture
nn. This value is simply Source-Sky Xnn /
Source Error Xnn.
• tot C cnts: the sum of the net integrated counts in
all comparison apertures. tot C cnts =
P
(Source-
Sky Cxx), where xx indexes all comparison apertures.
• tot C err: the error in tot C cnts. The error is cal-
culated by combining all Source Error Cxx values in
quadrature, where xx indexes all comparison stars.
• Peak Xnn: the highest pixel value in aperture nn (not
background subtracted)
• Mean Xnn: the mean pixel value in aperture nn (not
background subtracted)
• Sky/Pixel Xnn: the sky background estimate for aper-
ture nn. Depending on the options selected, the value
may be the mean value of all pixels, the mean value of
all pixels after iterative 2σ cleaning, or a plane fitted
to (possibly 2σ iteratively cleaned) pixels in the sky-
background annulus of aperture nn.
• X-Width Xnn: an estimate of the x-direction FWHM
of the PSF of the object in aperture nn. The aperture
radius should extend beyond 1.5 × FWHM in the x-
direction to enable the best estimate.
• Y-Width Xnn: an estimate of the y-direction FWHM
of the PSF of the object in aperture nn. The aperture
radius should extend beyond 1.5 × FWHM in the y-
direction to enable the best estimate.
• Width Xnn: the mean of the x- and y-direction FWHM
values for aperture nn. The aperture radius should ex-
tend beyond 1.5 × FWHM in the both the x- and y-
directions to enable the best estimate.
• Saturated: zero indicates that the peak value in all
apertures is less than the Saturation warning value set
in the Aperture Photometry Settings panel (see Ap-
pendix A.6). A number other than zero indicates the
highest peak value that exceeded the set limit.

27
• Source AMag Cnn: comparison aperture nn apparent
magnitude entered by the user. This column’s values
are the same in all rows since the comparison source is
assumed to be constant. This column does not exist if
apparent magnitude has not been entered for aperture
nn.
• Source AMag Tnn: target aperture nn apparent mag-
nitude calculated from all comparison apertures having
an apparent magnitude entry. This column does not ex-
ist if apparent magnitude has not been entered for any
comparison apertures. Equation C1 defines how this
value is calculated.
• Source AMag Err Tnn: target aperture nn apparent
magnitude uncertainty. This column does not exist if
apparent magnitude has not been entered for any com-
parison apertures. Equation C2 defines how this value
is calculated.
• Source AMag Err Cnn: comparison aperture nn ap-
parent magnitude uncertainty. This column does not
exist if apparent magnitude has not been entered for
aperture nn. Equation C3 defines how this value is cal-
culated.
The numeric values of FITS header keywords can also be
extracted from an image (or series of images) and included
in a measurements table when performing single aperture or
multi-aperture differential photometry. The associated col-
umn in the table will be labeled using the keyword name.
These keyword names must be specified in the Keywords
(comma separated) list in the Aperture Photometry Settings
panel (see Appendix A.6). As discussed in Appendix A.7,
DP provides the option to calculate new astronomical data
and add them to the FITS header of a calibrated image. A
keyword name specified in the Keywords (comma separated)
list in the Aperture Photometry Settings panel must match the
keyword name specified in the FITS Header Output Settings
sub-panel of the General FITS Header Settings panel to prop-
erly transfer the DP calculated astronomical data into the mea-
surements table. In addition, the FITS Header Update option
must be enabled and the target and observatory coordinates
must be provided through one of the various options in the
DP FITS Header Updates sub-panel. UTC date, time, and ex-
posure time information must also exist in the FITS header of
the raw image. Some keywords containing astronomical data
calculated by DP that are often extracted from the calibrated
image headers and added to the measurements table are listed
below.
• HJD UTC: UTC-based heliocentric Julian Date of
this measurement at the mid-point of the exposure
(see Eastman et al. 2010 for a complete definition of
HJDUTC)
• BJD TDB: TDB-based barycentric Julian Date of
this measurement at the mid-point of the exposure
(see Eastman et al. 2010 for a complete definition of
BJDTDB)
• ALT OBJ: altitude of the target coordinates above the
horizon at mid-exposure
• AIRMASS: airmass of the target coordinates at mid-
exposure
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