Aperture Photometry Tool

Click here for a tutorial on Aperture Photometry Tool.

Aperture Photometry Tool, v. 2.3.4, is now available:

http://www.aperturephotometry.org/aptool/download/

There are enhancements and bug fixes in this release.

Added a source de-blending algorithm to the “Source-List-Creation Tool”, which looks for peaks in aggregated image objects that are in accordance with the selected radial-profile sigma, a new input parameter on the “Source-List-Creation Tool” panel.

Added an new “Export Photometry Data to CSV File” option under the File menu-bar category, which has been given the keyboard shortcut of “Command-p” for Macs and “Control-p” for Windows machines.

Added a keyboard shortcut for clearing the current output aperture-photometry file, which is “Command-c” for Macs and “Control-c” for Windows machines.

Added a keyboard shortcut for bringing up the “More Settings” panel, which is “Command-m” for Macs and “Control-m” for Windows machines.

Added a keyboard shortcut for bringing up both the “Aperture Size, Shape, and Angle” and “Photometry Major Radii” panels, which is “Command-a” for Macs and “Control-a” for Windows machines.

Modified the software to write the Model-F non-annulus-based sky-background image to a FITS file in the scratch directory with filename skyBackgroundModelF.fits.

Modified the “Simple Photometric Calibration” tool to select only unambiguous matches (i.e., a source in list A was matched with a source in list B, each matched only once to each other).

Added a progress bar to the “Simple Photometric Calibration” tool.

Modified the software to do a nonlinear data fit to the radial-profile model and additionally compute sigma, as well as the linear model parameters, in order to minimize the chi-squared function of the data fit.

Defined a new column in the output aperture-photometry table called “RadialProfileFWHM”, in order to store the radial-profile model’s full width at half maximum (FWHM).

Minor bug fix: Added logic to reset the computed FWHM to approximately 2.35 times sigma for divergent cases where the radial profile’s half-width is determined to be greater than 3.0 times sigma or greater than the domain of the data used to derive the radial profile.

Minor bug fix: Modified the “Source-List-Creation Tool” to allow the input parameter “Number of image-edge pixels to skip” to be as little as zero (previously it was constrained to be one or greater).

Major bug fix: The “Preferences” menu option of automatically computing the aperture correction without the input dialog was broken and needed fixing.

Major bug fix: The yes/no dialogs for Windows and Linux machines were wired backwards (as a result of the button reordering that was done in a previous recent version).

Major bug fix: The “Export Image Data to Image File” option under the “File” menu-bar category was not hooked up and, therefore, this option was non-functional.

Aperture Photometry Tool, v. 2.3.3, is now available:

http://www.aperturephotometry.org/aptool/download/

There are bug fixes in this release.

Bug fix: Added missing code that prevented source-list creation via APT’s command-line batch mode.

Bug fix: Removed the call to APT’s JFrame.dispose() just before the System.exit( 0 ) call, so as not to wait for any APT threads that may be running to terminate, which ensures that APT and the JVM completely terminate upon user request.

Bug fix: A new bug (Windows and Linux only) was introduced in the last related to the “A”, “B”, “C”, “Cancel” button re-ordering on the “Open Image” dialog, which prevented it from working properly the second time around.

It was discovered that Aperture Photometry Tool, v. 2.3.2, installed from the *.dmg packages, was failing to launch on Macs. The problem was fixed by approximately 7:20 a.m. Pacific time on April 4, 2013. Changes to the jar-bundling build script was needed to accommodate the software’s new splash screen. The new *.dmg packages have been posted for downloading and their MD5 file checksums are as follows:

Full-size GUI: 0959f44be81c8397a079e41330d7aee8

Compact-size GUI: 981bc545f0f54907cc6ac5eef34d6171

The *.zip and *.tar.gz packages are unaffected.

Russ apologizes for any inconvenience that this problem may have caused.

Aperture Photometry Tool, v. 2.3.2, is now available:

http://www.aperturephotometry.org/aptool/download/

There are enhancements and a bug fix in this release.

Modified the software to output a list of available command-line options when the software is executed in a terminal window with the -h switch (for help).

For a ds9-like command line, modified the software to allow “-i” to be optional when specifying the input FITS-image filename as the first command-line argument. Also, modified the software to allow “-s” to be optional when specifying the input source-list filename as the second command-line argument. These two changes both retain the old command-line style (e.g., “APT.csh myImage.fits mySourceList.txt”), while allowing the new command-line style (e.g., “APT.csh -s mySourceList.txt -i myImage.fits “), which does not require the command-line options to be in any particular order.

Modified the “Primary-Image Thumbnail” panel to display grid-line sky coordinates labels in either decimal or sexagesimal, depending on the celestial-coordinates units selected under the Preferences menu.

Made code changes to get under control the writing of extraneous table headers to the output aperture-photometry-table file.

Modified all JOptionPane dialogs to have the same button ordering across different platforms (e.g. Macs vs. Windows and Linux machines).

Speeded up the “Aperture-Correction Tool” by replacing the single-threaded code for computing the thresholded and local background images with multi-threaded classes having similar functionality.

Speeded up the “Source-List-Creation Tool” by replacing the single-threaded code for computing the thresholded and local background images with multi-threaded classes having similar functionality.

Changed the progress-bar type from indeterminate to determinate for the “Source-List-Creation Tool”.

Modified the “Source-List-Creation Tool” to not issue a file-overwrite warning if the source-list filename is the default filename of “sourceListByAPT.dat”.

Modified the source algorithm called “Model 1″ to also perform radial-profile interpolation for saturated pixels.

Added a splash screen to indicate to users that the software requires some time to initialize before the interactive GUI is displayed.

Modifed the “APERTURE-PHOTOMETRY RESULTS” section on the main GUI to display the sky background for the sky algorithm selected (instead of simply displaying the sky median and the average).

Bug fix: Missing line of code “radio5.addActionListener( this );” was preventing the sky algorithm callled “Model E = Sky-annulus mode subtraction” from being selected and enabled.

Updated this documentation and added paragraph breaks to make it more readable.

There are some enhancements and one bug fix in this release.

Implemented a new sky algorithm called “Model F” that uses a local estimate for the sky background that is non-annulus-based and computed via bilinear interpolation of the mode statistic computed with a user-specifiable window size on a user-specifiable grid size (the median statistic is used instead if the window is less than 33 pixels).

Modified the “Aperture-Correction Tool” dialog to always be on top when executed in the automatic mode that uses stored preferences or default values as inputs and bypasses user interaction.

Modified the actions prompted by the “Clear Picks/Zaps”, “Hide/Show Aperture”, and “Close Window” buttons on the “Pick/Zap Tool” panel to include repainting the main GUI’s image-viewing panel so that any new zaps (or cleared zaps) are also shown there immediately (without having to wait until after the “Recompute Photometry” button is clicked.

Added a keyboard shortcut for setting the output aperture-photometry-table filename using a File-Chooser Dialog, which is “Command-s” for Macs and “Control-s” for Windows machines.

Changed the format of APT’s command line for batch-mode operations, in an effort to make APT more useful to power users. The command-line options must now be named, and no longer depend on the ordering of the command line. In this version, there are four different command-line options available:

Unix machine:

APT.csh -i input_FITS-image_filename
        -s input_source-list_filename
        -o output_aperture-photometry-table_filename
        -z zero_point

Windows machine:

APT.bat -i input_FITS-image_filename
        -s input_source-list_filename
        -o output_aperture-photometry-table_filename
        -z zero_point

At a minimum, the -i option must be specified for command-line options to be useful. No GUI will be displayed when both -i and -s options are specified (batch mode). The -z and -o options are optional.

Added a new column to the output aperture-photometry-table file, which is associated with the output of the new sky algorithm called “Model F”: SkyLocalNonAnnulusBkg.

Bug fix: Speeded up dramatically the image display when loading a new image.

Aperture Photometry Tool, v. 2.3.0, is now available:

http://www.aperturephotometry.org/aptool/download/

There is are several enhancements and one bug fix in this release.

Interchanged the positions of “Thumbnail” and “Source List” buttons, in order to better align these functions with the work flow (the former is a visualizer and the latter a results generator).

Switched from System property “mrj.version” to “os.name” for determining whether the host machine is a Mac.

Replaced the deprecated Mac code for handling the About, Preferences, and Quit options under the application’s menu on the menu bar with the up-to-date handlers.

For Mac machines, moved the Preferences menu to under the standard application menu (this is normal for Mac applications).

Moved the Preferences menu to the top of the list under the Edit menu on the menu bar for non-Mac machines.

Deprecated the preference called “apertureCorrectionsSourceDetectionThreshold”, and renamed it to “apertureCorrectionsBrightSourceDetectionThreshold”.

Added the following new preferences to the “Aperture Corrections” dialog: “apertureCorrectionsFaintSourceDetectionThreshold”, “apertureCorrectionsMaxPeakToCentroidDistance”, and “apertureCorrectionsSaturationLevel”.

Changed the default values for the following input parameters for the “Aperture-Correction Tool”: Largest aperture radius for which to compute an aperture correction, from 40 to 15 pixels; Minimum nearest-neighbor-source distance, from 40 to 30 pixels.

Added a Preferences option for APT’s interactive mode (non-batch mode) to compute aperture corrections (truly) automatically with input parameters from saved preferences or default values, so that, optionally, no user interaction is required in computing aperture corrections.

Added a keyboard shortcut for opening up a FITS image using a File-Chooser Dialog, which is “Command-o” for Macs and “Control-o” for Windows machines.

Added a keyboard shortcut for quitting the application, which is “Command-q” for Macs and “Control-q” for Windows machines.

Added a keyboard shortcut for poping up the Preferences menu, which is “Command-, (comma)” for Macs (as is normal), and “Alt-p” for Windows machines (for techical reasons, this is a keyboard mnemonic rather than an accelerator key).

Added a keyboard shortcut for poping up software documentation, which is “Command-d” for Macs and “Control-d” for Windows machines.

For non-Mac machines, added the new menu-bar category “APT”, and added under it the menu options “About APT”, “Preferences” (removed from the “Edit” menu), and “Quit APT” (removed from the “File” menu), in order to simulate the equivalent Mac behavior (which makes perfect sense).

For non-Mac machines, added keyboard mnemonics for all menu-bar categories: “Alt-a” for APT menu, “Alt-f” for File menu, “Alt-e” for Edit menu, “Alt-v” for View menu, “Alt-t” for Tools menu, and “Alt-h” for Help menu (keyboard mnemonics are recommended against in the Java Development Guide for Mac).

In the Preferences menu, moved “List Preferences” to just before “Load Preferences”.

Feature fix: converted HDU number from a zero-based counter to a one-based counter when displaying the HDU number in the FITS-header listing.

Bug fix: Forgot to close old output photometry file before new output photometry file is opened.

Aperture Photometry Tool, v. 2.2.9, is now available:

http://www.aperturephotometry.org/aptool/download/

There is are several enhancements and fixes in this release.

Modified the software to interrogate the computer for the number of available CPU cores and, by default, set the maximum number of threads to this value for multithreaded processing by the “Source-List Tool”.

Increased the selection in the drop-down menu for the maximum number of threads (under the Edit > Preferences menu) to include all values from 1 to 20 threads.

Modified the “Source-List Tool” to assure that the aperture-photometry outputs have the same ordering as the input source list.

Modified the software to use the local mode as a local backgound estimator when the window size is 33 or greater, and the local median otherwise (local image statistics are required by both the “Source-List-Creation Tool” and the “Aperture-Correction Tool”.

Updated the documentation to reflect the new column names of the output aperture-photometry table.

Typo fix: Changed column name “Sky_RMS” to “SkyRMS” (one intent of the related changes in the previous version was to get rid of the underscores).

Annoying-feature fix: added logic to disallow function lookUpAndSetApertureCorrection() from setting an aperture-correction value that is less than 1.0. Modified the “Aperture-Correction Tool” to set the aperture corrections to 1.0 in the event no bright, isolated sources are found in the image.

Fixed a scoping bug that was introduced in the last version, which may have been preventing background subtraction from being done properly for the plots associated with the curve of growth, radial profile, and source scatter.

Eliminated some unnecessary screen repainting and speeded up the calculations by almost a factor of 2!

Aperture Photometry Tool, v. 2.2.8, is now available:

http://www.aperturephotometry.org/aptool/download/

There are several enhancements and a minor bug fix in this release.

Added the red and green APT logo as an icon to the APT.exe Application file for Windows.

Added to the Preferences menu new options for setting the image-data saturation level and color for displaying saturated pixels, and modified the pixel-attributes class to display saturated pixels with the designated color when gray scale is selected or alternatively light gray if false color is selected.

Developed a new option to automatically compute the aperture correction as a function of aperture radius, and lood the correct value into the aperture-correction textfield on the “More Settings” panel (the output list of bright, isolated stars is written to brightIsolatedStars.dat in the scratch directory, and the output table of aperture radii, normalized curve-of-growth values, aperture corrections, and uncertainties is written to apertureCorrections.dat in the scratch directory).

Commented out the code that draws an image bounding box for indicating the image region that has been refreshed with the latest stretch and color-table settings (this is more of an annoyance than of any help).

Renamed the column headings in the output aperture-photometry table to simpler, more intuitive names.

Added an indeterminate progress bar to the “Source-List-Creation Tool” panel.

Fixed various bugs in the logic that checks the input-parameter values of the “Source-List-Creation Tool”.

Aperture Photometry Tool, v. 2.2.7, is now available:

http://www.aperturephotometry.org/aptool/download/

There is a minor bug fix and several enhancements in this release.

Minor bug fix: disallow multiple “Photometry File” panels (previously, only the last one created was active while the rest were zombies).

Modified the numerical formats in the output photometry file so that both Magnitude and Mag_unc always have 4 decimal places to the right of the decimal point.

Modified the “Photometry File” panel so that the “Close Window” button has the input focus; did the same for other panels.

Added a “Clear Contents” button to the “Photometry File” panel.

Increased the widths of the “X”, “Y”, “X_cen” and “Y_cen” columns in the output-photometry-table file by 3 spaces, in order to potentially handle very large images.

Reduced the size of the “Source-List Tool” panel from 950×630 pixels to 700×580 pixels, in order to make it less cramped on smaller computer screens.

Reduced the width of the “Source-List-Creation Tool” panel from 850 pixels to 700 pixels, in order to make it less cramped on smaller computer screens.

Increased the height of the “Simple Photometric-Calibration Tool” from 640 pixels to 770 pixels, as it was somewhat undersized.

On the “Source-List Creation Tool” panel, increased the defaults values of the “Source minimum number of pixels” and “Source maximum number of pixels” from 5 and 100 to 20 and 10000, respectively.

Modified the “Close” button on all graph panels to have the input focus.

On the “More Settings” panel, renamed sky algorithms from “Model B = Sky-median subtraction” and “Model D = Sky-average subtraction” to “Model B = Sky-annulus-median subtraction” and “Model D = Sky-annulus-average subtration”, respectively, in order to make it clear that these are local calculations involving the sky annulus.

Added new sky algorithm “Model E = Sky-annulus-mode subtraction”, and added new “Sky_mode/pix” column to the output-photometry-table file.

Added tool tips for the radio buttons on the “More Settings” panel.

Added a progress bar to the source-list tool.

Added dialogs to warn the user when the source-list tool is executed either before a source list has been specified or when there are no sources to process.

Modified the source-list tool’s “Automatically Process Source List” button to be disabled while processing the source list.

Made changes to the source-list tool to prevent a NullPointerException when the “Step Through Source List” button reaches the end of the list.

Changed the default representation of the sky coordinates from sexagesimal to decimal (this is better for students).

Modified the source-list creation code to skip a user-specifiable number of pixel rows and columns from the image edges, in order to avoid source detections near image edges.