Home

AstroImageJ 2.4.1 User Guide plus - University of Louisville Astronomy

1.
2. markers are still not displayed make sure the check boxes for each are selected 10 2 1 10 2 Detrend and Normalize Region Selection Finally the Detrend and Normalize Region Selection section at the bottom of the Multi Plot Main panel needs to be set to match your data In this simple case click the Copy icon cy to copy the V Markerl and V Marker2 values to the Left and Right boxes The V Marker lines are for display purposes only The Left and Right values are used to segment the data for normalization and detrending purposes The two sets of markers are not required to be at the same x axis location If the predicted ingress and egress are not accurate but you want to maintain those settings simply shift the Left and Right values to demark the desired normalization and detrending regions Your plot format should now look similar to the plot shown below SHORTCUT control left click in the plot to interactively set the Left value control right click in the plot to set the Right value 10 2 1 10 3 Detrend Mode Notice that three different Detrend Mode settings are used to produce this plot more are available but those are beyond the scope of this demonstration iu l L no detrending normalization is applied to the Y dataset EI 7 detrending normalization is fitted to the Y dataset values to the left of Left and to the right of Right In other words only the
3. AstroImageJ can be downloaded from http www astro louisville edu software astroimagej index html 2 1 Linux Installation Download AstroImageJ for Linux from http www astro louisville edu software astroimagej index html and extract AstroImageJ linux tar gz to the desired AstroImageJ folder A script file is available that shows how to set up AIJ for easy start up under Linux For Linux installation refer to the Linux section of the AA README AIJ page on the website For more information on generic ImageJ with Linux go to http rsbweb nih gov 1j docs install linux html 2 2 Windows Installation Download AstroImageJ for Windows from http www astro louisville edu software astroimagej index html and extract AstroImageJ windows zip to the desired AstroImageJ folder ex C Program Files x86 Be sure to read the Windows section of the AA README AIJ page on the website An AstroImageJ exe program is available in the upper most directory and can be used to start AstroImage J If preferred one can set up a file type to be automatically opened by AstroImageJ exe when double clicked by referencing that file type to the AstroImageJ exe program To change the maximum amount of memory allocated to AIJ start AIJ using the ImageJ exe program and then go to the Edit Options Memory amp Threads menu selection on the AIJ toolbar After changing the maximum memory allocation close and restart AIJ to enable the n
4. black mean 2 734 9092 white 3 851 1177 max 65 535 0000 5 1 Data Displayed Above the Image AIJ displays several data fields above the image that contain information specific to the mouse location within the image All of these values update as the mouse is moved Two pixel coordinate systems are displayed in the interface IJ s native origin i e x y 0 0 is at the top left of the image with x increasing to the right and y increasing toward the bottom IJ pixel coordinates are useful when using some of the built in IJ features The FITS standard origin is at the bottom left of the image with x increasing to the right and y increasing toward the top Pixel coordinates based on the FITS standard are often needed by astronomers and are particularly important when working with images containing World Coordinate System WCS headers The middle line displays RA and DEC when WCS headers are available from a FITS file The top right box labeled Value indicates the pixel value under the mouse cursor The Peak value indicates the highest pixel value within a circular aperture at the mouse cursor however if enabled in Preferences menu this label will read Mean and the value in the box is the mean within the aperture The aperture characteristics can be set by clicking the Set Aperture Icon amp and the mouse aperture display can be enabled disabled under the Preferences menu The Int
5. gt Import gt Image Sequence This icon is also available above all image windows MA can be automatically started as part of a DP run however it is often necessary to run MA on data that has already been calibrated Multi aperture outputs a table containing the photometry results Multi Plot Icon opens the Multi Plot MP module for plotting multiple curves on a single plot from the data table created by MA or any generic table opened from disk A data file can be opened by dragging and dropping it onto one of the two MP control panels or use the MP file menu A saved plot configuration will be automatically opened at the same time 1f a file with the same name but with suffix plotcfg exists in the same folder as the dropped file M Open Data Icon opens a previously saved measurements table or any generic tab comma csv space spc or prn or white space txt delimited file from disk for plotting with MP Alternatively a data file can be opened by dragging and dropping it onto one of the two MP control panels A saved plot configuration will be automatically opened at the same time if a file with the same name but with suffix plotcfg exists in the same folder as the dropped file ae Coordinate Converter Icon opens the astronomical coordinate and time converter module This feature retrieves coordinates from SIMBAD and converts them to other standard astronomical coordinate systems It converts time for those coor
6. AIJ can display an image as a negative by selecting the display as image negative icon above the image AIJ uses an inverting lookup table to display the image rather than modifying the underlying image In this mode high pixel values are displayed as black and low pixel values are displayed as white 5 5 Image Invert Flip and Rotate The image displayed in an AIJ astro mode window can be inverted flipped in the X and or Y axis and or rotated by 0 or 180 degrees by using the View menu above the image The View menu options change only how an image is displayed and do not change the orientation of the data in the underlying image in memory To flip or rotate the underlying image use the Flip and Rotate options under the Process menu above an image AIJ does not currently support rotation of images by 90 or 270 degrees or arbitrary angles These display features will be included in a future release of AIJ 5 6 Panning Left click and drag the mouse to pan the image A middle mouse click will center the image at the clicked location if enabled under preferences 5 7 Zooming If using a mouse with a scroll wheel the wheel can be used to zoom in and out of the image Place the mouse cursor at the point in the image where the zooming should take place and roll the wheel If a mouse wheel is not available click in the image at the desired zoom point and use the zoom buttons above the image AAA or press control and left click
7. AIJ plate solve setup panel Plate solving requires an internet link and a free user key from nova astrometry net FITS Header Editor Icon opens the AIJ FITS Header Editor module This feature allows the user to view or edit the FITS header associated with an image See FITS Header Viewing and Editing section for more details 5 14 Menus above the Image Display Pull down menus are provided at the top of the image display to allow direct access to many features commonly used by astronomers File menu provides several options for opening and saving image stack and data files The Save image display option saves the displayed image to a PNG or JPG file using the displayed size and current contrast settings and includes all information and apertures displayed in the image Other save options will save the full resolution image without the overlay information and or the displayed apertures The first image will need to be opened from either the OS by double clicking it if a file type association has been set up or by dragging and dropping a file onto the AIJ toolbar or by using the AIJ toolbar File menu Subsequent images can be opened from the AIJ File menu above an image by dragging and dropping a file onto an existing image opens in same window or the AIJ toolbar opens a new window through the OS or through the AIJ toolbar File menu Preferences menu provides several options for changing how an image is displayed W
8. If a master flat file has already been created and it is to be used to reduce the science data deselect Build select Enable and then point to the master flat file using the lower directory and file name fields To first create a master flat file from raw images also select Build and then select either ave or med to build the master by average or median combining the images Also specify the location and file name pattern for the raw files on the upper line of this section The master flat file will be saved at the location specified on the lower line and then as each science file is processed the same master flat file will be used to flat field the science data The value under Totals for the top line specifies the number of raw flat files matching the defined pattern and the value on the lower line indicates how many files match the master flat file name usually one or zero The Preferences menu contains an option to Remove gradient from calibrated raw flats when creating master flat If you suspect that your flat field surface sky dome etc is not evenly illuminated this option will fit a plane to all calibrated flat field images and divide out the illumination gradient prior to combining the raw images IMPORTANT NOTE When building a master flat unless all raw flat images are of the same exposure time as the master dark image it 1s necessary to have a master bias file defined and enabled so that a bias subtracted master dark
9. Overlay selection 6 Data Processor DP Module 6 1 Overview of Operation To start a data processing data reduction session click the DP icon on the AIJ toolbar or use an image s menu selection Process gt Data Reduction Facility DP operates much like a script in that it processes selected calibration and science images in a predefined sequence Fields are provided to define the directory folder locations and file name patterns of data to be processed Checkboxes are provided to enable and disable various tasks that can be included in the data processing session Each option or field in the display has tool tip help that pops up when the mouse pointer is positioned over the item for more than about a second The tool tip will disappear after 3 4 seconds The user often needs more than a few seconds to read the sometimes lengthy information so to keep the text displayed longer the mouse pointer can be slowly moved over the item after the tool tip is displayed Input and output files can be any format supported by generic ImageJ The input and output formats may be the same or may be different For example FITS files can to be processed as input and a TIFF files to be written as output 6 2 Post Processing vs Real Time Operation DP can be used in post processing mode by setting the Polling Interval at the bottom left of the DP panel to zero In this mode DP will process all images as set up in the control panel and t
10. account for new images written into the science directory until all of the previously matching images have been processed and a new polling cycle begins The Set Aperture button st provides direct access to the aperture settings panels To force the Multi Aperture settings panel to display after the next image has been calibrated press the button If a DP run is paused and continued or paused reset and restarted the same multi aperture settings and aperture locations will continue to be used unless the L button has been pressed When restarting a DP run it may be desired to remove all of the previous data from the measurements table To do so either press the Clear Measurements Table button ES or close the measurements table window 6 4 Sample Setup Figure 5 shows an example setup that would process 148 WASP 12b images first creating a master bias from files in the same directory as the science images that start with bias _ and end with fits similarly creating a master dark using a master flat that has previously been created and exists two directories up in a cals directory Wildcards are allowed in filename specifications with representing any single character and representing any number of characters RA and DEC of the target and latitude and longitude of the observatory are required if calculations of altitude airmass HJD are desired Check Use to calculate these values and
11. check Save to add the values to the output file s FITS header The processed files are placed in a subdirectory called pipelineout in this case and each file has the suffix bsdf added 1 e bias subtracted scaled for non linearity dark subtracted and flat fielded A key field to set up is the polling interval at the bottom right When set to 0 all matching files in the specified directory when the script is started will be reduced and then the process will stop If set to any other number the Primary Directory will be polled at that interval in seconds for new incoming files after all of the initial files have been processed This mode is useful for monitoring for the arrival of new images from a camera and provides for the capability of near real time light curve plotting during an observing session When all fields are setup as desired click the Start button to begin processing Any specified master calibration files will be created first followed by the science image processing If STOP 1s pressed processing will pause after the next image reduction has been completed Press Reset to start over or press Continue the Start button will now be labeled Continue to finish processing without starting over Note Most options and fields in the Data Processor interface have generous tooltips available to explain the feature s operation Hover the mouse over a field to see its tooltip To keep it displayed longer
12. opened by drag and drop Save Files Now Save Settings Only Cancel If you only want to save a subset of the files listed disable the unneeded files at the top To change the default file name suffix type in the relevant box Click Save Files Now and a file save dialog will open Navigate to the desired save folder and enter the desired file name prefix and click SAVE The selected files will be created 10 2 1 12 Save a subset of Data to Send to Collaborators Since the measurements table produced by Multi aperture contain large numbers of data columns it 1s often desirable to send a subset of the data to collaborators To do so use the Multi plot_Main gt File gt Save data subset to file menu item The following panel will open The settings shown will produce a 3 column table containing time relative flux normalized and relative flux error normalized recall that the rel flux T1 n and rel flux err T1 n data columns were added to the table using the New Col icon After clicking OK a file save dialog will open Navigate to the folder and enter the desired file name and click SAVE to create the file Bl Save data subset 2 Select datasets in the order to be saved Leave extra selections blank ifno more data is to be saved JD_UTC gt rel_flux_T1_n X rel_flux_err_T1_n v l Save column headings V Comment headings with l Save row numbers Save row labels OK Cancel
13. orignal method MV Show this panel of other aperture photometry parameters OK Cancel 10 Step by Step Guide to Differential Photometry in AlJ 10 1 Introduction This section provides a new AIJ user with basic step by step instructions on how to perform differential photometry and produce a light curve plot starting with a time series of calibrated images Most AIJ controls have verbose tool tip information that describes its use To access the tool tip information mouse over the control for about a half second and the help will appear on the screen To keep the information on the screen longer than the default time continue to slowly move the mouse over the control If images have not already been calibrated the Data Processor DP module on the AIJ toolbar provides the capability to create master bias dark and flat field images and to calibrate raw images using those master calibration files DP optionally operates in real time mode to calibrate data perform differential photometry and plot a light curve as images are written from the camera DP runs independent of and in parallel with any camera telescope control software For more information see the DP section NOTE an AIJ support user forum is available at http astroimagej 1065399 n5 nabble com 10 2 Step by Step Instructions 10 2 1 1 Install AIJ as described in the Installation section 10 2 1 2 Update the new installation to the latest version
14. out of transit data are fitted This setting is useful for transits or other light curves that show an eclipse all data in the Y dataset are used to normalize and or detrend This setting is useful for comparison star plots If airmass detrending is applied to a good comparison star the resulting plot should be flat unless other systematics are present 10 2 1 10 4 Plot Window Controls REMOVE BAD DATA if you have clouded or other bad data in your sequence the corresponding data point and table row can be deleted interactively in the plot by holding the shift key and moving the mouse in the plot until the bad data point is bolded While it is bolded carefully left click the mouse and the point and corresponding table row will be removed If a mistake is made when removing a point immediately right click while holding the shift key to re insert the data point ZOOM PLOT left click in the plot to zoom in right click to zoom out note this is different than in the image window which requires a control left or right click to zoom If a mouse with a scroll wheel 1s available roll the scroll wheel inside the plot to zoom in and out same as image window PAN PLOT left click and drag to pan the plot up down left right RETURN TO FULL PLOT right click inside plot to return to the un zoomed un panned standard plot ashi gt WASP 12b on UT2013 01 27 UofL MORC24 Telescope r filter 100sec fap 25 40 80 rel_flux_T1 1 025
15. rel flux THAIRMASS detrended rel_flux_C2 AIRMASS detrended bin size 2 1 020 x rel_flux_C3 AIRMASS detrended bin size 2 rel_flux_C4 AIRMASS detrended bin size 2 x rel_flux_C5 AIRMASS detrended bin size 2 1 015 rel flux C6 AIRMASS detrended bin size 2 x rel_flux_C7 AIRMASS detrended bin size 2 e rel_flux_C8 AIRMASS detrended bin size 2 Total Comparison Star Counts scaled 1 010 Negative Airmass scaled 1 005 Saturation indication Sky Pixel_T1 1 000 ot r a wo o n wpe J e e wo o So o l oe le pe 1 t o wo co n wo co i 0 975 wo in mee wo o wo a n Relative Flux normalized elette a wo a i wo n on wo n O 0 945 0 940 e an ee a oe ee As HH PE N tes a rete ten 1 0 935 s no 0 930 0 925 0 920 a ene Predicted PRIMES c gress Ingress 0 915 L 0 50 0 55 0 60 0 65 0 70 0 75 0 80 Geocentric Julian Date UTC 2456319 List Save Copy x 0 7572 y 0 9364 10 2 1 10 5 X data settings Most light curve plots are based on a common time data column For these normal cases the Default X data column can be set at the upper left of the Multi plot Main panel The selected dataset will be used to plot all Y axis data columns if default is selected for X data in
16. to zoom in or control and right click to zoom out Press the zoom in fast button b above the image or double left click in the image to zoom in fast Double right click to zoom out such that the image will fill the available area in the image display Press the zoom to fit icon X or triple right click to zoom out such that the full image is displayed on the screen which may leave white space at top bottom or left right of the image The keyboard up arrow or plus key will zoom in at the last clicked location in an image while the keyboard down arrow or minus key will zoom out 5 8 Mouse Pointer Live Photometer AIJ offers a live photometer which follows the mouse pointer around in the image and provides a peak pixel count in the aperture or mean pixel count if selected in the Preferences menu and a sky subtracted integrated count in the aperture The photometer radius and inner and outer background radii can be set by clicking the change aperture settings icon x above the image Display of the photometer can be disabled by deselecting the Preferences menu item Show photometer regions at mouse cursor The photometer peak and integrated counts will be updated above the image even if the photometer annuli are not showing 5 9 Single Aperture Photometry Shift left click on the mouse to run the single aperture photometer or click the Aperture Photometry Tool icon on the AIJ tool
17. values If the default settings do not display the desired results the constant factors can be changed by the user under the Scale menu Alternatively the arrows that define the blue region of the histogram can be dragged to adjust the image display manually The currently displayed range of pixel values is highlighted in blue in the histogram The blue region can be dragged with the mouse to adjust the brightness The pixel value corresponding to black is indicated in the histogram black box and the pixel value corresponding to white 1s indicated in the white box These numbers can be directly modified by clicking on an existing number and typing a new value and pressing lt Enter gt Alternatively a right mouse drag in the image will control the image brightness contrast similar to DS9 When right click dragging watch the histogram to see how the motion affects the settings Right dragging the mouse up and down changes the image brightness moves the range of values displayed up and down the same as dragging the blue region in the histogram Right dragging right and left changes the contrast by increasing and decreasing the width of the displayed range of pixel values Alternatively pressing the shift key while rolling the mouse wheel adjusts the image brightness and pressing the control key while rolling the mouse adjusts the contrast To return to auto scale setting click on the 7 icon above the image 5 4 Image Negative
18. 0 9 Save the Target star Normalized Relative Flux Back to the Table 8 39 LO 2 Veli Save all Workine Piles 16s ISK vxcecystatse nese ctetatacecaccuancealosare cannes cueciars anna 40 10 2 1 12 Save a subset of Data to Send to Collaborators ssesessesesesensesenensesesenseseserseserersesene 40 1 Introduction AstroImageJ AIJ is simply generic ImageJ IJ with customizations to the base code and a packaged set of astronomy specific plugins AIJ and IJ are public domain Java image processing programs inspired by NIH Image for the Macintosh IJ was developed by Wayne Rasband at the National Institutes of Health The plugins are based on the Astronomy Plugins package written by Frederic V Hessman et al of Inst f Astrophysik Georg August Universitat Gottingen The AstroImageJ customizations are written by Karen Collins karen collins at insightbb com and John Kielkopf of the University of Louisville The application is open source and the source code is embedded within the ij jar file and the Astronomy_ jar file To report bugs or suggest new features please email Karen Collins at the address indicated above For a step by step guide to getting started with AIJ jump to section 10 2 Installation Java must be installed on a computer before running AstroImageJ Java 64 bit is strongly recommended if supported by your OS Java can be downloaded from http www java com en download manual jsp
19. 00 10 2 1 4 Image Display Interface Overview A brief intro to the image display interface is provided here Please review the section AstroImageJ Image Display Interface for more information Default image scaling is Auto brightness and contrast There are a variety of related settings in the Scale menu The black and white values can be manually entered under the histogram region or the histogram region selectors can be dragged to change the display settings While in Auto brightness and contrast mode manually set values will automatically update when a new image in the stack is displayed To keep scaling values constant use Scale gt Fixed brightness and contrast North East arrows and distance scales are set automatically and show in yellow when compatible WCS headers are found If they are red no AIJ compatible WCS data has been found in the image header Directions and distance scales can be set manually in the WCS menu and or the overlay of this data on the image can be disabled in the View menu 22E6 These icons control which parts of apertures are displayed on the image when selected apertures will be placed at the centroid of the star near the mouse click This button should normally always be selected Centroid is either on or off for all apertures in versions 2 1 4 and below In versions 2 1 5 and above centroid can be controlled on a per aperture basis IRQ These icons con
20. Cnts value displays the sum of all the pixel values within the aperture less the mean of the pixel values in the background annulus The Int Cnts box label changes to either Length or Arclen to report length in pixels or arclength in decimal or sexagesimal format when the mouse is being dragged with the middle mouse button depressed Sexagesimal format can be selected deselected in the Preferences menu If WCS headers are available or if the pixel scale of the image has been set under the Preferences menu arclength will be displayed Otherwise distance in pixels will be displayed The length data can be written to a log window and saved if desired by selecting the corresponding option in the Preferences menu 5 2 Data Displayed in the Image The blue zoom box displayed in the up left of the image indicates the faction of the image that is currently displayed The size of the zoom box can be set under the preferences menu The green Y arrow points to what would be the top of the image prior to any inverting rotating see the View menu The green X arrow points to what would be the right of the image prior to any inverting rotating The N and E directional arrows and the distance scales show in either red or yellow If WCS headers are found in the image the display color is yellow and the directions and scales will be automatically set If no WCS headers are found the display color is red In the case of no
21. FITS dataset may contain extensions FITS Flexible Image Transport System format is defined in Astronomy land Astrophysics volume 376 page 359 bibcode 2001A8A 376 359H 11 0E 02 exposure time seconds 2009 11 05T06 30 45 date of observation UT Light Frame image type target R instrument OC O T E OP a telescope 2009 11 05706 32 44 fle creation date YYYY MM DDThh mm ss UT 2455140 771354167 Julian Date at start of exposure IJ 2455140 7719328706 Julian Date at mid exposure J 12455140 7753200424 Heliocentric JD at mid exposure IJ 6 509 108333333334 right ascension of target hours 13 129 672333333333334 dedination of target degrees IJ 138 25416666666667 geographic latitude of observation IJ 85 76027777777777 geographic longitude of observation IJ 55 32571849252983 altitude of target object at mid exposure IJ 1 215177268581516 airmass at mid exposure IJ Previous Filename wasp12b_26 fits E Lock keyword values 9 Aperture Settings To perform single aperture photometry in astro mode hold the lt shift gt key and left click near the object to be measured to place an aperture at its centroid Alternatively photometry mode can be entered by clicking on the IJ toolbar Aperture Photometry Tool icon to the right of the astro mode ico
22. In general the processing steps run in sequence from the top to the bottom of the panel 6 3 1 2 Options The options checkboxes allow various options to be enabled or disabled for each processing step Although the Macro 1 and Macro 2 checkboxes fall under the Options heading they are Control settings to enable or disable user created ImageJ macros as part of the data processing sequence 6 3 1 3 Directory The directory boxes define the directory folder location of each category of image files The directory path is automatically entered when a filename pattern is selected see below or the directory path can be directly typed into the box or the associated solid blue folder icon can be used to navigate to and select a directory The raw and master calibration file directories can either follow the science directory path or can operate independently by setting options in the Preferences menu at the top of the DP panel If a directory box is empty it will follow the science directory as well Unix Linux Dos current directory notation can be used to reference the science directory followed by relative subdirectory specification For example darks refers to a subdirectory of the science directory called darks The notation for up one directory can also be used to reference a parent directory For example cals refers to a directory two levels up called cals 6 3 1 4 Filename Pattern
23. NASA 5 Kentucky AstroImage 2 4 1 User Guide plus Getting Started with Differential Photometry an image analysis tool for astronomy website http www astro louisville edu software astroimage support forum http astroimage 1065399 n5 nabble com Feature Overview e General purpose but optimized for time series aperture photometry e Open source and written in Java so runs under Windows OS X Linux e Real time or post processed calibration analysis and plotting e DS9 like image display with live photometer and WCS support e Astrometry net plate solve capability internet connection required e FITS header handling viewing editing e Miulti image processing bias dark flat CCD non linearity correction e Miulti exposure multi aperture differential photometry e Interactive multi curve plotting e Interactive lightcurve detrending e Astronomical coord conversion J2000 EoD equatorial ecliptic galactic e Astronomical time conversion UTC local LST JD HJD BJDrpp Table of Contents koroe Oe n E E E N E A E E AOE E E EE 5 2e a O eee E E E E EE E E E E E E 5 SAd aaO aE a couoaswasacuenaesanstu_aaeeianvorous saveecee cctessceuanstsaeuensasaseonuesceeen J 2 2 Windows SEAN OI ssania EEr e ana A Ona a E aei 5 2 x VAG MINS aaO srn E N E E E A E E ETES 6 Dix Update AN tO Ware SCSI acs este tce ic heres nE aces cate ce ate ENETEIA EENEN 6 A AstrolmageJ vs Generic Ina GC 02 5 01sessesesssessesnndeseu
24. The file name pattern boxes specify which files in the directory are to be processed Unix wildcard notation using and should be used to define the filename patterns The blue and white folder icon to the right of each box can be used to navigate to a sample file that should be processed When a file is selected the associated directory path is loaded into the corresponding directory field and the file name 1s loaded into the filename pattern field By default a is automatically placed between the last underscore and last dot characters in the filename if both exist This behavior can be disabled in the preferences menu at the top of the DP panel 6 3 1 5 Totals The totals column indicates the number of files found that match each directory plus file name pattern The Control Panel section totals at the bottom of the panel indicate the number of files that have already been processed and the number of files remaining to be processed 6 3 2 Vertical Sections Starting from the top the vertical sections are labeled in the border of each section as 6 3 2 1 Science Image Processing This section is divided into two subsections In the Filename Pattern Matching subsection the directory and file name pattern should be set up and enabled If this subsection is disabled only master calibration files will be built if enabled Enable the Sort Num option to process the matching images in numerical order An image file
25. WCS headers the directions and scales can be set under the WCS menu Display of each of the zoom box X and Y direction arrows N and E direction arrows and the image scale indicator can be independently enabled or disabled under the View menu 5 3 Contrast Brightness Adjustment Under the Scale menu select either auto brightness amp contrast based on the image s pixel value standard deviation fixed brightness amp contrast keeps the same user defined levels from image to image or full dynamic range displays the full range of pixel values in the image The selected option 1s saved and recalled when new images are opened or a new image is displayed in a stack The black and white values indicated below the histogram can be directly entered in any mode but if auto mode is selected they will update when the image is updated or another image is opened The min and max histogram values are normally automatically set to the min and max pixel values of the displayed image However the values can be directly entered and will not change from image to image if the Scale menu item Use fixed min and max histogram values is enabled AIJ provides a number of ways to adjust the contrast and brightness of an image The simplest way is to click the Auto Scale button above the image Auto scale displays a range of pixel values based on a constant factor times the standard deviation of the images pixel
26. a master bias file has already been created and it is to be used to reduce the science data deselect Build select Enable and then point to the master bias file using the lower directory and file name fields To first create a master bias file from raw images also select Build and then select either ave or med to build the master by average or median combining the images Also specify the location and file name pattern for the raw files on the upper line of this section The master bias file will be saved at the location specified on the lower line and then as each science file is processed the same master bias file will be used to bias subtract the science data The value under Totals for the top line specifies the number of raw bias files matching the defined pattern and the value on the lower line indicates how many files match the master bias file name usually one or zero 6 3 2 3 Dark Subtraction This section allows the user to define locations and file names for raw and master dark images If a master dark file has already been created and it is to be used to reduce the science data deselect Build select Enable and then point to the master dark file using the lower directory and file name fields To first create a master dark file from raw images also select Build and then select either ave or med to build the master by average or median combining the images Also specify the location and file name pattern for the raw f
27. an image before running that selection The most commonly used ROI shapes are oval rectangular and line ROIs can be drawn by clicking on the related icon on the AIJ toolbar however astro mode panning and other convenient mouse functions will be lost while the ROI is being drawn If you use the AIJ toolbar to draw the regions remember to click on the astro mode icon after you are finished to restore astro mode functionality Short cuts are available to draw these three common ROI shapes without leaving astro mode Press and hold lt shift gt while left dragging to draw an oval ROI Press and hold lt control gt while left dragging to draw a rectangle ROI Press and hold lt alt gt while left dragging to draw a line ROI To move or edit an existing ROI press and hold the lt tab gt key then use the mouse to point at the ROI and drag it to the new location To edit the shape of an ROI hold the lt tab gt key and hover the mouse cursor over one of the ROI selection points until it changes to a finger shape then click and drag to change the ROI shape Currently to modify nonsymmetrical ROIs it may be necessary to set the image orientation to Invert None and 0 degrees under the View menu It may be quicker to simply redraw the ROI using the shortcuts described above This issue will be resolved in a future AIJ release ROIs can be cleared by clicking the clear aperture overlay icon above an image or by using the View menu Clear
28. and all underscore characters in the header value are replaced with a space before attempting a match If a match is not found DP will show an error message and stop running If FITS header latitude and longitude is selected as the observatory location source the science image headers must contain keywords as defined in the Observatory Latitude Keyword and Observatory Longitude Keyword fields of the FITS Header Settings input panel The header values associated with the keywords must be either real numbers or a string containing a sexagesimal representation of the geographic location of the observatory The latitude value should be north positive and the longitude value should be east positive If latitude is south positive or longitude is west positive check the appropriate negate box es in the input settings panel 6 3 2 6 5 FITS Header Output Settings DP can automatically add new FITS header keywords and values to output file headers if the input parameters have been set up as described in the previous four sections All of the keywords in the FITS Header Settings panel FITS Header Output Settings section shown in Figure 4 are enabled by default DP DPCC will calculate those values and write them to the output file headers Each keyword name can be customized and enabled disable in the settings panel Figure 6 Data Processor FITS Header Settings E General FITS Header Settings o e 2 FITS Header Inpu
29. as described in the Update section 29 10 2 1 3 Open the image sequence for processing ccceeeeeessssesesssseessseesesseseesseesseeeseseeeeeeeeeens 29 10 2 1 4 Image Display Interface Overview a ss geccsedcekcadacsselesdsceczavdea staves tnnedbasustlesdsdeeteuddastaesedtoneess 31 tO ke SCP Up AA Peruine Pal AMI CCC ts iss pasate A Sonu etoen teed atenveuneen ciao 32 10 2 1 6 Experiment to Find a Suitable Starting Aperture S1Z cc cccccccceceeeeeeeeeeeeeeeeeeeeeees 33 10 2 1 7 Run Multi Aperture Differential Photometry 0 cc cccccccccscceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeees 34 1O52 128 V arable A peruireW Sa Ge crn E RE eR 36 10 2 1 9 Load Default Plot Configuratio s sson nana a A 36 10 2 1 10 Understanding the Basics of Multi plot wo ccccccccceccccceceeeeeceeeeeeeeeeeeceeeeeeeeeeeeeeeees 36 POZO V Marker Wand V Markor 2 vec start cere ceas aceteveudetstueeitessvatctndecsten eta stanaie e 36 10 2 1 10 2 Detrend and Normalize Region Selection ccccscssccecceeeeeeeeeeeeeeeeeeeeeeeeeeeeeees 36 LOZ 1 1053 Dette Mode nestea sicetaciae hasan aiid eee 37 102 104 Plor Wmdow Controls ersero eosa E E A RE 37 102 Ue a dati seto S a S 38 102 10 6 Overview ofthe Y axis ata isteicacinsssstaatedcassdales a S 38 10 2 1 10 7 Changing the Comparison Star Ensemble without Rerunning Multi Aperture 39 10 2 1 10 8 Description of all Data Column Names Produced by Multi Aperture 39 10 2 1 1
30. as described in the Update section 10 2 1 3 Open the image sequence for processing Open an image sequence into an AIJ stack by clicking AIJ_Toolbar gt File gt Import gt Import Sequence If an image is already displayed go to its File menu and select Open sequence in new window In the file selection menu that pops up point to the folder or an image in the folder that contains your images Click Select and the following window will open Th Sequence Options ae Number of images Starting image Increment Scale images File name contains or enter pattern Convert to RGB if Sotnames numerically W Use virtual stack 4098 x 4096 x 168 10762 5MB OK Cancel Help There are 168 images in the folder used in the example above If there are some images in the folder that should be excluded type in a File name contains pattern to further refine to AIJ which files you want to open The easiest option is to put only the files you want to work on in the folder so that you don t need to worry about filtering Note that the bottom line displays the total number of images that will be loaded after any filtering and it shows the memory that will be required in this case 10 GB If all of your images will fit into the memory allocated to Java on your machine UNcheck Use virtual stack and all images will all be loaded into memory at once This mode will let you move back and forth in the Stac
31. bar The single aperture photometer results are listed in a measurements table and can be saved or plotted using Multi Plot The data values reported can be set by clicking the change aperture settings icon x above the image or by selecting Edit gt Aperture Settings in the menus above the image or by double clicking on the Aperture Photometry Tool icon on the AIJ toolbar See the Aperture Settings section for more details Apertures displayed on an image can be removed by clicking the clear apertures overlay icon above the image 5 10 Apertures Displayed in the Image Apertures are displayed as a non destructive overlay on the image at the mouse curser if enabled in Preferences as a result of single aperture photometry or multi aperture photometry Display of the background annulus of apertures from all three sources can be enabled or disabled by clicking the display sky background regions icon O above the image The display source integrated counts icon is applicable for both single and multi aperture photometry while the display source identification icon e is applicable only to multi aperture photometry The displayed source IDs indicate which aperture is related to similarly identified data in the measurements table The centroid aperture icon enables or disables the aperture centroid feature and is applicable to both single and multi aperture photometry Finally the clear aperture o
32. can be exposure time scaled to match the exposure time of each raw flat DP does not currently provide the capability to use multiple master dark images for different raw flat exposure times 6 3 2 5 Non Linearity Correction This section allows the user to define a formula for the correction of non linear characteristics of a CCD A master bias file must be defined and enabled for this option to work properly If non linear behavior has not been measured and characterized for your CCD deselect this option Otherwise the correction formula coefficients entered in the three fields will be used to correct the value of each pixel in a science image after bias subtraction but before dark subtraction and flat field division If non linearity correction is enabled while building master dark and master flat images the pixel values of the raw files will have non linearity correction applied after bias subtraction IMPORTANT NOTE If non linearity correction is used while processing science files the master calibration files should be created at the same time or should have previously been created using the same non linearity correction coefficients and the same set of master calibration files 6 3 2 6 FITS Header Updates This section provides the capability to add new keywords and values to the output file FITS header When this feature is enabled a DP instance of the Coordinate Converter DPCC module will be displayed as shown in Figur
33. ch limits network traffic and improves the solve time Click the plate solve icon C above an image or image stack to bring up the Astrometry Settings panel shown below Astrometry can also be performed as part of a Data Processor run To enable the feature in DP enable Plate Solve in the FITS Header Updates section of the DP CCD Data Processor panel and Click to set the astrometry options The first time the Astrometry module is used in AIJ a free user key will need to be obtained from nova astrometry net Copy the key into the User Key box below Figure 7 Astrometry Plate Solve Setup Panel LL User Key Get key from nova astrometry net Auto Save V Enable IMPORTANT WARNING overwrites original image Skip Images With WCS V Enable Radius pixels Annotate V Enable 30 00 2 m Start Slice Process Stack V Enable 16 _ Filter Radius pixels Median Filter V Enable 2E ae Max Peak ADU Noise Tol StdDev Max Num Stars Peak Find Options Limit Max Peaks 100002 0 104 50 Radius pixels Sky Inner pixels Sky Outer pixels Centroid Near Peaks Enable 20 00 50 00 E 30 002 Plate Scale arcsec pix Tolerance arcsec pix Constrain Plate Scale Enable 0 4002 0 20012 Center RA Hours Center Dec Degrees Radius arcmin Constrain Sky Location Enable 06 20 32 794 29 40 20 29 40 0 Show Results Log Enable START CANCEL An ent
34. d from to Anywhere You can restore the original setting once AstroImageJ is running the first time AstroImageJ does not work with Oracle Java 7 because the Apple launcher it uses does not support Java 7 To use Java 7 you have to move it to the top of the list in Applications Utilities Java Preferences and run AstroImageJ from the command line using something like java jar Xmx640m ij jar 3 Update AIJ to latest version After you have installed the full installation package as described in the previous section always update AIJ to the latest version using the semi automatic upgrade facility in AIJ you may need root user access for this feature to work properly since it writes files to your installation folder To update go to AIJ Toolbar gt Help gt Update AstroImageJ Select the latest build in the pull down menu the latest released build is the default Click OK and files will be downloaded and automatically installed in the proper location on your computer After the files have been installed AIJ will automatically close When you restart AIJ you will be running the new version 4 AstroImageJ vs Generic ImageJ 4 1 Important Notes This user guide assumes that the astro mode icon is selected on the AIJ Toolbar as shown in Figure 1 and as a result the image is displayed in the AIJ interface shown in Figure 2 In the default mode all images are opened in this format If any of the IJ specific tools are selected the icons t
35. dark will result in no dark exposure time scaling The full flat field creation algorithm first bias subtracts each flat image if selected scales the pixel values by the non linearity coefficients if selected dark subtracts the resulting image if selected removes any gradient from the image if selected near the bottom and normalizes the image to an average value of 1 0 After all specified flat images have been processed in this way the resulting images are either average or median combined to create the master flat field image Processed Images Science Images after any selected master calibration files have been created each science image matching the Primary Directory Filename Pattern and Filename Number Filter settings defined at the top of the window are processed according to the use values selected To use dark exposure time correction it must be selected and use must be selected for both master bias and master dark The full science processing algorithm first bias subtracts each image if selected scales the pixel values by the non linearity coefficients if selected dark subtracts the resulting image if selected and then divides by the master flat if selected If Cosmic Ray Removal is selected outlier pixels in the image are replaced by the average of its four neighbors Cosmic ray removal is not suggested for use with photometric data since it can clip stee
36. date and time must be defined in the science image s header by one of the following keywords DATE OBS DATEOBS DATE OBS UT DATE If both date and time are not found in one of those keywords DP searches for the date only in the same keywords If a date is found the following keywords are searched for UTC time TIME OBS TIMEOBS TIME OBS TM START TM START UT UTC UTSTART UT START UT START and UT_TIME 6 3 2 6 2 Exposure Time Source Exposure time is required for the calculation of mid exposure based time standards The following keywords are searched for exposure time EXPTIME and EXPOSURE If neither is found the following keyword pairs are searched for exposure start and exposure end times TM START TM END TM START TM END UT START UT END and UT START UT END 6 3 2 6 3 Target Coordinate Source The target s coordinates can be provided in five ways by selecting the desired Target Coordinate Source If Coordinate Converter manual entry is selected the SIMBAD Object ID and all coordinate fields of DPCC will be enabled for user manual data entry The target name field or any coordinate system pair may be used to define the target s coordinates however the lt Enter gt key must be pressed after typing data into any field If FITS header target name is selected as the target coordinate source all science images being processed must contain a FITS header keyword as defined in the FITS Header Settings panel which can be op
37. dinates and a specified observing location to from UTC local time Local Sidereal Time LST Julian Date JD Heliocentric JD HJD and Barycentric JD BJDrpp Lunar phase and proximity of the moon and of all major planets in the solar system are also provided Archival sky images can be displayed via the SK Y MAP org website Single Aperture Photometry Icon when selected single aperture photometry will be performed by left clicking the mouse at the desired location in an image Single aperture photometry can also be performed even if this icon is not depressed by holding the shift key when left clicking in an image If the centroid feature is enabled the aperture will be placed at the nearest centroid location The photometry results will be output to a measurements table and can be plotted or saved to disk 5 AstroImageJ Image Display Interface When a FITS image or any other supported image type is opened the image will be displayed in a window as shown Figure 2 Figure 2 AstroImageJ Image Display Interface i SOES File Preferences Scale View Edit Process Color Analyze WCS 1 168 wasp12b_9_bsdffits 4098x4098 pixels 16 bit 53GB WCS RA SIP DEC SIP TAN CD matrix ImageJ X 2 603 9375 ImageJ Y 55 0804 Value 2 696 0000 RA 06 30 15 804 DEC 29 27 19 22 Peak 2 864 0000 FITS X 2 604 4375 FITS Y 4 043 4196 Int Cnts 523 3604 geg Ea Z2OHe RARR P 0 0000 min 2 455 8571
38. e 5 The DPCC window can be alternately displayed or hidden by clicking the LZ icon in this section of the DP GUI DPCC will continue to operate as set up even if the window is closed hidden The DPCC instance runs independent of an instance started by clicking the Coordinate Converter icon on the AIJ toolbar Both instances running at the same time may be confusing at first but the DPCC instance is differentiated by the DP prefix in the window title and the Epoch of Interest time entry fields will be disabled grayed out since DP automatically enters a time which must be derived from the science image s FITS header Depending on settings described in the following sections other DPCC fields may be disabled as well In general if data that is normally manually entered into a field of the Coordinate Converter GUI is being derived from a FITS header value by DP the field and other associated fields will be disabled for manual entry in DPCC Four categories of new keywords and values may be added to the output image header including target coordinates observatory location airmass and various time standards To calculate new header values DP must be able to derive UTC based start of exposure time and exposure time from the science image header and the target coordinates and observatory location must either be derived by DP from the science image header or the user must manually enter that data into DPCC before starting the DP run Figure 5
39. eft blank The Suffix field defines a string of characters to be inserted into the input science image name after the primary part of the file name and before the dot in the file type to create the output file name For example with Suffix set to out an input science image file name of image fits becomes image_out fits Leave the Suffix field blank to use the input file name as the output file name without modification The Format field should be set to the desired output file format or simply leave it blank to write the output files in the same format as the input file Any output format supported by generic ImageJ may used Valid FITS file designations are fits fit FITS FIT fts and FTS Commonly used additional designations include tif jpg gif png bmp raw avi zip Saves as a zipped tif file Select GZIP to compress the output science files in gzip format The entire image is compressed including any header information fpack compression format excluding compression of the headers is not currently supported A gzipped image can be opened directly by AIJ without externally decompressing the image first Master calibration images can be saved in zipped format by including a gz suffix in the filename specification e g mdark fits gz 6 3 2 8 Post Processing This section allows the user to select Multi Aperture and Multi plot to run after each image has been calibrated The Multi Aperture setup panel will on
40. ened by clicking the SJ button The panel is shown in Figure 4 The keyword containing the target name not the target name should be entered in the field of the input settings section named Target Name Keyword The keyword value from a science image is transferred to DPCC s SIMBAD Object ID field and an attempt is made to resolve the object s coordinates via a SIMBAD query Internet access is required for this option The search is not case sensitive and all underscore characters in the header value are replaced with a space before starting the search If no valid SIMBAD ID is found DP will show an error message and stop running Duplicate target names from one science image to the next will not trigger a new SIMBAD query The FITS header target name less trailing alpha char option works the same as the previous option however if the object name has a trailing alpha character it is removed prior to the SIMBAD query This feature is useful since many exoplanet names in SIMBAD do not have proper motion entries while the host star name does For example at the time of this writing WASP 12 returns proper motion values from SIMBAD while WASP 12b does not If FITS header target RA DEC J2000 is selected as the target coordinate source the science file headers must contain keywords defined in Target RA Keyword and Target DEC Keyword and the values of those keywords must be either a real number containing the J2000 coordinate va
41. etl cadismae nc DA cus nota autiecadesmend ae Maman Ame 18 6 3 2 4 Flat DivisiOMcccicnhevtaccsue nina E a 18 623 225 NOn Lineari y COLL CHOON senesi ie a E E stevie E E S 19 02 0e PLILTS Header Update Sranannsi cores taste a cores a a nee eee 19 6 26 Exposure Start Date Time SOURCE sci eiahcdshet in aiir i a R eeaiaeds 20 O a0 Exposure Time SUIC Eakin R a a a 20 6k20 Taro CO0t dinate SOULCE ruoriin tor na E ame eeen 21 6 3 2 6 4 Observatory Location Source ssssseseeeeeesesesesseesssessessssssssssssssssssssssssssssssssssssssss 2l O2 O FITS Header OUPS EIDES aeea AAA 22 6 37227 Save Calibrated ima ES nai E T E R E made 22 G2 9a POSL ROC CS INO auiii e ie e e a 23 6 3 2 9 Control Pane lea 23 SAN UB E EE T ec E S E A E S E E A A es 24 0o Data Reduccion Algor imS ieena a ne a CR tee 23 7 Plate Solving using the Astrometry net Web Portal cccccccccccccceecceeeeeececeeeeeeeeeeeeeeeeeeeeeceeeeeeeeeeeeees 26 8 FITS Header Viewing and Editing misasi a a EL il eaaae 26 XAperure SeN ES saraa S E 28 10 Step by Step Guide to Differential Photometry in AIJ oo cccccceceeecceeeeeeeeceeeeeeeeeeeeeeeeeeeeeeeeeeees 29 DO Les Inrodtctio iann a E a A E E 29 102 SEP py Step SUP COINS sea hecncttees ceete be code ds cdl heseteies Coa tal ta cot chatted 29 10 2 1 1 Install AIJ as described in the Installation Section cc ececcseesesssseneeeeeeeeeeeeeeeeeeeeens 29 10 2 1 2 Update the new installation to the latest version
42. ew memory setting Do not start AIJ by double clicking on 1j jar because no more than 64MB of memory will be allocated to AIJ For more information on generic ImageJ with Windows go to http rsbweb nih gov 1j docs install windows html 2 3 Mac OS X Installation Download AstroImageJ for Mac OS X from http www astro louisville edu software astroimagej index html by clicking on AstroImageJ mac zip After the download completes extract the zip file to the AstroImageJ Move this folder to the Applications folder open it and copy either AstrolmageJ or AstrolmageJ64 to the dock or desktop for easy access AstrolmageJ runs in 32 bit mode using Java 1 5 Java 1 4 on OS X 10 3 and AstrolmageJ 64 runs in 64 bit mode using Java 1 6 AstrolmageJ64 is not limited to 1800MB of memory but it requires a 64 bit Intel Mac running Mac OS X 10 5 or later The AstroImageJ mac zip file can be deleted For more information on generic ImageJ with Mac OS X go to http rsbweb nih gov 1j docs install osx html There are several workarounds required for some OS X versions Since OS X 10 7 Lion Java is no longer pre installed so you are prompted to install it the first time you install a Java application With OS X 10 8 Mountain Lion you may get the message AstroImageJ64 is damaged and can t be opened To work around this problem go to System Preferences gt Security amp Privacy gt General and set Allow applications downloade
43. hen an image is closed its preference settings are saved to ImageJ memory If multiple image windows are open and the preference settings in more than one window have changed the settings of the last window closed are saved over any other previously saved settings Preference settings are not saved to hard disk until AIJ closes so if AIJ crashes or is terminated improperly using something like killall imagej in Linux the settings will not have been updated in the IJ_ Prefs txt file for use the next time ImageJ is started View menu provides several options for setting the displayed orientation of an image and for enabling informational overlays The Clear Overlay option clears any apertures or ROIs drawn on the image but not the informational overlays The View menu options are non destructive and do not change the underlying image data Edit menu provides options to edit various data associated with an image or stack These options include editing of aperture settings base IJ measurement settings FITS header entries and stack configuration Process menu provides various tools to modify the data within an image Analyze menu provides several options to measure the data within an image and to plot and or save those results These options do not modify the image data 5 15 Notes on Generic ImageJ Regions of Interest Some of the items in the Analyze menu require a region of interest ROI to be defined within
44. hen stop DP can be used in real time processing mode by setting the polling interval to a non zero value A value of 5 for 5 seconds is a good starting point In real time mode all images matching the settings in the DP panel will be processed and after the polling interval time DP will scan the science image directory folder for new files matching the patterns specified Each time new matching files are found they will be calibrated and then optionally Multi aperture and Multi plot can be enabled to run for each new image thus performing photometry and lightcurve plotting in real time as new exposures are being written from the camera 6 3 DP User Interface The DP graphical user interface is organized into five sections horizontally and nine sections vertically as shown in Figure 4 Figure 4 Data Processor User Interface P CCD Data Processor o B PX File Preferences View Control Options Directory Filename Pattern r Science Image Processing Filename Pattern Matching V Enable v Sort Num Q Observations _WASP 12b_qty 17 20130127_WASP 12b_r filter ed WASP 12b_ fits Filename Number Filtering v Enable in OS Max 10000000000000 WASP 12b_ fits r Bias Subtraction E Build ave med Q Observations _cals CDK20N_U16M_1_exposures 20121006_bias_ 10 y bias_ fits V Enable Q Observations _cals U16M_2_masters ea mbias_ 20_ 20131002 fits UUE
45. iles on the upper line of this section The master dark file will be saved at the location specified on the lower line and then as each science file 1s processed the same master dark file will be used to dark subtract the science data The value under Totals for the top line specifies the number of raw dark files matching the defined pattern and the value on the lower line indicates how many files match the master dark file name usually one or zero If the scale option is enabled the master dark pixel values will be scaled according to the ratio of the science image exposure time or raw flat image exposure time in the case of master flat creation to the master dark exposure time The master dark image must be bias subtracted and the exposure time must be available in both FITS headers for this feature to work as expected See the FITS header Updates section for compatible exposure time keywords IMPORTANT NOTES If bias subtraction is not enabled master darks created will contain the bias signal If bias subtraction is enabled master darks created will be bias subtracted using the master bias file defined in the bias subtraction section If Non Linearity Correction is Enabled AND Bias Subtraction is Enabled the bias subtracted dark 1s scaled using the three coefficients specified in the Non Linearity Correction section 6 3 2 4 Flat Division This section allows the user to define locations and file names for raw and master flat images
46. ire stack of images can be blind solved using settings similar to those shown above For defocused images enabling Centroid Near Peaks may give a better solution If your image has peaks above a certain level that should be ignored enable Limit Max Peaks and set the maximum accepted peak ADU in the Max Peak ADU box If the plate scale is known entering the nominal scale in arcsec pixel and a tolerance may speed up the plate solve Also the sky location can be constrained if the blind solve gets lost or is slow Click START to begin processing the stack 8 FITS Header Viewing and Editing WARNING Do not edit FITS header values unless you are confident that you understand which keyword and value changes will comprise the integrity of the FITS image The display FITS header icon above an image opens the image s FITS header into a table for viewing and editing as shown in Figure 4 To change keyword values the user must deselect Lock Keyword Values below the table To edit an item double click in the corresponding table cell and type the desired value To delete a header keyword and its associated value and comment single click on a row of the table to highlight it and then click the Delete button To insert a new row into the table single click on an existing row to highlight it and then click on the Insert button to insert a new row below the highlighted row Double click each cell of the row to e
47. it 5 3GB WCS RA SIP DEC SIP TAN CD matrix ImageJ X 2 055 2328 ImageJ Y 42 8149 Value 2 698 0000 RA 06 30 32 027 DEC 29 27 13 71 Peak 2 872 0000 FITS X 2 055 7328 FITS Y 4 055 6851 Int Cnts 17 1614 a NOERLOGEs BAEAS gaa T mean 2 726 3636 white 3 851 1177 max 10 000 0000 After the first image is processed a Measurements window opens The photometer measurements are added to the table contained within Two plot control windows will open Multi plot Main and Multi plot Y data and along with a plot of the data Plot of Measurements Light curves may or may not be displayed in the plot depending on the previous or default setting in the plot control windows 10 2 1 8 Variable Aperture Usage The Multi aperture Measurements setup panel that was discussed previously has an option labeled Vary photometer aperture radii based on FWHM and a FWHM multiplication factor below The variable aperture mode first estimates the FWHM of the object inside all of the apertures and calculates the mean FWHM for the image Then the aperture radii of all apertures in the image is set to FWHM x multiplication factor The idea is to allow the aperture radii to expand and contract with scintillation changes and or focus drift etc IMPORTANT NOTE The FWHM of each object is determined using only the pixels inside the defined fixed aperture radius It is important to set the fixed aperture
48. k and run photometry faster useful if photometry may be executed several times to explore the results of different aperture sizes etc If all of the images will not fit into memory at once select Use virtual stack This option loads only one image at a time into memory so photometry runs a little slower but the memory requirements are minimal In virtual mode the image window will still appear to contain all of the images but moving between images in the window will be slower since they are read from hard drive rather than memory when changing to a different image Individual images in an AIJ stack are referred to as a slice NOTE as a shortcut you can drag and drop a folder of images onto the toolbar for opening the virtual stack option is available but no file name filtering is available with the shortcut When OK is clicked note the file open progress bar at the bottom right of the AIJ toolbar When all images have been read from hard drive an image display similar to the one shown below will open File Preferences Scale View Edit Process Color Analyze WCS 1 168 wasp12b_9_bsdffits 4098x4098 pixels 16 bit 53GB WCS RA SIP DEC SIP TAN CD matrix ImageJ X 2 603 9375 ImageJ Y 55 0804 Value 2 696 0000 RA 06 30 15 804 DEC 29 27 19 22 Peak 2 864 0000 FITS X 2 604 4375 FITS Y 4 043 4196 Int Cnts 523 3604 Poe ices B08 RARA T mean 2 734 9092 white _3 851 1177 max 65 535 00
49. left click near a star A red aperture will be placed at the centroid of the star on the image and a measurements table will open The image display should look like this if background annulus display and integrated counts display are enabled If the aperture does not encircle the portion of the stars PSF that you desire open aperture settings and modify the radii as desired Click to clear the aperture image overlay and click to clear the old values from the table as needed Shift left click to place another aperture to make sure your aperture is sized to fit your needs If not repeat the above steps A future version will provide the capability to modify the aperture radii more conveniently 10 2 1 7 Run Multi Aperture Differential Photometry Start Multi Aperture MA setup by clicking the a icon above the image stack The following window will open Use the setting shown for a practice run except keep the aperture radii settings that you selected in the previous step fa Multi Aperture Measurements xs Maximum number of apertures perimage 500 right click in image to finalize Firstslice lt iz Lastslice lt 168 Radius of object aperture lt t 20 Inner radius of background annulus lt r 40 Outer radius of background annulus lt r fso M Use previous 9 apertures 1 click to set first aperture location l Use single step mode set new aperture locations for each image right click to exit V Repo
50. lue or a string containing a sexagesimal representation of the J2000 coordinate value The FITS header target RA DEC epoch of observation option works the same as the previous option however the values contained in the FITS header should be in epoch of observation rather than J2000 6 3 2 6 4 Observatory Location Source The observatory location can be defined by one of three options under the Observation Location Source If Coordinate Converter manual entry is selected DPCC s Observatory ID list is enabled for user input Select the observatory where the observations were conducted in the observatory ID list If the desired observatory is not listed choose Custom Lon Lat and Alt entry at the top of the observatory list and enter the observatory s coordinates and altitude manually in DPCC s Geographic Location of Observatory section Full DPCC help is available under the Help menu including instructions on how to customize the observatory list If FITS header observatory name is selected as the observatory location source all science images must contain the FITS header keyword defined in the Observatory Name Keyword field of the FITS Header Settings input panel see Figure 4 The keyword s value from the science image s header is used to search DPCC s Observatory ID list The first entry in the list that contains the string from the header will be selected The search is not case sensitive
51. ly be presented after the first image has been calibrated after opening DP or after pressing the ES button before or during a DP run Two ImageJ macros can also be executed after each image has been processed Enter the full path and file name or navigate to the desired macro file using the blue and white folder button to the right of macro path field The Totals column entry will show a 0 if the defined macro file is not found or 1 if it is found The ImageJ macro language is beyond the scope of this user guide however it is well documented at http rsbweb nih gow 1j docs The order which these items are processed if enabled is Macro 1 Macro 2 Multi Aperture Multi plot 6 3 2 9 Control Panel This section allows the user to start pause stop and reset DP runs and allows the control of related features Click the START button to begin processing all files While files are being processed this button shows RUNNING If PAUSE is pressed while in the RUNNING state this button shows CONTINUE Pressing CONTINUE resumes processing at the point where PAUSE was pressed Click the PAUSE button to pause processing of files while in the RUNNING state Click CONTINUE to resume processing files at the point where PAUSE was pressed or press RESET and then START to start processing all files again The RESET button resets the file processing queue causing all defined data processing to be executed again starting from the first ma
52. n In photometry mode left click without holding lt shift gt near an object to be measured to place an aperture at its centroid The photometric results will be written to a MeasurementsTable that will be created and displayed after creating the first aperture The parameters of the photometer and the data recorded in the MeasurementsTable can be set up by double clicking the single aperture icon on the IJ toolbar If an image is open the settings can be accessed clicking the icon above the image There are many options available but figures 4 and 5 below show the recommended settings Adjust the aperture sizes properly for the data being analyzed Be sure to select Show other configuration panel at the bottom of the first panel to display the second set of options after the first 1s closed Figure 9 Aperture Photometry Parameters Radius of object aperture j ri Inner radius of background annulus M List photometric errors Source Error yY j n j i Ouian casi s bad a V List photometric signal to noise Source SNR List error of multi aperture ratio rel flux err I Use variable aperture Multi Aperture only V List signal to noise of multi aperture ratio rel flux SNR Variable aperture FWHM multiplication factor lt 4 i CCD gain e count 1 50 List in Measurement Table CCD readout noise e 9 00 M filename Label CCD dark current e 4 00 IV slice number slice IZ centroid position in 1J c
53. name s numeric value is determined by combining all of the numeric digits in a matching filename The value under Totals indicates the number of files AIJ has found that match the defined pattern If the subsection is disabled the Totals value will be zero The Filename Number Filtering subsection can be used to filter out files that match the file name pattern but should not be included in processing if the file s numeric value is less than or greater than specified values in Min and Max The file name pattern in this subsection can be used to define which characters in a file name should be included when determining the numeric value of the file name Only numeric 66399 characters in a filename that fall under or characters in a pattern are used to determine a file name s numeric value If the full pattern is contained in a filename numeric characters after the pattern in the filename will also be included e g the file name mars0la34out fits with a pattern of mars has a numeric value of 134 The file name pattern in the number filtering subsection follows the pattern in the pattern matching subsection but can be altered after the pattern matching text has been entered 6 3 2 2 Bias Subtraction This section allows the user to define locations and file names for raw and master bias images The use of a master bias image is not required in general but is required for exposure time scaling and non linearity correction If
54. nter the desired data AIJ checks the validity of the contents of each cell that 1s changed to ensure that it meets the FITS standard A Keyword entry will be truncated to the first 8 characters and capitalized after pressing enter or clicking on another cell A Value entry can be a string an integer a real number or a Boolean T or F The Type value will be automatically set depending on the characters entered into the Value cell Comment can be any string but will be truncated after the entire length of the keyword entry exceeds 80 characters Comment truncating is done when the Save or Save File buttons is pressed To undo changes to the header press the Cancel button and reopen the FITS header into the editor if desired Press the Save button to save the changes into the copy of the image in AIJ memory To retain the header changes the file must then be saved to disk using the File menu above the image or the File menu in the AIJ toolbar To directly save the header changes to AIJ memory and to the hard drive click the Save File button at the bottom of the editor WARNING Save File will also save any changes that have been made to the pixel data of the image Figure 8 FITS Header Editor Comment Created by ImageJ FITS_Writer number of bits per data pixel number of data axes length of data axis 1 length of data axis 2 data range offset scaling factor
55. o the left of the astro mode icon operation will revert to standard IJ operation Clicking back on the astro mode icon will revert to AIJ operation A three button mouse with a scroll wheel and separate middle mouse button such as the Logitech Anywhere MX mouse provides the most convenient and efficient AIJ operation 4 2 AstroImageJ Toolbar When AstroImageJ AIJ is opened you will see the AIJ Toolbar as shown in Figure 1 with eight AIJ specific icons on the right side of the toolbar starting at the button shown depressed below The toolbar can be used the same as for generic IJ but for most operations with AIJ you will want the star field icon depressed as shown below The icon is called Astronomy Tool in the menubar and this mode is referred to as astro mode in this document AIJ defaults to this mode at startup An overview of each icon button is provided below NOTE although the right hand portion of the toolbar can be customized as with generic IJ it is highly recommended to leave the default AIJ icons installed as shown below Figure 1 AstrolmageJ Toolbar with AstroImageJ tools on right hand side a File Edit Image Process Analyze Plugins Window Help DOGO lt 4 N A e E Om gt gt Rectangularm or rounded rectangular selections right click to switch L 3 Ex Astro Mode Icon this button should normally be in the selected pressed state for AIJ operation When the button i
56. om X data J D 2400000_B W Add new column from data New column name from Y data rel_flux_T1_n W Add new column from Y error data New column name from Y error data rel_flux_e r_Ti_n New data columnis will be added to the open table Save table to save new columnis to disk Accept the default new column names and leave the new x data column deselected no x axis data changes have been made Click OK and the new data will be added to the table The plot control panels will disappear and reappear while the GUI elements are updated with the new data column names Auto Error can now be disabled if you prefer to submit a plot without the error bars displayed 10 2 1 11 Save all Working Files to Disk All working files can be saved in one operation by using Multi plot Main gt File gt Save all with options When the with options menu item is selected the following panel will open b Save all settings x Select items to save when using save all V Image V Plot V PlotConfig MV DataTable V Apertures MM Log Image suffix fed Plot image suffix _lighteuve Plot config file suffix measurements Data table file suff measurements ts Aperture file suffix measurements Log file suffix calibration IV Save images in PNG format uncheck for JPEG format Tip make plot config and data table suffix the same so thatthe plot config will auto load when a new data table file is
57. oordinates X 13 Y W FITS keyword for dark current e IV centroid position in FITS coordinates X FITS Y FITS needs gain readout noise and dark current info above IV aperture net integrated counts Source Sky MV List aperture moment x and y widths X Width Y Width IV List aperture radii Source Radius Sky Radius min Sky Radius max IV aperture peak pixel count Peak MV aperture mean pixel count Mean JV sky background per pixel Sky Pixel V Julian Date of image J D 2400000 if available V world coordinates RA DEC if available J mean PSF moment width Width Display in overlay V object aperture I sky annulus M source number l source net integrated counts Clear V ROI after use I overlay before use MV Reposition aperture to object centroid M Show other configuration panel OK Cancel List raw numbers e g if intensity calibrated I List orientation angle Angle V List roundness Roundness 0 if round 1 if a line WMV List variance square of std dev Variance M List a saturation warning Saturated for levels higherthan 60000 List the decimal values for the FITS keywords called comma separated keywords JD_SOBS JD_UTC HJD_UT Assume background is a plane V Ignore pixels gt 2 sigma from mean in photometer background region I Mark pixels gt 2 sigma from mean in photometer background region IV Use Howell Centroid Method disable to use
58. out noise e 9 00 CCD dark current e 4 00 FITS keyword for dark current e needs gain readout noise and dark current info above IV List aperture moment x and y widths X Width Y Width V List aperture radii Source Radius Sky Radius min Sky Radius max l Listraw numbers e g if intensity calibrated V List orientation angle Angle IV List roundness Roundness 0 if round 1 if a line IV List variance square of std dev Variance V List a saturation warning Saturated for levels higher than 60000 V List the decimal values for the FITS keywords called comma separated keywords JD_SOBS JD_UTC HJD_UT Assume background is a plane IV Ignore pixels gt 2 sigma from mean in photometer background region Mark pixels gt 2 sigma from mean in photometer background region IV Use Howell Centroid Method disable to use orignal method V Show this panel of other aperture photometry parameters OK Cancel 10 2 1 6 Experiment to Find a Suitable Starting Aperture Size Mouse the mouse cursor over the image and zoom in on a star of interest If you do not see the live aperture displayed at the mouse cursor enable Image Display gt Preferences gt Show photometer aperture at mouse cursor Enable or disable the display of the background annulus as desired using the icon above the image Also make sure the centroid icon is depressed enabled Now press and hold shift and
59. p peaks of stars The selection of gradient removal does not apply to science images If Save processed images is selected the new file will be written to the specified relative directory with the specified suffix added in either 16 bit integer or 32 bit float format as selected The filename format can be any natively supported image file type such as fits tif jpg gif bmp etc Show Log displays a list of the steps completed in a log window This data can be saved for reference if desired Show Master Images shows the master calibration creation process as it progresses and displays the final master calibration files However this option uses more memory The Auto Level selections can be ignored since this function is now implemented as an option in the image display window 7 Plate Solving using the Astrometry net Web Portal AIJ can plate solve images using an internet connection to the astrometry net web portal at nova astrometry net After a successful astrometric solution WCS headers will be added to the FITS image header and the file can optionally be automatically resaved with the new headers Source extraction is performed by AIJ and only the x y coordinates for the N brightest sources are sent to astrometry net where N is set by the user in the Max Num Stars box A setting of 50 works well for typical 0 5 arcmin telescope images The actual image is not transferred across the network whi
60. pdated automatically after each click making it easy to assess the quality of comparison stars b Multi plot Reference Star Selection eye xs Select reference stars to include in tot_C_cnts and rel_fiux calculations Reference Star Selection None all Set CydeEnabledStarsLessOne Cyde Individual Stars Ti C2 C3 C4 C5 C6 C7 O O M M M aa mw e Save Show Current Configuration Save Table Save Apertures Send to Multi aperture Show Apertures 10 2 1 10 8 Description of all Data Column Names Produced by Multi Aperture Go to Multi plot_ Main gt Help gt Data naming convention to see a comprehensive description of all data column names produced by Multi Aperture 10 2 1 10 9 Save the Target star Normalized Relative Flux Back to the Table The manipulated values normalized detrended shifted etc used to produce the plot are not automatically saved back to the table The target star normalized relative flux and normalized errors are often needed to submit to collaborators To save these plotted values back to the table the error calculation must first be enabled on the corresponding plot control row by selecting the Auto Error checkbox Now click the New Col icon m on the left side of the Y data panel that is on the plot control row corresponding to the desired data The following panel will open 4 Add new columns to table as Add new column from X data New column name fr
61. r Dark Subtraction Build ave med Q Observations _cals CDK20N_U16M_1_exposures 20121007_darks_ 10_100 a y dark_ fits Enable v scale Q Observations _cals U16M_2_masters ea mdark_ 20_100_20131002 fits Ot Division Build ave med Q Observations _cals CDK20N_U16M_1_exposures 20130223 flats_g_ 10 ed flat_ fits Enable Q Observations _cals U16M_2_masters ea mflat_r_ 20_20121117 fits Ot Linearity Correction Enable New pixel value 0 0E0 gt 1 0E0 x PixVal 8 0E 7 gt x PixVal 0 0E0 gt x PixVal r FITS Header Updates Target Coordinate Source Observatory Location Source 7 General V Plate Solve Coordinate Converter manual entry Coordinate Converter manual entry r Save Calibrated Images V Enable 1656 32 Sub dir pipelineout Suffix _bsdf Format fits r Post Processing v M Ap Save Image Q Observations static_plot DPimage jpg ow Macro 1 a v M Plot Save Plot Q Observations static_plot DPplot png a Macro 2 oa Control Panel Polling Interval gt 2 ince oO Sy al alee BESEL Remaining 6 3 1 Horizontal Sections Starting from the left the horizontal sections are labeled at the top of the panel as 6 3 1 1 Control The control checkboxes allow each of the possible processing capabilities to be enabled or disabled
62. radius to be larger than the largest FWHM in the image sequence In general double the size of a normal case aperture radius tends to work well NOTE AIJ currently overestimates FWHM However with the implementation in AIJ version 2 1 4 multiplication factors in the range 1 0 to 1 4 seem to work well 10 2 1 9 Load a Default Plot Configuration If the two Multi Plot MP control windows are not open from the previous step click Eel on the AIJ Toolbar to open them and automatically load the measurements table just created by Multi Aperture Now load the supplied plot configuration file using Multi Plot Main gt File gt Open plot configuration from file Navigate to the file transit_standard plotcfg that is supplied as part of this demonstration and click OPEN SHORTCUT drag and drop the plot configuration file transit standard plotcfg onto either of the Multi plot control windows to open it 10 2 1 10 Understanding the Basics of Multi plot 10 2 1 10 1 V Marker 1 and V Marker 2 The target light curve with up to 7 comparison stars should now be displayed However the ingress and egress markers may not be in the correct location for your dataset In the top right corner of Multi plot Main you will see settings for V marker 1 and V marker 2 Set the start of ingress time in the V Marker 1 box and the end of egress time in the V Marker 2 box If the red dashed ingress and egress
63. re will be shown in the image overlay centered at the star Then left click near additional stars to place red comparison star apertures To remove an aperture left click inside the aperture The image with aperture overlays should look similar to the example shown below When you have selected all desired comparison stars either press lt Enter gt or right click in the image to start processing all of the images NOTE Target star differential flux is calculated by dividing the integrated counts of the target star aperture by the sum of the integrated counts from all comparison star apertures Comparison star differential relative flux is calculated by dividing the integrated counts in that comparison star aperture by the sum of the integrated counts in all OTHER comparison star apertures More than one target star can be selected Shift left click after the first aperture 1s placed to add more target stars left Click Add target star aperture T1 shift4eft Click Add reference star aperture C1 shift contraltfeft Click right Click senter gt controlteft Click Zoom In control right Click Zoom Out roll mouse wheel Zoom In Out left dick drag Pan image up down left right middle dick Center dicked point in image display if enabled in Preferences menu lt escape gt Cancel Multi Aperture File Preferences Scale View Edit Process Color Analyze WCS 1 168 wasp12b_9_bsdffits 4099x4098 pixels 16 b
64. s in the deselected state mouse keyboard and image display manipulation revert to standard ImageJ operation This button will go into the deselected state if one of the base IJ toolbar icons has been pressed to draw a square circle etc Region of Interest ROI on the image These ROIs are not normally needed for AIJ operation but may be useful for custom measurements After drawing a ROI remember to press the astro mode icon to return to astro mode Pressing one of the following AIJ toolbar icons will not change the astro mode state DP Data Processing Icon opens the Data Processing DP module to perform image calibration bias dark flat linearity correction and to optionally perform FITs header updates plate solve to add WCS FITS headers requires internet access and free user key from nova astrometry net run Multi Aperture and or Multi plot after each image has been calibrated DP works in post processing mode by setting Polling Interval to zero or works in real time mode at the telescope by setting the polling rate to a non zero value 5 seconds tends to work well DP runs independent of and in parallel with any camera telescope control software Multi Aperture Icon opens the Multi Aperture MA photometry module to perform differential photometry on a series of usually already calibrated images A series of images can be opened into an AIJ Stack by using the AIJ toolbar menu item File
65. shows DPCC with all fields disabled which corresponds to a setup where all required data is being derived from the science image s FITS header As science images are processed all values in the DPCC GUI including the Phase Altitude Proximity indications will update to visually show the observing conditions during that exposure Figure 5 DP Coordinate Converter User Interface SIMBAD Object ID or 5 Target Proper Motion mas yr meal pmbec Standard Coordinates J2000 Equatorial J2000 Ecliptic E RA 00 00 00 Dec 00 00 00 Lon 00 00 00 Lat 00 00 00 SIMBAD B1950 Equatorial Galactic RA 23 57 26 234 00 16 42 286 96 20 14 117 Lat 60 11 18 79 Epoch of Interest UTC based Time Now UTC 2012 08 08 07 24 01 UT B39 o949em JD 2456147 808350 LST 22 50 45 Lock Local 2012 08 08 _ 03 24 01 AM Bi os47aMm_ HUD 2456147 812563 dT 00 06 04 Dynamical Time Update 4 Auto Leap secs OSUinternal BJD 2456147 813328 Equatorial Ecliptic RA 00 00 40 652 Dec 00 04 24 92 Lon 00 11 04 64 at 00 00 00 527 Horizontal Direction Hour Angle Zenith Distance Airmass Alt 48 30 23 83 Az 153 02 47 79 Dir HA 01 09 55 ZD 41 29 36 AM Phase Altitude Proximity Moon Mercury Venus Mars Jupiter Saturn Uranus r Neptune Fluto 43 41 Down Down Down 15 12 Down 4747 39 79 5 92 30 17 121 23 90 48 159 75 T1 29 155 69 8 31 28 04 83 22 6 3 2 6 1 Exposure Start Date Time Source UTC start of exposure
66. sition aperture to object centroid leave unchecked to center aperture at mouse click V Remove stars from background i e pixels gt 2 sigma from mean Assume background is a plane MV Update plot of measurements while running V Compute relative flux in all apertures TN Sum CX and CN Sum CX CN V Compute relative flux error only if you check Compute relative flux above MV Compute relative flux signal to noise only if you check Compute relative flux above V Compute total comparison star counts Vary photometer aperture radii based on FWHM FWHM multiplication factor lt t 1 20 V Allow leftright double click fast zoom in out adds slight delay to aperture placement V Always default first slice to slice 1 change effective next time MA is started V Show help panel during aperture selection PRESS Ok AND SELECT APERTURE LOCATIONS WITH LEFT CLICKS THEN RIGHT CLICK TO BEGIN PROCESSING to abort aperture selection or processing press lt ESC OK Cancel Now click OK The MA setup panel will close any apertures shown in the image overlay will be automatically cleared and the Multi Aperture Help window shown below will open Note that the help window is active so check for different mouse keyboard stroke actions available after each step in the aperture selection process For the normal case of one target star and several comparison stars left click on the target star first A green target apertu
67. splay 00000000000nnnnnnnnnnnnnnnnnnsnnnssnsnsnsnssssssssssssssssnns 13 5 14 Menus above the Image Display cccccccseseseeeeeeeeeeeeeeceeeecceceeeeeeceeeaeeececeeeeeeeeeeeeeeeeeeeeeeeseass 13 5 15 Notes on Generic ImageJ Regions of Interest ccccccecceeceeeeeecececeeeeececeeeeeeeeeeeeeeeeeeeeeeeeeees 14 6 Data Processor DP Mod le sesscresisninoairiin a e EEE EE 15 60l Overview or Opora oi ene ene nn ene ne ee ne ee ner 15 6 2 Post Processing vs Real Time Operation ccccccccccscsccccceececeeceeecceseeceecececeeceeceeceeeeeeeeeseseeeeeeeeas 15 C3 DP User nier AC Oo oaeneweioaetesnaaamaavonoscosnadonencnetanatannsguubernnnsteenarcaenas 15 6 3 1 Horizontal Sections cccccccecceccecceccescscoscosccsccsccsccsccecceccuscscescescescescescescessessesscescascescescess 16 ELE CONTO ogo eos es ccraden Wn te one otal eaten aha ant utlad ene yao canta otean oN cas lado an is E ete ate cae eta dae late aaa 16 E D a T E EEE E en oO EE eR Orne OTe ne en OTTER EE Tr eee OT 16 Oal DIECO eiaa A lasecbateancstalecsattatectheladiesctatedacst detente tcl beal ances 16 0 Le Filenin Paterno vaca asec sasuoonnsetaapteamstanenanepastd saduocoudetaapteamstanecanapastd varsounncetaneceamananexenanataas 17 Ol TOtalS a E asad iesal eee ae eeietee ea 17 Oi DD UC A CO E E E A E EE E A E OA E E 17 G37 Science Imate Process NE cann an ara A ee 17 6 3222 BIIO UDAC ON aciei E R A E E eaeteete Teese 17 O2 Dark SUD UAC ON se DA Sets usar
68. ssvaeaseasessevacnsenseusndesteasaasassasesseuectseateuandeateeadtenmesses 7 AE La Oaa IN UC a E E 7 AD AStrolmage Toolbar secs sverscceaeerseceaeeinecgceriaunnceeisessveriguns devia ETT ENOR ENDENE REENDER EEN 7 5 AstroImageJ Image Display Hitler lace sasaccsnccnaccisdisasacasdsenncisaeosadanndcnaceidisebacanddennaiiesleasadewndenaceisdsebaconddenneseseasacts 8 5 1 Data Displayed Aboye the mage gccsesiesdeasineccndwudendiacned sidwunesdeasunadendvadendiacmdehdweneddeassmdendvadeadiacumesties 9 53 2 Data Displayed in the MAA Oe a cccecdsecacesarenconseeeoesossvesedenasecsdesavetsonsesensaeadnassdenaeaadunsavensonsasenssendmeseceneees 10 5 3 Contrast BriOhtiess Adustineni srira 10 SA mage NETI sprer 11 5 5 Image Invert Flip and Rotate cesicesacasatenceronearaasenneomecensetyanesaneemectonraraacaaeeemeceneauaaanadsemecwnrashacesneenecemneee 11 S PANON AE E E EA E OEE E EE EOE TE AE OT 11 IPAO o E E E EEE E E EE E E E S 11 5 6 Mouse Pointer Live PHOtmeter sccisicosssccevintencswnratendscausisnonssaseuie E A T E E 11 5 9 Single Aperture PHOLOMEEY sccsicsscscacscncccaadoaseanaadaseanadeanssnansnnaaaadoaseanasnadeatansannsnmnsnnsanadoacsanannesecnannannes 12 5 10 Apertures Displayed in the Tima ge cs sdciacisnsasacnwnsanaasisasenadsndeepaacionsanadswnsanacsidasenadsndd nnadedecsadsentanaendaseans 12 zA Measuwrino Arc lenni Ren ee De EEA EAE EENE 12 ENM e a e eT ee IS o E a A TEA E IE A S T 12 5 13 Other Stack Related Icons above the Image Di
69. t Settings Target Name Keyword TARGET Target RA Keyword RA_OBJ Target DEC Keyword DEC_OBJ Observatory Name Keyword TELESCOP Observatory Latitude Keyword SITELAT Observatory Longitude Keyword SITELONG FITS Header Output Settings Target J2000 RA Keyword RAOQBJ2K Target J2000 DEC Keyword DECOBJ2K Target RA Keyword RA_OBJ Target DEC Keyword DEC OBJ Target Altitude Keyword ALT OBJ Target Azimuth Keyword A OBJ Target Hour Angle Keyword HA_OBJ Target Zenith Distance Keyword 7D OBJ Target Airmass Keyword AIRMASS JD UTC start Obs Keyword JD SOBS JD UTC mid Obs Keyword JD_UTC HJD UTC mid Obs Keyword HJD_UTC BJD TDB mid Obs Keyword BJD_TDB Observatory Latitude Keyword SITELAT Observatory Longitude Keyword SITELONG k 6 3 2 7 Save Calibrated Images This section defines how calibrated output images are saved if enable If Enable in the section is not selected no images will be output to disk however tasks in the Post Processing section may still be applied to the calibrated image in AIJ memory Calibrated images can be output in either 16 bit integer or 32 bit floating point pixel format by selecting either 6 or 32 if the output image format selected supports the pixel format Calibrated images may be saved into a subdirectory of the directory defined in the Science Image Processing section by entering the subdirectory name in the Sub dir field or back into the same directory if the field is l
70. t the animation speed and other parameters To delete the currently displayed image from a stack i e the current slice click the icon above the image The image is only removed from the stack in AIJ memory and is not deleted from the disk The delete current image feature will not delete the last two images of a stack Figure 3 Stack Control Panel P4 aten 1960 7 2862 7 3 64 7 4666 6 5568 6 6470 5 7372 5 B2745 9176 4 10000 0 0000 fmin 131 3451 black mean 306 3165 white 1 023 3473 max 10 000 0000 5 13 Other Stack Related Icons above the Image Display eal Clear Table Icon clears all data in the measurements table that is created by Single or Multi Aperture This button is useful when running back to back Multi Aperture sessions and the user desires to quickly delete the data from the previous session WARNING there is no undo for this operation eo Multi Aperture Icon opens the Multi Aperture MA photometry module to perform differential photometry on a series of usually already calibrated images E Image Alignment Icon opens the AIJ Stack Aligner module Stack Aligner allows the user to place apertures at one or more reference stars in a reference image of a stack It then uses the centroids of those reference stars in each image to align to the reference image by translating the image in the x and y axes image rotation is not supported Ka Plate Solve Icon opens the
71. t there are a few that require some initial per user per observatory changes Open the aperture settings window as described above As a starting point setup the parameters to match the settings shown in the figure below The aperture size parameters can be changed later in the Multi Aperture setup panel Radius of object aperture Inner radius of background annulus Outer radius of background annulus l Use variable aperture Multi Aperture only Variable aperture FWHM multiplication factor lt Listin Measurement Table iV filename Label IV slice number slice IV centroid position in IJ coordinates X IJ Y IJ V centroid position in FITS coordinates X FITS Y FITS IV aperture net integrated counts Source Sky IV aperture peak pixel count Peak IV aperture mean pixel count Mean IV sky background per pixel Sky Pixel iV Julian Date of image J D 2400000 if available IV world coordinates RA DEC if available IV mean PSF moment width Width Display in overlay V object aperture l sky annulus V source number l source net integrated counts Clear V ROI after use overlay before use V Reposition aperture to object centroid IV Show other configuration panel OK Cancel After ensuring that the option labeled Show other configuration panel at the bottom of the panel is checked click OK to go to the second panel of option settings The panel below will open Also start with
72. tching science file the next time the START button is pressed If in the RUNNING state PAUSE must be pressed first and then RESET Pressing START after RESET causes all files to be processed again if Process only new is deselected the default value in the Preferences menu If Process only new is selected only new files written to the directory defined in the Science Image Processing section will be processed To operate DP in post processing mode set the Polling Interval to zero 0 In this mode all images in the science directory matching the science image filters before pressing START will be processed and then execution will stop If a non zero Polling Interval is set all images in the science directory matching the science image filters before pressing START will be processed and then after a polling period delay the science image directory will be scanned again for matching science files Any new matching science files will then be processed and the cycle will repeat until PAUSE is pressed This real time processing mode is intended to be used to process data and optionally perform photometry and create a plot as images are written into the science directory from the camera The Totals fields in this section show how many files have been processed and how many files matching the filter settings are remaining to be processed The Remaining files number shown corresponds to the last polling cycle s directory scan and will not
73. the Multi plot Y data panel unfortunately this naming convention here is confusing Note that in this plot J D 2400000 is the selected Default X data in the main panel Since default is selected for X data in the Multi plot Y data panel J D 240000 is used to plot all y axis data AIJ recognizes J D 240000 as the Geocentric Julian Date of the middle of the exposure as long as the EXPTIME keyword is found in the header it is start of exposure time otherwise It is better to plot JD UTC or BJD_TDB is those have been placed in the FITS header by either AIJ or another program 10 2 1 10 6 Overview of the Y axis data Target star light curve the target star light curve is plotted twice The top blue dots light curve is the normalized relative flux of the target star with no detrending applied The second lightcurve is also the target star normalized flux but AIRMASS detrending has been fitted to the out of transit region of data and then the fit has been applied to the entire light curve In this case the AIRMASS trend is negligible so the two curves are nearly identical except that the red dot curve has been shifted down by 0 01 normalized units see the then Shift setting in the second row of plot settings Comparison star light curves 7 comparison star light curves are plotted below the target star light curves Notice that these are all AIRMASS detrended and normalized using
74. the full comparison star light curve for fitting Systematic checks and Page Rel plotting 4 curves are over plotted at the bottom as systematic checks Note that all of these curves are plotted with Page Rel enable Page Rel automatically scales a dataset to fit on a user specified portion of the plot In page relative mode the Scale setting indicates the percent of the overall plot Y axis that the dataset will cover Shift is also in percent of the plotted page The bottom dataset Sky Pixel T1 is scaled to cover 15 of the plot y axis and is shifted down from the center by 40 of the plot y axis Page relative plotting is useful when the shape of a light curve is the most interesting aspect and the plotted values correspondence to the absolute y axis values is less important 10 2 1 10 7 Changing the Comparison Star Ensemble without Rerunning Multi Aperture The comparison star ensemble can be changed in Multi Plot using the Multi Plot Reference Star Selection panel shown below If this panel is already open or is hidden behind another window click the Ref Stars button in the lower right corner of the Multi plot Main panel Deselecting a comparison star i e Cx will change the star to a target star i e Tx which removes it from the comparison star ensemble Buttons are available to cycle though all individual stars or to cycle through all enabled stars less one comparison star The table and plot are u
75. the values shown below except for the following customizations Modify these setting to make sure measurement error is calculated as accurately as possible for your observations CCD gain setting for your observations CCD read noise CCD dark current for the observations OR the FITS keyword for dark current Adjust the saturation warning level as needed A warning is generated if any one pixel within an aperture is above the specified ADU Keep in mind that the images have already been calibrated so you will need to compensate for bias and dark subtraction as well as flat fielding IMPORTANT Finally change the comma separated keywords to include all the FITS header keywords for which you want values extracted and placed in the measurements table It is recommended to paste the following text into that box to get started JD_SOBS JD_UTC HJD_UTC BJD_TDB ALT_OBJ AIRMASS CCD TEMP EXPTIME RAOBJ2K DECOBJ2K Then add any additional keywords for which you want values extracted from the FITS headers and placed in the measurements table If a keyword in the list is not found in the FITS headers the value NaN will be placed into the cells of the corresponding table column V List photometric errors Source Error V List photometric signal to noise Source SNR IV List error of multi aperture ratio rel flux err IV List signal to noise of multi aperture ratio rel flux SNR CCD gain e count 1 50 CCD read
76. trol image zoom Or shift left click to zoom in shift right click to zoom out or use the keyboard up and down arrows to zoom If you have a mouse with a scroll wheel roll it to zoom To pan the image left click and drag the image left right up down 7 Click this icon to return to automatic contrast settings after black and white have been manually changed Click to display and optionally edit the FITS header Value 696 0000 Peak 2 864 0000 Int Cnts 523 3604 The top right boxes above an image display the values from a live aperture that moves with the mouse If the live aperture does not show at the mouse pointer enable Preferences gt Show photometer aperture at mouse cursor to see it This is handy for selecting comp stars in the image In version 2 1 5 and later right click in an image with WCS headers to access object name information from SIMBAD requires internet connection In version 2 1 5 and later type or paste RA Dec coordinates in the boxes above an image that has WCS headers to identify the location in the image The slider at the bottom of the image can be used to move through all of your open images As mentioned previously the window will be slow to update if you used the virtual stack option 10 2 1 5 Set up Aperture Parameters Aperture settings can be accessed by clicking above an image or by double clicking on the AIJ Toolbar Most of these settings rarely need to be changed bu
77. verlay icon removes all apertures from the image 5 11 Measuring Arclength A middle mouse button click and drag shows distance in arclength in the bottom right box at the top of the image when a pixel scale is set in the Preferences menu or WCS headers are available Otherwise length is shown in pixels Click the clear apertures overlay icon to remove the line that was drawn during the measurement Two Preference menu options are available to enable image data to be written to a log file when the middle mouse button 1s clicked or dragged The resulting log file can be saved if desired 5 12 Image Stack Display Image sequences can be opened into an AIJ stack by using the AIJ toolbar menu item File gt Import gt Image Sequence or directory folder containing an image sequence can be dragged and dropped on the AIJ toolbar When a sequence of images has been opened into an AIJ image Stack they will be displayed in a single window as shown in Figure 2 with the addition of a stack control bar inserted between the image and histogram display as shown in Figure 3 The slider can be dragged left and right to move through the images or the left and right arrow buttons on either end can be used to move through the images one at a time The keyboard left and right arrow keys will also move through the images one at a time The play icon will display the stack as an animation Right click the play icon to se
78. while reading lengthy tooltips move the mouse back and forth slowly over the field after the tooltip has been displayed 6 5 Data Reduction Algorithms Master Dark when create is selected the specified images will be average or median combined to create the master dark file specified If use master bias is selected the resulting master dark image will be bias subtracted using the previously generated or specified master bias image If use master bias is not selected the master dark will not be bias subtracted If use non linearity correction is selected use bias must also be selected the bias subtracted dark is scaled using the three specified non linearity coefficients Master Flat when create is selected the specified images will be processed and average or median combined to create the master flat file specified If use master bias is selected each individual flat is bias subtracted before combining If use master dark is selected each individual flat is dark subtracted before combining If use is selected for both bias and dark the flat is both bias and dark subtracted before combining For dark exposure timing scaling to be applied when creating the master flat use master bias and master dark must both be selected and either created or available and Dark ExpTime Scaling must be selected Selecting it without selecting use bias and use

AstroImageJ 2.4.1 User Guide plus - University of Louisville Astronomy

Contents

Download Pdf Manuals

Related Search

Related Contents