AstroImageJ V2.0 User Guide - University of Louisville Astronomy
Contents
1. r Y o T x FITS Header Editor gt Keyword Value Comment ae 1 SIMPLE file does conform to FITS standard Em fx rer Fits per data pd pos po TT TN TT Tenth of datas SSS a ST ME z COMMENT FITS Hexble Image Transport System formatis denedin Astronomy SSS A aaa e Emo be o d range to tat of none short i o esae bo eat sing factor SSS 1d EXPTIME 1 06402 ee exposure time seconds CR 12 _ DATE OBS _ 2012 03 10700 36 12 es dateofobservation UT CS 13 IMAG ght Frame image type nome png SO TE 15 NSTRUE aPOGeE COS intuit E treze LH UoLRCZS A RC24 epe sR A o 10T00 38 11 A aS date YYYY MM DDThh mm ss UT a Jr 2162850000000009487 DO TT A A k 7 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 icon 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 t2. ESTAN AstroImage J V2 0 User Guide an image analysis tool for astronomy website http www astro lou1sville edu software astroimagej support forum http astroimage 1065399 n5 nabble com Feature Overview General purpose but optimized for time series aperture photometry Open source and written in Java so runs under Windows OS X Linux Real time or post processed calibration analysis and plotting DS9 like image display with live photometer and WCS support FITS header handling viewing editing Multi image processing bias dark flat CCD non linearity correction Multi exposure multi aperture differential photometry Interactive multi curve plotting Astronomical coord conversion J2000 EoD equatorial ecliptic galactic Astronomical time conversion UTC local LST JD HJD BJD 5p Table of Contents LAOL ar ol 4 Ze RISCA AUIOM eee E E E EE E E E E E E 4 Deel IDE AS PA AMO rs e oo 4 2 2 Windows ASEAN OI sssaaa a e e o 4 Zed MICONA MS CANA ON esarri E S E A A 5 3 Astrolm sclys Generic Mage added 5 EO NOO eae a EEE E E EEE E E E A s 5 A A Oe EN AN N RR 5 4 AstrolmageJ Image Display Interface cece cccceseeesseeeeeeseeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeeeeeeeeeees 7 4 1 Data Displayed Above the Image si A A a ele sosaausddanmeaoeaanacte 8 A2 Data Displayed Tah NN acid ra arado doada Canoa pondo doada 9 4 3 Contrast Brightness Adjustment ccccceeseseessssssssseeseseeeeseeeseeseee
3. FITS Header Updates Target Coordinate Source FITS header target name Enable 1 0E0 x PixVal 7 9060939E 7 gt x PixVal Observatory Location Source gt FITS header observatory name Save Calibrated Images Enable 016 32 Sub dir pipelineout Suffix _bsdf Format fits Post Processing Y M Ap Macro 1 CA oa 0 Y M Plot E Macro 2 CA oa 0 Control Panel Polling Interval 7 START Processed Remaining 5 3 1 Horizontal Sections Starting from the left the horizontal sections are labeled at the top of the panel as 5 3 1 1 Control The control checkboxes allow each of the possible processing capabilities to be enabled or disabled In general the processing steps run in sequence from the top to the bottom of the panel 5 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 5 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 dir
4. 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 is saved and recalled when new images are opened or a new image 1s displayed in a stack The black and white values indicated below the histogram can be directly entered in any mode but if auto mode 1s 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 Preferences 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 values If the default settings do not display the desired results the constant factors can be changed by the user under the Preferences menu Alternatively the arrows and blue region in the histogram can be dragged to adjust the image display manually The currently displayed range of pixel values is shown in blue in the histogram The blue r
5. 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 matching 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 1s 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
6. 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 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 5 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 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 or close the measurements table window 5 4 Sample Setup Figure 5 shows an example setup that would process 148 WASP 12b images
7. 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 1f calculations of altitude airmass HJD are desired Check Use to calculate these values and 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 d
8. 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 76 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 1n the Sub dir field or back into the same directory if the field is left 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 out
9. 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 5 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 then 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
10. 4 to the dock ImageJ runs in 32 bit mode using Java 1 5 Java 1 4 on OS X 10 3 and ImageJ64 runs in 64 bit mode using Java 1 6 ImageJ64 is not limited to 1800MB of memory but it requires a 64 bit Intel Mac running Mac OS X 10 5 or later The AstrolJ Mac _x x x zip file can be deleted For more information on running generic ImageJ with Mac OS X go to http rsbweb nth govw 1j docs install osx html 3 AstrolmageJ vs Generic ImageJ 3 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 1n this format If any of the IJ specific tools are selected the icons to 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 3 2 AstroImageJ Toolbar When AstrolmageJ AIJ is opened you will see the main AIJ Toolbar as shown in Figure 1 with eight AlJ 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 i
11. 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 4 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 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 overlay icon removes all apertures from the image 4 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 clea
12. JD 2456147 808350 LST 22 50 45 Lock Local 2012 08 08 03 24 01 AM EB 05 47am HUD 2456147 812563 dT 00 06 04 Dynamical Time Update Cb Auto Leap secs OsSUlinternal BJD 2456147 813328 Equatorial Ecliptic RA 00 00 40 652 Dec 00 04 24 02 Lon 00 11 04 84 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 47 47 39 79 5 92 30 17 121 23 90 48 159 75 71 29 155 69 8 31 28 04 83 22 5 3 2 6 1 Exposure Start Date Time Source UTC start of exposure 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 5 3 2 6 2 Exposure Time Source Exposure time 1s 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
13. TANT As long as the light curve plot is displayed the Multi Aperture settings dialog is bypassed and the previous aperture locations are used as reference If new Multi Aperture settings are desired close the light curve plot window and the settings dialog will be display for the next image that is processed Since a new set of Multi Plot control windows will be opened when a new plot is generated the old Multi Plot control windows should be closed as well All the settings will be saved and restored to the same state when the plot windows are opened If you want to start the run over with new data for all images close the MeasurementsTable window as well Otherwise new measurements will be appended to the old measurements 6 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
14. 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 enter the desired data AIJ checks the validity of the contents of each cell that is 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 7 FITS Header Editor
15. and UT START UT END 5 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 opened 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 1s 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 1s 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 t
16. 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 4 above an image or by using the View menu Clear Overlay selection 5 Data Processor DP Module 5 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
17. attern 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 5 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 a master bias file has already been created and it 1s 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 file
18. ce a AA AAAA AN 31 Ocima se Alon eee E ETE ETEO ETE E 34 1 Introduction AstrolmageJ 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 AstrolmageJ customizations are 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 1j jar file and the Astronomy jar file To report bugs or suggest new features please email Karen Collins at the address indicated above 2 Installation Java must be installed on a computer before running AstroImageJ Java can be downloaded from http www java com en download manual jsp AstroImageJ can be downloaded from http www astro louisville edu software imagej astronomy index html 2 1 Linux Installation Download AstroImageJ for Linux from http www astro louisville edu software astroimagej index html and extract AstrolJ x x x tar gz to the desired ImageJ folder A script file is available that shows how to set up AIJ for easy start up under Linux For Linux installatio
19. con 1s 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 and details are provided 1n separate sections of the user guide NOTE although the right hand portion of the toolbar can be customized as with generic IJ it is recommended to leave the default AIJ icons installed as shown below Figure 1 AstrolmageJ Toolbar with AstroImageJ tools on right hand side Ts Astrolmagel File Edit image Process Analyze Plugins Window Help DOGO lt 4 J NA e 2 O S EM ve Rectangular or rounded rectangular selections right click to switch P ha al Es Astro Mode Icon this button should normally be in the selected pressed state for AIJ operation When the button is 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 on of the following AIJ toolbar icons will not change the astro mode state DP Data Processing Icon opens the Data Processing DP module to perfo
20. e systems on the first and third lines of data above the image 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 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 4 2 Data Displayed in the Image The blue zoom box di
21. ectory 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 5 3 1 4 Filename Pattern The file name pattern boxes specify which files in the directory are to be processed Unix wildcard notation using 2 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 is loaded into the filename pattern field By default a 663099 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 5 3 1 5 Totals The totals column indicates the number of files found
22. een 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 4 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 ls 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 4 9 Single Aperture Photometry Shift left click on the mouse to run the full single aperture photometer or click the Aperture Photometry Tool icon on the AIJ toolbar The single aperture photometer provides full aperture photometry data which is displayed in a measurements table and can be saved or values from the table can be plotted 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
23. egion 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 P icon above the image 4 4 Image Negative 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 4 5 Image Invert Flip and Rotate The i
24. es menu Use astro window when images are opened checkbox Figure 2 AstrolmageJ Image Display Interface RA wasp 12b 00027 bsdf fits 13 7 a x File Preferences View Edit Process Analyze 4096x4096 pixels 16 bit 32MB ImageJ X 48 0178 ImageJ Y 1 064 0854 Value 299 0000 RA DEC Peak 477 0000 FITS Xx 48 5178 FITS 3032 4146 Int Ents 17 842 0648 TO 2 26 d 4 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 1 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 There 1s also an additional 0 5 pixel offset between the two coordinate systems IJ designates the top left of a pixel as the X 0 Y 0 location while FITS designates the center of a pixel as the X 0 Y 0 location AIJ displays pixel coordinates for both of thes
25. esired 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 while reading lengthy tooltips move the mouse back and forth slowly over the field after the tooltip has been displayed 5 9 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 fi
26. he macro options near the bottom provide the capability to perform real time data reduction and light curve plotting during an observing session To use this feature select use Macro 2 checkbox and then browse to the IJ plugins directory on your computer Then navigate to the Directory Watcher folder and select MultiApertureOnly txt as the macro file This macro runs Multi Aperture see Multi Aperture section below for description after each new image arrives and has been calibrated After the first file has been calibrated the Multi Aperture setup window will be displayed allowing any number of aperture locations to be selected in the image After then final aperture has been selected Multi Aperture runs differential photometry on the image and creates a MeasurementsTable containing the results Then the macro opens Multi Plot and plots the light curve as set up in the Multi Plot interface see below for details After the first image is completed each subsequent image is processed automatically Multi Aperture uses the same relative aperture positions without intervention Each aperture is repositioned at the centroid of the corresponding star in the new image unless the image field moves by more than the aperture radius from one image to the next in which case the process is halted The plot is automatically updated after Multi Aperture has completed photometric measurements and has updated the Measurements Table IMPOR
27. hing 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 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 5 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 correct
28. ing 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 4 15 Notes on Generic Image Regions of Interest Some of the items in the Analyze menu require a region of interest ROI to be defined within 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
29. ion 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 5 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 Figure 5 The DPCC window can be alternately displayed or hidden by clicking the L icon in this section of the DP GUI DPCC will continue to operate as set up even if the window 1s 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 no
30. ive check the appropriate negate box es in the input settings panel 5 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 FITS Header Input 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 T FITS Header Output Settings Target J2000 RA Keyword RAOBJ2K Target J2000 DEC Keyword DECOBJ2K lt q q Target RA Keyword RA_OBJ Target DEC Keyword DEC OBJ Target Altitude Keyword ALT OBJ Target Azimuth Keyword AZ OBJ a E Y ARTES Target Airmass Keyword AIRMASS JD start Obs Keyword JD SOBS JD mid Obs Keyword JD MOBS HJD mid Obs Keyword HJD_MOBS BJD mid Obs Keyword BJD_MOBS Observatory Latitude Keyword SITELAT Observatory Longitude Keyword SITELONG 5 3 2 7 Save Calibrated Images This section defines how calibrated output images are
31. le specified If use master bias is selected each individual flat is bias subtracted before combining If use master dark 1s 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 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 T
32. mage 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 4 6 Panning Left click and drag the mouse to pan the image A middle mouse click will center the image at the clicked location 4 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 ll or press control and left click to zoom in or control and right click to zoom out Press the zoom in fast button W 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 A or triple right click to zoom out such that the full image 1s displayed on the scr
33. 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 5 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 File Preferences View Control Options Science Image Processing Filename Pattern Matching V Enable Y Sort Num Q Observations _Qatar 1b_qty 12 20120821_Qatar 1b Filename Number Filtering Y Enable in 115 Bias Subtraction Build ave O med Q Observations _cals U16M_2_exposures 20120729 20 Biases Enable 7 7 Q Observations _cals U16M_2_masters Dark Subtraction Build ave O med Q Observations _cals U16M_2_exposures 20120706_ 20_Darks_100 Enable Ed Fi Q Observations _cals U16M_2_masters Y scale Division Build Enable O ave O med Q Observations _cals U16M_2_exposures Q Observations _cals U16M_2_masters gy Qatar 1b_ fits 1000000000 Qatar 1b_ fits es bias fits gy mbias_ 20_20120729 fits a dark_ fits gay mdark_ 20_100_20120706 fits gy mflat_ fits gy mflat_cbb_ 20_20120816 fits 4 Linearity Correction Y Enable New pixel value
34. n refer to the readme file at the AstroImageJ website For more information on running 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 AstroIJ_x x x zip to the desired ImageJ folder ex C Program Files x86 An ImageJ exe program is available in the upper most directory and can be used to start AstrolmageJ If preferred one can set up a file type to be automatically opened by ImageJ exe when double clicked by referencing that file type to the ImageJ 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 new memory setting When running AIJ by double clicking on 1 jar no more than 64MB of memory will be available to AIJ For more information on installing and running generic ImageJ with Windows go to http rsbweb nih gov 1j docs install windows html 2 3 Mac OS X Installation Download AstrolmageJ for Mac OS X from http www astro louisville edu software astroimagej index html and click on AstroIJ Mac _x x x zip to extract the ImageJ folder Move this folder to the Applications folder open it and copy either ImageJ or ImageJ6
35. o use dark exposure time correction 1t 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 steep 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 5 6 Real Time Light Curve Plotting T
36. oolbar If an image is open the settings can be accessed under the Edit menu Aperture Settings selection There are many options available but figures 4 and 5 below show an example of settings that should be a good starting point Adjust the aperture sizes properly for the data being analyzed Be sure to select Show other configuration panel to display the second set of options after the first set is closed
37. ovided 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 When 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 someth
38. put 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 5 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 only 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 gov 1 docs The order which these items are processed 1f enabled is Macro 1 Macro 2 Multi Aperture Multi plot 5 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
39. r apertures overlay icon Y 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 4 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 set 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 Fig
40. railing 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 1s 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 32000 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 value 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 5 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 observator
41. rm image calibration bias dark flat linearity correction and to optionally perform FITs header updates 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 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 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 la 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 Mm Open Data Icon opens a previously saved measurements table or any generic tab comma or space delimited file from disk for plotting with MP ri 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 sys
42. rmally 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 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 55 Target Proper Motion mas yr meal pmpec Standard Coordinates J2000 Equatorial J2000 Ecliptic a o Dec 00 00 00 Lon 00 00 00 Lat 00 00 00 B1950 Equatorial Galactic RA 23 57 26 234 00 16 42 28 96 20 14 17 Lat 60 11 18 79 Epoch of Interest UTC based Time Now UTC 2012 08 08 07 24 01 UT Ed og49Pm
43. s 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 5 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 files 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 is 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
44. seeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeees 9 A oO paca nda Naa O aaa iii as andas 10 4 5 Image Invert Flip and SA 10 I 6 DR 61010 DO SAAE o A nn unn 10 IP o O a ed 10 4 8 Mouse Pointer Live Photometer ooooocccccnncccnnnnonanononononnnnnnnnnnnnnnnnnnnnnnnnnnnn ono nnnnnnnnnnnnnnnnnnnnnannnnns 11 4 9 mole Aperture POLONIA aan 11 4 10 Apertures Displayed in the lMage oooocnnnnnccccunanonanonononanononnnnon nooo ono nono nono non nono nn nn non nn non n nn nro nan nro nn nnnnns 11 4 11 ia ie Ve TOU AR A Se PA ER OU EERE 11 AZ Hace tac DIS cese atleti 12 4 13 Other Stack Related Icons above the Image Display cccccsseessseesssesesssssssssessseeesseseeeeens 12 4 14 Menus above the Image Display aiii EE TE 13 4 15 Notes on Generic ImageJ Regions of Interest cccccceeeesssessesssessessesessseesessesseeseeseeeeeeeeeeeees 13 3 Data Processor DP Module eiii ranas 14 Sl ONCE OL OPS tal dades 14 5 2 Post Processing vs Real Time Operation occccccncnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnonnnnnnnnnnnnnnnnnnnnnnnnnss 14 ds DP Usor TOCA Ce o ateacees E A E E 14 Sad ls Hornzontal SCCUOUS A e e O o ER UA 15 5 3 2 Vertical Sections IN Sobeonedawanonaenes 16 SS DICA A MPS a Re NTP e R AA E E e E e A 23 So a Rc duc tion OA SS 24 56 Real Time Lia Curve A dados 24 6 FITS Header Viewing and Edinho aaa DESDE ADSENSE eae Ea 25 TI O ol 26 So MUA perturo PAOLO is 2I SEIOS PIO rr a rr n
45. splayed 1n 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 red N and E arrows point in the user defined directions that should indicate the proper north and east directions in the image The north and east directions are set under Preferences gt Set direction indicator angles The north offset should be entered as the CCW angle in degrees from the Y arrow in a non inverted rotated image The east offset should be entered as the CCW angle in degrees from the north direction in a non inverted rotated image note not from the X arrow Once set up the X Y N and E direction arrows will follow properly when the image is inverted or rotated The image scale indication at the top middle of an image will display the scale of the image in either pixels or in secs mins of arc if the pixel scale has been set in the Preferences 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 4 3 Contrast Brightness Adjustment Under the Preferences menu select either auto brightness amp contrast
46. tems It converts time for those coordinates and a specified observing location to from UTC local time Local Sidereal Time LST Julian Date JD Heliocentric JD HJD and Barycentric JD BJD x5p 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 SKY 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 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 4 AstrolmageJ Image Display Interface When a FITS image or any other native IJ image type is opened the image will be displayed in a window as shown Figure 2 The menubar the data fields and buttons at the top and the histogram and associated data fields at the bottom are specific to AIJ The custom AIJ display can be disabled by deselecting the checkbox under the Preferences menu labeled Use astro window when images are opened Then close and reopen the image to use the standard IJ image display with no controls or menus To reenter the AIJ style image display make sure that the star field icon 1s depressed and then click on the image To re enable AIJ style image display for all opened images check the Preferenc
47. 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 5 3 2 Vertical Sections Starting from the top the vertical sections are labeled in the border of each section as 5 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 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 characters in a filename that fall under 66399 or characters in a p
48. 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 is scaled using the three coefficients specified in the Non Linearity Correction section 5 3 2 4 Flat Division This section allows the user to define locations and file names for raw and master flat images 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 matc
49. ure 3 Stack Control Panel b P 4 j Eee 1960 2562 3 64 46666 5568 6 64 05 3 25 62 45 91764 10000 0 0000 min 131 3451 black mean 306 3165 white 1 023 3473 max10 000 0000 4 13 Other Stack Related Icons above the Image Display om ES Multi Aperture Icon opens the Multi Aperture MA photometry module to perform differential photometry on a series of usually already calibrated images See the Multi Aperture section for details 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 1s not supported See the Image Alignment section for more details 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 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 4 14 Menus above the Image Display Pull down menus are pr
50. y s coordinates and altitude manually in DPCC s Geographic Location of Observatory section Full DPCC help 1s 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 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 posit
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