the CF-EDIT Users Guide
Contents
1. CF EDIT D Lindler February 2004 V Dixon May 2004 1 0 Introduction CF_EDIT is an Interactive Data Language IDL visualization tool for the examination and modification of Far Ultraviolet Spectrographic Explorer FUSE intermediate data files IDF containing calibrated time tag photon lists It is started from IDL by typing cf_edit at the command prompt Figure 1 1 shows the layout of the primary CF EDIT interface It contains AE FILE Colors Scale Log Display Final X Y Overlay Event Selection GTI Selection Extract Spectrum Background Header Register Y CENTROID TTAG Analysis Exptime 9597 4 6012 7500 0 1022 6678 6780 634 736 Freeze Min Max Min 0 00000 5 Max lis 00000 Reset Min Max X i6496 y 1020 6 Val 0 00000 Figure 1 1 CF_EDIT Table 1 Summary of the CF_EDIT Menu Bar Section ES oe a a a EY CSS _ Read IDF File s Select and read CALFUSE intermediate data files 21 Write IDF File Write intermediate data file 22 _ Default Parameters Modify CF_EDIT control parameters 11 0 PS Output Produce PostScript file of the current display _2 3 Exit Colors Scale l Display Row Plotarow of the displayed image 40 Column Plot a column of the displayed image 40 RowSum___ Plot a sum of rows of the displayed image 40 _ Column Sum Plot a sum of columns of the displayed image 40 PHA P2. For example if you Night _ Day Either Day Night want to display an image of the burst events set Bursts to Bad You can limit the range of displayed pulse heights by entering new values in the PHA Range minimum and maximum fields _ Done Abort Reset SelectAll Use my GTI Selection allows you to turn off and on the use of any good time interval Selection that you may have done with the GTI Selection button Section 5 2 Good _ Bad _ Either High Voltage Good _ Bad _ Either Limb angle PHA Range Min 2 Max E Use my GTI selection _ No C Yes Figure 5 1 Event Selection When you have completed your Selections push Done The displayed images will be updated using only the events that you have selected Your Selections will also be used when Extract Spectrum or FILE Write IDF file are performed To exit the event Selection tool without BH aooe dd EXIT Zoom UnZoom X Log Log Delete All Delete Region Keep All Keep Region UNDO X 6969 89 Y 14 0741 FLAGS gt DAY BURSTS BKGD_CNT_RATE 0 5 0x10 1 ox10 1 5x10 Time seconds 213 000 X Max 19283 4 Y Min 0 935221 Y Max 28 5914 Figure 5 2 Selection of Good Time Intervals modifying the data press Abort Reset can be used to reset the Selections to those upon entry into the Event Selection interface Select All will cause all conditions to be ignored and all events selected 5
3. from all of the input files and may be reread by CF_EDIT However if you have changed the selection of good events with CF_EDIT you may have to go back to the original data to make additional changes For example if you told CF_EDIT to ignore the burst event flag it will be set to zero for all events in the output IDF file If you want to turn it back on you must go back and reread the original data 2 3 Postscript output of the displayed images Select PS output on the FILE menu to create a postscript file of the current images displayed by CF_EDIT It has three options B W for black and white B W reversed and Color 3 0 Controlling the Displayed Images 3 1 Selection of pseudo colors Push the Color button on the menu bar to change the pseudo color table used to display the images The standard IDL color table Selection interface will appear Select the desired color table and exit 3 2 Image Contrast Contrast can be controlled using the Scale pull down menu to the right of the Scale label button Four intensity transformations are available linear square root logarithmic and histogram equalization Further control of the intensity scaling is accomplished with the MIN and MAX fields see the region labeled with the number 5 in Figure 1 1 Anything with a value less than MIN is set to zero in the display Anything with a value greater then MAX is set to the maximum display value If you change the MIN or MAX value the new value d
4. 2 Selection of good time intervals The GTI Selection button on the menu bar allows you to reject events from time periods selected using plots of any of the following parameters LiF count rate SiC count rate 10 FEC count rate 11 AIC count rate 1 Time since sunrise 2 Time since sunset 3 Limb Angle 4 Spacecraft Longitude 5 Spacecraft Latitude 6 Orbital Velocity 7 High Voltage 8 9 12 Background count rate 13 Y centroid of the LiF target spectrum 14 Y centroid of the SiC target spectrum When you select a condition on the pull down menu of the GTI Selection button the tool shown in Figure 5 2 will appear Time regions that you flag as bad will appear in red Regions that are bad for other conditions as specified by the Event Selection tool Section 5 1 will appear as green As you move the cursor over a green region the condition that causes it to be bad is displayed below the menu bar To mark data as bad use the Delete All or Delete Region buttons Delete All marks all data as bad It is useful if most of the data is bad and you would prefer to mark it as all bad and then select the regions of good data Delete Region marks data within a user specified box as bad After pushing the button you must position the cursor on the first corner of the box and press the left mouse button Next position the cursor on the opposite corner and again press the left mouse button All data points lying within the box will be m
5. back to linear scaling When you exit from the GTI Selection tool the displayed images will be updated to remove data from the bad time intervals that you have selected provided that you have not turned off the Use my GTI Selection in the Event Selection Section 5 0 Any spectral extractions or output IDF files will also have your good bad time intervals flagged You may re enter the GTI Selection tool to make changes to your good time intervals or to apply additional selection criteria using a different plotted parameter 6 0 Background Region Selection With the Background button on the main menu you can adjust the background regions used to scale the background reference file in CalFUSE It has three options Adjust Region Create New Region and Delete Region When any of these options are selected the background overlay will be turned on and the background regions displayed on the images as rectangles Hint Change the X binning to 32 in the File Default Parameters Section 11 0 when changing the background regions This causes the entire spectral range to appear in the large display window If Adjust Region is selected place the cursor on one of the horizontal boundaries of a background region click a mouse button move cursor to the new location for the boundary and click again You need not worry about the light from the airglow lines These regions are automatically ignored by CalFUSE If New Region is selected p
6. the new plot Up to 10 overplots are supported See the documentation for LINEPLOT in the FUSE SCAN reference manual for additional information on the use of the plotting tool 5 0 Selection of Time Tag Events The Event Selection and GTI Selection buttons on the menu bar control which events are displayed in the image extracted with Extract Spectrum or flagged as usable in the output IDF file Event Selection allows you to turn Selection criteria on and off Section 5 1 GTI Selection allows you to specify the good and bad time intervals interactively using plots of various observation parameters versus time Section 5 2 5 1 Event Selection When you push Event Selection the interface shown in Figure 5 1 will appear Events are flagged with eight conditions that may make an event unusable or suspect 1 User Defined 2 J aer o Selection Criteria of Events to Display Extract 3 Not in OPUS good time interval Orial 5 riginal IDF Time Flags A Pursts C Good _ Bad _ Either User Defined Eit 5 High Voltage 00 _ bad _ Either ser Vetine 6 SAA C Good _ Bad _ Either Jitter 7 Limb Angle C Good _ Bad _ Either Notin OPUS GTI 8 Day Night l iK H Good _ Bad _ Either Bursts To reject events with any of these conditions select the Good button To ignore the condition press Either If Good _ Bad _ Either SAA you want to investigate what the bad m events look like without the good ones select the Bad
7. _EDIT can be run either in the standard IDL environment or using the IDL Virtual Machine VM IDL VM allows users who do not have an IDL license to run IDL packages prepared for VM To obtain IDL VM free of charge visit the Research Systems Inc web site E Image Binning X 2 8 ee Extracted wavelength spacing 0 0130000 Extracted spectral units _ Counts Flux erg cm2 sec A Cal File Directory V datat fuse cal fuse v3 0 calfiles DONE Figure 11 1 Default Parameters www rsinc com idlvm When installed load the file cf_edit sav into the IDL VM to start the program 13 0 Additional Information You ll find CF_EDIT easier to use if you know something about its internal logic First of all the program always ignores the status flags associated with individual photons in the first extension of an IDF file Instead it uses the status flags stored in the third extension the timeline table to determine the good and bad time intervals of an exposure or series of exposures It uses these intervals to determine whether individual photons are good or bad based on their arrival times If you use the Event Selection tool to change the definition of good and bad photons or the GTI selection tool to define time intervals as good or bad both the program s internal set of good time intervals and the list of photons included in the image display are modified accordingly Only when the program writes
8. ains the minimum and maximum image values and can be used to control the contrast of the displayed images Region 6 shows the X and Y position of the cursor position along with the image s intensity value at that point 2 0 File Input Output 2 1 Reading input IDF files Your first step when using CF_EDIT is to read one or more input IDF files Select Read IDF File s from the FILE menu A standard file Selection interface will appear You can move to the directory containing the data file s that you want Select the data files and exit Multiple files are selected by holding down the lt shift gt key to select a continuous range of files or the lt Ctrl gt key to select individual files It is sometimes helpful to limit the files on the Selection list by modifying the filter For example you might change the filter from idf fit to la idf fit to limit the list to segment la You can then quickly highlight the files you want by selecting the first file followed by the last file while pushing the shift key If you select multiple input files they must all be from the same detector segment Each segment must be processed independently 2 2 Writing the output IDF file Once you have completed your operations on the input IDF files you can write a merged IDF file Select Write IDF File s on the FILE menu The standard file selection interface will appear Use the default output filename or create your own The output file contains the events
9. are 10 0 Time Tag Event Analysis The TTAG Analysis button allows you to examine count rates and compute centroids of selected regions of the image When pressed it activates the tool shown in Figure 10 1 Initially the image display will be blank and the buttons below the PROCESS button will not be active To begin first home lindler fuse pro dev l _ Ej specify the range of data to be analyzed The default upon EXIT Movie entry is the area in the zoomed image of the main CF_EDIT display The range can be changed by editing the X Range and Y Range fields The area in the region will be centroided and the total counts within the region computed as a function of time Next you must specify a time interval by Time Intervals Seconds 120 which to bin the time tag events The default is 120 seconds The minimum counts needed within each time interval in order to attempt a centroid can also be changed When you are ready press the PROCESS button The HESA o rE E bottom display window will show the region of the image Bes Reno that you selected You can now generate plots of the centroids counts within the region and total counts within the image versus time using one of the four plot buttons PLOT X Centroids PLOT Y Centroids PLOT Counts or PLOT Total Counts Any of these buttons will bring up the line plotting widget LINEPLOT Refer to the FUSE_SCAN users manual for documentation on the use of LINEPLOT Exit the plo
10. arked as bad If you make a mistake in this process just hit the UNDO button or use Keep Region to select the portion of the data that you did not want marked as bad Keep Region works the same as Delete Region All data points within the selected box will be marked as good Keep All will mark all data points as good The X and Y ranges of the plot can be changed using the Zoom and UnZoom buttons on the menu bar After pushing the Zoom button position the cursor in the plot window at one corner of the rectangular region you want to expand Push the left mouse button and repeat for the opposite corner of the region Alternately you can zoom without first pushing the Zoom button by placing the cursor at one corner of the box pushing and holding the center mouse button while dragging the cursor to the opposite corner and releasing the center mouse button Another method of changing the X and Y ranges of the plot is to enter values into the X Min X Max Y Min and Y Max fields at the bottom of the widget Zooming in on selected regions allows you to refine the data masks By zooming to very small regions you can easily mark good and bad data points individually When zoomed to a sufficiently small region of the data individual data points will be marked as diamonds To change the X or Y axis to logarithmic scaling push the X Log or Y Log button The plot will change and the button will be renamed X Linear or Y Linear It can now be used to change
11. constructed by linearizing the wavelengths of the time tag events Only events with assigned wavelengths those within the aperture extraction regions are displayed The Wavelength Y coordinate system will show the results of the astigmatism correction You can adjust the binning of the data when constructing the image using the Default Parameters option on the menus File button Section 11 0 The default 2 x 2 binning is recommended as 1x1 binning may cause memory problems on some machines 3 6 Graphic Overlays E _ The Overlay button on the menu bar can be used to turn on and Wavelength Scales off graphic overlays on the images It will display the interface _ Background Regions shown in Figure 3 1 Push the buttons to turn the overlays on _ HIRS Extraction Region and off If an extraction region is selected CF EDIT must have _ MDRS Extraction Region access to the extraction limit calibration file listed in the FITS LWRS Extraction Region header keyword CHID_CAL The calibration file must be in the directory specified in the default parameters controlled by the Default Parameters option on the FILE button Section 11 0 The default value of this directory is the definition of the Figure 3 1 environment variable CF _CALDIR Graphic Overlays EXIT 4 0 Generation of Plots Plots of the data can be generated using the Plot button or the Extract Spectrum button on the menu bar The plot button offers five types o
12. f plots row column row sum column sum and PHA After selecting either the row or column option place the cursor on a row or column in any of the three display windows and push a mouse button When selecting a row or column sum place the cursor on the first row or column and push a mouse button Select the last row or column and push a mouse button again PHA will display a histogram of the pulse heights of the events With the Extract Spectrum button you must select the channel aperture to extract The spectrum will be extracted in wavelength bins versus flux or counts as specified in File Default Parameters Section 11 0 WARNING While spectra generated with the Extract Spectrum button may be written to an external file they are not background subtracted and are not meant for scientific analysis Instead we recommend that you write out your modified IDF file and use the CalFUSE extraction software to extract a final spectrum When a plot is requested with Plot or Extract Spectrum a plotting tool LINEPLOT will appear containing the plot This tool can remain active while you continue using CF_EDIT This will allow you to generate overplots If you leave the plotting tool active new plots will appear in the same window For example you could use the tool to compare an extraction of a spectrum with and without the daytime events included If you do not want the new plot to be overplotted you must exit the plotting tool before generating
13. f_idf 0 0123 and displayed in an interactive wavelength registration D15708870131attagf_idf 0 0035 tool Refer to the FUSE REGISTER user manual for _ D15709870121 attagf_idf 0 0012 instructions on using this tool The registration tool _ D15709870111attagf_idf 0 0455 will accept a maximum of ten spectra If you have read amp 45799870101 attagf_idf more than ten you will be asked to select up to 10 files to register Figure 8 1 Use the Selection buttons to select or deselect the files to process and then push D15709870091 attagf_idf D15709870081 attagf_idf DONE When you have registered the selected D15709870071attagf_idf spectra the Selection process will be repeated The _ D15709870061 attagf_idf computed wavelength shifts will be applied to all _ D15709870051 attagf_idf photons in the desired aperture Files previously _ D15709870041 attagf_idf processed will show the computed wavelength offsets in Angstroms to the right of the filename This will assist you so that you do not repeat or miss any of the files In the example in Figure 8 1 the first spectrum is used as a reference spectrum You are free to choose any of the spectra as a reference To exit the registration tool press DONE without selecting any files Figure 8 1 Registration File Selection _ D15709870031 attagf_idf _ D15709870021 attagf_idf _ D1570987001 1attagf_idf Although all of the capabilities in the FUSE_REGISTER registrati
14. lace the cursor at the first Y boundary and click a mouse button Move to the second position and click again The new region will be added If it overlaps with an existing region the boundary of the existing region will be adjusted to resolve the overlap If Delete Region is selected place the cursor in the region and push a mouse button WARNING background regions are specified in Final X Y coordinates Be sure your images are displayed in these coordinates Section 11 0 before adjusting the regions 7 0 Header Manipulation The Header button can be used to display the input headers and to add comments to an output header To display an input header select the Display option on the pull down menu If you have read multiple input files you will be requested to select which header to display The header is displayed in a scrollable text window When you finish examining the header push the DONE button at the top of the window The Add Comments option on the Header pull down menu allows you to enter comments to be placed into the output IDF file A text window will appear Enter the comments into the window and push DONE 8 0 Wavelength Registration idl E The Register button allows you to register the Select up to 10 files wavelengths of spectra from multiple exposures interactively Select the desired aperture from the pull down menu The requested spectra will be extracted D15709870151attagf_idf _ D15709870141attag
15. lot a histogram of the pulse heights of the time tag events W Ww bo AJN Overlay Control overlayed graphics on the displayed image Event Selection GTI Selection Extract Spectrum Select criteria for good events Select Modify Good time intervals Perform unweighted slit extraction of the specified aperture Overlay Event Selection GTI Selection banali ooz 60 6 0 6 0 el 7 0 8 0 9 0 Background Adjust Region Adjust region used for scaling the background Create New Region Create a new background region Delete a background region Delete Region Header Display Add Comments Register Y CENTROID TTAG Analysis Exptime Display FITS Header of the input IDF file s Add comments that will apear in the output header Wavelength registration Calculate Y centroid of a target spectrum Analyze time tag list count rates centriods movies Displays total exposure time for current good time intervals three graphic windows labeled 1 2 and 3 The long window at the bottom number 1 shows the entire detector image the large window number 2 shows a portion of the image with one data pixel per screen pixel and the small window in the upper right corner number 3 is a zoom window Commands are issued using the two row menu bar at the top of the widget labeled 4 in Figure 1 A summary of the menu bar commands is given in Table 1 The region of the interface labeled 5 cont
16. oaded Once the frames are loaded away it goes Use the top buttons on the animation widget to stop the movie or change directions The Frames Sec slider can be used to control the speed of the movie When done hit the End Animation button to return to the Movie Creator widget 11 0 Default Parameters The Default Parameters option on the File menu will allow you to a number of parameters used by E FUSE MOVIE CREATOR EXIT RANGE SELECTION X Range 6680 to 8782 Full Y Range 766 to B68 Full 1 Time Period to display in seconds from start of observation T Range a to 19066 Full BINNING SELECTION Binx p Bin p Zoom Factor 41 2 Time Interval 180 00 Seconds The estimated movie size in Megabytes will be 1 1 The value must be less than 128 To decrease increase bin sizes or or decrease range sizes Frame Size 103x103 Number of Frames 105 MOVIE CONTRAST Min counts b Max counts O LIGHTS CAMERA ACTION Figure 10 2 Movie Creation CF_EDIT When selected the tool in Figure 11 1 is displayed The Image Binning applied before displaying the images can be changed in the two pull down menus The Extracted wavelength spacing and Extracted spectral units give wavelength binsize and output units when spectra are extracted with the Extract Spectrum tool The Cal File Directory is the location of the CalFUSE calibration files 12 0 IDL Virtual Machine CF
17. oes not take effect until you either hit a carriage return while in the MIN or MAX window or select a new intensity transformation with the Contrast menu button If you plan to change both the MIN and MAX values you can save time by not hitting the carriage return until both values are changed The Reset Min Max button will reset the MIN and MAX fields to the original image minimum and maximum values The MIN and MAX fields are reset to the minimum and maximum image values whenever a new image is loaded If you want to freeze values to the current levels push the Freeze Min Max button The MIN and MAX values will be left unchanged when new images are loaded When hit the Freeze Min Max button will change to an UnFreeze Min Max button Hit the button again when you want to change back to normal operation 3 3 Controlling the region of the image displayed The long bottom display window region 1 in Figure 1 1 always shows the entire image binned to the window size Note that the x and y aspect ratios do not match Window number 2 in Figure 1 shows a portion of the image with the display pixel size equal to the image pixel size as binned during file reading see Section 11 0 There are two ways to control what region of the image is displayed in this window 1 Use the scroll bars on the side of the window If no scroll bar is present it indicates that the image fits within the display in either or both the X and Y directions 2 Move the curso
18. on tool are available only the wavelengths offsets are returned and have any effect on the output IDF file of CF_EDIT You are welcome to rescale the data and coadd it You can even write the coadded spectrum to a file However such actions have no effect on the operation of CF_ EDIT Also note that no statistical errors are loaded into the registration tool by CF_EDIT It is suggested that coaddition of extracted spectra be performed with the final CalFUSE outputs using FUSE REGISTER 9 0 Recomputing the Y Centroid The Y CENTROID button will allow you to recompute the Y centroid for a particular aperture Centroids for each aperture are stored in the IDF file header By default the header of the first input file is copied to any output IDF file created by CF_EDIT If your target is faint you may be able to improve on the YCENT values in the input header by recalculating centroids for the combined data set To do it press the Y CENTROID button and select and aperture Then decide how the centroid should be determined Target events only This is the standard Airglow events only Useful for diffuse or faint targets Default Reads value from aperture calibration file User select Presents a window in which to enter the Y centroid value To check your result use the Overlay button to plot the extraction window on the displayed image The new value of YCENT will be written to the output IDF file and used by the CalFUSE spectral extraction softw
19. out a new IDF file are the status flags of individual photons updated Because we lack arrival time information for data obtained in HIST mode exposures affected by bursts SAA s or low limb angles must be accepted or rejected in total These conditions are likely to increase the background level but probably not enough to overwhelm bright HIST targets CF_EDIT deals with such situations in two ways First if asked to read a file affected by one of these conditions that is if the header keyword EXP STAT gt 0 CF_EDIT issues a warning message but does not reject the data set Second CF_EDIT by default ignores the BRST SAA and LIMB flags in the timeline table You can see this in the Event Selection tool for HIST data the acceptance criteria for Bursts SAA and Limb Angle are set to Either
20. r to the lower window and hit any mouse button The position of the cursor in the lower window will be the center of the region displayed in display window 2 You can hold down the mouse button while moving the cursor in the lower window to roam around the image There are two ways to control the region of the image that is displayed in the zoomed image window number 3 in Figure 1 1 1 Move the cursor to the large window number 2 in Figure 1 1 and hit any mouse button The position of the cursor in the large window will be the center of the region displayed in the zoomed image window 2 Position the cursor at any point within the zoomed image window and push a mouse button The position of the image selected will be moved to the center of the zoomed image window The zoom factor of the zoomed image window can be changed using the Zoom Factor button above the zoom window 3 5 The image coordinate system Any of four coordinate systems can be selected with the Display button 1 Raw X Y 2 XFARF YFARF 3 Final X Y 4 Wavelength Y Click on the current coordinate system name to the right of the Display label and select the desired coordinate system from the pop up menu Raw X Y are the original raw X and Y coordinate system XFARF YFARE are the coordinates after correction for various detector distortions and Final X Y are the coordinates after the image motion correction In the Wavelength Y coordinate system the horizontal axis is
21. tting widget if you do not want the next plot you request to be overplotted on the existing plot X Range 6680 6782 Y Range 766 B68 Min counts needed to centroid 20 PROCESS PLOT Counts PLOT Total Counts The Movie button on the time tag analysis tool allows you to create a movie with the time tag events Pressing it will bring up the widget shown in Figure 10 2 There are four regions to this tool The first labeled 1 in Figure 10 2 Figure 10 1 controls the portion of the image and the time range to be TTAG Analysis displayed as a movie The default image range is the zoom window in the CF_EDIT main display The default time period is the entire observation The second region 2 controls the binning of the image and the time intervals binned for each movie frame Region 3 displays the size of the movie as specified and region 4 controls the contrast of the movie The total size must be less than 128 megabytes and typically should be much smaller If the movie is too large adjust the binning or range to make it an appropriate size Any time you edit one of the range or binning fields you must enter a carriage return within the field to update the information in the movie size region 3 of the widget When you are satisfied with your Selections hit the LIGHTS CAMERA ACTION button This will bring up the IDL animation tool Initially the movie will appear slow as the frames are created and l
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