CALFUSE Pipeline Status

December 5, 2008 -
Van Dixon -
v3.2/src/libcf/cf_calculate_y_centroid.c -
v3.2/src/libcf/cf_find_spectra.c -
v3.2/src/libcf/cf_screen_jitter.c - -

-In HIST mode, there are no spectra in other apertures to cause -confusion, so we need not require that the target centroid lie within X -pixels of either the airglow centroid or the tabulated centroid. Both -cf_find_spectra.c and cf_calculate_y_centroid.c were modified to effect -this change. - -

-Modified cf_screen_jitter.c so that the jitter correction is not -applied to ERO observations of Jupiter (program X006). - -

-
v3.2/include/calfuse.h -
v3.2/src/fuv/cf_bad_pixels.c -
v3.2/src/fuv/cf_screen_photons.c -
v3.2/src/libcf/cf_apply_filters.c -
v3.2/src/libcf/cf_fuv_init.c -
v3.2/src/libcf/cf_screen_jitter.c -
v3.2/src/libcf/cf_set_photon_flags.c -
v3.2/src/analysis/cf_combine.c -
v3.2/src/analysis/cf_xcorr.c -
v3.2/src/analysis/idf_combine.c -
v3.2/src/analysis/cf_make_all_obs.csh -
v3.2/src/analysis/cf_make_900_obs.csh - -

-I've modified CalFUSE to treat bright-earth and airglow observations -differently than before. Here are the details: -

-When creating the IDF files for bright-earth observations (programs -M106 and S100) or 900-level airglow exposures, CalFUSE sets the header -keyword EXP_STAT = 2. For 900-level exposures, the SRC_TYPE is set to -EE, and the following warning is written to the file header: -"Airglow exposure. Not an astrophysical target." -

-The pipeline then processes the file as usual. In particular, the -limb-angle flag is set in the timeline table (extension 3 of the IDF), -and the "Time with low limb angle" is written to the file header. -However, if EXP_STAT = 2, the following things change: - -

-The extracted spectra include photons obtained at low limb angles. The -detector-image plots do, too. But the count-rate plots indicate times -when the line of sight passes below the limb-angle limit. -

-For programs M106 and S100, all of the data are included in the -observation-level ALL, ANO, and NVO files. For all other programs, -900-level airglow exposures are excluded from the sum. A new -observation-level file is produced: a single quick-look (gif) plot -showing the summed spectrum from all of the 900-level exposures in the -observation. It has a name like M112580100900specttagf.gif. - -

April 11, 2008 -
Van Dixon -
v3.2/src/analysis/cf_xcorr.c -
v3.2/src/analysis/cf_combine.c -
v3.2/src/analysis/cf_make_all_obs.csh - -

-We've changed the logic used to combine individual exposures into -observation-level files for data obtained in HIST mode. If the target -is too faint to perform a cross-correlation, but is still in the slit -(i.e., its flux is within 50% of the reference spectrum), add the -spectra using a shift of zero. If an exposure suffers a limb-angle or -SAA violation, include it anyway, assuming that HIST targets are -bright enough that the additional background flux is not a problem. - -

-In HIST mode, there are no spectra in other apertures to cause -confusion, so we need not require that the target centroid lie -within 30 pixels of the expected value. - -

Feb 22, 2008 -
Benjamin Ooghe -
INSTALLING_CalFUSEv3.2.2 -
INSTALLING_A_FORTRAN_COMPILER -
FIXING_SELINUX_ISSUES - -

Added scripts to set environment variables in Bourne-based shells -(sh and bash) for systems without CSH and automated the setting of the -shell path. - -

-
v3.2/src/configure.linux -
v3.2/src/configure.linux64 -
v3.2/src/configure.macosx -
v3.2/src/configure.solaris -
v3.2/src/cfitsio/configure -
v3.2/src/Makefile.Linux -
v3.2/src/Makefile.Linux64 -
v3.2/src/Makefile.MacOSX -
v3.2/src/analysis/Makefile.Linux -
v3.2/src/analysis/Makefile.Linux64 -
v3.2/src/analysis/Makefile.MacOSX -
v3.2/src/analysis/idf_combine.c -
v3.2/src/analysis/cf_coadd.c -
v3.2/src/analysis/cf_arith.c -
v3.2/src/analysis/cf_combine.c -
v3.2/src/analysis/cf_pack.c -
v3.2/src/cal/jitter/Makefile.Linux -
v3.2/src/cal/jitter/Makefile.Linux64 -
v3.2/src/cal/jitter/Makefile.MacOSX -
v3.2/src/cal/jitter/cf_jitter.c -
v3.2/src/cal/jitter/cf_jitter_diag.c -
v3.2/src/fes/Makefile.Linux -
v3.2/src/fes/Makefile.Linux64 -
v3.2/src/fuv/Makefile.Linux -
v3.2/src/fuv/Makefile.Linux64 -
v3.2/src/fuv/Makefile.MacOSX -
v3.2/src/fuv/cf_gainmap.c -
v3.2/src/fuv/cf_countmap.c -
v3.2/src/libcf/Makefile.Linux -
v3.2/src/libcf/Makefile.Linux64 -
v3.2/src/libcf/Makefile.MacOSX -
v3.2/src/libcf/cf_idf_io.c -
v3.2/src/slalib/mk -
v3.2/src/slalib/mk.sv -
v3.2/src/slalib/sla_source.tar - -

Updated configure files and Makefiles for all systems in order to -compile with more different fortran compilers (f77, f90, g77, gfortran) -and on recent systems (Solaris 10, recent Linux, Mac OS X 10.4) -including 64-bit architecture machines. This required the modification -of source files to correct bad int/long declarations that cause -problems on 64-bit architectures, on Solaris 10 systems, and on some -fortran compilers. - -

-
v3.2/include/calfuse.h -
v3.2/src/libcf/cf_fes_proc_update.c -
v3.2/src/libcf/cf_fes_proc_check.c - -

Fixed warning messages from GCC compiler (missing brackets and -unused symbols). - -

Fixed memory problem causing occasional bad values in the NVO flux arrays. -In copy_spec, the shift+start value was sometimes negative, causing the -routine to read negative indexes in the flux and error arrays. Also, -the final values of the flux_nvo and error_nvo arrays weren't always -written. - -

In cf_generate_pseudo_photons, verify for each fill-data event that -the LOCATION_SHLD flag is not set to ensure that it does not -fall outside of the active area of the detector. - -

In cf_estimate_drift_coefficients, set max value of index to jmax-1 -rather than jmax. - - -

February 22, 2008 -
Van Dixon -
v3.2/src/fuv/cf_convert_to_farf.c -
v3.2/src/fuv/cf_flux_calibrate.c -
v3.2/src/fuv/cf_ttag_init.c -
v3.2/src/libcf/cf_modify_hist_pha.c -
v3.2/src/libcf/cf_screen_jitter.c -
v3.2/src/libcf/cf_set_good_time_intervals.c - -

-Modified cf_convert_to_farf to write out the new PHA values assigned -by cf_modify_hist_pha. - -

-Added -e flag to cf_ttag_init. It sets the header keyword HKEXISTS -to YES in the output IDF file. - -

-In cf_screen_jitter, don't apply jitter correction to observations -taken after the spacecraft lost pointing control. - -

-If HV array in HSKP file consists of a single 0 followed by all -1's, -use header info to populate timeline table. Change name of subroutine -fill_hv_array to hv_from_hskp and add hv_from_header. - -

-Within cf_bad_pixels, we scale nmax, the program's guess at the number -of bad pixels it will have to deal with, by 1.5 to help prevent array -overflows. To make warning messages more meaningful, we call -cf_error_init after each call to cf_extraction_limits and make -CF_PRGM_ID and CF_VER_NUM static variables. - -

March 29, 2007 -
Van Dixon -
v3.2/src/libcf/cf_init_support.c -
v3.2/src/cal/jitter/cf_jitter.c - -

-On error, cf_check_digitizer now sets EXP_STAT flag to -2, rather than --999, to be more consistent with cf_hist_init. - -

-We modified cf_jitter to handle the time period (in March 2007) when -the ACS telemetry rate was cut in half and generally made the code -more robust. - -

March 23, 2007 -
Van Dixon -
v3.2/src/fuv/cf_hist_init.c -
v3.2/src/libcf/cf_init_support.c -
v3.2/src/libcf/cf_screen_jitter.c -
v3.2/src/libcf/cf_satellite_jitter.c - -

-In cf_hist_init, set EXP_STAT to -1 if a raw hist file contains no -extensions. Treat the limits of the active area as good pixels. - -

-In cf_init_support, give a more detailed error message if the -housekeeping file is not usable. - -

-In cf_screen_jitter and cf_satellite_jitter, calculate time_diff (the -offset between the jitter and IDF versions of EXPSTART) once, rather -than each time it's used. - -
-

-In the subroutine cf_combine_pothole_data, if an entire dead spot falls -outside of the aperture, skip it and move on to the next one. - -

March 7, 2007 -
Van Dixon -
v3.2/src/libcf/cf_init_support.c -
v3.2/src/libcf/cf_velang.c -
v3.2/src/libcf/space_vel.c -
v3.2/include/calfuse.h v1.81 - -

-The subroutine space_vel used a convoluted scheme to compute what -is essentially a dot product. I simplified the code, deleted an -argument, and modified the subroutines that call it. - -

February 13, 2007 -
Van Dixon -
v3.2/src/fuv/cf_remove_motions.c - -
v3.2/src/libcf/cf_fifo_dead_time.c -
v3.2/src/libcf/cf_init_support.c - -

-When writing the LiF and SiC count rate arrays to the IDF file, -cf_remove_motions crashed if the array values were too large to be -stored as unsigned integers. As such enormous values are always wrong, -they are now set to zero. - -

-Sometimes, the header keyword TTPERIOD is erroneously set to 0. -If so, cf_init_support and cf_fifo_dead_time now set it to 1.0, -the most likely value. - -

January 2, 2007 -
Van Dixon -
v3.2/src/fuv/cf_screen_photons.c -
v3.2/src/fuv/cf_convert_to_farf.c -
v3.2/src/fuv/cf_remove_motions.c - -
v3.2/src/libcf/cf_apply_dead_time.c -
v3.2/src/libcf/cf_fifo_dead_time.c -
v3.2/src/libcf/cf_target_count_rate.c -
v3.2/src/libcf/pole_ang.c -
v3.2/src/libcf/cf_velang.c -
v3.2/src/libcf/cf_screen_high_voltage.c -
v3.2/src/libcf/cf_satellite_jitter.c -
v3.2/src/libcf/cf_grating_motion.c -
v3.2/src/libcf/cf_time_xy_distort.c -
v3.2/src/libcf/cf_init_support.c -
v3.2/src/libcf/cf_set_photon_flags.c - -
v3.2/src/cal/jitter/cf_jitter.c - -
v3.2/src/analysis/cf_combine.c -
v3.2/src/analysis/cf_nvo.c -
v3.2/src/analysis/cf_pack.c -
v3.2/src/analysis/idf_combine.c - - -

-To fix a bug in our correction for photon-event losses to FIFO -overflows, we modified the subroutine cf_screen_fifo_overflow, renamed -it cf_fifo_dead_time, and moved it from cf_screen_photons to -cf_convert_to_farf. The subroutine cf_apply_dead_time issues a warning -if DET_DEAD > 1.5, rather than TOT_DEAD. Because we no longer use -the HV status flag to denote FIFO overflows, mention of the FIFO flag -was removed from cf_set_photon_flags. Within cf_convert_to_farf, we -now set the header keywords DET_DEAD, IDS_DEAD, and TOT_DEAD to unity -by default. - -

-Within cf_remove_motions, we now treat the LiF and SiC count-rate -arrays as floats. We pass the WEIGHT array to cf_target_count_rate, -so that it returns dead-time corrected count rates. If these count -rates are too large to store as shorts, we use the TSCALE and TZERO -keywords to store them as unsigned shorts. For HIST data, we scale -the default LiF and SiC rates (read from the housekeeping file) by -the value of DET_DEAD to account for detector dead-time losses. - -

-The new subroutine pole_ang returns the angle between the orbit pole -and a given RA and DEC. It is called by cf_velang, which populates -the POLEANGL keyword. - -

-The subroutine cf_find_spectra has been modified: if the new argument -airglow_centroid is TRUE, then the program uses the airglow lines to -compute the centroid of the target spectrum. To invoke this option, -call cf_remove_motions with the -a flag. - -

-The program cf_jitter has been extensively modified. Among other -changes, it can (if necessary) compute the commanded quaternion from -the target coordinates in the housekeeping file header. Values of the -TRKFLG array now range from -1 to 5, with -1 meaning that tracking is -bad, 0 that no information is available, and 1 to 5 representing -increasingly reliable tracking estimates. The subroutines -cf_satellite_jitter and cf_screen_jitter have been modified -accordingly. In particular, the minimum value of TRKFLG that is to be -considered reliable and the X and Y aperture limits are read from the -pipeline parameter file. - -

-Both the subroutine cf_grating_motion and the grating-motion -calibration file have been completely revised. The new model depends -on the target's beta and pole angles. An additional set of corrections -tracks long-term drifts in the spectra's X and Y positions. - -

-A new subroutine, cf_time_xy_distort, corrects for long-term drifts -in the detector X and Y coordinate scales. It is called by -cf_convert_to_farf. - -

-We fixed a bug in the way that cf_init_support constructs the AIC -count-rate array. - -

-Lots of little changes in the analysis routines: When selecting which -detector segment to include in the composite spectrum, cf_nvo now -rejects segments with OBSTIME < 10 sec if the entire exposure is > 100 -s. The program idf_combine adds comment fields to the header keywords -WOFFS and WOFFL. The program cf_combine now counts SPEC### and WAVE### -using the variable ngood, rather than nfiles. Finally, we made small -changes to the way that cf_pack copies the SPEC keywords to the output -file header. - - -

June 22, 2006 -
Van Dixon -
v3.2/src/fuv/cf_hist_init.c -
v3.2/src/fuv/cf_extract_spectra.c -
v3.2/src/fuv/cf_ttag_init.c -
v3.2/src/libcf/cf_screen_jitter.c -
v3.2/src/libcf/cf_screen_burst.c -
v3.2/src/libcf/cf_optimal_extraction.c -
v3.2/src/libcf/cf_fuv_init.c -
v3.2/src/libcf/cf_error_msg.c - -

-The pipeline no longer issues WARNING messages when a raw or -intermediate data file is empty, either because it contains no photons -or because the entire exposure has been flagged as bad; when the jitter -file is missing (though out-of-date jitter files inspire a WARNING); -when the detector voltage is low; and when the pipeline cannot perform -optimal extraction. It issues level 1 verbose messages instead. - -

-Now that OPUS has been updated, the variable morekeys has been set to -zero in both cf_hist_init and cf_ttag_init. - -

May 24, 2006 -
Van Dixon -
v3.2/src/fuv/cf_extract_spectra.c -
v3.2/src/analysis/cf_combine.c -
v3.2/src/analysis/cf_nvo.c -
v3.2/src/analysis/cf_pack.c -
v3.2/src/analysis/cf_xcorr.c -
v3.2/src/analysis/idf_combine.c -
v3.2/idl/cf_obsplot.pro - -

-We modified cf_extract_spectra so that it will no longer discard (that -is, set to zero the flux and errors arrays of) spectra with non-zero -values of EXP_STAT. Those spectra are now rejected by cf_combine, -instead. - -

-The program cf_combine has been extensively revised: -it now runs through the input files with a single loop; -it supports the same command-line options as idf_combine; and -it ignores spectra with EXP_STAT != 0 (unless the -a flag is set). - -

-Both cf_nvo and cf_xcorr now use the Lyman beta line to align the -spectra of background observations. They use the interstellar O VI and -C II lines to align white dwarf spectra. For BKGD targets, cf_nvo -always selects the channel with the highest effective area, regardless -of its observed flux. The mean flux, used when deciding which segment -to use, is now calculated using the same wavelength regions for each -channel. For PC targets, the O VI lines are not included in the mean -flux calculation. - -

-The program cf_pack now writes an index to the various file extensions -to the primary HDU of the output *000all* file. - -

-Both cf_combine and idf_combine now write a number of header keywords -as longs, rather than floats. - -

-Three changes to cf_obsplot.pro: For BKGD targets, omit flux -comparison when selecting which detector segments to use. Compute mean -flux using same wavelength intervals for each band. For PC targets, -don't include O VI in the calculation of the mean flux. - -

-Divided cf_astigmatism_and_dispersion into two routines, incorporating -astig_check_input_image into the new program cf_astigmatism and -cf_x2lambda into cf_dispersion. Modified cf_assign_wavelength and -cf_bad_pixels to call the new routines. Because cf_astig_farf is not -used, it is no longer defined in calfuse.h or compiled by the -Makefile. - -

-For targets observed in HIST mode, cf_extraction_limits.c now pads -apertures by SPECBINY pixels. - -

-In cf_screen_burst, require that the number of windows in subroutine -median_filter be >= 1. -In cf_screen_fifo_overflow, changed length of data_rate array from -nevents to nseconds. -In cf_screen_jitter, screening is now applied to targets observed with -APERTURE = RFPT. -In cf_set_photon_flags, modify header keyword EXP_STAT only if was initially 0. - -

-In the analysis directory, modified cf_make_all_obs.csh to be smarter -when deciding whether to cross-correlate spectra or combine IDF files. -Also modified logic for discarding 000 files. In cf_nvo, ignore -segments with OBS_TIME = 0 and allow use of SiC data for 1000-1100 A -region. (Sometimes the LiF channels are not used.) In cf_pack, if a -segment is missing, write an empty image extension to the combined data -file. In cf_xcorr, scale each spectrum to the mean flux of the -reference spectrum. - -

February 3, 2006 -
Van Dixon -
v3.2/src/fuv/cf_compute_y_centroid.c -
v3.2/src/fuv/cf_find_spectra.c -
v3.2/src/libcf/cf_scale_bkgd.c -
v3.2/src/fuv/cf_extract_spectra.c - -

-We tightened the limits over which cf_find_spectra computes the -spectral centroid to prevent a bright star in a nearby aperture or the -enhanced background near the detector edge from pulling the extraction -window off center. In both cf_compute_y_centroid and cf_find_spectra, -we returned the EMAX_LIF and EMAX_SIC keywords to their original -behavior: if the centroid differs from the default value by more than -this limit, the default value is used. - -

-We fixed a bug introduced in the last modification of cf_scale_bkgd -that essentially turned off the background subtraction. - -

-We added a command-line flag to cf_extract_spectra that forces the use -of optimal extraction, even for extended sources. - -

January 24, 2006 -
Van Dixon -
v3.2/src/fuv/cf_screen_photons.c -
v3.2/src/libcf/cf_scale_bkgd.c - -

-Because cf_screen_burst wants to exclude airglow photons from the -calculated background, we must identify them before calling the -routine. To that end, I've made cf_screen_airglow the first of the -screening routines. - -

-The model background consists of a spatially-uniform component and a -scattered-light image. The scattered-light component was -over-estimated, because the data count totals were computed using a -larger region of the detector than the scattered-light model totals. -Now, we apply the same limits to both data and models. - -

-The program returns a slice of the background that is supposed to match -that covered by the probability array. Limit checks in the subroutine -get_limits prevented the background slice from falling off of the -detector. Sometimes, you want to background slice to fall off of the -detector. In such cases, the limit checks could introduce an unwanted -offset in the model background. We've deleted the limit checks and use -other means to avoid bad index values. - -

-cf_mirror_motion now exits without modifying the data if target is an -extended source. - -

December 2, 2005 -
Van Dixon -
v3.2/src/libcf/cf_astigmatism_and_dispersion.c -
v3.2/src/libcf/cf_apply_dead_time.c -
v3.2/src/libcf/cf_convert_to_ergs.c -
v3.2/src/libcf/cf_count_rate_y_distort.c -
v3.2/src/libcf/cf_doppler_and_heliocentric.c -
v3.2/src/libcf/cf_extraction_limits.c -
v3.2/src/libcf/cf_fpa_position.c -
v3.2/src/libcf/cf_init_support.c -
v3.2/src/libcf/cf_make_mask.c -
v3.2/src/libcf/cf_optimal_extraction.c -
v3.2/src/libcf/cf_satellite_jitter.c -
v3.2/src/libcf/cf_screen_bad_pixels.c (NEW) -
v3.2/src/libcf/cf_screen_fifo_overflow.c -
v3.2/src/libcf/cf_screen_jitter.c (NEW) -
v3.2/src/fuv/cf_bad_pixels.c -
v3.2/src/fuv/cf_extract_spectra.c -
v3.2/src/fuv/cf_remove_motions.c -
v3.2/src/fuv/cf_screen_photons.c - -

-To improve our bad-pixel correction, we've added a new routine, -cf_screen_bad_pixels, which flags photon events falling in known -pothole regions. cf_make_mask now fills gaps in the bad-pixel mask -that open when it is converted from pixels to wavelengths. In the -optimal-extraction algorithm, cf_optimal_extraction now scales the -variance estimate by the bad-pixel mask to better approximate the -observed counts. The main pothole routine, cf_bad_pixels, now uses -cf_x2lambda() and cf_get_potholes(), rather than its own subroutines -that do the same job. Also, it no longer adds random numbers to the -output pixel coordinates -- that's no longer necessary. Finally, -cf_bad_pixels no longer trims potholes at the edges of the -extraction windows. We modified cf_astigmatism_and_dispersion so that -it would not complain when events fall outside of the astig images. - -

-We added a test to cf_apply_dead_time to catch bad dead-time values: If -there is no housekeeping file, AND the engineering snapshot times are -bad, AND the mean value of either dead-time array is > 1.5, set the -array to unity and issue a warning. - -

-In cf_convert_to_ergs, we changed the effective-area arrays to type -double to match the AEFF_CAL files. - -

-For histogram data, cf_count_rate_y_distort must use a single count -rate value for all of the data. To better estimate it, we replace the -time-dependent FEC-rate array with its weighted mean value. - -

-To improve our calculation of the Doppler correction, we changed the -variables velocity and doppler to doubles in cf_doppler_and_heliocentric. - -

-Rather than using different HIST_PAD values for each aperture, -cf_extraction_limits now always pads the apertures by 8 pixels (top and -bottom) when in HIST mode. - -

-More efforts to catch corrupted keywords in cf_init_support: When -the housekeeping file is missing and the engineering snapshot times are -corrupted, we use EXPSTART and EXPEND to estimate eng_time. If EXPEND is -corrupted, we use EXPTIME. - -

-To improve the jitter-correction algorithm, we've removed the -data-screening functions from cf_satellite_jitter and moved them to a -new routine, cf_screen_jitter. The modules cf_remove_motions and -cf_screen_photons have been modified accordingly. - -

-We caught a bug in cf_screen_fifo_overflow: It was using the -RATE_LIF and RATE_SIC arrays to estimate the raw count rate, but those -arrays are populated from the housekeeping file and do not reflect data -losses due to FIFO overflows. Now we calculate the count rate across -the entire detector directly from the photon-event data. - -

-We added a flag to cf_extract_spectra that allows the user to disable -optimal extraction from the command line. - -

September 19, 2005 -
Van Dixon -
v3.1/src/libcf/cf_read_fpa_pos.c (RESTORED) - -

September 7, 2005 -
Van Dixon -
v3.1/src/analysis/cf_arith.c (RENAMED) -
v3.1/src/analysis/cf_coadd.c -
v3.1/src/analysis/cf_combine.c -
v3.1/src/analysis/cf_make_all_exp.c (NEW) -
v3.1/src/analysis/cf_nvo.c -
v3.1/src/analysis/cf_pack.c -
v3.1/src/analysis/cf_xcorr.c -
v3.1/src/analysis/getshift.c -
v3.1/src/analysis/modhead.c -
v3.1/src/libcf/cf_init_support.c -
v3.1/src/libcf/cf_fpa_position.c -
v3.1/src/libcf/cf_read_fpa_pos.c (DELETED) -
v3.1/src/libcf/cf_screen_burst.c -
v3.1/src/libcf/cf_write_extracted_spectrum.c - -

-We are required to provide MAST an all file for each exposure and -one set of all, ano, and nvo files per observation. -These files are created by cf_coadd, which has been completely re-written. -It calls cf_make_all_exp for each exposure and cf_make_all_obs.csh once -per observation. The new program cf_make_all_exp copies the primary HDU -of the channel with the longest EXPTIME into an otherwise empty file. -cf_nvo now sets the keyword NEXTEND back to 1. -In cf_pack, the keyword COMB_COR is set to COMPLETE. - -

-The name of cf_arith3 has been changed back to cf_arith. -If called with no arguments, cf_arith, cf_combine, cf_xcorr, and getshift -don't return an error, just a "usage" message. -If the input list given to cf_combine contains only file names (no shifts), -the program assumes that all shifts are zero. -The programs cf_xcorr and cf_combine have been modified -to use the same sign convention for spectral shifts as FUSE_REGISTER. -The program modhead now accepts multi-word strings as keyword values. - -

-In cf_init_support, use LWRS background limits for RFPT observations. -In cf_fpa_position, correct for both X and Z displacement of FPA's. -Delete call to cf_read_fpa_pos. -In cf_screen_burst, ignore photons with arrival times greater than MAX_EXPTIME. -In cf_write_extracted_spectrum, delete FITS_write_date from cf_copy_hist_header. - -

July 12, 2005 -
Van Dixon -
v3.1/src/analysis/cf_combine.c -
v3.1/src/analysis/cf_nvo.c -
v3.1/src/analysis/cf_pack.c -
v3.1/src/cal/jitter/cf_jitter.c -
v3.1/src/libcf/cf_satellite_jitter.c - -

-In cf_combine, we use fgets to read the input file and assume that pix_shift -is an integer. -In cf_nvo, we modify the cross-correlation routine to use LiF 2B as the -wavelength standard if header keyword FESCENT is set to FES B. -In cf_pack, we set the header keyword COMB_COR to COMPLETE. - -

-cf_jitter writes a new keyword, JIT_VERS, to the header of each jitter -file. If this keyword is missing or is less than 2, -cf_satellite_jitter now warns that the jitter file format is out -of date, which may result in the rejection of good data. - -

June 16, 2005 -
Van Dixon -
v3.1/src/libcf/cf_rebin_probability_array.c -
v3.1/src/libcf/cf_scale_bkgd.c -
v3.1/src/fuv/cf_extract_spectra.c -
v3.1/include/calfuse.h v1.71 - -

-A bug in the spectral-extraction subroutines caused CalFUSE always to -use the smaller, point-source extraction window, even for extended -sources. This could lead to an underestimate of the flux for extended -sources. The pipeline now uses either the point-source or -extended-source aperture, as appropriate. - -

June 8, 2005 -
Van Dixon -
v3.1/src/analysis/cf_combine.c -
v3.1/src/analysis/cf_make_all.csh -
v3.1/src/analysis/cf_nvo.c -
v3.1/src/analysis/cf_pack.c -
v3.1/src/analysis/cf_xcorr.c -
v3.1/src/analysis/extract_jitter.c -
v3.1/src/analysis/idf_combine.c -
v3.1/src/libcf/cf_calculate_y_centroid.c -
v3.1/src/libcf/cf_find_spectra.c -
v3.1/src/libcf/cf_idf_io.c -
v3.1/src/libcf/cf_modify_hist_pha.c -
v3.1/src/libcf/cf_rebin_probability_array.c - -
v3.1/include/calfuse.h v1.70 - -

-We modified cf_combine to support the generation of our new -observation-level spectral files. It now writes the keywords NSPEC, -SPEC###, and WOFF### to the primary HDU of the output file. - -

-Three C routines and a shell script generate a new set of -observation-level spectral files. For targets that are bright enough, -we cross-correlate and combine the extracted spectra from each -exposure. For fainter targets, we combine the IDF files from each -exposure and extract a single spectrum for the whole observation. Then -we repeat this exercise for the night-only data. Finally, we combine -observation-level spectra from the various channels into a single -spectral file for submission to the National Virtual Observatory. - -

-cf_make_all is the shell script that calls these routines. -
-cf_xcorr determines the relative wavelength offset of each exposure. -
-cf_pack combines the observation-level spectra from each channel into -a single ALL or ANO (all data, night-only) file. -
-cf_nvo selects data from the best channel for each waveband, shifts -it to a common wavelengh scale, and generates the NVO file. - -

-In idf_combine, comment out warning when FPA motion is detected. -The pipeline corrects for this. - -

-In cf_calculate_y_centroid, don't override user-specified centroid, -even if it is far from the expected value. Fixed bug in tabulation of -the expected Y centroids. - -

-In cf_find_spectra, use airglow centroid of LWRS aperture to constrain -airglow centroids of smaller apertures. Use airglow centroid of -target aperture to constrain search for centroid of target spectrum. - -

-In cf_rebin_probability_array, rounding errors left non-zero -probabilities in regions beyond the ends of the extraction windows. -Re-normalization raised these probabilities to unity. Now, if total -probability in a column is less than 0.1, it is set to zero. - -

April 19, 2005 -
Van Dixon - -
v3.0/include/calfuse.h v1.66, v1.67, v1.68, v1.69 - -

-Between August and December of 2004, pipeline modifications were -limited to bug fixes and a few new data-analysis routines. Since -January of 2005, we made extensive modifications to the code, both to -correct errors and to add new capabilities. All changes are documented -in the headers of the individual modules and subroutines. Rather than -repeat that information, we list here only the principal changes to the -pipeline's capabilities. - -

-In v3.0, data obtained during periods of uncertain pointing information -were often flagged as bad. Now, the jitter files are generated using a -simpler, more robust algorithm to determine when pointing information -is reliable. If it's not, the pipeline does nothing, rather than -flagging the data as bad. - -

-In v3.0, data obtained when the detector voltage was less than 95% of -the expected value were flagged as bad. Now, for detectors 1A, 1B, and -2B, the level is 85%. For detector 2A, data with HV > 90% of full is -processed without comment, data with HV > 80% of full generates a -warning message, and data with HV < 80% of full is flagged as bad. -(These limits are stored in the VOLT_CAL file.) For detector 2A data -in the 80-90% range, the user should examine the pulse-hight -distribution of photon events in the target aperture to ensure that the -peak of the distribution is well separated from the background. - -

-In v3.0, the geometric-distortion correction moved small segments of the -HIST spectra out of their extraction windows. The solution was to -increase the size of the HIST extraction windows in Y. A new keyword, -HIST_PAD, which depends on both the detector and the aperture, is read -from the header of the corresponding extension of the CHID_CAL file. -While making this change, we found and corrected a bug in the -calculation of the spectral Y centroid that affected both TTAG and -HIST data. - -

-In v3.0, the HIST and TTAG wavelength scales did not agree. This was a -result of the walk correction, which was applied to TTAG but not HIST -data. Since the walk correction is never zero, HIST data were never -fully converted to the FARF. We now assign a pulse height (the mean -for a particular date and aperture) to each HIST photon and apply the -walk correction to all data. - -

-When scaling the model background image to match the data, the -subroutine cf_scale_bkgd (formerly cf_ttag_bkgd) did not properly -account for regions of the detector excluded because of airglow -contamination. As a result, it underestimated the total background. -The program has been extensively revised. - -

-The final extracted spectral (*fcal.fit) files now have the standard -FITS binary table format that was employed in old (v2.4.3 and earlier) -versions of the pipeline. - -

-Errors in the calculation of TIME_SUNRISE and TIME_SUNSET have been -corrected. As these values are never greater than 6000 s, they are -now stored (and treated) as SHORTs. - -

-If the pipeline cannot compute the centroids of the detector stim -pulses, it now reads a new calibration file (STIM_CAL), in which the -time-dependent average values of the drift coefficients are tabulated. - -

-The burst-detection algorithm computes the mean count rate on the -unilluminated regions of the detector and writes it to the IDF. It now -does so for the entire exposure, not just for times previously -identified as good. - -

-Several keywords have been added to the IDF file headers, including -the limb-angle limits BRITLIMB and DARKLIMB from the SCRN_CAL file -and the calculated orbital period (ORBPERID). - -

-The AIRG_CAL files, which identify regions of each detector likely -to be contaminated by airglow features, are now expressed in FARF, -rather than RAW, coordinates. This change allows us to use smaller -airglow windows and thus to throw away less data. - -

-The default pulse-height limits (both upper and lower) have been -modified for all four detectors. - -

August 24, 2004 -
Van Dixon -
v3.0/src/libcf/cf_fes_proc_update.c -
v3.0/src/libcf/cf_fes_proc_check.c -
v3.0/src/libcf/cf_count_rate_y_distort.c -
v3.0/src/libcf/cf_calculate_y_centroid.c -
v3.0/src/libcf/cf_optimal_extraction.c - -
v3.0/include/calfuse.h v1.65 - -

-Installed two subroutines needed to process FES files. Modified calfuse.h -to support them. - -

-In cf_count_rate_y_distort, interpolate stretch correction among -tabulated Y values to prevent counts from piling up at 10-pixel -boundaries. - -

-In cf_calculate_y_centroid, confirm that all spectral centroids, not -just that of the target aperture, are within bounds. - -

-In cf_optimal_extraction, use QUALITY array to set X limits of -extraction region. Insure that sigma_out array is non-zero. - -

August 12, 2004 -
Van Dixon -
v3.0/src/fuv/cf_assign_wavelength.c -
v3.0/src/fuv/cf_bad_pixels.c -
v3.0/src/fuv/cf_extract_spectra.c -
v3.0/src/fuv/cf_remove_motions.c -
v3.0/src/fuv/cf_screen_photons.c -
v3.0/src/libcf/cf_astigmatism_and_dispersion.c -
v3.0/src/libcf/cf_apply_filters.c -
v3.0/src/libcf/cf_calculate_y_centroid.c -
v3.0/src/libcf/cf_fuv_init.c -
v3.0/src/libcf/cf_find_spectra.c -
v3.0/src/libcf/cf_grating_motion.c -
v3.0/src/libcf/cf_identify_channel.c -
v3.0/src/libcf/cf_init_support.c -
v3.0/src/libcf/cf_make_mask.c -
v3.0/src/libcf/cf_mirror_motion.c -
v3.0/src/libcf/cf_modify_hist_times.c -
v3.0/src/libcf/cf_optimal_extraction.c -
v3.0/src/libcf/cf_proc_check.c -
v3.0/src/libcf/cf_rebin_background.c -
v3.0/src/libcf/cf_satellite_jitter.c -
v3.0/src/libcf/cf_screen_burst.c -
v3.0/src/libcf/cf_screen_high_voltage.c -
v3.0/src/libcf/cf_screen_limb_angle.c -
v3.0/src/libcf/cf_set_photon_flags.c -
v3.0/src/libcf/cf_thermal_distort.c -
v3.0/src/libcf/cf_ttag_bkgd.c -
v3.0/src/libcf/cf_write_extracted_spectrum.c -
v3.0/src/libcf/eclipse.c -
v3.0/src/libcf/solar_ang.c -
v3.0/src/libcf/space_vel.c -
v3.0/src/libcf/state_geod.c -
v3.0/src/libcf/state_limb.c - -
v3.0/include/calfuse.h v1.64 - -

-Re-organized the pipeline, moving cf_screen_photons before -cf_remove_motions. This required changes to both programs, as well as -a number of subroutines. - -

-Numerous modifications to cf_fuv_init: We now allow for the possibility -that the time associated with a calibration file exactly equals -EXPSTART. If the BRIT_OBJ keyword is set to DEFOCUS, we modify -SRC_TYPE to E. Write CF_VERS to trailer file. Set ASTG_COR to -PERFORM, as the pipeline doesn't do it automatically. - -

-Changes to routines in cf_init_support: Add BRIT_OBJ keyword to header. -Rewrite fill_hv_array() to make it more robust. If HV values in header -are good, use them to determine whether HV arrays for 2A and 2B are -swapped. - -

-In both eclipse and state_geod, we corrected the FORTRAN call to sla_preces. -To address warnings from the Mac OS X compiler, we made minor -modifications to month_day. - -

-If more than 90% of an exposure is lost to a burst, jitter, etc., -cf_set_photon_flags will write the cause to the trailer file. - -

-Changes to cf_identify_channel: Don't bother shifting extraction -windows to correct for FPA position. If shift is known, it is not needed. -Because the extraction windows don't quite match the WGTS arrays, pad -windows by XPAD pixels in X. Change i (which steps through targ_ap -array) from long to int. - -

-Corrected bug in cf_mirror_motion that caused it to swap motion corrections -for sides 1 and 2. (This routine also got a new calibration file.) - -

-In cf_grating_motion, we estimate the time between sunrises using the -orbit period in the file header, rather than assuming a 6000-second orbit. - -

-In cf_satellite_jitter, we skip the jitter correction if the jitter -file lacks the JIT_STAT keyword. The program returns EXP_JITR -to the calling routine. - -

-Both cf_find_spectra and cf_calculate_y_centroid now use the photon -flags to exclude events arriving during bursts, etc., from their -centroid calculations. - -

-In cf_astigmatism_and_dispersion, must change ASTG_COR to COMPLETE or -SKIPPED by hand, as the pipeline won't do it automatically. - -

-Changes to bad-pixel routines: Fixed bug in cf_make_mask, changing & to &&. - -

-Changes to extraction subroutines: -Fixed bug in cf_ttag_bkgd: nxb was undefined if RUN_BKGD = NO. -Don't bother shifting the weights array to account for FPA motions, as -this should already have been corrected in the conversion to the FARF. -In cf_optimal_extraction: If weights_out[j] = 0, set variance = bkgd. -Iterate optimal extraction to accuracy of 0.01 counts. In the boxcar -extraction algorithm, we reduced the parray limit to 1E-4 to better -match fluxes from optimal extraction for bright stars. -The routine cf_write_extracted_spectrum now has an option (-o) -to override the default root name for the extracted spectra. - -

-Removed unused variables from the following routines: state_limb, -cf_rebin_background, cf_screen_high_voltage, cf_screen_limb_angle, -cf_thermal_distort, solar_ang, space_vel, and cf_bad_pixels. - -

-Made minor i/o changes to cf_screen_burst. The routine cf_proc_check -now calls cf_verbose rather than cf_if_warning when a pipeline step is -inappropriate for TTAG data. - -

-We made a lot of changes to the way that we deal with time for HIST -data: In cf_apply_filters, we mask the BRST, SAA, and LIMB flags when -calculating exposure time. In cf_set_photon_flags, we set only DAY -flag; we all write other flags to EXP_STAT keyword. A new routine, -cf_modify_hist_times, sets the photon-arrival times of photons in HIST -files to the midpoint of the longest good-time interval. - -

June 4, 2004 -
Van Dixon -
v2.4/src/fuv/cf_fuv_init.c -
v2.4/include/calfuse.h v1.175 - -

-Modified cf_fuv_init to allow for the possibility that the MJD for a -calibration file equals EXPSTART for an exposure. - -

May 13, 2004 -
Van Dixon -
v2.4/src/fuv/cf_update_qual.c -
v2.4/src/fuv/cf_dtcor.c -
v2.4/include/calfuse.h v1.174 - -

-Modified cf_update_qual and cf_dtcor to deal gracefully with bad -counters in the data file headers. - -

May 4, 2004 -
Van Dixon -
v3.0/src/fuv/cf_assign_wavelength.c -
v3.0/src/fuv/cf_countmap.c -
v3.0/src/fuv/cf_extract_spectra.c -
v3.0/src/fuv/cf_gainmap.c -
v3.0/src/fuv/cf_hist_init.c -
v3.0/src/fuv/cf_remove_motions.c -
v3.0/src/fuv/cf_ttag_init.c -
v3.0/src/libcf/cf_apply_dead_time.c -
v3.0/src/libcf/cf_calculate_y_centroid.c -
v3.0/src/libcf/cf_convert_to_ergs.c -
v3.0/src/libcf/cf_doppler_and_heliocentric.c.c -
v3.0/src/libcf/cf_error_msg.c -
v3.0/src/libcf/cf_find_spectra.c -
v3.0/src/libcf/cf_fuv_init.c -
v3.0/src/libcf/cf_init_support.c -
v3.0/src/libcf/cf_rebin_background.c -
v3.0/src/libcf/cf_set_good_time_intervals.c -
v3.0/src/libcf/cf_set_photon_flags.c -
v3.0/src/libcf/cf_set_user_gtis.c -
v3.0/src/libcf/cf_source_aper.c -
v3.0/src/libcf/cf_ttag_bkgd.c -
v3.0/src/libcf/cf_write_extracted_spectrum.c - -
v3.0/include/calfuse.h v1.61, v1.62, v1.63 - -

-Bernard performed housecleaning (removing unused variables, changing -variable types to match subroutine definitions, etc.) on the following -routines: cf_assign_wavelength, cf_hist_init, cf_ttag_init, cf_countmap, -and cf_bad_pixels.c. Also these subroutines: cf_apply_dead_time, -cf_calculate_y_centroid, cf_doppler_and_heliocentric.c, -cf_error_msg, cf_init_support, cf_set_good_time_intervals, -cf_set_photon_flags, cf_set_user_gtis, and cf_source_aper. - -In addition, he modified cf_ttag_init to create a photon list -containing a single dummy event when the raw file is empty and -cf_init_support to better catch errors in the header counter keywords. - -

-We made significant modifications to cf_extract_spectra, replacing -cf_rebin_and_flux_calibrate_background with cf_rebin_background. -cf_optimal_extraction now performs all calculations with the weights -array, rather than ergcm2. It returns counts and sigma arrays, rather -than flux and variance as before; cf_extract_spectra must -flux-calibrate each array, and cf_write_extracted_spectrum no longer -converts from variance to sigma. The boxcar algorithm now uses the -probability (weights) array to set the limits of the extraction window, -better replicating the results of optimal extraction. Optimal -extraction now iterates to 10% accuracy. The output weights and bkgd -arrays are calculated by the optimal-extraction routine, so better -match the final flux-calibrated spectra. - -

-In verbose mode, cf_convert_to_ergs prints out the relative weighting of -the two effective-area files. - -

-The first call to cf_identify_channel was moved from cf_find_spectra to -cf_remove_motions. The documentation of cf_remove_motions was improved. - -

-The keywords MKBK_COR and BKGD_COR are gone, so cf_fuv_init no longer -populates them. - -

-The routine cf_rebin_and_flux_calibrate_background was replaced by -cf_rebin_background. Flux calibration is now performed by -cf_extract_spectra. cf_ttag_bkgd returns a null-valued background -image if RUN_BKGD = NO. - -

April 5, 2004 -
Van Dixon -
v3.0/src/libcf/cf_geometric_distort.c -
v3.0/include/calfuse.h v1.60 - -

April 1,2004 -
Van Dixon -
v3.0/src/fuv/cf_extract_spectra.c -
v3.0/src/libcf/cf_geometric_distort.c -
v3.0/src/libcf/cf_hist_init.c -
v3.0/src/libcf/cf_init_support.c -
v3.0/src/libcf/cf_optimal_extraction.c -
v3.0/src/libcf/cf_proc_check.c -
v3.0/src/libcf/cf_rebin_probability_array.c -
v3.0/src/libcf/cf_ttag_bkgd.c -
v3.0/src/libcf/cf_write_extracted_spectrum.c -
v3.0/include/calfuse.h v1.59 - -

-Abandon use of WPC array throughout the pipeline. Instead, modify -cf_optimal_extraction to evenly distribute photon events across -one X pixel when in HIST mode. If optimal-extraction loop does not -converge within 50 iterations, exit and use results from boxcar extraction. -

-In cf_proc_check, call cf_verbose rather than cf_if_warning if program -not appropriate for HIST data. -

-Change the way that routines deal with empty data files. In -cf_hist_init, issue a warning -- but continue -processing -- if NEVENTS = 0. (A similar change for cf_ttag_init -will have to wait for the next version of the pipeline.) -In cf_extract_spectra, write null-valued -output spectra if either EXPTIME or NEVENTS = 0. In -cf_write_extracted_spectrum, if valid_spectrum = FALSE, write warning -message to file header. -

-Include math.h in cf_hist_init to define fmod(). This solves the -long-standing problem of the program crashing on Linux machines. -

-In cf_geometric_distort, modify header keyword SPECBINY to reflect -Y spacing in the FARF. -

-In cf_ttag_bkgd, set Y limits of 2-D background arrays equal to those -of the probability (weights) array. Since the sizes are now equal, -cf_optimal_extraction does not need to test them. Make centroid of -probability array a float in cf_extract_spectra and associated -subroutines. -

-In cf_rebin_probability_array, shift probability array to account -for position of FPA. - -

March 30, 2004 -
Van Dixon -
v2.4/src/fuv/cf_hist_init.c -
v2.4/include/calfuse.h v1.173 - -

March 16,2004 -
Van Dixon -
v3.0/src/fuv/cf_extract_spectra.c -
v3.0/src/fuv/cf_hist_init.c -
v3.0/src/fuv/cf_ttag_init.c -
v3.0/src/fuv/cf_bad_pixels.c -
v3.0/src/fuv/cf_countmap.c -
v3.0/src/fuv/cf_gainmap.c -
v3.0/src/fuv/cf_convert_to_farf.c -
v3.0/src/libcf/cf_astigmatism_and_dispersion.c -
v3.0/src/libcf/cf_init_support.c -
v3.0/src/libcf/cf_satellite_jitter.c -
v3.0/src/libcf/cf_thermal_distort.c -
v3.0/src/libcf/cf_write_extracted_spectrum.c -
v3.0/include/calfuse.h v1.57, v1.58 - -

-Implement WPC array in cf_extract_spectra and associated subroutines. -
In cf_hist_init.c, fix error in correcting hot pixels. -
In cf_ttag_init.c, exit if no photons in raw data file. -
In cf_bad_pixels.c, change maximum size of the output arrays in -cf_combine_pothole_data and insure that lif_cnt and sic_cnt arrays are -non zero. -
In cf_countmap.c and cf_gainmap.c, allow user to select coordinate -system: RAW, FARF (default), final. -
In cf_astigmatism_and_dispersion.c, make subroutine cf_x2lambda globally -accessible. -
In cf_convert_to_farf.c, pass weight array to cf_thermal_distort. -
In cf_init_support.c, read begin and end counters as float. -Set countrate to zero when cntb is more than 16777216. -
In cf_satellite_jitter.c, polulate the PLATESC keyword in the input file header. -
In cf_thermal_distort.c, added weights to the calculation (needed for -histogram mode) and corrected bug in procedure for finding stim pulses. -
In cf_write_extracted_spectrum.c, populate archive search keywords and -change name of POTHOLE column to QUALITY. - -

May 22, 2003 -
Van Dixon -
v2.4/src/idl/cf_plot_rate.pro -
v2.4/src/fuv/fcal.c -
v2.4/src/fuv/cf_make_ttag_bkgd.c -
v2.4/include/calfuse.h v1.172 - -

-Modified cf_plot_rate.pro, fcal.c, and cf_make_ttag_bkgd.c to deal -gracefully with zero-length exposures. Resulting spectral file has -FLUX and ERROR arrays set to zero. - -

May 19, 2003 -
Van Dixon -
v2.4/src/analysis/cf_combine.c -
v2.4/include/calfuse.h v1.171 - -

-Imported two of Jeff's modifications to cf_combine: -
-Close each input file in initial loop. -Without this, cfitsio crashes upon opening the 60th file. -
-Weight each pixel by exposure time after excluding ``bad'' pixels. - -

May 2, 2003 -
Van Dixon -
v2.4/src/analysis/cf_uninterp.c -
v2.4/include/calfuse.h v1.170 - -

-Added cf_uninterp.c to re-calibrate extracted spectra using only -the most recent flux-calibration file. - -

April 29, 2003 -
Van Dixon -
v2.3/src/fuv/cf_ttag_jitter.c -
v2.3/src/fuv/cf_hist_jitter.c -
v2.3/include/calfuse.h v1.169 - -

-Modified jitter routines to allow possiblity that jitter filename is in -lower-case letters. - -

April 25, 2003 -
Van Dixon -
v2.3/src/fuv/cf_fuv_init.c -
v2.3/include/calfuse.h v1.167, v1.168 - -

-In cf_fuv_init, never linearly extrapolate calibration files forward in -time. If an observation is not bracketed by calibration files, -simply use the latest one. - -

April 16, 2003 -
Van Dixon -
v2.3/src/fuv/cf_fuv_init.c -
v2.3/include/calfuse.h v1.166 - -

-In cf_fuv_init, test for corrupted detector bias values. Updated -comment field of HV_FLAG. Modified associated warning messages. - -

April 15, 2003 -
Van Dixon -
v2.3/src/fuv/cf_ttag_screen.c -
v2.3/include/calfuse.h v1.165, v1.166 - -

April 2, 2003 -
Van Dixon -
v2.3/src/fuv/cf_ttag_geodopp.c -
v2.3/src/fuv/cf_ttag_jitter.c -
v2.3/include/calfuse.h v1.164 - -

-Simplified DX/DY test in cf_ttag_geodopp. Test that TRKFLG is <= 5 -(the highest allowed value) in cf_ttag_jitter. - -

April 2, 2003 -
Van Dixon -
v2.3/src/fuv/cf_ttag_geodopp.c -
v2.3/include/calfuse.h v1.163 - -

-Test DX and DY values to make sure they are valid before combining -into mean Doppler shift. NaN values lead to bad-pixels masks full -of zeros, which lead to empty extracted spectra. - -

March 10, 2003 -
Van Dixon -
v2.3/src/fuv/cf_ttag_geodopp.c -
v2.3/include/calfuse.h v1.162 - -

-Alain Lecavelier points out that, for high-count-rate TTAG data, the -pipeline produces error bars that are about half of what one would -expect from SQRT(N) statistics. Turns out that the change that I made -to cf_ttag_geodopp in March 2002 was in error. I returned the code to -its previous state, and the error bars are now much better behaved. -Error bars for histogram data are unaffected by this change. - -

February 24, 2003 -
Van Dixon -
v2.2/src/fuv/cf_make_ttag_bkgd.c -
v2.2/src/fuv/cf_make_hist_bkgd.c -
v2.2/include/calfuse.h v1.161 - -

-Peter Young's Dec Alpha compiler identified a bug in these routines. -EXPNIGHT is stored in the header as type LONG, but these routines read -it as type FLOAT. CFITSIO should make the conversion automatically, -but apparently fails to do so on his machine. I've modified the calls -to FITS_read_key() in both routines. -

February 20, 2003 -
Van Dixon -
v2.2/src/libcf/read_tle.c -
v2.2/src/libcf/sgp4.c -
v2.2/src/fuv/cf_ttag_jitter.c -
v2.2/src/fuv/cf_make_ttag_bkgd.c -
v2.2/src/fuv/cf_extract.c -
v2.2/src/fuv/cf_driftcorr2.c -
v2.2/src/fuv/cf_coadd.c -
v2.2/src/analysis/ttag_combine.c -
v2.2/include/calfuse.h v1.160 - -

-Peter Young's Dec Alpha compiler identified two sets of bugs in these routines. -Several calls to FITS_read_key() or FITS_update_key() used an ampersand incorrectly: -
-FITS_read_key(fptr, TSTRING, "INSTRUME", &instrument, comment, &status); -
-and a few routines used abs() when fabs() is required. -

-P.Y.'s compiler refused to recognize one of the #define keywords in -sgp4.c, so Bryce Roberts replaced it with the actual value throughout -the routine. - -

December 13, 2002 -
Van Dixon -
v2.2/src/fuv/cf_ttag_screen.c -
v2.2/src/fuv/cf_hist_screen.c -
v2.2/src/fuv/cf_ttag_burst.c -
v2.2/src/fuv/cf_ttag_jitter.c -
v2.2/include/calfuse.h v1.159 - -

-Modify cf_ttag_screen and cf_hist_screen to write all EXP_* keywords as -type long. Modify cf_ttag_burst and cf_ttag_jitter to pass through all -photon events in the stim-pin regions, even during bad times. Have -them add EXP_BRST and EXP_JITR to EXP_BAD, and write all as type long. - -

November 8, 2002 -
Van Dixon -
v2.2/src/fuv/cf_extract.c -
v2.2/include/calfuse.h v1.158 - -

November 6, 2002 -
Van Dixon -
v2.2/src/fuv/cf_hist_jitter.c -
v2.2/src/fuv/cf_ttag_jitter.c -
v2.2/include/calfuse.h v1.157 - -

-Make cf_hist_jitter and cf_ttag_jitter issue warning, but continue -running, if keyword JIT_STAT is not found. - -

November 1, 2002 -
Van Dixon -
v2.2/src/fuv/cf_hist_jitter.c -
v2.2/idl/cf_plot_hist_rate.pro -
v2.2/include/calfuse.h v1.156 - -

-Make cf_hist_jitter and cf_plot_hist_rate exit gracefully if jitter -file not found. - -

October 29, 2002 -
Van Dixon -
v2.2/src/analysis/cf_arith.c -
v2.2/src/analysis/cf_combine.c -
v2.2/include/calfuse.h v1.155 - -

October 24, 2002 -
Van Dixon -
v2.2/src/fuv/Makefile -
v2.2/src/fuv/cf_make_hist_bkgd.c -
v2.2/include/calfuse.h v1.154 - -

-Add cf_hist_jitter to Makefiles. -Remove unused variables in cf_make_ttag_bkgd. - -

October 11, 2002 -
Van Dixon -
v2.2/src/fuv/cf_ttag_jitter.c -
v2.2/include/calfuse.h v1.153 - -

-Three changes to cf_ttag_jitter: Initialized nrej to 0, made program -exit quietly if jitter file not found, and set all times to floats in -test step, to correct bug whereby some photons were being erroneously -rejected. Note that the program still rejects photons with times later -than the end of the input good-time interval. This happens because the -burst-correction routine converts the GTI boundaries to integers. - -

August 29, 2002 -
Van Dixon -
v2.2/src/fuv/cf_hist_init.c -
v2.2/src/fuv/cf_ttag_init.c -
v2.2/include/calfuse.h v1.152 - -

August 28, 2002 -
Van Dixon -
v2.2/src/fuv/cf_hist_jitter.c -
v2.2/src/libcf/cf_fcal.c -
v2.2/idl/cf_plot_hist_rate.pro -
v2.2/include/calfuse.h v1.151 - -

-cf_hist_jitter reads the jitter file, determines how much time (if any) -the target spent out of the aperture, and writes this number to the -keyword EXP_JITR. cf_fcal subtracts this value from EXPTIME when -flux-calibrating the spectrum. The IDL procedure cf_plot_hist_rate.pro -plots the count rate during a histogram exposure using counter values -from the housekeeping file. - -

July 31, 2002 -
Van Dixon -
v2.2/src/fuv/cf_hist_count_map.c -
v2.2/src/fuv/cf_ttag_count_map.c -
v2.2/src/fuv/cf_ttag_gain_map.c -
v2.2/src/fuv/cf_make_ttag_bkgd.c -
v2.2/src/fuv/cf_ttag_jitter.c -
v2.2/src/fuv/cf_update_qual.c -
v2.2/src/libcf/cf_fuv_init.c -
v2.2/include/calfuse.h v1.150 - -

-The SDP group decided that CalFUSE 3.0 should use a radically different -scheme for processing time-tagged data. In the mean time, we have made -incremental progress on CalFUSE v2, and we have decided that this -version of the program should go behind the firewall as soon as -possible. Accordingly, I copied v2.1.7 to v2.2.0 and have continuued -to make incremental changes to the code. Highlights are - -

-Modify cf_hist_count_map, cf_ttag_count_map, cf_ttag_gain_map, and -cf_update_qual to read version 002 YSTR files. -
-Correct a Linux bug in cf_make_ttag_bkgd. -
-Add cf_ttag_jitter and modify cf_fuv_init to support it. - -

June 14, 2002 -
Van Dixon -
v2.1/src/fuv/cf_make_ttag_bkgd.c -
v2.1/include/calfuse.h v1.149 - -

June 14, 2002 -
Van Dixon -
cf_make_ttag_bkgd.c -
cf_undistort.c -
cf_driftcorr.c -
cf_extract.c -
cf_dpix.c -
cf_ttag_screen.c -
cf_hist_dopp.c -
cf_wcal.c -
cf_doppler_util.c -
calfuse.h v1.151 - -
-

-In cf_make_ttag_bkgd, correct error when using MKBK_COR=OMIT (1.15) and -fill in holes made by the removal of geocoronal lines. The latter is -needed in determination of X variations of scattered light. Re-wrote -cf_undistort to handle shifts as floats. Modified cf_driftcorr to -write output as an array of shorts. Modified cf_extract, cf_dpix to -read linear wavelength scale. Modified read_wavelengths in -cf_doppler_util and calls to it in cf_ttag_screen and cf_hist_dopp. -Modified cf_wcal to implement linear wavelength solution. -

May 30, 2002 -
Van Dixon -
cf_doppler_util.c -
cf_ttag_screen.c -
cf_hist_dopp.c -
cf_dpix.c -
cf_extract.c -
calfuse.h v1.150 - -
-

-In cf_doppler_util, modified read_wavelength no longer to generate and -return an xpix array, then modified the calling routines cf_ttag_screen -and cf_hist_dopp accordingly. Modified cf_dpix and cf_extract to -handle the linear wavelength scale. - -

May 29, 2002 -
Van Dixon -
cf_doppler_util.c -
cf_driftcorr.c -
cf_update_qual.c -
calfuse.h v1.149 - -
-

-In cf_doppler_util, modified the subroutine read_wavelength to handle a -linear wavelength scale. Installed Rich's new version of cf_driftcorr, -which puts a correction for the count-rate dependent Y stretch into the -DY image. Because we no longer need to correct the bad-pixel map for -the Y stretch, I moved back from v1.8 to v1.5 of cf_update_qual. - -

-Fixed a couple of bugs in cf_dpix: made LWRS the default aperture and -allowed the boundary between the SiC and LiF regions to vary with -detector. -

May 17, 2002 -
Van Dixon -
cf_dtcorr -
cf_undistort -
cf_wcal -
calfuse.h v1.147 - -
-

-Updated #define keywords in cf_dtcorr. Turned on X-distortion -correction in cf_undistort and moved it to follow cf_driftcorr2. -Implemented linear wavelength scale in cf_wcal. -

May 14, 2002 -
Van Dixon -
cf_make_ttag_bkgd -
cf_make_hist_bkgd -
calfuse.h v1.146 - -
-

April 16, 2002 -
Van Dixon -
cal_fuse_exp_ttag.csh -
cal_fuse_exp_hist.csh -
calfuse.h v1.145 - -
-

April 8, 2002 -
Van Dixon -
cf_make_hist_bkgd -
cf_make_ttag_bkgd -
cf_ttag_burst -
bchr*001.fit -
scrn*013.fit -
calfuse.h v1.144 - -
-

-New software from Rich: New BCHR (background characterization) files -contain the binary extensions that used to be in the SCRN files. -Pipeline modules were modified to read the new files. -

March 29, 2002 -
Van Dixon -
cf_make_ttag_bkgd -
cf_ttag_burst -
bkgd*005.fit -
bkgd*006.fit -
bkgd*007.fit -
bkgd*008.fit -
scrn*012.fit -
calfuse.h v1.143 - -
-

-New software from Rich: The burst module has been modified to update -the EXPNIGHT value. The background module has a new procedure for -determining the intrinsic background from the data. The background -files should do a better job at short wavelengths. The screening files -redefine the background sample regions and add a few more geocoronal -line positions. -

March 17, 2002 -
Van Dixon -
cf_make_ttag_bkgd -
cf_make_hist_bkgd -
cf_ttag_geodopp -
cf_hist_geodopp -
calfuse.h v1.142 - -
-

-Turns out that all of these programs were treating the error arrays as -sigmas rather than variances (sigma squared). Modified to propagate -errors correctly. - -

February 22, 2002 -
Van Dixon -
cf_fuv_init -
ttag_combine -
cf_dtcor -
calfuse.h v1.141 - -
-

-Introduced new keyword, RAWTIME, which is equal to EXPTIME before -CalFUSE starts tossing out data. Modified cf_fuv_init and ttag_combine -to propagate it correctly. -

-Modified cf_dtcor to determine exposure time from the keywords CTIME_B -and CTIME_E, which are the times of the initial and final engineering -packets from which the counter data were taken. -

February 13, 2002 -
Van Dixon -
cf_fuv_init -
ttag_combine -
calfuse.h v1.139 - -
-

-Modified logic of voltage test in cf_fuv_init. Add COMMENT lines -to data file header if low voltage found. Respond gracefully if -bias keywords do not exist. -

-Modified cf_fuv_init to check detector voltage and complain if low. -New volt***001.fit calibration files, VOLT_CAL keyword. -

-Richard's new version of cf_update_qual modifies the bad-pixel maps to -account for the count-rate dependence of the detector Y scale. - -

November 30, 2001 -
Van Dixon -
cf_dpix, cf_extract, cf_wormcorr, cf_optextract, cf_spexextract, -cf_plot_extract.pro, cal_fuse_exp_ttag.csh, cal_fuse_exp_hist.csh, -parm**007.fit -
calfuse.h v1.134 - -
-

-In earlier versions of the pipeline, the shift to correct for FPA -offsets was performed by cf_wcal. We have moved it earlier in the -pipeline, right after the astigmatism correction, and combine the -FPA corrections with the other shifts in order to have a single -float-to-integer conversion. The new module is called cf_dpix. - -

-cf_extract now reads the keyword RUN_OPTI, rather than OPT_EXTR, from -the parameter file. It also writes the Y centroid of each spectrum to -the corresponding output file header. - -

-Sylvestre added software to identify the worm in the LiF 1B spectrum: -cf_wormcorr reads the keyword RUN_WORM from the parameter file. If -RUN_WORM = LIF, SIC, or BOTH, the program attempts to identify the -region of the worm and write the range of affected pixels (WORM_BEG and -WORM_END) to the output file header. The IDL routine -cf_plot_extract.pro draws a ring around the worm, if found. - -

Modified cal_fuse_exp_ttag.csh and cal_fuse_exp_hist.csh to call -both cf_dpix and cf_wormcorr. Modified calfuse.h to include new -processing keywords DPIX_COR and WORM_COR. - -

-Changed the way that cf_ttag_screen treats user-defined good-time -intervals. Now takes intersection of them with pre-defined intervals -(from OPUS or cf_ttag_combine) before screening. Also changed the -module to apply all screens (SAA, day/night, limb angle, pulse height) -regardless of where the good-time intervals came from. Screening can -be turned off by modifying the scrn*.fit files, if desired. - -

-Defined NO_PIXEL in calfuse.h. Used by geometric-distortion and -extraction routines. - -

-Modified cf_dtcor to set counters to zero if values are too large to -read as longs. - -

-Modified cf_fuv_init to check header keyword OPUSVERS and complain if -the data file was processed using an old version of OPUS. - -

-Modified cf_ttag_init to reset the keywords SPECBINX, SPECBINY, -SIA_TBL, and NUM_HIST without checking their current value. -This code was moved from cf_ttag_image, where it had been -commented out in April 2001. -

October 10, 2001 -
Van Dixon -
ttag_combine -
flux*008.fit -
calfuse.h v1.127 - -
-

-Rich Robinson has made numerous upgrades to ttag_combine. Among other -things, it can now handle the DX, DY and DNFLG columns added by -cf_ttag_init. -

-Jeff Kruk has produced new flux-calibration files -based on the latest wavelength calibration. -

-Updated CALFUSE version to 2.0.5. -This is the release version of CalFUSE v2.0. - -

-Don Lindler has produced new wavelength files appropriate for data that -do NOT have the walk correction applied to their stim pins. -They were created by taking the previous line locations and correcting -them before fitting by: - -

-Version 008 had new PHA limits. Version 009 had new information for -background models. Version 010 has both. - -

-New version of background routine reads the keyword BKGDTYPE in the -screening file. Default value is 1; if set to -1, routine does not -perform an iterative fit to the observed scattered light. -

-Installed new wavelength calibration files, v013, which are corrected -for the motion of the stim pins due to walk correction in previous -versions of the pipeline. -

September 11, 2001 -
Van Dixon -
calfuse.h 1.125 -
cf_ttag_walk -
cf_hist_walk - -
-

-Don't apply walk correction to photons/pixels within STIM_PAD (512) -pixels of the detector edge. New walk-correction files (v003) have -zeros in the stim-pin region. - -

September 5, 2001 -
Van Dixon -
calfuse.h 1.124 -
cf_make_ttag_bkgd -
cf_extract - -
-

-If MKBK_COR is set to OMIT, cf_make_ttag_bkgd changes it to SKIPPED. -cf_extract copies the keyword OPT_EXTR into the FITS file headers. - -

-New cf_make_ttag_bkgd iteratively fits dark-count and scattered-light -components of the background to deal with the fact that the dark count -varies with time. Spits out a file filled with zeros if MKBK_COR -is set to OMIT. -

August 23, 2001 -
Van Dixon -
calfuse.h 1.122 -
cf_fuv_init -
cf_ttag_burst -
cf_ttag_walk -
cf_hist_walk -
cf_astig -
cf_make_hist_bkgd -
cf_make_ttag_bkgd -
cf_bkgd - -
-

-Enable user to turn off the burst rejection, walk correction, -background subtraction, or astigmatism correction by changing keywords -in parm**006.fit. cf_fuv_init reads the PARM file and changes the -appropriate keywords (e.g., BRST_COR) from PERFORM to OMIT. Subsequent -pipeline steps check their keyword; if it is OMIT, they change the -value to SKIPPED, issue a warning, and exit, copying input to output if -appropriate. Updated CALFUSE version to 2.0.2. - -

August 21, 2001 -
Van Dixon -
calfuse.h 1.121 -
cf_wcal -
cf_fpa_pos -
cf_ttag_init - -
-

-Moved cf_fpa_pos from cf_wcal to libcf. ttag_combine uses this routine -to determine the FPA positions and complains if an FPA moves by more -than 10 microns between exposures. - -

-Header keywords SPECBINX and SPECBINY should be 1 for ttag data. An -old version of OPUS set these to 0. Changed cf_ttag_init to update -these parameters if it finds them equal to 0. Also updated cf_dtcor to -use Dave Sahnow's new parameters for dead-time correction. Added a -check: if DET_DEAD > 2.0, assume it's wrong and set to 1.0. - -

-New version of cf_astig employs Sylvester's cross-correlation routine -to determine spectral centroids. New PHAM, WAVE, and FLUX files. -Updated CALFUSE version to 2.0.1. -
This is the beta-test version of CalFUSE v2.0. - -

July 2, 2001 -
Van Dixon -
calfuse.h 1.118 -
cf_ttag_init.c -
cf_ttag_screen.c -
cf_ttag_burst.c -
cf_make_ttag_bkgd.c -
cf_make_hist_bkgd.c - -
-

-Implemented Richard's new background modeling routine, which -independently computes the day- and night-time contributions to the -scattered-light background. To do so, he adds an extra column, DNFLG, -to all of the photon-event files. Package includes improvements -to the burst-screening algorithm. Updated CALFUSE version to 2.0.0. - -

-Changed sign returned by the LSR correction subroutines to conform with -astronomical standard. Updated CALFUSE version to 1.9.9 - -

-Alex Fullerton determined that we have been applying the heliocentric -velocity correction with the wrong sign. The orbital dopper correction -has been applied with the correct sign. The function helio_vel.c -inverts the sign returned by the SLALIB routines, so the simplest -correction is to remove this sign inversion. - -

April 10, 2001 -
Van Dixon -
calfuse.h 1.111 -
cf_hist_walk.c 1.1 -
cal_fuse_exp_hist.csh - -
-

-Installed new module to apply walk correction to histogram data. -Modified shell script cal_fuse_exp_hist.csh to call this routine. -Added PHAM entry to CALIBRATION_FILE_KEYS in calfuse.h. Updated -CALFUSE version to 1.9.8 - -

April 2, 2001 -
Van Dixon -
calfuse.h 1.110 -
cf_ttag_walk.c 1.1 -
cal_fuse_exp_ttag.csh -
cal_fuse_exp_hist.csh - -
-

-Installed new module to apply walk correction. Modified shell -scripts cal_fuse_exp_ttag.csh and cal_fuse_exp_hist.csh to call this -routine. Added WALK entry to CALIBRATION_FILE_KEYS in calfuse.h. -Updated CALFUSE version to 1.9.7 - -

March 28, 2001 -
Van Dixon -
calfuse.h 1.109 -
cf_extract.c 1.52 -
cal_fuse_exp_ttag.csh -
cal_fuse_exp_hist.csh - -
-

-Installed new module to perform optimal extraction. Modified shell -scripts cal_fuse_exp_ttag.csh and cal_fuse_exp_hist.csh to call this -routine. In calfuse.h, added definition of cf_optextract and new -arguments to cf_spextract. Updated CALFUSE version to 1.9.6 - -

March 27, 2001 -
Van Dixon -
calfuse.h 1.108 -
cf_make_bkgd.c 1.22 -
cal_fuse_exp_ttag.csh -
cal_fuse_exp_hist.csh - -
-

-Installed new module to scale background calibration file. Modified -shell scripts cal_fuse_exp_ttag.csh and cal_fuse_exp_hist.csh to call -this routine (instead of cf_make_bkgd_temp). Add AIRG entry to -CALIBRATION_FILE_KEYS in calfuse.h. Updated CALFUSE version to 1.9.5 - -

March 19, 2001 -
Van Dixon -
calfuse.h 1.107 -
cf_ttag_burst.c 1.9 -
cal_fuse_exp_ttag.csh -
cal_fuse_exp_hist.csh - -
-

-Installed new module to reject data during detector bursts. Modified -shell scripts cal_fuse_exp_ttag.csh and cal_fuse_exp_hist.csh to call -this routine. Modified Makefiles to install it. Updated CALFUSE -version to 1.9.4 - -

March 14, 2001 -
Van Dixon -
calfuse.h 1.106 -
cf_astig.c 1.8 -
cal_fuse_exp_ttag.csh -
cal_fuse_exp_hist.csh - -
-

-Installed new program to implement astigmatism correction, now called cf_astig. -Modified shell scripts cal_fuse_exp_ttag.csh and cal_fuse_exp_hist.csh to call -this routine. Modified Makefiles to install it. -Updated CALFUSE version to 1.9.3 - -

-Add checks to cf_ttag_screen.c to ensure that user-defined good time intervals -actually fit within the time spanned by the dataset, and that in each case the -end of a good time interval is later than the beginning. Invalid user GTI's -are ignored. Also added printout to trailer file of the number of events that -were rejected by pulse height limits. Updated CALFUSE version to 1.9.2 - -

February 8, 2001 -
J.C. Hsu -
calfuse.h 1.104 -
cf_linear.c 1.0 -
cf_transform1d.c 1.0 -
cf_1dff.c 1.0 -
cf_make_1dff.c 1.0 - -
-

-Install programs needed to perform 1-D flat fielding. All Makefiles updated. -The "official" pipeline shell scripts were not updated; users wishing to try -the 1-D flatfields should edit their local copies of the shell scripts for -the time being. Thus, the pipeline version was not updated. - -

December 21, 2000 -
Paul Barrett, J.C. Hsu -
Makefile.Alpha -
cf_ttag_screen.c 1.54 -
cf_ttag_image.c 1.22 -
cf_ttag_init.c 1.16 -
cf_wcal.c 1.25 - -
-

-In response to problems encountered by Vincent LeBrun installing -calfuse on a DEC Alpha running True64, we made a number of changes. -The main one was to correct type mismatches in cfitsio calls: -in a number of cases an "int" variable was referenced as TLONG and vice versa. -Added -ieee flag to compiler options in Makefile.Alpha. -cf_ttag_image: fix type mismatches in cfitsio calls -cf_ttag_init: fix type mismatches in cfitsio calls -cf_ttag_screen: fix type mismatches in cfitsio calls -cf_wcal: fix type mismatches in cfitsio calls -This is the first instance in which v1.9.1 differs from v1.8.7, and no -change in functionality was involved, so the pipeline version was -not updated. - -

November 15, 2000 -
Jeff Kruk -
cf_make_ff_temp.c 1.6 -
cf_make_bkgd_temp.c 1.6 -
cf_ttag_screen.c 1.53 - -
-

-Fixed typos in print statements in several routines. -No change in functionality resulted, so the pipeline version number -was not incremented. - -

-Created CALFUSE version 1.9.1 as the new development version. -calfuse.h was updated to reflect the new version number. - -

October 18, 2000 -
Martial Andre, Jeff Kruk -
cf_extract.c 1.47 -
calfuse.h 1.102 - -
-

-The image centroid (in Y) for extended sources is once again calculated -including airglow lines. In many cases extended sources are very faint -and the airglow will help locate the spectra. Extended sources will -ordinarily fill the slits in the same manner as airglow, so the accuracy -of the centroid calculation will not be adversely affected. -

October 13, 2000 -
Jeff Kruk -
cf_ttag_screen.c 1.52 -
cf_extract.c 1.46 -
cf_fuv_init.c 1.9 - -
-

-Three calls to FITS_read_key (infits, TSTRING, keyword, &arrayname,...) in the -program cf_ttag_screen were modified to remove the extraneous ampersand. -

-One call to FITS_read_key (infits, TSTRING, keyword, &arrayname,...) in -cf_extract.c was modified to remove the extraneous ampersand. Also -fixed a bug in the test for the variable ystop_bis being out of limits. -

October 2, 2000 -
Jeff Kruk, JC Hsu -
cf_hist_dopp 1.25 -
calfuse.h 1.101 -
cal_fuse_exp_ttag.csh -
cal_fuse_exp_hist.csh - -
-

-The program cf_hist_dopp was modified to incorporate corrections for -grating thermal motion. The mean motion for the exposure is added to -the doppler correction. -

-The shell script cal_fuse_exp_hist.csh was -modified to call cf_make_shift and to pass the resulting shift file -to cf_hist_dopp. -

-The include file calfuse.h was modified to include the function prototype -for lif_sic_border() (see below), and to change the MKSH_COR -histogram pipeline entry in CALIBRATION_STEP_KEYS to PERFORM. -

-The shell scripts cal_fuse_exp_ttag.csh and cal_fuse_exp_hist.csh were -modified to test cfstat before calling the idlplot routines. - -

October 2, 2000 -
Jeff Kruk -
cf_check_point 1.17 -
cf_hist_screen 1.21 -
cf_ttag_screen 1.51 - -
-

-The programs cf_hist_screen and cf_ttag_screen were modified to -update the keyword EXPNIGHT, newly created to provide the number of -seconds of exposure time (after screening) that were obtained during -the night side of the oribt. This keyword will be used by an upcoming -version of cf_bkgd. -

-The function cf_check_point was modified to return a flag indicating -whether the satellite was in daylight or night at the time being -checked. - -

The pipeline version number was updated for an additional change made -later in the day. - -

-The function lif_sic_border() was extracted from cf_hist_dopp.c -and make a function in libcf so that it would be available for -the upcoming 1-D version of cf_ff. The libcf Makefiles were modified -accordingly. - -

No change in functionality resulted, so no update to the pipeline -version number was made. - -

-The function state_limb() was modified (v1.08) to include fortran -function prototype wrappers for the new slalib calls introduced by -the previous change (slaDcc2s, slaEvp, slaDranrm). - -

This change was solely for running Make on the distribution version -of calfuse, so no update to the pipeline version number was made. - -

September 26, 2000 -
Martial Andre -
state_limb 1.05, 1.06, 1.07 -
cf_check_point 1.16 -
cf_orbit 1.03 -
calfuse.h 1.98, 1.99, 1.100 - -
-

-The function state_limb() was modified (v1.05) to calculate the limb angle -constraint in the same way as is done by the mission planners: -it checks if the limb itself is in daylight or night, rather than the -old simplistic method of seeing if the satellite was in day or night. -This required a modification to the call to state_limb. -Versions 1.06, 1.07 of state_limb were to fix minor bugs. -

-The function cf_check_point (v1.16) and the program cf_orbit (v1.03) were -modified to make use of this new limb angle constraint calculation. -

-The include file calfuse.h (v1.98, v1.99) was modified to provide the -proper function prototype for the new versions of state_limb and -cf_check_point. - -

These changes led to the increase in pipeline version number to 1.8.5 -(implemented by version 1.100 of calfuse.h). - - -

-Ed Murphy & Paul Barrett produce distribution version of pipeline. -Major change was to incorporate "makemake" files. - -

Since this routine is still in testing, I have not updated the -pipeline version number. The new version of cf_astig2.c is 1.07. - - -

-Jeff Kruk modified cf_dtcor.c to populate three new keywords -in the FUV header: -DEAD_DET Detector dead time factor -DEAD_IDS IDS dead time factor -DEAD_TOT Combined dead time factor - -New version of cf_dtcor.c is 1.18. He also changed sunmath.h to math.h. - -

-Modify cf_astig2 to get the calibration file from the ASTG_CAL keyword -rather than being hardcoded. - -

Since this routine is still in testing, I have not update the -pipeline version number. The new version of cf_astig2.c is 1.06. - -

-Jeff Kruk found that cf_astig2 crashed on all segment 1B data. The -routine lacked any boundary checking and was running off the bottom -of the image when attempting to centroid the SiC spectrum. The -centroiding routines have been updated to include boundary checking. - -

Since this routine is still in testing, I have not update the -pipeline version number. The new version of cf_astig2.c is 1.05. - -

-Martial fixed a bug in the initialization of column_sum that caused a -fatal bus error. -The change is too small to update the pipeline version number. -

-I added calls to cf_proc_check and cf_proc_update to cf_update_qual -to rid the trailer files of the warnings concerning the QUAL_COR -keyword. New version of cf_update_qual is 1.03. The change is too -small to update the pipeline version number. -

-To avoid the centroid to be shifted close to the bright edge, the procedure should compute the size of -the scanning window for each different channel (the changes done in version 1.41 were wrong!!!) -

-Propagation of quality should have been done with float since the very beginning (now fixed). -

July 26, 2000 -
J. C. Hsu, R. Robinson, Ed Murphy -
cf_update_qual v1.02 -
cf_driftcorr2 v1.23 - -

J. C. Hsu has written a program cf_update_qual to update the quality -flags in the *_img.fit files after the drift correction has been -determined. The FARF positions of the dead spots and edges of the detectors -were determined by Rich Robinson and are in the qual*001.fit calibration -files. The drift correction is used to correct for the strecth/shift -in going from the FARF to the observed data frame. - -

When implementing cf_update_qual, Ed Murphy noticed that cf_driftcorr2 -was centroiding the stims incorrectly. The error arose because the -algorithm was computing the stim centroid in a box that had an extent -of +-256 in X. Since the stims are at pixel ~230 (on segment 1a) the -centroiding box was including counts along the X=0 column, which -skewed the centroid. In the particular observation that he used -to test the routine (M999 flat field) the X=0 column was particularly -bright due to the high count rates in a stim lamp observation. This -problem probably does not effect most observations, since the X=0 column -is normally much weaker. He also modified cf_driftcorr2 to use the -FARF stim positions given in calfuse.h as opposed to the positions that -were hard coded into the routine. -

-Fixed bug of implementation of a pointer in im_centroid wich caused a bus error. -

Jeff Kruk added an IDS dead time correction to the dead time correction -routine cf_dtcor.c. - -

Now the default resolution of the coadded spectra is 0.1 Angstrom. This way, -we make sure that astronomers outside JHU don't use them for science purpose -(since some of the channels are currently misaligned => artefacts). Note that -the user is still free to have maximal resolution by tuning the arguments. - -

June 20, 2000 -
Ed Murphy -
cf_ttag_screen 1.49, cf_hist_dopp v1.23 -
PR 41926 - -
-

-Peter Young noticed that the Doppler shift in pixels for the SiC and -LiF spectra on segment 1a were both in the same direction. Since the -dispersions run in opposite directions, the two shifts should be opposite -in sign. The DISPAPIX keyword in the wavelength calibration file records -the average dispersion in Angstroms/pixel. It should be positive when -the wavelength increases with increasing pixel number and it should be -negative when the wavelength decreases with increasing pixel number -(SiC1 and LiF2). However, I found that the DISPAPIX keyword was always -positive in the recent versions of the wavelength calibration files. -Therefore, for SiC1 and LiF2, the sign of the Doppler and heliocentric -corrections are incorrect. - -

-I have modified the code in cf_ttag_screen and cf_hist_dopp to read in -the absolute value of DISPAPIX and compute the sign of the shift based -on the aperture to which the photon belongs. The new version of -cf_ttag_screen is 1.49 and the new version of cf_hist_dopp is 1.23. - -

-I have also removed the flat-fielding step from the pipeline. Even -though we do not have a flat-field file, we have been applying a flat -field (filled with 1's) to the data so that we could incorporate a bad -pixel mask. However, we are not stretching/shifting the flat field file -(since it is all 1's) to match the data which means that the bad pixel -mask does not line up with the data. J.C. Hsu is in the process of -writing a new module to properly apply the bad pixel mask. However, -the routine cf_ttag_geodopp.c still requires the _ff.fit file, so we -must still run cf_make_ff_temp. This intermediate _ff.fit data file -contains all 1's over the active area of the detectors, and 0's -everywhere else. Since we are not running the cf_ff, the locations -where the flat field is 0 are not being flagged as bad. This was -causing cf_ttag_geodopp to report a lot of "Divide by zero in ffbuf" -errors. For now, I have turned off the warning in cf_ttag_geodopp. - -

-The algorithm of finding the centroid has been totally changed. Now the position -of the spectrum is reached via a maximisation of the flux in the extraction window. -Moreover, the airglows are systematically screened to center only on the source. - -

-The way the windows are calculated changed drastically. Using the parameter of the distortion -correction, the shape of each window has been simplified (butterfly or trapeze) and the -weigth files are filled with parabolic profiles (first approximation). For more details -see /data1/fuse/calfuse/v1.8/src/cal/extraction_masks/README - - -

-Jeff Kruk upgraded cf_wcal to read either the new FPA keywords (FPASXPOS -or FPALXPOS) or the old keywords (FP1SXPOS, FP1LXPOS, FP2SXPOS, or -FP2LXPOS). New version is 1.24. -

-Ed Murphy found and corrected a bug in cf_extract that prevented the -SiC extraction windows from being reset to the default position if -the centroid was more than EMAX_SIC pixels from the exptected position. -

-Paul Barret changed the interpolation algorithm back to a constant (to -prevent ringing around the outside of the spectrum) and fixed a bug in -that implementation. - -

-Jeff Kruk has modified cf_wcal.c (now version 1.23) to correct the -wavelength scale for the position of the FPA. -

-Paul Barrett has produced new versions of the detector distortion -files: geom*005.fit in /data1/fuse/calfuse/calfiles. - -

-The pipeline can now generate a few diagnostic plots (using IDL) while -it is running if the CF_IDLDIR environment variable is set to point to -the location of the IDL programs. To set up the pipeline to make the -plots, add the following to your .cshrc or .login file:
-setenv CF_IDLDIR '/data1/fuse/calfuse/current/idl/' -

-The plots are in GIF format so that they can, at some future time, -be linked to the SDOG pages. -

-Development on V1.7.4 of the pipeline has been frozen. Only bug fixes -will be made from now on. The current stable version of the pipeline -now points to V1.7.4. You will need new calibration files, new -parameter files, and a new master_calib_file.dat -

It has been suggested that a higher order interpolation scheme be used -when expanding the binned histogram data, instead of the current constant -interpolation scheme. A quadratic average interpolation algorithm has been -implemented in cf_hist_init. This algorithm uses data from neighboring -pixels to interpolate the data in binned pixles while conserving the total -number of counts per binned pixel. This routine has been tested. -

This modification to cf_hist_init will now allow histogram data to be -used for determining distortion corrections by providing necessary spatial -resolution. -

In the SDOG report for P1320101 Jeff Kruk -found that the pipeline seemed to be excessively screening out data that -was near, but not violating, the night time limb angle limit. I found flawed -logic in the limb angle check in cf_check_point.c that meant that the bright -limb angle was always used regardless of the day/night flag. The problem -has been corrected (cf_check_point.c now V1.15) and the routine has been -tested. -
-

Bill Oegerle noticed that the pipeline was -not subtracting the background from some recently processed datasets. The -pipeline has been in this state since sometime around the end of December -1999. I fixed the problem in both versions of the pipeline: new versions -are V1.6.8 and V1.7.2 -

The problem was found in cf_make_bkgd_temp.c, which is a temporary module -designed to read in the background calibration file and write it into the -*ttagf_bkgd.fit file needed by the pipeline. The module does not stretch -or shift the background image but does scale the background by the integration -time. In the calibration file, the background image is composed of short -integers with the value 1 everywhere. The keyword BSCALE gives the number -of square cm per pixel, so that the file contains the number of counts -per pixel per second. The original version of cf_make_bkgd_temp.c read -in the calibration image and wrote it out directly, without converting -the input image to floats. All it did was multiply BSCALE by the integration -time, so that when cf_bkgd.c read in the file and scaled by BSCALE, the -resulting image would be background counts per pixel for the full integration. -

In late December 1999, it was decided to rewrite cf_make_bkgd_temp.c -to rebin the data for histogram mode observations. In this case, the new -routine read in the calibration file array (all 1), converted the background -image to floats by applying BSCALE, rebinned the data (if necessary), and -wrote out an array of floats. However, the header was copied from the input -file, so the BSCALE keyword still remained even though the data had already -been scaled as part of the routine. In addition, the step where BSCALE -was multiplied by the integration time also remained in the new version. -Therefore, when cf_bkgd.c read in the *ttagf_bkgd.fit intermediate file, -it used the BSCALE keyword a second time. The result was that the subtracted -background was about two orders of magnitude too small. -

Because the pipeline now unbins the histogram data, we have reverted -back to the original versions of the routines which do not rebin the data -and do not suffer from this problem. The new version of cf_make_bkgd_temp.c -is V1.4. -

A few histogram data sets were crashing the -pipeline becuause of a bad pixel value that was larger than 32767. This -value was large enough that it would not fit into a short integer in the -pipeline and cfitsio would return a data conversion error. Jim Rose has -agreed to modify the OPUS pipeline to find pixel values larger than 32767 -and change them to the data fill value 21865. As seen below, the pipeline -will convert the data fill value to 0.0 and change its quality flag to -bad. -

A number of histogram data sets have fill -data in them (decimal 21865) which the pipeline was not filtering out. -I have modifed v1.6.7 and v1.7.1 of the pipeline to check pixels for the -fill data value. If the fill data value is found, it will replace the data -with 0.0 and change the quality flag to bad. -

Until now, the DATE keyword in the header -was not modified by any of the modules in the pipeline, even though its -comment stated that it was the "date the file was written." I have modified -cf_proc_update.c to update the DATE keyword. Since cf_proc_update is called -at the end of each module of the pipeline, the output files and all intermediate -data products will now have accurate dates and times in the DATE keyword. -This change was made to both V.1.6.7 and V1.7.1 of the pipeline. -

Until now, the cf_extract procedure was unable -to perform a good centroiding in Y when very few counts were involved. -Since we used the formula : Ycenter = (å -Yi * nbcounts_i)/ånbcounts_i, where nbcounts_i -is the total number of counts along the row i, the result was depending -on the Y limits of the sum. For instance, if the upper limit equals infinity, -the result is infinity (do not forget that the noise is different of 0). -So, to use this formula, we need a first guess for the position of the -center in order - -

to choose a domain of calculation surrounding -it. At present, this first guess is the maximum peak. -
-

The new extraction windows are now available -(spex*005.fit). This is the first set of In Orbit Based Extraction Windows -: all the apertures have the same window (based on 100 percent with LWRS). - -

The associated weight files are also available -(wgts*003.fit). Note that since the raw windows extracted from In Orbit -Data are very noisy, I had to smooth and correct the geometrical distorsions -, sometimes " by hand ". -
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Detector	Data Used	Notes
1A (LiF)	/data2/fuse/CAL/M101/M1010201	Good
1A (SiC)	/data2/fuse/CAL/M103/M1030303	Good
1B (LiF)	/data2/fuse/CAL/M101/M1010201	Corrected by hand : mirror transformation applied
1B (SiC)	/data2/fuse/CAL/M103/M1030304	Corrected by hand : linear regression for the narrow domain
2A (LiF)	/data2/fuse/CAL/M101/M1010201	Good
2A (SiC)	/data2/fuse/CAL/M103/M1030304	Good
2B (LiF)	NOT AVAILABLE	Here I didn't find a signal strong enough ... I used the old Ground -Based Files + geometrical correction
2B (SiC)	/data2/fuse/CAL/M103/M1030304	Ground Based Files + geometrical correction

- -

Note also that you can change the windows -with "cf_modifwindows" wich apply an homothetic factor to the LiF channel -and the SiC channel : - -

By popular demand, I have written a program -to convert an ASCII file to the 1-D FITS extracted format that comes out -of the pipeline. The program is called ascii2fits and is in the /usr/local/fusesw/calfuse/current/bin -directory. The program takes 3 arguments: Calling sequence:ascii2fits ascii_file -template_fits_file output_fits_file The ASCII file must have six columns: -wavelength (float) flux (float) errors (float) quality flags (int) counts -(float) errors on counts (float) The template FITS file is used to populate -the header keywords. It can be any raw or pipeline processed file. -
-

Overlapping pixels are now averaged by cf_hist_geodopp. -This is a temporary fix to minimize the effect on the spectrum due to a -mis-match between the BARF and FARF, i.e. it removes the spikes from the -spectrum. -
-

Version 1.7.1 of the pipeline is now in the -FARF frame, however, the calibration files are not. -
-

The dead time correction step has been removed -from the pipeline. The new version of pipeline is V1.6.5. The pipeline -module itself was fine. However, Dave Sahnow has found that the on-board -counters behave strangely at low count rates (in addition to behaving strangely -in the SAA). Until this issue is resolved, we will not dead time correct -the data. -
-

Histogram data currently show strong spikes -approximately once per Angstrom. This behavior is not unexpected. It comes -from the fact that we have to compress the image in the X direction by -about 110 pixels in order to bring the data into the reference frame of -the calibration files. Until we can redefine the calibration file reference -frame and remake all our calibration files, this behavior will be present -in the data. -
-

Version 1.6.4 of the CALFUSE pipeline is now frozen. In the future, -only bug fixes will occur. The /usr/local/fusesw/calfuse/current directory -will now point to v1.6. All development will take place in v1.7. -

REMINDER: Many people directly reference -"v1.5" rather than "current" in their PATH and LD_LIBRARY_PATH. If you -do this, be sure to change both PATH and LD_LIBARARY_PATH to v1.6. Otherwise, -you will be running the pipeline with outdated copies of the library routines -since we are now using dynamically linked libraries (linked in at run time).

-CalFUSE Pipeline Status