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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="GENERATOR" content="Mozilla/4.6 [en] (X11; U; SunOS 5.7 sun4u) [Netscape]">
<meta name="CREATED" content="20000121;18144100">
<meta name="CHANGED" content="20000124;16081300">
<title>CALFUSE Pipeline Status</title>
</head>
<body bgcolor="#FFFFFF">
<h1>
CalFUSE Pipeline Status</h1>
<b>Final pipeline version is 3.2.3, dated December 5, 2008.</b>
<p STYLE="margin-bottom: 0in">Latest updates:
<p>December 5, 2008
<br>Van Dixon
<BR>v3.2/src/libcf/cf_calculate_y_centroid.c
<BR>v3.2/src/libcf/cf_find_spectra.c
<BR>v3.2/src/libcf/cf_screen_jitter.c
<P>
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.
<P>
Modified cf_screen_jitter.c so that the jitter correction is not
applied to ERO observations of Jupiter (program X006).
<P>
<hr WIDTH="100%">
<p>August 22, 2008
<br>Van Dixon
<P>
<BR>v3.2/include/calfuse.h
<BR>v3.2/src/fuv/cf_bad_pixels.c
<BR>v3.2/src/fuv/cf_screen_photons.c
<BR>v3.2/src/libcf/cf_apply_filters.c
<BR>v3.2/src/libcf/cf_fuv_init.c
<BR>v3.2/src/libcf/cf_screen_jitter.c
<BR>v3.2/src/libcf/cf_set_photon_flags.c
<BR>v3.2/src/analysis/cf_combine.c
<BR>v3.2/src/analysis/cf_xcorr.c
<BR>v3.2/src/analysis/idf_combine.c
<BR>v3.2/src/analysis/cf_make_all_obs.csh
<BR>v3.2/src/analysis/cf_make_900_obs.csh
<P>
I've modified CalFUSE to treat bright-earth and airglow observations
differently than before. Here are the details:
<P>
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."
<P>
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:
<UL>
<LI>no jitter correction is performed;
<LI>when the time-dependent flags are copied from the timeline
table to the individual photons, the limb-angle flag is masked
out;
<LI>when the good-time intervals and exposure time are
calculated, the limb-angle flag is ignored.
</UL>
<P>
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.
<P>
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.
<P>
Update version number to v3.2.3.
<P>
<hr WIDTH="100%">
<p>April 11, 2008
<br>Van Dixon
<BR>v3.2/src/analysis/cf_xcorr.c
<BR>v3.2/src/analysis/cf_combine.c
<BR>v3.2/src/analysis/cf_make_all_obs.csh
<P>
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.
<P>
<hr WIDTH="100%">
<p>March 21, 2008
<br>Van Dixon
<BR>v3.2/src/libcf/cf_find_spectra.c
<P>
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.
<P>
<hr WIDTH="100%">
<p>Feb 22, 2008
<br>Benjamin Ooghe
<BR>INSTALLING_CalFUSEv3.2.2
<BR>INSTALLING_A_FORTRAN_COMPILER
<BR>FIXING_SELINUX_ISSUES
<P>Updated installation information.
<P>
<BR>v3.2/bin/calfuse.sh
<BR>v3.2/bin/cfsetup.sh
<BR>v3.2/bin/cfsetup.csh
<P>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.
<P>
<BR>v3.2/src/configure.linux
<BR>v3.2/src/configure.linux64
<BR>v3.2/src/configure.macosx
<BR>v3.2/src/configure.solaris
<BR>v3.2/src/cfitsio/configure
<BR>v3.2/src/Makefile.Linux
<BR>v3.2/src/Makefile.Linux64
<BR>v3.2/src/Makefile.MacOSX
<BR>v3.2/src/analysis/Makefile.Linux
<BR>v3.2/src/analysis/Makefile.Linux64
<BR>v3.2/src/analysis/Makefile.MacOSX
<BR>v3.2/src/analysis/idf_combine.c
<BR>v3.2/src/analysis/cf_coadd.c
<BR>v3.2/src/analysis/cf_arith.c
<BR>v3.2/src/analysis/cf_combine.c
<BR>v3.2/src/analysis/cf_pack.c
<BR>v3.2/src/cal/jitter/Makefile.Linux
<BR>v3.2/src/cal/jitter/Makefile.Linux64
<BR>v3.2/src/cal/jitter/Makefile.MacOSX
<BR>v3.2/src/cal/jitter/cf_jitter.c
<BR>v3.2/src/cal/jitter/cf_jitter_diag.c
<BR>v3.2/src/fes/Makefile.Linux
<BR>v3.2/src/fes/Makefile.Linux64
<BR>v3.2/src/fuv/Makefile.Linux
<BR>v3.2/src/fuv/Makefile.Linux64
<BR>v3.2/src/fuv/Makefile.MacOSX
<BR>v3.2/src/fuv/cf_gainmap.c
<BR>v3.2/src/fuv/cf_countmap.c
<BR>v3.2/src/libcf/Makefile.Linux
<BR>v3.2/src/libcf/Makefile.Linux64
<BR>v3.2/src/libcf/Makefile.MacOSX
<BR>v3.2/src/libcf/cf_idf_io.c
<BR>v3.2/src/slalib/mk
<BR>v3.2/src/slalib/mk.sv
<BR>v3.2/src/slalib/sla_source.tar
<P>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.
<P>
<BR>v3.2/include/calfuse.h
<BR>v3.2/src/libcf/cf_fes_proc_update.c
<BR>v3.2/src/libcf/cf_fes_proc_check.c
<P>Fixed warning messages from GCC compiler (missing brackets and
unused symbols).
<P>
<BR>v3.2/src/analysis/cf_make_all_obs.csh
<P>Use airglow spectra when they are the only ones available.
<P>
<BR>v3.2/src/analysis/cf_nvo.c
<P>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.
<P>
<BR>v3.2/src/fuv/cf_bad_pixels.c
<P>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.
<P>
<BR>v3.2/src/libcf/cf_thermal_distort.c
<P>In cf_estimate_drift_coefficients, set max value of index to jmax-1
rather than jmax.
<P>
<hr WIDTH="100%">
<p>February 22, 2008
<br>Van Dixon
<BR>v3.2/src/fuv/cf_convert_to_farf.c
<BR>v3.2/src/fuv/cf_flux_calibrate.c
<BR>v3.2/src/fuv/cf_ttag_init.c
<BR>v3.2/src/libcf/cf_modify_hist_pha.c
<BR>v3.2/src/libcf/cf_screen_jitter.c
<BR>v3.2/src/libcf/cf_set_good_time_intervals.c
<P>
Modified cf_convert_to_farf to write out the new PHA values assigned
by cf_modify_hist_pha.
<P>
Cleaned up i/o in cf_flux_calibrate.
<P>
Added -e flag to cf_ttag_init. It sets the header keyword HKEXISTS
to YES in the output IDF file.
<P>
In cf_modify_hist_pha, fixed bug in loop through MJD array.
<P>
In cf_screen_jitter, don't apply jitter correction to observations
taken after the spacecraft lost pointing control.
<P>
Changed malloc to cf_malloc in cf_set_good_time_intervals.
<P>
Update version number to v3.2.2.
<P>
<hr WIDTH="100%">
<br>
<p>May 18, 2007
<br>Van Dixon
<BR>v3.2/src/libcf/cf_init_support.c
<P>
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.
<P>
Update version number to v3.2.1.
<P>
<hr WIDTH="100%">
<p>April 7, 2007
<br>Van Dixon
<BR>v3.2/src/fuv/cf_bad_pixels.c
<P>
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.
<P>
This is the release version of CalFUSE v3.2.0.
<P>
<hr WIDTH="100%">
<p>March 29, 2007
<br>Van Dixon
<BR>v3.2/src/libcf/cf_init_support.c
<BR>v3.2/src/cal/jitter/cf_jitter.c
<P>
On error, cf_check_digitizer now sets EXP_STAT flag to -2, rather than
-999, to be more consistent with cf_hist_init.
<P>
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.
<P>
<hr WIDTH="100%">
<br>
<p>March 23, 2007
<br>Van Dixon
<BR>v3.2/src/fuv/cf_hist_init.c
<BR>v3.2/src/libcf/cf_init_support.c
<BR>v3.2/src/libcf/cf_screen_jitter.c
<BR>v3.2/src/libcf/cf_satellite_jitter.c
<P>
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.
<P>
In cf_init_support, give a more detailed error message if the
housekeeping file is not usable.
<P>
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.
<br>
<p>March 20, 2007
<br>Van Dixon
<BR>v3.2/src/fuv/cf_bad_pixels.c
<P>
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.
<P>
<hr WIDTH="100%">
<p>March 7, 2007
<br>Van Dixon
<BR>v3.2/src/libcf/cf_init_support.c
<BR>v3.2/src/libcf/cf_velang.c
<BR>v3.2/src/libcf/space_vel.c
<BR>v3.2/include/calfuse.h v1.81
<P>
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.
<P>
This is version 3.2.0 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>February 13, 2007
<br>Van Dixon
<BR>v3.2/src/fuv/cf_remove_motions.c
<BR>v3.2/src/libcf/cf_fifo_dead_time.c
<BR>v3.2/src/libcf/cf_init_support.c
<P>
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.
<P>
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.
<P>
<hr WIDTH="100%">
<p>January 2, 2007
<br>Van Dixon
<BR>v3.2/src/fuv/cf_screen_photons.c
<BR>v3.2/src/fuv/cf_convert_to_farf.c
<BR>v3.2/src/fuv/cf_remove_motions.c
<BR>v3.2/src/libcf/cf_apply_dead_time.c
<BR>v3.2/src/libcf/cf_fifo_dead_time.c
<BR>v3.2/src/libcf/cf_target_count_rate.c
<BR>v3.2/src/libcf/pole_ang.c
<BR>v3.2/src/libcf/cf_velang.c
<BR>v3.2/src/libcf/cf_screen_high_voltage.c
<BR>v3.2/src/libcf/cf_satellite_jitter.c
<BR>v3.2/src/libcf/cf_grating_motion.c
<BR>v3.2/src/libcf/cf_time_xy_distort.c
<BR>v3.2/src/libcf/cf_init_support.c
<BR>v3.2/src/libcf/cf_set_photon_flags.c
<BR>v3.2/src/cal/jitter/cf_jitter.c
<BR>v3.2/src/analysis/cf_combine.c
<BR>v3.2/src/analysis/cf_nvo.c
<BR>v3.2/src/analysis/cf_pack.c
<BR>v3.2/src/analysis/idf_combine.c
<P>
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.
<P>
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.
<P>
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.
<P>
The subroutine cf_screen_high_voltage no longer sets the EXP_STAT keyword.
<P>
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.
<P>
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.
<P>
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.
<P>
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.
<P>
We fixed a bug in the way that cf_init_support constructs the AIC
count-rate array.
<P>
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.
<P>
<hr WIDTH="100%">
<p>June 22, 2006
<br>Van Dixon
<BR>v3.2/src/fuv/cf_hist_init.c
<BR>v3.2/src/fuv/cf_extract_spectra.c
<BR>v3.2/src/fuv/cf_ttag_init.c
<BR>v3.2/src/libcf/cf_screen_jitter.c
<BR>v3.2/src/libcf/cf_screen_burst.c
<BR>v3.2/src/libcf/cf_optimal_extraction.c
<BR>v3.2/src/libcf/cf_fuv_init.c
<BR>v3.2/src/libcf/cf_error_msg.c
<P>
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.
<P>
Now that OPUS has been updated, the variable morekeys has been set to
zero in both cf_hist_init and cf_ttag_init.
<P>
This is version 3.1.8 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<br>
<p>May 24, 2006
<br>Van Dixon
<BR>v3.2/src/fuv/cf_extract_spectra.c
<BR>v3.2/src/analysis/cf_combine.c
<BR>v3.2/src/analysis/cf_nvo.c
<BR>v3.2/src/analysis/cf_pack.c
<BR>v3.2/src/analysis/cf_xcorr.c
<BR>v3.2/src/analysis/idf_combine.c
<BR>v3.2/idl/cf_obsplot.pro
<P>
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.
<P>
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).
<P>
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.
<P>
The program cf_pack now writes an index to the various file extensions
to the primary HDU of the output *000all* file.
<P>
Both cf_combine and idf_combine now write a number of header keywords
as longs, rather than floats.
<P>
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.
<P>
<hr WIDTH="100%">
<br>Van Dixon
<BR>v3.2/src/fuv/cf_assign_wavelength.c
<BR>v3.2/src/fuv/cf_bad_pixels.c
<BR>v3.2/src/libcf/cf_astigmatism.c
<BR>v3.2/src/libcf/cf_dispersion.c
<BR>v3.2/src/libcf/cf_apply_dead_time.c
<BR>v3.2/src/libcf/cf_extraction_limits.c
<BR>v3.2/src/libcf/cf_init_support.c
<BR>v3.2/src/libcf/cf_screen_burst.c
<BR>v3.2/src/libcf/cf_screen_fifo_overflow.c
<BR>v3.2/src/libcf/cf_screen_jitter.c
<BR>v3.2/src/libcf/cf_set_photon_flags.c
<BR>v3.2/src/analysis/cf_make_all_obs.csh
<BR>v3.2/src/analysis/cf_nvo.c
<BR>v3.2/src/analysis/cf_pack.c
<BR>v3.2/src/analysis/cf_xcorr.c
<P>
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.
<P>
Cleaned up i/o in cf_apply_dead_time.
<P>
For targets observed in HIST mode, cf_extraction_limits.c now pads
apertures by SPECBINY pixels.
<P>
In cf_init_support, flag as bad all times after final OPUS GTI.
<P>
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.
<P>
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.
<P>
This is version 3.1.8 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>February 3, 2006
<br>Van Dixon
<BR>v3.2/src/fuv/cf_compute_y_centroid.c
<BR>v3.2/src/fuv/cf_find_spectra.c
<BR>v3.2/src/libcf/cf_scale_bkgd.c
<BR>v3.2/src/fuv/cf_extract_spectra.c
<P>
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.
<P>
We fixed a bug introduced in the last modification of cf_scale_bkgd
that essentially turned off the background subtraction.
<P>
We added a command-line flag to cf_extract_spectra that forces the use
of optimal extraction, even for extended sources.
<P>
This is version 3.1.7 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>January 24, 2006
<br>Van Dixon
<BR>v3.2/src/fuv/cf_screen_photons.c
<BR>v3.2/src/libcf/cf_scale_bkgd.c
<P>
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.
<P>
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.
<P>
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.
<P>
This is version 3.1.6 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>January 3, 2006
<br>Van Dixon
<BR>v3.2/src/libcf/cf_grating_motion.c
<P>
Correct LiF 1 data for residual zero-point errors in the wavelength scale.
<P>
<hr WIDTH="100%">
<p>December 2, 2005
<br>Van Dixon
<BR>v3.2/src/libcf/cf_mirror_motion.c
<P>
cf_mirror_motion now exits without modifying the data if target is an
extended source.
<P>
<hr WIDTH="100%">
<p>December 2, 2005
<br>Van Dixon
<BR>v3.2/src/libcf/cf_astigmatism_and_dispersion.c
<BR>v3.2/src/libcf/cf_apply_dead_time.c
<BR>v3.2/src/libcf/cf_convert_to_ergs.c
<BR>v3.2/src/libcf/cf_count_rate_y_distort.c
<BR>v3.2/src/libcf/cf_doppler_and_heliocentric.c
<BR>v3.2/src/libcf/cf_extraction_limits.c
<BR>v3.2/src/libcf/cf_fpa_position.c
<BR>v3.2/src/libcf/cf_init_support.c
<BR>v3.2/src/libcf/cf_make_mask.c
<BR>v3.2/src/libcf/cf_optimal_extraction.c
<BR>v3.2/src/libcf/cf_satellite_jitter.c
<BR>v3.2/src/libcf/cf_screen_bad_pixels.c (NEW)
<BR>v3.2/src/libcf/cf_screen_fifo_overflow.c
<BR>v3.2/src/libcf/cf_screen_jitter.c (NEW)
<BR>v3.2/src/fuv/cf_bad_pixels.c
<BR>v3.2/src/fuv/cf_extract_spectra.c
<BR>v3.2/src/fuv/cf_remove_motions.c
<BR>v3.2/src/fuv/cf_screen_photons.c
<P>
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.
<P>
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.
<P>
In cf_convert_to_ergs, we changed the effective-area arrays to type
double to match the AEFF_CAL files.
<P>
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.
<P>
To improve our calculation of the Doppler correction, we changed the
variables velocity and doppler to doubles in cf_doppler_and_heliocentric.
<P>
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.
<P>
We deleted unused variables in cf_fpa_position.
<P>
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.
<P>
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.
<P>
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.
<P>
We added a flag to cf_extract_spectra that allows the user to disable
optimal extraction from the command line.
<P>
This is version 3.1.5 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>September 19, 2005
<br>Van Dixon
<BR>v3.1/src/libcf/cf_read_fpa_pos.c (RESTORED)
<P>
Had to restore cf_read_fpa_pos, as it's called by ttag_combine.
<P>
This is version 3.1.3 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>September 7, 2005
<br>Van Dixon
<BR>v3.1/src/analysis/cf_arith.c (RENAMED)
<BR>v3.1/src/analysis/cf_coadd.c
<BR>v3.1/src/analysis/cf_combine.c
<BR>v3.1/src/analysis/cf_make_all_exp.c (NEW)
<BR>v3.1/src/analysis/cf_nvo.c
<BR>v3.1/src/analysis/cf_pack.c
<BR>v3.1/src/analysis/cf_xcorr.c
<BR>v3.1/src/analysis/getshift.c
<BR>v3.1/src/analysis/modhead.c
<BR>v3.1/src/libcf/cf_init_support.c
<BR>v3.1/src/libcf/cf_fpa_position.c
<BR>v3.1/src/libcf/cf_read_fpa_pos.c (DELETED)
<BR>v3.1/src/libcf/cf_screen_burst.c
<BR>v3.1/src/libcf/cf_write_extracted_spectrum.c
<P>
We are required to provide MAST an <b>all</b> file for each exposure and
one set of <b>all</b>, <b>ano</b>, and <b>nvo</b> 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.
<P>
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.
<P>
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.
<P>
<hr WIDTH="100%">
<p>July 12, 2005
<br>Van Dixon
<BR>v3.1/src/analysis/cf_combine.c
<BR>v3.1/src/analysis/cf_nvo.c
<BR>v3.1/src/analysis/cf_pack.c
<BR>v3.1/src/cal/jitter/cf_jitter.c
<BR>v3.1/src/libcf/cf_satellite_jitter.c
<P>
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.
<P>
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.
<P>
<hr WIDTH="100%">
<p>June 16, 2005
<br>Van Dixon
<BR>v3.1/src/libcf/cf_rebin_probability_array.c
<BR>v3.1/src/libcf/cf_scale_bkgd.c
<BR>v3.1/src/fuv/cf_extract_spectra.c
<BR>v3.1/include/calfuse.h v1.71
<P>
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.
<P>
This is version 3.1.2 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>June 8, 2005
<br>Van Dixon
<BR>v3.1/src/analysis/cf_combine.c
<BR>v3.1/src/analysis/cf_make_all.csh
<BR>v3.1/src/analysis/cf_nvo.c
<BR>v3.1/src/analysis/cf_pack.c
<BR>v3.1/src/analysis/cf_xcorr.c
<BR>v3.1/src/analysis/extract_jitter.c
<BR>v3.1/src/analysis/idf_combine.c
<BR>v3.1/src/libcf/cf_calculate_y_centroid.c
<BR>v3.1/src/libcf/cf_find_spectra.c
<BR>v3.1/src/libcf/cf_idf_io.c
<BR>v3.1/src/libcf/cf_modify_hist_pha.c
<BR>v3.1/src/libcf/cf_rebin_probability_array.c
<BR>v3.1/include/calfuse.h v1.70
<P>
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.
<P>
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.
<P>
cf_make_all is the shell script that calls these routines.
<br>
cf_xcorr determines the relative wavelength offset of each exposure.
<br>
cf_pack combines the observation-level spectra from each channel into
a single ALL or ANO (all data, night-only) file.
<br>
cf_nvo selects data from the best channel for each waveband, shifts
it to a common wavelengh scale, and generates the NVO file.
<P>
In extract_jitter, fixed a bug that set EXPSTART equal to EXPEND.
<P>
In idf_combine, comment out warning when FPA motion is detected.
The pipeline corrects for this.
<P>
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.
<P>
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.
<P>
In cf_idf_io, allow arrays of floats to be read as doubles.
<P>
In cf_modify_hist_pha, fixed bug in loop through MJD array.
<P>
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.
<P>
<hr WIDTH="100%">
<p>April 19, 2005
<br>Van Dixon
<BR>v3.0/include/calfuse.h v1.66, v1.67, v1.68, v1.69
<P>
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.
<P>
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.
<P>
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.
<P>
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.
<P>
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.
<P>
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.
<P>
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.
<P>
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.
<P>
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.
<P>
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.
<P>
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).
<P>
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.
<P>
The default pulse-height limits (both upper and lower) have been
modified for all four detectors.
<P>
<hr WIDTH="100%">
<p>August 24, 2004
<br>Van Dixon
<BR>v3.0/src/libcf/cf_fes_proc_update.c
<BR>v3.0/src/libcf/cf_fes_proc_check.c
<BR>v3.0/src/libcf/cf_count_rate_y_distort.c
<BR>v3.0/src/libcf/cf_calculate_y_centroid.c
<BR>v3.0/src/libcf/cf_optimal_extraction.c
<BR>v3.0/include/calfuse.h v1.65
<P>
Installed two subroutines needed to process FES files. Modified calfuse.h
to support them.
<P>
In cf_count_rate_y_distort, interpolate stretch correction among
tabulated Y values to prevent counts from piling up at 10-pixel
boundaries.
<P>
In cf_calculate_y_centroid, confirm that all spectral centroids, not
just that of the target aperture, are within bounds.
<P>
In cf_optimal_extraction, use QUALITY array to set X limits of
extraction region. Insure that sigma_out array is non-zero.
<P>
<hr WIDTH="100%">
<p>August 12, 2004
<br>Van Dixon
<BR>v3.0/src/fuv/cf_assign_wavelength.c
<BR>v3.0/src/fuv/cf_bad_pixels.c
<BR>v3.0/src/fuv/cf_extract_spectra.c
<BR>v3.0/src/fuv/cf_remove_motions.c
<BR>v3.0/src/fuv/cf_screen_photons.c
<BR>v3.0/src/libcf/cf_astigmatism_and_dispersion.c
<BR>v3.0/src/libcf/cf_apply_filters.c
<BR>v3.0/src/libcf/cf_calculate_y_centroid.c
<BR>v3.0/src/libcf/cf_fuv_init.c
<BR>v3.0/src/libcf/cf_find_spectra.c
<BR>v3.0/src/libcf/cf_grating_motion.c
<BR>v3.0/src/libcf/cf_identify_channel.c
<BR>v3.0/src/libcf/cf_init_support.c
<BR>v3.0/src/libcf/cf_make_mask.c
<BR>v3.0/src/libcf/cf_mirror_motion.c
<BR>v3.0/src/libcf/cf_modify_hist_times.c
<BR>v3.0/src/libcf/cf_optimal_extraction.c
<BR>v3.0/src/libcf/cf_proc_check.c
<BR>v3.0/src/libcf/cf_rebin_background.c
<BR>v3.0/src/libcf/cf_satellite_jitter.c
<BR>v3.0/src/libcf/cf_screen_burst.c
<BR>v3.0/src/libcf/cf_screen_high_voltage.c
<BR>v3.0/src/libcf/cf_screen_limb_angle.c
<BR>v3.0/src/libcf/cf_set_photon_flags.c
<BR>v3.0/src/libcf/cf_thermal_distort.c
<BR>v3.0/src/libcf/cf_ttag_bkgd.c
<BR>v3.0/src/libcf/cf_write_extracted_spectrum.c
<BR>v3.0/src/libcf/eclipse.c
<BR>v3.0/src/libcf/solar_ang.c
<BR>v3.0/src/libcf/space_vel.c
<BR>v3.0/src/libcf/state_geod.c
<BR>v3.0/src/libcf/state_limb.c
<BR>v3.0/include/calfuse.h v1.64
<P>
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.
<P>
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.
<P>
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.
<P>
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.
<P>
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.
<P>
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.
<P>
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.)
<P>
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.
<P>
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.
<P>
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.
<P>
In cf_astigmatism_and_dispersion, must change ASTG_COR to COMPLETE or
SKIPPED by hand, as the pipeline won't do it automatically.
<P>
Changes to bad-pixel routines: Fixed bug in cf_make_mask, changing & to &&.
<P>
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.
<P>
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.
<P>
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.
<P>
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.
<P>
This is the release version 3.0.7 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>June 4, 2004
<br>Van Dixon
<BR>v2.4/src/fuv/cf_fuv_init.c
<BR>v2.4/include/calfuse.h v1.175
<P>
Modified cf_fuv_init to allow for the possibility that the MJD for a
calibration file equals EXPSTART for an exposure.
<P>
This is version 2.4.4 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>May 13, 2004
<br>Van Dixon
<BR>v2.4/src/fuv/cf_update_qual.c
<BR>v2.4/src/fuv/cf_dtcor.c
<BR>v2.4/include/calfuse.h v1.174
<P>
Modified cf_update_qual and cf_dtcor to deal gracefully with bad
counters in the data file headers.
<P>
This is version 2.4.3 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>May 4, 2004
<br>Van Dixon
<BR>v3.0/src/fuv/cf_assign_wavelength.c
<BR>v3.0/src/fuv/cf_countmap.c
<BR>v3.0/src/fuv/cf_extract_spectra.c
<BR>v3.0/src/fuv/cf_gainmap.c
<BR>v3.0/src/fuv/cf_hist_init.c
<BR>v3.0/src/fuv/cf_remove_motions.c
<BR>v3.0/src/fuv/cf_ttag_init.c
<BR>v3.0/src/libcf/cf_apply_dead_time.c
<BR>v3.0/src/libcf/cf_calculate_y_centroid.c
<BR>v3.0/src/libcf/cf_convert_to_ergs.c
<BR>v3.0/src/libcf/cf_doppler_and_heliocentric.c.c
<BR>v3.0/src/libcf/cf_error_msg.c
<BR>v3.0/src/libcf/cf_find_spectra.c
<BR>v3.0/src/libcf/cf_fuv_init.c
<BR>v3.0/src/libcf/cf_init_support.c
<BR>v3.0/src/libcf/cf_rebin_background.c
<BR>v3.0/src/libcf/cf_set_good_time_intervals.c
<BR>v3.0/src/libcf/cf_set_photon_flags.c
<BR>v3.0/src/libcf/cf_set_user_gtis.c
<BR>v3.0/src/libcf/cf_source_aper.c
<BR>v3.0/src/libcf/cf_ttag_bkgd.c
<BR>v3.0/src/libcf/cf_write_extracted_spectrum.c
<BR>v3.0/include/calfuse.h v1.61, v1.62, v1.63
<P>
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.
<P>
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.
<P>
In verbose mode, cf_convert_to_ergs prints out the relative weighting of
the two effective-area files.
<P>
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.
<P>
The keywords MKBK_COR and BKGD_COR are gone, so cf_fuv_init no longer
populates them.
<P>
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.
<P>
This is version 3.0.7 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>April 5, 2004
<br>Van Dixon
<BR>v3.0/src/libcf/cf_geometric_distort.c
<BR>v3.0/include/calfuse.h v1.60
<P>
Rescale SPECBINY only if it is > 1.
<P>
<hr WIDTH="100%">
<p>April 1,2004
<br>Van Dixon
<BR>v3.0/src/fuv/cf_extract_spectra.c
<BR>v3.0/src/libcf/cf_geometric_distort.c
<BR>v3.0/src/libcf/cf_hist_init.c
<BR>v3.0/src/libcf/cf_init_support.c
<BR>v3.0/src/libcf/cf_optimal_extraction.c
<BR>v3.0/src/libcf/cf_proc_check.c
<BR>v3.0/src/libcf/cf_rebin_probability_array.c
<BR>v3.0/src/libcf/cf_ttag_bkgd.c
<BR>v3.0/src/libcf/cf_write_extracted_spectrum.c
<BR>v3.0/include/calfuse.h v1.59
<P>
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.
<p>
In cf_proc_check, call cf_verbose rather than cf_if_warning if program
not appropriate for HIST data.
<p>
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.
<p>
Include math.h in cf_hist_init to define fmod(). This solves the
long-standing problem of the program crashing on Linux machines.
<p>
Modify cf_init_support to better deal with counter errors.
<p>
In cf_geometric_distort, modify header keyword SPECBINY to reflect
Y spacing in the FARF.
<p>
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.
<p>
In cf_rebin_probability_array, shift probability array to account
for position of FPA.
<P>
This is version 3.0.6 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>March 30, 2004
<br>Van Dixon
<BR>v2.4/src/fuv/cf_hist_init.c
<BR>v2.4/include/calfuse.h v1.173
<P>
Modified cf_hist_init to produce
null-valued data file if NEVENTS=0.
<P>
This is version 2.4.2 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>March 16,2004
<br>Van Dixon
<BR>v3.0/src/fuv/cf_extract_spectra.c
<BR>v3.0/src/fuv/cf_hist_init.c
<BR>v3.0/src/fuv/cf_ttag_init.c
<BR>v3.0/src/fuv/cf_bad_pixels.c
<BR>v3.0/src/fuv/cf_countmap.c
<BR>v3.0/src/fuv/cf_gainmap.c
<BR>v3.0/src/fuv/cf_convert_to_farf.c
<BR>v3.0/src/libcf/cf_astigmatism_and_dispersion.c
<BR>v3.0/src/libcf/cf_init_support.c
<BR>v3.0/src/libcf/cf_satellite_jitter.c
<BR>v3.0/src/libcf/cf_thermal_distort.c
<BR>v3.0/src/libcf/cf_write_extracted_spectrum.c
<BR>v3.0/include/calfuse.h v1.57, v1.58
<P>
Implement WPC array in cf_extract_spectra and associated subroutines.
<br>In cf_hist_init.c, fix error in correcting hot pixels.
<br>In cf_ttag_init.c, exit if no photons in raw data file.
<br>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.
<br>In cf_countmap.c and cf_gainmap.c, allow user to select coordinate
system: RAW, FARF (default), final.
<br>In cf_astigmatism_and_dispersion.c, make subroutine cf_x2lambda globally
accessible.
<br>In cf_convert_to_farf.c, pass weight array to cf_thermal_distort.
<br>In cf_init_support.c, read begin and end counters as float.
Set countrate to zero when cntb is more than 16777216.
<br>In cf_satellite_jitter.c, polulate the PLATESC keyword in the input file header.
<br>In cf_thermal_distort.c, added weights to the calculation (needed for
histogram mode) and corrected bug in procedure for finding stim pulses.
<br>In cf_write_extracted_spectrum.c, populate archive search keywords and
change name of POTHOLE column to QUALITY.
<P>
This is version 3.0.5 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>February 16, 2004
<br>Van Dixon
<BR>v3.0/include/calfuse.h v1.56
<P>
Release CalFUSE v3.0.4 for beta testing.
<P>
<hr WIDTH="100%">
<p>May 22, 2003
<br>Van Dixon
<BR>v2.4/src/idl/cf_plot_rate.pro
<BR>v2.4/src/fuv/fcal.c
<BR>v2.4/src/fuv/cf_make_ttag_bkgd.c
<BR>v2.4/include/calfuse.h v1.172
<P>
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.
<P>
This is version 2.4.1 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>May 19, 2003
<br>Van Dixon
<BR>v2.4/src/analysis/cf_combine.c
<BR>v2.4/include/calfuse.h v1.171
<P>
Imported two of Jeff's modifications to cf_combine:
<br>
Close each input file in initial loop.
Without this, cfitsio crashes upon opening the 60th file.
<br>
Weight each pixel by exposure time after excluding ``bad'' pixels.
<P>
<hr WIDTH="100%">
<p>May 2, 2003
<br>Van Dixon
<BR>v2.4/src/analysis/cf_uninterp.c
<BR>v2.4/include/calfuse.h v1.170
<P>
Added cf_uninterp.c to re-calibrate extracted spectra using only
the most recent flux-calibration file.
<P>
This is version 2.4.0 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>April 29, 2003
<br>Van Dixon
<BR>v2.3/src/fuv/cf_ttag_jitter.c
<BR>v2.3/src/fuv/cf_hist_jitter.c
<BR>v2.3/include/calfuse.h v1.169
<P>
Modified jitter routines to allow possiblity that jitter filename is in
lower-case letters.
<P>
<hr WIDTH="100%">
<p>April 25, 2003
<br>Van Dixon
<BR>v2.3/src/fuv/cf_fuv_init.c
<BR>v2.3/include/calfuse.h v1.167, v1.168
<P>
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.
<P>
This is version 2.3.2 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>April 16, 2003
<br>Van Dixon
<BR>v2.3/src/fuv/cf_fuv_init.c
<BR>v2.3/include/calfuse.h v1.166
<P>
In cf_fuv_init, test for corrupted detector bias values. Updated
comment field of HV_FLAG. Modified associated warning messages.
<P>
This is version 2.3.1 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>April 15, 2003
<br>Van Dixon
<BR>v2.3/src/fuv/cf_ttag_screen.c
<BR>v2.3/include/calfuse.h v1.165, v1.166
<P>
Test only first letter of scrn*.fit keyword DAYNIGHT in cf_ttag_screen.
<P>
<hr WIDTH="100%">
<p>April 2, 2003
<br>Van Dixon
<BR>v2.3/src/fuv/cf_ttag_geodopp.c
<BR>v2.3/src/fuv/cf_ttag_jitter.c
<BR>v2.3/include/calfuse.h v1.164
<P>
Simplified DX/DY test in cf_ttag_geodopp. Test that TRKFLG is <= 5
(the highest allowed value) in cf_ttag_jitter.
<P>
<hr WIDTH="100%">
<p>April 2, 2003
<br>Van Dixon
<BR>v2.3/src/fuv/cf_ttag_geodopp.c
<BR>v2.3/include/calfuse.h v1.163
<P>
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.
<P>
<hr WIDTH="100%">
<p>March 10, 2003
<br>Van Dixon
<BR>v2.3/src/fuv/cf_ttag_geodopp.c
<BR>v2.3/include/calfuse.h v1.162
<P>
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.
<P>
This is version 2.3.0 of the CalFUSE pipeline.
<P>
<hr WIDTH="100%">
<p>February 24, 2003
<br>Van Dixon
<BR>v2.2/src/fuv/cf_make_ttag_bkgd.c
<BR>v2.2/src/fuv/cf_make_hist_bkgd.c
<BR>v2.2/include/calfuse.h v1.161
<P>
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.
<P>
<font color=red>This is the release version of CalFUSE v2.2.3.</font>
<P>
<hr WIDTH="100%">
<p>February 20, 2003
<br>Van Dixon
<BR>v2.2/src/libcf/read_tle.c
<BR>v2.2/src/libcf/sgp4.c
<BR>v2.2/src/fuv/cf_ttag_jitter.c
<BR>v2.2/src/fuv/cf_make_ttag_bkgd.c
<BR>v2.2/src/fuv/cf_extract.c
<BR>v2.2/src/fuv/cf_driftcorr2.c
<BR>v2.2/src/fuv/cf_coadd.c
<BR>v2.2/src/analysis/ttag_combine.c
<BR>v2.2/include/calfuse.h v1.160
<P>
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:
<br>
FITS_read_key(fptr, TSTRING, "INSTRUME", &instrument, comment, &status);
<br>
and a few routines used abs() when fabs() is required.
<P>
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.
<P>
<hr WIDTH="100%">
<p>December 13, 2002
<br>Van Dixon
<BR>v2.2/src/fuv/cf_ttag_screen.c
<BR>v2.2/src/fuv/cf_hist_screen.c
<BR>v2.2/src/fuv/cf_ttag_burst.c
<BR>v2.2/src/fuv/cf_ttag_jitter.c
<BR>v2.2/include/calfuse.h v1.159
<P>
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.
<P>
Updated CALFUSE version to 2.2.3.
<P>
<hr WIDTH="100%">
<p>November 8, 2002
<br>Van Dixon
<BR>v2.2/src/fuv/cf_extract.c
<BR>v2.2/include/calfuse.h v1.158
<P>
Modify cf_extract to write keyword SPECYCNT to outfits, not infits.
<P>
<hr WIDTH="100%">
<p>November 6, 2002
<br>Van Dixon
<BR>v2.2/src/fuv/cf_hist_jitter.c
<BR>v2.2/src/fuv/cf_ttag_jitter.c
<BR>v2.2/include/calfuse.h v1.157
<P>
Make cf_hist_jitter and cf_ttag_jitter issue warning, but continue
running, if keyword JIT_STAT is not found.
<P>
<hr WIDTH="100%">
<p>November 1, 2002
<br>Van Dixon
<BR>v2.2/src/fuv/cf_hist_jitter.c
<BR>v2.2/idl/cf_plot_hist_rate.pro
<BR>v2.2/include/calfuse.h v1.156
<P>
Make cf_hist_jitter and cf_plot_hist_rate exit gracefully if jitter
file not found.
<P>
<hr WIDTH="100%">
<p>October 29, 2002
<br>Van Dixon
<BR>v2.2/src/analysis/cf_arith.c
<BR>v2.2/src/analysis/cf_combine.c
<BR>v2.2/include/calfuse.h v1.155
<P>
Corrected error in history lines of both routines.
<P>
<hr WIDTH="100%">
<p>October 24, 2002
<br>Van Dixon
<BR>v2.2/src/fuv/Makefile
<BR>v2.2/src/fuv/cf_make_hist_bkgd.c
<BR>v2.2/include/calfuse.h v1.154
<P>
Add cf_hist_jitter to Makefiles.
Remove unused variables in cf_make_ttag_bkgd.
<P>
<hr WIDTH="100%">
<p>October 11, 2002
<br>Van Dixon
<BR>v2.2/src/fuv/cf_ttag_jitter.c
<BR>v2.2/include/calfuse.h v1.153
<P>
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.
<P>
Updated CALFUSE version to 2.2.2.
<P>
<hr WIDTH="100%">
<p>August 29, 2002
<br>Van Dixon
<BR>v2.2/src/fuv/cf_hist_init.c
<BR>v2.2/src/fuv/cf_ttag_init.c
<BR>v2.2/include/calfuse.h v1.152
<P>
The initialization routines now exit with an error if NEVENTS = 0.
<P>
<hr WIDTH="100%">
<p>August 28, 2002
<br>Van Dixon
<BR>v2.2/src/fuv/cf_hist_jitter.c
<BR>v2.2/src/libcf/cf_fcal.c
<BR>v2.2/idl/cf_plot_hist_rate.pro
<BR>v2.2/include/calfuse.h v1.151
<P>
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.
<P>
Updated CALFUSE version to 2.2.1.
<P>
<hr WIDTH="100%">
<p>July 31, 2002
<br>Van Dixon
<BR>v2.2/src/fuv/cf_hist_count_map.c
<BR>v2.2/src/fuv/cf_ttag_count_map.c
<BR>v2.2/src/fuv/cf_ttag_gain_map.c
<BR>v2.2/src/fuv/cf_make_ttag_bkgd.c
<BR>v2.2/src/fuv/cf_ttag_jitter.c
<BR>v2.2/src/fuv/cf_update_qual.c
<BR>v2.2/src/libcf/cf_fuv_init.c
<BR>v2.2/include/calfuse.h v1.150
<P>
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
<P>
Modify cf_hist_count_map, cf_ttag_count_map, cf_ttag_gain_map, and
cf_update_qual to read version 002 YSTR files.
<BR>
Correct a Linux bug in cf_make_ttag_bkgd.
<BR>
Add cf_ttag_jitter and modify cf_fuv_init to support it.
<P>
Updated CALFUSE version to 2.2.0.
<P>
<font color=red>This version of CalFUSE will go behind the firewall on
1 August 2002.</font>
<P>
<hr WIDTH="100%">
<p>June 14, 2002
<br>Van Dixon
<BR>v2.1/src/fuv/cf_make_ttag_bkgd.c
<BR>v2.1/include/calfuse.h v1.149
<p>
Moved v1.16 of cf_make_ttag_bkgd back to CalFUSE v2.1.
<P>
Updated CALFUSE version to 2.1.7.
<hr WIDTH="100%">
<p>June 14, 2002
<br>Van Dixon
<BR>cf_make_ttag_bkgd.c
<BR>cf_undistort.c
<BR>cf_driftcorr.c
<BR>cf_extract.c
<BR>cf_dpix.c
<BR>cf_ttag_screen.c
<BR>cf_hist_dopp.c
<BR>cf_wcal.c
<BR>cf_doppler_util.c
<BR>calfuse.h v1.151
<br>
<p>
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.
<P>
Updated CALFUSE version to 3.0.1.
<hr WIDTH="100%">
<p>May 30, 2002
<br>Van Dixon
<BR>cf_doppler_util.c
<BR>cf_ttag_screen.c
<BR>cf_hist_dopp.c
<BR>cf_dpix.c
<BR>cf_extract.c
<BR>calfuse.h v1.150
<br>
<p>
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.
<hr WIDTH="100%">
<p>May 29, 2002
<br>Van Dixon
<BR>cf_doppler_util.c
<BR>cf_driftcorr.c
<BR>cf_update_qual.c
<BR>calfuse.h v1.149
<br>
<p>
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.
<hr WIDTH="100%">
<p>May 21, 2002
<br>Van Dixon
<BR>cf_dpix
<BR>calfuse.h v1.148
<br>
<p>
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.
<p>
Made this change to both v2.1 and v3.0.
<hr WIDTH="100%">
<p>May 17, 2002
<br>Van Dixon
<BR>cf_dtcorr
<BR>cf_undistort
<BR>cf_wcal
<BR>calfuse.h v1.147
<br>
<p>
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.
<p>
Updated CALFUSE version to 3.0.0.
<hr WIDTH="100%">
<p>May 14, 2002
<br>Van Dixon
<BR>cf_make_ttag_bkgd
<BR>cf_make_hist_bkgd
<BR>calfuse.h v1.146
<br>
<p>
Teach background modules to read compressed background-calibration files.
<P>
<font color=red>This is the release version of CalFUSE v2.1.</font>
<hr WIDTH="100%">
<p>April 16, 2002
<br>Van Dixon
<BR>cal_fuse_exp_ttag.csh
<BR>cal_fuse_exp_hist.csh
<BR>calfuse.h v1.145
<br>
<p>
Remove cf_wormcorr from pipeline for now.
<P>
Updated CALFUSE version to 2.1.6.
<hr WIDTH="100%">
<p>April 8, 2002
<br>Van Dixon
<BR>cf_make_hist_bkgd
<BR>cf_make_ttag_bkgd
<BR>cf_ttag_burst
<BR>bchr*001.fit
<BR>scrn*013.fit
<BR>calfuse.h v1.144
<br>
<p>
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.
<P>
Updated CALFUSE version to 2.1.5.
<hr WIDTH="100%">
<p>March 29, 2002
<br>Van Dixon
<BR>cf_make_ttag_bkgd
<BR>cf_ttag_burst
<BR>bkgd*005.fit
<BR>bkgd*006.fit
<BR>bkgd*007.fit
<BR>bkgd*008.fit
<BR>scrn*012.fit
<BR>calfuse.h v1.143
<br>
<p>
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.
<P>
Updated CALFUSE version to 2.1.4.
<hr WIDTH="100%">
<p>March 17, 2002
<br>Van Dixon
<BR>cf_make_ttag_bkgd
<BR>cf_make_hist_bkgd
<BR>cf_ttag_geodopp
<BR>cf_hist_geodopp
<BR>calfuse.h v1.142
<br>
<p>
Turns out that all of these programs were treating the error arrays as
sigmas rather than variances (sigma squared). Modified to propagate
errors correctly.
<P>
Updated CALFUSE version to 2.1.3.
<hr WIDTH="100%">
<p>February 22, 2002
<br>Van Dixon
<BR>cf_fuv_init
<BR>ttag_combine
<BR>cf_dtcor
<BR>calfuse.h v1.141
<br>
<p>
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.
<p>
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.
<P>
Updated CALFUSE version to 2.1.2.
<hr WIDTH="100%">
<p>February 15, 2002
<br>Van Dixon
<BR>calfuse.h v1.140
<br>
<p>
Changed OPUS_VERSION to 2.5.
<hr WIDTH="100%">
<p>February 13, 2002
<br>Van Dixon
<BR>cf_fuv_init
<BR>ttag_combine
<BR>calfuse.h v1.139
<br>
<p>
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.
<p>
Modified ttag_combine to respond gracefully if EXPNIGHT does not exist.
<hr WIDTH="100%">
<p>February 12, 2002
<br>Van Dixon
<BR>cf_fuv_init
<BR>calfuse.h v1.138
<br>
<p>
Modified cf_fuv_init to check detector voltage and complain if low.
New volt***001.fit calibration files, VOLT_CAL keyword.
<P>
Updated CALFUSE version to 2.1.1.
<hr WIDTH="100%">
<p>January 25, 2002
<br>Van Dixon
<BR>cf_ttag_burst
<BR>calfuse.h v1.137
<br>
<p>
Modified cf_ttag_burst to write a list of bursts to an ASCII file.
<hr WIDTH="100%">
<p>January 15, 2002
<br>Van Dixon
<BR>ttag_combine
<BR>calfuse.h v1.136
<br>
<p>
Modified ttag_combine to update keyword EXPNIGHT in output file.
<hr WIDTH="100%">
<p>December 7, 2001
<br>Van Dixon
<BR>cf_update_qual
<BR>calfuse.h v1.135
<br>
<p>
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.
<hr WIDTH="100%">
<p>November 30, 2001
<br>Van Dixon
<BR>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
<BR>calfuse.h v1.134
<br>
<p>
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.
<p>
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.
<p>
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.
<p> 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.
<hr WIDTH="100%">
<p>November 27, 2001
<br>Van Dixon
<BR>cf_ttag_screen
<BR>calfuse.h v1.133
<br>
<p>
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 <tt>scrn*.fit</tt> files, if desired.
<hr WIDTH="100%">
<p>November 21, 2001
<br>Van Dixon
<BR>cf_update_qual
<BR>calfuse.h v1.132
<br>
<p>
Installed Rich's new QUAL files. Modified cf_update_qual to read them.
<hr WIDTH="100%">
<p>November 16, 2001
<br>Van Dixon
<BR>calfuse.h v1.131
<br>
<p>
Defined NO_PIXEL in calfuse.h. Used by geometric-distortion and
extraction routines.
<hr WIDTH="100%">
<p>October 26, 2001
<br>Van Dixon
<BR>cf_dtcor
<BR>calfuse.h v1.130
<br>
<p>
Modified cf_dtcor to set counters to zero if values are too large to
read as longs.
<hr WIDTH="100%">
<p>October 26, 2001
<br>Van Dixon
<BR>cf_fuv_init
<BR>calfuse.h v1.129
<br>
<p>
Modified cf_fuv_init to check header keyword OPUSVERS and complain if
the data file was processed using an old version of OPUS.
<hr WIDTH="100%">
<p>October 10, 2001
<br>Van Dixon
<BR>cf_ttag_init
<BR>calfuse.h v1.128
<br>
<p>
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.
<p>
Added keyword OPUS_VERSION to calfuse.h
<p>
Updated CALFUSE version to 2.1.0.
<hr WIDTH="100%">
<p>October 10, 2001
<br>Van Dixon
<BR>ttag_combine
<BR>flux*008.fit
<BR>calfuse.h v1.127
<br>
<p>
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.
<p>
Jeff Kruk has produced new flux-calibration files
based on the latest wavelength calibration.
<p>
Updated CALFUSE version to 2.0.5.
<font color=red>This is the release version of CalFUSE v2.0.</font>
<hr WIDTH="100%">
<p>October 2, 2001
<br>Van Dixon
<BR>wave*014.fit
<br>
<p>
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:
<pre>
xx = ((x-leftF)/(rightF-leftF))*(right1-left1)+left1
xcor = ((xx-left2)/(right2-left2))*(rightF-leftF)+leftF
where:
left1,right1 are the measured STIM positions when the walk correction
was applied to the STIMs
left2,right2 are the measured STIM positions when the walk correction
was not applied to the STIMs
leftF, rightF - are the FARF STIM positions
x - is the measured x position in the spectra that had the walk
correction applied to the STIMs
xcor is the corrected x position that would be expected if the walk
correction was not applied to the STIMs
</pre>
<hr WIDTH="100%">
<p>September 21, 2001
<br>Van Dixon
<BR>scrn*010.fit
<br>
<p>
Version 008 had new PHA limits. Version 009 had new information for
background models. Version 010 has both.
<hr WIDTH="100%">
<p>September 17, 2001
<br>Van Dixon
<br>calfuse.h 1.126
<BR>cf_make_ttag_bkgd
<br>
<p>
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.
<P>
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.
<P>
Updated CALFUSE version to 2.0.4.
<hr WIDTH="100%">
<p>September 11, 2001
<br>Van Dixon
<br>calfuse.h 1.125
<BR>cf_ttag_walk
<BR>cf_hist_walk
<br>
<p>
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.
<hr WIDTH="100%">
<p>September 5, 2001
<br>Van Dixon
<br>calfuse.h 1.124
<BR>cf_make_ttag_bkgd
<BR>cf_extract
<br>
<p>
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.
<hr WIDTH="100%">
<p>August 30, 2001
<br>Van Dixon
<br>calfuse.h 1.123
<BR>cf_make_ttag_bkgd
<br>
<p>
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.
<P>
New wavelength calibration files. Updated CALFUSE version to 2.0.3.
<hr WIDTH="100%">
<p>August 23, 2001
<br>Van Dixon
<br>calfuse.h 1.122
<br>cf_fuv_init
<br>cf_ttag_burst
<br>cf_ttag_walk
<br>cf_hist_walk
<br>cf_astig
<BR>cf_make_hist_bkgd
<BR>cf_make_ttag_bkgd
<BR>cf_bkgd
<br>
<p>
Replaced keyword TBURST with EXP_BRST in cf_ttag_burst.
<p>
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.
<hr WIDTH="100%">
<p>August 21, 2001
<br>Van Dixon
<br>calfuse.h 1.121
<br>cf_wcal
<br>cf_fpa_pos
<br>cf_ttag_init
<br>
<p>
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.
<hr WIDTH="100%">
<p>August 20, 2001
<br>Van Dixon
<br>calfuse.h 1.120
<br>cf_ttag_init
<br>cf_dtcor
<br>
<p>
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.
<hr WIDTH="100%">
<p>July 25, 2001
<br>Van Dixon
<br>calfuse.h 1.119
<br>cf_astig.c
<br>
<p>
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.
<br><font color=red>This is the beta-test version of CalFUSE v2.0.</font>
<hr WIDTH="100%">
<p>July 2, 2001
<br>Van Dixon
<br>calfuse.h 1.118
<br>cf_ttag_init.c
<br>cf_ttag_screen.c
<br>cf_ttag_burst.c
<br>cf_make_ttag_bkgd.c
<br>cf_make_hist_bkgd.c
<br>
<p>
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.
<hr WIDTH="100%">
<p>June 29, 2001
<br>Van Dixon
<br>calfuse.h 1.114
<br>lsrd_vel.c
<br>lsrk_vel.c
<br>
<p>
Changed sign returned by the LSR correction subroutines to conform with
astronomical standard. Updated CALFUSE version to 1.9.9
<hr WIDTH="100%">
<p>June 19, 2001
<br>Jeff Kruk
<br>helio_vel.c
<p>
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.
<hr WIDTH="100%">
<p>April 10, 2001
<br>Van Dixon
<br>calfuse.h 1.111
<br>cf_hist_walk.c 1.1
<br>cal_fuse_exp_hist.csh
<br>
<p>
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
<hr WIDTH="100%">
<p>April 2, 2001
<br>Van Dixon
<br>calfuse.h 1.110
<br>cf_ttag_walk.c 1.1
<br>cal_fuse_exp_ttag.csh
<br>cal_fuse_exp_hist.csh
<br>
<p>
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
<hr WIDTH="100%">
<p>March 28, 2001
<br>Van Dixon
<br>calfuse.h 1.109
<br>cf_extract.c 1.52
<br>cal_fuse_exp_ttag.csh
<br>cal_fuse_exp_hist.csh
<br>
<p>
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
<hr WIDTH="100%">
<p>March 27, 2001
<br>Van Dixon
<br>calfuse.h 1.108
<br>cf_make_bkgd.c 1.22
<br>cal_fuse_exp_ttag.csh
<br>cal_fuse_exp_hist.csh
<br>
<p>
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
<hr>
<p>March 19, 2001
<br>Van Dixon
<br>calfuse.h 1.107
<br>cf_ttag_burst.c 1.9
<br>cal_fuse_exp_ttag.csh
<br>cal_fuse_exp_hist.csh
<br>
<p>
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
<hr>
<p>March 14, 2001
<br>Van Dixon
<br>calfuse.h 1.106
<br>cf_astig.c 1.8
<br>cal_fuse_exp_ttag.csh
<br>cal_fuse_exp_hist.csh
<br>
<p>
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
<hr>
<p>February 9, 2001
<br>Jeff Kruk
<br>calfuse.h 1.105
<br>cf_ttag_screen.c 1.55
<br>
<p>
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
<hr>
<p>February 8, 2001
<br>J.C. Hsu
<br>calfuse.h 1.104
<br>cf_linear.c 1.0
<br>cf_transform1d.c 1.0
<br>cf_1dff.c 1.0
<br>cf_make_1dff.c 1.0
<br>
<p>
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.
<hr>
<p>December 21, 2000
<br>Paul Barrett, J.C. Hsu
<br>Makefile.Alpha
<br>cf_ttag_screen.c 1.54
<br>cf_ttag_image.c 1.22
<br>cf_ttag_init.c 1.16
<br>cf_wcal.c 1.25
<br>
<p>
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.
<hr>
<p>November 15, 2000
<br>Jeff Kruk
<br>cf_make_ff_temp.c 1.6
<br>cf_make_bkgd_temp.c 1.6
<br>cf_ttag_screen.c 1.53
<br>
<p>
Fixed typos in print statements in several routines.
No change in functionality resulted, so the pipeline version number
was not incremented.
<hr>
<p>October 19, 2000
<br>Jeff Kruk
<br>CALFUSE 1.9.1
<br>calfuse.h 1.103
<br>
<p>
Created CALFUSE version 1.9.1 as the new development version.
calfuse.h was updated to reflect the new version number.
<hr>
<p>October 18, 2000
<br>Martial Andre, Jeff Kruk
<br>cf_extract.c 1.47
<br>calfuse.h 1.102
<br>
<p>
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.
<p>
Changed CALFUSE version to 1.8.7.
<hr>
<p>October 13, 2000
<br>Jeff Kruk
<br>cf_ttag_screen.c 1.52
<br>cf_extract.c 1.46
<br>cf_fuv_init.c 1.9
<br>
<p>
Three calls to FITS_read_key (infits, TSTRING, keyword, &arrayname,...) in the
program cf_ttag_screen were modified to remove the extraneous ampersand.
<p>
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.
<p>
CF_VER_NUM was brought up to date in cf_fuv_init.c
<P>These changes are too small to update the version number of the pipeline.
<hr>
<p>October 2, 2000
<br>Jeff Kruk, JC Hsu
<br>cf_hist_dopp 1.25
<br>calfuse.h 1.101
<br>cal_fuse_exp_ttag.csh
<br>cal_fuse_exp_hist.csh
<br>
<p>
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.
<p>
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.
<p>
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.
<p>
The shell scripts cal_fuse_exp_ttag.csh and cal_fuse_exp_hist.csh were
modified to test cfstat before calling the idlplot routines.
<P>The pipeline version number was incremented to 1.8.6.
<hr>
<p>October 2, 2000
<br>Jeff Kruk
<br>cf_check_point 1.17
<br>cf_hist_screen 1.21
<br>cf_ttag_screen 1.51
<br>
<p>
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.
<p>
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.
<P>The pipeline version number was updated for an additional change made
later in the day.
<hr>
<p>October 2, 2000
<br>Jeff Kruk, JC Hsu
<br>lif_sic_border() 1.00
<br>
<p>
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.
<P>No change in functionality resulted, so no update to the pipeline
version number was made.
<hr>
<p>October 2, 2000
<br>Jeff Kruk
<br>state_limb 1.08
<br>
<p>
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).
<P>This change was solely for running Make on the distribution version
of calfuse, so no update to the pipeline version number was made.
<hr>
<p>September 26, 2000
<br>Martial Andre
<br>state_limb 1.05, 1.06, 1.07
<br>cf_check_point 1.16
<br>cf_orbit 1.03
<br>calfuse.h 1.98, 1.99, 1.100
<br>
<p>
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.
<p>
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.
<p>
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.
<P>These changes led to the increase in pipeline version number to 1.8.5
(implemented by version 1.100 of calfuse.h).
<hr>
<p>September 18, 2000
<br>Ed Murphy
<br>Pipeline Distribution Version
<br>
<p>
Ed Murphy & Paul Barrett produce distribution version of pipeline.
Major change was to incorporate "makemake" files.
<P>Update the version number of the pipeline to v1.8.4.
<hr>
<p>September 18, 2000
<br>Ed Murphy
<br>cf_astig2 1.07
<br>
<p>
Ed made some change, not documented in the header.
<P>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.
<hr>
<p>September 6, 2000
<br>Jeff Kruk
<br>cf_dtcor 1.18
<br>
<p>
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.
<P>These changes are too small to update the version number of the pipeline.
<hr>
<p>September 5, 2000
<br>Ed Murphy
<br>cf_astig2 1.06
<br>
<p>
Modify cf_astig2 to get the calibration file from the ASTG_CAL keyword
rather than being hardcoded.
<P>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.
<hr>
<p>August 25, 2000
<br>Ed Murphy
<br>cf_astig2 1.05
<br>
<p>
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.
<P>I also added the ability for the routine to check the number
of arguments.
<P>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.
<hr>
<p>August 23, 2000
<br>Martial Andre
<br>cf_extract 1.44
<br>
<p>
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.
<P>
<hr>
<p>August 18, 2000
<br>Ed Murphy
<br>cf_update_qual 1.03
<br>
<p>
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.
<P>
<hr>
<p>August 14, 2000
<br>Martial
<br>cf_extract 1.43
<br>
<p>
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!!!)
<P>
<hr>
<p>August 13, 2000
<br>Martial
<br>cf_coadd 1.17
<br>
<p>
Propagation of quality should have been done with float since the very beginning (now fixed).
<P>
<hr>
<p>August 9, 2000
<br>Martial
<br>cf_extract 1.42
<br>
<p>
Added a define statement to use sunmath only ifdef SOLARIS.
<P>
<hr>
<p>July 26, 2000
<br>J. C. Hsu, R. Robinson, Ed Murphy
<br>cf_update_qual v1.02
<br>cf_driftcorr2 v1.23
<p>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.
<p>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.
<P>
Ed Murphy created V1.8.3.
<hr>
<p>July 21, 2000
<br>Martial
<br>cf_extract 1.41
<br>
<p>
Fixed bug of implementation of a pointer in im_centroid wich caused a bus error.
<P>
<hr>
<p>June 27, 2000
<br>Jeff Kruk
<br>cf_dtcor v1.17
<p>Jeff Kruk added an IDS dead time correction to the dead time correction
routine cf_dtcor.c.
<P>
Ed Murphy created V1.8.2 and V1.7.8.
<hr>
<p>June 26, 2000
<br>Martial
<br>cf_coadd v1.15
<p>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.
<hr>
<p>June 20, 2000
<br>Ed Murphy
<br>cf_ttag_screen 1.49, cf_hist_dopp v1.23
<br>PR 41926
<br>
<p>
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.
<P>
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.
<P>
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.
<P>
Ed Murphy created V1.8.1 and V1.7.7.
<hr>
<p>June 13, 2000
<br>Martial
<br>cf_extract 1.40
<br>
<br>
<p>
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.
<hr>
<p>June 9, 2000
<br>Martial
<br>cf_extract 1.39
<br>
<p>
Airglow screened while computing the centroid.
<P>
<hr>
<p>June 9, 2000
<br>Martial
<br>cf_extract 1.38
<br>
<p>
Major change to calculate the centroid. Center is reached for flux maximum.
<P>
<hr>
<p>June 4, 2000
<br>Martial
<br>Version 7 of the extraction windows
<br>
<br>
<p>
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
<hr>
<p>May 24, 2000
<br>Martial
<br>cf_extract 1.37
<br>
<p>
Added a define statement for the cpp and DEC
<P>
<hr>
<br>
<hr>
<p>May 18, 2000
<br>Jeff Kruk, Ed Murphy
<br>cf_wcal 1.24
<br>
<p>
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.
<P>
Ed Murphy created V1.8.0.
<hr>
<p>May 17, 2000
<br>Jeff Kruk, Ed Murphy, Paul Barrett
<br>CALFUSE v1.7.6
<br>
<p>
Jeff Kruk has completed the new version of cf_dtcor.
<P>
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.
<P>
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.
<hr>
<p>May 12, 2000
<br>Jeff Kruk, Paul Barrett
<br>CALFUSE v1.7.5
<br>
<p>
Jeff Kruk has modified cf_wcal.c (now version 1.23) to correct the
wavelength scale for the position of the FPA.
<P>
Paul Barrett has produced new versions of the detector distortion
files: geom*005.fit in /data1/fuse/calfuse/calfiles.
<hr>
<p>April 24, 2000
<br>Ed Murphy
<br>CALFUSE v1.7.4
<br>
<p>
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:<BR>
setenv CF_IDLDIR '/data1/fuse/calfuse/current/idl/'
<P>
The plots are in GIF format so that they can, at some future time,
be linked to the SDOG pages.
<hr>
<p>April 24, 2000
<br>Ed Murphy
<br>CALFUSE v1.7.4
<br>
<p>
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
<P>
Upgrades (besides those listed in previous messages) include:
<ol>
<li> Both the code (V1.7.*) and calibration files are now in the
Flight Alignment Reference Frame. This means that the stretch and
shift has been reduced from about 120 pixels in X to less than 10
pixels in X.
<li> Improved wavelength calibration from Don Lindler.
<li> Improved flux calibration from Jeff Kruk.
<li> Improved distortion correction from Paul Barrett.
<li> The user now has the ability to scale the background by a simple
scalar value when using pulse height screening. The value to scale
the background is in the PHA_BKGD keyword in the screening parameter
file.
<li> The user now has the ability to limit the motion of the spectral
extraction windows based on the pipeline determined centroid. If the
difference between the expected and actual positions is larger than
the limit, the pipeline defaults to the expected position. The limit
is set using the EMAX_LIF and EMAX_SIC keywords in the parm**002.fit
files.
<li> The user now has the ability to ignore the pipeline determined
centroid and place the extraction windows where ever they wish using
the SPEX_SIC and SPEX_LIF keywords in the parm**002.fit files. Note
that the maximum motion limit described above still applies.
</ol>
<hr WIDTH="100%">
<p>March 24, 2000
<br>Paul Barrett
<br>CALFUSE v1.7.4
<br>PR 41000
<p>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.
<p>This modification to cf_hist_init will now allow histogram data to be
used for determining distortion corrections by providing necessary spatial
resolution.
<hr WIDTH="100%">
<p>March 7, 2000
<br>Ed Murphy
<br>CALFUSE V1.6.9 and V1.7.3
<br>PR 40864
<p STYLE="margin-bottom: 0in">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.
<br>
<hr>
<p>February 10, 2000
<br>Ed Murphy
<br>CALFUSE V1.6.8 and V1.7.2
<br>PR 40661
<p STYLE="margin-bottom: 0in">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
<p>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.
<p>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.
<p>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.
<hr>
<p>February 1, 2000
<br>Ed Murphy
<br>CALFUSE V1.6.7 and V1.7.1
<br>PR 40541
<p STYLE="margin-bottom: 0in">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.
<hr>
<p>February 1, 2000
<br>Ed Murphy
<br>CALFUSE V1.6.7 and V1.7.1
<br>PR 40544
<p STYLE="margin-bottom: 0in">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.
<hr>
<p>January 31, 2000
<br>Ed Murphy
<br>CALFUSE V1.6.7 and V1.7.1
<br>PR 40553
<p STYLE="margin-bottom: 0in">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.
<hr>
<p>January 24, 2000
<br>Martial
<br>CALFUSE V1.6 and V1.7
<p STYLE="margin-bottom: 0in">CENTROIDING PROBLEMS FIXED :
<p STYLE="margin-bottom: 0in">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 = (<font face="symbol">å</font>
Yi * nbcounts_i)/<font face="symbol">å</font>nbcounts_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
<p STYLE="margin-bottom: 0in">to choose a domain of calculation surrounding
it. At present, this first guess is the maximum peak.
<br>
<hr>
<p>January 21, 2000
<br>Martial
<br>CALFUSE V1.6 and V1.7
<p STYLE="margin-bottom: 0in">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).
<p STYLE="margin-bottom: 0in">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 ".
<br>
<table BORDER CELLSPACING=3 CELLPADDING=4 >
<caption><COL WIDTH=85><COL WIDTH=85><COL WIDTH=85><THEAD>
<br></THEAD><TBODY>
<br></TBODY></caption>
<tr VALIGN=TOP>
<th>Detector</th>
<th>Data Used</th>
<th>Notes</th>
</tr>
<tr VALIGN=TOP>
<td>1A (LiF)</td>
<td>/data2/fuse/CAL/M101/M1010201</td>
<td>Good </td>
</tr>
<tr VALIGN=TOP>
<td>1A (SiC)</td>
<td>/data2/fuse/CAL/M103/M1030303</td>
<td>Good </td>
</tr>
<tr VALIGN=TOP>
<td>1B (LiF)</td>
<td>/data2/fuse/CAL/M101/M1010201</td>
<td>Corrected by hand : mirror transformation applied</td>
</tr>
<tr VALIGN=TOP>
<td>1B (SiC)</td>
<td>/data2/fuse/CAL/M103/M1030304</td>
<td>Corrected by hand : linear regression for the narrow domain</td>
</tr>
<tr VALIGN=TOP>
<td>2A (LiF)</td>
<td>/data2/fuse/CAL/M101/M1010201</td>
<td>Good</td>
</tr>
<tr VALIGN=TOP>
<td>2A (SiC)</td>
<td>/data2/fuse/CAL/M103/M1030304</td>
<td>Good </td>
</tr>
<tr VALIGN=TOP>
<td>2B (LiF)</td>
<td>NOT AVAILABLE</td>
<td>Here I didn't find a signal strong enough ... I used the old Ground
Based Files + geometrical correction</td>
</tr>
<tr VALIGN=TOP>
<td>2B (SiC)</td>
<td>/data2/fuse/CAL/M103/M1030304</td>
<td>Ground Based Files + geometrical correction</td>
</tr>
</table>
<div STYLE="margin-bottom: 0in"></div>
<p STYLE="margin-bottom: 0in">Note also that you can change the windows
with "cf_modifwindows" wich apply an homothetic factor to the LiF channel
and the SiC channel :
<p STYLE="margin-bottom: 0in">>cf_modifwindows filename 0.8 (80% for LiF)
0.9 (90% for SiC)
<br>
<hr>
<br>
<br>
<br>
<p>January 5, 2000
<br>Ed Murphy
<br>CALFUSE V1.6 and V1.7
<p STYLE="margin-bottom: 0in">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.
<br>
<hr>
<p>January 03, 2000
<br>Paul Barrett
<br>CALFUSE V1.6.5
<p STYLE="margin-bottom: 0in">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.
<br>
<hr>
<p>December 21, 1999
<br>Ed Murphy
<br>CALFUSE V1.7.1
<p STYLE="margin-bottom: 0in">Version 1.7.1 of the pipeline is now in the
FARF frame, however, the calibration files are not.
<br>
<hr>
<p>December 21, 1999
<br>Ed Murphy
<br>CALFUSE V1.6.5
<p STYLE="margin-bottom: 0in">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.
<br>
<hr>
<p>December 21, 1999
<br>Ed Murphy
<br>CALFUSE V1.6.4
<p STYLE="margin-bottom: 0in">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.
<br>
<hr>
<p>December 17, 1999
<br>Ed Murphy
<br>CALFUSE V1.6.4
<p>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.
<p>Upgrades include:
<ol>
<div STYLE="margin-bottom: 0in">The histogram pipeline finally works. The
histogram images are, for now, expanded out to 16384x1024 in size to avoid
some of the binning problems we were encountering.</div>
<p STYLE="margin-bottom: 0in">The spectral thermal shifts are now removed
from the data using Kathy's algorithm. If you have a local copy of the
calibration files, will need to copy the new version of master_calib_file.dat
from /data1/fuse/calfuse/parmfiles and the new calibration file shft001.fit
from /data1/fuse/calfuse/calfiles.
<p STYLE="margin-bottom: 0in">In ttag data, the calculated centroid of
the target aperture is used to offset all apertures to account for movememnt
in the Y direction. In the past, each aperture was centroided and offset
independently. However, because of the overlapping spectra on side 2, the
HIRS aperture centroid often caused the HIRS extraction to contain significant
flux from the LWRS aperture.
<p>A large number of small items were taken care of (keyword updates, minor
bug fixes, etc.).</ol>
<div STYLE="margin-bottom: 0in">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).</div>
<br>
<hr>
<address><a href="mailto:emurphy@pha.jhu.edu">Ed Murphy</a></address>
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