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Version 0.1.0 - All Versions before 2020-06-01
----------------------------------------------
> Created phot2lc.py as a python replacement for
WQED. Included just the basic functionality
to work with output from Antonio Kanaan's
IRAF hsp_nd and data from McDonald Observatory.
Version 1.0.0 - 2020-06-01
--------------------------
> Created the teledat.py and photfunc.py scripts
-teledat.py stores information related to each
telescope and has a unique 4-letter code
associated with each one. This script is
similar in purpose to the file whiff.dat
for WQED.
-photfunc.py stores several functions used
within the main script below. This was
created just to help clean things up.
> Included functionality that allows phot2lc
to be used with output from both hsp_nd and
Maestro. For Maestro, only the "counts" files
can currently be used.
> Improved the formatting for the .lc and .phot
output files. The headers are now more easily
readable and contain more information. There
are also two time columns now, one for the raw
uncorrected times, and one for the barycentric
corrected times.
Version 1.1.0 - 2020-06-04
--------------------------
> Created a new function in photfunc.py, get_loc,
which gets the Astropy Earth Locations for each
telescope available in the teledat.py file
> Added LCOGT 1.0m telescopes to teledat.py with
codename 'lco1'
> Fixed bug related to object names. If object name
taken from the FITS header has any spaces in it,
those spaces will now be automatically removed,
since the object names in stars.dat cannot have
spaces.
> Removed plot that shows the size of apertures and
sky annuli around each object. Too many issues,
and not a very useful plot.
> Fixed bug in get_time function. Times were being
improperly re-formatted when DATE-OBS was already
in ISO or ISOT in the FITS header. Now, these
times are fed directly into an Astropy Time object
which can auto-interpret the format.
Version 1.2.0 - 2020-06-09
--------------------------
> Added a new command line input parameter for
providing the object name. Originally the object
name was grabbed solely from the FITS header, but
not all FITS files will have an object entry. The
object name is required, however, for grabbing the
corresping RA and Dec from the star.dat file.
Judi Provencal recommended adding a command line
option. The new command line option is -o, or
--object. By default this option is set to None,
in which case the header is used.
> Changed activation and deactivation functionality
of the Garbage and Zoom rectangle selectors.
Originally, once activated with the "g" or "z"
input keys, they would remain active until
deactivated using the same input keys. This would
lead to some confusion during use, as it was often
easy to forget one selector was activated which
then blocked activation of the other selector.
Now, each selector is automatically deactivated
after use, though it can still be manually
deactivated if, once a user activates it, they
realize they don't want to use it.
> Added a Reverse Garbage Selector which, when you
draw a box, will delete all of the points OUTSIDE
of the box rather than inside the box. This
feature can be activated and deactivated using
the "r" keyboard input.
Version 1.3.0 - 2020-06-12
--------------------------
> Added a sigma clipping function. This feature can
be used with the "x" key. User will be prompted
for their choice of lower and upper sigma
rejection thresholds. The user can also choose
the window size, i.e. how many points are
considered at a time when rejecting data points.
Smaller windows are useful when dealing with
stars that are variable on short timescales. The
default window size is 25 data points.
> Changed periodogram calculation/plot so that it
only goes out to 10,000 uHz, for easier viewing.
> Added "#!/usr/bin/env python" to script so it can
be executed on the command line without having
to invoke Python beforehand.
> Also removed .py extension on phot2lc so it looks
more like a regular executable.
> Removed version history from phot2lc script, it now
lives only in this text file.
> Cleaned up the inputs. Deleted some unused modules
and reorganized the rest. Now checks to make sure
the python version is 3.6 or later.
> Added a new configuration script, a convenience
function which new users can use to set the
defaults. This was needed in order to prevent
users from having to go into the code and manually
change hard-coded variables in order to make
phot2lc work. Now, the "photconfig" function can
be called which edits the config.dat file, which
is then loaded into phot2lc during initialization.
Version 1.3.1 to 1.3.4 - 2020-06-13
-----------------------------------
> Made phot2lc into a python package available on PyPI
> Fixed bugs so that phot2lc and photconfig work
properly once they have been pip installed
Version 1.4.0 - 2020-06-14
--------------------------
> Removed some extraneous print commands.
> Changed the light curve and photometry header
descriptions for DATE, UTC, MJD, and BJED to be
more descriptive.
> Finally got the weldlc functions working again with
the new .lc output formats. wildly can be used now
to stitch .lc files together for multi-night or
multi-site data sets.
Version 1.4.1 - 2020-06-14
--------------------------
> Small changes to the PyPI README.md file
Version 1.4.2 - 2020-06-14
--------------------------
> config.dat didn't get uploaded with the previous
version due to an error in setup.py. Fixed the
error and this version appears fully functional.
Version 1.4.3 - 2020-06-14
--------------------------
> Forgot to include the most up-to-date version of
this file (version_history.txt) with the last
one. Now it should be complete.
Version 1.4.4 - 2020-06-15
--------------------------
> A few small bug fixes.
> Fixed an indexing error related to the grid search.
The wrong index was being used to save information
into the output .phot files related to the optimal
aperture being used when using "G" to save the
final light curve. This has been fixed in this
version.
Version 1.4.5 - 2020-06-21
--------------------------
> Changed weldlc output to include both time columns
present in the original .lc files (Raw T-mid and
BaryCorr T-mid). This way, the column format does
not change between original and welded light curves.
Version 1.4.6 - 2020-06-21
--------------------------
> Fixed small bugs.
Version 1.5.0 - 2020-06-21
--------------------------
> Found and fixed a significant issue related to the
calculation of the Barycentric Julian Date (BJD) at
the start of the exposure sequence which gets saved
as the header keyword BJED in the .lc and .phot files.
The BJD should have have been referencing the very
first image, regardless of whether the first data point
got removed from the final light curve. Instead, it was
referencing the first non-deleted data point. The
barycentric corrected timestamps were shifted to
reference this time, so the timings from previous versions
won't be incorrect, but the raw timings were not shifted
to reference this time, so large discrepancies could
sometimes be seen when comparing the raw and barycorr
time columns. This has been fixed so that the BJED
keyword now always references the first image of a run,
and both time columns now reference the same BJED.
Version 1.5.1 - 2020-06-25
--------------------------
> Fixed bug related to improper exposure time format. The
"get_time" function within photfunc.py assumed that
FITS header's exposure time value was a float, but
occasionally it would be a different format. This
resulted in errors within phot2lc when doing float
arithmetic on the exposure time parameter. Now, the
get_time function will convert the exposure time to
type float upon loading it from the header.
Version 1.5.2 - 2020-06-28
--------------------------
> Fixed the command list printed with "?" to include all
available options, a few had been missing from the
"Aperture Selection" list.
> Improved the layout of the Aperture Selection Window.
- Now show significance thresholds for both the
User and Grid periodograms.
- Uses only red and white color scheme to more
clearly indicate what lines/markers/values
correspond to the Grid vs. User light curves.
- Now shows the maximum signal-noise of the highest
peak in the periodogram:
(Max S/N = Max Peak Height / Average Noise Level)
> Created a new command line tool named "quicklook"
which generates a plot of an extracted light curve
along with its periodogram and marks significant
peaks determined by a pre-whitening routine.
Version 1.5.3 - 2020-07-01
--------------------------
> Forgot to edit the setup.py file to include the new
"quicklook" tool as a script. Bug has been fixed
and quicklook is now available.
Version 1.5.4 - 2020-07-01
--------------------------
> Added more functionality to the "quicklook" tool.
- Now includes 4 command line options:
1) -f --files
Input file(s) to perform quicklook on.
2) -s --show
Whether to display the quicklook plot.
3) -p --prewhiten
Whether to perform a pre-whitening sequence.
4) -w --wqedlc
Whether the input file(s) are from WQED.
5) -h --help
Print out command line options.
Version 1.5.5 - 2020-07-01
--------------------------
> Bug in quicklook's import statements. Fixed.
Version 1.5.6 - 2020-07-02
--------------------------
> Improved layout of the periodogram plot in the
aperture selection window. The y-axis scaling
no longer pushes the significance threshold
text off the top of the plot.
Version 1.5.7 - 2020-07-02
--------------------------
> Fixed a bug in quicklook which loaded in the
incorrect date for welded phot2lc light curves.
Version 1.5.8 - 2020-07-03
--------------------------
> Fixed bug related to the calculation of an
object's declination coordinate after loading it
from the stars.dat file. Objects with negative
declinations were being improperly formatted,
where the minute and second components were being
added as positive values to the degree value
instead of being subtracted.
> Due to the above bug, if you have used phot2lc
prior to this version to calculate barycentric
corrections for objects with negative declinations,
it is highly recommended that you rerun phot2lc
on those objects with this or later versions.
Version 1.5.9 - 2020-07-10
--------------------------
> Updates to the quicklook program. Added new command
line options for when performing pre-whitening:
-l --lower, Lower frequency limit for pre-whitening
search (micro-Hertz, default = 500).
-u --upper, Upper frequency limit for pre-whitening
search (micro-Hertz, default = 100,000).
-n --num , Maximum number of pre-whitening iterations
(default = 10).
These new options provide the user with more control
over the pre-whitening process, in particular when the
object of interest shows low-frequency variability.
Version 1.5.10 - 2020-07-12
---------------------------
> Improved the x,y coordinates for text in the "First Image"
window so that each star's label no longer overlaps the
star or circle marker.
> Added an additional curve to the P2P Scatter vs. Aperture
size plot when the Grid search option is used. This
curve, colored red, shows the P2P vs. Ap Size trend for
the grid search's determination of the optimal comp
star combination.
> Improved y-axis scaling of the periodogram plot in the
Aperture Selection window.
> Added legend to P2P vs. ApSize plot showing the comparison
stars used and the minimum P2P scatter value.
> Added a "Time" keyword in the welded light curve header.
> Changed the "UTC" keyword in .lc and .phot file headers to
"Time" to be consistent with the welded file header.
> The quicklook -s option is now for optionally saving rather
than optionally showing the resulting plot. The plot is
now always shown.
> The quicklook output file naming convention was changed
from quicklook_object_date.pdf to quicklook_filename.pdf
where "filename" is the input .lc file's name.
> Fixed bug in photfunc.py's prewhiten function which
calculated one more pre-whitening step than requested.
Version 1.5.11 - 2020-07-13
---------------------------
> Small bug fix in the pp_scat function within photfunc.py.
Denominator should have been N-1, not N.
Version 1.5.12 - 2020-08-05
---------------------------
> Changed .lc and .phot file format. Instead of two time
columns, there is now only one. The time column is
either the raw times or the barycentric corrected
times. The user has control over which output occurs
using the new -b (--barycorr) command line option
when calling phot2lc.
Version 1.5.13 - 2020-08-07
---------------------------
> Updated the weldlc and quicklook programs to work
properly with the newly formatted .lc file.
> Minor modifications to the quicklook plot format.
The text displayed on the periodogram plots is
now positioned more efficiently to prevent overlap.
Version 1.6.0 - 2020-11-15
--------------------------
> Added a new capability to phot2lc which allows Users
to perform sigma rejections when fitting a polynomial
to the light curve. This optimizes the fitting procedure
for objects which are expected to exhibit many points
below or above the average flux, for example objects
in eclipsing binaries or flare stars. The -f keyword
is still available for simple polynomial fitting without
sigma rejections where only the polynomial degree needs
to be defined. A new keword, -F, is used to define the
sigma rejections parameters:
- Polymial Degree , e.g. 3
- Rejection Iterations , e.g. 10
- Lower Sigma Threshold , e.g. 2.5
- Upper Sigma Threshold , e.g. 5.0
> Fixed the weldlc header which still indicated two time
time columns were present though now only one is
included.
> Refined treatment of light curves which have not been
barycentric corrected. When corrections are not
performed, the .lc and .phot headers now have "None"
entered for the BJED value. In addition there is a
headder keyword "BaryCorr" with a value of True or
False indicating whether corrections have been
performed.
> Related to the above point, the weldlc header looks
different now depending on whether the input light
curve files have all been barycentric corrected or
not. If they have, all of the times referencing the
start of the welded light curve (T0) are in TDB time
scales. If they haven't, the times are instead in the
UTC scale, or some combination of the UTC and TDB scales.
Unless specified using weldlc's new -b (--bypass) option,
however, weldlc will throw an error if not ALL of the
input light curves have been barycentric corrected.
Regardless of whether you use the -b option, though,
weldlc still works the same in the sense that it simply
takes the time columns from each .lc file and concatenates
them together. The only true difference is that the -b
option will reference all times to the earliest MJD value
found rather than the earliest BJED value.
Version 1.6.1 through 1.6.6 - 2020-11-15
----------------------------------------
> Small bug fixes
Version 1.6.7 - 2021-02-10
--------------------------
> Chooses between QT5agg and TKagg backends for different
platforms.
> Updated the RTD documentation
Version 1.6.8 - 2021-02-10
--------------------------
> Fallback to DejaVu Sans Mono for non macOSX platforms
Version 1.6.9 - 2021-02-10
--------------------------
> Command line option description and RTD docs updates
Version 1.7.0 - 2022-01-28
--------------------------
> Fixed some dependency issues with Matplotlib 3.5
> Added support for the KPED instrument on the Kitt Peak 2.1m
> Changed the Layout of the Divided Light Curve Panel so that
the comparison star light curve and divided target light
curve share the same x-axis for easier identification of
bad point removal.
> The "s" key command now toggles the display of deleted
summed comparison star points in addition to the divided
light curve points.
> Changed the matplotlib backend to be system dependent for
the quicklook program. QT5Agg was distorted on some
Linux machines, switched to using TKAgg.
Version 1.7.1 - 2023-02-07
--------------------------
> Added support for the CHIMERA instrument on the Palomar
200-inch Hale Telescope.
> Changed how error estimation is being performed. The
photometric noise is now being normalized using the
comparison star flux as a normalization factor. A
scaling factor has also been introduced to help
reduce over/under estimation of errorbars. The scaling
factor is designed to make sure that the average
1-sigma errorbar matches the standard deviation of the
light curve.
> Added support for the HiPERCAM photometry pipeline:
Version 1.2.0
https://cygnus.astro.warwick.ac.uk/phsaap/hipercam/docs/html/index.html
The photometry source parameter (source) defined in
the configuration file, or set on the command line
using the -s or --source option, can now be set to
"hcm". In this mode, it will assume that a file with
a name like output*log exists containing the raw
photometry. It will also assume that a .hcm file needs
to be loaded in order to display the first image, and
use a HiPERCAM aperture file (.ape) to display the
initial source aperture positions.
Some caveats for handling HiPERCAM output include:
- Can only handle single-CCD output.log files.
The HiPERCAM pipeline is designed to reduce
multiple CCDs simulatneously since the actual
HiPERCAM instrument is a 5-channel photometer,
but the phot2lc code is not yet designed to
parse multi-CCD output.
- So far it has only been tested for data acquired
from the McDonald 2.1m ProEM instrument or the
Palomar 200-in CHIMERA instrument. Data from
from other instruments reduced using the
HiPERCAM pipeline may not yet play nice with phot2lc.
Version 1.7.2 - 2023-02-08
---------------------------
> Improved error messaging for missing object name
from the stars.dat file.
> Improved header descriptions for the .lc and .phot files.
- Added new header row in .lc file listing the IDs of
comparison stars used to generate divided light curve.
- Added new header row in both .phot and .lc files
naming the observer that acquired the data.
- Made description of BJED header entry more clear
in the .lc file.
- Made description of the Time column in both the
.lc and .phot file more clear.
> Added support for Ultracam pipeline output, version
19/12/2005. Since the ultracam pipeline requires
specially formatted image files (.ucm), an additional
script, ucm_utils.py, has been added to the package.
This script contains functions that can read and decode
the binary .ucm files, namely the read_ucm function. This
code was taken and modified from Tom Marsh's ultracam
pipeline package:
https://github.com/trmrsh/trm-ultracam
Such a function was not needed for the HiPERCAM .hcm
files, since these are basically just FITS files and
can easily be read with astropy.io.fits.
The photometry source parameter (source) defined in
the configuration file, or set on the command line
using the -s or --source option, can now be set to
"ucm". Similar to the HiPERCAM option, it will assume
that a file with a name like output*log exists containing
the raw photometry. It will also assume that a .ucm file
needs to be loaded in order to display the first image,
and use an ULTRACAM aperture file (.ape) to display the
initial source aperture positions.
Version 1.7.3 (2023-02-09)
---------------------------
> Minor bug fixes
Version 1.7.4 (2023-04-28)
---------------------------
> Added new location info for the Tenerife site of the
Las Cumbres Observatory 1.0-m telescopes.
> Added new option for the config.dat file called
phot_basename, which allows users to specify the base
filename for the output from the photometry pipeline
being used (e.g. "runbase" for ccd_hsp or "output.log"
for ULTRA/HiPERCAM). There is also a new command line
option for phot2lc (-p, --photname), which allows users
to specify the basename at runtime or override whatever
the default value is in the config.dat file.
> Added a new command line convenience program "addstar"
that allows users to add a new entry into the stars.dat
file. Example usage:
addstar SDSSJ0000+1111 00:00:00.0 +11:11:11.1
Version 1.7.5 (2023-04-28)
---------------------------
> Minor bug fixes
Version 1.7.6 (2023-05-02)
---------------------------
> Minor bug fixes in addstar
Version 1.7.7 (2023 May 4)
---------------------------
> Better handling of NaN values in HiPERCAM and
ULTRACAM output.
> Better information print out from the addstar
command line function.
Version 1.7.8 (2023 May 16)
----------------------------
> Changed how the light curve "author" is handled. The
default now is to use your system username, which
happens when the "author" parameter in the config.dat
file is set to "sys-user". You can change this parameter
to any custom value you like by running the photconfig
script as usual, or there is now a command line option
-a/--author for phot2lc which allows you to override
the value in the config.dat file, e.g.:
phot2lc --author 'Zach Vanderbosch'
This update makes it easier for multiple people to use
the same phot2lc installation, e.g. on a computer that
a whole research group may use to store and reduce
their data. Now, different users no longer have to run
the photconfig script to change the author name in order
to get the correct author metadata into the .lc file.
Version 1.8.0 (2024 July 31)
----------------------------
> Updated the weldlc program to be compatible with the
updated headers of the .lc files.
> Removed deprecated 'delim_whitespace' parameters from
pandas read_csv function calls, now using sep='\\s+'
> Fixed all microhertz axis labels from '$\mu$' to '$\\mu$'
to avoid syntax warnings.
Version 1.8.1 (2024 July 31)
----------------------------
> Minor bug fixes.