CHANGELOG.txt

*****  Sun May 28 23:48:48 CEST 2017  *****

Calling sequence:
  ./pup.py pup.cfg

This seems to be enough.  All required info can be contained into the
pup.cfg file, including what steps to run, and over which folders.

Main steps:
+ load
+ badpixel
- centering
- photometry
- modeling
- mcmc


centering:
- run_centering
    driver: load files, launch runs (series)
- centering
    main: 
- do_center
    low level centering
- centerdriver

TBD centering:
- read in data, mask, uncert


*****  Sat Aug 19 20:19:37 CEST 2017  *****

Let's make puppies work.
puppies must work from the command line or from an interactive session:

## Interactive:
import puppies as p

# New puppy:
pup = p.init("cfile.cfg")

# New step:
pup.badpix()
pup.center()

# Load:
pup = p.io.load(path + "wa043b.p")

## Command line:
  TBD

On now puppy, take the location of the config file as the root where
to place the outputs.

*****

repository structure (so far):
puppies
|--puppies
|  |--tools
|  |--stats
|  |--lib
|  |--image
|  `--io
|--examples
|--inputs
|--src_c
|--modules
`--docs

*****

Got a basic package import working, and interactive init() running.
Added required files.
Need to find a solution for all_spitzer.vec (file too large),
download during 'make'?


*****  Sun Aug 20 22:26:40 CEST 2017  *****

Moved getpar() from spitzer.py to tools.

*****

Got badpix working.
Added pup_badpix.py and stats module.


*****  Sun Sep  3 20:09:46 CEST 2017  *****

Implemented disk routine for Python and C.

*****

Implemented imedit.py, tied together with disk.py into image
module.


*****  Sun Sep 24 18:51:34 CEST 2017  *****

Implemented gaussian functions into center module.
TBD: give them their own submodule inside the center module.


*****  Mon Sep 25 23:09:32 CEST 2017  *****

Implemented least-asymetry routines into center module.


*****  Tue Sep 26 21:01:11 CEST 2017  *****

Cleaned up the disk.py and cdisk.c functions.


*****  Sun Oct  1 15:04:01 CEST 2017  *****

Sorted up gaussian, made it its own module inside the center module.

*****

Implemented center-of-light calculation into center module.

*****

Implemented center driver.py routine.


*****  Sun Oct  8 22:55:49 CEST 2017  *****

Got pup_center running (yay!).
Added temporary calling sequence to pup_center.
Fixed minor bug in center/driver.py for least-asym calls.
Tweaked main driver (removed parse() def).
Put user-input dict (from config files) into pup.inputs.


*****  Sat Oct 21 18:56:15 CEST 2017  *****

Rewrote disk C extension, moving most of the work into the cdisk.h
header, such it can be called from other C extentions.


*****  Fr 27. Okt 17:23:32 CEST 2017  *****

Implemented and documented the low-level aperture photometry routine
in aphot.c (a C extension).

*****

Incorporated aperture photometry in the puppies.photometry submodule.


*****  Sun Oct 29 17:05:52 CET 2017  *****

Implemented aperture photometry module.
Optimal photometry is TBI.

*****

Renamed centering's expand input to psfscale (pixel scale ratio
between the PSF and data images) to avoid conflict with photometry's
expand interpolating factor.


*****  Sat Nov  4 11:59:41 CET 2017  *****

Added some extra information about the Spitzer bad-pixel-mask bits,
still not completely sure it's the right one.


*****  Sun Nov 12 20:47:00 CET 2017  *****

Revampled spitzer.py to handle time stamps with astropy.time objects
for the ephtime and fp.time values.  This simplifies the light
travel time corrections, bjd-utc corrections, phase calculation.
The pipeline now takes the spacecraft location from the headers
instead of the horizons file.
All of these calculation are now in Spitzer.py rather than after
the photometry step.

Also, revamped the main object's FrameParameter from 2D into 1D.
This commit breaks all further steps of the pipeline.


*****  Sat Nov 18 22:09:59 CET 2017  *****

Adapted pup_badpix.py to the new data shape.

*****

Adapted pup_centering.py to the new data shape.


*****  Sun Nov 26 11:29:16 CET 2017  *****

Moved telemetry frame parameters into its own subclass.

*****

Adapted pup_photom.py to the new data shape.

*****

Added new plots module, to make plots (duh!).
Implemented YX plot vs. phase for centering.

*****

Added stats calculations at the end of pup_centering.py to print
means, median, std, and RMS.  Also make yx plots.


*****  Sun Dec 10 16:29:52 CET 2017  *****

Added MC3 submodule.

*****

Added background() and rawflux() to plots module.
Generate raw flux and background plots at the end of pup_photom.py.


*****  Sun Jan 28 17:56:23 CET 2018  *****

Added models module with lightcurve models.
Added linramp(), mandelecl(), and bliss() light-curve models.
TBD: Need to doublecheck bliss model works.


*****  So 18. Feb 18:21:45 CET 2018  *****

Implemented linramp, quadramp, expramp, mandelecl, mandeltr, and bliss
light-curve models.

*****

Added tools.cat(), a shorthand for numpy concatenate.
Removed tools.parray().

*****

Added parse.py file which implements tools.parse_model() to handle the
light-cruve modeling configuration files.
It also implements tools.parray().

*****

Added paramedit.py which implements tools.loadparams() to read-in
light-curve model parameters, bounds, and stepsizes.

*****

Added pup_model.py which implements the Model() and Fit() clasess
(for light-curve modeling).  It also implements the puppies.setup()
method, which prepares the code for a light-curve fitting/posterior
sampling.

TBI in this file: the fit() and mcmc() methods, which do the
least-square optimization and posterior sampling of the light-curve
modeling.


*****  So 25. Feb 18:54:17 CET 2018  *****

Implemented pup_model.fit(). Need to tie some loose ends (write file,
output, pickle file).
Sorted out variables in pup_model.setup().
Cleaned up pup_model.evalmodel().
Enabled chiscale and optimizer arguments for light-curve modeling.

*****

Implemented sigrej at the begining of pup_model.setup().
Need to think what to do if the data veries significantly from stat to
end, messing up the sigma rejection (do piecewise?, what's a good
recipe for this).
Also could do a sigrej from the residuals, after an initial fit
(consider if fit fails, it may mess up things as well).


*****  Sun Apr  8 20:01:23 CEST 2018  *****

Implemented newparams() and saveparams() in puppies.tool submodule.
This let's the user create a new modelparams file with default values
and to update an existing file with values from a Fit() object,
respectively.

*****

Minor corrections in _quadramp.c, _mandeltr.c, and _mandelecl.c
light-curve models.

*****

Updated fit() in pup_model.py to return the Model() object and store
best-fitting values into modelparams file(s).
Added update argument in evalmdel to update the models' parameters.


*****  Di 17. Apr 16:27:31 CEST 2018  *****

Combined all ramp models into ramps.py, where the specific models
inherit from the Ramp() superclass.
Files need to be properly documented.

*****

Updated bliss and ramp light-curve classes, renamed the pup argument
to obj in the settup() method.

*****

Added eclipse submodule, which implements mandelecl() and eclipse()
light-curve models.

*****

Adapted puppies.models' init to new ramps.py file and eclipse module.  
Removed mandelecl.py file (replaced with eclipse submodule).

*****

Updated Makefile to include submodules
and make it less verbose.

*****

Adapted pup_model.py to latest changes in puppies.models.


*****  Sun May 27 22:57:36 CEST 2018  *****

Renamed pup.model.fit() to lcfit() to avoid variable name conflict.
Added SDR and BIC calculations to laika object during lcfit().
For multiple model fits per pup requesting chiscale, scale according
to fit with lowest SDR.


*****  Mon Jun 11 01:06:49 CEST 2018  *****

Updated MC3 submodule.

*****

Got Light-curve MCMC up and running.
Wrote a basic screen summary output.
TBD: LC plot.
TBD: Put LC modeling into output folder.
TBD: Setup LC log.
TBD: Store LC output into pickle file.


*****  Sat Jun 16 10:57:25 CEST 2018  *****

Renamed spitzer.py to pup_spitzer.py


*****  Sun Jun 17 12:48:05 CEST 2018  *****

Reorganized the project, adding the core and inst modules that
contain the main reduction steps and the dataset initialization
routines, respectively.

*****

Renamed uncd variable to uncert.

*****

Return to original location after running core.center() and
core.photom().


*****  Sun Oct 14 17:00:00 CEST 2018  *****

Use datafile variable for the filepath to data, rather than using the
data variable itself (same for uncert and bdmskd).
Revamped io.save() accordingly.


*****  Di 5. Feb 15:43:13 CET 2019  *****

Some cosmetics.

*****

Added fitting and retrieval fixes from Bell's run.


*****  Sun Mar 7 22:37:09 CET 2021  *****

Synced with WASP-12b version.


*****  Mon Mar 8 21:39:18 CET 2021  *****

Sorted out files in stats module.

*****

Added __version__ variable into VERSION.py

*****

Added ophase.py into models module with orbital-phase lightcurve
model.
Fixed a few other bugs to get the pupppies package to import without
breaking.

*****

Got setup.py up to speed, puppies is now installable.

*****

Removed MCcubed submodule.
Added mc3 requirement.

*****

Added .readthedocs.yml file.
Updated docs conf.py and other docs.
Removed CONTRIBUTING.md

*****

Added pyproject.toml file.

*****

Updated mc3 required version to 3.0.6.


*****  Thu Mar 11 11:53:47 CET 2021  *****

Removed eclipse submodule, replaced with source files.
Fixed some bugs related to mc3 dependency.

*****

Updated LICENSE.

*****

PEP8ed puppies/driver.py.

*****

Added ROOT constant into tools module with puppies root location.

*****

PEP8ed pup_spitzer.py

*****

Renamed io/loadsave.py to io/io.py

*****

PEP8ed io.py.

*****

Renamed inst module to instruments.

*****

PEP8ed pup_badpix.py.

*****

PEP8ed stats.py.

*****

Moved update() from pup_center.py to io.py.

*****

PEP8ed pup_center.py.


*****  Sun Mar 14 20:17:18 CET 2021  *****

Updated logo and README files.

*****

Added pup entry point.


*****  Sun Mar 21 16:40:37 CET 2021  *****

Refactored io.update to process whatever is passed on in the config
file, regardless of the step.  Do not set defaults.  Moved checks
into the respective steps.

*****

PEP8ed pup_photom.py and got it working.

*****

Tweaked README file.


*****  Do 25. Mär 11:46:27 CET 2021  *****

PEP8ed image module.
Added image module into main package.

*****

PEP8ed pup_model.py.
Got light-curve fitting and retrieval running.

*****

Updated docs adding getting started and draft of WASP43b eclipse
worked example.

*****

Added pup_marker.py with code to enable pup matplotlib markers.
Updated getting started with pup-marker example.
Moved all figures to puppies/docs/figures/ folder.

*****

PEP8ed a bunch of files.
Updated copyright headers.

*****

Updated Makefile (do I even need this file anymore [question mark])

*****

Bumped puppies version to 0.2.0.


*****  Fr 26. Mär 10:22:20 CET 2021  *****

Updated MANIFEST.in file.

*****

Updated setup.py, set lon_description text, set name to exo_puppies
(since puppies is already taken on PyPI), and updated email.

*****

Retracted puppies version to 0.2.0a1 (to align with PyPI release).

*****

Updated pyproject.toml file to consider python>3.7 versions.


*****  Do 24. Feb 14:05:15 CET 2022  *****

Updated requirements.

*****

Updated pyproject.toml to use oldest-supported-numpy dependency.

*****

Added .travis.yml file.

*****

Added .gitignore in puppies/lib/
Removed Makefile.

*****

Updated version.py file and setup.py.

*****

Fixed bug with version.py filename.

*****

Renamed gauss.c to _gauss.c

*****

Prevented deprecation warning with
scipy.ndimage.interpolation.map_coordinates

*****

Corrected includes in C source files.

*****

Debugging edits to figure out problem with C code.

*****

Bringing (renamed) _asymmetry.c back.

*****

Bringing _expramp.c back.

*****

Bringing _linramp.c back.

*****

Bringing _eclipse.c back.

*****

Bringing _mandeltr.c back.
This one shoulf break because there no preceeding underscore
in PyModuleDef of the file.

*****

Bringing _bilinint.c back.
Previous commit did not break...

*****

Bringing _disk.c back.

*****

Bringing _aphot.c back.

*****

Bringing _gauss.c back. The final one, will it break...

*****

Attempt number one at approaching a passing gauss test.
Replaced gauss2D code with exponential ramp.
Work in progress.

*****

One step closed, get names of functions as they should be.

*****

Getting closer.

*****

OK, it's either the name of PyMethodDef gauss_methods
or something inside the gauss2D function.

*****

It seems that the problem is the content of the function.
Reverting edits.

*****

Not breaking once again.
Try changing stuff in the PyArg_ParseTuple().

*****

So far so good. Updated the rest of the PyArg_ParseTuple variables.

*****

Broken again. Reverted PyArg_ParseTuple edits.
Updated for loops.

*****

Updated everything except the PyArg_ParseTuple.

*****

Removed height calculation.

*****

Added y_sigma and x_sigma into the PyArg_ParseTuple.

*****

Added height and backgroun into optional PyArg_ParseTuple.

*****

Try now changing the input arguments, receive array, edit in place.

*****

What if, packing the inputs in an array.


*****  Tue Mar 15 23:55:10 CET 2022  *****

There is absolutely no reason why this keeps failing.
I'm giving up. Wrote code in the python module.
Removed src_c/_gauss.c entirely.

*****

Fixed bug with relative import.

*****

Updated puppies version to 0.2.0a2.

*****

Changed license to GNU GPL v2.


*****  Fri Mar 18 21:35:35 CET 2022  *****

Housekeeping.
pup_spitzer.py is running clean.


*****  Tue Mar 22 22:30:31 CET 2022  *****

Got Spitzer pipeline running intil badpix.

*****

Updated README conda links.

*****

Updated mc3 requirement.


*****  Wed Mar 23 09:55:19 CET 2022  *****

Got Spitzer pipeline running intil centering.


*****  Wed Mar 27 22:06:12 CET 2024  *****

Updated the pup marker to work with matplotlib v3.4+
(as well as keeping compatibility with older versions).

*****

Getting the docs back to life.

*****

Replaced travis CI with github workflows for automated testing.

*****

Cleaning up the code.
Raise NotImplementedError for PSF optimal photometry routines.

*****

Cleaned up centering.

*****

Cleaned up plots code.

*****

Cleaned up badpix.

*****

Cleaned up pup_model.py

*****

Updated workflow versions.

*****

Updated copyright and version to 0.3.0


*****  Do 28 Mär 2024 11:12:26 CET  *****

Updated setup.py and pyproject.toml.
(Moving most of the configuration options to the latter)

*****

Updated README and docs' index and license.

*****

Split getstarted.rst into install.rst and pup_marker.rst.
Also added top-level section for Dog of the day.
 
*****

Fixed pup entry point in pyproject.toml.


*****  Sat Mar 30 16:14:00 CET 2024  *****

Moved inputs folder to puppies/data.
Renamed data/spitzer/filter to data/spitzer_filters
Renamed data/spitzer/psf to data/spitzer_psf

*****

Fixed bug reinstating puppies.input() from puppies/laika.py file.

*****

Revamped 'pup --day' entry point since the dogperday.com does not
update as frequent as it used to do. Now this command will bring up
a random dog of the day.
If on wants the most recent dog, it should call 'pup --today'.
Added puppies/tools/pup_scrapper.py file, which collects the
dogs of the day and save to a file.
Added puppies/data/dogs_of_the_day.txt file with the dogs of the day.

*****

Updated version to 0.4.0

*****

Updated version to 0.4.0b1 for pypi testing.

*****

Renamed puppies.core.Model() to Laika().
Turned into a proper class, moving the lightcurve_fit() and mcmc()
functions into methods of the class.
Fixed a couple of typos.
Made Laika.summary() method also save the screen output to file.

*****

Renamed Laika.lightcurve_fit() to Laika.bestfit().
Renamed Laika.mcmc() to Laika.retrieval().

*****

Updated logo. Goes into docs and README.md.

*****

Implemented tools.cd() context manager.
Ensured user always end on the current folder.
Added zoomed plot of frame when the data [nx,ny] is too large.
Also, avoid using the first frame in case the telescope is not on point.


*****  Sun Mar 31 10:16:05 CEST 2024  *****

Updated docs, Spitzer tutorial for WASP-18b.

*****

Updated version to 0.5.0

*****

Some docs little fixes.