Closed stormnick closed 1 year ago
added pd df of results and their plotting
added extra plots and comments
took out scripts into their own file
changed internal structure to pd for results
added title with fitted results
removed plotted figures
fixed issue when plotting only 1 point
not saving overlapping spectra if closeby linemasks anymore
cleaned the outputs
cleaned the debug stuff
fixed bug when only 1 line in fitlist
decreased the tolerance for line fitting
fixed bug with saving the results
fixed bug when no slash given in path
updated readme: adding more instructions
cleaned up reading of config + trimming in temp dir
updated readme file with installation and usage a bit
micro interpolation fix by Jeff and temp dir clean up crash fix
code refactoring
decreased the tolerance for fitting
Update Readme + default example for Fe fitting
Updated README.md
fixed bug with commented line
fixed crash when no output
fixed crash when no output 2
Update turbospectrum_class_nlte.py
loading of observed spectra only for columns 0 and 1 for plotting
fixed bug where plotting of all spectra would duplicate for multiple lines
added paramater whether to plot title or not
added parameter to save figure
save figure with wavelength center as well
fixed bug with saving
fixed crash when lte didnt generate
fixed bug where correct atmos were not taken
removed unnecessary code/comments and faster LTE creation
removed unnecessary scripts
copies config into output folder, so it is easier to plot
fixed bug with copying config
added ability to print average of columns
made printing of avg results better
can now just print specific values
changed printed error to normal std error
added abund limits
fixed that teff fits rotation when not needed
maybe h was not nlte in teff
code cleaning and added nlte_filenames.cfg for config
can now choose elements to do in nlte much easier
fixed where config is not auto updated with new change
changed order how nlte_config is written
added deprecation warning as print statement too
now checks if nlte file exists before using it
fixed bug with location of model_atoms
added spaces to depreciation warning
fixed bug where macro was fitted for rotation
now can use molecules in NLTE and removed old code
can plot synthetic data directly from jupyter notebook
can plot synthetic data now
fixed imports
bug fixes of the plotting tool
fixed lmin and lmax being too small
returns calculated spectra if needed for later
can remove bad lines now
change named of variable
saves good lines now as well
fixed bug
fixed bug when loading 1 column?
can specify xlim and ylim during plotting now
changed file location + unittest for trimming
updated config reading + added .cfg config
fixed molecules in nlte
changed how code is called
added default values for guess for old config
fixed old config loading nlte
fixed old config loading nlte again
auto convert paths to the new format
fixed ts path
fixing new way of calling for old paths
fixed bug with old config loading
fixed segment creation
fixed segment creation and ts call + added unittest
trying absolute paths for TS
fixed temp dir creation
trying to fix location of temp dir
trying to fix temp dir
trying to convert all paths to absolute
test
need to add config into spectra now
added font size for plotting
hopefully now spectra config is loaded correctly
bug fixes with referencing unassigned variables
fixed loading atmo type config
fixed Spectra. calling
fixed more config calling
debugging no output
addede todo for tuesday
fixed linelist loading
fixed bug with saving fitted spectra
trying to update scripts for plotting for the new version
fixed saving convolved fitted spectra
removed bug printing
fixed problem with experimental perhaps interferign with each other
added TODO
fixed bug crashing lbl not fitting rot or vmac
using pickle to read tsconfig
fixed bug with vmac fitting
fixed? vmic slow fitting
fixed guess vmic slow
fixed pickled path
fixed micro guess
fixed where elem abundance is not passed vmic slow
fixed logic of the program vmic slow
fixed trimming for vmic slow
can fit several elements for vmic slow now
fixed abund passed into ts vmic slow
fixed crash when not converging something
updating the conversion of old config to new one
supports conversion of old config into new one
new config has new paths now
changed behaviour of old config conversion
config conversion fixed output folder
fixed temp directory cfg conversion
added Y 3D grid
updating paths for plotting tools
fixed slow trimming without molecules
updated unittest
avg of columns is now done based on unique specnames
raise error if not together with script
fixed printing of mean of tables
fixed how specname is chosen
added better title to the output
changed name of the nlte flag saving
fixed min max wavelength passed for all in old config
fixed conversion output filename and config in output name
auto sorts observed spectra
fixed ts path old config conversion and new config loading plotting
changed default values for plotting to be Halpha
not crash if calling now
fixed loading of new config guess or known abund
fixed model atmo list
trying to fit rv separate to macro and rot
reduced tolerance for vmac and doppler
reverting the last 2 changes. rv and broad fitted together again
trying different tolerance
trying different limits
trying to add 5 sigma bound
fixing 5sig
now upper limit is general, not just 5 sigma
trying different upepr limit
better output upper limit
temp upper limit always
trying root for the upper limit
fixing root finder
uhm fixing output root
trying fix root finder
added default debug mode for old config
trying to fix run_wrapper
fixed some bugs with running wrapper
changed loading of nlte
started adding grid generation code
still working on this
fixing NLTE molecules for new TS version
trying to fix upper limit
upper limit doesnt crash if not good bounds
trying different upper limit
removed unnecessary comment
now saves with atmosphere type
turned off upper limit
trying upper limit with EW
trying to check if it works
fixing plotting tools
added ew calc function
bug EW measurement for upper limit
fixed bug EW calc for upper limit
fixing nlte corrections
fixed calc nlte corr line
fixed crash
tring to fix crash
tring to convert old config
fixing input path fitlist
fix linemask path and pickle
load of atmo list
pickled data folder creation
only convert non .cfg files
fixed config load
trying diff abundance limits
hopefully fixed bug where inptu abund is not used
actually fixed bug where inptu abund is not used
fixed crash saving output
trying different guess
trying instead root method for correction
trying different chi squared formula
chi squared upper limit too
fixed crash with variance cut
debug messages added
fixed upper limit crash
trying to catch more warnings
more debug
remove debug messages 1 and debugging chi squared calc
fixed bug with chosen variance
removed debug print
turned off upper limits
fixed duplicate Y entry
fixed bug with plotting density results
testing upper limit
fixed bug with upper limits calculation
added check if config file exists
added warning about sigma column in spectra
fixing crash for method all
added error message teff failing
fixed a bug in conversion script
removed unneeded segments
fixed bug where only default nlte_grid config was read
added upper limits into the config
added upper limits to config
added where to check the status dask
fixed teff fitting hopefully
updating readme
fixed crash when no upper limit given in config
fixed teff not saving output
removed one todo
WIP on the generating synthetic grids
removed bad fitlist columns
added pd df of results and their plotting
added extra plots and comments
took out scripts into their own file
changed internal structure to pd for results
added title with fitted results
removed plotted figures
fixed issue when plotting only 1 point
not saving overlapping spectra if closeby linemasks anymore
cleaned the outputs
cleaned the debug stuff
fixed bug when only 1 line in fitlist
decreased the tolerance for line fitting
fixed bug with saving the results
fixed bug when no slash given in path
updated readme: adding more instructions
cleaned up reading of config + trimming in temp dir
updated readme file with installation and usage a bit
micro interpolation fix by Jeff and temp dir clean up crash fix
code refactoring
decreased the tolerance for fitting
Update Readme + default example for Fe fitting
Updated README.md
fixed bug with commented line
fixed crash when no output
fixed crash when no output 2
Update turbospectrum_class_nlte.py
loading of observed spectra only for columns 0 and 1 for plotting
fixed bug where plotting of all spectra would duplicate for multiple lines
added paramater whether to plot title or not
added parameter to save figure
save figure with wavelength center as well
fixed bug with saving
fixed crash when lte didnt generate
fixed bug where correct atmos were not taken
removed unnecessary code/comments and faster LTE creation
removed unnecessary scripts
copies config into output folder, so it is easier to plot
fixed bug with copying config
added ability to print average of columns
made printing of avg results better
can now just print specific values
changed printed error to normal std error
added abund limits
fixed that teff fits rotation when not needed
maybe h was not nlte in teff
code cleaning and added nlte_filenames.cfg for config
can now choose elements to do in nlte much easier
fixed where config is not auto updated with new change
changed order how nlte_config is written
added deprecation warning as print statement too
now checks if nlte file exists before using it
fixed bug with location of model_atoms
added spaces to depreciation warning
fixed bug where macro was fitted for rotation
now can use molecules in NLTE and removed old code
can plot synthetic data directly from jupyter notebook
can plot synthetic data now
fixed imports
bug fixes of the plotting tool
fixed lmin and lmax being too small
returns calculated spectra if needed for later
can remove bad lines now
change named of variable
saves good lines now as well
fixed bug
fixed bug when loading 1 column?
can specify xlim and ylim during plotting now
changed file location + unittest for trimming
updated config reading + added .cfg config
fixed molecules in nlte
changed how code is called
added default values for guess for old config
fixed old config loading nlte
fixed old config loading nlte again
auto convert paths to the new format
fixed ts path
fixing new way of calling for old paths
fixed bug with old config loading
fixed segment creation
fixed segment creation and ts call + added unittest
trying absolute paths for TS
fixed temp dir creation
trying to fix location of temp dir
trying to fix temp dir
trying to convert all paths to absolute
test
need to add config into spectra now
added font size for plotting
hopefully now spectra config is loaded correctly
bug fixes with referencing unassigned variables
fixed loading atmo type config
fixed Spectra. calling
fixed more config calling
debugging no output
addede todo for tuesday
fixed linelist loading
fixed bug with saving fitted spectra
trying to update scripts for plotting for the new version
fixed saving convolved fitted spectra
removed bug printing
fixed problem with experimental perhaps interferign with each other
added TODO
fixed bug crashing lbl not fitting rot or vmac
using pickle to read tsconfig
fixed bug with vmac fitting
fixed? vmic slow fitting
fixed guess vmic slow
fixed pickled path
fixed micro guess
fixed where elem abundance is not passed vmic slow
fixed logic of the program vmic slow
fixed trimming for vmic slow
can fit several elements for vmic slow now
fixed abund passed into ts vmic slow
fixed crash when not converging something
updating the conversion of old config to new one
supports conversion of old config into new one
new config has new paths now
changed behaviour of old config conversion
config conversion fixed output folder
fixed temp directory cfg conversion
added Y 3D grid
updating paths for plotting tools
fixed slow trimming without molecules
updated unittest
avg of columns is now done based on unique specnames
raise error if not together with script
fixed printing of mean of tables
fixed how specname is chosen
added better title to the output
changed name of the nlte flag saving
fixed min max wavelength passed for all in old config
fixed conversion output filename and config in output name
auto sorts observed spectra
auto sorts observed spectra
fixed ts path old config conversion and new config loading plotting
changed default values for plotting to be Halpha
not crash if calling now
fixed loading of new config guess or known abund
fixed model atmo list
trying to fit rv separate to macro and rot
reduced tolerance for vmac and doppler
reverting the last 2 changes. rv and broad fitted together again
trying different tolerance
trying different limits
trying different limits
trying different tolerance
trying different tolerance
trying to add 5 sigma bound
fixing 5sig
now upper limit is general, not just 5 sigma
trying different upepr limit
better output upper limit
temp upper limit always
trying root for the upper limit
fixing root finder
uhm fixing output root
trying fix root finder
trying fix root finder
added default debug mode for old config
trying to fix run_wrapper
fixed some bugs with running wrapper
changed loading of nlte
started adding grid generation code
still working on this
fixing NLTE molecules for new TS version
trying to fix upper limit
upper limit doesnt crash if not good bounds
trying different upper limit
removed unnecessary comment
now saves with atmosphere type
turned off upper limit
trying upper limit with EW
trying to check if it works
fixing plotting tools
added ew calc function
bug EW measurement for upper limit
fixed bug EW calc for upper limit
fixing nlte corrections
fixed calc nlte corr line
fixed crash
tring to fix crash
tring to convert old config
fixing input path fitlist
fixing input path fitlist
fix linemask path and pickle
load of atmo list
pickled data folder creation
fixed crash
only convert non .cfg files
fixed config load
fixed crash
fixed crash
fixed crash
trying diff abundance limits
hopefully fixed bug where inptu abund is not used
actually fixed bug where inptu abund is not used
fixed crash saving output
trying different guess
trying instead root method for correction
trying different chi squared formula
chi squared upper limit too
fixed crash with variance cut
debug messages added
fixed upper limit crash
trying to catch more warnings
more debug
remove debug messages 1 and debugging chi squared calc
fixed bug with chosen variance
removed debug print
turned off upper limits
fixed duplicate Y entry
fixed bug with plotting density results
testing upper limit
fixed bug with upper limits calculation
added check if config file exists
added warning about sigma column in spectra
fixing crash for method all
added error message teff failing
fixed a bug in conversion script
removed unneeded segments
fixed bug where only default nlte_grid config was read
added upper limits into the config
added upper limits to config
added where to check the status dask
fixed teff fitting hopefully
updating readme
fixed crash when no upper limit given in config
fixed teff not saving output
removed one todo
WIP on the generating synthetic grids
removed bad fitlist columns