# QSoas

## Change log

# What’s new in version 2.2 ?

Version 2.2 brings in a lot of new features and improvements, notably
greatly improved memory use for massive multifits, a fit for linear
(in)activation processes, a new way to transform “numbers” like peak
position or stats into new datasets and SVG output ! It also finally
brings back the peak area output in `find-peaks`

and related
commands !

See the full list of changes below

# What’s new in version 2.1 ?

Version 2.1 brings in a number of new functionalities, such as a command to solve equations, and ways to reparametrize fits, along with numerous improvements of already existing commands.

See the full list of changes below

# What’s new in version 2.0 ?

Version 2.0 brings a whole new set of functionalities for fits, namely a fit engine with enormous performance increases in massive multibuffer fits (easy to reach a 1000 times speed increase !), definition of fits with a distribution of parameters, and many new functions.

See the full list of changes below

# Changes in version 2.2

## New commands

- a
`load-as-parameters`

load function to load saved fit parameters as normal datasets `pop`

, which can be combined with the various`/accumulate=`

options to create datasets on the fly, from the results of commands like`stats`

or`1`

## Fits

- new fit:
`linear-kinetic-system`

, which is useful for fitting the time traces of potential step experiments with linear inactivation (like in Fourmond*el al*,*Nat Chem*2014) - new time-dependent parameter:
`ramps`

- interpolation of parameters in the “Parameters Spreadsheet”
- chi-squared “goodness of fit”
`qsoas`

and`multi`

a much more memory-efficient for massive multi-buffer fits`arbitrary`

has more “automatic” parameters- all the
`sim-`

commands now also take the`/style=`

and`/set-meta=`

options

## Improvements of previous commands

- new picking modes available for all commands that pick points: the local min (Ctrl+M) and max (Ctrl+Shift+M)
- possibility to track the point selected for commands that pick points
- an
`/exclusive=yes`

option to`flag`

to remove all the other flags - most data-producing commands now have an
`/accumulate`

option to generate buffers step-by-step, to combine with`pop`

- new
`stats`

:`stddev`

, and quantiles:`q10`

,`q25`

,`q75`

and`q90`

`save-buffers`

can now avoid to overwrite files- threshold option for
`strip-if`

(to avoid creating near-empty buffers) `load-as-csv`

now correctly parses CSV files with quotes`print`

can now export SVG files`bin`

can now use a column for weights, and normalize the sum to 1.- Finally bring back the peak area for
`find-peaks`

,`1`

and`2`

! `expand`

can now group the Y columns 2 by 2, (or 3 by 3, etc.)- Improvements of
`unwrap`

, including the possibility to reverse its effects

## Other improvements

- possibility to load a saved stack by just double-clicking on it
- in kinetic systems, can now use either Butler-Volmer or Marcus-Hush-Chidsey kinetics for interfacial electron transfers
- now fully compatible with Qt 5, still not the default build
- switched to using embedded mruby rather than plain ruby, which finally fixes a hard crash on Windows
- new special functions: incomplete gamma functions
- many bug fixes and other minor improvements

# Changes in version 2.1

## New commands

`solve`

, to solve equations`reparametrize-fit`

, to manipulate the parameters of a fit

## Fits

- Reparametrization of the wave shape fits for 1- and 2-electron
reversible catalysts
`ecr-wave`

and`eecr-wave`

- Implementation of the corresponding fits for irreversible
catalysts,
`eci-wave`

and`eeci-wave`

- The commands that define fits,
`reparametrize-fit`

,`combine-fits`

,`define-distribution-fit`

and`define-derived-fit`

can now redefine existing fits with the option`/redefine=true`

. - The
`qsoas`

and`multi`

fit engines can now use scaling, see the “Fit Options” dialog - Improvements of the parameters spreadsheet

## Improvements of previous commands

`echem-peaks`

now offers all the options of the other peak-finding commands, with the same meaning- When several datasets are specified, commands that pick points
`cursor`

,`baseline`

, etc. can switch between all displayed datasets (with the`n`

and`N`

keys) - Commands that write to the output file can now also save the data
as meta-data through the use of the
`/set-meta`

option. - It is now possible to select the statistics one wants to
display/save with the
`stats`

command `diff`

can now compute an arbitrary derivative to an arbitrary order`print`

can now overwrite output PDF file without asking via the`/overwrite=true`

option- most of the commands that can produce several datasets now take a
`/flag=`

option and a`/style=`

, the exception being the`sim-`

commands which still only support the`/flag=`

option at this stage.

## Other improvements

- Now compiles and runs with Ruby 2.3 and the most recent GSL releases
- The
`--stdout`

command-line option writes the content of the terminal to the standard output - Sketch of an Emacs major mode,
`misc/qsoas-mode.el`

in the tarball - A series of bug fixes

# Changes in version 2.0

## New commands

`auto-flag`

, to automatically add flags to all newly created datasets`auto-reglin`

, another way to compute the derivative of a signal`define-distribution-fit`

, to define fits with distribution of values for parameters`hide-buffer`

, to hide buffers from view`mintegrate-formula`

, to integrate functions depending on one parameter`reverse`

, to reverse the order of data points`split-on-values`

, to split datasets on the values of certain colunms`system`

, to run external commands`timer`

, that measures the time between two calls`add`

and`multiply`

commands- a
`debug`

function to save debug information in a directory, helpful for debugging (reproducible) crashes

## Fits

- Load parameters using interpolation on Z values
- Shortcut to fix/unfix a parameter for all datasets (right-clicking)
- Spreadsheet mode for editing parameters
- A “Multi” fit engine that performs very well for large number of buffers
- Can now cancel the current fit using the shell command
`killall QSoas -SIGUSR1`

on Linux and MacOS - better convergence for the QSoas and Multi fit engines
- Generalize the use of “time-dependent parameters” (the
`/with=co:2,exp`

options to`fit-kinetic-system`

) to`fit-ode`

and`fit-arb`

- New types of time dependent parameters:
`rexp`

(exponential relaxation) and`steps`

(discrete steps) - The
`sim-`

commands can now compute the jacobian and reexport parameters (to the output file) - Now, the fit dialog detects when there are NaNs in the data, which avoid hard-to-understand problems of convergence of fits
- a new
`pseudo-voigt`

fit - a new
`polynomial`

fit - Now, the commands that define fits can redefine existing (custom)
fits if given the
`/redefine=true`

option - One can now specify the fit engine from the command-line

## Improvements of previous commands

`eval`

can now use statistics and meta-data of the current buffer- Can now push the transform using uppercase T in
`filter-fft`

, and using the`/transform`

option in`auto-filter-fft`

`save-buffers`

can now be used to name files (or buffers) based on meta-data; it can also simply rename without saving, and create directories if necessary (using`/mkpath=true`

)`run`

can change to the directory of a script when it is running it, using`/cd-to-script=true`

`flag`

can now clear all flags before adding new ones (with`/set=true`

)`generate-buffers`

can now generate several buffers at once when using the`/number`

option- More control in
`split-monotonic`

: can now keep only the first and/or last parts, and group several segments into datasets - In
`apply-formula`

and`strip-if`

, one can now use`i_0`

and`x_0`

to refer to the index and value of x of the first point of the segment `strip-if`

is now aware of the metadata and stats, like`apply-formula`

## Other improvements

`latest`

and`latest:`

*n*specifications to refer to the datasets generated by the latest command (or the _n_th before)- Faster startup time
- New special functions: Dawson integral, Debye functions, the clausen function, a couple of Fermi-Dirac integrals, multigamma functions, some hypergeometric functions, and an approximation of Marcus-Hush-Chidsey kinetics
- One can now use the
`--run`

and`--exit-after-running`

command-line options to QSoas to run scripts from the command-line - possibility to run “inline” Ruby code from within scripts and from QSoas itself
- Can now run QSoas commands from within Ruby code, for instance
`QSoas::load("file")`

. This is still experimental. - Now supports GSL 2.0
- Quite a few bug fixes

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