What’s new in version 3.2 ?

Version 3.2 is mostly a bug-fix release, fixing a mistake in the EEC reversible with relay fits, see the correction of the original article. All users of the eecr-relay-wave fit are strongly encouraged to rerun their fits with the new version.

In addition to this important fix, new possibilities have been added, including a way to make fits with “partially global” parameters, to pick the best parameters dataset-by-dataset within fit trajectories, a parameter space explorer trying all possible permutations of a set of parameters, and the possibility to save the results of a command to a global ruby variable.

It also includes a series of improvements of already existing commands.

See the full list of changes below

What’s new in version 3.1 ?

Version 3.1 brings many improvements to the fit system, including more flexibility in loading parameters, processing fit trajectories (after parameter space exploration), and improvements in individual fits.

It brings in also a series of new commands, to look at files and directories, to add noise and remove it, to run linear least squares minimisations and facilitate the handling of column and row names.

It features also many other improvements, such as the possibility to define “virtual files” inside script files, to define reusable parameters, basic handling of complex numbers and many useability fixes.

See the full list of changes below

What’s new in version 3.0 ?

Version 3.0 brings an “expert” fit mode, with a fit command line that makes it possible to automate fitting or do parameter space exploration, running many fits with random initial starting positions to greatly increase the likelihood of finding the best parameters (along with many other new features for fits).

Another improvement in the fits is a new implicit fit, to fit an implicit equation to data.

This release also brings in a command to permanently record information about a file, such as the conditions in which the experiments were made (the sample used, the temperature, etc…), in a format that QSoas automatically reads when reading the file. This makes it possible to quickly browse through data to find the experiments you need.

Finally, this release brings in a whole new offline documentation system, with and index and search facilities, startup tips, cross-reference examples and the possibility to specify manually all the command arguments and options in a dialog box when running a command from the menus.

See the full list of changes below

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 3.2 (22.03.2023)

Fits

• important the eecr-relay-wave fits were using a false formula, leading to wrong fits. This version provides a corrected and validated formula (see the correction);
• the define-indexed-fit command makes it possible to define fits in which a parameter is indexed on a meta-data, to make fits with “partially global” parameters;
• parameter space explorers now save the trajectories on each iteration;
• a compute command to recompute the fit;
• a pick-from-trajectories to pick the best parameters, dataset-by-dataset from a list of trajectories;
• a permutation-explorer explorer that allows one to try all the possible permutations of one or several sets of parameters;
• enable the use of reporters in plain ODE fits;
• improvements of the trajectory displays, with better ways to hide parameters and a new tab showing the parameters as a function of perpendicular coordinates.

New command

• a run-for-values command to run scripts passing as arguments the contents of a dataset, row by row.

Improvements of previous commands

• all the commands generating values (like stats, etc…) can now also save their results into the global ruby variable $values using the /set-global option;
• the linear-least-squares command can now optionally generate datasets with the fits or the residuals.

Other improvements

• better loading of fit parameter files as datasets;
• several bug fixes/small improvements.
• better handling of mruby 2.1, mruby 3 is currently not supported

Changes in version 3.1 (28.09.2022)

Fits

• now the main terminal is also accessible via a tab on from the fit window, which makes it much easier to follow the output of the various fit commands
• more flexibility in load for loading parameters, matching datasets, even renaming parameters on the fly
• ode and kinetic-system now have a /voltammogram option to work better with the time and potential dependence of voltammograms
• kinetic-system now provide means to use various interfacial electron transfer models, including Marcus-Hush-Chidsey
• definition of species names in nernst
• more flexibility to designate datasets for fix, unfix, set
• a sort-trajectories command to sort the trajectories
• the time-dependent parameters now allow to have several parameters controlled by the same time dependence (with different values)
• it is now possible to use j_elec as a reporter in the kinetic-system fit to represent the electrical current at the electrode
• the fit engines are now more robust to the appearance of NaN, and also the trajectory sorting now handles them better too
• the sim commands can now push the parameters as a dataset with /operation=push
• the fit interface now has menus instead of the previously used combo boxes
• trajectory loading is more resistant to manually modified trajectory files
• the use of reparametrize-fit now also creates a command that can regenerate the parameters of the original fit from a dataset containing parameters of the reparametrized one

New commands

• a add-noise command to add random, controlable, noise to datasets
• a files-browser command to browse files on the local storage and display/modify their meta-data
• a contour to compute contour lines at a certain level from a y = f(x,z) dataset
• a clear-segments command to remove all the segments of a dataset
• an save-meta command to save the meta defined on the current dataset back to the original data file
• a head command to display the beginning of a file (as text), as QSoas is seeing it (helpful for when load doesn’t do what you want)
• a ls command to list the files in the current directory
• a linear-least-squares command that performs the (exact) determination of the parameters in the case of linear least squares, very powerful for data extraction
• a pause command to temporarily stop the execution of a script
• a rotate command to move points of a dataset from the beginning to the end
• the set-column-names and set-row-names commands to set the column and row names of a dataset
• a let command to define named parameters to be used inside scripts
• a sort-datasets command to sort a series of datasets directly from within the stack
• a kernel-filter command offering several kernel-like filters

Improvements of previous commands

• use of $c.column to read the value of a column in strip-if and apply-formula
• apply-formula got several new modes of action, one in which a new column is added, another in which the dataset is considered as a global function y = f(x,z) (z is the perpendicular coordinate)
• apply-formula can also use column names for both reading and modifying
• truncate the dataset using the Ruby function break in apply-formula
• many commands got the possibility to work on several datasets at the same time, and others that already had this also were given the /for-which option to better fine-tune the datasets they work on
• possibilty to specify min and max in bin
• browse got all the backend-specific options of the load command
• eval got greatly improved, with the possibility to evaluate several formulas on several datasets at the same time, making it the best command for data extraction on series of datasets
• eval can now also modify the row and column names
• film-loss got a new mode for determining the film loss rate constant on a given segment
• the find-peaks command now can save the peak data into parameter files to help with initial parameters in fits
• generate-dataset can generate different columns with different formulas in one go, and can directly give a name to the generated datasets with the /name option
• generate-dataset can also have the X values logarithmically spaced
• loading of row names from text files with the /text-columns option of load
• the possibility to get the status of the accumulator with pop
• the possibility to toggle between datasets in reglin
• more flexibility in controling the format used for saving by save and save-datasets
• the commands that generate several datasets in one go can now push them in the reverse order of what they usually do by using /reversed=true
• the sort command can now work on any column, not just the X one
• edit shows the perpendicular coordinates
• a /select= option to tweak-columns that selects only a given number of (possibly named) columns from a dataset
• conditional execution of scripts in run
• load plays better with QSoas’s own files, including the saved parameters files (which can be loaded as normal data files)
• edit shows the column and row names
• all the commands now preserve column and row names whenever possible, or handle them as they should
• cursor can now quit subtracting X values
• greatly improved speed for load
• save now saves the meta-data in the .qsm files
• commands that produce many datasets from one, or one from many now offer the possibilty to expand or contract the meta-data to lists
• auto-reglin can also now be used as a filter
• record-meta can now also be used to remove meta-data

Other improvements

• inline files: it is now possible to define “inline files” inside files already, which makes subroutine construction/calling much much easier to write and maintain
• better handling of files that QSoas should not try to load (PDF files, etc…)
• better display of the segments delimitation
• it is now possible to specify columns using their name, via the name:column or $c.column syntax (with completion)
• handling of complex numbers from within Ruby formulas
• a --headless command-line option to run non-interactively
• a --run-script command-line option to run directly a script
• a true Win64 build, allowing you to use much more ram should the need arise
• the tooltip over a dataset point also shows the row name when applicable
• the terminal now uses bold and color when useful
• now understands the QSOAS_DEBUG environment variable
• a --write-deps command-line option that writes the dependency of all the generated files on the files QSoas had to read to generate them, in Makefile format
• quite a few bug fixes, in particular concerning the interaction with Ruby
• implemented a dataset rendering cache to greatly improve the responsivity when using commands like cursor on very “jaggy” datasets
• disable the ugly “black console” window on Win platforms
• NaN in datasets are now shown as a “cross” next to the non NaN points they are next to

Changes in version 3.0 (03.12.2020)

Fits

The fit system has been greatly improved, with an /expert=true mode featuring:

• a command-line interface with over 50 commands in the fit dialog to run fits non-interactively
• parameter space explorers, which run fits systematically with different starting parameters, to improve the chance of finding the best parameters
• possibility to run scripts, even as a fit- command-line option, which means one can now perform fully automatic fits
• the display, handling, reuse of all the previous fit attempts in a fit session (“fit trajectories”), including ways to highlight changes
• the possibility to set the fit dialog title bar
• a Particle Swarm Optimizer fit engine
• the GSL implementation of the simplex as fit engine
• a mode in sim- that just writes the residuals
• a mode in sim- to export subfunctions
• improvements to the parameters spreadsheet
• a new fit, implicit, that fits the results of equations to data, together with a define-implicit-fit to create named implicit fits
• the arb fit now has its corresponding sim-arb function

New commands

• a mem command to query for memory usage and set the size of the cache for loading datasets
• a record-meta command to permanently set meta-data to a given file
• a verify command that aborts the current script if a condition is not verified
• a define-distribution command to define distribution of parameters in fits

Improvements of previous commands

• apply-formula, eval and stats can now work on several buffers
• browse-stack, browse-stack, overlay-buffer now accept the /for-which= option to further select the buffers
• apply-formula now better handles mathematical errors (like sqrt(-1))
• load and related commands now take an /expected= option to abort with an error if the number of loaded datasets is not what one expects
• run, run-for-each and run-for-datasets now provide several ways to deal with errors in the execution of the script: ignore, abort or fail
• reglin can now be used to define a baseline to characterize peaks, and it can also show the exponential equivalent to the line
• cursor has new symmetry operations, and can work effectively with many curves
• set-perp can now take the values of perpendicular coordinates from a dataset row
• possibility to disable optimization in auto-filter-bs
• show-stack can also list the meta-data now
• Gauss-Kronrod integration for distribution of parameters and other multidimensional integrators
• help can now be run without argument to start the new documentation system. With a command argument, it will still take to the documentation of the command.

Other improvements

• new syntax for statistics and meta: one can now use $stats.y_max (etc.) in addition to $stats["y_max"] to refer to the y_max stats (and for all stats and meta too), which means that there is no need anymore for cumbersome double quoting like in eval '$stats["y_max"]'
• completion on the meta/stats names for the code
• a %{ruby code} expansion in scripts or command-line
• a set of functions (k_mhc and k_mhc_double) to Marcus-Hush-Chidsey rate constants (using the integral formula)
• a trumpet_bv function to compute the position of peaks in so-called “trumpet plots” when using Butler-Volmer kinetics
• several additional functions like ln_erfc(x), ln_gamma(x)
• a --log command-line option to choose the log file name
• a --version command-line option
• Gauss-Kronrod integrators for parameter distributions
• full support for Qt5 (support for Qt4 is dropped)
• running a command from the menu now spawns a full dialog box with the possibility to set options
• it is now possible to deduce rate constants from thermodynamic constraints in kinetic systems
• new statistics: y_a and y_b, which correspond to parameters of the linear regression of $y = f(x)$. Available for y2 and all the others, still as a function of x.
• a _sum statistic that corresponds to the sum of all elements (available for each column)
• a new comprehensive offline documentation system with index, search capacities, cross-referenced examples, and the possibility to execute commands directly from within it
• a series of startup tips
• now, using the menus to start a command will show a dialog box in which one can choose the arguments and options

Changes in version 2.2 (2018.03.21)

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
• arb 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-datasets 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 (2017.01.02)

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 (2016.07.19)

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-datasets 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-dataset 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