THIS CHANGELOG FILE CONTANS PRE-SVN CHANGELOGS AND SUMMARIES OF POST-SVN CHANGELOGS. FROM 0.8.4 ONWARD, DETAILED CHANGELOGS ARE AVAILABLE ON THE HOOKE SUBVERSION REPOSITORY. 0.8.4 (2008-x-x) PLUGINS: macro.py: hooke does not crash if it doesn't have permissions to create the folder fixed overwriting of export for curves with the same name and different numerical extension fixed macrodir (out of try-catch) cleaned debug output in execmacro DRIVERS: alternative version of picoforce driver INPUT merged (partially) libinput (so far in hooke_cli) OUTLET merged liboutlet 0.8.3 (2008-04-16) PLUGINS: generalvclamp.py: fixed autopeak header fixed autopeak slope (now unwanted slope values are discarded) 0.8.2 (2008-04-10) PLUGINS: flatfilts.py: convfilt does not crash if a file is not a curve generalvclamp.py: autopeak now saves curve data correctly autopeak now generates a dummy note (so that copylog/notelog is aware you measured the curve) 0.8.1 (2008-04-07) PLUGINS: generalvclamp.py: fixed DeprecationWarning in flatten flatfilts.py convfilt now working 0.8.0: (2008-04-04) hooke.py: sanity check of CLI plugins to avoid function overloading at startup hooke_cli.py ; libhooke.py: now playlists keep the index (when you reload the playlist, it starts from the last observed curve) updated plot to use _send_plot() hooke.conf accepts lists as arguments for variables in txt, export now have consistent argument order (thanks to A.G.Casado for pointing me that) txt crashes no more if no filename is given (thanks to A.G.Casado for pointing me that) libhookecurve.py: added add_set() , remove_set() methods to make life easier for plugin writers procplots.py: plotmanip_correct() works with new picoforce.py deflection output (see) PLUGINS: fit.py: updated wlc to use _send_plot() wlc noauto now keeps the contact point wlc reclick to click again the contact point temperature now set in hooke.conf generalvclamp.py: implemented slope (thanks to Marco Brucale) implemented autopeak flatfilts.py: convfilt,peaks use flattened curve macro.py: (new) added macro plugin (thanks to Alberto Gomez Casado) DRIVERS: picoforce.py: fixed trigger bug! (thanks to Alberto Gomez Casado) better deflection output (separated extension,retraction) 0.7.5: (2008-03-27) hooke_cli.py: removed outdated size command PLUGINS: generalvclamp.py: implemented flatten DRIVERS: added tutorialdriver.py driver csvdriver.py: fixed (forgot close_all() method) 0.7.4: (2008-03-19) added csvdriver driver hooke_cli.py: fixed plot manipulators handling (now it's safe to comment a plot manipulator on hooke.conf) PLUGINS: fit.py: fixed possible crash when clicking two times the same point on wlc 0.7.3: (2008-01-10) hooke_cli.py: fixed crash on copylog PLUGINS: massanalysis.py: Initial release tutorial.py: Tutorial plugin, initial release 0.7.2.1: (2007-11-30) PLUGINS: flatfilt.py: fixed crash on Windows 0.7.2: (2007-11-29) hooke.py: new configuration variable hookedir hooke_cli.py: copylog now checks if the destination is a real directory fixed crashes in set PLUGINS: generalvclamp.py: fixed a crash in forcebase when picking two times the same point flatfilt.py: fixed crash due to convfilt.conf impossible to load initial implementation of the blind window for convfilt initial data set maps (NOT FINISHED) 0.7.1: (2007-11-26) PLUGINS: flatfilts.py: fixed possible crash in convfilt implemented configuration file convfilt.conf convfilt defaults are now 5 peaks 5 times more the noise absdev implemented convconf implemented setconf libpeakspot.py: fixed:now it really uses noise_absdev 0.7.0: (2007-11-15) hooke_cli.py: implemented _send_plot() helper API function PLUGINS: generalvclamp.py: fixed forcebase to work with subtplot flatfilts.py: implemented convfilt! added libpeakspot.py (helping library for convolution filter) 0.6.5: (2007-11-06) hooke_cli.py, hooke.py: plateau and contact (unmaintained) deleted and scheduled for re-release in generalvramp implemented _measure_N_points() PLUGINS: generalvclamp.py: implemented forcebase fit.py: wlc now accepts and uses temperature as an argument wlc has been cleaned and uses new APIs 0.6.4: (2007-10-23) hooke_cli.py, libhooke.py: implemented support for defining order of plotmanip methods in hooke.conf hooke_cli.py: implemented delta implemented point attempted fix to bug 0033 (notelog crashing Hooke when using Unicode characters) PLUGINS: generalvramp.py: began to move velocity ramp force spectroscopy-specific things in separate plugin procplots.py: added detriggerize; "set detrigger" 0/1 disables/enables it. DRIVERS: picoforce.py: removed detriggerize() from driver 0.6.3: (2007-10-02) hooke_cli.py: rewritten txt command, now working DRIVERS: picoforce.py: implemented detriggerize() to bypass the Picoforce trigger bug PLUGINS: superimpose.py: implemented plotavgimpose 0.6.2: (2007-09-27) hooke_cli.py: fixed error handling in notelog smarter handling of directory names in genlist unexpected error handling in do_plot() hooke.py: implemented GetDisplayedPlot event and handlers PLUGINS: fit.py: fixed (bug 0029) about replotting of wlc on a subtplot curve multiple fitting displayed (to refine...) 0.6.1: (2007-08-06) libhooke.py , hooke.py: initial support for workdir configuration variable libhooke.py: fixed Driver() etc. semantics for gracefully handling unrecognized plots hooke_cli.py: fixed export namehandling fixed plot error handling PLUGINS: flatfilts.py: fixed memory leak generalclamp.py: fixed step command 0.6.0 "Anko": (2007-07-25) hooke.py: initial plugin support for the gui wlc fitting now 100% plugin measure_points replaces measure_couple etc. and provides much better extensibility hooke_cli.py: curves are sorted at beginning PLUGINS: procplots.py: fft now allows for user selection of curve segment; select the plot; etc. fit.py: added gui section of plugin, now completely independent fixed bug of wlc output superimpose.py: new plugin for superimposition of curve segments (still in development) generalclamp.py: all clamp commands now in a single plugin implemented step 0.5.4: (2007-06-15) procplots.py: fixed fft crash with Numpy 1.0.1 hooke.py: fixed crashes if plot.scatter[] was empty fixed management of multiple plots (bug #0025) hooke_cli.py fixed zpiezo error in measurement hemingclamp.py, picoforce.py: implemented close_all() method in drivers to avoid too many open files error flatfilts.py: fixed memory leak 0.5.3: (2007-06-06) wlc.py, hooke.py: fixing and cleaning fit code: now the fit is part of a PlotObject and 100% coded in wlc.py plotting of the wlc.py clicked points also begin to be part of a PlotObject management of 'scatter' style property of plots hooke_cli.py fixed measuring error in defl, zpiezo flatfilts.py: slightly optimized has_features() routine procplots.py: fixed derivplot for every number of vectors fixed possible crash of subtplot if applied on a file with != 2 plots added fft command libhookecurve.py: fixed xaxis, yaxis for non-default plots: now defined from PlotObject PlotObject now defines a styles[] vector 0.5.2: (2007-05-21) versioning a bit cleaned fixed bug in hemingclamp.py preventing filename to appear fixed wxversion problem for 2.8 fixed too many open files bug (bug 0024) added index command 0.5.1: (2007-05-09) using wxversion to choose from multiple wx versions fixed old dependencies remaining 0.5.0 "Ingyo": (2007-05-03) general code updating and rewriting due to plugin support/better plot management hooke.py: initial plugin architecture for the command line. initial plugin architecture for file drivers initial plugin architecture for processing plots export can now export both top and bottom plot (not together) hooke_cli.py: wlc fitting moved to fit.py plugin flatfilt moved to flatfilts.py plugin subtplot, derivplot moved to procplots.py plugin double plot temporarily fixed for previous commands export can now export both top and bottom plot (not together) 0.4.1: (2007-02-13) hooke_cli.py: double plot now default for clamp experiments libhooke.py: fixed bug that prevented flatfilt to work (maybe) fixed memory leak in flatfilt 0.4.0 "Hanzei": (2007-02-08) general code updating and rewriting due to double plot/force clamp supports hooke.py: initial dummy menu sketch hooke.py, hooke_cli.py: first general support in code for double plot: - derivplot now in separate plot - implemented show and close commands - all functions should be double plot-aware - clicking a point is double plot-aware libhooke.py, hooke_cli.py: general code cleanup: vectors_to_plot(), subtract_plot(), find_contact_point() and derivplot routines are now methods of class HookeCurve hooke_cli.py: implemented quit (alias of exit) implemented version libhooke.py, hooke.py, hooke_cli.py: initial support for force clamp experiments: - hemingclamp driver supported - "experiment" flag describes what kind of experiment is a curve - time, zpiezo, defl commands implemented libhemingclamp.py: inital release. 0.3.1: hooke.py: fixed stupid bug in plateau fixed bug in derivplot and subtplot not taking into account xaxes/yaxes variables 0.3.0: from now on, all changelog is stored in CHANGELOG hooke.py, libhooke.py, hooke_cli.py: fixed plot and flatfilt crash when processing corrupt files flatfilt output now more verbose implemented system (execute an external OS command) implemented copylog (copies annotated curves to a given directory) (todo 0033) initial txt implementation (exports the current curve as a text file) (todo 0023) fixed exit behaviour (bug 0013) xaxes and yaxes variables now control visualization of plot (todo 0018) new (better) contact point algorithm + workaround for the picoforce trigger bug 0.2.2 : hooke.py, hooke_cli.py, libhooke.py: support for fixed persistent length in WLC 0.2.1 : hooke.py , libhooke.py: fixed 'wlc noauto' bug (0012) preventing correct contact point to be used 0.2.0 : hooke_cli.py: implemented getlist (alias of genlist) implemented contact (to plot the contact point) fixed bug 0001 (Hooke crashes when opening a non-pf file) fixed bug 0008 (Hooke crashes when generating a playlist with malformed namefiles/nonexistent files) now the plot is refreshed after a "set" command (todo 0014) wlc fit can use the (new) automatic contact point detection (old behaviour is preserved with "noauto" option) hooke.py: fixed versioning printing complete refactoring of contact point routines wlc fit adapted to use the (new) automatic contact point detection wlc fit code a bit cleaned; parts moved to libhooke.py libhooke.py: new contact point algorithm (new algorithm) wlc fit now uses a fancier domain (from contact point to a bit more than last point); initial chunk preparation section moved from hooke.py OLDER CHANGELOGS: hooke.py: 0.1.1 : From now on, all changelog is stored in hooke.py hooke_cli.py: corrected bug 0010 (addtolist bug), alerts when hitting start/end of playlist 2006_09_15_devel=0.1.0: initial WLC fit support. We hit 0.1 milestone :D 2006_08_28_devel: refactoring of plot interaction 2006_06_14_devel: fixed libhooke calls 2006_06_08_devel: initial automatic contact point finding 2006_05_30_devel: configuration file support hooke_cli.py: 0.1.1 : from now on, all changelog is in hooke.py 2006_09_15_devel: implemented wlc; 0.1.0 milestone. 2006_08_28_devel: refactoring of plot interaction 2006_07_23_devel: implemented note; implemented flatfilt; implemented notelog; exit now warns if playlist/notes have not been saved. 2006_07_18_devel: implemented subtplot; bug 0007 ("cd" crashing) fixed 2006_06_16_devel: moved math helper functions in libhooke.py 2006_06_14_devel: fixed "jump" output; fixed "exit" (now it works!); fixed off-by-one bug in deflection-correction 2006_06_08_devel: fixed "loadlist" output; 2006_05_30_devel: initial configuration file support; added "set" command; initial deflection-correction support; added "ls" command as an alias of "dir" 2006_05_23_devel: rewriting of playlist-handling code due to major rewrite of hooke_playlist.py libhooke.py 0.1.1 : from now on, all changelog is in hooke.py 2006_09_15_devel : initial WLC support 2006_09_14_devel : initial support for Hemingway velocity clamp files, minor refactorings 2006_07_22_devel : implemented math function has_features 2006_06_16_devel : math functions moved here 2006_06_08_devel : hooke_playlist.py becomes libhooke.py 2006_05_30_devel : support for deflection in HookeCurve 2006_05_29_devel : Initial configuration file support 2006_05_23_devel : Major rewrite. Fixed bug 0002