{"id":18963935,"url":"https://github.com/janeliascicomp/tmt","last_synced_at":"2025-04-19T12:48:23.944Z","repository":{"id":137881527,"uuid":"12250647","full_name":"JaneliaSciComp/tmt","owner":"JaneliaSciComp","description":"A toolbox of Matlab functions useful for data analysis, especially of electrophysiology data.","archived":false,"fork":false,"pushed_at":"2025-03-28T21:34:38.000Z","size":1500,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":22,"default_branch":"main","last_synced_at":"2025-03-28T22:30:57.218Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"MATLAB","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/JaneliaSciComp.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2013-08-20T18:25:20.000Z","updated_at":"2025-03-28T21:34:42.000Z","dependencies_parsed_at":null,"dependency_job_id":"bc0a6865-1304-469c-8ef8-92cfbbb5dde0","html_url":"https://github.com/JaneliaSciComp/tmt","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Ftmt","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Ftmt/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Ftmt/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Ftmt/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JaneliaSciComp","download_url":"https://codeload.github.com/JaneliaSciComp/tmt/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249201117,"owners_count":21229004,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-08T14:22:34.368Z","updated_at":"2025-04-16T05:31:32.134Z","avatar_url":"https://github.com/JaneliaSciComp.png","language":"MATLAB","readme":"TMT\n===\n\nTMT is a library of Matlab functions, centered around the analysis \nof electrophysiology data.\n\n\nSystem Requirements\n-------------------\n\nMatlab R2013b or later (64-bit)\n\n\nInstallation\n------------\n\n1.  Unzip the .zip file to a place of your choosing.\n\n2.  In Matlab, go to File \u003e Set Path... \n\n3.  Remove any paths for older versions of TMT.\n\n3.  Still in File \u003e Set Path, click on \"Add with Subfolders...\" and\n    select the tmt-release_(whatever) folder that was created when\n    you unzipped the .zip file.\n\n\nCopyright\n---------\n\nAll files included in TMT present in version 1.09 are copyright Adam\nL. Taylor, 1997-2011.  All files after this point, and additions to\nexisting files, are copyright Howard Hughes Medical Institute,\n2011-infinity.\n\n\nLicense\n-------\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are\nmet:\n\n* Redistributions of source code must retain the above copyright\n  notice, this list of conditions and the following disclaimer.\n\n* Redistributions in binary form must reproduce the above copyright\n  notice, this list of conditions and the following disclaimer in the\n  documentation and/or other materials provided with the distribution.\n\n* Neither the name of HHMI nor the names of its contributors may be\n  used to endorse or promote products derived from this software\n  without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS\n\"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT\nLIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR\nA PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT\nOWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\nSPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\nLIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,\nDATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY\nTHEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT\n(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\nOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n\n\nAuthor\n------\n\n[Adam L. Taylor](http://www.janelia.org/people/research-resources-staff/adam-taylor), taylora@hhmi.org  \n[Scientific Computing](http://www.janelia.org/research-resources/computing-resources)  \n[Janelia Research Campus](http://www.janelia.org)  \n[Howard Hughes Medical Institute](http://www.hhmi.org)\n\n[![Picture](/hhmi_janelia_160px.png)](http://www.janelia.org)\n\n\nVersion History\n---------------\n\n1.01\n\nAdded hds/ directory, the \"Hessian direction set\" optimization routine.  \nNote that it now has a switch so that you can do fixed direction set, \nPowell's method, or my \"Hessian direction set\" method.\n\nAdded help for the function event_triggered().\n\nDeleted event_triggered_double(), since one can just call \nevent_triggered() twice.\n\nDeleted fig_triggered_average(), redundant.\n\nRenamed four functions with names like fig_spike_triggered_whatever() to \nfig_event_triggered_whatever, for consistency.\n\nChanged hist_from_data() to more recent version.\n\nDeleted histc_from_data(), so hist_from_data() and histc_from_data() \nweren't out-of-register.  Should probably rewrite histc_from_data() to\nbe parallel to new hist_from_data().\n\n-----\n\n1.02\n\nRemoved cov(), because there's a cov() function built into Matlab that \ndoes the same thing.  How did I miss that?\n\nAdded bipolar(), a colormap function.\n\nChanged to using newer version (2.31) of MATLAB SON Library.  Changed my \nfunctions that do SON stuff to be compatible.  Ted Brookings did the\nmodification of load_smr().\n\nChanged to making the user download MATLAB SON Library themselves, because \nMalcolm Lidierth asked us to.\n\n-----\n\n1.03\n\nMoved testing code out of the library, so that adding the library to path\ndoesn't add any 'modpath.m' files to the path.\n\nDeleted analyze_*.m functions, Z_all_sweeps() from \ndata_analysis/impedance_fitting.  Those functions are really not of general \nutility.\n\nAdded get_home_dir_name() function.\n\n-----\n\n1.04\n\nAdded stg_spectra directory under data_analysis.  This includes code for \nmaking spectrograms and cohereograms in a way that's tailored for use\nwith STG rhythms.  Some functions also added in other places to support this.\nThe code for the plots is similar to what we used for Kris' paper, except we\nno longer do the gaussian filtering before calculating the spectra.\n\n-----\n\n1.05\n\nAdded function for plotting classic phase diagrams.\n\nAdded functions for setting ylims on all axes in a figure.\n\nAdded functions mean_circular() and std_circular, for calculating the\nmean and standard deviation of angles.\n\nAdded function set_axes_size().\n\nChanged print_pdf() to use ghostscript, and to work on UNIX.\n\nChanged print_png() to work on UNIX.\n\nChanged print_tiff() to work on UNIX.\n\nFixed bug in save_tabular_data() -- didn't open file in text mode.\n\n-----\n\n1.06\n\nChanged some of the spectrogram and coherogram plotting functions to\nbe more rational.\n\n-----\n\n1.07\n\nAdded get_figure_size() function.\n\nChanged times_to_rate_gaussian() so it no longer uses convn().\n  Assuming there are not too many spikes, this should make it\n  faster most of the time.\n\nChanged print_png(), print_eps(), print_pdf(), print_tiff() to not use\n  deprecated -adobecset switch to the built-in print() function.\n\nDeleted show(), because I decided it was too special-purpose.\n\nDeleted chart(), because I decided it was too special-purpose.\n\nDeleted browse(), because I decided it was too special-purpose.\n\nDeleted vcr(), because I decided it was too special-purpose.\n\nDeleted stg_spectra(), because I decided it was too special-purpose.\n\nDeleted impedance_fitting(), because I decided it was too special-purpose.\n\nDeleted load_abf(), replaced it with Michael Sorenson's excellent\n  readabf(), because readabf() is better.\n\nAdded some documentation to line_wrap().\n\nAdded patch_eb(), a simple function to make plotting error bars as patches \n  easier.\n\nAdded patch_eb_wrap(), a function for plotting error bars on angular \n  quantities as patches.\n\nAdded break_at_wrap_points(), a function that factors out common functionality\n  in line_wrap() and patch_eb_wrap().\n\n-----\n\n1.08  (March 7, 2011)\n\nGot rid of readabf(), because had some problems with it.  Put\n  load_abf() back in.\n\nChanged all the multitaper code to versions that analyze one signal,\n  or a pair of signals, at a time.\n\nAdded utility scripts ll and la.\n\nAdded get_axes_size()\n\nAdded set_axes_size_fixed_center()\n\nAdded rate_from_times_and_timeline_gaussian()\n\nAdded rate_from_times_and_timeline_simple()\n\nGot rid of plot_wrap()\n\nGot rid of break_at_wrap_points_with_eb(), wasn't used.\n\nAdded load_tiff_series()\n\nAdded load_multi_image_tiff_file()\n\n-----\n\n1.09 (May 12, 2011)\n\nFixed bug in coh_mt that lead to NaN's in Cxy_mag getting converted to 1's.\n\n-----\n\n1.10 (August 29, 2011)\n\nAdded blue_to_yellow() colormap function.\n\nAdded set_axes_position().\n\nRenamed figure_cohereogram() to figure_cohgram().\n\nRenamed figure_spectrogram_amp() to figure_powgram().\n\nRenamed plot_cohereogram() to plot_cohgram().\n\nRenamed plot_spectrogram_amp() to plot_powgram().\n\nRenamed fig_coh_polar() to figure_coh_polar().\n\nChanged figure_cohgram(), plot_cohgram() so that they accept the\n  spectrogram in the same units as returned by powgram_mt(), and takes\n  an additional argument that specifies the units for plotting.\n\nChanged load_abf() so it now returns the channel names and channel\n  units for each channel read in.\n\nAdded a function called load_abf_by_channel_name(), which does what\n  you would imagine.\n\nChanged patch_eb() so that it divides up the data to make no single\n  patch too big.\n\nFixed patch_eb_wrap() so that it actually returns an array of patch\n  object handles.\n\nAdded line_eb(), line_eb_wrap() as drop-in replacements for\n  patch_eb(), and patch_eb_wrap(), for cases where patches are too\n  slow.\n\nAdded pow_mt_windowed(), coh_mt_windowed(), that make it more\n  convenient to average over windows when calculating spectral\n  estimates.\n\nChanged load_named_event_channel_from_smr() to have better error\n  messages.\n\nChanged print_pdf() so that it uses the executable gswin64c on 64-bit\n  windows machines.\n\nAdded tf_mt(), estimates transfer functions of two signals.\n\nChanged coh_mt() to make internal variable names agree with tf_mt(),\n  but no user-visible changes.\n\nAdded tf_mt_windowed(), analogous to coh_mt_windowed().\n\nAdded tfgram_mt(), analogous to cohgram_mt().\n\nAdded figure_tf(), figure_coh().\n\nAdded a number of functions for reading and writing .tcs files, a file\n  format I made up for storing trace data that is easy to import into\n  Spike2.\n\n-----\n\n1.11 (December 16, 2011)\n\nMinor changes to several of the spectral plotting functions.\n\n-----\n\n1.12 (March 6, 2012)\n\nAdded functions for doing motion-correction of video.\n\nAdded functions for doing 'anonymous' saving and loading of .mat files.\n\n-----\n\n1.13 (April 24, 2012)\n\nMinor improvements.\n\n-----\n\n1.14 (November 16, 2012)\n\nMinor improvements.\n\n-----\n\n1.15 (July 28, 2014)\n\nMinor improvements.\n\n-----\n\n1.16 (May 3, 2015)\n\nFixed bugs with under-specification of character sets in load_abf()\nand .tcs reading and writing files.\n\n-----\n\n1.17 (June 29, 2015)\n\nUpdated README, added license notice.\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjaneliascicomp%2Ftmt","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjaneliascicomp%2Ftmt","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjaneliascicomp%2Ftmt/lists"}