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Function listing

jamesjun edited this page Oct 31, 2017 · 3 revisions

Spike sorting

  • makeprm_(): Create a new parameter file. Called by "jrc makeprm myrecording.bin myprobe.prb".
  • clear_(): Clear memory used by JRCLUST. Called by "jrc clear" or "jrc clear myparam.prm"
  • edit_(): Edit .prm file. Called by "jrc edit myparam.prm".
  • detect_(): Spike detection and feature extraction. Called by "jrc detect myparam.prm"
  • auto_(): Post-cluster automated merging. Called by "jrc auto myparam.prm".
  • describe_(): Describe the clustered data. Called by "jrc describe myparam.prm".
  • sort_(): Cluster spikes. Called by "jrc sort myparam.prm"

Installation

Documentation and help functions

  • wiki_(): Open a Github Wiki page. Called by "jrc wiki" or "jrc wiki command page_name".
  • wiki_download_(): Download the entire Github wiki page. Called by "jrc wiki-download".
  • doc_(): Open a PDF manual ("JRCLUST manual.pdf"). Called by "jrc doc". To be removed since Github Wiki contains the latest documentation.
  • help_(): Print a help text. Called by "jrc help"

Batch process

  • batch_(): Batch process. Called by "jrc batch mylist.batch".
  • batch_mat_(): Batch process a .mat file containing .
  • batch_plot_(): Plot spiking activities from multiple sessions. Called by "jrc batch-plot mylist.batch".
  • batch_verify_(): Batch process and verify ground truth.
  • dir_files_(): Find list of files that matches the wild card. Called by "jrc dir e:\myfiles*.bin".

Deployment

  • update_(): Download the latest version by copying from the local Dropbox folder location. Called by "jrc download". Dropbox location must be specified in "user.cfg\path_dropbox".
  • jrc_version_(): Display JRCLUST version number and last updated date. Called by "jrc version".
  • about_(): Display version, author, and requirements. Called by "jrc about".
  • git_pull_(): Download the latest version from Github. Called by "jrc git-pull" or "jrc git-pull version_name".
  • disp_dependencies_(): Display code and toolbox dependencies. Called by "jrc dependencies".
  • download_(): Download sample data. Called by "jrc download sample".
  • issue_(): Leave an issue on Github. Called by "jrc issue"

GUI functions

  • traces_(): Plot traces GUi. Called by "jrc traces myparam.prm".
  • plot_drift_(): Plot spike position vs. time. Called by "jrc drift myparam.prm".
  • plot_rd_(): Plot Rho vs. Delta plot (Rodriguez-Laio). Called by "jrc plot-rd".
  • probe_(): Plot probe layout. Called by "jrc probe myprobe.prb".
  • preview_(): preview GUI. Called by "jrc preview myparam.prm".
  • manual_(): manual sorting GUI. Called by "jrc manual myparam.prm"
  • plot_activity_(): Plot activity rate vs. time. Called by "jrc plot-activity myparam.prm".
  • gui_(): Launch a main GUI. Called by "jrc gui".

Developer's functions

Other spike sorting

  • kilosort_(): Run Kilosort. Called by "jrc kilosort myparam.prm".

Export

Import

Utility functions

find_site_spk23_ mn2tn_wav_spk2_ disp_cs_ find_prb_ jrcpath_ keyPressFcn_Fig_traces_ str_toggle_ key_modifier_ spk_pos_ trWav2fet_cov_ spkwav_car_ tr_sort_ref_ mr2vr_sub2ind_ mem_max_ plan_load_ setlim_ load_file_preview_ load_file_ get_ loadParam_ calc_maxSite_ get_filter_ spikeMerge_ spikeMerge_single_ findNearSite_ car_reject_ expand_vr_ find_peak_ cell2mat_ findRange_ centroid_mr_ fet2clu_ partition_vi_ eucl2_dist_ cluster_spacetime_ cuda_rho_ cuda_delta_ compute_dc2_ quantile_ fet12_site_ fet12_site_1_ validate_ load_gt_ gt2spk_ sgfilt4_ sgfilt_init_ mr2rms_ post_merge_

Struct

struct_get_ remove_struct_ write_struct_

File handling

fopen_ read_cfg_ load_cached_ load_prb_ search_file_ subsDir_ write_bin_ load_bin_multi_

GUI support

change_amp_

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