From b2ef37ad8c96635ba276a99762a0b533400ddd74 Mon Sep 17 00:00:00 2001
From: Henry Nomeland <nomeland@waisman.wisc.edu>
Date: Thu, 22 Feb 2024 10:39:42 -0600
Subject: [PATCH 01/11] testing

---
 .gitignore    | 4 ++++
 wave_viewer.m | 7 ++-----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/.gitignore b/.gitignore
index 454c7ff..b5dd851 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,7 @@
 # matlab autosave files
 *.asv
 *.m~
+# other files being used in testing
+audioGUI.m
+*.mat
+*/*
diff --git a/wave_viewer.m b/wave_viewer.m
index dec0bff..2165e7c 100644
--- a/wave_viewer.m
+++ b/wave_viewer.m
@@ -124,7 +124,7 @@
 %% set up GUI
 
 % create new figure
-hf = figure('Name',p.plot_params.name,'Units','normalized','Position',p.plot_params.figpos);
+hf = figure('Name',p.plot_params.name,'Units','normalized','Position',p.plot_params.figpos); 
 set(hf,'DeleteFcn',@delete_func);
 
 p.guidata = guihandles(hf);
@@ -390,10 +390,6 @@ function edit_events(hObject,eventdata) % callback for h_button_edit_events
         end
     end
 
-
-
-
-
 % clear events button
 clearEventsButtonPos = [padL+buttonWidth*1/2 horiz_orig buttonWidth*1/2 buttonHeight];
 hbutton.clear_events = uicontrol(p.guidata.buttonPanel,'Style','pushbutton',...
@@ -669,6 +665,7 @@ function toggle_formants(hObject,eventdata) % callback for hbutton.toggle_forman
         end
         set(gram_ax,'UserData',axinfo);
     end
+
 % calc button
 calcButtonPos = [padL horiz_orig buttonWidth buttonHeight];
 hbutton.calc = uicontrol(p.guidata.buttonPanel,'Style','pushbutton',...

From 32260d63c668069077947c07d54d06fd33476ebd Mon Sep 17 00:00:00 2001
From: Henry Nomeland <nomeland@waisman.wisc.edu>
Date: Thu, 21 Mar 2024 09:34:33 -0500
Subject: [PATCH 02/11] small updates

---
 get_formant_tracks.m | 203 ++++---------------------------------------
 1 file changed, 15 insertions(+), 188 deletions(-)

diff --git a/get_formant_tracks.m b/get_formant_tracks.m
index 8fab430..43d90b1 100644
--- a/get_formant_tracks.m
+++ b/get_formant_tracks.m
@@ -1,8 +1,5 @@
 function [ftrack_out,ftrack_mstaxis,ftrack_lpc_coeffs] = get_formant_tracks(y,fs,faxis,ms_framespec,nlpc_coeffs,yes_preemph,nformants,ftrack_method,yes_verbose)
 
-frames_per_dot = 10;
-dots_per_line = 50;
-
 if nargin < 2 || isempty(fs), fs = 11025; end
 if nargin < 3 || isempty(faxis), faxis = linspace(0,fs/2,1025); end
 if nargin < 4 || isempty(ms_framespec), ms_framespec = 'narrowband'; end
@@ -15,9 +12,6 @@
 params.fs = fs;
 params.nlpc = nlpc_coeffs;
 switch ftrack_method
-    case 'colea', ftrack_func = @colea_ftrack_func; params.nformants_max = 3; params.yes_trackperframe = 1;
-    case 'mine',  ftrack_func = @my_ftrack_func;    params.nformants_max = 3; params.yes_trackperframe = 1;
-    case 'mine2', ftrack_func = @my_ftrack_func2;   params.nformants_max = 4; params.yes_trackperframe = 1;
     case 'praat', ftrack_func = @praat_ftrack_func; params.nformants_max = 5; params.yes_trackperframe = 0;
     otherwise, error('formant tracking method(%s) unrecognized',ftrack_method);
 end
@@ -26,41 +20,18 @@
 params.nformants = nformants;
 params.faxis = faxis;
 
-starting_formants = [500 1500 2500 3500];
-
-[nsamps,yes_y_is_rowvec] = get_len_yvec(y);
+[nsamps,~] = get_len_yvec(y);
 [ms_awin,ms_astep,nsamps_frame,nsamps_astep] = get_ms_framespec(ms_framespec,fs);
-win = hann(nsamps_frame)/sum(hann(nsamps_frame));
-if ~yes_y_is_rowvec, win = win'; end
 y = my_preemph(y,yes_preemph);
 nframes = floor((nsamps - nsamps_frame)/nsamps_astep);
-ftrack = zeros(nformants,nframes);
-ftrack_mstaxis = zeros(1,nframes);
-lpc_coeffs = zeros((nlpc_coeffs+1),nframes);
 
-if params.yes_trackperframe % if tracker operates on a frame-by-frame basis within Matlab
-    for iframe = 1:nframes
-        yframe = y((iframe-1)*nsamps_astep + (1:nsamps_frame));
-        ftrack_mstaxis(iframe) = 1000*mean((iframe-1)*nsamps_astep + (1:nsamps_frame))/fs;
-        ywinframe = win .* yframe;
-        if iframe > 1, params.Fprev = ftrack(:,iframe-1); else params.Fprev = starting_formants; end
-        output = ftrack_func(ywinframe,params);
-        ftrack(:,iframe) = output{1};
-        lpc_coeffs(:,iframe) = output{2};
-        if yes_verbose
-            if ~rem(iframe,frames_per_dot), fprintf('.'); end
-            if ~rem(iframe,frames_per_dot*dots_per_line), fprintf('%d\n',iframe); end
-        end
-    end
-else                        % if we want to pass entire utterance to external tracker
-    params.window_size = ms_awin/1000;
-    params.step_size = ms_astep/1000;
-    params.nframes = nframes;
-    output = ftrack_func(y,params);
-    ftrack = output{1};
-    lpc_coeffs = output{2};
-    ftrack_mstaxis = output{3};
-end
+params.window_size = ms_awin/1000;
+params.step_size = ms_astep/1000;
+params.nframes = nframes;
+output = ftrack_func(y,params);
+ftrack = output{1};
+lpc_coeffs = output{2};
+ftrack_mstaxis = output{3};
 
 % ftrack_out(1:nformants,1:nframes) = ftrack(1:nformants,1:nframes);
 ftrack_out(1:nformants,:) = ftrack(1:nformants,:); %removing nframes allows for praat tracking
@@ -69,64 +40,6 @@
 end
 if nargout >= 3, ftrack_lpc_coeffs = lpc_coeffs; end
 
-
-% must have colea on matlab path to use this function
-function output = colea_ftrack_func(ywinframe,params)
-
-fs = params.fs;
-nlpc_coeffs = params.nlpc;
-nformants = params.nformants;
-
-lpc_coeffs = lpc(ywinframe,nlpc_coeffs);
-[frmnt(1),frmnt(2),frmnt(3)] = frmnts(lpc_coeffs,fs);
-formant(1:nformants) = frmnt(1:nformants);
-
-output{1} = formant;
-output{2} = lpc_coeffs;
-
-function output = my_ftrack_func(ywinframe,params)
-
-fs = params.fs;
-nlpc_coeffs = params.nlpc;
-nformants = params.nformants;
-
-lpc_coeffs = lpc(ywinframe,nlpc_coeffs);
-[frmnt(1),frmnt(2),frmnt(3)] = my_frmnts(lpc_coeffs,fs);
-
-formant(1:nformants) = frmnt(1:nformants);
-
-output{1} = formant;
-output{2} = lpc_coeffs;
-
-
-function output = my_ftrack_func2(ywinframe,params)
-
-fs = params.fs;
-faxis = params.faxis;
-nlpc_coeffs = params.nlpc;
-nformants = params.nformants;
-Fprev = params.Fprev;
-
-lpc_coeffs = lpc(ywinframe,nlpc_coeffs);
-lpc_magspec = get_lpc_magspec(lpc_coeffs,faxis,fs);
-[lpc_magspec_peaks,nlpc_magspec_peaks] = peakfind(lpc_magspec);
-for iformant = 1:nformants
-  if iformant < nlpc_magspec_peaks
-    formant(iformant) = faxis(lpc_magspec_peaks(iformant));
-  elseif iformant == nlpc_magspec_peaks
-    formant(iformant) = faxis(lpc_magspec_peaks(iformant));
-    if abs(Fprev(iformant)-formant(iformant)) > 75
-        formant(iformant) = Fprev(iformant);
-    end
-  else
-    formant(iformant) = Fprev(iformant);
-  end
-end
-
-output{1} = formant;
-output{2} = lpc_coeffs;
-
-
 function output = praat_ftrack_func(y,params)
 % execute Praat script using params
 %must be in git repo folder to run praat function, so save current location and go there
@@ -136,8 +49,6 @@
 cd(praat_path)
 
 fs = params.fs;
-faxis = params.faxis;
-nlpc_coeffs = params.nlpc;
 nformants = params.nformants;
 
 %%% Praat wrapper code here
@@ -158,10 +69,10 @@
     error('Something went wrong in Praat analysis')
 end
 
-% clean up praat output text file to eliminate uniterpretable characters
+% clean up praat output text file to eliminate uninterpretable characters
 A = regexp( fileread('temp_wav_formants.txt'), '\n', 'split');
 headers = strsplit(A{1},'\t');
-if length(headers) == 1 %for some reason Praat sometimes uses a space to separate headers
+if length(headers) == 1 % for some reason Praat sometimes uses a space to separate headers
     headers = strsplit(A{1},' ');
 end
 for i = 1:length(headers)
@@ -180,7 +91,7 @@
 % load formant tracks from file written by Praat and put in 'formant' output
 formant_vals = readtable('temp_wav_formants.txt','Delimiter','\t');
 
-%find number of formant values returbned by praat
+%find number of formant values returned by praat
 for nf = 1:nformants
     form=['F' num2str(nf)];
     formant(nf,:) = formant_vals.(form)';
@@ -189,96 +100,12 @@
 %find times of formants
 msaxis = formant_vals.time';
 
-% load LPC values from file written by Praat and put in 'lpc_coeffs' output
-% lpc_coeffs = dlmread('temp_wav_lpc.txt','\t');
-lpc_coeffs = [];
-% clean up by deleting files that were created and return to previous
-% directory
-delete temp_wav.wav temp_wav_formants.txt %temp_wav_lpc.txt
+% clean up by deleting files and return to previous directory
+delete temp_wav.wav temp_wav_formants.txt
 cd(curr_dir)
 
+% establish outputs
+lpc_coeffs = [];
 output{1} = formant;
 output{2} = lpc_coeffs;
 output{3} = msaxis * 1000; %covert from s to ms
-
-
-% my version of the colea frmnts function,
-% orinally copyright (c) 1998 by Philipos C. Loizou
-function [F1,F2, F3]=my_frmnts(lpc_coeffs,fs)
-
-global F1prev F2prev F3prev
-
-min_formant_freq =   90;
-max_formant_freq = 4000;
-max_formant_bw   =  500;
-defaultF1 = 300; defaultF2 = 1200; defaultF3 = 3000;
-
-max_allowable_F1dev     = 150;
-max_allowable_F2dev     = 150;
-min_initial_formant_sep =  80;
-min_formant_sep         =  50;
-
-const = fs/(2*pi);
-rts = roots(lpc_coeffs);
-k = 1;
-for i=1:length(lpc_coeffs)-1
-  re = real(rts(i)); im = imag(rts(i));
-  the_formant_cand = const*atan2(im,re);   %--formant frequencies
-  formant_bw = -0.5*const*log(abs(rts(i)));%--formant bandwidth
-  if (the_formant_cand < max_formant_freq) & ...
-     (the_formant_cand > min_formant_freq) & ...
-     (formant_bw < max_formant_bw)
-    unsort_candidate_formant(k) = the_formant_cand;
-    bandw(k) = formant_bw;
-    k = k + 1;
-  end
-end
-candidate_formant = sort(unsort_candidate_formant);
-ncand_formants = length(candidate_formant);
-
-if isempty(F1prev) %++++++++++++++++ the first frame ++++++++++++++++++
-  if 2 > ncand_formants
-    F1 = defaultF1; F2 = defaultF2; F3 = defaultF3;
-  elseif abs(candidate_formant(1)-candidate_formant(2)) < min_initial_formant_sep
-    F1 = candidate_formant(2); F2 = candidate_formant(3);
-    if 3 > ncand_formants, F3 = candidate_formant(4); else F3 = defaultF3; end
-  elseif 4 == ncand_formants
-    F1 = candidate_formant(2); F2 = candidate_formant(3);
-    F3 = candidate_formant(4);
-  else
-    F1 = candidate_formant(1); F2 = candidate_formant(2); 
-    if 3 > ncand_formants, F3 = defaultF3; else F3 = candidate_formant(3); end
-  end
-else %++++++++++++++++ all frames after the first ++++++++++++++++++
-     %----Impose some formant continuity constraints -------------------
-  in1 = find(abs(F1prev-candidate_formant) < max_allowable_F1dev);
-  in2 = find(abs(F2prev-candidate_formant) < max_allowable_F2dev);
-  if length(in1) > 1, i1 = in1(2); else i1 = in1; end
-  if length(in2) > 1, i2 = in2(2); else i2 = in2; end
-  
-  switch (10*(~isempty(i1)) + (~isempty(i2)))
-    case 11
-      if i1 == i2
-        if 1 > ncand_formants, F1 = F1prev; else F1 = candidate_formant(1); end
-        if 2 > ncand_formants, F2 = F2prev; else F2 = candidate_formant(2); end
-        if 3 > ncand_formants, F3 = F3prev; else F3 = candidate_formant(3); end
-      else
-        F1 = candidate_formant(i1); F2 = candidate_formant(i2); 
-        if i2 + 1 > ncand_formants, F3 = F3prev; else F3 = candidate_formant(i2 + 1); end
-      end
-    case 10
-      F1 = candidate_formant(i1);
-      if i1 + 1 > ncand_formants, F2 = F2prev; else F2 = candidate_formant(i1 + 1); end
-      if i1 + 2 > ncand_formants, F3 = F3prev; else F3 = candidate_formant(i1 + 2); end
-    otherwise
-      F1 = candidate_formant(1);
-      if 2 > ncand_formants, F2 = F2prev; else F2 = candidate_formant(2); end
-      if 3 > ncand_formants, F3 = F3prev; else F3 = candidate_formant(3); end
-  end
-end
-
-% --last check .. --------
-if abs(F2-F3) < min_formant_sep, F2 = F2prev; F3 = F3prev; end
-if abs(F2-F1) < min_formant_sep, F2 = F2prev; F3 = F3prev; end
-
-F1prev = F1; F2prev = F2; F3prev = F3;

From 002bbc25887fa9efe8d39ae42fa6ce12a4deb5db Mon Sep 17 00:00:00 2001
From: Henry Nomeland <nomeland@waisman.wisc.edu>
Date: Tue, 2 Apr 2024 10:40:54 -0500
Subject: [PATCH 03/11] fast track testing

---
 .gitignore                                    |   1 +
 ...mant_tracks.praat => get_fast_tracks.praat |  26 ++--
 get_formant_tracks.m                          | 138 +++++++++---------
 3 files changed, 86 insertions(+), 79 deletions(-)
 rename get_formant_tracks.praat => get_fast_tracks.praat (50%)

diff --git a/.gitignore b/.gitignore
index b5dd851..9e85ac2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@
 audioGUI.m
 *.mat
 */*
+temp_wav.wav
diff --git a/get_formant_tracks.praat b/get_fast_tracks.praat
similarity index 50%
rename from get_formant_tracks.praat
rename to get_fast_tracks.praat
index 01d2d66..20d4cd8 100644
--- a/get_formant_tracks.praat
+++ b/get_fast_tracks.praat
@@ -1,19 +1,22 @@
-# get_formants.praat
-# BEN PARRELL 18 DEC 2017
+# get_fast_tracks.praat by Henry Nomeland, 21 Mar 2024
+# adapted from get_formants.praat by Ben Parrell, 18 Dec 2017
 #
-# Measure formants for whole .wav file
-# For use with wave_viewer
+# measures formants for a .wav file utilizing tools and utils of FastTrack
+# FastTrack code available here: https://github.com/santiagobarreda/FastTrack/
+# for use with wave_viewer
+
+include utils/trackAutoselectProcedure.praat
 
 #Inputs
 form Measure formant values for segments in a textgrid
     sentence directory_name: /Users/Ben/Documents/MATLAB/wave_viewer
-	sentence file_name: temp_wav
+    sentence file_name: temp_wav
+    positive minimum_formant 0
     positive maximum_formant 5500
-    positive number_of_formants 5
-	positive window_size 0.025
-    positive time_step 0.005
-	positive preemphasis 50
-	positive fs 11025
+    positive number_steps 100
+    positive num_coefs 10
+    positive num_formants 3
+    sentence tracking_method: burg
 endform
 
 #open the sound and select it
@@ -22,7 +25,8 @@ Read from file... 'directory_name$'/'wav_name$'
 soundID1$ = selected$("Sound")
 
 #extract formants
-To Formant (burg)... 'time_step' 'number_of_formants' 'maximum_formant' 'window_size' 'preemphasis'
+@trackAutoselectProcedure: soundID1$, directory_name$, minimum_formant, maximum_formant, number_steps, num_coefs, num_formants, tracking_method$, 0, soundID1$, 0, 5500, 2, 0, 0
+selectObject: soundID1$
 formant = selected ("Formant")
 
 #write formants
diff --git a/get_formant_tracks.m b/get_formant_tracks.m
index 43d90b1..feb2496 100644
--- a/get_formant_tracks.m
+++ b/get_formant_tracks.m
@@ -6,7 +6,7 @@
 if nargin < 5 || isempty(nlpc_coeffs), nlpc_coeffs=14; end
 if nargin < 6 || isempty(yes_preemph), yes_preemph = 1; end
 if nargin < 7 || isempty(nformants), nformants = 0; end
-if nargin < 8 || isempty(ftrack_method), ftrack_method = 'mine'; end
+if nargin < 8 || isempty(ftrack_method), ftrack_method = 'praat'; end
 if nargin < 9 || isempty(yes_verbose), yes_verbose = 0; end
 
 params.fs = fs;
@@ -41,71 +41,73 @@
 if nargout >= 3, ftrack_lpc_coeffs = lpc_coeffs; end
 
 function output = praat_ftrack_func(y,params)
-% execute Praat script using params
-%must be in git repo folder to run praat function, so save current location and go there
-curr_dir = pwd;
-temp_str = which('get_formant_tracks.praat');
-praat_path = fileparts(temp_str);
-cd(praat_path)
-
-fs = params.fs;
-nformants = params.nformants;
-
-%%% Praat wrapper code here
-% write y to file (this will be deleted later, it is just written to the
-% current directory)
-audiowrite('temp_wav.wav',y,fs)
-
-% set praat params that are not changeable
-max_formant = 5500;
-preemphasis = 50;
-
-if ismac
-    status = system(['"/Applications/Praat.app/Contents/MacOS/Praat" --run get_formant_tracks.praat "' pwd '" "temp_wav" ' num2str(max_formant) ' ' num2str(params.nlpc/2) ' ' num2str(params.window_size) ' ' num2str(params.step_size) ' ' num2str(preemphasis) ' ' num2str(params.fs)]);
-else
-    status = system(['"C:\Users\Public\Desktop\Praat.exe" --run get_formant_tracks.praat "' pwd '" "temp_wav" ' num2str(max_formant) ' ' num2str(params.nlpc/2) ' ' num2str(params.window_size) ' ' num2str(params.step_size) ' ' num2str(preemphasis) ' ' num2str(params.fs)]);
-end
-if status ~= 0
-    error('Something went wrong in Praat analysis')
-end
-
-% clean up praat output text file to eliminate uninterpretable characters
-A = regexp( fileread('temp_wav_formants.txt'), '\n', 'split');
-headers = strsplit(A{1},'\t');
-if length(headers) == 1 % for some reason Praat sometimes uses a space to separate headers
-    headers = strsplit(A{1},' ');
-end
-for i = 1:length(headers)
-    curTxt = headers{i};
-    startUnits = strfind(curTxt,'(');
-    if ~isempty(startUnits)
-        curTxt = curTxt(1:startUnits-1);
-        headers{i} = curTxt;
+%%% function which executes Praat script using params
+    %must be in git repo folder to run praat function, so save current location and go there
+    curr_dir = pwd;
+    temp_str = which('get_fast_tracks.praat');
+    praat_path = fileparts(temp_str);
+    cd(praat_path)
+    
+    fs = params.fs;
+    nformants = params.nformants;
+    
+    %%% Praat wrapper code here
+    % write y to file (this will be deleted later, it is just written to the
+    % current directory)
+    audiowrite('temp_wav.wav',y,fs)
+    
+    % set praat params that are not changeable
+    max_formant = 5500;
+    preemphasis = 50;
+    
+    if ismac
+        status = system(['"/Applications/Praat.app/Contents/MacOS/Praat" --run get_fast_tracks.praat "' pwd '" "temp_wav" ' num2str(max_formant) ' ' num2str(params.nlpc/2) ' ' num2str(params.window_size) ' ' num2str(params.step_size) ' ' num2str(preemphasis) ' ' num2str(params.fs)]);
+    else
+        status = system(['"C:\Users\Public\Desktop\Praat.exe" --run get_fast_tracks.praat "' pwd '" "temp_wav" ' num2str(max_formant) ' ' num2str(params.nlpc/2) ' ' num2str(params.window_size) ' ' num2str(params.step_size) ' ' num2str(preemphasis) ' ' num2str(params.fs)]);
     end
-end
-A{1} = strjoin(headers,'\t');
-fid = fopen('temp_wav_formants.txt','w');
-fprintf(fid, '%s\n', A{:});
-fclose(fid);
-
-% load formant tracks from file written by Praat and put in 'formant' output
-formant_vals = readtable('temp_wav_formants.txt','Delimiter','\t');
-
-%find number of formant values returned by praat
-for nf = 1:nformants
-    form=['F' num2str(nf)];
-    formant(nf,:) = formant_vals.(form)';
-end
-
-%find times of formants
-msaxis = formant_vals.time';
-
-% clean up by deleting files and return to previous directory
-delete temp_wav.wav temp_wav_formants.txt
-cd(curr_dir)
-
-% establish outputs
-lpc_coeffs = [];
-output{1} = formant;
-output{2} = lpc_coeffs;
-output{3} = msaxis * 1000; %covert from s to ms
+    if status ~= 0
+        error('Something went wrong in Praat analysis')
+    end
+    
+    % clean up praat output text file to eliminate uninterpretable characters
+    A = regexp( fileread('temp_wav_formants.txt'), '\n', 'split');
+    headers = strsplit(A{1},'\t');
+    if length(headers) == 1 % for some reason Praat sometimes uses a space to separate headers
+        headers = strsplit(A{1},' ');
+    end
+    for i = 1:length(headers)
+        curTxt = headers{i};
+        startUnits = strfind(curTxt,'(');
+        if ~isempty(startUnits)
+            curTxt = curTxt(1:startUnits-1);
+            headers{i} = curTxt;
+        end
+    end
+    A{1} = strjoin(headers,'\t');
+    fid = fopen('temp_wav_formants.txt','w');
+    fprintf(fid, '%s\n', A{:});
+    fclose(fid);
+    
+    % load formant tracks from file written by Praat and put in 'formant' output
+    formant_vals = readtable('temp_wav_formants.txt','Delimiter','\t');
+    
+    %find number of formant values returned by praat
+    for nf = 1:nformants
+        form=['F' num2str(nf)]; % finds the particular formant number
+        formant(nf,:) = formant_vals.(form)'; % updates row in formant
+    end
+    
+    %find times of formants
+    msaxis = formant_vals.time';
+    
+    % clean up by deleting files and return to previous directory
+    delete temp_wav.wav 
+    % delete temp_wav_formants.txt
+    cd(curr_dir)
+    
+    % establish outputs
+    lpc_coeffs = [];
+    output{1} = formant;
+    output{2} = lpc_coeffs;
+    output{3} = msaxis * 1000; %covert from s to ms
+%%% end of praat function

From 60e4bd77f9caa107d610423d103a88cdb964891d Mon Sep 17 00:00:00 2001
From: Henry Nomeland <nomeland@waisman.wisc.edu>
Date: Thu, 4 Apr 2024 10:28:22 -0500
Subject: [PATCH 04/11] added autocontinue

---
 get_formant_tracks.m |  6 +++---
 wave_viewer.m        | 14 +++++++++++---
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/get_formant_tracks.m b/get_formant_tracks.m
index feb2496..476c2f2 100644
--- a/get_formant_tracks.m
+++ b/get_formant_tracks.m
@@ -44,7 +44,7 @@
 %%% function which executes Praat script using params
     %must be in git repo folder to run praat function, so save current location and go there
     curr_dir = pwd;
-    temp_str = which('get_fast_tracks.praat');
+    temp_str = which('get_formant_tracks.praat');
     praat_path = fileparts(temp_str);
     cd(praat_path)
     
@@ -61,9 +61,9 @@
     preemphasis = 50;
     
     if ismac
-        status = system(['"/Applications/Praat.app/Contents/MacOS/Praat" --run get_fast_tracks.praat "' pwd '" "temp_wav" ' num2str(max_formant) ' ' num2str(params.nlpc/2) ' ' num2str(params.window_size) ' ' num2str(params.step_size) ' ' num2str(preemphasis) ' ' num2str(params.fs)]);
+        status = system(['"/Applications/Praat.app/Contents/MacOS/Praat" --run get_formant_tracks.praat "' pwd '" "temp_wav" ' num2str(max_formant) ' ' num2str(params.nlpc/2) ' ' num2str(params.window_size) ' ' num2str(params.step_size) ' ' num2str(preemphasis) ' ' num2str(params.fs)]);
     else
-        status = system(['"C:\Users\Public\Desktop\Praat.exe" --run get_fast_tracks.praat "' pwd '" "temp_wav" ' num2str(max_formant) ' ' num2str(params.nlpc/2) ' ' num2str(params.window_size) ' ' num2str(params.step_size) ' ' num2str(preemphasis) ' ' num2str(params.fs)]);
+        status = system(['"C:\Users\Public\Desktop\Praat.exe" --run get_formant_tracks.praat "' pwd '" "temp_wav" ' num2str(max_formant) ' ' num2str(params.nlpc/2) ' ' num2str(params.window_size) ' ' num2str(params.step_size) ' ' num2str(preemphasis) ' ' num2str(params.fs)]);
     end
     if status ~= 0
         error('Something went wrong in Praat analysis')
diff --git a/wave_viewer.m b/wave_viewer.m
index 2165e7c..b3821de 100644
--- a/wave_viewer.m
+++ b/wave_viewer.m
@@ -846,7 +846,15 @@ function fig_resize_func(src,event)
 set(hf,'KeyPressFcn',@key_press_func);
 set(hf,'ResizeFcn',@fig_resize_func);
 if yes_profile, profile off; end
-if yes_start_blocking, uiwait(hf); end
+if yes_start_blocking && p.sigproc_params.autocont ~= 1, uiwait(hf); end
+
+%%% CODE FOR AUTOCONTINUE
+if p.sigproc_params.autocont
+    if p.sigproc_params.autocont == 1
+        contprogram([],[]);
+    end
+end
+
 end
 
 %%
@@ -2308,8 +2316,8 @@ function set_viewer_axlims(hax,t_min,t_max,dat4minmax,yax_fact2use)
     'ptrack_voicing_thresh', 0.45, ...
     'ptrack_octave_cost', 0.01, ...
     'ptrack_octave_jump_cost', 0.35, ...
-    'ptrack_voiced_unvoiced_cost', 0.14);
-
+    'ptrack_voiced_unvoiced_cost', 0.14, ...
+    'autocont', 0);
 end
 
 %% get figure params (used to be global vars)

From 1ea75571fa4229c506c0ced6e8932efa2eff7d63 Mon Sep 17 00:00:00 2001
From: Henry Nomeland <nomeland@waisman.wisc.edu>
Date: Thu, 18 Apr 2024 10:44:56 -0500
Subject: [PATCH 05/11] fast track implementation

---
 get_fast_tracks.praat | 31 ++++++++++++++++++-------------
 get_formant_tracks.m  |  6 +++---
 2 files changed, 21 insertions(+), 16 deletions(-)

diff --git a/get_fast_tracks.praat b/get_fast_tracks.praat
index 20d4cd8..1cf91c9 100644
--- a/get_fast_tracks.praat
+++ b/get_fast_tracks.praat
@@ -5,28 +5,33 @@
 # FastTrack code available here: https://github.com/santiagobarreda/FastTrack/
 # for use with wave_viewer
 
-include utils/trackAutoselectProcedure.praat
-
 #Inputs
 form Measure formant values for segments in a textgrid
-    sentence directory_name: /Users/Ben/Documents/MATLAB/wave_viewer
+    sentence dir: /Users/Ben/Documents/MATLAB/wave_viewer
     sentence file_name: temp_wav
-    positive minimum_formant 0
-    positive maximum_formant 5500
-    positive number_steps 100
-    positive num_coefs 10
-    positive num_formants 3
-    sentence tracking_method: burg
 endform
 
-#open the sound and select it
+include utils/trackAutoselectProcedure.praat
+@getSettings
+
+formants = 3
+time_step = 0.002
+method$ = burg
+steps = 20
+coefficients = 5
+out_formant = 2
+fastTrackMinimumDuration = 0.030000000000001
+lowestAnalysisFrequency = 0
+highestAnalysisFrequency 5500
+
 wav_name$ = file_name$ + ".wav"
 Read from file... 'directory_name$'/'wav_name$'
 soundID1$ = selected$("Sound")
+select Sound 'soundID1$'
+
+if windowDuration >= fastTrackMinimumDuration
+      @trackAutoselect: selected(), dir$, lowestAnalysisFrequency, highestAnalysisFrequency, steps, coefficients, formants, method$, 0, selected(), 0, 4000, 2, 2, 0
 
-#extract formants
-@trackAutoselectProcedure: soundID1$, directory_name$, minimum_formant, maximum_formant, number_steps, num_coefs, num_formants, tracking_method$, 0, soundID1$, 0, 5500, 2, 0, 0
-selectObject: soundID1$
 formant = selected ("Formant")
 
 #write formants
diff --git a/get_formant_tracks.m b/get_formant_tracks.m
index 476c2f2..16f3f36 100644
--- a/get_formant_tracks.m
+++ b/get_formant_tracks.m
@@ -44,7 +44,7 @@
 %%% function which executes Praat script using params
     %must be in git repo folder to run praat function, so save current location and go there
     curr_dir = pwd;
-    temp_str = which('get_formant_tracks.praat');
+    temp_str = which('get_fast_tracks.praat');
     praat_path = fileparts(temp_str);
     cd(praat_path)
     
@@ -61,9 +61,9 @@
     preemphasis = 50;
     
     if ismac
-        status = system(['"/Applications/Praat.app/Contents/MacOS/Praat" --run get_formant_tracks.praat "' pwd '" "temp_wav" ' num2str(max_formant) ' ' num2str(params.nlpc/2) ' ' num2str(params.window_size) ' ' num2str(params.step_size) ' ' num2str(preemphasis) ' ' num2str(params.fs)]);
+        status = system(['"/Applications/Praat.app/Contents/MacOS/Praat" --run get_fast_tracks.praat "' pwd]);
     else
-        status = system(['"C:\Users\Public\Desktop\Praat.exe" --run get_formant_tracks.praat "' pwd '" "temp_wav" ' num2str(max_formant) ' ' num2str(params.nlpc/2) ' ' num2str(params.window_size) ' ' num2str(params.step_size) ' ' num2str(preemphasis) ' ' num2str(params.fs)]);
+        status = system(['"C:\Users\Public\Desktop\Praat.exe" --run get_fast_tracks.praat "' pwd]);
     end
     if status ~= 0
         error('Something went wrong in Praat analysis')

From ff4955a3fc2dda4db292454935b7c54c3d024029 Mon Sep 17 00:00:00 2001
From: Henry Nomeland <nomeland@waisman.wisc.edu>
Date: Thu, 25 Apr 2024 12:16:30 -0500
Subject: [PATCH 06/11] fast track implementation

---
 get_fast_tracks.praat | 11 +++++------
 get_formant_tracks.m  | 16 ++++++++--------
 2 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/get_fast_tracks.praat b/get_fast_tracks.praat
index 1cf91c9..dbafe25 100644
--- a/get_fast_tracks.praat
+++ b/get_fast_tracks.praat
@@ -16,28 +16,27 @@ include utils/trackAutoselectProcedure.praat
 
 formants = 3
 time_step = 0.002
-method$ = burg
 steps = 20
 coefficients = 5
 out_formant = 2
 fastTrackMinimumDuration = 0.030000000000001
 lowestAnalysisFrequency = 0
-highestAnalysisFrequency 5500
+highestAnalysisFrequency = 5500
 
+method$ = "burg"
 wav_name$ = file_name$ + ".wav"
-Read from file... 'directory_name$'/'wav_name$'
+Read from file... 'dir$'/'wav_name$'
 soundID1$ = selected$("Sound")
 select Sound 'soundID1$'
 
-if windowDuration >= fastTrackMinimumDuration
-      @trackAutoselect: selected(), dir$, lowestAnalysisFrequency, highestAnalysisFrequency, steps, coefficients, formants, method$, 0, selected(), 0, 4000, 2, 2, 0
+@trackAutoselect: selected(), dir$, lowestAnalysisFrequency, highestAnalysisFrequency, steps, coefficients, formants, method$, 0, selected(), 0, 4000, 2, 0, 0
 
 formant = selected ("Formant")
 
 #write formants
 formant_name$ = file_name$ + "_formants.txt"
 Down to Table... yes yes 6 no 3 yes 3 no 
-Save as tab-separated file... 'directory_name$'/'formant_name$'
+Save as tab-separated file... 'dir$'/'formant_name$'
 
 #extract LPC parameters
 #selectObject: formant
diff --git a/get_formant_tracks.m b/get_formant_tracks.m
index 16f3f36..11f4bbc 100644
--- a/get_formant_tracks.m
+++ b/get_formant_tracks.m
@@ -41,7 +41,7 @@
 if nargout >= 3, ftrack_lpc_coeffs = lpc_coeffs; end
 
 function output = praat_ftrack_func(y,params)
-%%% function which executes Praat script using params
+%%% function which executes Fast Track script using params
     %must be in git repo folder to run praat function, so save current location and go there
     curr_dir = pwd;
     temp_str = which('get_fast_tracks.praat');
@@ -49,21 +49,21 @@
     cd(praat_path)
     
     fs = params.fs;
+    faxis = params.faxis;
+    nlpc_coeffs = params.nlpc;
     nformants = params.nformants;
-    
+
     %%% Praat wrapper code here
     % write y to file (this will be deleted later, it is just written to the
     % current directory)
     audiowrite('temp_wav.wav',y,fs)
-    
-    % set praat params that are not changeable
     max_formant = 5500;
     preemphasis = 50;
     
     if ismac
-        status = system(['"/Applications/Praat.app/Contents/MacOS/Praat" --run get_fast_tracks.praat "' pwd]);
+        status = system(['"/Applications/Praat.app/Contents/MacOS/Praat" --run get_fast_tracks.praat "' pwd '" "temp_wav"']);
     else
-        status = system(['"C:\Users\Public\Desktop\Praat.exe" --run get_fast_tracks.praat "' pwd]);
+        status = system(['"C:\Users\nomeland\Documents\Praat.exe" --run get_fast_tracks.praat "' pwd '" "temp_wav"']);
     end
     if status ~= 0
         error('Something went wrong in Praat analysis')
@@ -102,7 +102,7 @@
     
     % clean up by deleting files and return to previous directory
     delete temp_wav.wav 
-    % delete temp_wav_formants.txt
+    delete temp_wav_formants.txt
     cd(curr_dir)
     
     % establish outputs
@@ -110,4 +110,4 @@
     output{1} = formant;
     output{2} = lpc_coeffs;
     output{3} = msaxis * 1000; %covert from s to ms
-%%% end of praat function
+%%% end of Fast Track function

From ef9ac6656f28796a99246a1a7127a4012b3b8070 Mon Sep 17 00:00:00 2001
From: Henry Nomeland <nomeland@waisman.wisc.edu>
Date: Fri, 26 Apr 2024 09:38:40 -0500
Subject: [PATCH 07/11] details

---
 get_fast_tracks.praat    | 12 ++++++------
 get_formant_tracks.m     |  4 ----
 get_formant_tracks.praat | 40 ++++++++++++++++++++++++++++++++++++++++
 3 files changed, 46 insertions(+), 10 deletions(-)
 create mode 100644 get_formant_tracks.praat

diff --git a/get_fast_tracks.praat b/get_fast_tracks.praat
index dbafe25..7d2b1c0 100644
--- a/get_fast_tracks.praat
+++ b/get_fast_tracks.praat
@@ -15,15 +15,15 @@ include utils/trackAutoselectProcedure.praat
 @getSettings
 
 formants = 3
-time_step = 0.002
-steps = 20
-coefficients = 5
+time_step = 0.01
+steps = 10
+coefficients = 2
 out_formant = 2
 fastTrackMinimumDuration = 0.030000000000001
-lowestAnalysisFrequency = 0
-highestAnalysisFrequency = 5500
+lowestAnalysisFrequency = 2400
+highestAnalysisFrequency = 3200
 
-method$ = "burg"
+method$ = "robust"
 wav_name$ = file_name$ + ".wav"
 Read from file... 'dir$'/'wav_name$'
 soundID1$ = selected$("Sound")
diff --git a/get_formant_tracks.m b/get_formant_tracks.m
index 11f4bbc..d08c6c4 100644
--- a/get_formant_tracks.m
+++ b/get_formant_tracks.m
@@ -49,16 +49,12 @@
     cd(praat_path)
     
     fs = params.fs;
-    faxis = params.faxis;
-    nlpc_coeffs = params.nlpc;
     nformants = params.nformants;
 
     %%% Praat wrapper code here
     % write y to file (this will be deleted later, it is just written to the
     % current directory)
     audiowrite('temp_wav.wav',y,fs)
-    max_formant = 5500;
-    preemphasis = 50;
     
     if ismac
         status = system(['"/Applications/Praat.app/Contents/MacOS/Praat" --run get_fast_tracks.praat "' pwd '" "temp_wav"']);
diff --git a/get_formant_tracks.praat b/get_formant_tracks.praat
new file mode 100644
index 0000000..66b86d5
--- /dev/null
+++ b/get_formant_tracks.praat
@@ -0,0 +1,40 @@
+# get_formants.praat
+# BEN PARRELL 18 DEC 2017
+#
+# Measure formants for whole .wav file
+# For use with wave_viewer
+
+#Inputs
+form Measure formant values for segments in a textgrid
+    sentence directory_name: /Users/Ben/Documents/MATLAB/wave_viewer
+    sentence file_name: temp_wav
+    positive maximum_formant 5500
+    positive number_of_formants 5
+    positive window_size 0.025
+    positive time_step 0.005
+    positive preemphasis 50
+    positive fs 11025
+endform
+
+#open the sound and select it
+wav_name$ = file_name$ + ".wav"
+Read from file... 'directory_name$'/'wav_name$'
+soundID1$ = selected$("Sound")
+
+#extract formants
+To Formant (burg)... 'time_step' 'number_of_formants' 'maximum_formant' 'window_size' 'preemphasis'
+formant = selected ("Formant")
+
+#write formants
+formant_name$ = file_name$ + "_formants.txt"
+Down to Table... yes yes 6 no 3 yes 3 no 
+Save as tab-separated file... 'directory_name$'/'formant_name$'
+
+#extract LPC parameters
+#selectObject: formant
+#To LPC... fs
+#Down to Matrix (lpc)
+
+#save LPC parameters
+#lpc_name$ = file_name$ + "_lpc.txt"
+#Save as headerless spreadsheet file... 'directory_name$'/'lpc_name$'

From 20402f7b81c7cd62a71cf44157276239990cb93d Mon Sep 17 00:00:00 2001
From: Henry Nomeland <nomeland@waisman.wisc.edu>
Date: Fri, 26 Apr 2024 09:57:06 -0500
Subject: [PATCH 08/11] formant tracking updates

---
 get_formant_tracks.m | 261 +++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 252 insertions(+), 9 deletions(-)

diff --git a/get_formant_tracks.m b/get_formant_tracks.m
index d08c6c4..cdca2f1 100644
--- a/get_formant_tracks.m
+++ b/get_formant_tracks.m
@@ -1,18 +1,25 @@
 function [ftrack_out,ftrack_mstaxis,ftrack_lpc_coeffs] = get_formant_tracks(y,fs,faxis,ms_framespec,nlpc_coeffs,yes_preemph,nformants,ftrack_method,yes_verbose)
 
+frames_per_dot = 10;
+dots_per_line = 50;
+
 if nargin < 2 || isempty(fs), fs = 11025; end
 if nargin < 3 || isempty(faxis), faxis = linspace(0,fs/2,1025); end
 if nargin < 4 || isempty(ms_framespec), ms_framespec = 'narrowband'; end
 if nargin < 5 || isempty(nlpc_coeffs), nlpc_coeffs=14; end
 if nargin < 6 || isempty(yes_preemph), yes_preemph = 1; end
 if nargin < 7 || isempty(nformants), nformants = 0; end
-if nargin < 8 || isempty(ftrack_method), ftrack_method = 'praat'; end
+if nargin < 8 || isempty(ftrack_method), ftrack_method = 'mine'; end
 if nargin < 9 || isempty(yes_verbose), yes_verbose = 0; end
 
 params.fs = fs;
 params.nlpc = nlpc_coeffs;
 switch ftrack_method
+    case 'colea', ftrack_func = @colea_ftrack_func; params.nformants_max = 3; params.yes_trackperframe = 1;
+    case 'mine',  ftrack_func = @my_ftrack_func;    params.nformants_max = 3; params.yes_trackperframe = 1;
+    case 'mine2', ftrack_func = @my_ftrack_func2;   params.nformants_max = 4; params.yes_trackperframe = 1;
     case 'praat', ftrack_func = @praat_ftrack_func; params.nformants_max = 5; params.yes_trackperframe = 0;
+    case 'fasttrack', ftrack_func = @fasttrack_ftrack_func; params.nformants_max = 5; params.yes_trackperframe = 0;
     otherwise, error('formant tracking method(%s) unrecognized',ftrack_method);
 end
 if ~nformants, nformants = params.nformants_max; end
@@ -20,18 +27,41 @@
 params.nformants = nformants;
 params.faxis = faxis;
 
-[nsamps,~] = get_len_yvec(y);
+starting_formants = [500 1500 2500 3500];
+
+[nsamps,yes_y_is_rowvec] = get_len_yvec(y);
 [ms_awin,ms_astep,nsamps_frame,nsamps_astep] = get_ms_framespec(ms_framespec,fs);
+win = hann(nsamps_frame)/sum(hann(nsamps_frame));
+if ~yes_y_is_rowvec, win = win'; end
 y = my_preemph(y,yes_preemph);
 nframes = floor((nsamps - nsamps_frame)/nsamps_astep);
+ftrack = zeros(nformants,nframes);
+ftrack_mstaxis = zeros(1,nframes);
+lpc_coeffs = zeros((nlpc_coeffs+1),nframes);
 
-params.window_size = ms_awin/1000;
-params.step_size = ms_astep/1000;
-params.nframes = nframes;
-output = ftrack_func(y,params);
-ftrack = output{1};
-lpc_coeffs = output{2};
-ftrack_mstaxis = output{3};
+if params.yes_trackperframe % if tracker operates on a frame-by-frame basis within Matlab
+    for iframe = 1:nframes
+        yframe = y((iframe-1)*nsamps_astep + (1:nsamps_frame));
+        ftrack_mstaxis(iframe) = 1000*mean((iframe-1)*nsamps_astep + (1:nsamps_frame))/fs;
+        ywinframe = win .* yframe;
+        if iframe > 1, params.Fprev = ftrack(:,iframe-1); else params.Fprev = starting_formants; end
+        output = ftrack_func(ywinframe,params);
+        ftrack(:,iframe) = output{1};
+        lpc_coeffs(:,iframe) = output{2};
+        if yes_verbose
+            if ~rem(iframe,frames_per_dot), fprintf('.'); end
+            if ~rem(iframe,frames_per_dot*dots_per_line), fprintf('%d\n',iframe); end
+        end
+    end
+else                        % if we want to pass entire utterance to external tracker
+    params.window_size = ms_awin/1000;
+    params.step_size = ms_astep/1000;
+    params.nframes = nframes;
+    output = ftrack_func(y,params);
+    ftrack = output{1};
+    lpc_coeffs = output{2};
+    ftrack_mstaxis = output{3};
+end
 
 % ftrack_out(1:nformants,1:nframes) = ftrack(1:nformants,1:nframes);
 ftrack_out(1:nformants,:) = ftrack(1:nformants,:); %removing nframes allows for praat tracking
@@ -40,8 +70,140 @@
 end
 if nargout >= 3, ftrack_lpc_coeffs = lpc_coeffs; end
 
+
+% must have colea on matlab path to use this function
+function output = colea_ftrack_func(ywinframe,params)
+
+fs = params.fs;
+nlpc_coeffs = params.nlpc;
+nformants = params.nformants;
+
+lpc_coeffs = lpc(ywinframe,nlpc_coeffs);
+[frmnt(1),frmnt(2),frmnt(3)] = frmnts(lpc_coeffs,fs);
+formant(1:nformants) = frmnt(1:nformants);
+
+output{1} = formant;
+output{2} = lpc_coeffs;
+
+function output = my_ftrack_func(ywinframe,params)
+
+fs = params.fs;
+nlpc_coeffs = params.nlpc;
+nformants = params.nformants;
+
+lpc_coeffs = lpc(ywinframe,nlpc_coeffs);
+[frmnt(1),frmnt(2),frmnt(3)] = my_frmnts(lpc_coeffs,fs);
+
+formant(1:nformants) = frmnt(1:nformants);
+
+output{1} = formant;
+output{2} = lpc_coeffs;
+
+
+function output = my_ftrack_func2(ywinframe,params)
+
+fs = params.fs;
+faxis = params.faxis;
+nlpc_coeffs = params.nlpc;
+nformants = params.nformants;
+Fprev = params.Fprev;
+
+lpc_coeffs = lpc(ywinframe,nlpc_coeffs);
+lpc_magspec = get_lpc_magspec(lpc_coeffs,faxis,fs);
+[lpc_magspec_peaks,nlpc_magspec_peaks] = peakfind(lpc_magspec);
+for iformant = 1:nformants
+  if iformant < nlpc_magspec_peaks
+    formant(iformant) = faxis(lpc_magspec_peaks(iformant));
+  elseif iformant == nlpc_magspec_peaks
+    formant(iformant) = faxis(lpc_magspec_peaks(iformant));
+    if abs(Fprev(iformant)-formant(iformant)) > 75
+        formant(iformant) = Fprev(iformant);
+    end
+  else
+    formant(iformant) = Fprev(iformant);
+  end
+end
+
+output{1} = formant;
+output{2} = lpc_coeffs;
+
+
 function output = praat_ftrack_func(y,params)
+% execute Praat script using params
+%must be in git repo folder to run praat function, so save current location and go there
+curr_dir = pwd;
+temp_str = which('get_formant_tracks.praat');
+praat_path = fileparts(temp_str);
+cd(praat_path)
+
+fs = params.fs;
+faxis = params.faxis;
+nlpc_coeffs = params.nlpc;
+nformants = params.nformants;
+
+%%% Praat wrapper code here
+% write y to file (this will be deleted later, it is just written to the
+% current directory)
+audiowrite('temp_wav.wav',y,fs)
+
+% set praat params that are not changeable
+max_formant = 5500;
+preemphasis = 50;
+
+if ismac
+    status = system(['"/Applications/Praat.app/Contents/MacOS/Praat" --run get_formant_tracks.praat "' pwd '" "temp_wav" ' num2str(max_formant) ' ' num2str(params.nlpc/2) ' ' num2str(params.window_size) ' ' num2str(params.step_size) ' ' num2str(preemphasis) ' ' num2str(params.fs)]);
+else
+    status = system(['"C:\Users\Public\Desktop\Praat.exe" --run get_formant_tracks.praat "' pwd '" "temp_wav" ' num2str(max_formant) ' ' num2str(params.nlpc/2) ' ' num2str(params.window_size) ' ' num2str(params.step_size) ' ' num2str(preemphasis) ' ' num2str(params.fs)]);
+end
+if status ~= 0
+    error('Something went wrong in Praat analysis')
+end
+
+% clean up praat output text file to eliminate uniterpretable characters
+A = regexp( fileread('temp_wav_formants.txt'), '\n', 'split');
+headers = strsplit(A{1},'\t');
+if length(headers) == 1 %for some reason Praat sometimes uses a space to separate headers
+    headers = strsplit(A{1},' ');
+end
+for i = 1:length(headers)
+    curTxt = headers{i};
+    startUnits = strfind(curTxt,'(');
+    if ~isempty(startUnits)
+        curTxt = curTxt(1:startUnits-1);
+        headers{i} = curTxt;
+    end
+end
+A{1} = strjoin(headers,'\t');
+fid = fopen('temp_wav_formants.txt','w');
+fprintf(fid, '%s\n', A{:});
+fclose(fid);
+
+% load formant tracks from file written by Praat and put in 'formant' output
+formant_vals = readtable('temp_wav_formants.txt','Delimiter','\t');
+
+%find number of formant values returbned by praat
+for nf = 1:nformants
+    form=['F' num2str(nf)];
+    formant(nf,:) = formant_vals.(form)';
+end
+
+%find times of formants
+msaxis = formant_vals.time';
+
+% load LPC values from file written by Praat and put in 'lpc_coeffs' output
+% lpc_coeffs = dlmread('temp_wav_lpc.txt','\t');
+lpc_coeffs = [];
+% clean up by deleting files that were created and return to previous
+% directory
+delete temp_wav.wav temp_wav_formants.txt %temp_wav_lpc.txt
+cd(curr_dir)
+
+output{1} = formant;
+output{2} = lpc_coeffs;
+output{3} = msaxis * 1000; %covert from s to ms
+
 %%% function which executes Fast Track script using params
+function output = fasttrack_ftrack_func(y,params)
     %must be in git repo folder to run praat function, so save current location and go there
     curr_dir = pwd;
     temp_str = which('get_fast_tracks.praat');
@@ -107,3 +269,84 @@
     output{2} = lpc_coeffs;
     output{3} = msaxis * 1000; %covert from s to ms
 %%% end of Fast Track function
+
+% my version of the colea frmnts function,
+% orinally copyright (c) 1998 by Philipos C. Loizou
+function [F1,F2, F3]=my_frmnts(lpc_coeffs,fs)
+
+global F1prev F2prev F3prev
+
+min_formant_freq =   90;
+max_formant_freq = 4000;
+max_formant_bw   =  500;
+defaultF1 = 300; defaultF2 = 1200; defaultF3 = 3000;
+
+max_allowable_F1dev     = 150;
+max_allowable_F2dev     = 150;
+min_initial_formant_sep =  80;
+min_formant_sep         =  50;
+
+const = fs/(2*pi);
+rts = roots(lpc_coeffs);
+k = 1;
+for i=1:length(lpc_coeffs)-1
+  re = real(rts(i)); im = imag(rts(i));
+  the_formant_cand = const*atan2(im,re);   %--formant frequencies
+  formant_bw = -0.5*const*log(abs(rts(i)));%--formant bandwidth
+  if (the_formant_cand < max_formant_freq) & ...
+     (the_formant_cand > min_formant_freq) & ...
+     (formant_bw < max_formant_bw)
+    unsort_candidate_formant(k) = the_formant_cand;
+    bandw(k) = formant_bw;
+    k = k + 1;
+  end
+end
+candidate_formant = sort(unsort_candidate_formant);
+ncand_formants = length(candidate_formant);
+
+if isempty(F1prev) %++++++++++++++++ the first frame ++++++++++++++++++
+  if 2 > ncand_formants
+    F1 = defaultF1; F2 = defaultF2; F3 = defaultF3;
+  elseif abs(candidate_formant(1)-candidate_formant(2)) < min_initial_formant_sep
+    F1 = candidate_formant(2); F2 = candidate_formant(3);
+    if 3 > ncand_formants, F3 = candidate_formant(4); else F3 = defaultF3; end
+  elseif 4 == ncand_formants
+    F1 = candidate_formant(2); F2 = candidate_formant(3);
+    F3 = candidate_formant(4);
+  else
+    F1 = candidate_formant(1); F2 = candidate_formant(2); 
+    if 3 > ncand_formants, F3 = defaultF3; else F3 = candidate_formant(3); end
+  end
+else %++++++++++++++++ all frames after the first ++++++++++++++++++
+     %----Impose some formant continuity constraints -------------------
+  in1 = find(abs(F1prev-candidate_formant) < max_allowable_F1dev);
+  in2 = find(abs(F2prev-candidate_formant) < max_allowable_F2dev);
+  if length(in1) > 1, i1 = in1(2); else i1 = in1; end
+  if length(in2) > 1, i2 = in2(2); else i2 = in2; end
+  
+  switch (10*(~isempty(i1)) + (~isempty(i2)))
+    case 11
+      if i1 == i2
+        if 1 > ncand_formants, F1 = F1prev; else F1 = candidate_formant(1); end
+        if 2 > ncand_formants, F2 = F2prev; else F2 = candidate_formant(2); end
+        if 3 > ncand_formants, F3 = F3prev; else F3 = candidate_formant(3); end
+      else
+        F1 = candidate_formant(i1); F2 = candidate_formant(i2); 
+        if i2 + 1 > ncand_formants, F3 = F3prev; else F3 = candidate_formant(i2 + 1); end
+      end
+    case 10
+      F1 = candidate_formant(i1);
+      if i1 + 1 > ncand_formants, F2 = F2prev; else F2 = candidate_formant(i1 + 1); end
+      if i1 + 2 > ncand_formants, F3 = F3prev; else F3 = candidate_formant(i1 + 2); end
+    otherwise
+      F1 = candidate_formant(1);
+      if 2 > ncand_formants, F2 = F2prev; else F2 = candidate_formant(2); end
+      if 3 > ncand_formants, F3 = F3prev; else F3 = candidate_formant(3); end
+  end
+end
+
+% --last check .. --------
+if abs(F2-F3) < min_formant_sep, F2 = F2prev; F3 = F3prev; end
+if abs(F2-F1) < min_formant_sep, F2 = F2prev; F3 = F3prev; end
+
+F1prev = F1; F2prev = F2; F3prev = F3;

From b9b757994cc5d46d7670d5e4c5c6c2f551a37eb7 Mon Sep 17 00:00:00 2001
From: Henry Nomeland <nomeland@waisman.wisc.edu>
Date: Fri, 26 Apr 2024 10:05:22 -0500
Subject: [PATCH 09/11] removed autocont

---
 wave_viewer.m | 13 ++-----------
 1 file changed, 2 insertions(+), 11 deletions(-)

diff --git a/wave_viewer.m b/wave_viewer.m
index b3821de..ad5f5c0 100644
--- a/wave_viewer.m
+++ b/wave_viewer.m
@@ -846,15 +846,7 @@ function fig_resize_func(src,event)
 set(hf,'KeyPressFcn',@key_press_func);
 set(hf,'ResizeFcn',@fig_resize_func);
 if yes_profile, profile off; end
-if yes_start_blocking && p.sigproc_params.autocont ~= 1, uiwait(hf); end
-
-%%% CODE FOR AUTOCONTINUE
-if p.sigproc_params.autocont
-    if p.sigproc_params.autocont == 1
-        contprogram([],[]);
-    end
-end
-
+if yes_start_blocking, uiwait(hf); end
 end
 
 %%
@@ -2316,8 +2308,7 @@ function set_viewer_axlims(hax,t_min,t_max,dat4minmax,yax_fact2use)
     'ptrack_voicing_thresh', 0.45, ...
     'ptrack_octave_cost', 0.01, ...
     'ptrack_octave_jump_cost', 0.35, ...
-    'ptrack_voiced_unvoiced_cost', 0.14, ...
-    'autocont', 0);
+    'ptrack_voiced_unvoiced_cost', 0.14);
 end
 
 %% get figure params (used to be global vars)

From 387c78b4c1de12572d5ad3257e2ab2a4c4ab3047 Mon Sep 17 00:00:00 2001
From: Henry Nomeland <nomeland@waisman.wisc.edu>
Date: Tue, 30 Apr 2024 09:50:28 -0500
Subject: [PATCH 10/11] fixed windows path

---
 get_fast_tracks.praat | 14 +++++++-------
 get_formant_tracks.m  |  4 ++--
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/get_fast_tracks.praat b/get_fast_tracks.praat
index 7d2b1c0..04ff565 100644
--- a/get_fast_tracks.praat
+++ b/get_fast_tracks.praat
@@ -1,4 +1,4 @@
-# get_fast_tracks.praat by Henry Nomeland, 21 Mar 2024
+    # get_fast_tracks.praat by Henry Nomeland, 21 Mar 2024
 # adapted from get_formants.praat by Ben Parrell, 18 Dec 2017
 #
 # measures formants for a .wav file utilizing tools and utils of FastTrack
@@ -15,15 +15,15 @@ include utils/trackAutoselectProcedure.praat
 @getSettings
 
 formants = 3
-time_step = 0.01
-steps = 10
-coefficients = 2
+time_step = 0.002
+steps = 30
+coefficients = 3
 out_formant = 2
 fastTrackMinimumDuration = 0.030000000000001
-lowestAnalysisFrequency = 2400
-highestAnalysisFrequency = 3200
+lowestAnalysisFrequency = 4800
+highestAnalysisFrequency = 5500
 
-method$ = "robust"
+method$ = "burg"
 wav_name$ = file_name$ + ".wav"
 Read from file... 'dir$'/'wav_name$'
 soundID1$ = selected$("Sound")
diff --git a/get_formant_tracks.m b/get_formant_tracks.m
index cdca2f1..eefec15 100644
--- a/get_formant_tracks.m
+++ b/get_formant_tracks.m
@@ -18,7 +18,7 @@
     case 'colea', ftrack_func = @colea_ftrack_func; params.nformants_max = 3; params.yes_trackperframe = 1;
     case 'mine',  ftrack_func = @my_ftrack_func;    params.nformants_max = 3; params.yes_trackperframe = 1;
     case 'mine2', ftrack_func = @my_ftrack_func2;   params.nformants_max = 4; params.yes_trackperframe = 1;
-    case 'praat', ftrack_func = @praat_ftrack_func; params.nformants_max = 5; params.yes_trackperframe = 0;
+    case 'praat', ftrack_func = @fasttrack_ftrack_func; params.nformants_max = 5; params.yes_trackperframe = 0;
     case 'fasttrack', ftrack_func = @fasttrack_ftrack_func; params.nformants_max = 5; params.yes_trackperframe = 0;
     otherwise, error('formant tracking method(%s) unrecognized',ftrack_method);
 end
@@ -221,7 +221,7 @@
     if ismac
         status = system(['"/Applications/Praat.app/Contents/MacOS/Praat" --run get_fast_tracks.praat "' pwd '" "temp_wav"']);
     else
-        status = system(['"C:\Users\nomeland\Documents\Praat.exe" --run get_fast_tracks.praat "' pwd '" "temp_wav"']);
+        status = system(['"C:\Users\Public\Desktop\Praat.exe" --run get_fast_tracks.praat "' pwd '" "temp_wav"']);
     end
     if status ~= 0
         error('Something went wrong in Praat analysis')

From d7b4196941e210753b1d3bb05089411f69895de7 Mon Sep 17 00:00:00 2001
From: Henry Nomeland <nomeland@waisman.wisc.edu>
Date: Wed, 1 May 2024 12:24:41 -0500
Subject: [PATCH 11/11] tiny updates

---
 get_fast_tracks.praat | 3 +--
 get_formant_tracks.m  | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/get_fast_tracks.praat b/get_fast_tracks.praat
index 04ff565..0e2c0b7 100644
--- a/get_fast_tracks.praat
+++ b/get_fast_tracks.praat
@@ -19,7 +19,6 @@ time_step = 0.002
 steps = 30
 coefficients = 3
 out_formant = 2
-fastTrackMinimumDuration = 0.030000000000001
 lowestAnalysisFrequency = 4800
 highestAnalysisFrequency = 5500
 
@@ -45,4 +44,4 @@ Save as tab-separated file... 'dir$'/'formant_name$'
 
 #save LPC parameters
 #lpc_name$ = file_name$ + "_lpc.txt"
-#Save as headerless spreadsheet file... 'directory_name$'/'lpc_name$'
+#Save as headerless spreadsheet file... 'dir$'/'lpc_name$'
diff --git a/get_formant_tracks.m b/get_formant_tracks.m
index eefec15..54c5748 100644
--- a/get_formant_tracks.m
+++ b/get_formant_tracks.m
@@ -18,7 +18,7 @@
     case 'colea', ftrack_func = @colea_ftrack_func; params.nformants_max = 3; params.yes_trackperframe = 1;
     case 'mine',  ftrack_func = @my_ftrack_func;    params.nformants_max = 3; params.yes_trackperframe = 1;
     case 'mine2', ftrack_func = @my_ftrack_func2;   params.nformants_max = 4; params.yes_trackperframe = 1;
-    case 'praat', ftrack_func = @fasttrack_ftrack_func; params.nformants_max = 5; params.yes_trackperframe = 0;
+    case 'praat', ftrack_func = @praat_ftrack_func; params.nformants_max = 5; params.yes_trackperframe = 0;
     case 'fasttrack', ftrack_func = @fasttrack_ftrack_func; params.nformants_max = 5; params.yes_trackperframe = 0;
     otherwise, error('formant tracking method(%s) unrecognized',ftrack_method);
 end