function varargout = muscle_track_v1(varargin)
% MUSCLE_TRACK_V1 M-file for muscle_track_v1.fig
% MUSCLE_TRACK_V1, by itself, creates a new MUSCLE_TRACK_V1 or raises the existing
% singleton*.
%
% H = MUSCLE_TRACK_V1 returns the handle to a new MUSCLE_TRACK_V1 or the handle to
% the existing singleton*.
%
% MUSCLE_TRACK_V1('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in MUSCLE_TRACK_V1.M with the given input arguments.
%
% MUSCLE_TRACK_V1('Property','Value',...) creates a new MUSCLE_TRACK_V1 or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before muscle_track_v1_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to muscle_track_v1_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
%
% Edit the above text to modify the response to help muscle_track_v1
%
% Last Modified by GUIDE v2.5 26-Aug-2011 15:11:06
%
% Written by Dr Glen Lichtwark (The Univesity of Queensland)
% Copyright Dr Glen Lichtwark 2011.
%
% Please cite the following manuscripts in any academic publications arising
% from this contribution -
%
% Jarred G. Gillett, Rod S. Barrett, Glen A. Lichtwark
% Reliability and accuracy of an automatic tracking algorithm to measure
% passive and active muscle fascicle length changes from ultrasound.
%
% Cronin, NJ, Carty, CP, Barrett, RS and Lichtwark, G. (In Press).
% Automatic tracking of medial gastrocnemius fascicle length during human
% locomotion. Journal of Applied Physiology.
% doi:10.?1152/?japplphysiol.?00530.?2011
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @muscle_track_v1_OpeningFcn, ...
'gui_OutputFcn', @muscle_track_v1_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before muscle_track_v1 is made visible.
function muscle_track_v1_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to muscle_track_v1 (see VARARGIN)
% Choose default command line output for muscle_track_v1
handles.output = hObject;
set(0,'RecursionLimit',3000)
% set some standard values for processing
% default depth setting - please change if you have a standard
% depth you want to use all of the time
handles.ID = 60;
% default settings for affine flow tracking
handles.SIGMA = 3;
handles.S_STEP = 3;
% try prevent flickering in figure
set(gcf,'DoubleBuffer','on');
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes muscle_track_v1 wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = muscle_track_v1_OutputFcn(~, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --------------------------------------------------------------------
function File_Callback(hObject, eventdata, handles)
% hObject handle to File (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function Image_Callback(hObject, eventdata, handles)
% hObject handle to Image (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function Tracking_Callback(hObject, eventdata, handles)
% hObject handle to Tracking (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function Fascicle_Callback(hObject, eventdata, handles)
% hObject handle to Fascicle (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --- Executes on button press in cut_frames_before.
function cut_frames_before_Callback(hObject, eventdata, handles)
% hObject handle to cut_frames_before (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles,'movObj')
% this function effectively trims the video sequence in case there are
% frames you don't want to analyse in the video - trims frames before
% the current frame
frame_no = round(get(handles.frame_slider,'Value'));
handles.start_frame = frame_no + handles.start_frame;
handles.NumFrames = handles.movObj.NumberOfFrames-handles.start_frame+1;
% reset the slider bar
set(handles.frame_slider,'Min',1);
set(handles.frame_slider,'Max',handles.NumFrames);
set(handles.frame_slider,'Value',1);
set(handles.frame_slider,'SliderStep',[1/handles.NumFrames 5/handles.NumFrames]);
handles.fas_x(1:handles.start_frame-1)=[];
handles.fas_y(1:handles.start_frame-1)=[];
% set the string in the frame_number to 1
set(handles.frame_number,'String',1);
% update the image axes using show_image function (bottom)
show_image(hObject,handles)
end
% --- Executes on button press in cut_frames_after.
function cut_frames_after_Callback(hObject, eventdata, handles)
% hObject handle to cut_frames_after (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles,'movObj')
% this function effectively trims the video sequence in case there are
% frames you don't want to analyse in the video - trims frams after
% current frame
frame_no = round(get(handles.frame_slider,'Value'));
handles.NumFrames = frame_no;
% reset the slider bar
set(handles.frame_slider,'Min',1);
set(handles.frame_slider,'Max',handles.NumFrames);
set(handles.frame_slider,'Value',handles.NumFrames);
set(handles.frame_slider,'SliderStep',[1/handles.NumFrames 5/handles.NumFrames]);
handles.fas_x(frame_no+1:end)=[];
handles.fas_y(frame_no+1:end)=[];
% set the string in the frame_number to 1
set(handles.frame_number,'String',frame_no);
% update the image axes using show_image function (bottom)
show_image(hObject,handles)
end
% --- Executes on slider movement.
function frame_slider_Callback(hObject, eventdata, handles)
% hObject handle to frame_slider (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'Value') returns position of slider
% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
% get the current value from the slider (round to ensure it is integer)
frame_no = round(get(handles.frame_slider,'Value'));
% set the string in the frame_number box to the current frame value
set(handles.frame_number,'String',num2str(frame_no));
% update the image axes using show_image function (bottom)
show_image(hObject,handles)
% --- Executes during object creation, after setting all properties.
function frame_slider_CreateFcn(hObject, eventdata, handles)
% hObject handle to frame_slider (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor',[.9 .9 .9]);
end
function frame_number_Callback(hObject, eventdata, handles)
% hObject handle to frame_number (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of frame_number as text
% str2double(get(hObject,'String')) returns contents of frame_number as a double
% goto frame number
frame_no = str2num(get(handles.frame_number,'String'));
set(handles.frame_slider,'Value',round(frame_no));
% update the image axes using show_image function (bottom)
show_image(hObject,handles)
% --- Executes during object creation, after setting all properties.
function frame_number_CreateFcn(hObject, eventdata, handles)
% hObject handle to frame_number (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% -----------------------------------------------
% -----------------------------------------------
function goto_next_frame(hObject, handles)
if get(handles.autorun_but,'BackgroundColor') == [0 1 0]
% get the current value from the slider (round to ensure it is integer)
frame_no = round(get(handles.frame_slider,'Value'))+1;
if frame_no < get(handles.frame_slider,'Max')
% set the slider
set(handles.frame_slider,'Value',frame_no);
% set the string in the frame_number box to the current frame value
set(handles.frame_number,'String',num2str(frame_no));
else handles.run = 0;
set(handles.autorun_but,'BackgroundColor',[1 0 0]);
end
% update the image axes using show_image function (bottom)
show_image(hObject,handles)
end
% --- Executes on button press in define_roi.
function define_roi_Callback(hObject, eventdata, handles)
% hObject handle to define_roi (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles,'movObj')
% define a region of interest in the current image using the roipoly
% function from the image processing toolbox
axes(handles.axes1)
[handles.ROI,handles.ROIx, handles.ROIy] = roipoly;
handles.CIm = handles.Im;
% show the ROI on the image
show_image(hObject,handles)
end
% --- Executes on button press in define_fascicle.
function define_fascicle_Callback(hObject, eventdata, handles)
% hObject handle to define_fascicle (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles,'movObj')
% find current frame number from slilder
frame_no = round(get(handles.frame_slider,'Value'));
if ~isempty(handles.fas_x{frame_no})
handles.fas_x{frame_no} = [];
handles.fas_y{frame_no} = [];
end
% make the image axes the current axes
axes(handles.axes1)
imshow(handles.Im)
% select the two points that define the fascicle line of action -
% image this with the rbline function
[p1,p2]=rbline(handles.axes1);
% store these points in specific locations
handles.fas_x{frame_no}(1) = p1(1);
handles.fas_x{frame_no}(2) = p2(1);
handles.fas_y{frame_no}(1) = p1(2);
handles.fas_y{frame_no}(2) = p2(2);
% correct which is the upper and with is the lower points relative to
% the image - to standardise
if handles.fas_y{frame_no}(1) > handles.fas_y{frame_no}(2)
handles.fas_y{frame_no} = fliplr(handles.fas_y{frame_no});
handles.fas_x{frame_no} = fliplr(handles.fas_x{frame_no});
end
% make the fascicle end points the current points for subsequent
% tracking
handles.current_xy = [handles.fas_x{frame_no};handles.fas_y{frame_no}]';
% calculate the length and pennation for the current frame
handles.fas_pen(frame_no) = atan2(abs(diff(handles.fas_y{frame_no})),abs(diff(handles.fas_x{frame_no})));
scalar = handles.ID/handles.movObj.Height;
handles.fas_length(frame_no) = scalar*sqrt(diff(handles.fas_y{frame_no}).^2 + diff(handles.fas_x{frame_no}).^2);
handles.CIm = handles.Im;
% show the fascicle on the image
show_image(hObject,handles)
end
% --- Executes on button press in clear_fascicle.
function clear_fascicle_Callback(hObject, eventdata, handles)
% hObject handle to clear_fascicle (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles,'movObj')
% clear the current fascicle points to start again
if isfield(handles,'fas_length')
handles = rmfield(handles,'fas_length');
handles = rmfield(handles,'fas_pen');
handles = rmfield(handles,'current_xy');
for i = 1:handles.movObj.NumberOfFrames
handles.fas_x{i}=[];
handles.fas_y{i}=[];
end
end
if isfield(handles,'ROI')
handles = rmfield(handles,'ROI');
end
% set current frame to 1
set(handles.frame_slider,'Value',1);
set(handles.frame_number,'String',1);
show_image(hObject,handles)
end
% --- Executes on button press in process_all.
function process_all_Callback(hObject, eventdata, handles)
% hObject handle to process_all (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles,'movObj') && isfield(handles,'current_xy') && isfield(handles,'ROI')
% perform the affine flow tracking on the muscle ultrasound for all
% frames from current frame
% find current frame number from slilder
frame_no = round(get(handles.frame_slider,'Value'));
if isempty(handles.fas_length(frame_no))
f = warndlg('First frame must have fascicle and ROI marked', 'Warning');
else
% create image from movie frame
Im = read(handles.movObj, handles.start_frame+frame_no-1);
% crop image with current cropping value
Im = imcrop(Im,handles.crop_rect);
% set image as current image
handles.CIm = Im;
% define end frame to get o
end_frame = get(handles.frame_slider,'Max');
h = waitbar(0,'Please wait while processing...');
image_depth = handles.ID;
for i = frame_no+1:end_frame
% create image from movie frame
Im = read(handles.movObj, handles.start_frame+i-1);
% crop image with current cropping value
Im = imcrop(Im,handles.crop_rect);
handles.Im = Im;
% set new image
handles.NIm = handles.Im;
% convert current and new images to greyscale
im1 = double(rgb2gray(handles.CIm))/256;
im2 = double(rgb2gray(handles.NIm))/256;
sigmaXY = handles.SIGMA;
sampleStep = handles.S_STEP;
% determine affine flow on region of interest (roi) and convert
% this into a flow warp to be applied to fascicle end points
af = affine_flow('image1', im1, 'image2', im2, 'sigmaXY',sigmaXY,'sampleStep',sampleStep,'regionOfInterest',handles.ROI);
af = af.findFlow;
flow = af.flowStruct;
w = affine_flow.warp(flow);
% apply flow warp (affine transformation) to the fascicle end
% points of current frame
pos = [handles.fas_x{i-1}(:) handles.fas_y{i-1}(:) ones(length(handles.current_xy),1)] * w;
% save these as the fascicle end points of new frame
handles.fas_x{i}(1:2) = pos(:,1);
handles.fas_y{i}(1:2) = pos(:,2);
% calculate the length and pennation for the new frame
handles.fas_pen(i) = atan2(abs(diff(handles.fas_y{i})),abs(diff(handles.fas_x{i})));
scalar = image_depth/handles.movObj.Height;
handles.fas_length(i) = scalar*sqrt(diff(handles.fas_y{i}).^2 + diff(handles.fas_x{i}).^2);
% make the new frame the current frame for the next iteration
handles.CIm = handles.NIm;
% update wait bar
waitbar(i/end_frame,h)
end
%close waitbar
close(h)
set(handles.frame_slider,'Value',frame_no);
set(handles.frame_number,'String',num2str(frame_no));
% update the image axes using show_image function (bottom)
show_image(hObject,handles)
end
end
% Update handles structure
guidata(hObject, handles);
% --------------------------------------------------------------------
function menu_affine_settings_Callback(hObject, eventdata, handles)
% hObject handle to menu_affine_settings (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% change the two important parameters used in the affine flow algorithm
if ~isfield(handles, 'SIGMA')
handles.SIGMA = 3;
end
if ~isfield(handles, 'S_STEP')
handles.SIGMA = 3;
end
% use a dialog box to get the two variables
A = inputdlg({'Sigma','Sample Step'}, 'Affine Flow Settings', 1,...
{num2str(handles.SIGMA),num2str(handles.S_STEP)});
handles.SIGMA = str2double(A{1});
handles.S_STEP = str2double(A{2});
% Update handles structure
guidata(hObject, handles);
% --------------------------------------------------------------------
function menu_crop_image_Callback(hObject, eventdata, handles)
% hObject handle to menu_crop_image (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles,'movObj')
% define current axes
axes(handles.axes1)
% use imcrop tool to determine croppable area
[~,handles.crop_rect] = imcrop;
handles.crop_rect = round(handles.crop_rect);
% update the image axes using show_image function (bottom)
show_image(hObject,handles)
end
% --------------------------------------------------------------------
function menu_reset_image_Callback(hObject, eventdata, handles)
% hObject handle to menu_reset_image (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles,'movObj')
% set the image croppable area to the maximum area
handles.crop_rect = [1 1 handles.movObj.Width handles.movObj.Height];
% update the image axes using show_image function (bottom)
show_image(hObject,handles)
end
% --------------------------------------------------------------------
function menu_set_depth_Callback(hObject, eventdata, handles)
% hObject handle to menu_set_depth (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles,'movObj')
if ~isfield(handles, 'ID')
handles.ID = 60.4;
end
A = inputdlg('Enter image depth', 'Image Depth', 1, {num2str(handles.ID)});
handles.ID = str2double(A{1});
% Update handles structure
guidata(hObject, handles);
end
% --------------------------------------------------------------------
function menu_save_tracking_Callback(hObject, eventdata, handles)
% hObject handle to menu_save_tracking (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles,'movObj') && isfield(handles,'fas_length')
dt = 1/handles.FrameRate;
time = (dt:dt:length(handles.fas_length)*dt)+((handles.start_frame-1)*dt);
%determine any non-zero entries in fascicle length array
nz = logical(handles.fas_length ~= 0);
T = time(nz)';
FL = handles.fas_length(nz);
PEN = handles.fas_pen(nz);
[filename, pathname] = uiputfile('*.txt', 'Save Fasicle Tracking as');
% open a new text file for writing
fid = fopen([pathname filename],'w');
fprintf(fid,'TIME\tFASCICLE LENGTH\tPENNATION ANLE\n');
fprintf(fid,'%3.4f\t%3.6f\t%3.6f\n',[T FL' PEN']');
fclose(fid);
end
% --------------------------------------------------------------------
function menu_load_fascicle_Callback(hObject, eventdata, handles)
% hObject handle to menu_load_fascicle (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles,'movObj')
% load a fascicle from a previously saved MAT file with the fascicle
% end points - from menu_save_fascicle function
% find current frame number from slilder
frame_no = round(get(handles.frame_slider,'Value'));
if isfield(handles,'fas_x')
[fname, pname] = uigetfile('*.mat','Load tracking MAT file');
a = load([pname fname]);
handles.fas_x{frame_no} = a.fas_x;
handles.fas_y{frame_no} = a.fas_y;
handles.current_xy(1,1) = handles.fas_x{frame_no}(1);
handles.current_xy(1,2) = handles.fas_y{frame_no}(1);
handles.current_xy(2,1) = handles.fas_x{frame_no}(2);
handles.current_xy(2,2) = handles.fas_y{frame_no}(2);
% update the image axes using show_image function (bottom)
show_image(hObject,handles)
end
end
% --------------------------------------------------------------------
function menu_save_fascicle_Callback(hObject, eventdata, handles)
% hObject handle to menu_save_fascicle (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles,'movObj')
% save the current fascicle end points in a MAT file so that the
% fascicle can be re-loaded at any time
% find current frame number from slilder
frame_no = round(get(handles.frame_slider,'Value'));
if isfield(handles,'fas_x_corr')
fas_x = handles.fas_x_corr{frame_no};
fas_y = handles.fas_y_corr{frame_no};
[fname, pname] = uiputfile('*.mat', 'Save tracking MAT file');
save([pname fname],'fas_x','fas_y');
elseif isfield(handles,'fas_x')
fas_x = handles.fas_x{frame_no};
fas_y = handles.fas_y{frame_no};
[fname, pname] = uiputfile('*.mat', 'Save tracking MAT file');
save([pname fname],'fas_x','fas_y');
end
end
% --------------------------------------------------------------------
function menu_save_image_Callback(hObject, eventdata, handles)
% hObject handle to menu_save_image (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles,'movObj')
% save the current frame as an image including any fascicles and/or ROI
% drawings
[fileout, pathout, FI] = uiputfile('*.tif', 'Save video as');
if FI > 0
IM_out = getframe(handles.axes1);
imwrite(IM_out.cdata,[pathout fileout], 'TIFF');
end
end
% --------------------------------------------------------------------
function menu_load_file_Callback(hObject, eventdata, handles)
% hObject handle to menu_load_file (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% load a new video file
% if a video is already opened then delete current video and any current
% fascicles etc
if isfield(handles,'movObj')
handles = rmfield(handles,'mov');
handles = rmfield(handles,'movObj');
end
if isfield(handles,'fas_length')
handles = rmfield(handles,'fas_length');
handles = rmfield(handles,'fas_pen');
handles = rmfield(handles,'fas_x');
handles = rmfield(handles,'fas_y');
end
version = ver;
% do some checking to make sure the image processing toolbox is available
if isempty(strfind([version.Name],'Image Processing Toolbox'))
error('This application requires the Matlab Image Processing Toolbox to be installed')
end
% determine the release date and use the appropriate file loading function
% newer versions > 2010b use VideoReader, older versions use mmreader
if datenum(version(1).Date) >= 734353
reader = 'VideoReader';
else reader = 'mmreader';
end
% if post 2010a version of Matlab then look at the available video formats
% for the list
if datenum(version(1).Date) >= 734202
%determine the available video formats
file_formats = eval([reader '.getFileFormats']);
format_list{1,1} = [];
format_list{1,2} = 'All Video Files (';
for i = 1:length(file_formats)
format_list{1,1} = [format_list{1,1} '*.' file_formats(i).get.Extension ';'];
format_list{1,2} = [format_list{1,2} file_formats(i).get.Description ', '];
format_list{i+1,1} = ['*.' file_formats(i).get.Extension];
format_list{i+1,2} = ['*.' file_formats(i).get.Extension ' - ' file_formats(i).get.Description];
end
format_list{1,2} = [format_list{1,2}(1:end-2) ')'];
%load the avi file
[handles.fname, handles.pname] = uigetfile(format_list, 'Pick a movie file');
else % pre 2010a mmreader function cannot use the getFileFormats method so only allow AVI files to be selected
[handles.fname, handles.pname] = uigetfile('*.avi', 'Pick a movie file');
end
if isequal(handles.fname,0) || isequal(handles.pname,0)
return;
end
cd (handles.pname)
handles.movObj = eval([reader '([handles.pname handles.fname])']);
handles.NumFrames = handles.movObj.NumberOfFrames;
vidHeight = handles.movObj.Height;
vidWidth = handles.movObj.Width;
handles.FrameRate = handles.movObj.NumberOfFrames/handles.movObj.Duration;
% display the path and name of the file in the filename text box
set(handles.filename,'String',[handles.pname handles.fname])
% set the string in the frame_number box to the current frame value (1)
set(handles.frame_number,'String',num2str(1))
handles.start_frame = 1;
% set the limits on the slider - use number of frames to set maximum (min =
% 1)
set(handles.frame_slider,'Min',1);
set(handles.frame_slider,'Max',handles.NumFrames);
set(handles.frame_slider,'Value',1);
set(handles.frame_slider,'SliderStep',[1/handles.NumFrames 10/handles.NumFrames]);
% set the image croppable area to the maximum area
if ~isfield(handles,'crop_rect')
handles.crop_rect = [1 1 vidWidth vidHeight];
end
for i = 1:handles.NumFrames
handles.fas_x{i}=[];
handles.fas_y{i}=[];
end
cd(handles.pname)
% make a timeline which corresponds to the ultrasound frame data
handles.Time = (1/handles.FrameRate:1/handles.FrameRate:handles.NumFrames/handles.FrameRate)';
% update the image axes using show_image function (bottom)
show_image(hObject,handles)
%---------------------------------------------------------
% Function to show image with appropriate image processing
%---------------------------------------------------------
function show_image(hObject, handles)
if isfield(handles,'movObj')
% find current frame number from slilder
frame_no = round(get(handles.frame_slider,'Value'));
image_depth = handles.ID;
handles.mov.cdata = read(handles.movObj, frame_no+handles.start_frame-1);
% create image from movie frame
Im = handles.mov.cdata;
% crop image with current cropping value
Im = imcrop(Im,handles.crop_rect);
% make the image axes the current axes
axes(handles.axes1)
cla
% show the image
imshow(Im)
handles.Im = Im;
handles.NIm = handles.Im;
% plot the ROI if available
if isfield(handles,'ROI')
hold on
plot(handles.ROIx,handles.ROIy,'r:','LineWidth',2)
hold off
end
if isfield(handles,'current_xy')
% if the new frame hasn't been tracked yet and a fascicle for the
% previous viewed frame is determined along with a ROI defined then
% perform the tracking to the new frame
if isempty(handles.fas_x{frame_no}) && isfield(handles,'ROI')
% convert current and new images to greyscale
im1 = double(rgb2gray(handles.CIm))/256;
im2 = double(rgb2gray(handles.NIm))/256;
sigmaXY = handles.SIGMA;
sampleStep = handles.S_STEP;
% determine affine flow on region of interest (roi) and convert
% this into a flow warp to be applied to fascicle end points
af = affine_flow('image1', im1, 'image2', im2, 'sigmaXY',sigmaXY,'sampleStep',sampleStep,'regionOfInterest',handles.ROI);
af = af.findFlow;
flow = af.flowStruct;
w = affine_flow.warp(flow);
% apply flow warp (affine transformation) to the fascicle end
% points of current frame
pos = [handles.current_xy(:,1) handles.current_xy(:,2) ones(length(handles.current_xy),1)] * w;
% save these as the fascicle end points of new frame and the
% current points for the next iteration
handles.current_xy = pos;
handles.fas_x{frame_no}(1) = handles.current_xy(1,1);
handles.fas_y{frame_no}(1) = handles.current_xy(1,2);
handles.fas_x{frame_no}(2) = handles.current_xy(2,1);
handles.fas_y{frame_no}(2) = handles.current_xy(2,2);
% make the new frame the current frame for the next iteration
handles.CIm = handles.NIm;
% calculate the length and pennation for the current frame
handles.fas_pen(frame_no) = atan2(abs(diff(handles.fas_y{frame_no})),abs(diff(handles.fas_x{frame_no})));
scalar = image_depth/handles.movObj.Height;
handles.fas_length(frame_no) = scalar*sqrt(diff(handles.fas_y{frame_no}).^2 + diff(handles.fas_x{frame_no}).^2);
else % if the tracking has been performed already then just display
% the fascicle for this frame and make the fascicle end points
% for this frame current
handles.current_xy(1,1) = handles.fas_x{frame_no}(1);
handles.current_xy(1,2) = handles.fas_y{frame_no}(1);
handles.current_xy(2,1) = handles.fas_x{frame_no}(2);
handles.current_xy(2,2) = handles.fas_y{frame_no}(2);
handles.fas_pen(frame_no) = atan2(abs(diff(handles.fas_y{frame_no})),abs(diff(handles.fas_x{frame_no})));
scalar = image_depth/handles.movObj.Height;
handles.fas_length(frame_no) = scalar*sqrt(diff(handles.fas_y{frame_no}).^2 + diff(handles.fas_x{frame_no}).^2);
end
% display the current fascicle on the current frame image
hold on
plot(handles.axes1,handles.fas_x{frame_no},handles.fas_y{frame_no},'ro-','LineWidth',2)
hold off
end
% Update handles structure
guidata(hObject, handles);
end
