other libraries to make code independent

batch_execute.m

@@ -13,6 +13,10 @@ function batch_execute(job_dir)
 		hostname= getenv('HOSTNAME');
 	end
 	
+	%% add to path
+	cur_dir			= fileparts(mfilename('fullpath'));
+	addpath(genpath(cur_dir));
+	
 	%% report
 	fprintf('--------------------------------------------------------------\n');
 	fprintf('[%s] %s BATCH PROCESSING BEGIN\n', hostname, datestr(now));

job_create.m

@@ -5,6 +5,7 @@
 %				j.m.lawson@soton.ac.uk
 % Created:		11/09/2019
 %
+addpath(genpath(fileparts(mfilename('fullpath'))));
 
 %% input parameters: file paths
 % where to save jobs
@@ -29,7 +30,7 @@ vec_pat         = '%s/B%05d.mat';		% output vector field file pattern
 % processing flags
 b_use_mask		= true;					% use mask file?
 b_overwrite     = true;                 % overwrite existing vector fields?
-b_execute_now	= false;					% start processing now?
+b_execute_now	= true;					% start processing now?
 
 % PIV correlation settings
 i_frames		= {[1 2],[3 4]};		% indices of frame pairs to cross-correlate

misc/clim.m

+function clim(lim)
+	set(gca, 'clim', lim);
+end
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misc/hms.m

+function ret = hms(seconds_elapsed)
+	ret = fix(mod(seconds_elapsed, [0, 3600, 60]) ./ [3600, 60, 1]);
+end
\ No newline at end of file

misc/lsqgradient2d.m

+function [dFdx, dFdy] = lsqgradient2d(F, dx, dy)
+	%% [dFdx, dFdy] = lsqgradient(F, dx, dy)
+	% computes numerical gradient based on second order,
+	% least squares approximation as detailed in PIV: A Practical Guide
+	%
+	% dF/dx_i ~=  2 f_(i+2) + f_(i+1) - f(i-1) - 2f_(i-2)
+	%              ------------------------------------
+	%                          10 dx_i
+	%
+	% F must be a 2D array of size Nx x Ny
+	% dFdx_i an Nx x Ny array
+	% at the edges,
+	% dFdx_i is calculated with either first order central 
+	% differences or at the very edges, forwards/backwards differences 
+	% 
+
+	%% parse input
+	if nargin < 2
+		dx = 1;
+		dy = 1;
+	elseif nargin < 3
+		dy = 1;
+	end
+	
+	%% allocate memory for dFdx
+	Nx		= size(F, 1);
+	Ny    = size(F, 2);
+	dFdx	= nan(size(F), class(F));
+	dFdy  = nan(size(F), class(F));
+	
+	%% forwards and backwards difference at edges
+	dFdx(1, :)		= (F(2,:)	- F(1,:)		) / dx;
+	dFdy(:, 1)		= (F(:,2)	- F(:,1)		) / dy;
+	dFdx(end,:)		= (F(end,:) - F(end-1,:)) / dx; 
+	dFdy(:,end)		= (F(:,end)	- F(:,end-1)) / dy;
+	
+	%% first order central difference near edges
+	if Nx >= 3
+		for i = [2 Nx-1]
+			dFdx(i, :) = (F(i+1,:) - F(i-1,:)) / (2*dx);
+		end
+	end
+	if Ny >= 3
+		for j = [2 Ny-1]
+			dFdy(:, j) = (F(:,j+1) - F(:,j-1)) / (2*dy);
+		end
+	end
+	
+	%% second order least squares near middle
+	% use an expansion of f(x)' which is accurate to O(dx^4)
+	for i = 3:(Nx-2)
+		dFdx(i, :) = (2*F(i+2,:) + F(i+1,:) - F(i-1,:) - 2*F(i-2,:)) / (10*dx);
+	end
+	for j = 3:(Ny-2)
+		dFdy(:, j) = (2*F(:,j+2) + F(:,j+1) - F(:,j-1) - 2*F(:,j-2)) / (10*dy);
+	end
+end

misc/redblue.m

+function c = redblue(m)
+%REDBLUE    Shades of red and blue color map
+%   REDBLUE(M), is an M-by-3 matrix that defines a colormap.
+%   The colors begin with bright blue, range through shades of
+%   blue to white, and then through shades of red to bright red.
+%   REDBLUE, by itself, is the same length as the current figure's
+%   colormap. If no figure exists, MATLAB creates one.
+%
+%   For example, to reset the colormap of the current figure:
+%
+%             colormap(redblue)
+%
+%   See also HSV, GRAY, HOT, BONE, COPPER, PINK, FLAG, 
+%   COLORMAP, RGBPLOT.
+
+%   Adam Auton, 9th October 2009
+
+if nargin < 1, m = size(get(gcf,'colormap'),1); end
+
+if (mod(m,2) == 0)
+    % From [0 0 1] to [1 1 1], then [1 1 1] to [1 0 0];
+    m1 = m*0.5;
+    r = (0:m1-1)'/max(m1-1,1);
+    g = r;
+    r = [r; ones(m1,1)];
+    g = [g; flipud(g)];
+    b = flipud(r);
+else
+    % From [0 0 1] to [1 1 1] to [1 0 0];
+    m1 = floor(m*0.5);
+    r = (0:m1-1)'/max(m1,1);
+    g = r;
+    r = [r; ones(m1+1,1)];
+    g = [g; 1; flipud(g)];
+    b = flipud(r);
+end
+
+c = [r g b]; 
+

readimx/MakeFrameInfo.m

+function [frameInfo]=MakeFrameInfo(Frame)
+
+Names = Frame.ComponentNames;
+frameInfo.choices = zeros(12,1);
+for i=1:size(Names,1),
+	if strcmp(Names{i},'U0')==1, frameInfo.choices( 1) = i; end; 
+	if strcmp(Names{i},'V0')==1, frameInfo.choices( 2) = i; end; 
+	if strcmp(Names{i},'W0')==1, frameInfo.choices( 3) = i; end; 
+	if strcmp(Names{i},'U1')==1, frameInfo.choices( 4) = i; end; 
+	if strcmp(Names{i},'V1')==1, frameInfo.choices( 5) = i; end; 
+	if strcmp(Names{i},'W1')==1, frameInfo.choices( 6) = i; end; 
+	if strcmp(Names{i},'U2')==1, frameInfo.choices( 7) = i; end; 
+	if strcmp(Names{i},'V2')==1, frameInfo.choices( 8) = i; end; 
+	if strcmp(Names{i},'W2')==1, frameInfo.choices( 9) = i; end; 
+	if strcmp(Names{i},'U3')==1, frameInfo.choices(10) = i; end; 
+	if strcmp(Names{i},'V3')==1, frameInfo.choices(11) = i; end; 
+	if strcmp(Names{i},'W3')==1, frameInfo.choices(12) = i; end; 
+	if strcmp(Names{i},'ACTIVE_CHOICE')== 1, frameInfo.best   = i; end;
+	if strcmp(Names{i},'ENABLED')      == 1, frameInfo.enable = i; end; 
+	if strcmp(Names{i},'MASK')         == 1, frameInfo.mask   = i; end; 
+end
+frameInfo.Grids  = Frame.Grids;
+frameInfo.Scales.X = Frame.Scales.X;
+frameInfo.Scales.Y = Frame.Scales.Y;
+frameInfo.Scales.Z = Frame.Scales.Z;
+frameInfo.Scales.I = Frame.Scales.I;
+frameInfo.is3D = (frameInfo.choices(3) > 0);	
+frameInfo.hasChoices = (frameInfo.choices(4) > 0);
\ No newline at end of file