N = 500;
pattern = zeros(N,N);
grid on
plot(pattern)
% gets coordinates of modified cells
[x,y] = ginput;
% convert coordinates to integers
X = uint8(x);
Y = uint8(y);
% convert (X,Y) into linear indices
indx = sub2ind([N,N],x,y);
% switch desired cells on (value of 1)
pattern(indx) = 1;
I'm trying to assign several elements of a zeros array the value of 1. Basically I want to create an interactive plot where the user decides what cells he wants to turn on and then save his drawing as a matrix. In Python it's very simple to use the on_click with Matplotlib, but Matlab is weird and I can't find a clear answer. What's annoying is you can't see where you clicked until you save your changes and check the final matrix. You also can't erase a point if you made a mistake.
Moreover I get the following error : Error using sub2ind Out of range subscript. Error in createPattern (line 12) indx = sub2ind([N,N],X,Y);
Any idea how to fix it?
function CreatePattern
hFigure = figure;
hAxes = axes;
axis equal;
axis off;
hold on;
N = 3; % for line width
M = 20; % board size
squareEdgeSize = 5;
% create the board of patch objects
hPatchObjects = zeros(M,M);
for j = M:-1:1
for k = 1:M
hPatchObjects(M - j+ 1, k) = rectangle('Position', [k*squareEdgeSize,j*squareEdgeSize,squareEdgeSize,squareEdgeSize], 'FaceColor', [0 0 0],...
'EdgeColor', 'w', 'LineWidth', N, 'HitTest', 'on', 'ButtonDownFcn', {#OnPatchPressedCallback, M - j+ 1, k});
end
end
Board = zeros(M,M);
playerColours = [1 1 1; 0 0 0];
xlim([squareEdgeSize M*squareEdgeSize]);
ylim([squareEdgeSize M*squareEdgeSize]);
function OnPatchPressedCallback(hObject, eventdata, rowIndex, colIndex)
% change FaceColor to player colour
value = Board(rowIndex,colIndex);
if value == 1
set(hObject, 'FaceColor', playerColours(2, :));
Board(rowIndex,colIndex) = 0; % update board
else
set(hObject, 'FaceColor', playerColours(1, :));
Board(rowIndex,colIndex) = 1; % update board
end
end
end
I found this link and modified the code to be able to expand the board and also select cells that have been turned on already to switch them off.
Now I need a way to extract that board value to save the array.
The Goal
(Forgive me for length of this, it's mostly background and detail.)
I'm contributing to a TOML encoder/decoder for MATLAB and I'm working with numerical arrays right now. I want to input (and then be able to write out) the numerical array in the same format. This format is the nested square-bracket format that is used by numpy.array. For example, to make multi-dimensional arrays in numpy:
The following is in python, just to be clear. It is a useful example though my work is in MATLAB.
2D arrays
>> x = np.array([1,2])
>> x
array([1, 2])
>> x = np.array([[1],[2]])
>> x
array([[1],
[2]])
3D array
>> x = np.array([[[1,2],[3,4]],[[5,6],[7,8]]])
>> x
array([[[1, 2],
[3, 4]],
[[5, 6],
[7, 8]]])
4D array
>> x = np.array([[[[1,2],[3,4]],[[5,6],[7,8]]],[[[9,10],[11,12]],[[13,14],[15,16]]]])
>> x
array([[[[ 1, 2],
[ 3, 4]],
[[ 5, 6],
[ 7, 8]]],
[[[ 9, 10],
[11, 12]],
[[13, 14],
[15, 16]]]])
The input is a logical construction of the dimensions by nested brackets. Turns out this works pretty well with the TOML array structure. I can already successfully parse and decode any size/any dimension numeric array with this format from TOML to MATLAB numerical array data type.
Now, I want to encode that MATLAB numerical array back into this char/string structure to write back out to TOML (or whatever string).
So I have the following 4D array in MATLAB (same 4D array as with numpy):
>> x = permute(reshape([1:16],2,2,2,2),[2,1,3,4])
x(:,:,1,1) =
1 2
3 4
x(:,:,2,1) =
5 6
7 8
x(:,:,1,2) =
9 10
11 12
x(:,:,2,2) =
13 14
15 16
And I want to turn that into a string that has the same format as the 4D numpy input (with some function named bracketarray or something):
>> str = bracketarray(x)
str =
'[[[[1,2],[3,4]],[[5,6],[7,8]]],[[[9,10],[11,12]],[[13,14],[15,16]]]]'
I can then write out the string to a file.
EDIT: I should add, that the function numpy.array2string() basically does exactly what I want, though it adds some other whitespace characters. But I can't use that as part of the solution, though it is basically the functionality I'm looking for.
The Problem
Here's my problem. I have successfully solved this problem for up to 3 dimensions using the following function, but I cannot for the life of me figure out how to extend it to N-dimensions. I feel like it's an issue of the right kind of counting for each dimension, making sure to not skip any and to nest the brackets correctly.
Current bracketarray.m that works up to 3D
function out = bracketarray(in, internal)
in_size = size(in);
in_dims = ndims(in);
% if array has only 2 dimensions, create the string
if in_dims == 2
storage = cell(in_size(1), 1);
for jj = 1:in_size(1)
storage{jj} = strcat('[', strjoin(split(num2str(in(jj, :)))', ','), ']');
end
if exist('internal', 'var') || in_size(1) > 1 || (in_size(1) == 1 && in_dims >= 3)
out = {strcat('[', strjoin(storage, ','), ']')};
else
out = storage;
end
return
% if array has more than 2 dimensions, recursively send planes of 2 dimensions for encoding
else
out = cell(in_size(end), 1);
for ii = 1:in_size(end) %<--- this doesn't track dimensions or counts of them
out(ii) = bracketarray(in(:,:,ii), 'internal'); %<--- this is limited to 3 dimensions atm. and out(indexing) need help
end
end
% bracket the final bit together
if in_size(1) > 1 || (in_size(1) == 1 && in_dims >= 3)
out = {strcat('[', strjoin(out, ','), ']')};
end
end
Help me Obi-wan Kenobis, y'all are my only hope!
EDIT 2: Added test suite below and modified current code a bit.
Test Suite
Here is a test suite to use to see if the output is what it should be. Basically just copy and paste it into the MATLAB command window. For my current posted code, they all return true except the ones more than 3D. My current code outputs as a cell. If your solution output differently (like a string), then you'll have to remove the curly brackets from the test suite.
isequal(bracketarray(ones(1,1)), {'[1]'})
isequal(bracketarray(ones(2,1)), {'[[1],[1]]'})
isequal(bracketarray(ones(1,2)), {'[1,1]'})
isequal(bracketarray(ones(2,2)), {'[[1,1],[1,1]]'})
isequal(bracketarray(ones(3,2)), {'[[1,1],[1,1],[1,1]]'})
isequal(bracketarray(ones(2,3)), {'[[1,1,1],[1,1,1]]'})
isequal(bracketarray(ones(1,1,2)), {'[[[1]],[[1]]]'})
isequal(bracketarray(ones(2,1,2)), {'[[[1],[1]],[[1],[1]]]'})
isequal(bracketarray(ones(1,2,2)), {'[[[1,1]],[[1,1]]]'})
isequal(bracketarray(ones(2,2,2)), {'[[[1,1],[1,1]],[[1,1],[1,1]]]'})
isequal(bracketarray(ones(1,1,1,2)), {'[[[[1]]],[[[1]]]]'})
isequal(bracketarray(ones(2,1,1,2)), {'[[[[1],[1]]],[[[1],[1]]]]'})
isequal(bracketarray(ones(1,2,1,2)), {'[[[[1,1]]],[[[1,1]]]]'})
isequal(bracketarray(ones(1,1,2,2)), {'[[[[1]],[[1]]],[[[1]],[[1]]]]'})
isequal(bracketarray(ones(2,1,2,2)), {'[[[[1],[1]],[[1],[1]]],[[[1],[1]],[[1],[1]]]]'})
isequal(bracketarray(ones(1,2,2,2)), {'[[[[1,1]],[[1,1]]],[[[1,1]],[[1,1]]]]'})
isequal(bracketarray(ones(2,2,2,2)), {'[[[[1,1],[1,1]],[[1,1],[1,1]]],[[[1,1],[1,1]],[[1,1],[1,1]]]]'})
isequal(bracketarray(permute(reshape([1:16],2,2,2,2),[2,1,3,4])), {'[[[[1,2],[3,4]],[[5,6],[7,8]]],[[[9,10],[11,12]],[[13,14],[15,16]]]]'})
isequal(bracketarray(ones(1,1,1,1,2)), {'[[[[[1]]]],[[[[1]]]]]'})
I think it would be easier to just loop and use join. Your test cases pass.
function out = bracketarray_matlabbit(in)
out = permute(in, [2 1 3:ndims(in)]);
out = string(out);
dimsToCat = ndims(out);
if iscolumn(out)
dimsToCat = dimsToCat-1;
end
for i = 1:dimsToCat
out = "[" + join(out, ",", i) + "]";
end
end
This also seems to be faster than the route you were pursing:
>> x = permute(reshape([1:16],2,2,2,2),[2,1,3,4]);
>> tic; for i = 1:1e4; bracketarray_matlabbit(x); end; toc
Elapsed time is 0.187955 seconds.
>> tic; for i = 1:1e4; bracketarray_cris_luengo(x); end; toc
Elapsed time is 5.859952 seconds.
The recursive function is almost complete. What is missing is a way to index the last dimension. There are several ways to do this, the neatest, I find, is as follows:
n = ndims(x);
index = cell(n-1, 1);
index(:) = {':'};
y = x(index{:}, ii);
It's a little tricky at first, but this is what happens: index is a set of n-1 strings ':'. index{:} is a comma-separated list of these strings. When we index x(index{:},ii) we actually do x(:,:,:,ii) (if n is 4).
The completed recursive function is:
function out = bracketarray(in)
n = ndims(in);
if n == 2
% Fill in your n==2 code here
else
% if array has more than 2 dimensions, recursively send planes of 2 dimensions for encoding
index = cell(n-1, 1);
index(:) = {':'};
storage = cell(size(in, n), 1);
for ii = 1:size(in, n)
storage(ii) = bracketarray(in(index{:}, ii)); % last dimension automatically removed
end
end
out = { strcat('[', strjoin(storage, ','), ']') };
Note that I have preallocated the storage cell array, to prevent it from being resized in every loop iteration. You should do the same in your 2D case code. Preallocating is important in MATLAB for performance reasons, and the MATLAB Editor should warm you about this too.
I'm essentially trying to accomplish this and then this but with a 3D matrix, say (128,128,60,6). The 4th dimension is an array vector that represents the diffusion array at that voxel, e.g.:
d[30,30,30,:] = [dxx, dxy, dxz, dyy, dyz, dzz] = D_array
Where dxx etc. are diffusion for a particular direction. D_array can also be seen as a triangular matrix (since dxy == dyx etc.). So I can use those 2 other answers to get from D_array to D_square, e.g.
D_square = [[dxx, dxy, dxz], [dyx, dyy, dyz],[dzx, dzy, dzz]]
I can't seem to figure out the next step however - how to apply that unit transformation of a D_array into D_square to the whole 3D volume.
Here's the code snippet that works on a single tensor:
#this solves an linear eq. that provides us with diffusion arrays at each voxel in a 3D space
D = np.einsum('ijkt,tl->ijkl',X,bi_plus)
#our issue at this point is we have a vector that represents a triangular matrix.
# first make a tri matx from the vector, testing on unit tensor first
D_tri = np.zeros((3,3))
D_array = D[30][30][30]
D_tri[np.triu_indices(3)] = D_array
# then getting the full sqr matrix
D_square = D_tri.T + D_tri
np.fill_diagonal(D_square, np.diag(D_tri))
So what would be the numpy-way of formulating that unit transformation of the Diffusion tensor to the whole 3D volume all at once?
Approach #1
Here's one using row, col indices from triu_indices for indexing along last two axes into an initialized output array -
def squareformnd_rowcol_integer(ar, n=3):
out_shp = ar.shape[:-1] + (n,n)
out = np.empty(out_shp, dtype=ar.dtype)
row,col = np.triu_indices(n)
# Get a "rolled-axis" view with which the last two axes come to the front
# so that we could index into them just like for a 2D case
out_rolledaxes_view = out.transpose(np.roll(range(out.ndim),2,0))
# Assign permuted version of input array into rolled output version
arT = np.moveaxis(ar,-1,0)
out_rolledaxes_view[row,col] = arT
out_rolledaxes_view[col,row] = arT
return out
Approach #2
Another one with the last two axes merged into one and then indexing with linear indices -
def squareformnd_linear_integer(ar, n=3):
out_shp = ar.shape[:-1] + (n,n)
out = np.empty(out_shp, dtype=ar.dtype)
row,col = np.triu_indices(n)
idx0 = row*n+col
idx1 = col*n+row
ar2D = ar.reshape(-1,ar.shape[-1])
out.reshape(-1,n**2)[:,idx0] = ar2D
out.reshape(-1,n**2)[:,idx1] = ar2D
return out
Approach #3
Finally altogether a new method using masking and should be better with performance as most masking based ones are when it comes to indexing -
def squareformnd_masking(ar, n=3):
out = np.empty((n,n)+ar.shape[:-1] , dtype=ar.dtype)
r = np.arange(n)
m = r[:,None]<=r
arT = np.moveaxis(ar,-1,0)
out[m] = arT
out.swapaxes(0,1)[m] = arT
new_axes = range(out.ndim)[2:] + [0,1]
return out.transpose(new_axes)
Timings on (128,128,60,6) shaped random array -
In [635]: ar = np.random.rand(128,128,60,6)
In [636]: %timeit squareformnd_linear_integer(ar, n=3)
...: %timeit squareformnd_rowcol_integer(ar, n=3)
...: %timeit squareformnd_masking(ar, n=3)
10 loops, best of 3: 103 ms per loop
10 loops, best of 3: 103 ms per loop
10 loops, best of 3: 53.6 ms per loop
A vectorized way to do it:
# Gets the triangle matrix
d_tensor = np.zeros(128, 128, 60, 3, 3)
triu_idx = np.triu_indices(3)
d_tensor[:, :, :, triu_idx[0], triu_idx[1]] = d
# Make it symmetric
diagonal = np.zeros(128, 128, 60, 3, 3)
idx = np.arange(3)
diagonal[:, :, :, idx, idx] = d_tensor[:, :, :, idx, idx]
d_tensor = np.transpose(d_tensor, (0, 1, 2, 4, 3)) + d_tensor - diagonal
I have two array, the first one is data_array(50,210), the second one is dest_array(210,210). The goal, using data from data_array to calculate the values of dest_array at specific indicies, without using for-loop.
I do it in such way:
function [ out ] = grid_point( row,col,cg_row,cg_col,data,kernel )
ker_len2 = floor(length(kernel)/2);
op1_vals = data((row - ker_len2:row + ker_len2),(col - ker_len2:col + ker_len2));
out(cg_row,cg_col) = sum(sum(op1_vals.*kernel)); %incorre
end
function [ out ] = sm(dg_X, dg_Y)
%dg_X, dg_Y - arrays of size 210x210, the values - coordinates of data in data_array,
%index of each element - position this data at 210x210 grid
data_array = randi(100,50,210); %data array
kernel = kernel_sinc2d(17,'hamming'); %sinc kernel for calculations
ker_len2 = floor(length(kernel)/2);
%adding the padding for array, to avoid
%the errors related to boundaries of data_array
data_array = vertcat(data_array(linspace(ker_len2+1,2,ker_len2),:),...
data_array,...
data_array(linspace(size(data_array,1)-1,size(data_array,1) - ker_len2,ker_len2),:));
data_array = horzcat(data_array(:,linspace(ker_len2+1,2,ker_len2)),...
data_array,...
data_array(:,linspace(size(data_array,2)-1,(size(data_array,2) - ker_len2,ker_len2)));
%cg_X, cg_Y - arrays of indicies for X and Y directions
[cg_X,cg_Y] = meshgrid(linspace(1,210,210),linspace(1,210,210));
%for each point at grid(210x210) formed by cg_X and cg_Y,
%we should calculate the value, using the data from data_array(210,210).
%after padding, data_array will have size (50 + ker_len2*2, 210 + ker_len2*2)
dest_array = arrayfun(#(y,x,cy,cx) grid_point(y, x, cy, cx, data_array, kernel),...
dg_Y, dg_X, cg_Y, cg_X);
end
But, it seems that arrayfun cannot resolve my problem, because I use arrays with different sizes. Have somebody the ideas of this?
I am not completely sure, but judging from the title, this may be what you want:
%Your data
data_array_small = rand(50,210)
data_array_large = zeros(210,210)
%Indicating the points of interest
idx = randperm(size(data_array_large,1));
idx = idx(1:size(data_array_small,1))
%Now actually use the information:
data_array_large(idx,:) = data_array_small