Index in position 2 exceeds array bounds (must not exceed 1).

Hello!

I am getting an error while running the code as given below"

Index in position 2 exceeds array bounds (must not exceed 1).

Error in Untitled4 (line 32)

imagesc(data{1,3});

The main code is:

% A = imread('Filename');
%%
close all;
load_data_flag =1;
%% Load data
if load_data_flag ==1;
%
% las_file = load('Curves.txt');
% log_depth = las_file(:,1);
% caliper3 = las_file(:,3:5); % 1) depth, 3-4-5) calipers
% caliper_ave = mean(caliper3(:,3:end),2);
%%
tifffiles = dir('*.tif');
nfiles = length(tifffiles);
 for n= 1:nfiles;

 data{n} = imread(tifffiles(n).name);
 end % endfor
 % concatenate all log data into one matrix

% DATA = data;
 DATA = data{1,1};

 for i = 2:length(data(1,:))

 DATA=vertcat(DATA,data{1,i});

 end

%% Subsection of data
clf
imagesc(data{1,3});
reply = input ('Input depth axis, subsection and 0-360 coordinates?[Y]/[N]:', 's');
 if reply == ('Y')||('y')

I would appreciate if anyone can help?

Answer 1

[Walter Roberson]

You only have one .tif file in your current directory so you are only storing data{1} .

[Rock Interpreter]

Hi Walter,

Thank you so much for your quick response. I understood this later and tried with 3 Tiff images. However, I could not proceed further with the following error:

Error using vertcat

Dimensions of arrays being concatenated are not consistent.

Error in Untitled4 (line 26)

DATA=vertcat(DATA,data{1,i});

[Walter Roberson]

If that code was going to work at all, you would be able to do it without the for loop, by using

DATA = vertcat(data{:});

However, this is not going to work in your situation. It looks to me as if your images do not all have the same number of columns, and so cannot all be put above each other in the same matrix.

You could consider imresize() as you read them in, to get them to a standardized size.

I have to wonder, though, whether putting them all as one big image with a lot of rows is really what you want to do. It would typically make more sense to imresize() them as you read them in, and then either

DATA = cat(3, data{:});     %if they are grayscale images

or

DATA = cat(4, data{:});     %if they are RGB images

[Rock Interpreter]

Hi Walter,

Many thanks. I tried your suggestion, bt no luck. Maybe I am not doing correctly. Could you please fix this?

Now Error is:

-----------------------------------------------------------------------

Error using imresize>parsePreMethodArgs (line 336)

Invalid input syntax; input image missing from argument list.

Error in imresize>parseInputs (line 260)

[params.A, params.map, params.scale, params.output_size] = ...

Error in imresize (line 146)

params = parseInputs(args{:});

Error in Untitled4 (line 18)

data{n} = imresize(tifffiles(n).name);

--------------------------Main Part-------------------------------------

close all;
load_data_flag =1;
%% Load data
if load_data_flag ==1;
tifffiles = dir('*.tif');
nfiles = length(tifffiles);
 for n= 1:nfiles;

 data{n} = imread(tifffiles(n).name);
 data{n} = imresize(tifffiles(n).name);
 end % endfor
 % concatenate all log data into one matrix

% DATA = data;
 DATA = data{1,1};
 DATA = vertcat(data {:});
 DATA = cat(4, data{:}); %if they are RGB images

% for i = 2:length(data(1,:))
% DATA=vertcat(DATA,data{1,i});
%end

---------------------------------------------------------------

[Walter Roberson]

load_data_flag = 1;

%% Load data
if load_data_flag == 1
    force_rows = 512; force_columns = 512;
    
    tifffiles = dir('*.tif');
    nfiles = length(tifffiles);
    data = cell(nfiles, 1);
    
    for n = 1:nfiles
        input_image = imread(tifffiles(n).name);
        data{n} = imresize(input_image, [force_rows, force_columns]);
    end % endfor
    
    % concatenate all log data into one matrix
    DATA = cat(ndims(data{1})+1, data{:});

end

This code forces all images to be the same size, controlled by force_rows and force_columns. Using a fixed aspect ratio can distort the image. You should think more about how you want to handle the case where the images are not the same size. Sometimes it makes sense to imresize() them to a common size. Sometimes it makes more sense to pad them to a common size. Sometimes it makes more sense to pad them as needed to fit the widest and heighest image. Sometimes it makes most sense to pad relative to the center rather than padding on bottom or right all the time. Sometimes it makes more sense to do image registration to find the best scaling and translation to bring them into alignment.

[Rock Interpreter]

Dear Walter,

Many thanks for your kind response. I am still struglling to get the image for further analyis. Would appreciate if you could help.

Now the error is:

Index in position 2 exceeds array bounds (must not exceed 1).

Error in Untitled4 (line 36)

imagesc(data{1,n});

The main script is given below:

-----------------------------------------------------

close all;

load_data_flag =1;

%% Load data

if load_data_flag ==1;

force_rows = 512; force_columns = 512;

tifffiles = dir('*.tif');

nfiles = length(tifffiles);

data = cell(nfiles, 1);

for n = 1:nfiles

input_image = imread(tifffiles(n).name);

data{n} = imresize(input_image, [force_rows, force_columns]);

end % endfor

% concatenate all log data into one matrix

DATA = cat(ndims(data{1})+1, data{:});

end

%% Subsection of data

clf

imagesc(data{1,n});

reply = input ('Input depth axis, subsection and 0-360 coordinates?[Y]/[N]:', 's');

if reply == ('Y')||('y')

%% 1) DEPTH AXIS - INPUT

[ null, depths] = ginput(2); % log input for depth axis

%% 2) SUBSECTION - INPUT

[L, r] = ginput(2); % input for subsection of data

left = ceil(L(1,1));

right = ceil(L(2,1));

subsection_data = DATA;

subsection_data = subsection_data(:,left:right,:); % need last colon cause its image with RGB

clf

imagesc(subsection_data);

%% 3) 0-360 AZIMUTH - INPUT

[beg, en] = ginput(2); %coordinates for 0-360 the axis of FMI

zero = ceil(beg(1,1));

three60 = ceil(beg(2,1));

end % endif

%%

% appended = vertcat(A,B) ==> appended = [A | B]'

imagesc(subsection_data);

counterrow=0;

% countery=0;

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