Error in tgspcread and reshape

I have been encountering some difficulty processing my data in MATLAB for 14 of 40 files fail because of the following two errors. I have included the full scripts/functions in the hope someone can tell me where I'm going wrong. I am uncertain why it works for most but not all. Please help?

extract_data_AJ

%% PNT2_DMSO_50uM_5

cd('/Users/Ewan/Desktop/MATLAB')

mkdir('PNT2_DMSO_50uM_5')

cd('PNT2_DMSO_50uM_5')

[PNT2_DMSO_50uM_5,shift,ratio1,ratio2,output]= extract_lipid_fixed_AJ('/Users/Ewan/Desktop/MATLAB/PNT2 cm5/PNT2 50uM DMSO x55 y43.spc',55,43);

close all

save('/Users/Ewan/Desktop/MATLAB/Extracted files/PNT2_DMSO_50uM_5.mat')

clear

Function - extract_lipid_fixed_AJ

function [extracted_spectra ,shift,ratio1,ratio2,output]= extract_lipid_fixed_AJ(filename,x,y)

%%e.g. filename = 'C:\Users\laure\Dropbox\CENSIS postodc\Lipid big experiment\27022017 Dreadnought\PC3 DMSO 0.5s 50% centre3000 2 x59y39_Copy_Copy.spc'

%% read in spc file change file

tgspcread(filename)

%% assign shift and data variables from spc file

shift=ans.X;

data=ans.Y;

%% change dimensions according to map

%x=59;

%y=39;

%% reshape data to match original image

data=data';

data = reshape(data, x, y ,[]);

data=rot90(data,-1);

data=fliplr(data);

imagescnan(sum(data,3));axis image;

%% select cell area

ti = sum(data,3);

[level,mask] = thresh_tool(ti);

maskrows = reshape(mask, [], 1);

data = reshape(data, y*x,[]);

mask_1_rows = find(mask == 1);

data_maskrows = data(mask_1_rows,:);

emptymatrix = NaN(y*x, length(shift));

emptymatrix(mask_1_rows,:) = data_maskrows;

output = reshape(emptymatrix, y, x, []);

imagescnan(sum(output, 3));axis image

close all

%% plot average spectrum

output = reshape(output,[],1);

rows_of_spectra = find(output==output);

extracted_spectra = output(rows_of_spectra,:);

extracted_spectra = reshape(extracted_spectra,[],length(shift));

figure; lplot(shift, mean(extracted_spectra));

%% reshape

image = reshape(extracted_spectra,[],1);

matrix = NaN(y*x,length(shift));

matrix = reshape(matrix,[],1);

matrix(rows_of_spectra,:)=image;

image = reshape(matrix, y, x, []);

%% ratio 1 map = 2850/2935

image=reshape(image,y*x,[]);

[a b]=size(image);

intensity_2850=image(:,418);

intensity_2935=image(:,355);

for i=1:a

ratio1(i,1)=intensity_2850(i,1)/(intensity_2935(i,1));

end

ratio1=reshape(ratio1,y,x,1);

imagescnan(ratio1); axis image; set(gca,'FontSize',20,'FontName','Arial');colorbar;caxis([0 1.0]);colormap(jet);

print('-dtiffn','-r600','Ratio1.tif');

close all

%% ratio 2 map = 2880/2935

intensity_2880=image(:,396);

intensity_2935=image(:,355);

for i=1:a

ratio2(i,1)=intensity_2880(i,1)/(intensity_2935(i,1));

end

ratio2=reshape(ratio2,y,x,1);

imagescnan(ratio2); axis image; set(gca,'FontSize',20,'FontName','Arial');colorbar;caxis([0 1.0]);colormap(jet);

print('-dtiffn','-r600','Ratio2.tif');

close all

end

Error 1 - Reshape

>> extract_data_AJ

Reading header for file: /Users/Ewan/Desktop/MATLAB/PNT2 cm5/PNT2 50uM DMSO x55 y43.spc

File contains 1596 scans

ans =

struct with fields:

Header: [1×1 struct]

X: [633×1 single]

Y: [633×1596 single]

Z: [1×1596 single]

Error using reshape

Product of known dimensions, 2365, not divisible into total number of elements, 1010268.

Error in extract_lipid_fixed_AJ (line 15)

data = reshape(data, x, y ,[]);

Error in extract_data_AJ (line 5)

[PC3_DMSO_5uM_1,shift,ratio1,ratio2,output]= extract_lipid_fixed_AJ('/Users/Ewan/Desktop/MATLAB/PNT2 cm5/PNT2

50uM DMSO x55 y43.spc',55,43);

Error 2 - tgspcread

extract_data_AJ

%% PNT2_5uM_TOFA_1

cd('/Users/Ewan/Desktop/MATLAB')

mkdir('PNT2_5uM_TOFA_1')

cd('PNT2_5uM_TOFA_1')

[PNT2_5uM_TOFA_1,shift,ratio1,ratio2,output]= extract_lipid_fixed_AJ('/Users/Ewan/Desktop/MATLAB/PNT2 cm1/PNT2 5uM TOFA x66, y87..spc',66,87);

close all

save('/Users/Ewan/Desktop/MATLAB/Extracted files/PNT2_5uM_TOFA_1.mat')

clear

>> extract_data_AJ

Reading header for file: /Users/Ewan/Desktop/MATLAB/PNT2 cm1/PNT2 5mM TOFA x66, y87.spc

File contains 5742 scans

Operands to the || and && operators must be convertible to logical scalar values.

Error in tgspcread (line 313)

if(headeronly) || subheader(traceCount).subtime < zrange(1) || subheader(traceCount).subtime > zrange(2)

|| ~ismember(traceCount,scanindices)

Error in extract_lipid_fixed_AJ (line 6)

tgspcread(filename)

Error in extract_data_AJ (line 5)

[PC3_DMSO_5uM_1,shift,ratio1,ratio2,output]= extract_lipid_fixed_AJ('/Users/Ewan/Desktop/MATLAB/PNT2 cm1/PNT2

5mM TOFA x66, y87.spc',66,87);

Any expert help would be much appreciated :)

[Rik]

Do not delete the contents of your question. If you want private help, hire a consultant. If you want free help on this forum, keep your post up as it was so others can benefit as well. Removing your question after it has been answered is extremely rude.

[Rena Berman]

(Answers Dev) Restored edit

Answer 1

[Pavel]

Error 1:

This may be related only to variable data, it have such size that can't be reshaped to desired numbers of rows (x) and columns (y).

data = reshape(data, x, y ,[]);

Error 2:

I'm guessing that you use one of the past MATLAB release, because debugger told about error at 313 line with the following code, while it located on 321 line of file tgspcread.m in latest release 2018b.

if(headeronly) || subheader(traceCount).subtime < zrange(1) || subheader(traceCount).subtime > zrange(2)

So this error can be a bug in older version of function tgspcread. There are two ways: try to debug this function on your own or try to use a newer version of MATLAB.

If you choose first variant, you can find the code with "edit" command:

    edit tgspcread