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Help preallocating variables for a table

7 vues (au cours des 30 derniers jours)
Julian
Julian le 13 Sep 2018
Commenté : Julian le 13 Sep 2018
Hi everyone,
so i have written some code which goes like this:
function caTable = makeCaTable(caCM)
% creates a table with information about the frames(coordinates of the
% centroids and the total number of cells in the frame)
Frame = {};
PosX = {};
PosY = {};
NumberOfCells = {};
for i = 1:size(caCM,2)
C = chop(caCM{1,i},0);
for j = 1:size(C,1)
Frame{end+1,1} = i;
PosX{end+1,1} = C(j,1);
PosY{end+1,1} = C(j,2);
if(j == 1)
NumberOfCells{end+1,1} = size(C,1);
else
NumberOfCells{end+1,1} = '-';
end
end
end
% write the table
caTable = table(Frame, PosX, PosY, NumberOfCells);
it works and gives me the results i want. But now i want to preallocate the variables. I thought I do it like this:
[nrows,ncols] = cellfun(@size,caCM);
rows = sum(nrows);
Frames = cell(rows,1);
PosX = cell(rows,1);
PosY = cell(rows,1);
NumberOfObjects = cell(rows,1);
But if i do so i cant use my for loop the way i wrote it, since it would always put the values at the end of the preallocated matrices. But if i simply use:
Frames(j,1) = i
my table will not have all the fields. I really don't know how i can fix this. Maybe some of you could help me with that.
Thank you very much!
  2 commentaires
Guillaume
Guillaume le 13 Sep 2018
Modifié(e) : Guillaume le 13 Sep 2018

Please get rid of all the extra blank lines you've added to the code and in the future use the {}Code button to format code as such, as I've done for you now.

What is C (returned by chop)? A cell array? A matrix?

Why are PosX, PosY and particularly Frame cell arrays. Frame only stores scalar numerics. Not sure about PosX and PosY (depends on what C is).

Julian
Julian le 13 Sep 2018
Thank you Guillaume. C is a matrix with doubles in it. They don't necessarly have to be cell arrays. I just built it that way because it was the first thing that came to my mind. They actually all hold scalar numerics.

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Guillaume
Guillaume le 13 Sep 2018
Modifié(e) : Guillaume le 13 Sep 2018
C is a matrix with doubles in it
In that case,
function caTable = makeCaTable(caCM)
%doc goes here
% caCM: a 2D(?) cell array
% caTable:a table with 4 variables: Frame, PosX, PosY, NumberOfCells
chopped = cellfun(@(x) chop(x, 0), caCM(1, :), 'UniformOutput', false)'; %transpose for easier repelem and cell2mat
NumberOfCells = cellfun(@(m) size(m, 1), chopped);
NumberOfCells = repelem(NumberOfCells , NumberOfCells );
Frame = repelem((1:size(chopped, 1))', NumberOfCells);
chopped = cell2mat(chopped);
PosX = chopped(:, 1);
PosY = chopped(:, 2);
caTable = table(Frame, PosX, posY, NumberOfCells);
end
As a rule you shouldn't be using cell arrays unless you need to, they're slower to process and takes a lot more memory than a matrix (15 times more if each cell is just a scalar double).
Note that I'm replicating the number of cells for all rows of a frame instead of having '-' for all rows but the first of the frame. It's rarely a good idea to mix numbers and characters in a variable. If you want a different value for all but the first row, I'd recommend using NaN instead. It's trivially done:
NumberOfCells = repelem(NumberOfCells, NumberOfCells); %continuing on from there
NumberOfCells([false; diff(NumberOfCells) == 0]) = NaN;
If you really want a '-', then it's slightly more complicated:
ncells = repelem(NumberOfCells, NumberOfCells);
NumberOfCells = num2cell(ncells);
NumberOfCells([false; diff(NumberOfCells) == 0]) = {'-'};
  5 commentaires
Guillaume
Guillaume le 13 Sep 2018

No, I understood the intent the first time round. It's my mistake, I meant to use the original NumberOfCell before it got repelem'd on that Frame line. Swapping the order of the two lines will fix the error:

   NumberOfCells = cellfun(@(m) size(m, 1), chopped);
   Frame = repelem((1:size(chopped, 1))', NumberOfCells);    %to be done first
   NumberOfCells = repelem(NumberOfCells , NumberOfCells);

Better would be not to reuse NumberOfCells for different purpose so replace the above three by:

ncells = cellfun(@(m) size(m, 1), chopped);
NumberOfCells = repelem(ncells, ncells);
Frame = repelem((1:size(chopped, 1))', ncells);

and then the order doesn't matter.

Julian
Julian le 13 Sep 2018
Thank you so much Guillaume. I really learnt a lot! It works just fine now

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Plus de réponses (1)

Steven Lord
Steven Lord le 13 Sep 2018
I think you want to use the T = table('Size',sz,'VariableTypes',varTypes) syntax shown on the documentation page for the table function.
  2 commentaires
Julian
Julian le 13 Sep 2018
Modifié(e) : Julian le 13 Sep 2018

Yes i did that:

    [nrows,ncols] = cellfun(@size,caCM);
rows = sum(nrows);
varTypes = {'double', 'double', 'double', 'double'};
varNames = {'Frame', 'PosX', 'PosY', 'NumberOfCells'};
sz = [rows 4];
caTable = table('Size', sz, 'VariableTypes', varTypes, 'VariableNames',varNames);

but I still don't know how to use the for loop to make it fill out the empty fields the right way.

Peter Perkins
Peter Perkins le 13 Sep 2018
The preallocation syntax that Steve is referring to was introduced in R2018a.
But Guillaume's answer avoids needing to preallocate the table, because nothing is growing dynamically, and everything is a vectorized assignment. +1.

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