I wrote a loop code to extract my table files names into a string or an array and meanwhile collect the data into arrays. But I found my code went wrong as only one file was read and repeated in the loop over and over again. I had no idea where my code is wrong and it already took me several hours to look for the problem. Could somebody help me?
DataCircle = dir('*-circle.xls');
MeanAreaCircle = [];
ColonyNumCircle = [];
PlateNameCircle = [];
for zz = 1:numel(DataCircle)
basefilenamedata1 = DataCircle(w).name; % generate the base name
DataName1 = regexprep(basefilenamedata1,'-circle.xls',''); %replace part of the name and the extension
PlateNameCircle = [PlateNameCircle DataName1]; % collect the file name into a string
T1 = readtable(basefilenamedata1); % read data in
MeanAreaCircle = [MeanAreaCircle mean(T1.area)]; % collect the mean for area
end
What I got is like this, which is wrong:
>> PlateNameCircle
PlateNameCircle ='IMG_0813IMG_0813IMG_0813IMG_0813IMG_0813IMG_0813IMG_0813IMG_0813IMG_0813IMG_0813'
>> MeanAreaCircle
MeanAreaCircle =
1.0e+03 *
6.4152 6.4152 6.4152 6.4152 6.4152 6.4152 6.4152 6.4152 6.4152 6.4152
My input file list:
IMG_0809-CC.xls
IMG_0809-circle.xls
IMG_0810-CC.xls
IMG_0810-circle.xls
IMG_0812-CC.xls
IMG_0812-circle.xls
IMG_0813-CC.xls
IMG_0813-circle.xls
What I want is a column or a character array or a string like this:
PlateNameCircle = 'IMG_0809' 'IMG_0810' 'IMG_0811' 'IMG_0812' 'IMG_0813'
Issues
1: you're using w to index the name, instead of zz, the loop variable. Apparently, there is a stray variable called w in your workspace, equal to 8. That's why you're always reading the same file, regardless of iteration number.
2: you're not adding a space in the name:
PlateNameCircle = [PlateNameCircle ' ' DataName1];
3: you're adding the same name on each two consecutive iterations:
PlateNameCircle = 'IMG_0809-CC IMG_0809 IMG_0810-CC IMG_0810 ...'
Improvements
vectorize and use cell strings
preallocate instead of grow-on-the-fly
give your variables even-better names (although you already did a pretty good job there already, tbh)
something like:
filenames = {D.name};
PlateNameCircle = regexprep(filenames,'-circle.xls',''); %...doubt this is actually what you want, but it *is* what you've written...
MeanAreaCircle = zeros(numel(filenames),1);
ColonyNumCircle = []; % <- not used?
for zz = 1:numel(filenames)
T1 = readtable(filenames{zz}); % read data in
MeanAreaCircle(zz) = mean(T1.area); % collect the mean for area
end
I think the w in
basefilenamedata1 = DataCircle(w).name;
should be zz instead. Otherwise you are always looking at the first file in the list.
Related
I have a code like below. I want to generate an array with all the file names and combine with the data that I collected from each file.
DataCC = dir('*-CC.xls'); %select the file type
MeanAreaCC=[];
PlateNameCC=[];
for w = 1: numel(DataCC)
basefilenamedata=DataCC(w).name; %extract the file name
T=readtable(basefilenamedata); %read table in
PlateNameCC=[PlateNameCC basefilenamedata]; %generate the file name array
MeanAreaCC = [MeanAreaCC mean(T.Area)]; %generate the data array
end
x=array2table([PlateNameCC, transpose(MeanAreaCC)],'VariableNames',{'Iso-Condi-Rep','MeanAreaCC'}); %combine two arrays just generated
writetable(x,fullfile(DataFolder,'DataSummary.xls'),'Sheet',1,'Range','A1');
But my code didn't work, as the PlateNameCC is generated as one character but not an array. This came to an error complaining different array size, when I combine PlateNameCC with MeanAreaCC. Could somebody check it for me? Thank you!
There are a couple things wrong here.
First, PlateNameCC = [PlateNameCC basefilenamedata]; is going to create one long string of garbage.
For example:
fnames = dir('*.m')
namelist = [];
for ii = 1:numel(fnames)
namelist = [namelist fnames(ii).name]
end
Gives me:
namelist =
'SOcode.mcallbacksclass.mtestcode.m'
You want to use a string array or a cell array:
fnames = dir('*.m');
namelist1 = string({fnames.name});
namelist2 = {fnames.name};
Which returns:
namelist1 =
1×3 string array
"SOcode.m" "callbacksclass.m" "testcode.m"
namelist2 =
1×3 cell array
{'SOcode.m'} {'callbacksclass.m'} {'testcode.m'}
Second, there's no point trying to concatenate two (very) unlike arrays to create a table when you can just use the table constructor itself:
fnames = dir('*.m');
namelist = string({fnames.name});
data = [1, 2, 3];
T = table(namelist.', data.');
Which gives:
T =
3×2 table
Var1 Var2
__________________ ____
"SOcode.m" 1
"callbacksclass.m" 2
"testcode.m" 3
I am beginner in MATLAB. I would like to load 200 image files (size 192x192) in a specific folder by using a for loop.
The image names are '1.png', '2.png', '3.png' and so on.
My code is as below.
list = dir('C:/preds/*.png');
N = size(list,1);
sum_image = zeros(192,192,200);
for i = 1:N
sum_image(:,:,i) = imread('C:/preds/i.png');
end
Which part should I change ?
I would probably do it like the code below:
You are currently getting the list of filenames then not really doing much with it. Iterating over the list is safer otherwise if there is a missing number you could have issues. Also, the sort maybe unnecessary depending if you image numbering is zero-padded so they come out in the correct order ... but better safe than sorry. One other small change initializing the array to size N instead of hard-coding 200. This will make it more flexible.
searchDir = 'C:\preds\';
list = dir([searchDir '*.png']);
nameList = {list.name}; %Get array of names
imNum = str2double(strrep(nameList,'.png','')); %Get image number
[~,idx] = sort(imNum); %sort it
nameList = nameList(idx);
N = numel(nameList);
sum_image = zeros(192,192,N);
for i=1:N
sum_image(:,:,i) = imread(fullfile(searchDir,nameList{i}));
end
I would suggest changing the line within the loop to the following:
sum_image(:,:,i) = imread(['C:/preds/', num2str(i), '.png']);
MATLAB treats the i in your string as a character and not the variable i. The above line of code builds your string piece by piece.
If this isn't a homework problem, the right answer to this question is don't write this as a for loop. Use an imageDatastore:
https://www.mathworks.com/help/matlab/ref/imagedatastore.html
ds = imageDatastore('C:/preds/');
sumImageCellArray = readall(ds);
sumImage = cat(3,sumImageCellArray{:});
I am trying to take the averages of a pretty large set of data, so i have created a function to do exactly that.
The data is stored in some struct1.struct2.data(:,column)
there are 4 struct1 and each of these have between 20 and 30 sub-struct2
the data that I want to average is always stored in column 7 and I want to output the average of each struct2.data(:,column) into a 2xN array/double (column 1 of this output is a reference to each sub-struct2 column 2 is the average)
The omly problem is, I can't find a way (lots and lots of reading) to point at each structure properly. I am using a string to refer to the structures, but I get error Attempt to reference field of non-structure array. So clearly it doesn't like this. Here is what I used. (excuse the inelegence)
function [avrg] = Takemean(prefix,numslits)
% place holder arrays
avs = [];
slits = [];
% iterate over the sub-struct (struct2)
for currslit=1:numslits
dataname = sprintf('%s_slit_%02d',prefix,currslit);
% slap the average and slit ID on the end
avs(end+1) = mean(prefix.dataname.data(:,7));
slits(end+1) = currslit;
end
% transpose the arrays
avs = avs';
slits = slits';
avrg = cat(2,slits,avs); % slap them together
It falls over at this line avs(end+1) = mean(prefix.dataname.data,7); because as you can see, prefix and dataname are strings. So, after hunting around I tried making these strings variables with genvarname() still no luck!
I have spent hours on what should have been 5min of coding. :'(
Edit: Oh prefix is a string e.g. 'Hs' and the structure of the structures (lol) is e.g. Hs.Hs_slit_XX.data() where XX is e.g. 01,02,...27
Edit: If I just run mean(Hs.Hs_slit_01.data(:,7)) it works fine... but then I cant iterate over all of the _slit_XX
If you simply want to iterate over the fields with the name pattern <something>_slit_<something>, you need neither the prefix string nor numslits for this. Pass the actual structure to your function, extract the desired fields and then itereate them:
function avrg = Takemean(s)
%// Extract only the "_slit_" fields
names = fieldnames(s);
names = names(~cellfun('isempty', strfind(names, '_slit_')));
%// Iterate over fields and calculate means
avrg = zeros(numel(names), 2);
for k = 1:numel(names)
avrg(k, :) = [k, mean(s.(names{k}).data(:, 7))];
end
This method uses dynamic field referencing to access fields in structs using strings.
First of all, think twice before you use string construction to access variables.
If you really really need it, here is how it can be used:
a.b=123;
s1 = 'a';
s2 = 'b';
eval([s1 '.' s2])
In your case probably something like:
Hs.Hs_slit_01.data= rand(3,7);
avs = [];
dataname = 'Hs_slit_01';
prefix = 'Hs';
eval(['avs(end+1) = mean(' prefix '.' dataname '.data(:,7))'])
I was just wondering if there is a clean way to store a matrix after each iteration with a different name? I would like to be able to store each matrix (uMatrix) under a different name depending on which simulation I am on eg Sim1, Sim2, .... etc. SO that Sim1 = uMatrix after first run through, then Sim2 = uMatrix after 2nd run through. SO that each time I can store a different uMatrix for each different Simulation.
Any help would be much appreciated, and sorry if this turns out to be a silly question. Also any pointers on whether this code can be cleaned up would be great too
Code I am using below
d = 2;
kij = [1,1];
uMatrix = [];
RLABEL=[];
SimNum = 2;
for i =1:SimNum
Sim = ['Sim',num2str(i)] %Simulation number
for j=1:d
RLABEL = [RLABEL 'Row','',num2str(j) ' '];
Px = rand;
var = (5/12)*d*sum(kij);
invLam = sqrt(var);
u(j) = ((log(1-Px))*-invLam)+kij(1,j);
uMatrix(j,1) = j;
uMatrix(j,2) = u(j);
uMatrix(j,3) = kij(1,j);
uMatrix(j,4) = Px;
uMatrix(j,5) = invLam;
uMatrix(j,6) = var;
end
printmat(uMatrix,'Results',RLABEL,'SECTION u kij P(Tij<u) 1/Lambda Var')
end
There are really too many options. To go describe both putting data into, and getting data our of a few of these methods:
Encode in variable names
I really, really dislike this approach, but it seems to be what you are specifically asking for. To save uMatrix as a variable Sim5 (after the 5th run), add the following to your code at the end of the loop:
eval([Sim ' = uMatrix;']); %Where the variable "Sim" contains a string like 'Sim5'
To access the data
listOfStoredDataNames = who('Sim*')
someStoredDataItem = eval(listOfStoredDataNames {1}) %Ugghh
%or of you know the name already
someStoredDataItem = Sim1;
Now, please don't do this. Let me try and convince you that there are better ways.
Use a structure
To do the same thing, using a structure called (for example) simResults
simResults.(Sim) = uMatrix;
or even better
simResults.(genvarname(Sim)) = uMatrix;
To access the data
listOfStoredDataNames = fieldnames(simResults)
someStoredDataItem = simResults.(listOfStoredDataNames{1})
%or of you know the name already
someStoredDataItem = simResults.Sim1
This avoids the always problematic eval statement, and more importantly makes additional code much easier to write. For example you can easily pass all simResults into a function for further processing.
Use a Map
To use a map to do the same storage, first initialize the map
simResults = containers.Map('keyType','char','valueType','any');
Then at each iteration add the values to the map
simResults(Sim) = uMatrix;
To access the data
listOfStoredDataNames = simResults.keys
someStoredDataItem = simResults(listOfStoredDataNames{1})
%or of you know the name already
someStoredDataItem = simResults('Sim1')
Maps are a little more flexible in the strings which can be used for names, and are probably a better solution if you are comfortable.
Use a cell array
For simple, no nonsense storage of the results
simResults{i} = uMatrix;
To access the data
listOfStoredDataNames = {}; %Names are Not available using this method
someStoredDataItem = simResults{1}
Or, using a slight level of nonesense
simResults{i,1} = Sim; %Store the name in column 1
simResults{i,2} = uMatrix; %Store the result in column 2
To access the data
listOfStoredDataNames = simResults(:,1)
someStoredDataItem = simResults{1,2}
Just to add to the detailed answer given by #Pursuit, there is one further method I am fond of:
Use an array of structures
Each item in the array is a structure which stores the results and any additional information:
simResults(i).name = Sim; % store the name of the run
simResults(i).uMatrix = uMatrix; % store the results
simResults(i).time = toc; % store the time taken to do this run
etc. Each element in the array will need to have the same fields. You can use quick operations to extract all the elements from the array, for example to see the timings of each run at a glance you can do:
[simResults.time]
You can also use arrayfun to to a process on each element in the array:
anon_evaluation_func = #(x)( evaluate_uMatrix( x.uMatrix ) );
results = arrayfun( anon_evaluation_func, simResults );
or in a more simple syntax,
for i = 1:length(simResults)
simResults(i).result = evaluate_uMatrix( simResults(i).uMatrix );
end
I would try to use a map which stores a <name, matrix>.
the possible way to do it would be to use http://www.mathworks.com/help/matlab/map-containers.html
I have written a function that takes the names and values of the input variables and writes them to a file. eg.
a = 10;
b = 100;
writevars('file.txt',a,b);
gives me a file file.txt that contains:
\def\a{\num{10}}
\def\b{\num{100}}
It would now like to be able to pass on all variables that are found using the who command. Eg if who returns:
a b z
I would like to be able to use writevars as if I called writers('file.txt', a, b, z).
The main problem I have is that writevars makes use of inputname... (temporary variables won't work e.g. writevars('file.txt', 100) doesn't work since there is no name to be given in the file).
ANSWER
var_names = who;
for i = 1 : length(var_names)
evalin('caller',['writevars(''file.txt'', ' char(var_names(i)) ' )']);
end
You can use EVALIN to run who from within writevars, e.g.
function writevars(filename,varargin)
%# get a list of variable names in the calling workspace and read their values
if isempty(varargin)
listOfVars = evalin('caller','who');
values = cell(size(listOfVars));
for i=1:length(listOfVars)
values{i} = evalin('caller',listOfVars{i});
end
else
%# use inputname to read the variable names into listOfVars
end
%# --- rest of writevars is here ---
It can be used by using the return value of whos command:
function GetAllVars
a = 45;
x = 67;
ff = 156;
z = who();
for i=1:numel(z)
if ~isequal(z{i},'z')
fprintf(1,'%s = %f\n',z{i},eval(z{i}));
end
end