loop over branch of subfolders to copy files, without pattern in file name, in folders with specific name scheme

Hi everyone,

this will be a complex task.

I have following structure of folder and subfolders: starting with "movie":

Timepoint_1 many tif-files ...

2019_1 3245 Timepoint_2 *.tif

Timepoint_3 *.tif

Timepoint_4 tif-files ...

movie 2019_2 3245 Timepoint_5 *.tif

Timepoint_6 *.tif

Timepoint_7 tif-files ...

2019_3 3245 Timepoint_8 *.tif

Timepoint_9 *.tif

In all Timepoint_x folders are many tif-files. I want to:

1. loop over all folders and subfolders to find all tif-files
2. copy to another folder and
3. rename them by
4. sorting them in new folders with specific name scheme

How can I loop over all folders and subfolders till the function finds the tif files in a smart way? There are many existing functions to loop over subfolders. But I neither undertand nor even use them.

How can I combine the missing task with my existing code?

aim:

3_2_1_RFP_1.tif

3_2_1 3_2_1_RFP_10.tif

3_2_1_CFP_13.tif

image_sorted

3_2_1_RFP_1.tif

3_2_2 3_2_2_RFP_2.tif

3_2_2_YFP_2.tif

%  create  folder for sorted images = dest
outputFolder = fullfile(pwd, 'image_sorted')
if ~exist(outputFolder, 'dir')
  mkdir(outputFolder);
end

%
path1 ='C:\Users\Desktop\rename_microscope_files\movie\2019_1\3245\TimePoint_1'
dest = 'C:\Users\Desktop\rename_microscope_files\image_sorted'

source =fullfile(path1,'*.tif');
myfile= dir(source);

% to do: 1. loop over all folders, number of timePoint_x folders can vary


% 2. loop over files, copy all tif files without thumb in filename to folder B
for i = 1:numel(myfile)   
    if ~contains(myfile(i).name, '_thumb')
        copyfile(fullfile(path1, myfile(i).name), dest);
    end   
end


% to do:  3. rename files, assign file format 
% e.g. tif file name in folder timePoint_1: movie_C02_w1_B9D7398B.tif 
%                                             --> 3_2_1_RFP_1.tif 
%                                            (row_column_site_wave_timepoint)
% this file should be put in folder 3_2_1

for i = 1:size(file_names)
    fname = file_names(i).name;
    
    fname = strsplit(fname,'_');
    fname = char(fname);
    
    row = fname(1);    % takes 1. letter
    col = str2num(fname(2:3)); % 2. and 3. letter
    
    switch row
        case 'A'
            row = 1;
        case 'B'
            row = 2;
        case 'C'
            row = 3;
        case 'D'
            row = 4;
        case 'E'
            row = 5;
        case 'F'
            row = 6;
        case 'G'
            row = 7;
        case 'H'
            row = 8;        
            
    end
    
    switch wave
        case 'w1'
            wave = RFP;
        case 'w2'
            wave = YFP;
        case 'w3'
            wave = CFP;
    end
    
    % build structure .row = defined features
    new_fname_info(i).row = row;
    new_fname_info(i).col = col;
    new_fname_info(i).site = 1;
    new_fname_info(i).org_fname = file_names(i).name;
    new_fname_info.channel = wave;
    new_fname_info.timepoint = -1; % space holder, return struct 
    
end

% to do: 4. to do: sorting files and moving into parent folder like 3_2_1

Answer 1

[meghannmarie]

Are you trying to do something like this?

outputFolder = fullfile(pwd, 'image_sorted')
if ~exist(outputFolder, 'dir')
  mkdir(outputFolder);
end

path1 ='C:\Users\Desktop\rename_microscope_files\movie\2019_1\3245\TimePoint_1'
dest = 'C:\Users\Desktop\rename_microscope_files\image_sorted'


% to do: 1. loop over all folders, number of timePoint_x folders can vary
source =fullfile(path1,'**\*.tif');
myfiles = dir(source);

% 2. loop over files, copy all tif files without thumb in filename to folder B

for i = 1:numel(myfiles)   
    myfile = myfiles(i).name;
    if ~contains(myfile, '_thumb')
        copyfile(fullfile(myfiles(i).folder, myfiles(i).name), dest);
    end   

end

[Dung Vu]

Yes, I mean this. But your script doesn't copy the not-thumb files into destination.

[meghannmarie]

I had a typo, I edited code above.

[Dung Vu]

unfortunatly it still doesn't copy the files :(

[meghannmarie]

Are all the files and folders you are searching through in path1?

[Dung Vu]

In path1 is only a part of the files

[meghannmarie]

Try this, does the variable myfiles contain the path names of the files you want to move? Otherwise maybe I ma not undertanding problem/question.

outputFolder = fullfile(pwd, 'image_sorted');
if ~exist(outputFolder, 'dir')
  mkdir(outputFolder);
end

%Folder with fubfolders that contain .tif files
input_folder = 'C:\Users\Desktop\rename_microscope_files\movie';

% Create structure with all .tif files in folder and subfolders
source =fullfile(input_folder,'**\*.tif');
myfiles = dir(source);

%Remove files with _thumb in file name. Create cell array to file to copy.
idx = ~contains({myfiles.name}, '_thumb');
myfiles = fullfile({myfiles(idx).folder}, {myfiles(idx).name});

% Loop over cell array and copy files to output folder.
for f = 1:numel(myfiles)
   copyfile(myfiles{f},outputFolder); 
end

Answer 2

[Image Analyst]

Try imageDatastore().