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

6 ビュー (過去 30 日間)
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

回答 (2 件)

meghannmarie
meghannmarie 2019 年 11 月 15 日
編集済み: meghannmarie 2019 年 11 月 18 日
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
  6 件のコメント
Dung Vu
Dung Vu 2019 年 11 月 21 日
In path1 is only a part of the files
meghannmarie
meghannmarie 2019 年 11 月 21 日
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

サインインしてコメントする。


Image Analyst
Image Analyst 2019 年 11 月 19 日
Try imageDatastore().

カテゴリ

Help Center および File ExchangeFile Operations についてさらに検索

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Translated by