Applying Function to Structure

Currently, here is my code:

% Specify the folder where the files live.
myFolder = 'C:\Users\Irwin\Desktop\Matlab\Scintillator_project\advanced';
% Check to make sure that folder actually exists.  Warn user if it doesn't.
if ~isdir(myFolder)
  errorMessage = sprintf('Error: The following folder does not exist:\n%s', 
  myFolder);
  uiwait(warndlg(errorMessage));
  return;
end

% Get a list of all files in the folder with the desired file name pattern.
filePattern = fullfile(myFolder, '*.spe'); 
theFiles = dir(filePattern);
for k = 1 : length(theFiles)
  baseFileName = theFiles(k).name;
  fullFileName = fullfile(myFolder, baseFileName);
  fprintf(1, 'Now reading %s\n', fullFileName);
end

I currently have a structure in which each entry contains a .spe file. I would like to apply the function readSPE https://www.mathworks.com/matlabcentral/fileexchange/35940-readspe to each entry in the structure to convert them from .spe format to a 3D array.

Please help!

Thanks :)

Answer 1

[Walter Roberson]

In terms of your existing code, you would just add a readSPE(fullFileName) after your fprintf().

If you want to use more compact code then

filePattern = fullfile(myFolder, '*.spe'); 
dinfo = dir(filePattern);
filenames = fullfile(myFolder, {dinfo.name});
output = arrayfun(@readSPE, filenames, 'uniform', 0);

[Jan]

Typo fixed.

[itend]

Thank you for your response!

So if I then want to convert the data to type double and apply a median filter across the "3rd" dimension of each matrix (after readSPE has converted the files from .spe to 3D arrays), can I do this:

% Get a list of all files in the folder with the desired file name pattern.
filePattern = fullfile(myFolder, '*.spe'); % Change to whatever pattern you need.
theFiles = dir(filePattern);
for k = 1 : length(theFiles)
  baseFileName = theFiles(k).name;
  fullFileName = fullfile(myFolder, baseFileName);
  fprintf(1, 'Now reading %s\n', fullFileName);
  readSPE(fullFileName);
  double(median(fullFileName,3));
end

Furthermore, how can I call the files if I want to generate an image from them, say using imagesc?

Thanks again!!

[itend]

I also wanted to add that when I use your condensed code, I get the following error:

Error using fopen
First input must be a file name or a file identifier.
Error in readSPE (line 231)
fd = fopen(filename,'r');
Error in avdanced2 (line 14)
output = arrayfun(@readSPE, filenames, 'uniform', 0);

Here is the code with your condensed insert:

% Specify the folder where the files live.
myFolder = 'C:\Users\Irwin\Desktop\Matlab\Scintillator_project\advanced';
% Check to make sure that folder actually exists.  Warn user if it doesn't.
if ~isdir(myFolder)
  errorMessage = sprintf('Error: The following folder does not exist:\n%s', myFolder);
  uiwait(warndlg(errorMessage));
  return;
end
% Get a list of all files in the folder with the desired file name pattern.
filePattern = fullfile(myFolder, '*.spe'); 
dinfo = dir(filePattern);
filenames = fullfile(myFolder, {dinfo.name});
output = arrayfun(@readSPE, filenames, 'uniform', 0);

What do you think?

Thanks again!!

[Walter Roberson]

Sorry, the arrayfun should be cellfun:

output = cellfun(@readSPE, filenames, 'uniform', 0);

[Walter Roberson]

filt_order = 3;   
% Get a list of all files in the folder with the desired file name pattern.
filePattern = fullfile(myFolder, '*.spe'); % Change to whatever pattern you need.
theFiles = dir(filePattern);
num_files = length(theFiles);
filt_results = cell(num_files, 1);
for k = 1 : num_files
  baseFileName = theFiles(k).name;
  fullFileName = fullfile(myFolder, baseFileName);
  fprintf(1, 'Now reading %s\n', fullFileName);
  this_spe = readSPE(fullFileName);
  filt_result{k} = medfilt1(this_spe, filt_order, 3);
end

You cannot use imagesc or anything similar to create images from them. The result of median filtering is going to be 3 dimensional if the input is 3 dimensional. You need to decide how you want to create the images of the 3D arrays:

• as iso surfaces using isosurface()
• as slices, using slice()
• using the R2017a voxelViewer() app
• as animation
• as voxels, using some other routine

[itend]

Thank you so much for your help!!!