From c610c6368652bd722ca0498a45929385c4040d83 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 9 Mar 2026 21:39:14 +0000
Subject: [PATCH 1/2] Initial plan


From cd280439075e69efc24222b100f7cab01d6d955f Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 9 Mar 2026 22:00:08 +0000
Subject: [PATCH 2/2] Fix write function performance for filenames with
 underscores

- Replace str2num with str2double in make_img_filename to avoid eval-based
  path searches that are extremely slow on clusters with large MATLAB paths.
  str2double handles non-numeric strings by returning NaN (fast) instead of
  triggering a full MATLAB function path search via eval.
- Fix warning('off') to use warning('off', 'all') with proper save/restore
  state pattern, fixing deprecated usage in MATLAB R2020a+.
- Fix O(N^2) char concatenation loop in slice write path to use cell array
  pre-allocation (O(N)) instead of repeated char() matrix building.

Fixes slow write for filenames like TYPEB_FITHRF.nii where str2num called
with the identifier would trigger expensive MATLAB path lookups.

Co-authored-by: torwager <6262700+torwager@users.noreply.github.com>
---
 .../iimg_reconstruct_3dvol.m                      |  9 ++++++---
 .../iimg_reconstruct_vols.m                       | 15 +++++++++------
 2 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/CanlabCore/Index_image_manip_tools/iimg_reconstruct_3dvol.m b/CanlabCore/Index_image_manip_tools/iimg_reconstruct_3dvol.m
index c65261f2..58a83c66 100644
--- a/CanlabCore/Index_image_manip_tools/iimg_reconstruct_3dvol.m
+++ b/CanlabCore/Index_image_manip_tools/iimg_reconstruct_3dvol.m
@@ -129,9 +129,9 @@ function write_file(voldata, volInfo, outname, descrip, varargin)
         % correct .private loaded from file by re-mapping volume.
         spm_write_plane(spm_vol(volInfo.fname), voldata, slice_number);
     else
-        warning('off'); % empty images return many warnings
+        warnstate = warning('off', 'all'); % empty images return many warnings
         spm_write_vol(volInfo, voldata);
-        warning('on');
+        warning(warnstate);
     end
 end
 
@@ -149,7 +149,10 @@ function write_file(voldata, volInfo, outname, descrip, varargin)
     t = t(1);
     n1 = ext((t+1):end);
     if ~isempty(n1),
-        n   = str2num(n1);
+        n = str2double(n1);
+        if isnan(n)
+            n = 1;  % Fall back to 1 for non-numeric values
+        end
         ext = ext(1:(t-1));
     end
 end
diff --git a/CanlabCore/Index_image_manip_tools/iimg_reconstruct_vols.m b/CanlabCore/Index_image_manip_tools/iimg_reconstruct_vols.m
index 3e77c855..3d5770b0 100644
--- a/CanlabCore/Index_image_manip_tools/iimg_reconstruct_vols.m
+++ b/CanlabCore/Index_image_manip_tools/iimg_reconstruct_vols.m
@@ -232,18 +232,18 @@ function write_file(voldata, volInfo, outname, descrip, varargin)
         % write one slice for a series of images
         slice_number = varargin{1};
 
-        filenames = [];
+        filenames_cell = cell(nimgs, 1);
         for i = 1:nimgs
-            filenames = char(filenames, make_img_filename(outname, i));
+            filenames_cell{i} = make_img_filename(outname, i);
         end
-        filenames = filenames(2:end, :);
+        filenames = char(filenames_cell);
 
         % Note: pinfo is set to [1 0 0] for new images; no rescaling of
         % images.
         scn_write_plane(filenames, voldata, slice_number, volInfo);
 
     else
-        warning('off'); % empty images return many warnings
+        warnstate = warning('off', 'all'); % empty images return many warnings
         for i = 1:nimgs
             [volInfo.fname, volInfo.n(1)] = make_img_filename(outname, i);
             volInfo.descrip = descrip;
@@ -254,7 +254,7 @@ function write_file(voldata, volInfo, outname, descrip, varargin)
 
             spm_write_vol(volInfo, squeeze(voldata(:, :, :, i)));
         end
-        warning('on');
+        warning(warnstate);
     end
 end
 
@@ -278,7 +278,10 @@ function write_file(voldata, volInfo, outname, descrip, varargin)
         t = t(1);
         n1 = ext((t+1):end);
         if ~isempty(n1),
-            n = str2num(n1);
+            n = str2double(n1);
+            if isnan(n)
+                n = imagenum;  % Fall back to imagenum for non-numeric values
+            end
             ext = ext(1:(t-1));
         end
     else