From 80db5847f1e04355a1eb96fabbe82575654f9875 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 19 Sep 2024 08:26:06 +0200
Subject: [PATCH 1/4] start

---
 fmrwhy_util_createMontage.m        | 114 +++++++++++++++++++++++++++++
 fmrwhy_util_createOverlayMontage.m |  97 ++++++++++++++++++++++++
 miss_hit.cfg                       |   6 +-
 untitled.m                         |  37 ++++++++++
 4 files changed, 251 insertions(+), 3 deletions(-)
 create mode 100644 fmrwhy_util_createMontage.m
 create mode 100644 fmrwhy_util_createOverlayMontage.m
 create mode 100644 untitled.m

diff --git a/fmrwhy_util_createMontage.m b/fmrwhy_util_createMontage.m
new file mode 100644
index 00000000..2dbd9521
--- /dev/null
+++ b/fmrwhy_util_createMontage.m
@@ -0,0 +1,114 @@
+function montage = fmrwhy_util_createMontage(img, columns, rotate, str, clrmp, visibility, shape, cxs)
+
+  % (C) Copyright 2022 bidspm developers
+
+  % Simple function to create a montage / mosaic of multiple slices from a single 3D
+  % image matrix. TODO: Needs improvement i.t.o RAS/LAS orientation specification
+  % and image layout...
+  %
+  % INPUT:
+  % img           - 3D (x,y,z) image matrix
+  % columns       - number of columns in montage (rows are calculated accordingly)
+  % rotate        - rotate images 90 deg clockwise? yes = 1; no = 0.
+  % str           - figure title
+  % clrmp         - figure colormap
+  % visibility    - show figure?
+  %
+  % OUTPUT:
+  % output        - structure with montage data
+
+  montage = struct;
+  [Ni, Nj, Nk] = size(img);
+
+  % Rotate image slices if required
+  if rotate
+    img_orig = img;
+    clear img;
+    for p = 1:Nk
+      img(:, :, p) = rot90(img_orig(:, :, p));
+    end
+  end
+
+  % Determine amount of rows and filler slices
+  rows = floor(Nk / columns);
+  if rows == 0
+    rows = 1;
+  end
+  fill = mod(Nk, columns);
+  if fill == 0
+    N_fill = 0;
+  else
+    N_fill = columns - mod(Nk, columns);
+  end
+  if rotate
+    filler = zeros(Nj, Ni);
+  else
+    filler = zeros(Ni, Nj);
+  end
+
+  montage.rows = rows;
+  montage.columns = columns;
+  montage.N_fill = N_fill;
+
+  parts = {};
+  % 1 - Concatenate slices together horizontally, per row (except last).
+  % 2 - Concatenate rows together vertically
+  for i = 1:rows
+    for j = 1:columns
+      if j == 1
+        parts{i} = img(:, :, columns * (i - 1) + j);
+      else
+        parts{i} = cat(2, parts{i}, img(:, :, columns * (i - 1) + j));
+      end
+    end
+    if i == 1
+      whole = parts{i};
+    else
+      whole = cat(1, whole, parts{i});
+    end
+  end
+
+  % 1 - Concatenate filler slices to last row, if required.
+  % 2 - Concatenate last row to whole matrix, if required.
+  if N_fill ~= 0
+    % last row
+    last_parts = img(:, :, rows * columns + 1);
+    for k = (rows * columns + 2):Nk
+      last_parts = cat(2, last_parts, img(:, :, k));
+    end
+    for m = 1:N_fill
+      last_parts = cat(2, last_parts, filler);
+    end
+    montage.whole_img = cat(1, whole, last_parts);
+  else
+    montage.whole_img = whole;
+  end
+
+  % Get screen size for plotting - [1 1 w h]
+  scr_size = get(0, 'ScreenSize');
+  dist = scr_size(4);
+  if scr_size(3) < dist
+    dist = scr_size(3);
+  end
+
+  % Create figure - outerposition = [left bottom width height]
+  if strcmp(shape, 'max')
+    f = figure('visible', visibility, 'units', 'normalized', 'outerposition', [0 0 1 1]);
+  elseif strcmp(shape, 'square')
+    f = figure('visible', visibility, 'units', 'pixels', 'outerposition', [0 0 dist dist]);
+  else
+    f = figure('visible', visibility, 'units', 'pixels', 'outerposition', [0 0 dist dist]);
+    % daspect manual;
+  end
+  ax = subplot(1, 1, 1);
+  im = imagesc(ax, montage.whole_img);
+  colormap(clrmp); % colorbar;
+  if nargin == 8
+    if ~isempty(cxs)
+      caxis(ax, cxs);
+    end
+  end
+  % title(str);
+  montage.im = im;
+  montage.f = f;
+  montage.ax = ax;
diff --git a/fmrwhy_util_createOverlayMontage.m b/fmrwhy_util_createOverlayMontage.m
new file mode 100644
index 00000000..43bed597
--- /dev/null
+++ b/fmrwhy_util_createOverlayMontage.m
@@ -0,0 +1,97 @@
+function output = fmrwhy_util_createOverlayMontage(templateImg, overlayImg, columns, rotate, str, clrmp, visibility, shape, cxs, rgbcolors, saveAs)
+
+  % (C) Copyright 2022 bidspm developers
+
+  % fmrwhy_util_createOverlayMontage(tsnr_img{i}, overlayImg, 9, 1, '', ...
+  % 'hot', 'off', 'max', [0 250], [33, 168, 10], tsnr_saveAss{i});
+
+  % Function to create montages of images/rois overlaid on a template image
+
+  % Structure to save output
+  output = struct;
+  alpha = 0.2;
+  plot_contour = 1;
+  if rgbcolors == 0
+    rgbcolors = [255, 255, 191; 215, 25, 28; 253, 174, 97; 171, 217, 233; 44, 123, 182] / 255;
+  else
+    rgbcolors = rgbcolors / 255;
+  end
+
+  % Create background montage
+  montage_template = fmrwhy_util_createMontage(templateImg, columns, rotate, 'Template volume', clrmp, 'off', shape, cxs);
+  % Get screen size for plotting
+  scr_size = get(0, 'ScreenSize');
+  dist = scr_size(4);
+  if scr_size(3) < dist
+    dist = scr_size(3);
+  end
+
+  % Create figures with background montage and overlaid masks
+  % f(i) = figure('units','pixels','outerposition',[0 0 dist dist]);
+  f = figure('units', 'normalized', 'outerposition', [0 0 1 1], 'visible', visibility);
+  im1 = imagesc(montage_template.whole_img);
+  colormap(clrmp);
+  if ~isempty(cxs)
+    caxis(cxs);
+  end
+  ax = gca;
+  outerpos = ax.OuterPosition;
+  ti = ax.TightInset;
+  left = outerpos(1) + ti(1);
+  bottom = outerpos(2) + ti(2);
+  ax_width = outerpos(3) - ti(1) - ti(3);
+  ax_height = outerpos(4) - ti(2) - ti(4);
+  ax.Position = [left bottom ax_width ax_height];
+  hold(ax, 'on');
+  [Nimx, Nimy] = size(montage_template.whole_img);
+  oo = ones(Nimx, Nimy);
+  zz = zeros(Nimx, Nimy);
+  red = cat(3, oo, zz, zz);
+  green = cat(3, zz, oo, zz);
+  blue = cat(3, zz, oo, oo);
+
+  if iscell(overlayImg)
+    for i = 1:numel(overlayImg)
+      montage_overlay{i} = fmrwhy_util_createMontage(overlayImg{i}, columns, rotate, 'Overlay', clrmp, 'off', shape, 'auto');
+    end
+  else
+    montage_overlay = {};
+    montage_overlay{1} = fmrwhy_util_createMontage(overlayImg, columns, rotate, 'Overlay', clrmp, 'off', shape, 'auto');
+  end
+
+  for i = 1:numel(montage_overlay)
+    rbgclr = rgbcolors(i, :);
+    clr = cat(3, rbgclr(1) * oo, rbgclr(2) * oo, rbgclr(3) * oo);
+    imC = imagesc(ax, clr);
+    set(imC, 'AlphaData', alpha * montage_overlay{i}.whole_img);
+    if plot_contour
+      bound_whole_bin = bwboundaries(montage_overlay{i}.whole_img);
+      Nblobs_bin = numel(bound_whole_bin);
+      for b = 1:Nblobs_bin
+        p = plot(ax, bound_whole_bin{b, 1}(:, 2), bound_whole_bin{b, 1}(:, 1), 'color', rbgclr, 'LineWidth', 1);
+      end
+    end
+  end
+
+  hold(ax, 'off');
+  set(ax, 'xtick', []);
+  set(ax, 'xticklabel', []);
+  set(ax, 'ytick', []);
+  set(ax, 'yticklabel', []);
+  set(ax, 'ztick', []);
+  set(ax, 'zticklabel', []);
+
+  output.ax = ax;
+  output.f = f;
+
+  if saveAs ~= 0
+    print(f, saveAs, '-dpng', '-r0');
+  end
+  % Close necessary figure handles
+  close(montage_template.f);
+  for i = 1:numel(montage_overlay)
+    close(montage_overlay{i}.f);
+  end
+  if strcmp(visibility, 'off')
+    close(f);
+  end
diff --git a/miss_hit.cfg b/miss_hit.cfg
index cd8e82be..184ae47f 100644
--- a/miss_hit.cfg
+++ b/miss_hit.cfg
@@ -3,7 +3,7 @@ project_root
 octave: true
 
 # style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
-line_length: 100
+line_length: 250
 
 # camelCase
 regex_function_name: "[a-z]+(_*[a-zA-Z0-9]+[a-z]*)*"
@@ -36,7 +36,7 @@ copyright_entity: "Wellcome Trust Centre for Neuroimaging"
 tab_width: 2
 
 # metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
-metric "cnest": limit 5
+metric "cnest": limit 9
 metric "file_length": limit 1000
 metric "cyc": limit 22
-metric "parameters": limit 7
+metric "parameters": limit 12
diff --git a/untitled.m b/untitled.m
new file mode 100644
index 00000000..aeabd316
--- /dev/null
+++ b/untitled.m
@@ -0,0 +1,37 @@
+% (C) Copyright 2022 bidspm developers
+
+bidspm_dir = '/home/remi/github/cpp-lln-lab/bidspm';
+
+overlay_img = fullfile(bidspm_dir, 'demos/MoAE/outputs/derivatives/bidspm-stats/sub-01/task-auditory_space-MNI152NLin6Asym_FWHM-8/mask.nii');
+
+template_img = fullfile(bidspm_dir, 'demos/MoAE/outputs/derivatives/bidspm-preproc/sub-01/func/sub-01_task-auditory_space-MNI152NLin6Asym_desc-smth8_bold.nii');
+
+columns = 9;
+
+rotate = 1;
+
+str = '';
+
+clrmp = 'gray';
+
+visibility = 'on';
+
+saveAs_fn = 0;
+
+template_hdr = spm_vol(template_img);
+template = spm_read_vols(template_hdr(1));
+
+mask_hdr = spm_vol(overlay_img);
+mask = spm_read_vols(mask_hdr);
+
+fmrwhy_util_createOverlayMontage(template, ...
+                                 mask, ...
+                                 columns, ...
+                                 rotate, ...
+                                 '', ...
+                                 clrmp, ...
+                                 visibility, ...
+                                 'max', ...
+                                 [0 255], ...
+                                 [33, 168, 10], ...
+                                 saveAs_fn);

From ba79b3ba4ff78ed0b936c41bd66e60d217b8907b Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 19 Sep 2024 09:22:50 +0200
Subject: [PATCH 2/4] ref

---
 createMontage.m                    | 153 +++++++++++++++++++++++++++++
 createOverlayMontage.m             | 132 +++++++++++++++++++++++++
 fmrwhy_util_createOverlayMontage.m |  15 +--
 untitled.m                         |  26 +----
 4 files changed, 290 insertions(+), 36 deletions(-)
 create mode 100644 createMontage.m
 create mode 100644 createOverlayMontage.m

diff --git a/createMontage.m b/createMontage.m
new file mode 100644
index 00000000..6ca3c474
--- /dev/null
+++ b/createMontage.m
@@ -0,0 +1,153 @@
+function montage = createMontage(varargin)
+  %
+  % USAGE
+  %
+  % montage = createMontage(img, ...
+  %                         'columns', 9, ...
+  %                         'rotate', true, ...
+  %                         'cmap', 'gray', ...
+  %                         'visibility', 'on', ...
+  %                         'shape', 'max', ...
+  %                         'cxs', [0 255])
+  %
+  %
+  % Simple function to create a montage / mosaic of multiple slices from a single 3D
+  % image matrix.
+  %
+  % INPUT:
+  % img           - 3D (x,y,z) image matrix
+  % columns       - number of columns in montage (rows are calculated accordingly)
+  % rotate        - rotate images 90 deg clockwise? yes = 1; no = 0.
+  % cmap          - figure colormap
+  % visibility    - show figure?
+  %
+  % OUTPUT:
+  % output        - structure with montage data
+
+  % (C) Copyright 2022 bidspm developers
+
+  % TODO: Needs improvement i.t.o RAS/LAS orientation specification
+  %  and image layout...
+
+  args = inputParser;
+
+  addRequired(args, 'img');
+  addParameter(args, 'columns', 9, @isnumeric);
+  addParameter(args, 'rotate', true, @islogical);
+  addParameter(args, 'cmap', 'gray', @ischar);
+  addParameter(args, 'visibility', 'on', @ischar);
+  addParameter(args, 'shape', 'max', @ischar); % max or square
+  addParameter(args, 'cxs', 'auto');
+
+  parse(args, varargin{:});
+
+  img = args.Results.img;
+  columns = args.Results.columns;
+  rotate = args.Results.rotate;
+  cmap = args.Results.cmap;
+  visibility = args.Results.visibility;
+  shape = args.Results.shape;
+  cxs = args.Results.cxs;
+
+  montage = struct;
+  [Ni, Nj, Nk] = size(img);
+
+  % Rotate image slices if required
+  if rotate
+    img_orig = img;
+    clear img;
+    for p = 1:Nk
+      img(:, :, p) = rot90(img_orig(:, :, p));
+    end
+  end
+
+  % Determine amount of rows and filler slices
+  rows = floor(Nk / columns);
+  if rows == 0
+    rows = 1;
+  end
+  fill = mod(Nk, columns);
+  if fill == 0
+    N_fill = 0;
+  else
+    N_fill = columns - mod(Nk, columns);
+  end
+  if rotate
+    filler = zeros(Nj, Ni);
+  else
+    filler = zeros(Ni, Nj);
+  end
+
+  montage.rows = rows;
+  montage.columns = columns;
+  montage.N_fill = N_fill;
+
+  parts = {};
+  % 1 - Concatenate slices together horizontally, per row (except last).
+  % 2 - Concatenate rows together vertically
+  for i = 1:rows
+    for j = 1:columns
+      if j == 1
+        parts{i} = img(:, :, columns * (i - 1) + j);
+      else
+        parts{i} = cat(2, parts{i}, img(:, :, columns * (i - 1) + j));
+      end
+    end
+    if i == 1
+      whole = parts{i};
+    else
+      whole = cat(1, whole, parts{i});
+    end
+  end
+
+  % 1 - Concatenate filler slices to last row, if required.
+  % 2 - Concatenate last row to whole matrix, if required.
+  if N_fill ~= 0
+    % last row
+    last_parts = img(:, :, rows * columns + 1);
+    for k = (rows * columns + 2):Nk
+      last_parts = cat(2, last_parts, img(:, :, k));
+    end
+    for m = 1:N_fill
+      last_parts = cat(2, last_parts, filler);
+    end
+    montage.whole_img = cat(1, whole, last_parts);
+  else
+    montage.whole_img = whole;
+  end
+
+  % Get screen size for plotting - [1 1 w h]
+  scr_size = get(0, 'ScreenSize');
+  dist = scr_size(4);
+  if scr_size(3) < dist
+    dist = scr_size(3);
+  end
+
+  % Create figure - outerposition = [left bottom width height]
+  if strcmp(shape, 'max')
+    f = figure('visible', visibility, ...
+               'units', 'normalized', ...
+               'outerposition', [0 0 1 1]);
+  elseif strcmp(shape, 'square')
+    f = figure('visible', visibility, ...
+               'units', 'pixels', ...
+               'outerposition', [0 0 dist dist]);
+  else
+    f = figure('visible', visibility, ...
+               'units', 'pixels', ...
+               'outerposition', [0 0 dist dist]);
+  end
+
+  ax = subplot(1, 1, 1);
+  im = imagesc(ax, montage.whole_img);
+
+  colormap(cmap);
+  if ~isempty(cxs)
+    caxis(ax, cxs);
+  end
+
+  montage.im = im;
+  montage.f = f;
+  montage.ax = ax;
+
+end
diff --git a/createOverlayMontage.m b/createOverlayMontage.m
new file mode 100644
index 00000000..1296d9b5
--- /dev/null
+++ b/createOverlayMontage.m
@@ -0,0 +1,132 @@
+function output = createOverlayMontage(varargin)
+
+  % (C) Copyright 2022 bidspm developers
+
+  % fmrwhy_util_createOverlayMontage(tsnr_img{i}, overlayImg, 9, 1, '', ...
+  % 'hot', 'off', 'max', [0 250], [33, 168, 10], tsnr_saveAss{i});
+
+  % Function to create montages of images/rois overlaid on a template image
+
+  rgbcolors = [255, 255, 191; ...
+               215, 25, 28; ...
+               253, 174, 97; ...
+               171, 217, 233; ...
+               44, 123, 182];
+
+  args = inputParser;
+
+  addRequired(args, 'templateImg');
+  addRequired(args, 'overlayImg');
+  addParameter(args, 'columns', 9, @isnumeric);
+  addParameter(args, 'rotate', true, @islogical);
+  addParameter(args, 'cmap', 'gray', @ischar);
+  addParameter(args, 'visibility', 'on', @ischar);
+  addParameter(args, 'shape', 'max', @ischar); % max or square
+  addParameter(args, 'cxs', 'auto');
+  addParameter(args, 'rgbcolors', rgbcolors);
+  addParameter(args, 'saveAs', '');
+
+  parse(args, varargin{:});
+
+  templateImg = args.Results.templateImg;
+  overlayImg = args.Results.overlayImg;
+  columns = args.Results.columns;
+  rotate = args.Results.rotate;
+  cmap = args.Results.cmap;
+  visibility = args.Results.visibility;
+  shape = args.Results.shape;
+  cxs = args.Results.cxs;
+  rgbcolors = args.Results.rgbcolors;
+  saveAs = args.Results.saveAs;
+
+  % Structure to save output
+  output = struct;
+  alpha = 0.2;
+  plot_contour = 1;
+  rgbcolors = rgbcolors / 255;
+
+  % Create background montage
+  montage_template = createMontage(templateImg, ...
+                                   'columns', columns, ...
+                                   'rotate', rotate, ...
+                                   'cmap', cmap, ...
+                                   'visibility', 'off', ...
+                                   'shape', shape, ...
+                                   'cxs', cxs);
+
+  % Create figures with background montage and overlaid masks
+  f = figure('units', 'normalized', ...
+             'outerposition', [0 0 1 1], ...
+             'visible', visibility);
+  imagesc(montage_template.whole_img);
+  colormap(cmap);
+  if ~isempty(cxs)
+    caxis(cxs);
+  end
+  ax = gca;
+  outerpos = ax.OuterPosition;
+  ti = ax.TightInset;
+  left = outerpos(1) + ti(1);
+  bottom = outerpos(2) + ti(2);
+  ax_width = outerpos(3) - ti(1) - ti(3);
+  ax_height = outerpos(4) - ti(2) - ti(4);
+  ax.Position = [left bottom ax_width ax_height];
+  hold(ax, 'on');
+  [Nimx, Nimy] = size(montage_template.whole_img);
+  oo = ones(Nimx, Nimy);
+
+  if iscell(overlayImg)
+    for i = 1:numel(overlayImg)
+      montage_overlay{i} = createMontage(overlayImg{i},   'columns', columns, ...
+                                         'rotate', rotate, ...
+                                         'cmap', cmap, ...
+                                         'visibility', 'off', ...
+                                         'shape', shape, ...
+                                         'cxs', 'auto');
+    end
+  else
+    montage_overlay = {};
+    montage_overlay{1} = createMontage(overlayImg,   'columns', columns, ...
+                                       'rotate', rotate, ...
+                                       'cmap', cmap, ...
+                                       'visibility', 'off', ...
+                                       'shape', shape, ...
+                                       'cxs', 'auto');
+  end
+
+  for i = 1:numel(montage_overlay)
+    rbgclr = rgbcolors(i, :);
+    clr = cat(3, rbgclr(1) * oo, rbgclr(2) * oo, rbgclr(3) * oo);
+    imC = imagesc(ax, clr);
+    set(imC, 'AlphaData', alpha * montage_overlay{i}.whole_img);
+    if plot_contour
+      bound_whole_bin = bwboundaries(montage_overlay{i}.whole_img);
+      Nblobs_bin = numel(bound_whole_bin);
+      for b = 1:Nblobs_bin
+        p = plot(ax, bound_whole_bin{b, 1}(:, 2), bound_whole_bin{b, 1}(:, 1), 'color', rbgclr, 'LineWidth', 1);
+      end
+    end
+  end
+
+  hold(ax, 'off');
+  set(ax, 'xtick', []);
+  set(ax, 'xticklabel', []);
+  set(ax, 'ytick', []);
+  set(ax, 'yticklabel', []);
+  set(ax, 'ztick', []);
+  set(ax, 'zticklabel', []);
+
+  output.ax = ax;
+  output.f = f;
+
+  if saveAs ~= 0
+    print(f, saveAs, '-dpng', '-r0');
+  end
+  % Close necessary figure handles
+  close(montage_template.f);
+  for i = 1:numel(montage_overlay)
+    close(montage_overlay{i}.f);
+  end
+  if strcmp(visibility, 'off')
+    close(f);
+  end
diff --git a/fmrwhy_util_createOverlayMontage.m b/fmrwhy_util_createOverlayMontage.m
index 43bed597..bcea0aaf 100644
--- a/fmrwhy_util_createOverlayMontage.m
+++ b/fmrwhy_util_createOverlayMontage.m
@@ -19,17 +19,10 @@
 
   % Create background montage
   montage_template = fmrwhy_util_createMontage(templateImg, columns, rotate, 'Template volume', clrmp, 'off', shape, cxs);
-  % Get screen size for plotting
-  scr_size = get(0, 'ScreenSize');
-  dist = scr_size(4);
-  if scr_size(3) < dist
-    dist = scr_size(3);
-  end
 
   % Create figures with background montage and overlaid masks
-  % f(i) = figure('units','pixels','outerposition',[0 0 dist dist]);
   f = figure('units', 'normalized', 'outerposition', [0 0 1 1], 'visible', visibility);
-  im1 = imagesc(montage_template.whole_img);
+  imagesc(montage_template.whole_img);
   colormap(clrmp);
   if ~isempty(cxs)
     caxis(cxs);
@@ -45,10 +38,6 @@
   hold(ax, 'on');
   [Nimx, Nimy] = size(montage_template.whole_img);
   oo = ones(Nimx, Nimy);
-  zz = zeros(Nimx, Nimy);
-  red = cat(3, oo, zz, zz);
-  green = cat(3, zz, oo, zz);
-  blue = cat(3, zz, oo, oo);
 
   if iscell(overlayImg)
     for i = 1:numel(overlayImg)
@@ -68,7 +57,7 @@
       bound_whole_bin = bwboundaries(montage_overlay{i}.whole_img);
       Nblobs_bin = numel(bound_whole_bin);
       for b = 1:Nblobs_bin
-        p = plot(ax, bound_whole_bin{b, 1}(:, 2), bound_whole_bin{b, 1}(:, 1), 'color', rbgclr, 'LineWidth', 1);
+        plot(ax, bound_whole_bin{b, 1}(:, 2), bound_whole_bin{b, 1}(:, 1), 'color', rbgclr, 'LineWidth', 1);
       end
     end
   end
diff --git a/untitled.m b/untitled.m
index aeabd316..893894ea 100644
--- a/untitled.m
+++ b/untitled.m
@@ -1,4 +1,5 @@
 % (C) Copyright 2022 bidspm developers
+close all;
 
 bidspm_dir = '/home/remi/github/cpp-lln-lab/bidspm';
 
@@ -6,32 +7,11 @@
 
 template_img = fullfile(bidspm_dir, 'demos/MoAE/outputs/derivatives/bidspm-preproc/sub-01/func/sub-01_task-auditory_space-MNI152NLin6Asym_desc-smth8_bold.nii');
 
-columns = 9;
-
-rotate = 1;
-
-str = '';
-
-clrmp = 'gray';
-
-visibility = 'on';
-
-saveAs_fn = 0;
-
 template_hdr = spm_vol(template_img);
 template = spm_read_vols(template_hdr(1));
 
 mask_hdr = spm_vol(overlay_img);
 mask = spm_read_vols(mask_hdr);
 
-fmrwhy_util_createOverlayMontage(template, ...
-                                 mask, ...
-                                 columns, ...
-                                 rotate, ...
-                                 '', ...
-                                 clrmp, ...
-                                 visibility, ...
-                                 'max', ...
-                                 [0 255], ...
-                                 [33, 168, 10], ...
-                                 saveAs_fn);
+% createMontage(template, 'shape', 'square');
+createOverlayMontage(template, mask, 'rgbcolors', [255, 0, 0], 'shape', 'square');

From b0ffa5251c1f2cc759f957269762deda03212e3f Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 19 Sep 2024 09:23:22 +0200
Subject: [PATCH 3/4] ref

---
 fmrwhy_util_createMontage.m        | 114 -----------------------------
 fmrwhy_util_createOverlayMontage.m |  86 ----------------------
 miss_hit.cfg                       |   6 +-
 3 files changed, 3 insertions(+), 203 deletions(-)
 delete mode 100644 fmrwhy_util_createMontage.m
 delete mode 100644 fmrwhy_util_createOverlayMontage.m

diff --git a/fmrwhy_util_createMontage.m b/fmrwhy_util_createMontage.m
deleted file mode 100644
index 2dbd9521..00000000
--- a/fmrwhy_util_createMontage.m
+++ /dev/null
@@ -1,114 +0,0 @@
-function montage = fmrwhy_util_createMontage(img, columns, rotate, str, clrmp, visibility, shape, cxs)
-
-  % (C) Copyright 2022 bidspm developers
-
-  % Simple function to create a montage / mosaic of multiple slices from a single 3D
-  % image matrix. TODO: Needs improvement i.t.o RAS/LAS orientation specification
-  % and image layout...
-  %
-  % INPUT:
-  % img           - 3D (x,y,z) image matrix
-  % columns       - number of columns in montage (rows are calculated accordingly)
-  % rotate        - rotate images 90 deg clockwise? yes = 1; no = 0.
-  % str           - figure title
-  % clrmp         - figure colormap
-  % visibility    - show figure?
-  %
-  % OUTPUT:
-  % output        - structure with montage data
-
-  montage = struct;
-  [Ni, Nj, Nk] = size(img);
-
-  % Rotate image slices if required
-  if rotate
-    img_orig = img;
-    clear img;
-    for p = 1:Nk
-      img(:, :, p) = rot90(img_orig(:, :, p));
-    end
-  end
-
-  % Determine amount of rows and filler slices
-  rows = floor(Nk / columns);
-  if rows == 0
-    rows = 1;
-  end
-  fill = mod(Nk, columns);
-  if fill == 0
-    N_fill = 0;
-  else
-    N_fill = columns - mod(Nk, columns);
-  end
-  if rotate
-    filler = zeros(Nj, Ni);
-  else
-    filler = zeros(Ni, Nj);
-  end
-
-  montage.rows = rows;
-  montage.columns = columns;
-  montage.N_fill = N_fill;
-
-  parts = {};
-  % 1 - Concatenate slices together horizontally, per row (except last).
-  % 2 - Concatenate rows together vertically
-  for i = 1:rows
-    for j = 1:columns
-      if j == 1
-        parts{i} = img(:, :, columns * (i - 1) + j);
-      else
-        parts{i} = cat(2, parts{i}, img(:, :, columns * (i - 1) + j));
-      end
-    end
-    if i == 1
-      whole = parts{i};
-    else
-      whole = cat(1, whole, parts{i});
-    end
-  end
-
-  % 1 - Concatenate filler slices to last row, if required.
-  % 2 - Concatenate last row to whole matrix, if required.
-  if N_fill ~= 0
-    % last row
-    last_parts = img(:, :, rows * columns + 1);
-    for k = (rows * columns + 2):Nk
-      last_parts = cat(2, last_parts, img(:, :, k));
-    end
-    for m = 1:N_fill
-      last_parts = cat(2, last_parts, filler);
-    end
-    montage.whole_img = cat(1, whole, last_parts);
-  else
-    montage.whole_img = whole;
-  end
-
-  % Get screen size for plotting - [1 1 w h]
-  scr_size = get(0, 'ScreenSize');
-  dist = scr_size(4);
-  if scr_size(3) < dist
-    dist = scr_size(3);
-  end
-
-  % Create figure - outerposition = [left bottom width height]
-  if strcmp(shape, 'max')
-    f = figure('visible', visibility, 'units', 'normalized', 'outerposition', [0 0 1 1]);
-  elseif strcmp(shape, 'square')
-    f = figure('visible', visibility, 'units', 'pixels', 'outerposition', [0 0 dist dist]);
-  else
-    f = figure('visible', visibility, 'units', 'pixels', 'outerposition', [0 0 dist dist]);
-    % daspect manual;
-  end
-  ax = subplot(1, 1, 1);
-  im = imagesc(ax, montage.whole_img);
-  colormap(clrmp); % colorbar;
-  if nargin == 8
-    if ~isempty(cxs)
-      caxis(ax, cxs);
-    end
-  end
-  % title(str);
-  montage.im = im;
-  montage.f = f;
-  montage.ax = ax;
diff --git a/fmrwhy_util_createOverlayMontage.m b/fmrwhy_util_createOverlayMontage.m
deleted file mode 100644
index bcea0aaf..00000000
--- a/fmrwhy_util_createOverlayMontage.m
+++ /dev/null
@@ -1,86 +0,0 @@
-function output = fmrwhy_util_createOverlayMontage(templateImg, overlayImg, columns, rotate, str, clrmp, visibility, shape, cxs, rgbcolors, saveAs)
-
-  % (C) Copyright 2022 bidspm developers
-
-  % fmrwhy_util_createOverlayMontage(tsnr_img{i}, overlayImg, 9, 1, '', ...
-  % 'hot', 'off', 'max', [0 250], [33, 168, 10], tsnr_saveAss{i});
-
-  % Function to create montages of images/rois overlaid on a template image
-
-  % Structure to save output
-  output = struct;
-  alpha = 0.2;
-  plot_contour = 1;
-  if rgbcolors == 0
-    rgbcolors = [255, 255, 191; 215, 25, 28; 253, 174, 97; 171, 217, 233; 44, 123, 182] / 255;
-  else
-    rgbcolors = rgbcolors / 255;
-  end
-
-  % Create background montage
-  montage_template = fmrwhy_util_createMontage(templateImg, columns, rotate, 'Template volume', clrmp, 'off', shape, cxs);
-
-  % Create figures with background montage and overlaid masks
-  f = figure('units', 'normalized', 'outerposition', [0 0 1 1], 'visible', visibility);
-  imagesc(montage_template.whole_img);
-  colormap(clrmp);
-  if ~isempty(cxs)
-    caxis(cxs);
-  end
-  ax = gca;
-  outerpos = ax.OuterPosition;
-  ti = ax.TightInset;
-  left = outerpos(1) + ti(1);
-  bottom = outerpos(2) + ti(2);
-  ax_width = outerpos(3) - ti(1) - ti(3);
-  ax_height = outerpos(4) - ti(2) - ti(4);
-  ax.Position = [left bottom ax_width ax_height];
-  hold(ax, 'on');
-  [Nimx, Nimy] = size(montage_template.whole_img);
-  oo = ones(Nimx, Nimy);
-
-  if iscell(overlayImg)
-    for i = 1:numel(overlayImg)
-      montage_overlay{i} = fmrwhy_util_createMontage(overlayImg{i}, columns, rotate, 'Overlay', clrmp, 'off', shape, 'auto');
-    end
-  else
-    montage_overlay = {};
-    montage_overlay{1} = fmrwhy_util_createMontage(overlayImg, columns, rotate, 'Overlay', clrmp, 'off', shape, 'auto');
-  end
-
-  for i = 1:numel(montage_overlay)
-    rbgclr = rgbcolors(i, :);
-    clr = cat(3, rbgclr(1) * oo, rbgclr(2) * oo, rbgclr(3) * oo);
-    imC = imagesc(ax, clr);
-    set(imC, 'AlphaData', alpha * montage_overlay{i}.whole_img);
-    if plot_contour
-      bound_whole_bin = bwboundaries(montage_overlay{i}.whole_img);
-      Nblobs_bin = numel(bound_whole_bin);
-      for b = 1:Nblobs_bin
-        plot(ax, bound_whole_bin{b, 1}(:, 2), bound_whole_bin{b, 1}(:, 1), 'color', rbgclr, 'LineWidth', 1);
-      end
-    end
-  end
-
-  hold(ax, 'off');
-  set(ax, 'xtick', []);
-  set(ax, 'xticklabel', []);
-  set(ax, 'ytick', []);
-  set(ax, 'yticklabel', []);
-  set(ax, 'ztick', []);
-  set(ax, 'zticklabel', []);
-
-  output.ax = ax;
-  output.f = f;
-
-  if saveAs ~= 0
-    print(f, saveAs, '-dpng', '-r0');
-  end
-  % Close necessary figure handles
-  close(montage_template.f);
-  for i = 1:numel(montage_overlay)
-    close(montage_overlay{i}.f);
-  end
-  if strcmp(visibility, 'off')
-    close(f);
-  end
diff --git a/miss_hit.cfg b/miss_hit.cfg
index 184ae47f..d7a1a245 100644
--- a/miss_hit.cfg
+++ b/miss_hit.cfg
@@ -3,7 +3,7 @@ project_root
 octave: true
 
 # style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
-line_length: 250
+line_length: 100
 
 # camelCase
 regex_function_name: "[a-z]+(_*[a-zA-Z0-9]+[a-z]*)*"
@@ -36,7 +36,7 @@ copyright_entity: "Wellcome Trust Centre for Neuroimaging"
 tab_width: 2
 
 # metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
-metric "cnest": limit 9
+metric "cnest": limit 7
 metric "file_length": limit 1000
 metric "cyc": limit 22
-metric "parameters": limit 12
+metric "parameters": limit 9

From 8ee871bac389f0fa85a430fc98f3d2c7e83f4a67 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 19 Sep 2024 09:44:56 +0200
Subject: [PATCH 4/4] ref

---
 miss_hit.cfg                                  |  6 ++--
 .../plotting/createMontage.m                  | 28 ++++---------------
 .../plotting/createOverlayMontage.m           | 15 +++++-----
 src/plotting/initMontageFigure.m              | 24 ++++++++++++++++
 untitled.m                                    | 13 +++++++--
 5 files changed, 50 insertions(+), 36 deletions(-)
 rename createMontage.m => src/plotting/createMontage.m (78%)
 rename createOverlayMontage.m => src/plotting/createOverlayMontage.m (90%)
 create mode 100644 src/plotting/initMontageFigure.m

diff --git a/miss_hit.cfg b/miss_hit.cfg
index d7a1a245..727d20b4 100644
--- a/miss_hit.cfg
+++ b/miss_hit.cfg
@@ -36,7 +36,7 @@ copyright_entity: "Wellcome Trust Centre for Neuroimaging"
 tab_width: 2
 
 # metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
-metric "cnest": limit 7
+metric "cnest": limit 4
 metric "file_length": limit 1000
-metric "cyc": limit 22
-metric "parameters": limit 9
+metric "cyc": limit 20
+metric "parameters": limit 6
diff --git a/createMontage.m b/src/plotting/createMontage.m
similarity index 78%
rename from createMontage.m
rename to src/plotting/createMontage.m
index 6ca3c474..550bdef4 100644
--- a/createMontage.m
+++ b/src/plotting/createMontage.m
@@ -11,12 +11,14 @@
   %                         'cxs', [0 255])
   %
   %
-  % Simple function to create a montage / mosaic of multiple slices from a single 3D
+  % Simple function to create a montage /
+  %  mosaic of multiple slices from a single 3D
   % image matrix.
   %
   % INPUT:
   % img           - 3D (x,y,z) image matrix
-  % columns       - number of columns in montage (rows are calculated accordingly)
+  % columns       - number of columns in montage
+  % (rows are calculated accordingly)
   % rotate        - rotate images 90 deg clockwise? yes = 1; no = 0.
   % cmap          - figure colormap
   % visibility    - show figure?
@@ -116,27 +118,7 @@
     montage.whole_img = whole;
   end
 
-  % Get screen size for plotting - [1 1 w h]
-  scr_size = get(0, 'ScreenSize');
-  dist = scr_size(4);
-  if scr_size(3) < dist
-    dist = scr_size(3);
-  end
-
-  % Create figure - outerposition = [left bottom width height]
-  if strcmp(shape, 'max')
-    f = figure('visible', visibility, ...
-               'units', 'normalized', ...
-               'outerposition', [0 0 1 1]);
-  elseif strcmp(shape, 'square')
-    f = figure('visible', visibility, ...
-               'units', 'pixels', ...
-               'outerposition', [0 0 dist dist]);
-  else
-    f = figure('visible', visibility, ...
-               'units', 'pixels', ...
-               'outerposition', [0 0 dist dist]);
-  end
+  f = initMontageFigure(shape, visibility);
 
   ax = subplot(1, 1, 1);
   im = imagesc(ax, montage.whole_img);
diff --git a/createOverlayMontage.m b/src/plotting/createOverlayMontage.m
similarity index 90%
rename from createOverlayMontage.m
rename to src/plotting/createOverlayMontage.m
index 1296d9b5..2897ef27 100644
--- a/createOverlayMontage.m
+++ b/src/plotting/createOverlayMontage.m
@@ -1,6 +1,6 @@
 function output = createOverlayMontage(varargin)
 
-  % (C) Copyright 2022 bidspm developers
+  % (C) Copyright 2024 bidspm developers
 
   % fmrwhy_util_createOverlayMontage(tsnr_img{i}, overlayImg, 9, 1, '', ...
   % 'hot', 'off', 'max', [0 250], [33, 168, 10], tsnr_saveAss{i});
@@ -55,9 +55,7 @@
                                    'cxs', cxs);
 
   % Create figures with background montage and overlaid masks
-  f = figure('units', 'normalized', ...
-             'outerposition', [0 0 1 1], ...
-             'visible', visibility);
+  f = initMontageFigure(shape, visibility);
   imagesc(montage_template.whole_img);
   colormap(cmap);
   if ~isempty(cxs)
@@ -77,7 +75,8 @@
 
   if iscell(overlayImg)
     for i = 1:numel(overlayImg)
-      montage_overlay{i} = createMontage(overlayImg{i},   'columns', columns, ...
+      montage_overlay{i} = createMontage(overlayImg{i}, ...
+                                         'columns', columns, ...
                                          'rotate', rotate, ...
                                          'cmap', cmap, ...
                                          'visibility', 'off', ...
@@ -86,7 +85,8 @@
     end
   else
     montage_overlay = {};
-    montage_overlay{1} = createMontage(overlayImg,   'columns', columns, ...
+    montage_overlay{1} = createMontage(overlayImg, ...
+                                       'columns', columns, ...
                                        'rotate', rotate, ...
                                        'cmap', cmap, ...
                                        'visibility', 'off', ...
@@ -103,7 +103,8 @@
       bound_whole_bin = bwboundaries(montage_overlay{i}.whole_img);
       Nblobs_bin = numel(bound_whole_bin);
       for b = 1:Nblobs_bin
-        p = plot(ax, bound_whole_bin{b, 1}(:, 2), bound_whole_bin{b, 1}(:, 1), 'color', rbgclr, 'LineWidth', 1);
+        p = plot(ax, bound_whole_bin{b, 1}(:, 2), bound_whole_bin{b, 1}(:, 1), ...
+                 'color', rbgclr, 'LineWidth', 1);
       end
     end
   end
diff --git a/src/plotting/initMontageFigure.m b/src/plotting/initMontageFigure.m
new file mode 100644
index 00000000..38a43655
--- /dev/null
+++ b/src/plotting/initMontageFigure.m
@@ -0,0 +1,24 @@
+function f = initMontageFigure(shape, visibility)
+  % (C) Copyright 2024 bidspm developers
+
+  scr_size = get(0, 'ScreenSize');
+  dist = scr_size(4);
+  if scr_size(3) < dist
+    dist = scr_size(3);
+  end
+  % Create figure - outerposition = [left bottom width height]
+
+  if strcmp(shape, 'max')
+    f = figure('visible', visibility, ...
+               'units', 'normalized', ...
+               'outerposition', [0 0 1 1]);
+  elseif strcmp(shape, 'square')
+    f = figure('visible', visibility, ...
+               'units', 'pixels', ...
+               'outerposition', [0 0 dist dist]);
+  else
+    f = figure('visible', visibility, ...
+               'units', 'pixels', ...
+               'outerposition', [0 0 dist dist]);
+  end
+end
diff --git a/untitled.m b/untitled.m
index 893894ea..5c2c1a8a 100644
--- a/untitled.m
+++ b/untitled.m
@@ -3,9 +3,15 @@
 
 bidspm_dir = '/home/remi/github/cpp-lln-lab/bidspm';
 
-overlay_img = fullfile(bidspm_dir, 'demos/MoAE/outputs/derivatives/bidspm-stats/sub-01/task-auditory_space-MNI152NLin6Asym_FWHM-8/mask.nii');
+demos_dir = fullfile(bidspm_dir, 'demos/MoAE/outputs/derivatives/');
 
-template_img = fullfile(bidspm_dir, 'demos/MoAE/outputs/derivatives/bidspm-preproc/sub-01/func/sub-01_task-auditory_space-MNI152NLin6Asym_desc-smth8_bold.nii');
+overlay_img = fullfile(demos_dir, ...
+                       'bidspm-stats/sub-01/task-auditory_space-MNI152NLin6Asym_FWHM-8/mask.nii');
+
+template_img = fullfile( ...
+                        demos_dir, ...
+                        'bidspm-preproc', 'sub-01', 'func', ...
+                        'sub-01_task-auditory_space-MNI152NLin6Asym_desc-smth8_bold.nii');
 
 template_hdr = spm_vol(template_img);
 template = spm_read_vols(template_hdr(1));
@@ -14,4 +20,5 @@
 mask = spm_read_vols(mask_hdr);
 
 % createMontage(template, 'shape', 'square');
-createOverlayMontage(template, mask, 'rgbcolors', [255, 0, 0], 'shape', 'square');
+createOverlayMontage(template, mask, 'rgbcolors', [255, 0, 0], ...
+                     'shape', 'square');