[3/3] Fastgraph: Plot Fastgraphs

external/subtightplot/license.txt

@@ -0,0 +1,26 @@
+Copyright (c) 2012, Felipe G. Nievinski
+Copyright (c) 2010, Pekka Kumpulainen
+Copyright (c) 2011, Nikolay S.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in
+      the documentation and/or other materials provided with the distribution
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

external/subtightplot/subtightplot.m

@@ -0,0 +1,67 @@
+function h=subtightplot(m,n,p,gap,marg_h,marg_w,varargin)
+%function h=subtightplot(m,n,p,gap,marg_h,marg_w,varargin)
+%
+% Functional purpose: A wrapper function for Matlab function subplot. Adds the ability to define the gap between
+% neighbouring subplots. Unfotrtunately Matlab subplot function lacks this functionality, and the gap between
+% subplots can reach 40% of figure area, which is pretty lavish.  
+%
+% Input arguments (defaults exist):
+%   gap- two elements vector [vertical,horizontal] defining the gap between neighbouring axes. Default value
+%            is 0.01. Note this vale will cause titles legends and labels to collide with the subplots, while presenting
+%            relatively large axis. 
+%   marg_h  margins in height in normalized units (0...1)
+%            or [lower uppper] for different lower and upper margins 
+%   marg_w  margins in width in normalized units (0...1)
+%            or [left right] for different left and right margins 
+%
+% Output arguments: same as subplot- none, or axes handle according to function call.
+%
+% Issues & Comments: Note that if additional elements are used in order to be passed to subplot, gap parameter must
+%       be defined. For default gap value use empty element- [].      
+%
+% Usage example: h=subtightplot((2,3,1:2,[0.5,0.2])
+
+if (nargin<4) || isempty(gap),    gap=0.01;  end
+if (nargin<5) || isempty(marg_h),  marg_h=0.05;  end
+if (nargin<5) || isempty(marg_w),  marg_w=marg_h;  end
+if isscalar(gap),   gap(2)=gap;  end
+if isscalar(marg_h),  marg_h(2)=marg_h;  end
+if isscalar(marg_w),  marg_w(2)=marg_w;  end
+gap_vert   = gap(1);
+gap_horz   = gap(2);
+marg_lower = marg_h(1);
+marg_upper = marg_h(2);
+marg_left  = marg_w(1);
+marg_right = marg_w(2);
+
+%note n and m are switched as Matlab indexing is column-wise, while subplot indexing is row-wise :(
+[subplot_col,subplot_row]=ind2sub([n,m],p);  
+
+% note subplot suppors vector p inputs- so a merged subplot of higher dimentions will be created
+subplot_cols=1+max(subplot_col)-min(subplot_col); % number of column elements in merged subplot 
+subplot_rows=1+max(subplot_row)-min(subplot_row); % number of row elements in merged subplot   
+
+% single subplot dimensions:
+%height=(1-(m+1)*gap_vert)/m;
+%axh = (1-sum(marg_h)-(Nh-1)*gap(1))/Nh; 
+height=(1-(marg_lower+marg_upper)-(m-1)*gap_vert)/m;
+%width =(1-(n+1)*gap_horz)/n;
+%axw = (1-sum(marg_w)-(Nw-1)*gap(2))/Nw;
+width =(1-(marg_left+marg_right)-(n-1)*gap_horz)/n;
+
+% merged subplot dimensions:
+merged_height=subplot_rows*( height+gap_vert )- gap_vert;
+merged_width= subplot_cols*( width +gap_horz )- gap_horz;
+
+% merged subplot position:
+merged_bottom=(m-max(subplot_row))*(height+gap_vert) +marg_lower;
+merged_left=(min(subplot_col)-1)*(width+gap_horz) +marg_left;
+pos_vec=[merged_left merged_bottom merged_width merged_height];
+
+% h_subplot=subplot(m,n,p,varargin{:},'Position',pos_vec);
+% Above line doesn't work as subplot tends to ignore 'position' when same mnp is utilized
+h=subplot('Position',pos_vec,varargin{:});
+
+if (nargout < 1),  clear h;  end
+
+end

toolbox/io/export_channel_atlas.m

@@ -1,19 +1,28 @@
-function TsvFile = export_channel_atlas(ChannelFile, Modality, TsvFile, Radius, isProba, isInteractive)
+function [TsvFile, ChanTable] = export_channel_atlas(ChannelFile, Modality, TsvFile, Radius, isProba, isInteractive, AtlasFilter)
 % EXPORT_CHANNEL_ATLAS: Compute anatomical labels for SEEG/ECOG contacts from volume and surface parcellations
 %
-% USAGE:  TsvFile = export_channel_atlas(ChannelFile, Modality='ECOG+SEEG', TsvFile=[ask], Radius=[ask], isProba=[ask], isInteractive=1)
-%         TsvFile = export_channel_atlas(ChannelFile, iChannels,            TsvFile=[ask], Radius=[ask], isProba=[ask], isInteractive=1)
+% USAGE:  TsvFile = export_channel_atlas(ChannelFile, Modality='ECOG+SEEG', TsvFile=[ask], Radius=[ask], isProba=[ask], isInteractive=1, AtlasFilter='')
+%         TsvFile = export_channel_atlas(ChannelFile, iChannels,            TsvFile=[ask], Radius=[ask], isProba=[ask], isInteractive=1, AtlasFilter='')
 %
 % INPUT: 
 %     - ChannelFile   : Path to Brainstorm channel file to be processed
 %     - Modality      : String, export only the channel with the selected modality
 %     - iChannels     : Array of integers, export only the selected channel indices
 %     - TsvFile       : Output text file (tab-separated values)
 %     - Radius        : Size in millimeters of the neighborhood to consider around each contact
+%     - isProba       : If 1, for each volume atlas, add a column indicating the spatial probability (100 * nVoxelWithLabel / nVoxelsInSphere)
 %     - IsInteractive : If 1, display the output table at the end of the process
-%                     : If 0, use all available Coodinates, Parcellations (anat) and Atlases (surface),
-%                       and do not display output table 
-%     - iChannels     : Limit export to a subset of channel indices
+%                     : If 0, use all available Coodinates, and the Parcellations (anat) and Atlases (surface) filtered by 'AtlasFilter'
+%                       and do not display output table
+%     - AtlasFilter   : Used with IsInteractive=0. If absent or empty, use all the Parcellations (anat) and Atlases (surface).
+%                       Otherwise use the string in AtlasFilter to indicate the Parcellations and Atlases to return.
+% OUTPUT: 
+%     - TsvFile       : Output text file (tab-separated values). Empty when no file was selected or requested.
+%     - ChanTable     : Cell array containing the complete output table. The same information is written to TsvFile 
+%                       when an output file is requested.
+%                       - The first column always contains channel names
+%                       - The remaining columns contain available coordinates, anatomical labels, 
+%                         and optional probabilities corresponding to each channel
 % 
 % REFERENCES:
 %     - MERCIER M, 2021:
@@ -47,6 +56,9 @@
 
 
 % ===== PASRSE INPUTS =====
+if (nargin < 7) || isempty(AtlasFilter)
+    AtlasFilter = [];
+end
 if (nargin < 6) || isempty(isInteractive)
     isInteractive = 1;
 end
@@ -78,7 +90,7 @@
 
 
 % ===== SELECT OUTPUT FILE =====
-if isempty(TsvFile)
+if isempty(TsvFile) && isInteractive
     % Get default directories and formats
     LastUsedDirs = bst_get('LastUsedDirs');
     % Default output filename
@@ -240,6 +252,31 @@
 end
 
 
+% ===== FILTER ATLASES =====
+if ~isInteractive && ~isempty(AtlasFilter)
+    % === Volume ===
+    iColVol = find(~cellfun(@(c)isempty(strfind(c, tagVol)), Columns(:,2)));
+    % Try match, if nothing found, try regular expression
+    iVolValid = find(strcmpi(Columns(iColVol,1), AtlasFilter));
+    if isempty(iVolValid)
+        iVolValid = find(~cellfun(@isempty, regexp(Columns(iColVol,1), AtlasFilter)));
+    end
+    % Remove non-matching volume atlases
+    Columns(setdiff(iColVol, iColVol(iVolValid)), :) = [];
+    % Update iColSurf in case volumes were removed
+    iColSurf = find(~cellfun(@(c)isempty(strfind(c, tagSurf)), Columns(:,2)));
+
+    % === Surface ===
+    % Try match, if nothing found, try regular expression
+    iSurfValid = find(strcmpi(SurfAtlases, AtlasFilter));
+    if isempty(iSurfValid)
+        iSurfValid = find(~cellfun(@isempty, regexp(SurfAtlases, AtlasFilter)));
+    end
+    % Keep only matching surface atlases
+    SurfAtlases = SurfAtlases(iSurfValid);
+end
+
+
 % ===== SPHERE PROBE =====
 % Ask sphere radius to users
 if isempty(Radius)