Added all the stuff for stitching

Author: adamltaylor

build_raw_tile_index_for_neighborhood.m

@@ -0,0 +1,32 @@
+function tile_index = build_raw_tile_index_for_neighborhood(raw_tile_root_folder_path, center_tile_relative_path, sample_memo_folder_path, do_force_computation)
+    % Build the full tile index
+    raw_tile_index = compute_or_read_from_memo(sample_memo_folder_path, ...
+                                               'raw-tile-index', ...
+                                               @()(build_raw_tile_index(raw_tile_root_folder_path)), ...
+                                               do_force_computation) ;
+    full_tile_index_from_full_tile_ijk1 = raw_tile_index.tile_index_from_tile_ijk1 ;
+    full_tile_ijk1_from_full_tile_index = raw_tile_index.ijk1_from_tile_index ;
+    xyz_from_full_tile_index = raw_tile_index.xyz_from_tile_index ;
+    relative_path_from_full_tile_index = raw_tile_index.relative_path_from_tile_index ;
+    %full_tile_grid_shape = size(full_tile_index_from_full_tile_ijk1)
+    %full_tile_count = length(relative_path_from_full_tile_index) 
+
+    % Get out just the tiles around the center_tile
+    [tile_index_from_tile_ijk1, ...
+     tile_ijk1_from_tile_index, ...
+     xyz_from_tile_index, ...
+     relative_path_from_tile_index] = ...
+        extract_tiles_near_tile(full_tile_index_from_full_tile_ijk1, ...
+                                full_tile_ijk1_from_full_tile_index, ...
+                                xyz_from_full_tile_index, ...
+                                relative_path_from_full_tile_index, ...
+                                center_tile_relative_path) ;
+    %tile_count = length(relative_path_from_tile_index)
+
+    % Store the tile subset indices in a single structure
+    tile_index = struct() ;
+    tile_index.tile_index_from_tile_ijk1 = tile_index_from_tile_ijk1 ;
+    tile_index.ijk1_from_tile_index = tile_ijk1_from_tile_index ;
+    tile_index.xyz_from_tile_index = xyz_from_tile_index ;
+    tile_index.relative_path_from_tile_index = relative_path_from_tile_index ;
+end

common/io/recdir.m

@@ -0,0 +1,84 @@
+function recdir(inputfolder,args,level)
+%%
+% args.level = opt.level;
+% args.ext = opt.ext;
+% if exist(opt.seqtemp, 'file') == 2
+%     % load file directly
+% else
+%     args.fid = fopen(opt.seqtemp,'w');
+%     recdir(opt.inputfolder,args)
+% end
+% fid=fopen(opt.seqtemp,'r');
+% myfiles = textscan(fid,'%s');
+% myfiles = myfiles{1};
+% fclose(fid)
+
+% get sequence
+if nargin ==0 
+    inputfolder = '/nobackup2/mouselight/cluster/SitchedProbability_GN1/2015-06-19-erhan-GN1-maskProb'
+    args.level = 5;
+    args.fid = fopen('paths.txt','w');
+    args.ext = 'tif'
+%     try
+%         recdir(inputfolder,args,level)
+%     catch
+%         fclose(args.fid)
+%     end
+end
+%%
+if nargin <3
+    level = 0;
+end
+if args.ext(1) == '.'
+    args.ext(1) = [];
+end
+dirinfo = dir(inputfolder);
+dirinfo(~[dirinfo.isdir]) = [];  %remove non-directories
+tf = cellfun(@(x) x(1)=='.',{dirinfo.name}); %remove hidded and parent folders
+% ismember( {dirinfo.name}, {'.', '..','.log','.backup'});
+dirinfo(tf) = [];  %remove current and parent directory.
+
+if isfield(args,'pattern')
+    matches = regexp({dirinfo(:).name},args.pattern);
+    keep_these = zeros(1,length(dirinfo));
+    for ifold = 1:length(matches)
+        if matches{ifold} & matches{ifold}(1)==1
+            keep_these(ifold) = 1;
+        end
+    end
+    dirinfo(~keep_these) = []; %remove any folder that doesn't follow pattern
+end
+%%
+if level == args.level
+    % search file
+    % get files with argument
+    myfiles = dir([inputfolder,'/*.',args.ext]);
+    % append to xls file
+    for ii=1:length(myfiles)
+        if 0&exist(fullfile(inputfolder,[myfiles(ii).name(1:end-3),'.tif']),'file')
+            
+        else
+            fprintf(args.fid,'%s\n',fullfile(inputfolder,myfiles(ii).name));
+        end
+    end
+%     % append to xls file
+%     for ii=1:length(myfiles)
+%         if myfiles(ii).bytes~=789753938
+%             fprintf(args.fid,'%s\n',fullfile(inputfolder,myfiles(ii).name));
+%         end
+%     end
+    %return
+else
+    % recursion
+    for idx=1:length(dirinfo)
+        recdir(fullfile(inputfolder,dirinfo(idx).name),args,level+1)
+    end
+    if level == 1
+        disp(sprintf('Finished %d : %s',level,inputfolder))
+    end
+end
+if level==0
+    fclose(args.fid);
+end
+
+end

common/stat/getmod.m

@@ -0,0 +1,20 @@
+function mod = getmod(x)
+% assumes x[Nxdim]
+if ndims(x) ==1
+    mod = gtmd(x);
+else
+    if size(x,1)<=size(x,2)
+        error('input has more columns then rows, use getmod(x'') if input is correct')
+    end
+    mod = size(x,2);
+    for dim = 1:size(x,2)
+        mod(dim) = gtmd(x(:,dim));
+    end
+end
+end
+
+function md = gtmd(x)
+    [n,edges] = histcounts(x);
+    [maxn,indmax] = max(n);
+    md = (edges(indmax)+edges(indmax+1))/2;
+end

common/third-party/altmany-export_fig-4c015d5/.gitignore

@@ -0,0 +1,5 @@
+/.ignore
+*.txt
+*.asv
+*~
+*.mex*

common/third-party/altmany-export_fig-4c015d5/ImageSelection.class

@@ -0,0 +1,38 @@
+/*
+ * Based on code snippet from
+ * http://java.sun.com/developer/technicalArticles/releases/data/
+ *
+ * Copyright © 2008, 2010 Oracle and/or its affiliates. All rights reserved. Use is subject to license terms.
+ */
+
+import java.awt.image.BufferedImage;
+import java.awt.datatransfer.*;
+
+public class ImageSelection implements Transferable {
+    
+    private static final DataFlavor flavors[] =
+    {DataFlavor.imageFlavor};
+    
+    private BufferedImage image;
+    
+    public ImageSelection(BufferedImage image) {
+        this.image = image;
+    }
+    
+    // Transferable
+    public Object getTransferData(DataFlavor flavor) throws UnsupportedFlavorException {
+        if (flavor.equals(flavors[0]) == false) {
+            throw new UnsupportedFlavorException(flavor);
+        }
+        return image;
+    }
+    
+    public DataFlavor[] getTransferDataFlavors() {
+        return flavors;
+    }
+    
+    public boolean isDataFlavorSupported(DataFlavor
+    flavor) {
+        return flavor.equals(flavors[0]);
+    }
+}

common/third-party/altmany-export_fig-4c015d5/ImageSelection.java

@@ -0,0 +1,27 @@
+Copyright (c) 2014, Oliver J. Woodford, Yair M. Altman
+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.
+
+* Neither the name of the {organization} nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+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 HOLDER 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.