matlab实战中一些重要的函数总结

这段时间看了一些大型的matlab工程文件(如：faster r-cnn)，对于工程中经常要用到的一些函数进行一个总结。
1、路径问题。
这主要涵括文件路径的包含和组合。

curdir = fileparts(mfilename('fullpath'));
addpath(genpath(fullfile(curdir, 'utils')));
mkdir_if_missing(fullfile(curdir, 'utils'));
caffe_path = fullfile(curdir, 'external', 'caffe', 'matlab');
if exist(caffe_path, 'dir') == 0
   error('matcaffe is missing from external/caffe/matlab; See README.md');
end

我们经常需要引用不同文件夹下的文件或是函数。
mfilename 表示正在运行的函数的路径
fileparts 则返回文件上层的文件夹路径
fullfile 则返回组合文件的全路径
genpath 递归的产生该文件夹下的所有文件的路径
addpath 路径加入到函数或文件搜索的范围内
exist 查看路径是否存在
mkdir_if_missing 如果不存在就创建对应的文件夹

dirpath = '/home/Deeplearning';
filepath = [dirpath, '/%s.txt'];
for i=1:10
    filepath_real = sprintf(filepath, num2str(i));
end

这时路径组合中经常出现的情况
用[]拼接通用路径，具体情况时再加入需要改动的部分，需改动的部分在拼接通用路径时预留
2、查找和排序

[B,I] = sort(A,mode,dim)

A为输入矩阵或向量，mode为排序的模式，升序还是降序，dim表示按第几维进行排序；B为排序后的矩阵或向量，I为排序后的各元素的序号。

X = [3 2 0; -5 0 7; 0 0 1] [row,col,v] = find(X>1)

X>1为条件,即矩阵X中元素大小比1大的元素，row，col, v分别为返回的元素的位置横、纵坐标、元素本身。
3、随机过程与函数
randi ,random等
4、维度转换

A = [1 2; 3 4]; permute(A,[2 1])
ans =
     1     3
     2     4

squeeze移除掉多余的某一纬度

Create a 2-by-1-by-3 array and remove the singleton column dimension to form a 2-by-3 matrix.
y = rand(2,1,3)
z = squeeze(y)
y(:,:,1) =
    0.8147
    0.9058
y(:,:,2) =
    0.1270
    0.9134
y(:,:,3) =

    0.6324
    0.0975
z =

    0.8147    0.1270    0.6324
    0.9058    0.9134    0.0975

5、画图
plot , subplot, figure, meshgrid等
对于如何在一幅图片中的指定位置加入文字和标注可参考我的上一篇博文http://blog.csdn.net/sunnyxiaohu/article/details/51150430
中 function showboxes(im, boxes, legends, color_conf)的解析。
6、数据的转换
round:
Round to nearest decimal or intege
这个在处理数据时很有用
cell2mat:
num2str, str2num
cat(1,some_cell);
unique();
这些函数在进行各种格式之间的数据转换用的很多，可以自行查阅文档。
matlab中经常强调向量化编程，这样能加快运行的速度。那么对于array或者cell，我们怎样尽量的少使用for循环而用向量化编程呢？

A = randi(10,4,2)%假设你有4组数据，每一组数据有2维，你需要对每组数据进行某个处理

     7     7
     8     2
     8     8
     4     1
A_cell = num2cell(A,2)%先将其按行转化为cell

    [1x2 double]
    [1x2 double]
    [1x2 double]
    [1x2 double] 
y_hat = cellfun(@(x) (x.*10) ,A_cell, 'UniformOutput', false)%这样就可用cellfun进行向量化处理了
    [1x2 double]
    [1x2 double]
    [1x2 double]
    [1x2 double]
%处理完成之后，又变换回原来的格式
y = cat(1,y_hat{:})
    70    70
    80    20
    80    80
    40    10

7、文档的读写
这里主要讲两种

[gtids,t]=textread(sprintf(VOCopts.imgsetpath,VOCopts.testset),'%s %d');

[A,B,C,...] = textread(filename,format)
[A,B,C,...] = textread(filename,format,N)
[...] = textread(...,param,value,...)

对于txt文件的读取，用textread基本就已经够用了，这里面有很多个参数可选，自己琢磨一下。

xmlwrite() xmlread()

这里有一个文档可供参考，讲得很详细。

%% Tutorial for xml_io_tools Package
% *By Jarek Tuszynski*
%
% Package xml_io_tools can read XML files into MATLAB struct and writes 
% MATLAB data types to XML files with help of simple interface to 
% MATLAB's xmlwrite and xmlread functions.
% 
% Two function to simplify reading and writing XML files from MATLAB:
%
% * Function xml_read first calls MATLAB's xmlread function and than 
% converts its output ('Document Object Model' tree of Java objects) 
% to tree of MATLAB struct's. The output is in the format of nested 
% structs and cells. In the output data structure field names are based on
% XML tags.
%
% * Function xml_write first convert input tree of MATLAB structs and cells 
% and other types to tree of 'Document Object Model' nodes, and then writes 
% resulting object to XML file using MATLAB's xmlwrite function. .
%
%% This package can:
% * Read most XML files, created inside and outside of MATLAB environment, 
%   and convert them to MATLAB data structures.
% * Write any MATLAB's struct tree to XML file
% * Handle XML attributes and special XML nodes like comments, processing  
%   instructions and CDATA sections
% * Supports base64 encoding and decoding to allow handling embeded binary
%   data
% * Be studied, modified, customized, rewritten and used in other packages 
%   without any limitations. All code is included and documented. Software
%   is distributed under BSD Licence (included).   
%
%% This package does not:
% * Guarantee to recover the same Matlab objects that were saved. If you 
% need to be able to recover carbon copy of the structure that was saved 
% than you will have to use one of the packages that uses special set of 
% tags saved as xml attributes that help to guide the parsing of XML code. 
% This package does not use those tags.
% * Guarantee to work with older versions of MATLAB. Functions do not work
% with versions of MATLAB prior to 7.1 (26-Jul-2005). 
%
%% Change History
% * 2006-11-06 - original version
% * 2006-11-26 - corrected xml_write to handle writing Matlab's column
%   arrays to xml files. Bug discovered and diagnosed by Kalyan Dutta.
% * 2006-11-28 - made changes to handle special node types like: 
%   COMMENTS and CDATA sections 
% * 2007-03-12 - Writing CDATA sections still did not worked. The problem 
%   was diagnosed and fixed by Alberto Amaro. The fix involved rewriting
%   xmlwrite to use Apache Xerces java files directly instead of MATLAB's 
%   XMLUtils java class.
% * 2007-06-21 - Fixed problem reported by Anna Kelbert in Reviews about 
%   not writing attributes of ROOT node. Also: added support for Processing
%   Instructions, added support for global text nodes: Processing
%   Instructions and comments, allowed writing tag names with special
%   characters
% * 2007-07-20 - Added tutorial script file. Extended support for global
%   text nodes. Added more Preference fields.
% * 2008-01-23 - Fixed problem reported by Anna Krewet of converting dates 
%   in format '2007-01-01' to numbers. Improved and added warning messages.
%   Added detection of old Matlab versions incompatible with the library.
%   Expanded documentation.
% * 2008-06-23 - Fixed problem with writing 1D array reported by Mark Neil. 
%   Extended xml_read's Pref.Num2Str to 3 settings (never, smart and always) 
%   for better control. Added parameter Pref.KeepNS for keeping or ignoring 
%   namespace data when reading. Fixed a bug related to writing 2D cell
%   arrays brought up by Andrej's Mosat review. 
% * 2008-09-11 - Resubmitting last upload - zip file is still old
% * 2009-02-26 - Small changes. More error handling. More robust in case of
%   large binary objects. Added support for Base64 encoding/decoding of
%   binary objects (using functions by Peter J. Acklam).
% * 2009-06-26 - changes to xml_read: added CellItem parameter to allow
%   better control of reading files with 'item' notation (see comment by
%   Shlomi); changed try-catch statements so xml_read would work for mablab
%   versions prior to 7.5 (see Thomas Pilutti comment)
% * 2009-12-03 - added PreserveSpace parameter for contolling empty string
%   handling as suggested by Sebastiaan. Fix suggested by Michael Murphy.
%   Fixed number recognition code as suggested by Yuan Ren.  
% * 2010-05-04 - implemented fixes suggested by Dylan Reynolds from Airbus.  
% * 2010-07-28 - implemented support for 2D arrays of cells and structs 
%   suggested by Rodney Behn from MIT Lincoln Laboratory. Also attempted
%   large scale cleanup of xml_write function
% * 2010-08-18 - minor extension to allow better handling of logical
%   scalars and arrays and function handles suggested by Andreas Richter 
%   and others
% * 2010-09-20 - allow reading and writing of sparse matrices. Improve
%   reading of 1D boolean arrays.
% * 2010-11-05 - Fix problem with empty cells reported by Richard Cotton;
%   fixed issues with reading boolean arrays reported by Zohar Bar-Yehuda;
%   Improved speed of base64 coding and decoding by switching to java based 
%   code.
%% Licence
% The package is distributed under BSD License
format compact; % viewing preference
clear variables;
type('license.txt')

%% Write XML file based on a Struct using "xml_write"
% Any MATLAB data struct can be saved to XML file.
MyTree=[];
MyTree.MyNumber = 13;
MyTree.MyString = 'Hello World';
xml_write('test.xml', MyTree);
type('test.xml')

%% Read XML file producing a Struct using "xml_read"
[tree treeName] = xml_read ('test.xml');
disp([treeName{1} ' ='])
gen_object_display(tree)

%% "Pref.XmlEngine" flag in "xml_write"
% Occasionaly some operations are performed better by Apache Xerces XML 
% engine than default xmlread function. That is why xml_write provide an 
% option for choosing the underlaying xml engine. Code below performs the 
% same operation as the previous section but using Apache Xerces XML engine.
% Notice that in this case name of root element 
% was passed as variable and not extracted from the variable name.
% Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
% xml_write('test.xml', MyTree, 'TreeOfMine', Pref);
% type('test.xml')
% 
% %% Writing Struct with different type MATLAB arrays
% MyTree=[];
% MyTree.Empty   = [];                   % Empty variable
% MyTree.Num_1x1 = 13;                   % simple scalar
% MyTree.Vec_1x3 = [1 2 3];              % horizontal vector
% MyTree.Vec_4x1 = [1; 2; 3; 4];         % vertical vector
% MyTree.Mat_2x2 = [1, 2; 3, 4];         % 2D matrix
% MyTree.Cube_3D = reshape(1:8,[2 2 2]); % 3D array
% MyTree.String1 = '[2003 10 30]';       % number string with    [] brackets
% MyTree.String2 = ' 2003 10 30 ';       % number string without [] brackets
% MyTree.Logical_1x1 = false;            % single logical
% MyTree.Logical_2x2 = [false, true; true, false]; % 2D matrix of logicals
% MyTree.Logical_Str = 'False False True True';
% MyTree.Int_2x2 = uint8([1 2;3 4]);     % 2D matrix of uint8 integers
% MyTree.Complex_1x1 = complex(1, 7);    % complex scalar
% MyTree.Complex_2x2 = complex([1 2;3 4],[2 2;7 7]); % 2D matrix of complex numbers
% MyTree.Sparse_9x9 = sparse(1:9,1:9,1); % sparse 9x9 matrix
% MyTree.Function = @sum;                % function handle
% xml_write('test.xml', MyTree);
% type('test.xml')
% 
% %% Read Struct with MATLAB arrays
% % Notice that 'Cube_3D' did not preserve original dimentions 
% [tree treeName] = xml_read ('test.xml');
% disp([treeName{1} ' ='])
% gen_object_display(tree)
% 
% %% "Pref.StructItem" flag in "xml_write" (controls 1D arrays of structs)
% % *Create a simple structure with 1D array of struct's*
MyTree = [];
MyTree.a(1).b = 'jack';
MyTree.a(2).b = 'john';
gen_object_display(MyTree)
%%
% *Write XML with "StructItem = true" (default).  Notice single 'a' 
% section and multiple 'item' sub-sections. Those subsections are used 
% to store array elements*
wPref.StructItem = true;
xml_write('test.xml', MyTree, 'MyTree',wPref);
type('test.xml')
fprintf('\nxml_read output:\n')
gen_object_display(xml_read ('test.xml'))
%%
% *Write XML with "StructItem = false". Notice multiple 'a' sections*
wPref.StructItem = false;
xml_write('test.xml', MyTree, 'MyTree',wPref);
type('test.xml')
fprintf('\nxml_read output:\n')
gen_object_display(xml_read ('test.xml'))
%%
% *Notice that xml_read function produced the same struct when reading both files*
%%
% *Potential problems with "StructItem = true":*
wPref.StructItem = true;
MyTree1 = []; MyTree1.a.b    = 'jack';
MyTree2 = []; MyTree2.a(1).b = 'jack';
MyTree3 = []; MyTree3.a(2).b = 'jack';
xml_write('test.xml', MyTree1, [], wPref); type('test.xml');
xml_write('test.xml', MyTree2, [], wPref); type('test.xml');
xml_write('test.xml', MyTree3, [], wPref); type('test.xml');
%%
% *Notice that MyTree1 and MyTree2 produce identical files with no 'items',
% while MyTree2 and MyTree3 produce very different file structures. It was
% pointed out to me that files produced from MyTree2 and MyTree3 can not 
% belong to the same schema, which can be a problem. The solution is to use 
% cells.* 
wPref.CellItem = true;
wPref.NoCells  = true;
MyTree2 = []; MyTree2.a{1}.b = 'jack';
MyTree3 = []; MyTree3.a{2}.b = 'jack';
xml_write('test.xml', MyTree2, [], wPref); type('test.xml');
xml_write('test.xml', MyTree3, [], wPref); type('test.xml');


%% "Pref.CellItem" flag in "xml_write" (controls 1D arrays of cells)
% *Create a simple structure with cell arrays*
MyTree = [];
MyTree.a = {'jack', 'john'};
disp(MyTree)
%%
% *Write XML with "CellItem = true" (default).  Notice single 'a' 
% section and multiple 'item' sections*
Pref=[]; Pref.CellItem = true;
xml_write('test.xml', MyTree, 'MyTree',Pref);
type('test.xml')
fprintf('\nxml_read output:\n');
disp(xml_read ('test.xml'))
%%
% *Write XML with "CellItem = false". Notice multiple 'a' sections*
Pref=[]; Pref.CellItem = false;
xml_write('test.xml', MyTree, 'MyTree',Pref);
type('test.xml')
fprintf('\nxml_read output:\n');
disp(xml_read ('test.xml'))
%%
% *Notice that xml_read function produced the same struct when reading both files*

%% "Pref.NoCells" flag in "xml_read"
% *Create a cell/struct mixture object*
MyTree = [];
MyTree.a{1}.b = 'jack';
MyTree.a{2}.b = [];
MyTree.a{2}.c = 'john';
gen_object_display(MyTree);
%%
% *Save it to xml file*
Pref=[]; Pref.CellItem = false;
xml_write('test.xml', MyTree, 'MyTree',Pref);
type('test.xml')
%%
% *Read above file with "Pref.NoCells=true" (default) - output is quite different then input*
% By default program is trying to convert everything to struct's and arrays
% of structs. In case arrays of structs all the structs in array need to have the
% same fields, and if they are not than MATLAB creates empty fields.
Pref=[]; Pref.NoCells=true;
gen_object_display(xml_read('test.xml', Pref))
%%
% *Read above file with "Pref.NoCells=false" - now input and output are the same*
% Cell arrays of structs allow structs in array to have different fields.
Pref=[]; Pref.NoCells=false;
gen_object_display(xml_read('test.xml', Pref))

%% "Pref.ItemName" flag in "xml_write" (customize 1D arrays of structs and cells)
% *Create a cell/struct mixture object*
MyTree = [];
MyTree.a{1}.b = 'jack';
MyTree.a{2}.c = 'john';
gen_object_display(MyTree);
%%
% *Save it to xml file, using 'item' notation but with different name*
Pref=[]; 
Pref.CellItem = true;
Pref.ItemName = 'MyItem';
xml_write('test.xml', MyTree, 'MyTree',Pref);
type('test.xml')

%% "Pref.ItemName" flag in "xml_read"
% *Read above file with default settings ("Pref.ItemName = 'item'")*
% The results do not match the original structure
Pref=[]; Pref.NoCells  = false;
gen_object_display(xml_read('test.xml', Pref))
%%
% *Read above file with "Pref.ItemName = 'MyItem'" - now saved and read 
% MATLAB structures are the same*
Pref=[]; 
Pref.ItemName = 'MyItem';
Pref.NoCells  = false;
gen_object_display(xml_read('test.xml', Pref))

%% "Pref.CellItem" flag in "xml_read"
% "Pref.ItemName" is used to create xml files with clearly marked arrays
% "Pref.CellItem" flag in "xml_read" ensures that they are always read as
% arrays by forcing output to stay in cell format. In cell format s{1} is
% different than s, while s(1) is indistinguishable from s.
%%
% *Create a test file*
MyTree = [];
MyTree.a1{1}.b = 'jack'; % a1 - single struct
MyTree.a2{1}.b = 'jack'; % a2 - cell array of structs with the same fields
MyTree.a2{2}.b = 'john';
MyTree.a3{1}.b = 'jack'; % a3 - cell array of structs with the different fields
MyTree.a3{2}.c = 'john';
Pref=[]; 
Pref.CellItem = true;
Pref.Debug = true;
xml_write('test.xml', MyTree, 'MyTree',Pref);
type('test.xml')
%%
% *Read above file with "Pref.CellItem = true" (default)*
% All outputs are in cell format
Pref=[]; 
Pref.NoCells  = false;  % allow cell output
Pref.CellItem = true;   % keep 'item' arrays as cells 
gen_object_display(xml_read('test.xml', Pref))
%%
% *Read above file with "Pref.CellItem = false"*
% Outputs format is determined by content
Pref=[]; 
Pref.NoCells  = false; % allow cell output
Pref.CellItem = false; % allow 'item' arrays to beheave like other fields 
gen_object_display(xml_read('test.xml', Pref))
%%
% *Read above file with "Pref.CellItem = false" and "Pref.NoCells = true"*
% All outputs are in struct format
Pref=[]; 
Pref.NoCells  = true;  % don't allow cell output 
Pref.CellItem = false; % allow 'item' arrays to beheave like other fields
gen_object_display(xml_read('test.xml', Pref))

%% "Pref.CellTable" flag in "xml_write" (controls 2D arrays of cells)
% *Create a structure with 2D arrays of cells*
MyTree = [];
MyTree.M = {[1,2;3,4], 'M12'; struct('a','jack'), {11, 'N12'; 21, 'N22'}};
gen_object_display(MyTree)
%%
% *Write XML with "CellTable = 'Html" (default). This option mimics use of  
%  HTML "tr" and "td" tags to encode 2D tables. Tag names can  
%  be changed using TableName parameter (see below)*
wPref = [];
wPref.CellTable = 'Html';
xml_write('test.xml', MyTree, 'MyTree',wPref);
type('test.xml')
fprintf('\nxml_read output:\n')
rPref=[]; rPref.NoCells=false;
gen_object_display(xml_read('test.xml', rPref))
%%
% *Write XML with "CellTable = 'Vector'".*
%  Converts 2D arrays to 1D array and item or regular notation. This option 
%  is mostly provided for backward compatibility since this was the 
%  behavior in prior verions of the code
wPref = [];
wPref.CellTable = 'Vector';
xml_write('test.xml', MyTree, 'MyTree',wPref);
type('test.xml')
fprintf('\nxml_read output:\n')
rPref=[]; rPref.NoCells=false;
gen_object_display(xml_read('test.xml', rPref))
%%
% *Create a simpler structure without struct's*
MyTree = [];
MyTree.M = {[1,2;3,4], 'M12'; 'M21', {11, 'N12'; 21, 'N22'}};
gen_object_display(MyTree)
%%
% *Write XML with "CellTable = 'Matlab". This option encodes tables
% consisting of numbers, strings and other cell arrays as MATLAB command
% string. Unlike 'Html' option it does not work if one of the cells is 
% a struct*
wPref = [];
wPref.CellTable = 'Matlab';
xml_write('test.xml', MyTree, 'MyTree',wPref);
type('test.xml')
fprintf('\nxml_read output:\n')
rPref=[]; rPref.NoCells=false;
gen_object_display(xml_read('test.xml', rPref))

%% Write 2D cell array in HTML format
MyTree = [];
MyTree.table.ATTRIBUTE.border=1;
MyTree.table.CONTENT = {'Apples', '44%'; 'Bannanas', '23%'; 'Oranges', '13%'; 'Other', '10%'};
xml_write('html/test.html', MyTree);
type('html/test.html')
%%
% Click on <test.html> to opened this file with a web brouwser

%% "Pref.StructTable" flag in "xml_write" (controls 2D arrays of structs)
% *Create a simple structure with arrays of struct's*
MyTree = [];
MyTree.a(1,1).b = 'jack';
MyTree.a(1,2).b = 'john';
MyTree.a(2,1).b = 'jim';
MyTree.a(2,2).b = 'jill';
gen_object_display(MyTree)
%%
% *Write XML with "StructTable = 'Html" (default). This option mimics use of  
%  HTML "tr" and "td"  tags to encode 2D tables. Tag names can  
%  be changed using TableName parameter (see below)*
wPref = [];
wPref.StructTable = 'Html';
xml_write('test.xml', MyTree, 'MyTree',wPref);
type('test.xml')
fprintf('\nxml_read output:\n')
gen_object_display(xml_read ('test.xml'))
%%
% *Write XML with "CellTable = 'Vector'".*
%  Converts 2D arrays to 1D array and item or regular notation. This option 
%  is mostly provided for backward compatibility since this was the 
%  behavior in prior verions of the code
wPref = [];
wPref.StructTable = 'Vector';
xml_write('test.xml', MyTree, 'MyTree',wPref);
type('test.xml')
fprintf('\nxml_read output:\n')
gen_object_display(xml_read ('test.xml'))

%% "Pref.TableName" flag in "xml_write" (controls encoding tags used for 2D arrays)
% *Create a cell object*
MyTree = [];
MyTree.M = {[1,2;3,4], 'M12'; 21, {11, 'N12'; 21, 'N22'}};
gen_object_display(MyTree);
%%
% *Save it to xml file, using 'Html' notation but with different names for 
%  rows and cells*
Pref=[]; Pref.TableName = {'row','cell'};
xml_write('test.xml', MyTree, 'MyTree',Pref);
type('test.xml')

%% "Pref.TableName" flag in "xml_read"
% *Read above file with default settings ("Pref.TableName = {'tr','td'}")*
% The results do not match the original structure
Pref=[]; Pref.NoCells  = false;
gen_object_display(xml_read('test.xml', Pref))
%%
% *Read above file with "Pref.TableName = {'row','cell'}" - now saved and read 
% MATLAB structures are the same*
Pref=[]; 
Pref.TableName = {'row','cell'};
Pref.NoCells  = false;
gen_object_display(xml_read('test.xml', Pref))

%% "Pref.Str2Num" flag in xml_read (control conversion to numbers while reading)
% *Create a cell/struct mixture object*
MyTree = [];
MyTree.str     = 'sphere';
MyTree.num1    =  123;
MyTree.num2    = '123';
MyTree.num3    = '[Inf,NaN]';
MyTree.calc    = '1+2+3+4';
MyTree.func    = 'sin(pi)/2';
MyTree.String1 = '[2003 10 30]'; 
MyTree.String2 = '2003 10 30';   % array resembling date
MyTree.ISO8601 = '2003-10-30';   % date in ISO 8601 format
MyTree.US_date = '2003/10/30';   % US style date format
MyTree.complex = '2003i-10e-30'; % complex number resembling a date
gen_object_display(MyTree);
%%
% *Save it to xml file*
xml_write('test.xml', MyTree);
type('test.xml')
%%
% *Read above file with default settings*
% ("Pref.Str2Num = true" or "Pref.Str2Num = 'smart'"). Under this setting all
% strings that look like numbers are converted to numbers, except for 
% strings that are recognized by MATLAB 'datenum' function as dates
gen_object_display(xml_read('test.xml'))
%%
% *Note that all the fields of 'MyTree' can be converted to numbers (even 
% 'sphere') but by default the function is trying to 'judge' if a string  
% should be converted to a number or not*
MyCell = {'sphere','1+2+3+4','sin(pi)/2','2003 10 30','2003-10-30','2003/10/30','2003i-10e-30'};
cellfun(@str2num, MyCell, 'UniformOutput', false)
%%
% *Read above file with "Pref.Str2Num = false" or "Pref.Str2Num = 'never'" 
% to keep all the fields in string format*
Pref=[]; Pref.Str2Num = false;
gen_object_display(xml_read('test.xml', Pref))
%%
% *Read above file with "Pref.Str2Num = always"  
% to convert all strings that look like numbers to numbers* note the likelly 
% unintendet conversion of 'ISO8601'
Pref=[]; Pref.Str2Num   = 'always';
gen_object_display(xml_read('test.xml', Pref))
%%
% *Notice that all three settings will produce the same output for "num1" and
% "num2" and there is no way to reproduce the original "MyTree" structure.*

%% "Pref.PreserveSpace" flag in xml_write (control handling of strings with leading/trailing spaces)
% *Create a struct with strings*
MyTree=[];
MyTree.Empty     = '';
MyTree.OneSpace  = ' ';
MyTree.TwoSpaces = '  '; 
MyTree.String1   = ' Hello      World ';
%%
% *Write XML with "PreserveSpace = false" (default).*
Pref=[]; Pref.PreserveSpace = false; % (default setting)
xml_write('test.xml', MyTree, [], Pref);
type('test.xml')
%%
% *Write XML with "PreserveSpace = true".*
Pref=[]; Pref.PreserveSpace = true; 
xml_write('test.xml', MyTree, [], Pref);
type('test.xml')

%% "Pref.PreserveSpace" flag in xml_read
% *Read file while using "PreserveSpace = false" (default).*
Pref=[]; Pref.PreserveSpace = false; % (default setting)
gen_object_display(xml_read('test.xml',Pref))
%%
% *Read file while using "PreserveSpace = true".*
Pref=[]; Pref.PreserveSpace = true; 
gen_object_display(xml_read('test.xml',Pref))


%% Write XML files with ATTRIBUTEs 
% In order to add node attributes a special ATTRIBUTE field is used. 
% ATTRIBUTEs have to be of simple types like numbers or strings (not
% struct or cells). Attributes are easy to attach to structs nodes like 
% MyTree below. 
MyTree=[];
MyTree.MyNumber = 13;
MyTree.MyString = 'Hello World'; % simple case
MyTree.ATTRIBUTE.Num = 2;
xml_write('test.xml', MyTree);
type('test.xml')

%%  
% In case when one needs to attach attributes to nodes which are not
% structs (for example strings, numbers or calls) then special CONTENT 
% field needs to be used to make the node a struct node.
MyTree=[];
MyTree.MyNumber = 13;
MyTree.MyString.CONTENT = 'Hello World'; % simple case
MyTree.MyString.ATTRIBUTE.Num = 2;
xml_write('test.xml', MyTree);
type('test.xml')

%% "Pref.Str2Num" flag in file with ATTRIBUTEs
% *Create a cell/struct mixture object*
MyTree = [];
MyTree.X.ATTRIBUTE.str     = 'sphere';
MyTree.X.ATTRIBUTE.num1    =  123;
MyTree.X.ATTRIBUTE.num2    = '123';
MyTree.X.ATTRIBUTE.num3    = '[Inf,NaN]';
MyTree.X.ATTRIBUTE.calc    = '1+2+3+4';
MyTree.X.ATTRIBUTE.func    = 'sin(pi)/2';
MyTree.X.ATTRIBUTE.String1 = '[2003 10 30]'; 
MyTree.X.ATTRIBUTE.String2 = '2003 10 30';   % array resembling date
MyTree.X.ATTRIBUTE.ISO8601 = '2003-10-30';   % date in ISO 8601 format
MyTree.X.ATTRIBUTE.US_date = '2003/10/30';   % US style date format
MyTree.X.ATTRIBUTE.complex = '2003i-10e-30'; % complex number resembling a date
gen_object_display(MyTree);
%%
% *Save it to xml file*
xml_write('test.xml', MyTree);
type('test.xml')
%%
% *Read above file with default settings*
% ("Pref.Str2Num = true" or "Pref.Str2Num = 'smart'"). Under this setting all
% strings that look like numbers are converted to numbers, except for 
% strings that are recognized by MATLAB 'datenum' function as dates
gen_object_display(xml_read('test.xml'))

%%
% *Read above file with "Pref.Str2Num = false" or "Pref.Str2Num = 'never'" 
% to keep all the fields in string format*
Pref=[]; Pref.Str2Num = false;
gen_object_display(xml_read('test.xml', Pref))
%%
% *Read above file with "Pref.Str2Num = always"  
% to convert all strings that look like numbers to numbers* 
Pref=[]; Pref.Str2Num   = 'always';
gen_object_display(xml_read('test.xml', Pref))
%%
% *Notice that all three settings will produce the same output for "num1" and
% "num2" and there is no way to reproduce the original "MyTree" structure.*


%% Write XML files with COMMENTs
% Insertion of Comments is done with help of special COMMENT field.
% Note that MATLAB's xmlwrite is less readable due to lack of end-of-line 
% characters around comment section. 
MyTree=[];
MyTree.COMMENT = 'This is a comment';
MyTree.MyNumber = 13;
MyTree.MyString.CONTENT = 'Hello World';
xml_write('test.xml', MyTree);
type('test.xml')

%%
% *Same operation using Apache Xerces XML engine*
% gives the same result
Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
xml_write('test.xml', MyTree, 'MyTree', Pref);
type('test.xml')

%%
% *Comments in XML top level (method #1)*
% This method uses cell array 
MyTree=[];
MyTree.MyNumber = 13;
MyTree.MyString = 'Hello World';
xml_write('test.xml', MyTree, {'MyTree', [], 'This is a global comment'});
type('test.xml')
%%
% *Same operation using Apache Xerces XML engine* 
% gives even nicer results.
Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
xml_write('test.xml', MyTree, {'MyTree', [], 'This is a global comment'}, Pref);
type('test.xml')

%%
% *Comments in XML top level (method #2)*
% This method adds an extra top layer to the struct 'tree' and sets
% "Pref.RootOnly = false", which informs the function about the extra 
% layer. Notice that RootName is also saved as a part of
% the 'tree', and does not have to be passed in separately.
MyTree=[];
MyTree.COMMENT = 'This is a global comment';
MyTree.MyTest.MyNumber = 13;
MyTree.MyTest.MyString = 'Hello World';
Pref=[]; Pref.RootOnly = false;
xml_write('test.xml', MyTree, [], Pref);
type('test.xml')
%%
% *Same operation using Apache Xerces XML engine*
Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
Pref.RootOnly  = false;
xml_write('test.xml', MyTree, [], Pref);
type('test.xml')

%% Write XML files with PROCESSING_INSTRUCTIONs 
% Insertion of Processing Instructions is done through use of special 
% PROCESSING_INSTRUCTION field, which stores the instruction string. The
% string has to be in 'target data' format separated by space.
MyTree=[];
MyTree.PROCESSING_INSTRUCTION = 'xml-stylesheet type="a" href="foo"';
MyTree.MyNumber = 13;
MyTree.MyString = 'Hello World';
xml_write('test.xml', MyTree);
type('test.xml')

%%
% *Same operation using Apache Xerces XML engine*
Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
xml_write('test.xml', MyTree, 'MyTree', Pref);
type('test.xml')

%%
% *PROCESSING_INSTRUCTIONs in XML top level (method #1)*
% This method uses cell array 
MyTree=[];
MyTree.MyNumber = 13;
MyTree.MyString = 'Hello World';
xml_write('test.xml', MyTree, {'MyTree', 'xml-stylesheet type="a" href="foo"'});
type('test.xml')
%%
% *Same operation using Apache Xerces XML engine*
Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
xml_write('test.xml', MyTree, {'MyTree', 'xml-stylesheet type="a" href="foo"'}, Pref);
type('test.xml')

%%
% *PROCESSING_INSTRUCTIONs in XML top level (method #2)*
% This method adds an extra top layer to the struct 'tree' and sets
% pref.RootOnly=false, which informs the function about the extra 
% layer. Notice that RootName is also saved as a part of
% the 'tree', and does not have to be passed in separately.
MyTree=[];
MyTree.PROCESSING_INSTRUCTION =  'xml-stylesheet type="a" href="foo"';
MyTree.MyTest.MyNumber = 13;
MyTree.MyTest.MyString = 'Hello World';
Pref=[]; Pref.RootOnly = false;
xml_write('test.xml', MyTree, [], Pref);
type('test.xml')
%%
% *Same operation using Apache Xerces XML engine*
Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
Pref.RootOnly  = false;
xml_write('test.xml', MyTree, 'MyTree', Pref);
type('test.xml')

%% Write XML files with CDATA Sections 
% "In an XML document a CDATA (Character DATA) section is a section of % element content that is marked for the parser to interpret as only % character data, not markup." (from Wikipedia) 
% To insert CDATA Sections one use special CDATA_SECTION field,
%  which stores the instruction string. Note that MATLAB's xmlwrite created
%  wrong xml code for CDATA section
MyTree=[];
MyTree.CDATA_SECTION = '<A>txt</A>';
MyTree.MyNumber = 13;
MyTree.MyString = 'Hello World';
xml_write('test.xml', MyTree);
type('test.xml')
%%
% *Same operation using Apache Xerces XML engine produces correct results*
Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
xml_write('test.xml', MyTree, 'MyTree', Pref);
type('test.xml')

%% Write XML files with special characters in TAG names
% The input to xml_write requires that all tags one wants in XML document 
% have to be encoded as field names of MATLAB's struct's. Matlab has a lot
% of restrictions on variable names. This section is about XML tags with
% names not allowed as MATLAB variables, or more specifically with
% characters allowed as xml tag names but not allowed as MATLAB variable
% names. Characters like that can be replaced by their hexadecimal
% representation just as it is done by genvarname function. Alternative way
% of writing the first example is:
MyTree=[];
MyTree.('MyNumber') = 13;               % same as MyTree.MyNumber = 13;
MyTree.MyString.CONTENT = 'Hello World';
MyTree.MyString.ATTRIBUTE.('Num') = 2;  % same as MyTree.MyString.ATTRIBUTE.Num = 2;
xml_write('test.xml', MyTree);
type('test.xml')

%%
% *This approach fails for some characters like dash '-', colon ':', and
% international characters.*
MyTree=[];
try
  MyTree.('My-Number') = 13;
  MyTree.MyString.CONTENT = 'Hello World';
  MyTree.MyString.ATTRIBUTE.('Num_锟�) = 2;
catch  %#ok<CTCH>
  err = lasterror; %#ok<LERR>
  disp(err.message);
end

%%
% It can be overcome by replacing offending characters with their 
% hexadecimal representation. That can be done manually or with use of 
% genvarname function. Note that MATLAB 'type' function does not show
% correctly '锟� letter in xml file, but opening the file in editor shows 
% that it is correct.
MyTree=[];
MyTree.(genvarname('My-Number')) = 13;
MyTree.MyString.CONTENT = 'Hello World';
MyTree.MyString.ATTRIBUTE.Num_0xF6 = 2;
gen_object_display(MyTree);
xml_write('test.xml', MyTree);
type('test.xml')

%%
% *Also two of the characters '-' and ':' can be encoded by a special strings:
% '_DASH_' and '_COLON_' respectively*
MyTree=[];
MyTree.My_DASH_Number = 13;
MyTree.MyString.CONTENT = 'Hello World';
MyTree.MyString.ATTRIBUTE.Num0xF6 = 2;
xml_write('test.xml', MyTree);
type('test.xml')

%% Write XML files with Namespaces
% No extra special fields are needed to define XML namespaces, only colon 
% character written using '0x3A' or '_COLON_'. Below is an
% example of a namespace definition
MyTree=[];
MyTree.f_COLON_child.ATTRIBUTE.xmlns_COLON_f = 'http://www.foo.com';
MyTree.f_COLON_child.f_COLON_MyNumber = 13;
MyTree.f_COLON_child.f_COLON_MyString = 'Hello World';
xml_write('test.xml', MyTree, 'MyTree');
type('test.xml')
%%
% *Same operation using Apache Xerces XML engine*
Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
xml_write('test.xml', MyTree, 'f_COLON_MyTree', Pref);
type('test.xml')

%% "Pref.KeepNS" flag in "xml_read"
% Thise option allow keeping  or exclusion of namespaces in tag names. 
% By default the namespace data is kept but it produces much longer field
% names in the output structure. Ignoring namespace will produce more
% readible output.
% Perform default read of file with namespace
tree = xml_read('test.xml');
gen_object_display(tree);

%%
% Now the same operation with KeepNS = false. 
Pref=[]; Pref.KeepNS = false; % do not read attributes
tree = xml_read('test.xml', Pref);
gen_object_display(tree);

%% Read XML files with special node types
% Display and read the file, then show the data structure. Note that 
% MATLAB 'type' function shows '锟� letter incorrectly as 'A锟� in xml file, 
% but opening the file in editor shows that it is correct.
fprintf('Test xml file:\n');
type('test_file.xml')
%%
% Read only the Root Element (default) 
[tree GlobalTextNodes] = xml_read('test_file.xml');
fprintf('Global Data (Root name, Global Processing Instructions and Global Comments):\n');
disp(GlobalTextNodes')
fprintf('\nStructure read from the file (uncludes COMMENT and CDATA sections):\n');
gen_object_display(tree);
%%
% Read the whole tree including global Comments and Processing Instructions
Pref=[]; Pref.RootOnly = false;
[tree GlobalTextNodes] = xml_read('test_file.xml', Pref);
fprintf('Global Data (Root name, Global Processing Instructions and Global Comments):\n');
disp(GlobalTextNodes')
fprintf('\nStructure read from the file (uncludes COMMENT and CDATA sections):\n');
gen_object_display(tree);

%% "Pref.ReadAttr" flag in "xml_read" (control handling of nodes with attributes)
% Those option allow exclusion of attributes 
Pref=[]; Pref.ReadAttr = false; % do not read attributes
tree = xml_read('test_file.xml', Pref);
gen_object_display(tree);

%% "Pref.ReadSpec" flag in "xml_read"
% Those option allow exclusion of special nodes, like
% comments, processing instructions, CData sections, etc.
Pref=[]; Pref.ReadSpec = false; % do not read special node types
tree = xml_read('test_file.xml', Pref);
gen_object_display(tree);

%% "Pref.RootOnly" flag in "xml_read"
% As it was shown in previous examples RootOnly parameter can be used to
% capture global (top level) special nodes (like COMMENTs and
% PROCESSING_INSTRUCTIONs) which are ignored by default
Pref=[]; Pref.RootOnly = false; % do not read special node types
tree = xml_read('test_file.xml', Pref);
gen_object_display(tree);

%% "Pref.RootOnly" flag in "xml_write"
% Writing previously read tree with default "Pref.RootOnly = true" gives
% wrong output file
Pref=[]; Pref.RootOnly = true; % do not read special node types
xml_write('test.xml', tree, [], Pref);
fprintf('Test xml file:\n');
type('test.xml')
%%
% Writing the same tree with "Pref.RootOnly = false" gives correct output
Pref=[]; Pref.RootOnly = false; % do not read special node types
xml_write('test.xml', tree, [], Pref);
fprintf('Test xml file:\n');
type('test.xml')

%% "Pref.NumLevels" flag in "xml_read"
% This parameter allows user to skip parts of the tree in order to save
% time and memory. Usefull only in a rare case when a small portion of
% large XML file is needed.
%
% Create test tile
MyTree = [];
MyTree.Level1 = 1;
MyTree.Level1_.Level2 = 2;
MyTree.Level1_.Level2_.Level3 = 3;
MyTree.Level1_.Level2_.Level3_.Level4 = 4;
xml_write('test.xml', MyTree);
fprintf('Test xml file:\n');
type('test.xml')
%%
% *Use Default ("Pref.NumLevels = infinity") setting*
tree = xml_read('test.xml');
gen_object_display(tree);
%%
% *Limit the read to only 2 levels*
Pref=[]; Pref.NumLevels = 2; 
tree = xml_read('test.xml', Pref);
gen_object_display(tree);




%% Create DOM object based on a Struct using "xml_write"
% *Create Struct tree*
MyTree=[];
MyTree.MyNumber = 13;
MyTree.MyString = 'Hello World';
%%
% *Convert Struct to DOM object using xml_write*
DOM = xml_write([], MyTree); 
xmlwrite('test.xml', DOM);   % Save DOM object using MATLAB function 
type('test.xml')

%% Convert DOM object to Struct using "xml_read"
DOM = xmlread('test.xml');       % Read DOM object using MATLAB function
[tree treeName] = xml_read(DOM); % Convert DOM object to Struct
disp([treeName{1} ' ='])
gen_object_display(tree)

%% Write XML file based on a DOM using "xml_write_xerces"
xmlwrite_xerces('test.xml', DOM); % Save DOM object using Xerces library 
type('test.xml')

%% Write XML to string instead of a file
DOM = xml_write([], MyTree);
str = xmlwrite(DOM);
disp(str)

%% Write XML file with embedded binary data encoded as Base64 (using java version)
fid = fopen('football.jpg', 'rb');       
raw1 = uint8(fread(fid, 'uint8'));                % read image file as a raw binary
fclose(fid);

MyTree=[];
MyTree.Size = 13;
MyTree.MyString = 'Hello World'; % simple case
MyTree.MyImage.ATTRIBUTE.EncodingMIMEType = 'base64';
MyTree.MyImage.CONTENT = base64encode(raw1,'java');% perform base64 encoding of the binary data
xml_write('test.xml', MyTree);             % write xml file

%% Read XML file with embedded binary data encoded as Base64 (using java version)
tree = xml_read('test.xml', Pref);         % read xml file
raw  = base64decode(tree.MyImage.CONTENT, '', 'java');   % convert xml image to raw binary
fid = fopen('MyFootball.jpg', 'wb');  
fwrite(fid, raw, 'uint8');                 % dumb the raw binary to the hard disk 
fclose(fid);
I = imread('MyFootball.jpg');              % read it as an image
imshow(I);

%% Write XML file with embedded binary data encoded as Base64 (simpler version using only matlab code
% Notice that process of writing to xml stripped all end-of-lie characters
% from base64 code.
isChunked = true; % break into chunks 76 characters long
url_safe  = true; % 'base64url' encoding
code = base64encode('license.txt', 'matlab', isChunked, url_safe);
disp(code)
MyTree=[];
MyTree.Size = 13;
MyTree.MyString = 'Hello World'; 
MyTree.MyImage.ATTRIBUTE.EncodingMIMEType = 'base64';
MyTree.MyImage.CONTENT = code;   % perform base64 encoding of the binary data
xml_write('test.xml', MyTree);   % write xml file
type('test.xml')

%% Read XML file with embedded binary data encoded as Base64 (simpler version using only matlab code
tree = xml_read('test.xml', Pref);         % read xml file
base64decode(tree.MyImage.CONTENT, 'license2.txt', 'matlab'); % save xml image as raw binary
type('license2.txt')