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user documentation on sqw_op and sqw_op_bin_pixels #1891

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301a4e9
Re #1844 minor comments to the documentation
abuts Jul 23, 2025
ef3f853
Re #1844 minor comments and improvements to the doc
abuts Jul 24, 2025
04e574b
Merge branch '1844_sqw_op_and_bin_doc' of https://github.com/abuts/Ho…
abuts Jul 24, 2025
f037d11
Re #1844 minor typo
abuts Nov 12, 2025
a32d113
Re #1844 autocr/lf changes
abuts Jan 12, 2026
1587c4a
Re #1844 Merge branch 'master' into 1844_sqw_op_and_bin_doc
abuts Jan 12, 2026
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39 changes: 7 additions & 32 deletions admin/make_horace_distribution_kit.m
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Original file line number Diff line number Diff line change
Expand Up @@ -3,15 +3,12 @@ function make_horace_distribution_kit(varargin)
% Horace to work into single zip file
%
%Usage:
%>>make_horace_distribution_kin(['-reveal_code','-compact'])
%>>make_horace_distribution_kin(['-compact'])
%
%where optional arguments are:
%'-reveal_code' -- if present, do not request p-code Horace; default pCode
% the private Horace folders
%'-compact' -- if present, request dropping the demo and test files
% with test folders, default -- compress demo and tests
% together with main code.
%'-noherbert' -- do not pack Herbert together with Horace
%
% excludes (not copies to distribution) all files and subfolders of a folder where
% _exclude_all.txt file is found
Expand All @@ -30,8 +27,6 @@ function make_horace_distribution_kit(varargin)
% after renaming the file Horace_on.m.template to horace_on.m.
%
%
% $Revision:: 1759 ($Date:: 2020-02-10 16:06:00 +0000 (Mon, 10 Feb 2020) $)
%
%
% known keys
options = {'-reveal_code','-compact','-noherbert'};
Expand All @@ -40,7 +35,7 @@ function make_horace_distribution_kit(varargin)
error('MAKE_HORACE_DISTRIBUTION_KIT:invalid_argument',err_mess);
end% default key values
%
common_files_to_distribute = {'LICENSE','README.md','CMakeLists.txt'};
common_files_to_distribute = {'LICENSE','README.md','CMakeLists.txt','VERSION'};

pths = horace_paths;
hor_root_dir = pths.root; % MUST have rootpath so that horace_init, horace_off are included
Expand All @@ -67,16 +62,13 @@ function make_horace_distribution_kit(varargin)

% copy everything, which can be found core Horace folder
copy_files_list(fullfile(hor_root_dir,'horace_core'),fullfile(horace_targ_dir,'horace_core'),'+_');
copy_files_list(fullfile(hor_root_dir,'herbert_core'),fullfile(horace_targ_dir,'herbert_core'),'+_');
% copy source code files from system directory
copy_files_list(fullfile(hor_root_dir,'_LowLevelCode'),fullfile(horace_targ_dir,'_LowLevelCode'),...
'+_','h','cpp','c','sln','vcproj');
copy_files_list(fullfile(hor_root_dir,'admin'),fullfile(horace_targ_dir,'admin'));
copy_files_list(fullfile(hor_root_dir,'cmake'),fullfile(horace_targ_dir,'cmake'));
%
hor_on_template = fullfile(horace_targ_dir,'admin','horace_on.m.template');
copyfile(hor_on_template,fullfile(target_Dir,'horace_on.m.template'),'f');
delete(hor_on_template);
%
common_files_to_distribute = cellfun(@(x)(fullfile(hor_root_dir,x)),common_files_to_distribute,...
'UniformOutput',false);
for i=1:numel(common_files_to_distribute)
Expand All @@ -92,36 +84,19 @@ function make_horace_distribution_kit(varargin)
% if necessary, copy demo and test folders
if ~no_demo
% copy source code files from system directory
copy_files_list(fullfile(hor_root_dir,'_test'),fullfile(horace_targ_dir,'_test'),'+_')
copy_files_list(fullfile(hor_root_dir,'demo'),fullfile(horace_targ_dir,'demo'),'+_')
copy_files_list(fullfile(hor_root_dir,'_test'),fullfile(horace_targ_dir,'_test'),'+_');
copy_files_list(fullfile(hor_root_dir,'demo'),fullfile(horace_targ_dir,'demo'),'+_');
end
%
disp('! The HORACE program files collected successfully ==============!')
if(~reveal_code)
disp('! p-coding private Horace parts and deleting unnecessary folders=!')
pCode_Horace_kit(fullfile(horace_targ_dir,'horace_core'));
disp('! Horace p-coding completed =====================================!')
end

% if Herbert used, add Herbert distribution kit to the distribution
if ~no_herbert
argi{1}='-run_by_horace';
if ~no_demo
argi{2} = '-full';
end
make_herbert_distribution_kit(target_Dir,argi{:});
pref='';
else
pref='_only';
end
%
%
disp('! Start compressing all necessary files together ================!')
%
if no_demo
horace_file_name=['Horace',pref,'_nodemo.zip'];
horace_file_name='Horace_nodemo_distribution_kit.zip';
else
horace_file_name= ['horace',pref,'_distribution_kit.zip'];
horace_file_name= 'Horace_distribution_kit.zip';
end
horace_file_name=fullfile(current_dir,horace_file_name);
if(exist(horace_file_name,'file'))
Expand Down
21 changes: 12 additions & 9 deletions documentation/user_docs/docs/manual/Generic_Transformation.rst
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Expand Up @@ -3,10 +3,10 @@ Generic Transformations
#######################

The previous chapters describe how one may do various
:doc:`unary </manual/Unary_operations>` or :doc:`binary operations </manual/Binary_operations>` over your data or build analytical model and :doc:`simulate it over whole sqw file </manual/Simulation>`.
:doc:`unary </manual/Unary_operations>` or :doc:`binary operations </manual/Binary_operations>` over your data, apply :doc:`symmetry operations </manual/Symmetrising_etc>` or build analytical model and :doc:`simulate it over whole sqw file </manual/Simulation>`.
As whole ``sqw`` file can not be generally placed in memory, all these operations are
based on special ``PageOp`` family of algorithms, which operate loading a page of data in memory
and applying various operations to these data. For :doc:`unary </manual/Unary_operations>` and :doc:`binary </manual/Binary_operations>` operations we wrote these transformations for users and the ``sqw_eval`` algorithm from :doc:`Simulation </manual/Simulation>` section
and applying various operations to these data. For :doc:`unary </manual/Unary_operations>`, :doc:`binary </manual/Binary_operations>` and :doc:`symmetry operations </manual/Symmetrising_etc>` we wrote these transformations for users and the ``sqw_eval`` algorithm from :doc:`Simulation </manual/Simulation>` section
gives user a set of rules to write his own model in `hklE` coordinate system and apply it to whole ``sqw`` object.

Introduction
Expand Down Expand Up @@ -106,9 +106,9 @@ This is simple code, but if your objects are filebased, this will requests two s
function output_sig_err = sqw_op_unary(in_page_op,varargin)
% Apply two simple transformations of signal of an sqw object in one go.

data = in_page_op.data; % get access to page of pixel data
data(8,:) = 2*data-1; % change pixel data signal by multiplying it by 2 and extracting 1
output_sig_err = data(8:9,:); % combine signal and unchanged error into form, requested by algorithm
data = in_page_op.data; % get access to page of pixel data
data(8,:) = 2*data(8,:)-1; % change pixel data signal by multiplying it by 2 and extracting 1
output_sig_err = data(8:9,:); % extract signal and unchanged error into form, requested by algorithm
end

and apply ``sqw_op`` algorithm:
Expand Down Expand Up @@ -184,7 +184,8 @@ The page-function with actually used to remove background in the code above is:
% As this is special projection, it needs 5 rows of pixel data (needs run_id)
% rather then the standard projection, which takes 4 rows.
pix = bg_data.proj.transform_pix_to_img(data(1:5,:)); % you may define your own
% complex transformation to convert pixels in Cry
% complex transformation to convert pixels from Crystal Cartesian coordinates to
% image coordinates, but here you have your projection already defined to do that.

% interpolate background signal on the pixels coordinates expressed
% in instrument coordinate system.
Expand Down Expand Up @@ -221,7 +222,7 @@ Let's assume you are interested in magnetic signal which is present at relativel
:alt: Sample differential cross-section measured on MAPS

Sample differential cross-section measured on MAPS and showing
magnetic signal within read-cycle surrounded area and background signal (phonons)
magnetic signal within red-cycle surrounded area and background signal (phonons)
inside and outside of this area. Yellow box represents double-size Brillouin zone where
data moved using shift operation and its top right quadrant -- the area where data should
be finally moved using folding and reflection.
Expand Down Expand Up @@ -404,7 +405,8 @@ The similarities and differences between these two algorithms are summarized in
| | | operations | |
+---------+--------------------------+------------------------------+-------------------------------------------+
| 2 | Multiple transformations | Not allowed | simple modifications to standard script |
| | applied to single data | | |
| | applied to symmetrized | | |
| | data | | |
+---------+--------------------------+------------------------------+-------------------------------------------+
| 3 | Include same pixels from | No. Efficient exclusion | request complex coding. Probably |
| | multiple symmetry op. | algorithm | not very efficient but possible. |
Expand Down Expand Up @@ -484,7 +486,8 @@ Simplest form of the function, which allows combining multiple cuts into single
% into coordinate system, related to target projection
for i=1:numel(proj_array)
% input projections used for cut do not have lattice set up for them.
% They need lattice so let's set it up here.
% They need lattice to be fully defined and use projection methods so let's set it up here.
% may be taken out of loop for performance though it is fast anyway.
proj_array(i).alatt = targ_proj.alatt;
proj_array(i).angdeg = targ_proj.angdeg;
% transform momentum transfer values from current page of data into
Expand Down