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160 lines
6.7 KiB
Matlab
160 lines
6.7 KiB
Matlab
% function used to correct the image orientation of mcs_mesh data.
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% [output, output_pos] = adjust_projection(input, snake_scan, fast_axis_x, positions)
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% input = data to be corrected. For mcs the data should be a 2D matrix.
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% snake_scan = 0 for off and 1 for on
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% fast_axis_x = 1 for fast axis along x, 0 for fast axis along y
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%
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% output = corrected data
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% output_pos = corrected output positions, could be used to see if
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% there was a problem with the correction
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% For snake scans the routine decides the flipping based on the positions
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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function [output, output_pos] = adjust_projection(input, snake_scan, fast_axis_x, positions)
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if nargin < 4
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positions = [];
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end
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output_temp = input;
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output_pos = positions;
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%%% Sanity checks %%%
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if ~isempty(output_pos)
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%%% fast axis direction %%%
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average_x_step_fast_axis = mean(mean(abs(diff(output_pos(:,:,1),1,1))));
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average_y_step_fast_axis = mean(mean(abs(diff(output_pos(:,:,2),1,1))));
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fast_axis_x_from_pos = fast_axis_x;
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if (fast_axis_x)&&(average_x_step_fast_axis < average_y_step_fast_axis)
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warning('You specified fast_axis_x true, but the positions seem to be for fast axis along y')
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fast_axis_x_from_pos = false;
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fast_axis_ind = 2;
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slow_axis_ind = 1;
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elseif (~fast_axis_x)&&(average_x_step_fast_axis > average_y_step_fast_axis)
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warning('You specified fast_axis_x false, but the positions seem to be for fast axis along x')
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fast_axis_x_from_pos = true;
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fast_axis_ind = 1;
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slow_axis_ind = 2;
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elseif fast_axis_x
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fast_axis_ind = 1;
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slow_axis_ind = 2;
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elseif ~fast_axis_x
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fast_axis_ind =2;
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slow_axis_ind = 1;
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end
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%%% Scan quality check %%%
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if ~any(output_pos(:)==0)
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aux_fast = abs(diff(output_pos(:,:,fast_axis_ind),1,1));
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aux_slow = abs(diff(output_pos(:,:,slow_axis_ind),1,2));
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average_fastaxis_absstep = mean(aux_fast(:));
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average_slowaxis_absstep = mean(aux_slow(:));
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std_fastaxis_absstep = std(aux_fast(:));
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std_slowaxis_absstep = std(aux_slow(:));
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step_text = sprintf('\n Step, (fast axis,slow axis) +/- (std,std) = (%.2f,%.2f) +/- (%.2f,%.2f) microns.',...
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average_fastaxis_absstep*1e3,average_slowaxis_absstep*1e3,std_fastaxis_absstep*1e3,std_slowaxis_absstep*1e3);
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if (std_fastaxis_absstep>average_fastaxis_absstep*0.05)||(std_slowaxis_absstep>average_slowaxis_absstep*0.05)
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warning(step_text)
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pause(2)
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else
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if nargout>1
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disp(step_text);
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end
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end
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end
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%%% snake scans %%%
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average_fastaxis_step = mean(diff(output_pos(:,:,fast_axis_ind),1,1));
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% is this a snake scan?
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if abs(average_fastaxis_step(2)-average_fastaxis_step(3))==0
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% Do nothing, data has not been loaded
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snake_scan_from_pos = snake_scan;
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elseif abs(average_fastaxis_step(2)-average_fastaxis_step(3))>abs(average_fastaxis_step(1))
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snake_scan_from_pos = true;
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else
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snake_scan_from_pos = false;
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end
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if snake_scan ~= snake_scan_from_pos
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warning(['You specified snake_scan = ' num2str(snake_scan) ' but from the positions it seems that snake_scan = ' num2str(snake_scan_from_pos)])
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end
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end
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%%% Handling the flipping of the data %%%
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if snake_scan %
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startflipind = 1;
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if ~isempty(output_pos)
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if mean(diff(output_pos(:,1,fast_axis_ind),1,1))>0
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startflipind = 2;
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else
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startflipind = 1;
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end
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output_pos(:,startflipind:2:end,:) = flipud(output_pos(:,startflipind:2:end,:));
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end
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output_temp(:,startflipind:2:end,:,:) = flipud(output_temp(:,startflipind:2:end,:,:));
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end
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if fast_axis_x
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output_temp = permute(output_temp,[2 1 3]);
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output_pos = permute(output_pos, [2 1 3]);
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end
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output = rot90(output_temp,2);
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output_pos = rot90(output_pos,2);
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% if ~isempty(output_pos)
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% if (mean(mean(diff(output_pos(:,:,1),1,2)))>0)||(mean(mean(diff(output_pos(:,:,2),1,2)))>0)
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% warning('Something is wrong with the positions, I dont know what so Ill show you in a figure of the positions after adjusting them. Positions should monotonically decrease with increase x or y coordinate')
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% figure(123)
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% subplot(1,2,1)
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% imagesc(output_pos(:,:,1))
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% title('X position')
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% subplot(1,2,2)
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% imagesc(output_pos(:,:,2))
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% title('Y position')
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% end
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% end
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return
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