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Commit cfdea3e1 authored by Wolfgang Ludwig's avatar Wolfgang Ludwig
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Change xop default directory path 


Signed-off-by: default avatarWolfgang Ludwig <wolfgang.ludwig@esrf.fr>
parent 78e3f1e4
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zUtil_Cryst/gtCrystXopInitializeDirectory.m
+ 3
− 3
View file @ cfdea3e1
......@@ -10,9 +10,9 @@ function [xop_dir,msg] = gtCrystXopInitializeDirectory(name, material)
% xop_dir = the name of the directory created
%
top_xop_dir=fullfile('/data','id11','graintracking','file_xop');
dataset_xop_dir=fullfile('/data','id11','graintracking','file_xop', name);
material_xop_dir=fullfile('/data','id11','graintracking','file_xop', name, material);
top_xop_dir=fullfile('/data','id11','archive','file_xop');
dataset_xop_dir=fullfile('/data','id11','archive','file_xop', name);
material_xop_dir=fullfile('/data','id11','archive','file_xop', name, material);
% create top level directory if needed
if ~exist(top_xop_dir,'dir')
......
zUtil_GUI/inputwdefaultnumeric.m
+ 1
− 1
View file @ cfdea3e1
......@@ -9,5 +9,5 @@ function answer = inputwdefaultnumeric(question, default)
% OUTPUT:
% answer = <double> User input (take the default one if empty)
answer = inputwdefault(question, default, true);
answer = str2num(inputwdefault(question, default));
end
zUtil_Imaging/gtCheckSegmentation.m
+ 10
− 8
View file @ cfdea3e1
......@@ -23,19 +23,21 @@ function gtCheckSegmentation(imnum,parameters,clims)
cont=bwperim(spots);
cont=bwmorph(cont,'dilate');
cont=255*uint8(cont);
cont(:,:,2:3)=0;
cont=double(cont);
%cont(:,:,2:3)=0;
full=mat2gray(full,clims);
figure();
h=imshow(full);
h=imshow(full-cont,clims);
set(gcf,'Renderer','OpenGL');
hold on;
imshow(cont);
hold off;
set(h,'Alphadata',0.3);
% set(gcf,'Renderer','OpenGL');
% hold on;
% imshow(cont);
% hold off;
% set(h,'Alphadata',0.3);
end
......
zUtil_Topotomo/calc_pole_tilts_id06.m 0 → 100644
+ 110
− 0
View file @ cfdea3e1
function [phx, phy] = calc_pole_tilts_id11(im1, im2)
% position a given reflection in the pole
% modified for ID11 goniometer: W. Ludwig, March 2014
% input parameters:
disp('this version assumes that the lower tilt (SAMRY) of the goniometer is at 0 position and aligned with Lab X at diffrz = 0 !')
basedir = '/data/id11/inhouse/align';
prefix = 'spot_';
[im1, info1] = edf_read('%s/%s_%04d.edf', basedir, prefix, close);
[im2, info2] = edf_read('%/%s_%04d.edf', basedir, prefix, far);
diffrz_offset = -90;
ps = 0.0014 % pixelsize in mm
dist = 6.3;
figure(1); imshow(im1 + im2, []);
[u, v] = ginput(2);
pos1 = [-dist, -u(1) * ps, v(1) * ps];
pos2 = [ dist, -(2048-u(2)) * ps, v(2) * ps];
dx = pos2 - pos1;
%--------------------------------------------------------------------------
energy = parameters.acq.energy; % keV.
lambda = gtConvEnergyToWavelength(energy);
hkl = [1 1 1];
a = 4.05; % Al lattice spacing....
theta = asind(lambda*norm(hkl)/2/a);
tth = 2 * theta
% Coordinate systems are identical to 3DXRD convensions.
% All rotation matrices are right hand rotations.
eta_measured = atand(dx(2)/dx(3))
tth_measured = atand( sqrt(dx(2)^2 + dx(3)^2) / dx(1) )
% output parameters:
% phi_x_final (deg) : final setting for x-Tilt
% phi_y_final (deg) : final setting for y-Tilt
% --------------------------------------------------------------------
diffrz = info1.motor.diffrz + diffrz_offset;
diffry = info1.motor.diffry;
samrx = info1.motor.samrx;
samry = info1.motor.samry;
%% Laboratory Reference defined by X beam (X along beam) and gravity (negative Z)
% Coincicent with sample reference system for omega = 0 (diffrz = -90)
LabX = [1 0 0]';
LabY = [0 1 0]';
LabZ = [0 0 1]';
%% Instrument reference system
% Coincident with Sample system for diffrz = -90 since we run scans from diffrz: -90 to 270 degre
instrgeo.dirx = [ 1 0 0];
instrgeo.diry = [ 0 1 0];
instrgeo.dirz = [ 0 0 1];
%% Sample reference system
samgeo.dirx = [0 -1 0];
samgeo.diry = [1 0 0];
samgeo.dirz = [0 0 1];
%% Rotation Matrix (based on angle & axis -> Rodrigues Rotation Formula) v_rotated = R(angle, axis) * v
R = @(angle,axis)gtMathsRotationTensor(angle, gtMathsRotationMatrixComp(axis, 'col'));
% Plane normal in Sample Reference system
% G = cosd(tth_measured/2)*[-tand(tth_measured/2) -sind(eta_measured) cosd(eta_measured)];
% G_sam = R(-samry, LabY) * R(-diffrz, LabZ) * R(-diffry, LabY) * G; % rotate SAMRY back to 0: SAMRX will now rotate around Lab X
%% GInstr = Plane normal in Instrument reference system:
% samrx is upper tilt and rotates around LabX at diffrz = 0 (omega = 90)
% ramry is lower tile and rotates around LabY at diffrz = 0 (omega = 90)
G_instr = gtGeoSam2Sam(G_sam, samgeo, instrgeo, 1, 1);
% first solve for upper tilt: RX * G_sam = [r 0 s] -> G_sam(2)*cos(phx) - G_sam(3)*sin(phx) = 0
phx = atand(G_instr(2)/G_instr(3));
tmp = R(phx, LabX) * G_instr';
% now solve for lower tilt: RY * tmp = [0 0 1], RY = [cos(phy) 0 sin(phy); 0 1 0; -sin(phy) 0 cos(phy)]; ->
% phy = atand(-tmp(1)/tmp(3));
phy = atand(-tmp(1)/tmp(3)) ;
G_aligned = R(phy, LabY) * tmp;
['mvr samrx ',num2str(phx)]
['mvr samry ',num2str(phy)]
zUtil_Topotomo/calc_pole_tilts_id11.m 0 → 100644
+ 110
− 0
View file @ cfdea3e1
function [phx, phy] = calc_pole_tilts_id11(im1, im2)
% position a given reflection in the pole
% modified for ID11 goniometer: W. Ludwig, March 2014
% input parameters:
disp('this version assumes that the lower tilt (SAMRY) of the goniometer is at 0 position and aligned with Lab X at diffrz = 0 !')
basedir = '/data/id11/inhouse/align';
prefix = 'spot_';
[im1, info1] = edf_read('%s/%s_%04d.edf', basedir, prefix, close);
[im2, info2] = edf_read('%/%s_%04d.edf', basedir, prefix, far);
diffrz_offset = -90;
ps = 0.0014 % pixelsize in mm
dist = 6.3;
figure(1); imshow(im1 + im2, []);
[u, v] = ginput(2);
pos1 = [-dist, -u(1) * ps, v(1) * ps];
pos2 = [ dist, -(2048-u(2)) * ps, v(2) * ps];
dx = pos2 - pos1;
%--------------------------------------------------------------------------
energy = parameters.acq.energy; % keV.
lambda = gtConvEnergyToWavelength(energy);
hkl = [1 1 1];
a = 4.05; % Al lattice spacing....
theta = asind(lambda*norm(hkl)/2/a);
tth = 2 * theta
% Coordinate systems are identical to 3DXRD convensions.
% All rotation matrices are right hand rotations.
eta_measured = atand(dx(2)/dx(3))
tth_measured = atand( sqrt(dx(2)^2 + dx(3)^2) / dx(1) )
% output parameters:
% phi_x_final (deg) : final setting for x-Tilt
% phi_y_final (deg) : final setting for y-Tilt
% --------------------------------------------------------------------
diffrz = info1.motor.diffrz + diffrz_offset;
diffry = info1.motor.diffry;
samrx = info1.motor.samrx;
samry = info1.motor.samry;
%% Laboratory Reference defined by X beam (X along beam) and gravity (negative Z)
% Coincicent with sample reference system for omega = 0 (diffrz = -90)
LabX = [1 0 0]';
LabY = [0 1 0]';
LabZ = [0 0 1]';
%% Instrument reference system
% Coincident with Sample system for diffrz = -90 since we run scans from diffrz: -90 to 270 degre
instrgeo.dirx = [ 1 0 0];
instrgeo.diry = [ 0 1 0];
instrgeo.dirz = [ 0 0 1];
%% Sample reference system
samgeo.dirx = [0 -1 0];
samgeo.diry = [1 0 0];
samgeo.dirz = [0 0 1];
%% Rotation Matrix (based on angle & axis -> Rodrigues Rotation Formula) v_rotated = R(angle, axis) * v
R = @(angle,axis)gtMathsRotationTensor(angle, gtMathsRotationMatrixComp(axis, 'col'));
% Plane normal in Sample Reference system
% G = cosd(tth_measured/2)*[-tand(tth_measured/2) -sind(eta_measured) cosd(eta_measured)];
% G_sam = R(-samry, LabY) * R(-diffrz, LabZ) * R(-diffry, LabY) * G; % rotate SAMRY back to 0: SAMRX will now rotate around Lab X
%% GInstr = Plane normal in Instrument reference system:
% samrx is upper tilt and rotates around LabX at diffrz = 0 (omega = 90)
% ramry is lower tile and rotates around LabY at diffrz = 0 (omega = 90)
G_instr = gtGeoSam2Sam(G_sam, samgeo, instrgeo, 1, 1);
% first solve for upper tilt: RX * G_sam = [r 0 s] -> G_sam(2)*cos(phx) - G_sam(3)*sin(phx) = 0
phx = atand(G_instr(2)/G_instr(3));
tmp = R(phx, LabX) * G_instr';
% now solve for lower tilt: RY * tmp = [0 0 1], RY = [cos(phy) 0 sin(phy); 0 1 0; -sin(phy) 0 cos(phy)]; ->
% phy = atand(-tmp(1)/tmp(3));
phy = atand(-tmp(1)/tmp(3)) ;
G_aligned = R(phy, LabY) * tmp;
['mvr samrx ',num2str(phx)]
['mvr samry ',num2str(phy)]
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