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Commit 10291599 authored by Wolfgang Ludwig's avatar Wolfgang Ludwig
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Support for carrying over en existing parameter file 

Signed-off-by: default avatarWolfgang Ludwig <wolfgang.ludwig@esrf.fr>
parent 67f7cfa8
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1_preprocessing/gtFindDirectBeamBB.m
+ 192
− 179
View file @ 10291599
......@@ -22,205 +22,218 @@ function bbdir = gtFindDirectBeamBB(acq)
% to be more tolerant of missing images
% (incorporating Sabine's modifications for interlaced scans)
%
% Version 003 March 2020 by W Ludwig
% now allows checking an existing bounding box.
%
% Operates at the start of preprocessing, so images have been undistorted and
% interlaced images renamed, and placed in the 0_rawdata/scanname/ folder
%
%
refarea = 100;
refarea = 200;
lim_directbeam = 0.4;
ref = get_refimage(acq);
disp(' ');
disp('Determining direct beam bounding box...');
disp(' ');
% get the first reference image
name1 = fullfile(acq.dir,'0_rawdata',acq.name,'refHST0000.edf');
name2 = fullfile(acq.dir,'0_rawdata',acq.name,'ref0000_0000.edf');
if exist(name1, 'file')
ref0 = edf_read(name1);
elseif exist(name2, 'file')
ref0 = edf_read(name2);
if ~isempty(acq.bbdir)
bbdir = display_bbdir(acq, acq.bbdir, ref);
else
disp('No initial reference image found!');
ref0 = [];
end
disp(' ');
disp('Determining direct beam bounding box...');
disp(' ');
% if possible get the last reference image
% after renaming of interlaced scans, so no special naming conventions
if strcmp(acq.type, '360degree')
totproj = 2*acq.nproj;
elseif strcmp(acq.type, '180degree')
totproj = acq.nproj;
else
gtError('ACQ:invalid_parameter', ...
'Unknown type of scan: "%s". Check parameters.acq.type!', acq.type);
end
name1 = fullfile(acq.dir, '0_rawdata', acq.name, sprintf('refHST%04d.edf', totproj));
name2 = fullfile(acq.dir, '0_rawdata', acq.name, sprintf('ref0000_%04d.edf', totproj));
if exist(name1, 'file')
ref1 = edf_read(name1);
elseif exist(name2, 'file')
ref1 = edf_read(name2);
else
disp('No final reference image found...');
ref1 = [];
end
% calculate mean value m in central part of the image
m = gtImgMeanValue(ref(round(acq.ydet/2-refarea:acq.ydet/2+refarea+1), ...
round(acq.xdet/2-refarea:acq.xdet/2+refarea+1)));
cen = double(ref > (lim_directbeam*m)); % should correspond to direct beam footprint
% find the direct beam region bb automatically (supposes fairly homogeneous
% beam profile - attention with ID11 data here... !
marker = zeros(acq.ydet, acq.xdet);
marker(round(acq.ydet/2), round(acq.xdet/2)) = 1;
cen = imreconstruct(marker, cen);
tmp = regionprops(cen, 'BoundingBox');
if isempty(tmp)
disp('Please select (zoom onto) the direct beam area and disable zoom afterwards');
hfig = figure('name', 'Direct beam bounding box');
colormap gray;
imagesc(ref);
drawnow;
h = zoom(hfig); set(h, 'Enable', 'on'); waitfor(h, 'Enable', 'off'), hold on;
disp('-> Now click top-left and bottom-right corners for final selection');
bbdir = ginput(2);
bbdir = round([bbdir(1, 1) bbdir(1, 2) bbdir(2, 1)-bbdir(1, 1)+1 bbdir(2, 2)-bbdir(1, 2)+1]);
% Make sure the bbox width and height are even numbers (needed for correlation)
bbdir(3:4) = ceil(bbdir(3:4)/2)*2;
cen = gtPlaceSubImage(ones(bbdir(4),bbdir(3)), zeros(acq.ydet, acq.xdet), bbdir(1), bbdir(2));
else
bbdir = tmp.BoundingBox;
end
% get dark image
darkname = fullfile(acq.dir,'0_rawdata',acq.name,'dark.edf');
if exist(darkname, 'file')
d = edf_read(darkname);
%shouldn't need these work arounds
% elseif exist('darkend0000.edf', 'file')
% % try to make it
% d = edf_read('darkend0000.edf')/acq.ndark;
% else
% % work around
% d = ones(size(ref0))*median(ref0(:));
end
% Tighten bb until it's fully filled
bbdir = [ceil(bbdir(1:2)), bbdir(3:4)-1];
goon = true;
while goon
cenbb = gtCrop(cen, bbdir);
goon = false;
if any(~cenbb(:, 1)) % tighten bb on the left
bbdir(1) = bbdir(1)+1;
bbdir(3) = bbdir(3)-1;
goon = true;
end
if any(~cenbb(:, end)) % tighten bb on the right
bbdir(3) = bbdir(3)-1;
goon = true;
end
cenbb = gtCrop(cen, bbdir);
if any(~cenbb(1, :)) % tighten bb at the top
bbdir(2) = bbdir(2)+1;
bbdir(4) = bbdir(4)-1;
goon = true;
end
if any(~cenbb(end, :)) % tighten bb at the bottom
bbdir(4) = bbdir(4)-1;
goon = true;
end
end
% apply dark image
if ~isempty(ref0)
ref0 = ref0-d;
end
if ~isempty(ref1)
ref1 = ref1-d;
end
% Loosen bb if it can be on any side
goon = true;
while goon
goon = false;
tmpbb = bbdir+[-1 0 1 0]; % loose bb on the left
tmpim = gtCrop(cen, tmpbb);
if all(tmpim(:))
bbdir = tmpbb;
goon = true;
end
tmpbb = bbdir+[0 0 1 0]; % loose bb on the right
tmpim = gtCrop(cen, tmpbb);
if all(tmpim(:))
bbdir = tmpbb;
goon = true;
end
tmpbb = bbdir+[0 -1 0 1]; % loose bb at the top
tmpim = gtCrop(cen, tmpbb);
if all(tmpim(:))
bbdir = tmpbb;
goon = true;
end
tmpbb = bbdir+[0 0 0 1]; % loose bb at the bottom
tmpim = gtCrop(cen, tmpbb);
if all(tmpim(:))
bbdir = tmpbb;
goon = true;
end
end
%take the minimum of the two references if available
if (~isempty(ref0) && ~isempty(ref1))
ref = min(ref0, ref1); % min of ref-s at beginning and end of scan
elseif (~isempty(ref0))
ref = ref0;
else % no images found!
disp('%%%%%%% missing images %%%%%%%%');
disp('no reference images found in this directory!');
disp('using a default guess');
disp('%%%%%%% missing images %%%%%%%%');
disp(' ');
bbdir = [512 512 1024 1024];
return
% make sure the bbox width and height are even numbers (needed for correlation)
bbdir(3:4) = ceil(bbdir(3:4)/2)*2;
bbdir = display_bbdir(acq, bbdir, ref);
end
end % end of function
% calculate mean value m in central part of the image
m = gtImgMeanValue(ref(round(acq.ydet/2-refarea:acq.ydet/2+refarea+1), ...
round(acq.xdet/2-refarea:acq.xdet/2+refarea+1)));
cen = double(ref > (lim_directbeam*m)); % should correspond to direct beam footprint
% find the direct beam region bb automatically (supposes fairly homogeneous
% beam profile - attention with ID11 data here... !
marker = zeros(acq.ydet, acq.xdet);
marker(round(acq.ydet/2), round(acq.xdet/2)) = 1;
cen = imreconstruct(marker, cen);
tmp = regionprops(cen, 'BoundingBox');
bbdir = tmp.BoundingBox;
% Tighten bb until it's fully filled
bbdir = [ceil(bbdir(1:2)), bbdir(3:4)-1];
goon = true;
while goon
cenbb = gtCrop(cen, bbdir);
goon = false;
if any(~cenbb(:, 1)) % tighten bb on the left
bbdir(1) = bbdir(1)+1;
bbdir(3) = bbdir(3)-1;
goon = true;
end
if any(~cenbb(:, end)) % tighten bb on the right
bbdir(3) = bbdir(3)-1;
goon = true;
end
cenbb = gtCrop(cen, bbdir);
if any(~cenbb(1, :)) % tighten bb at the top
bbdir(2) = bbdir(2)+1;
bbdir(4) = bbdir(4)-1;
goon = true;
end
if any(~cenbb(end, :)) % tighten bb at the bottom
bbdir(4) = bbdir(4)-1;
goon = true;
function bbdir = display_bbdir(acq, bbdir, ref)
hfig = figure('name', 'Direct beam bounding box');
% plot bbox found, its center-line and center-line of image
bbcenter_abs = ((2*bbdir(1))+bbdir(3)-1)/2;
colormap gray;
imagesc(ref);
drawnow;
hold on;
plot([bbdir(1), bbdir(1)+bbdir(3)-1, bbdir(1)+bbdir(3)-1, bbdir(1), bbdir(1)], [bbdir(2), bbdir(2), bbdir(2)+bbdir(4)-1, bbdir(2)+bbdir(4)-1, bbdir(2)], 'r-');
plot([acq.xdet/2+0.5 acq.xdet/2+0.5], [1 acq.ydet], 'b-.'); % centre of the ccd
plot([bbcenter_abs bbcenter_abs], [bbdir(2) bbdir(2)+bbdir(4)-1], 'c-.'); % centre of the direct beam
% interactive check
questionMsg = 'Are you satisfied with this bounding box for the direct beam? [y/n]';
while (strcmpi(inputwdefault(questionMsg, 'n'), 'n'))
disp('Please select (zoom onto) the direct beam area and disable zoom afterwards');
figure(hfig), clf, imagesc(ref), h = zoom(hfig); set(h, 'Enable', 'on'); waitfor(h, 'Enable', 'off'), hold on;
disp('-> Now click top-left and bottom-right corners for final selection');
bbdir = ginput(2);
bbdir = round([bbdir(1, 1) bbdir(1, 2) bbdir(2, 1)-bbdir(1, 1)+1 bbdir(2, 2)-bbdir(1, 2)+1]);
% Make sure the bbox width and height are even numbers (needed for correlation)
bbdir(3:4) = ceil(bbdir(3:4)/2)*2;
% Plot the new bounding box
plot([bbdir(1), bbdir(1)+bbdir(3)-1, bbdir(1)+bbdir(3)-1, bbdir(1), bbdir(1)], [bbdir(2), bbdir(2), bbdir(2)+bbdir(4)-1, bbdir(2)+bbdir(4)-1, bbdir(2)], 'r-');
bbcenter_abs = ((2*bbdir(1))+bbdir(3)-1)/2;
plot([acq.xdet/2+0.5 acq.xdet/2+0.5], [1 acq.ydet], 'b-.');
plot([bbcenter_abs bbcenter_abs], [bbdir(2) bbdir(2)+bbdir(4)-1], 'c-.'); % centre of the direct beam
end
close(hfig);
end
% Loosen bb if it can be on any side
goon = true;
while goon
goon = false;
tmpbb = bbdir+[-1 0 1 0]; % loose bb on the left
tmpim = gtCrop(cen, tmpbb);
if all(tmpim(:))
bbdir = tmpbb;
goon = true;
function ref = get_refimage(acq)
% get dark image
darkname = fullfile(acq.dir,'0_rawdata',acq.name,'dark.edf');
if exist(darkname, 'file')
d = edf_read(darkname);
end
tmpbb = bbdir+[0 0 1 0]; % loose bb on the right
tmpim = gtCrop(cen, tmpbb);
if all(tmpim(:))
bbdir = tmpbb;
goon = true;
% get the first reference image
name1 = fullfile(acq.dir,'0_rawdata',acq.name,'refHST0000.edf');
name2 = fullfile(acq.dir,'0_rawdata',acq.name,'ref0000_0000.edf');
if exist(name1, 'file')
ref0 = edf_read(name1) - d;
elseif exist(name2, 'file')
ref0 = edf_read(name2) - d;
else
disp('No initial reference image found!');
ref0 = [];
end
tmpbb = bbdir+[0 -1 0 1]; % loose bb at the top
tmpim = gtCrop(cen, tmpbb);
if all(tmpim(:))
bbdir = tmpbb;
goon = true;
% if possible get the last reference image
% after renaming of interlaced scans, so no special naming conventions
if strcmp(acq.type, '360degree')
totproj = 2*acq.nproj;
elseif strcmp(acq.type, '180degree')
totproj = acq.nproj;
else
gtError('ACQ:invalid_parameter', ...
'Unknown type of scan: "%s". Check parameters.acq.type!', acq.type);
end
tmpbb = bbdir+[0 0 0 1]; % loose bb at the bottom
tmpim = gtCrop(cen, tmpbb);
if all(tmpim(:))
bbdir = tmpbb;
goon = true;
name1 = fullfile(acq.dir, '0_rawdata', acq.name, sprintf('refHST%04d.edf', totproj));
name2 = fullfile(acq.dir, '0_rawdata', acq.name, sprintf('ref0000_%04d.edf', totproj));
if exist(name1, 'file')
ref1 = edf_read(name1) - d;
elseif exist(name2, 'file')
ref1 = edf_read(name2) - d;
else
disp('No final reference image found...');
ref1 = [];
end
end
% make sure the bbox width and height are even numbers (needed for correlation)
bbdir(3:4) = ceil(bbdir(3:4)/2)*2;
% plot bbox found, its center-line and center-line of image
bbcenter_abs = ((2*bbdir(1))+bbdir(3)-1)/2;
hfig = figure('name', 'Direct beam bounding box');
colormap gray;
imagesc(ref);
drawnow;
hold on;
plot([bbdir(1), bbdir(1)+bbdir(3)-1, bbdir(1)+bbdir(3)-1, bbdir(1), bbdir(1)], [bbdir(2), bbdir(2), bbdir(2)+bbdir(4)-1, bbdir(2)+bbdir(4)-1, bbdir(2)], 'r-');
plot([acq.xdet/2+0.5 acq.xdet/2+0.5], [1 acq.ydet], 'b-.'); % centre of the ccd
plot([bbcenter_abs bbcenter_abs], [bbdir(2) bbdir(2)+bbdir(4)-1], 'c-.'); % centre of the direct beam
% interactive check
questionMsg = 'Are you satisfied with this bounding box for the direct beam? [y/n]';
while (strcmpi(inputwdefault(questionMsg, 'n'), 'n'))
disp('Please select (zoom onto) the direct beam area and disable zoom afterwards');
figure(hfig), clf, imagesc(ref), h = zoom(hfig); set(h, 'Enable', 'on'); waitfor(h, 'Enable', 'off'), hold on;
disp('-> Now click top-left and bottom-right corners for final selection');
bbdir = ginput(2);
bbdir = round([bbdir(1, 1) bbdir(1, 2) bbdir(2, 1)-bbdir(1, 1)+1 bbdir(2, 2)-bbdir(1, 2)+1]);
% Make sure the bbox width and height are even numbers (needed for correlation)
bbdir(3:4) = ceil(bbdir(3:4)/2)*2;
% Plot the new bounding box
plot([bbdir(1), bbdir(1)+bbdir(3)-1, bbdir(1)+bbdir(3)-1, bbdir(1), bbdir(1)], [bbdir(2), bbdir(2), bbdir(2)+bbdir(4)-1, bbdir(2)+bbdir(4)-1, bbdir(2)], 'r-');
bbcenter_abs = ((2*bbdir(1))+bbdir(3)-1)/2;
plot([acq.xdet/2+0.5 acq.xdet/2+0.5], [1 acq.ydet], 'b-.');
plot([bbcenter_abs bbcenter_abs], [bbdir(2) bbdir(2)+bbdir(4)-1], 'c-.'); % centre of the direct beam
end
close(hfig);
end % end of function
%take the minimum of the two references if available
if (~isempty(ref0) && ~isempty(ref1))
ref = min(ref0, ref1); % min of ref-s at beginning and end of scan
elseif (~isempty(ref0))
ref = ref0;
else % no images found!
disp('%%%%%%% missing images %%%%%%%%');
disp('no reference images found in this directory!');
disp('using a default guess');
disp('%%%%%%% missing images %%%%%%%%');
disp(' ');
bbdir = [512 512 1024 1024];
return
end
end
\ No newline at end of file
1_preprocessing/gtFindRotationAxis.m
+ 5
− 10
View file @ 10291599
......@@ -34,7 +34,7 @@ try
name_ref1 = name_ref0;
else
sprintf('Using images DURING scan for determination of rotation axis posistion\n')
% SECOND CHOICE: IMAGES DURING SCAN
% SECOND CHOICE: IMAGES DURING SCAN
% WL May 2009
% changed to use per default the images at end of scan - should be more accurate;
indx_next = acq.nproj/(acq.interlaced_turns+1);
......@@ -51,7 +51,10 @@ try
end
end
% If there is already a sample bounding box, we will use it
if ~isempty(acq.bb)
bbdir = acq.bb;
end
im0 = edf_read(name_curr, bbdir, 'nodisp');
im1 = edf_read(name_next, bbdir, 'nodisp');
ref0 = edf_read(name_ref0, bbdir, 'nodisp');
......@@ -82,15 +85,7 @@ try
im0 = (im0-d)./(ref0-d);
im1 = (im1-d)./(ref1-d);
% determine centre of rotation
% shift=[];
% assignin('base', 'shift', shift);
shift = gtFindShifts(im0, fliplr(im1), 'block', 'on');
% set(gcf,'name','Manual correlation to find rotation axis...')
% while isempty(shift)
% drawnow;
% shift = evalin('base','shift');
% end
% working in the direct beam bounding box
rotu = bbdir(1) - 1 + (bbdir(3)/2) + 0.5 + (shift(2)/2);
......
1_preprocessing/gtFindSampleEdges.m
+ 25
− 23
View file @ 10291599
function acqbb = gtFindSampleEdges(acq, prep, bb)
function acqbb = gtFindSampleEdges(acq, prep)
% GTFINDSAMPLEEDGES
% acqbb = gtFindSampleEdges(acq, prep, bb)
% ----------------------------------------
......@@ -22,7 +22,11 @@ function acqbb = gtFindSampleEdges(acq, prep, bb)
disp('Trying to determine a tight BoundingBox around the sample and a region for intensity normalization');
intervals = 6;
if ~isempty(prep.bbox)
bb = prep.bbox;
else
bb = acq.bbdir;
end
%use bb when reading the files in.
ims = zeros(bb(4),bb(3));
count = 0; %how many images read?
......@@ -78,8 +82,8 @@ for ii = 0:round(im_turn/intervals):im_turn
end
if (count > 0)
ims = min(ims, [], 3); % using minimum for better contrast at edges...
ims = min(ims, [], 3); % using minimum for better contrast at edges..
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% analyse images
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
......@@ -147,6 +151,22 @@ if (count > 0)
disp('default "last" value')
last = bb(3)-prep.margin+1;
end
disp('centering bb on rotx')
%rotation axis position
bb_rotu = acq.rotu-bb(1)+1;
% check that enough of a margin is left for normalisation
min_first = prep.margin + 1;
max_last = bb(3) - prep.margin;
% shouldn't exceed either of these
max_width = min(bb_rotu-min_first, max_last-bb_rotu);
% we have previously tried to guess first and last
width = max(bb_rotu-first, last-bb_rotu);
% apply the limit
width = min(width, max_width);
first = floor(bb_rotu-width);
last = ceil(bb_rotu+width);
else
disp('%%%%%%% missing images %%%%%%%%')
disp('no useful images found! - using defaults')
......@@ -165,24 +185,6 @@ else
end
disp('centering bb on rotx')
%rotation axis position
bb_rotu = acq.rotu-bb(1)+1;
% check that enough of a margin is left for normalisation
min_first = prep.margin + 1;
max_last = bb(3) - prep.margin;
% shouldn't exceed either of these
max_width = min(bb_rotu-min_first, max_last-bb_rotu);
% we have previously tried to guess first and last
width = max(bb_rotu-first, last-bb_rotu);
% apply the limit
width = min(width, max_width);
first = floor(bb_rotu-width);
last = ceil(bb_rotu+width);
%pass to operator for final decision
h = figure();
......@@ -223,7 +225,7 @@ close(h);
incr = 1;
end
if ((first > prep.margin+incr+1) && (last < bb(3)-prep.margin-incr-1))
if ((first > prep.margin+incr) && (last < bb(3)-prep.margin-incr+1))
first = first-incr;
last = last+incr;
else
......
1_preprocessing/gtPreprocessing.m
+ 13
− 11
View file @ 10291599
......@@ -170,7 +170,7 @@ if (parameters.acq.no_direct_beam)
check = inputwdefault('Is it like a taper scan with the sample still in the images? [y/n]', 'y');
if strcmpi(check,'y')
% define the sample envelope - assume centred on direct beam
labgeo_tmp = gtGeoSamEnvFromAcq(parameters.labgeo, parameters.acq);
labgeo_tmp = gtGeoSamEnvFromAcq(parameters.labgeo, parameters.detgeo, parameters.acq);
parameters.labgeo.samenvtop = labgeo_tmp.samenvtop;
parameters.labgeo.samenvbot = labgeo_tmp.samenvbot;
parameters.labgeo.samenvrad = labgeo_tmp.samenvrad;
......@@ -214,21 +214,23 @@ else
check = inputwdefault(['Do you want to (re)-define the Sample BoundingBox (currently ' sprintf('[%d %d %d %d]',parameters.acq.bb) ')? [y/n]'], 'n');
end
if strcmpi(check,'y')
parameters.acq.bb = gtFindSampleEdges(parameters.acq,parameters.prep,bbdir);
parameters.prep.bbox = parameters.acq.bb+[-parameters.prep.margin 0 2*parameters.prep.margin 0];
% define the sample envelope - assume centred on direct beam
labgeo_tmp = gtGeoSamEnvFromAcq(parameters.labgeo, parameters.acq);
parameters.labgeo.samenvtop = labgeo_tmp.samenvtop;
parameters.labgeo.samenvbot = labgeo_tmp.samenvbot;
parameters.labgeo.samenvrad = labgeo_tmp.samenvrad;
parameters.acq.bb = gtFindSampleEdges(parameters.acq,parameters.prep);
end
parameters.prep.bbox = parameters.acq.bb+[-parameters.prep.margin 0 2*parameters.prep.margin 0];
save(parameters_name,'parameters');
end % end no_direct_beam case
% Update Detector reference position
parameters.detgeo = gtGeoDetDefaultParameters(parameters.acq);
save(parameters_name,'parameters');
if isempty(parameters.acq.masterdir)
parameters.detgeo = gtGeoDetDefaultParameters(parameters.acq);
save(parameters_name,'parameters');
end
% Calculate sample envelope
labgeo_tmp = gtGeoSamEnvFromAcq(parameters.labgeo, parameters.detgeo, parameters.acq);
parameters.labgeo.samenvtop = labgeo_tmp.samenvtop;
parameters.labgeo.samenvbot = labgeo_tmp.samenvbot;
parameters.labgeo.samenvrad = labgeo_tmp.samenvrad;
if isempty(parameters.acq.maxradius)
check='y';
......
1_preprocessing/gtSetup.m
+ 52
− 8
View file @ 10291599
......@@ -93,7 +93,43 @@ redColor = sprintf(gtGetANSIColour('red'));
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Create parameters structure, move/correct datafiles
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Copy parameters from a different acquisition
check = inputwdefault('Would you like to copy an existing parameter file? [y/n]', 'y');
if strcmpi(check, 'y')
masterpath = uigetdir('../','Select a directory');
p = gtLoadParameters(masterpath);
p.acq.dir = pwd;
p.acq.name = gtGetLastDirName(p.acq.dir);
p.acq.pair_tablename = sprintf('%sspotpairs', p.acq.name);
p.acq.calib_tablename = sprintf('%spaircalib', p.acq.name);
p.acq.collection_dir = pwd;
p.acq.collection_dir_old = pwd;
p.acq.masterdir = masterpath;
gtSaveParameters(p);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Set up the database tables
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
gtDBSetupTables(p.acq);
% Make directories
disp(['Setting up directory structure in ' p.acq.dir]);
[~,msg] = mkdir( fullfile(p.acq.dir, '0_rawdata') ); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, '0_rawdata', p.acq.name)); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, '0_rawdata', 'Orig') ); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, '1_preprocessing') ); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, '1_preprocessing', 'full') ); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, '1_preprocessing', 'abs') ); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, '1_preprocessing', 'ext') ); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, '2_difspot') ); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, '3_pairmatching') ); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, '4_grains') ); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, '5_reconstruction') ); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, '6_rendering') ); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, '7_fed') ); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, '8_analysis') ); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, '8_analysis', 'figures') ); disp(msg);
[~,msg] = mkdir( fullfile(p.acq.dir, 'OAR_log') ); disp(msg);
end
% If the parameters are already set up, start moving and correction
if exist(fullfile(pwd,'parameters.mat'), 'file')
disp('A parameters.mat file already exists in this directory');
......@@ -155,9 +191,9 @@ end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Set up directory structure.
% If in a visitor directory, make a DCT_Analysis directory, otherwise
% use ID11/graintracking.
parameters.acq.dir = gtSetAnalysisDir(pwd());
% For the moment we process in the acquisition directory - this will have to
% change with ESRF data policy
parameters.acq.dir = pwd; % gtSetAnalysisDir(pwd());
hasChosen = false;
while (~hasChosen)
......@@ -181,6 +217,12 @@ freeSpace = round(jdir.getUsableSpace() / 10^6);
fprintf('You have about %d Mb free space\n', freeSpace);
jdir.delete();
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Set up the database tables
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
gtDBSetupTables(parameters.acq);
% Make directories
disp(['Setting up directory structure in ' parameters.acq.dir]);
[~,msg] = mkdir(parameters.acq.dir); disp(msg);
......@@ -244,7 +286,7 @@ else
parameters.acq = gtAddMatFile(parameters.acq, params_acq, true, false, false);
clear params_acq;
parameters = gtCheckParameters(parameters, 'acq', 'verbose', true);
%parameters = %gtCheckParameters(parameters, 'acq', 'verbose', true);
gtSaveParameters(parameters);
% Default SAMPLE REFERENCE
......@@ -252,7 +294,7 @@ else
% omega=0.
parameters.samgeo = gtGeoSamDefaultParameters();
parameters = gtCheckParameters(parameters, 'samgeo', 'verbose', true);
%parameters = %gtCheckParameters(parameters, 'samgeo', 'verbose', true);
gtSaveParameters(parameters);
% Default RECONSTRUCTION REFERENCE
......@@ -260,7 +302,7 @@ else
% but scaled to microns.
parameters.recgeo = gtGeoRecDefaultParameters();
parameters = gtCheckParameters(parameters, 'recgeo', 'verbose', true);
%parameters = %gtCheckParameters(parameters, 'recgeo', 'verbose', true);
gtSaveParameters(parameters);
end
......@@ -293,11 +335,13 @@ if isfield(info, 'motor')
parameters.acq.rotation_name = 'pmo';
elseif ismember('diffrz', tmp_motors)
parameters.acq.rotation_name = 'diffrz';
elseif ismember('srot', tmp_motors)
parameters.acq.rotation_name = 'srot';
else
parameters.acq.rotation_name = 'unknown';
end
else
parameters.acq.rotation_name = 'unknown';
parameters.acq.rotation_name = 'diffrz';
end
......@@ -342,7 +386,7 @@ else
end
parameters = gtCheckParameters(parameters, 'labgeo', 'verbose', true);
%parameters = %gtCheckParameters(parameters, 'labgeo', 'verbose', true);
gtSaveParameters(parameters);
header = 'Parameters dealing with arbitrary geometry:';
......
2_difspot/gtSegmentationLaunchOAR.m
+ 3
− 7
View file @ 10291599
......@@ -3,13 +3,9 @@ function handles = gtSegmentationLaunchOAR(handles)
set(handles.status_label, 'string', 'Launching OAR', 'backgroundColor', 'y')
drawnow()
totproj = gtAcqTotNumberOfImages(handles.parameters) - 1;
handles.parameters.seg.segmentation_stack_size = 600;
list = build_list_v2();
ind_tmp = findValueIntoCell(list.seg(:,1), {'segmentation_stack_size'});
list.seg{ind_tmp(1),4} = 2;
handles.parameters.seg = gtModifyStructure(handles.parameters.seg, list.seg, 2, 'Segmentation stack size:');
handles = gtSegmentationSaveParameters(handles);
......@@ -30,7 +26,7 @@ if strcmpi(check,'Yes')
handles.parameters.oar.mem_core_mb = 8000; %Mb
handles.parameters.oar.node = 1;
handles.parameters.oar.core = 6;
list = build_list_v2();
list.oar(end+1,:) = {'mem_core_mb','Memory for each core in Mb','double', 2};
......@@ -38,7 +34,7 @@ if strcmpi(check,'Yes')
list.oar(end+1,:) = {'core','Number of cores per node','double', 2};
handles.parameters.oar = gtModifyStructure(handles.parameters.oar, list.oar, 2, 'OAR parameters:');
handles.parameters.seg.segmentation_stack_size = ceil(totproj ./ handles.parameters.oar.njobs);
parameters = handles.parameters;
save('parameters.mat','parameters')
......
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