From cc45aab02093a4a3ad86e8bd4895fa70554d27bc Mon Sep 17 00:00:00 2001
From: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>
Date: Sat, 14 Jun 2014 14:33:01 +0200
Subject: [PATCH] initialize horizontal rotation axis offset in
labgeo.detrefpos
Signed-off-by: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>
---
1_preprocessing/gtPreprocessing.m | 1 +
zUtil_Imaging/gtCheckSegmentation.m | 10 +++++-----
zUtil_Indexter/gtINDEXIndividualSpots.m | 16 ++++++++++++----
3 files changed, 18 insertions(+), 9 deletions(-)
diff --git a/1_preprocessing/gtPreprocessing.m b/1_preprocessing/gtPreprocessing.m
index e7e34cde..e2764227 100644
--- a/1_preprocessing/gtPreprocessing.m
+++ b/1_preprocessing/gtPreprocessing.m
@@ -200,6 +200,7 @@ else
if strcmpi(check,'y')
parameters.acq.rotu = gtFindRotationAxis(parameters.acq,bbdir);
parameters.acq.rotx = parameters.acq.rotu;
+ parameters.labgeo.detrefpos(2) = (parameters.acq.rotu - parameters.acq.xdet / 2) * parameters.acq.pixelsize;
end
save(parameters_name,'parameters');
diff --git a/zUtil_Imaging/gtCheckSegmentation.m b/zUtil_Imaging/gtCheckSegmentation.m
index b750c1ed..c2a2b0df 100644
--- a/zUtil_Imaging/gtCheckSegmentation.m
+++ b/zUtil_Imaging/gtCheckSegmentation.m
@@ -1,7 +1,7 @@
function gtCheckSegmentation(imnum,parameters,clims)
%querie1 = sprintf('select XIndex,YIndex from %sdifblobdetails where ZIndex=%d',parameters.acq.name,imnum);
- querie2 = sprintf('select difspotID,BoundingBoxXOrigin,BoundingBoxYOrigin from %sdifspot where StartImage<%d AND EndImage>%d', parameters.acq.name, imnum, imnum);
+ querie2 = sprintf('select difspotID,BoundingBoxXOrigin,BoundingBoxYOrigin from %sdifspot where StartImage<=%d AND EndImage>=%d', parameters.acq.name, imnum, imnum);
full=gtGetFullImage(imnum,parameters);
spots=zeros(parameters.acq.ydet,parameters.acq.xdet);
@@ -10,15 +10,15 @@ function gtCheckSegmentation(imnum,parameters,clims)
% for i=1:length(x)
% spots(y(i),x(i))=1;
% end
-
- [difspotID, bb(:,1), bb(:,2)] = mym(querie2);
+ mym(querie2)
+ [difspotID, bb(:,1), bb(:,2)] = mym(querie2)
for i=1:length(difspotID)
spot = gtGetSummedDifSpot(difspotID(i),parameters,true);
- spots = gtPlaceSubVolume(spots, spot, [bb(i,1)-1, bb(i,2)-1, 0],1,'assign');
+ spots = gtPlaceSubVolume(spots, spot, [bb(i,2)-1, bb(i,1)-1, 0],1,'assign');
end
cont=bwperim(spots);
@@ -30,7 +30,7 @@ function gtCheckSegmentation(imnum,parameters,clims)
full=mat2gray(full,clims);
- figure();
+ figure(1);
h=imshow(full-cont,clims);
% set(gcf,'Renderer','OpenGL');
diff --git a/zUtil_Indexter/gtINDEXIndividualSpots.m b/zUtil_Indexter/gtINDEXIndividualSpots.m
index bb78ce80..9ee0db7c 100644
--- a/zUtil_Indexter/gtINDEXIndividualSpots.m
+++ b/zUtil_Indexter/gtINDEXIndividualSpots.m
@@ -102,8 +102,9 @@ if ~exist('spin','var') || isempty(spin)
fprintf('Loading diff. spot data from difspottable %s ...\n', difspottable)
gtDBConnect;
- mysqlcmd = sprintf('SELECT difspotID,CentroidX,CentroidY,CentroidImage,BoundingBoxXsize,BoundingBoxYsize,Integral FROM %s ORDER BY difspotID',difspottable);
- [spin.id, spin.cu, spin.cv, spin.cw, spin.bbx, spin.bby, spin.int] = mym(mysqlcmd);
+ mysqlcmd = sprintf('SELECT difspotID,CentroidX,CentroidY,CentroidImage,BoundingBoxXsize,BoundingBoxYsize', ...
+ 'BoundingBoxXOrigin, BoundingBoxYOrigin, Integral FROM %s ORDER BY difspotID',difspottable);
+ [spin.id, spin.cu, spin.cv, spin.cw, spin.bbx, spin.bby, spin.bbxo, spin.bbyo, spin.int] = mym(mysqlcmd);
end
@@ -112,7 +113,11 @@ end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Active grains
-actgr = gtFitAllGrainValues(grain,'active',[],1);
+if isfield('grain','active')
+ actgr = gtFitAllGrainValues(grain,'active',[],1);
+else
+ actgr = ones(length(grain), 1);
+end
gr.cu = [];
@@ -349,6 +354,8 @@ spot.simw = [];
spot.mesu = [];
spot.mesv = [];
spot.mesw = [];
+spot.bbxo = [];
+spot.bbyo = [];
indspot = 0;
ovspot = 0;
okspot = 0;
@@ -425,7 +432,8 @@ for ii = 1:length(grain)
spot.mesu = [spot.mesu; spin.cu(spind)];
spot.mesv = [spot.mesv; spin.cv(spind)];
spot.mesw = [spot.mesw; spin.cw(spind)];
-
+ spot.bbxo = [spot.bbxo; spin.bbxo(spind)];
+ spot.bbyo = [spot.bbyo; spin.bbyo(spind)];
% Check multiplicity
mult = histc(grain{ii}.spot.hklspind, bins);
--
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