diff --git a/2_difspot/gtDBBlob2SpotTable.m b/2_difspot/gtDBBlob2SpotTable.m
index 8d01655a5af5d8575811a2461c02a9a37cb56235..a8e061ce788ae3d6ee401a1fed85544b8c4e164e 100644
--- a/2_difspot/gtDBBlob2SpotTable.m
+++ b/2_difspot/gtDBBlob2SpotTable.m
@@ -158,14 +158,17 @@ for difspotID = first:last
% Write edf file on disk
if flag_writeedf
- % Read full edf-s, create summed image
- im = zeros(bb(5),bb(4));
-
- for fullID = bb(3):bb(3)+bb(6)-1
- im = im + edf_read(sprintf('1_preprocessing/full/full%04d.edf', fullID),...
- bb([1 2 4 5]));
+ if any(strcmp(seg.difspotmask,{'none', 'blob2D'}))
+ % Read full edf-s, create summed image
+ im = zeros(bb(5),bb(4));
+
+ for fullID = bb(3):bb(3)+bb(6)-1
+ im = im + edf_read(sprintf('1_preprocessing/full/full%04d.edf', fullID),...
+ bb([1 2 4 5]));
+ end
end
+
% Check minimum area condition
if isempty(thr_area)
mask2D = [];
diff --git a/2_difspot/gtPostSegmentation.m b/2_difspot/gtPostSegmentation.m
index bfd99c4c5689285671512472ca7e76cac1fb2e1f..a0397ed27563d6222b9fc39f0d15d9cc51a8137f 100644
--- a/2_difspot/gtPostSegmentation.m
+++ b/2_difspot/gtPostSegmentation.m
@@ -74,8 +74,7 @@ if test~=0
overwrite_flag=true;
gtDBCreateDifspotTable(parameters.acq.name, overwrite_flag);
else
- disp('Keeping difspot data. Quitting gtPostSegmentation')
- return
+ disp('Keeping difspot data')
end
end
diff --git a/5_reconstruction/gtForwardSimulate_v2.m b/5_reconstruction/gtForwardSimulate_v2.m
index 7e6d71394fa69870c69bb38c25d78b66c29a82ad..2b37fbcb3d2908d33d6e64bfd942cf343e630ebc 100644
--- a/5_reconstruction/gtForwardSimulate_v2.m
+++ b/5_reconstruction/gtForwardSimulate_v2.m
@@ -67,12 +67,10 @@ phases_num = length(parameters.cryst); % number of phases in the material
cryst = parameters.cryst(phaseID);
grainfilename = fullfile(acq.dir, '4_grains', sprintf('phase_%02d', phaseID), 'index.mat');
+fprintf('\nLoading indexing results...\n');
grains = load(grainfilename);
grain_num = length(grains.grain);
-name = acq.name;
-difspottable = [name,'difspot'];
-
%%% this section should be replaced with a function dealing with different
% versions of parameters names: fed, v1, v2...
@@ -83,14 +81,53 @@ detdirv0 = labgeo.detdirv;
rotdir = labgeo.rotdir;
beamdir = labgeo.beamdir;
detrefpos = labgeo.detrefpos / acq.pixelsize; % detector reference position in pixels
-detposcorner = labgeo.detorig; % the (0,0) corner of the detector in Lab system (edge of detector pixel)
+detposcorner = labgeo.detorig / acq.pixelsize; % the (0,0) corner of the detector in Lab system (edge of detector pixel)
rotcomp = gtMathsRotationMatrixComp(rotdir,'row');
omstep = 180 / acq.nproj;
imagerange = round(fsim.omegarange/omstep); % number of images summed up when searching raw data for a missing spot
-for n = first : last
+fprintf('\nLoading reflections from database...\n');
+difspottable = [parameters.acq.name,'difspot'];
+
+% Load difspot data in 'allspots' / spotpair data in 'allpairs'
+mymcmd = sprintf(['SELECT difspotID, CentroidX, CentroidY, CentroidImage, '...
+ 'BoundingBoxXsize, BoundingBoxYsize, BoundingBoxXorigin, BoundingBoxYorigin '...
+ 'FROM %s'],difspottable);
+
+[difspotIDs, CentroidXs, CentroidYs, CentroidImages, BoundingBoxXsizes, ...
+ BoundingBoxYsizes, BoundingBoxXorigins, BoundingBoxYorigins] = mym(mymcmd);
+
+numspots = max(difspotIDs);
+difspotID = NaN(numspots, 1);
+CentroidX = NaN(numspots, 1);
+CentroidY = NaN(numspots, 1);
+CentroidImage = NaN(numspots, 1);
+BoundingBoxXsize = NaN(numspots, 1);
+BoundingBoxYsize = NaN(numspots, 1);
+BoundingBoxXorigin = NaN(numspots, 1);
+BoundingBoxYorigin = NaN(numspots, 1);
+
+for ii = 1: length(difspotIDs)
+ jj = difspotIDs(ii);
+ difspotID(jj) = jj;
+ CentroidX(jj) = CentroidXs(ii);
+ CentroidY(jj) = CentroidYs(ii);
+ CentroidImage(jj) = CentroidImages(ii);
+ BoundingBoxXsize(jj) = BoundingBoxXsizes(ii);
+ BoundingBoxYsize(jj) = BoundingBoxYsizes(ii);
+ BoundingBoxXorigin(jj) = BoundingBoxXorigins(ii);
+ BoundingBoxYorigin(jj) = BoundingBoxYorigins(ii);
+end
+
+
+mymcmd = sprintf('select ldirX, ldirY, ldirZ, omega, omegaB, difAID, difBID from %s ',acq.pair_tablename);
+[allpairs.ldirX, allpairs.ldirY, allpairs.ldirZ, allpairs.omegaA, allpairs.omegaB, allpairs.difAID, allpairs.difBID] = mym(mymcmd);
+
+for n = first : last
+ fprintf('\nRunning forward simulation for grain %d...\n',n);
+
gr = grains.grain{n}; % output from INDEXTER
graincenter = gr.center / acq.pixelsize; % graincenter contains COM coordinates in pixels
@@ -149,22 +186,24 @@ for n = first : last
bb = zeros(numspots, 4); % difspot BoundingBox from database
status = cell(numspots, 1); % string corresponding to flag (summarizing result of forward simulation)
spotid = zeros(numspots, 1); % Mysql difspottable difspotID
- check = zeros(numspots, 5);
+ check = zeros(numspots, 2);
hklsp = zeros(numspots,size(gr.hkl,1)); % signed hk(i)l indices of reflection
omega = zeros(numspots, 1); % rotation angle in degrees
proj_geom = zeros(numspots, 12); % Vector used for ROI grain reconstruction in ASTRA (grain shifted to center of roi volume)
proj_geom_full = zeros(numspots, 12); % Vector describing full projection geometry (full images, grain at nominal position in sample volume)
proj_geom_abs = zeros(numspots, 12); % Vector describung absorption image projection geometry
- r = zeros(numspots, 3); % direction of diffracted beam
+ r = zeros(numspots, 3); % direction of diffracted beam used in ASTRA
r_th = zeros(numspots, 3); % theoretically predicted direction of diffracted beam (based on R_vector)
r_ex = zeros(numspots, 3); % estimated direction of diffracted beam, based on grain & difspot COM positions
U = zeros(numspots, 1); % COM u positions of difspots from difspottable
V = zeros(numspots, 1); % COM v positions of difspots from difspottable
full = zeros(acq.xdet, acq.ydet);
- %%% Main loop: examine all hklsp and search corresponding spots / intensity on the detector...
-
+
+
+
+ %%% Main loop: examine all hklsp and search corresponding spots / intensity on the detector..
for ii = 1 : numspots
currentSpotID = ondet(ii);
pl = gr.allblobs.pl(currentSpotID, :);
@@ -180,27 +219,19 @@ for n = first : last
% improved...
thr_max_offset = round(min(fsim.MaxOmegaOffset, (fsim.omegarange/(abs(sind(eta)))))/omstep);
- % loose search criteria - is there any intensity at the predicted spot
- % position ?
- firstquery = sprintf(...
- ['SELECT difspotID, CentroidX, CentroidY, CentroidImage, ' ...
- 'BoundingBoxXsize, BoundingBoxYsize, BoundingBoxXorigin, ' ...
- 'BoundingBoxYorigin' ...
- ' FROM %sdifspot' ...
- ' WHERE (%d between CentroidImage-%d and CentroidImage+%d) '...
- 'and (abs(CentroidX-%d) / BoundingBoxXsize) < 0.5 '...
- 'and (abs(CentroidY-%d) / BoundingBoxYsize) < 0.5 '...
- ' ORDER BY ((abs(BoundingBoxXsize-%d)/%d)+(abs(BoundingBoxYsize-%d)/%d)) limit 1'],...
- name, ...
- image_n, thr_max_offset, thr_max_offset, ...
- u(currentSpotID), ...
- v(currentSpotID), ...
- dif_Xsize, dif_Xsize, dif_Ysize, dif_Ysize);
-
- [difspotID, CentroidX, CentroidY, CentroidImage, BoundingBoxXsize, ...
- BoundingBoxYsize, BoundingBoxXorigin, BoundingBoxYorigin] = mym(firstquery);
-
- if isempty(difspotID)
+ % Look for difspots appying loose search criteria - is there any intensity at the predicted spot
+ % position ? Choose the one which is closest to the expected size
+
+
+
+ image_ok = find((CentroidImage >= image_n - thr_max_offset) & (CentroidImage <= image_n + thr_max_offset));
+ intensity_ok = find(abs(CentroidX(image_ok) - u(currentSpotID)) < max(dif_Xsize/2, BoundingBoxXsize(image_ok)/2 - dif_Xsize/2) & ...
+ abs(CentroidY(image_ok) - v(currentSpotID)) < max(dif_Ysize, BoundingBoxYsize(image_ok)/2 - dif_Ysize/2));
+
+ candidateIDs = image_ok(intensity_ok);
+
+
+ if isempty(candidateIDs)
% no candidates have been found: segmentation / overlap / intensity / ... problem ?
flag(ii) = 1; % No intensity at expected spot position
@@ -244,58 +275,52 @@ for n = first : last
end % app.assemble_figure
end % app.check_spot
- else % isempty(difspotID)
- U(ii) = CentroidX;
- V(ii) = CentroidY;
- Z(ii) = CentroidImage;
- bb(ii, :) = [BoundingBoxXorigin, BoundingBoxYorigin, ...
- BoundingBoxXsize, BoundingBoxYsize];
- spotid(ii) = difspotID;
+ else % isempty(candidateIDs)
+ % in case there are several candidates, take the one which has
+ % the Area close to the expected Area. This selection "rule" could be
+ % improved...
+
+ [area, area_index] = sort(abs(BoundingBoxXsize(candidateIDs) .* BoundingBoxYsize(candidateIDs) - dif_Xsize*dif_Ysize));
+ [image, image_index] = sort(abs(CentroidImage(candidateIDs) - image_n));
+ candidateID = candidateIDs(image_index(1));
+
+ U(ii) = CentroidX(candidateID);
+ V(ii) = CentroidY(candidateID);
+ Z = CentroidImage(candidateID);
+ bb(ii, :) = [BoundingBoxXorigin(candidateID), BoundingBoxYorigin(candidateID), ...
+ BoundingBoxXsize(candidateID), BoundingBoxYsize(candidateID)];
+ spotid(ii) = candidateID;
+
flag(ii) = 3; % Found a segmented difspot at expected position - we will check if it does match strict criteria
- spot = gtGetSummedDifSpot(difspotID, parameters, 1);
+ spot = gtGetSummedDifSpot(candidateID, parameters, 1);
spot = spot / sum(spot(:)) * dif_Xsize * dif_Xsize * dif_Ysize; % here we force the intensity to be the same in all spots -
if (fsim.assemble_figure)
full = gtPlaceSubImage2(spot, full, bb(ii, 1), bb(ii, 2), 'summed');
end
-
- image_ok = between(CentroidImage, image_n - thr_max_offset, image_n + thr_max_offset);
- centx_ok = abs(CentroidX - u(currentSpotID)) < dif_Offset;
- centy_ok = abs(CentroidY - v(currentSpotID)) < dif_Offset;
- xsize_ok = between(BoundingBoxXsize, dif_XsizeMin, dif_XsizeMax);
- ysize_ok = between(BoundingBoxYsize, dif_YsizeMin, dif_YsizeMax);
-
- if (fsim.verbose)
- % useful feedback to find out which of the more strict search criteria fail...
- sprintf('%d < %d < %d : %d',image_n - thr_max_offset, CentroidImage, image_n + thr_max_offset, image_ok)
- sprintf('abs(%d - %d) < %d : %d', CentroidX, u(currentSpotID), dif_Offset, centx_ok)
- sprintf('abs(%d - %d) < %d : %d', CentroidY, v(currentSpotID), dif_Offset, centy_ok)
- sprintf('%d < %d < %d : %d', dif_XsizeMin, BoundingBoxXsize, dif_XsizeMax, xsize_ok)
- sprintf('%d < %d < %d : %d', dif_YsizeMin, BoundingBoxYsize, dif_YsizeMax, ysize_ok)
- inputwdefault('continue','yes')
- end
-
- check(ii,:) = [image_ok, centx_ok, centy_ok, xsize_ok, ysize_ok];
-
+
+ cent_ok = sqrt((U(ii) - u(currentSpotID)).^2 + (V(ii) - v(currentSpotID)).^2) <= dif_Offset;
+ size_ok = all([between(bb(ii,3), dif_XsizeMin, dif_XsizeMax), between(bb(ii,4), dif_YsizeMin, dif_YsizeMax)]);
+
+
+ check(ii,:) = [cent_ok, size_ok];
+
+
if all(check(ii,:)), flag(ii) = 4; end % otherwise we keep flag == 3
- if find(gr.difspotidA == difspotID)
+ if find(gr.difspotidA == candidateID)
% If available, we want to use the angles as determined from the
% Friedel pairs - interrogate spotpair table
- flag(ii) = 5; % This spot is part of a pair and has been used by INDEXTER
- query = sprintf('select ldirX, ldirY, ldirZ, omega from %s where difAID=%d', ...
- parameters.acq.pair_tablename, difspotID);
- [ldirX, ldirY, ldirZ, omegaA] = mym(query);
- omega(ii) = omegaA;
- r(ii,:) = [ldirX, ldirY, ldirZ];
+ flag(ii) = 5; % This spot is part of a pair and has been used by INDEXTER
+ index = find(allpairs.difAID == candidateID);
+ omega(ii) = allpairs.omegaA(index);
+ r(ii,:) = [allpairs.ldirX(index), allpairs.ldirY(index), allpairs.ldirZ(index)];
Rottens = gtMathsRotationTensor(-omega(ii), rotcomp);
- elseif find(gr.difspotidB == difspotID)
+ elseif find(gr.difspotidB == candidateID)
flag(ii) = 5; % This spot is part of a pair and has been used by INDEXTER
- query = sprintf('select ldirX, ldirY, ldirZ, omegaB from %s where difBID=%d', ...
- parameters.acq.pair_tablename, difspotID);
- [ldirX, ldirY, ldirZ, omegaB] = mym(query);
- omega(ii) = omegaB; % in this case we have to reverse the line direction
- r(ii,:) = -[ldirX, ldirY, ldirZ];
+ index = find(allpairs.difBID == candidateID);
+ omega(ii) = allpairs.omegaB(index); % in this case we have to reverse the line direction
+ r(ii,:) = -[allpairs.ldirX(index), allpairs.ldirY(index), allpairs.ldirZ(index)];
Rottens = gtMathsRotationTensor(-omega(ii), rotcomp);
else
% we found a segmentedd spot - can use the theoretically
@@ -303,7 +328,7 @@ for n = first : last
% COM of grain and spot) for backprojection
% theoretically prediceted omega angle
- Rottens = gtMathsRotationTensor(-om_th, rotcomp);
+ Rottens = gtMathsRotationTensor(-om_th, rotcomp);
% theoretically predicted beam direction
r_th(ii,:) = beamdir*Rottens + 2*sind(theta)*pl;
@@ -317,6 +342,7 @@ for n = first : last
end
end
+
hoffset = round((hsize - bb(ii,3)) / 2);
voffset = round((vsize - bb(ii,4)) / 2);
@@ -348,7 +374,7 @@ for n = first : last
detposFull = detposcorner + detrefu*detdiru0 + detrefv*detdirv0;
proj_geom_full(ii, :) = proj_geom(ii,:);
proj_geom_full(ii, 4:6) = (detposFull * Rottens);
- end % if isempty(difspotID)
+ end % if isempty(candidateID)
end % loop over predicted spot positions
found_reflections = length(find(flag > 1));
@@ -374,8 +400,13 @@ for n = first : last
%%% Now fill in the information for the output
% remove reflections for which no segmented spot has been found
- ind = find(flag >= 3); % indices of spots to be included in output structure
-
+ if fsim.include_cand
+ ind = find(flag >= 3); % indices of spots to be included in output structure
+ else
+ ind = find(flag >= 4);
+ end
+
+
out.selected = flag(ind) >= 4; % vector of logicals with pre-selected spots active
out.id = gr.id;
out.phaseid = phaseID;
@@ -406,7 +437,9 @@ for n = first : last
out.proj.vol_size_y = hsize;
out.proj.vol_size_z = vsize;
out.proj.num_iter = parameters.rec.num_iter;
-
+ out.vol = [];
+ out.segbb = zeros(6,1);
+ out.threshold = 0;
out.shift(1) = round((acq.bb(3)-hsize)/2 + graincenter(1)) + 1;
out.shift(2) = round((acq.bb(3)-hsize)/2 + graincenter(2)) + 1;
out.shift(3) = round((acq.bb(4)-vsize)/2 + graincenter(3)) + 1;
@@ -441,9 +474,13 @@ function [spot, m] = sfGetRoi(start_image, end_image, acq, bb)
if all([bb(1) > 0, bb(2) > 0, bb(1)+bb(3) < acq.xdet, bb(2)+bb(4) < acq.ydet])
fullImgsDir = fullfile(acq.dir, '1_preprocessing', 'full');
indexes = start_image : end_image;
+ filename = fullfile(fullImgsDir, sprintf('full%04d.edf', indexes(1)));
+ info = edf_info(filename);
+
+
for img_n = 1:nimages
fullImgName = fullfile(fullImgsDir, sprintf('full%04d.edf', indexes(img_n)));
- spot(:, :, img_n) = edf_read(fullImgName, bb);
+ spot(:, :, img_n) = edf_read(fullImgName, bb, [], info);
m(img_n) = gtImgMeanValue2(spot(centery, centerx, img_n));
end
end
diff --git a/5_reconstruction/gtFsimDefaultParameters.m b/5_reconstruction/gtFsimDefaultParameters.m
index 996a74ab0023a8ac966503726341a8b19aa547c1..4b282d35888e1bc1a75d975768a117e926fdd39d 100644
--- a/5_reconstruction/gtFsimDefaultParameters.m
+++ b/5_reconstruction/gtFsimDefaultParameters.m
@@ -5,12 +5,12 @@ fsim.omegarange = 0.5; % look in +/- 1 degrees from predicted image
fsim.MaxOmegaOffset = 1; % Maximum omega offset
fsim.bb_size = []; % default dimensions of ROI, read from the FULL images - if empty the zeropadded projection size will be used
fsim.assemble_figure = true; % assemble the results of forward simulation into a full image saved in the grain%d_.mat file
-fsim.display_figure = true; %
+fsim.display_figure = false; %
fsim.Grayscale = [-20 200]; % default colorlimits when visualizing diffraction spots
fsim.Rdist_factor = 3; % allow for multiple times Rdiststd in calulcation of lateral spot offset
fsim.bbsize_factor = 2; % allow for +/- times std difference in horizontal and vertical bb size
fsim.oversize = 1.5; % projections are zeropadded before reconstruction
fsim.use_th = true; % use theoretically predicted diffraction angles for new detected spots
-fsim.verbose = false; %
-
+fsim.verbose = false; % tell which search criteria has failed
+fsim.include_cand = false; % include candidate spots (flag = 3 : wrong size) into difspot stack (deselected)
end
diff --git a/5_reconstruction/gtSetupReconstruction.m b/5_reconstruction/gtSetupReconstruction.m
index bc3c34d7870ffebfb488a23adbc98ce4cc05f21a..b590be24b4e7e033f1df18d5ff3a5a221bafc203 100644
--- a/5_reconstruction/gtSetupReconstruction.m
+++ b/5_reconstruction/gtSetupReconstruction.m
@@ -49,7 +49,12 @@ disp(['Setting up Reconstruction for phase ' num2str(phaseID) ' (' parameters.cr
samplefile = fullfile(parameters.acq.dir, '4_grains', 'sample.mat');
if exist(samplefile, 'file')
+ check=inputwdefault('4_grains/sample.mat already exists - do you want to reinitialize it ? [y/n]','n');
+ if strcmpi(check,'y')
+ sample = GtSample();
+ else
sample = GtSample.loadFromFile(samplefile);
+ end
else
sample = GtSample();
end
@@ -87,7 +92,7 @@ last = length(grain);
% get reconstruction parameters
-check = inputwdefault('Use default parameters? [y/n]', 'y');
+check = inputwdefault('Use default parameters for grain reconstruction ? [y/n]', 'y');
if ~strcmpi(check, 'y')
list = build_list_v2();
parameters.rec = gtModifyStructure(parameters.rec, list.rec(:,1:2));
diff --git a/zUtil_DataStructures/gtCreateGtSample.m b/zUtil_DataStructures/gtCreateGtSample.m
index d1acd8088ca54160e2181bd26e2eb494844f4184..962f6f5bca1d815172b2f3e73e3aba0e8a23cd32 100644
--- a/zUtil_DataStructures/gtCreateGtSample.m
+++ b/zUtil_DataStructures/gtCreateGtSample.m
@@ -33,26 +33,38 @@ for phaseid = 1 : phaseNum
phaseDir = sprintf('phase_%02d', phaseid);
fprintf('Phase %02d: ', phaseid);
+
+ %% Check if we have already reconstructed volumes or not
+ grainFile = sprintf('grain_%04d.mat', 1);
+ grainPath = fullfile('4_grains', phaseDir, grainFile);
+ grainInfo = load(grainPath);
+
+ if all(isfield(grainInfo,{'vol', 'segbb', 'threshold'}))
+ variables = {'shift', 'vol', 'segbb', 'selected', 'threshold', 'completeness', 'difspotID'};
+ reconstructed = 1;
+ else
+ variables = {'shift', 'selected', 'completeness', 'difspotID'};
+ reconstructed = 0;
+ end
+
for grainid = 1 : grainsNum
fprintf('%04d/%04d', grainid, grainsNum);
grainFile = sprintf('grain_%04d.mat', grainid);
grainPath = fullfile('4_grains', phaseDir, grainFile);
- grainInfo = load(grainPath, 'shift', 'vol', 'segbb', 'selected', 'threshold', 'completeness', 'difspotID');
+ grainInfo = load(grainPath, variables{:});
phase.setR_vector(grainid, grain{grainid}.R_vector);
phase.setCenter(grainid, grain{grainid}.center);
- if (~isfield(grainInfo, 'segbb'))
- phase.setBoundingBox(grainid, [grainInfo.shift, size(grainInfo.vol)]);
- else
+ if reconstructed
phase.setBoundingBox(grainid, grainInfo.segbb);
+ phase.setThreshold(grainid, grainInfo.threshold);
end
selected = zeros(length(grainInfo.difspotID),1);
selected(grainInfo.selected) = 1;
phase.setSelectedDiffspots(grainid, selected);
-
- phase.setThreshold(grainid, grainInfo.threshold);
+
phase.setCompleteness(grainid, grainInfo.completeness);
phase.setDifspotID(grainid, grainInfo.difspotID);
diff --git a/zUtil_Imaging/gtCheckSegmentation.m b/zUtil_Imaging/gtCheckSegmentation.m
index a3c79dce92cc9182fee99a5cd5a3be20f12038a5..4af4cf39ed5c8285e881863efbc4d6a84f013c85 100644
--- a/zUtil_Imaging/gtCheckSegmentation.m
+++ b/zUtil_Imaging/gtCheckSegmentation.m
@@ -1,7 +1,7 @@
function gtCheckSegmentation(imnum,parameters,clims)
querie=sprintf('select XIndex,YIndex from %sdifblobdetails where ZIndex=%d',parameters.acq.name,imnum);
- full=gtGetFullImage(imnum,clims);
+ full=gtGetFullImage(imnum,parameters);
spots=zeros(parameters.acq.ydet,parameters.acq.xdet);
[x,y]=mym(querie);
for i=1:length(x)
diff --git a/zUtil_Parameters/build_list_v2.m b/zUtil_Parameters/build_list_v2.m
index a88bdbf2ed27aa8db602e5e1fd8853b67763b007..e0595a21515f288fc36c75c49277a8100c6fdde6 100644
--- a/zUtil_Parameters/build_list_v2.m
+++ b/zUtil_Parameters/build_list_v2.m
@@ -737,6 +737,9 @@ list.fsim{11,1} = 'use_th'; list.fsim{11,2} = 'Use th
list.fsim{12,1} = 'verbose'; list.fsim{12,2} = 'Display the search criteria for each of the spots';
list.fsim{12,3} = 'logical';
list.fsim{12,4} = 2;
+list.fsim{13,1} = 'include_cand'; list.fsim{13,2} = 'Include difspot candidates into the stack - automatically disabled';
+ list.fsim{13,3} = 'logical';
+ list.fsim{13,4} = 2;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% reconstruction