diff --git a/1_preprocessing/gtCopyCorrectUndistortCondor.m b/1_preprocessing/gtCopyCorrectUndistortCondor.m
index ab93baf973db4f9893293c4736be5bb311ada884..06f4a6ad10ded34719e88d598d54efc6737e9782 100644
--- a/1_preprocessing/gtCopyCorrectUndistortCondor.m
+++ b/1_preprocessing/gtCopyCorrectUndistortCondor.m
@@ -39,7 +39,7 @@ destdir = fullfile( parameters.acq.dir, '0_rawdata', parameters.acq.name );
destdir_orig = fullfile( parameters.acq.dir, '0_rawdata', 'Orig' );
%database connect
-gtDBConnect();
+gtDBConnect('graindb.esrf.fr', 'gtadmin', 'gtadmin', 'graintracking');
filetable=[parameters.acq.name '_filetable'];
diff --git a/4_grains/gtCalculateGrain.m b/4_grains/gtCalculateGrain.m
index fffd4089ef28d39b361caa8a483a908a61f6b4a5..0e5565522006a8010151019197065f37c740bd38 100644
--- a/4_grains/gtCalculateGrain.m
+++ b/4_grains/gtCalculateGrain.m
@@ -103,7 +103,7 @@ detrefv = labgeo.detrefv;
Qdet = gtFedDetectorProjectionTensor(detdiru,detdirv,1,1);
tn = cross(detdiru,detdirv);
-pixelsize = [labgeo.pixelsizeu labgeo.pixelsizeu labgeo.pixelsizev];
+pixelsize = mean([labgeo.pixelsizeu labgeo.pixelsizev]);
detpos = (labgeo.detrefpos./pixelsize)';
diff --git a/5_reconstruction/gtAstraReconstructGrain.m b/5_reconstruction/gtAstraReconstructGrain.m
index efbf2038329d60b892d83f040da0e57fbc7bc59d..a67a3365936394a658048a2719cda091250433c8 100644
--- a/5_reconstruction/gtAstraReconstructGrain.m
+++ b/5_reconstruction/gtAstraReconstructGrain.m
@@ -1,4 +1,4 @@
-function vol = gtAstraReconstructGrain(grainID, phaseID, parameters)
+function vol = gtAstraReconstructGrain(grainID, phaseID, parameters, sample)
% GTASTRARECONSTRUCTGRAIN 3D ART (ASTRA) reconstruction on a GPU machine
% gtAstraReconstructGrain(grainID, phaseID, [parameters])
% -------------------------------------------------------
@@ -14,23 +14,14 @@ function vol = gtAstraReconstructGrain(grainID, phaseID, parameters)
%
-
-% try
-% d = gpuDevice;
-% OK = d.SupportsDouble;
-% catch mexc1
-% mexc = MException('ASTRA:no_GPU', ...
-% 'gtAstraReconstructGrain: Submit this job on a GPU machine! Exiting...');
-% mexc = addCause(mexc, mexc1);
-% throw(mexc)
-% end
-
if ~exist('parameters','var') || isempty(parameters)
load('parameters.mat');
end
-samplefile = fullfile(parameters.acq.dir, '4_grains', 'sample.mat');
-sample = GtSample.loadFromFile(samplefile);
+if ~exist('sample','var')
+ samplefile = fullfile(parameters.acq.dir, '4_grains', 'sample.mat');
+ sample = GtSample.loadFromFile(samplefile);
+end
selected = logical(sample.phases{phaseID}.grains{grainID}.selectedDiffspots);
diff --git a/5_reconstruction/gtChangeThreshold3D.m b/5_reconstruction/gtChangeThreshold3D.m
index 9a08c0616458f501c8f11ec9c195f2fec057a544..ff11f60aa55b6edc8bbab6350c6f7658dd496fc4 100644
--- a/5_reconstruction/gtChangeThreshold3D.m
+++ b/5_reconstruction/gtChangeThreshold3D.m
@@ -24,6 +24,7 @@ if isdeployed
firstID = str2double(firstID);
lastID = str2double(lastID);
phaseID = str2double(phaseID);
+ gtDBConnect('graindb.esrf.fr','gtadmin','gtadmin','graintracking');
% else
% % Here is for the lazy who wants to launch from CMD line.
% if (ischar(firstID) && strcmpi(firstID, 'first'))
@@ -36,6 +37,17 @@ end
phaseDir = fullfile(parameters.acq.dir, '4_grains', sprintf('phase_%02d', phaseID));
+filetable = sprintf('%s_filetable', parameters.acq.name);
+filename = fullfile(parameters.acq.dir, '4_grains', 'sample.mat');
+
+if exist(filename, 'file')
+ sample = GtSample.loadFromFile(filename);
+else
+ disp('Can not find 4_grains/sample.mat !');
+ exit;
+end
+
+
if (~isdeployed), fprintf('Phase %02d: ', phaseID); end
for grainID = firstID : lastID
if (~isdeployed), fprintf('%04d/(%04d..%04d)', grainID, firstID, lastID); end
@@ -44,17 +56,22 @@ for grainID = firstID : lastID
grain = load(grain_file, 'vol', 'shift', 'id');
grain = gtThresholdGrain3D(grain, rec);
seg = grain.seg;
+ Area = grain.Area;
segbb = grain.segbb;
threshold = grain.threshold;
- Area = grain.Area;
if ~isempty(seg)
save(grain_file, '-append', 'seg', 'segbb', 'threshold', 'Area');
+ sample.phases{phaseID}.setBoundingBox(grainID, segbb);
+ sample.phases{phaseID}.setThreshold(grainID, threshold);
end
if (~isdeployed), fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b'); end
end
if (~isdeployed), fprintf('(%04d..%04d) Done.\n', firstID, lastID); end
+disp('now writing to sample.mat')
+sample.mergeToFile(filetable, filename, 'sample');
+
end % end of function
diff --git a/5_reconstruction/gtForwardSimulate_v2.m b/5_reconstruction/gtForwardSimulate_v2.m
index 130cf6f185b5d8daba6f156551695324f0528b10..6f7be299587073acf91b95a3e5b2e63b3f0e42a2 100644
--- a/5_reconstruction/gtForwardSimulate_v2.m
+++ b/5_reconstruction/gtForwardSimulate_v2.m
@@ -94,7 +94,7 @@ detdiru0 = labgeo.detdiru; % will use detdiru0 to distinguish from ro
detdirv0 = labgeo.detdirv;
rotdir = labgeo.rotdir;
beamdir = labgeo.beamdir;
-pixelsize = [labgeo.pixelsizeu labgeo.pixelsizeu labgeo.pixelsizev];
+pixelsize = mean([labgeo.pixelsizeu, labgeo.pixelsizev]);
detrefpos = labgeo.detrefpos ./ pixelsize; % detector reference position in pixels
detposcorner = labgeo.detorig ./ pixelsize; % the (0,0) corner of the detector in Lab system (edge of detector pixel)
@@ -140,6 +140,22 @@ 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);
+difspot_num = length(difspotIDs); % number of difspots in database
+spot2grain = cell(difspot_num, 1); % cell array linking difspots with grainids
+spot2phase = cell(difspot_num, 1);
+
+filetable = sprintf('%s_filetable',acq.name);
+filename = fullfile(acq.dir,'4_grains','spot2grain.mat');
+spotTable = GtMergeTable(filetable, filename, {'spot2grain', 'spot2phase'});
+
+samplefile = fullfile(acq.dir,'4_grains','sample.mat');
+sample = GtSample(phases_num);
+sample.fileTable = sprintf('%s_filetable',parameters.acq.name);
+% initialise sample structure
+phase = GtPhase(parameters.cryst(phaseID).name, grain_num);
+sample.phases{phaseID} = phase;
+
+
for n = first : last
fprintf('\nRunning forward simulation for grain %d...\n',n);
@@ -462,9 +478,9 @@ for n = first : last
out.vol = [];
out.segbb = zeros(1,6);
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;
+ out.shift(1) = round((acq.bb(3)-out.proj.vol_size_x)/2 + graincenter(1)) + 1;
+ out.shift(2) = round((acq.bb(3)-out.proj.vol_size_y)/2 + graincenter(2)) + 1;
+ out.shift(3) = round((acq.bb(4)-out.proj.vol_size_z)/2 + graincenter(3)) + 1;
if fsim.display_figure
out.full = full;
@@ -475,9 +491,21 @@ for n = first : last
filename = fullfile(acq.dir, '4_grains', sprintf('phase_%02d',phaseID), ...
sprintf('grain_%04d.mat', gr.id));
save(filename, '-struct', 'out');
+
+ spot2grain(spotid(included)) = {n};
+ spot2phase(spotid(included)) = {phaseID};
+
+ sample.phases{phaseID}.setR_vector(n, gr.R_vector);
+ sample.phases{phaseID}.setCompleteness(n, completeness);
+ sample.phases{phaseID}.setCenter(n, graincenter);
+ sample.phases{phaseID}.setSelectedDiffspots(n, out.selected);
+
+end
+spotTable.fillTable(spot2grain, 'spot2grain');
+spotTable.fillTable(spot2phase, 'spot2phase');
-end
+sample.mergeToFile(filetable, samplefile, 'sample');
end % end of function
diff --git a/5_reconstruction/gtReconstructGrains.m b/5_reconstruction/gtReconstructGrains.m
index 5ec54dd47eacdd8751b092d7bab17a62d928a895..9ba1b639b7944df20a6d56229eeb1a0e6b6de8c8 100644
--- a/5_reconstruction/gtReconstructGrains.m
+++ b/5_reconstruction/gtReconstructGrains.m
@@ -50,12 +50,15 @@ if ~OK
disp('ASTRA:no_GPU gtAstra3D: You should submit this job on a GPU machine ! Exiting...');
end
+samplefile = fullfile(parameters.acq.dir, '4_grains', 'sample.mat');
+sample = GtSample.loadFromFile(samplefile);
+
if ~isempty(rec.list)
if OK
for ii = 1 : length(rec.list)
fprintf('%04d/%04d', ii, length(rec.list));
- gtAstraReconstructGrain(ii, phaseID, parameters);
+ gtAstraReconstructGrain(ii, phaseID, parameters, sample);
fprintf('\b\b\b\b\b\b\b\b\b');
end
else
@@ -66,7 +69,7 @@ else
if OK
for ii = first : last
fprintf('%04d/(%04d..%04d)', ii, first, last);
- gtAstraReconstructGrain(ii, phaseID, parameters);
+ gtAstraReconstructGrain(ii, phaseID, parameters, sample);
fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b');
end
else
diff --git a/5_reconstruction/gtSetupForwardSimulation.m b/5_reconstruction/gtSetupForwardSimulation.m
index aae1ca7974eeb1937f34a732a2b36f7be51151fc..579ef6a30cd45d164722cef073b004d6143ef072 100644
--- a/5_reconstruction/gtSetupForwardSimulation.m
+++ b/5_reconstruction/gtSetupForwardSimulation.m
@@ -1,45 +1,59 @@
-function gtSetupForwardSimulation(phaseID)
+function gtSetupForwardSimulation
% simple helper function to run gtForwardSimulate
% whatever the current version is ;-)
parameters = [];
load('parameters.mat');
+gtDBConnect();
nof_phases = length(parameters.cryst);
-if ~exist('phaseID','var')
+if nof_phases > 1
+ phaseID = inputwdefaultnumeric('Enter phaseID', num2str(1));
+else
phaseID = 1;
end
-phaseID_str = sprintf('%02d',phaseID);
-disp(['Setting up Forward Simulation for phase ' phaseID_str ' ' parameters.cryst(1).name]);
+phaseID_str = sprintf('%02d',phaseID);
+disp(['Setting up Forward Simulation for phase ' phaseID_str ' ' parameters.cryst(phaseID).name]);
+filetable = sprintf('%s_filetable', parameters.acq.name);
% get the latest version of indexter output
grain = [];
filename = fullfile(parameters.acq.dir, '4_grains', ['phase_' phaseID_str], 'index.mat');
+
load(filename, 'grain');
% how many grains in this dataset?
ngrains = length(grain);
-% sample.mat unused in gtForwardSimulate_v2!!! So no reason to load it here :)
-
-% create / reset sample.mat spot2grain.mat
-% filename = fullfile(parameters.acq.dir, '4_grains', 'sample.mat');
-% if exist(filename, 'file')
-% sample = GtSample.loadFromFile(filename); % do not create from scratch - we want to keep information related to other phases
-% else
-% sample = GtSample(nof_phases);
-% end
-%
-% phase = GtPhase(parameters.cryst(phaseID).name, ngrains);
-% sample.phases{phaseID} = phase;
-% save(filename, 'sample');
-% disp(['Reset phase number ' num2str(phaseID) ' in the sample.mat:'])
-% disp(['Name : ' parameters.cryst(phaseID).name])
-% disp(['nof_grains: ' ngrains])
-%
-% filename = fullfile(parameters.acq.dir,'4_grains','spot2grain.mat');
-% spotTable = GtMergeTable(filename, {'spot2grain', 'spot2phase'});
+
+%create / reset sample.mat spot2grain.mat
+filename = fullfile(parameters.acq.dir, '4_grains', 'sample.mat');
+if exist(filename, 'file') && (nof_phases > 1)
+ sample = GtSample.loadFromFile(filetable, filename); % do not create from scratch - we want to keep information related to other phases
+else
+ sample = GtSample(nof_phases);
+ sample.fileTable = sprintf('%s_filetable',parameters.acq.name);
+end
+
+phase = GtPhase(parameters.cryst(phaseID).name, ngrains);
+sample.phases{phaseID} = phase;
+save(filename, 'sample');
+disp(['Reset phase number ' num2str(phaseID) ' in the sample.mat:'])
+disp(['Name : ' parameters.cryst(phaseID).name])
+disp(['nof_grains: ' num2str(ngrains)])
+
+
+filename = fullfile(parameters.acq.dir,'4_grains','spot2grain.mat');
+difspot_num = mym(sprintf('select count(*) from %sdifspot', parameters.acq.name));
+
+if exist(filename, 'file') && nof_phases>1
+ check = inputwdefault('Do you want to reset spot2grain? [y/n]', 'n');
+ if ~strcmpi(check, 'y')
+ spot2grain = cell(difspot_num, 1); % cell array linking difspots with grainids
+ spot2phase = cell(difspot_num, 1);
+ end
+end
% get reconstruction parameters
check = inputwdefault('Use default parameters? [y/n]', 'y');
diff --git a/5_reconstruction/gtSetupReconstruction.m b/5_reconstruction/gtSetupReconstruction.m
index b590be24b4e7e033f1df18d5ff3a5a221bafc203..baa76f5c65e245e92674edf103f107ffc83462e3 100644
--- a/5_reconstruction/gtSetupReconstruction.m
+++ b/5_reconstruction/gtSetupReconstruction.m
@@ -45,18 +45,22 @@ parameters_savefile = fullfile(parameters.acq.dir, 'parameters.mat');
nof_phases = length(parameters.cryst);
+if nof_phases > 1
+ phaseID = inputwdefaultnumeric('Enter phaseID', num2str(1));
+end
+
+phaseID_str = sprintf('%02d',phaseID);
+
+
disp(['Setting up Reconstruction for phase ' num2str(phaseID) ' (' parameters.cryst(phaseID).name ')']);
+filetable = sprintf('%s_filetable', parameters.acq.name);
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
+ sample = GtSample.loadFromFile(samplefile);
else
- sample = GtSample();
+ disp('Can not find 4_grains/sample.mat - have you run gtSetupForwardSimulation ?');
+ exit;
end
absorption_volume = fullfile(parameters.acq.dir, '5_reconstruction', 'volume_absorption.mat');
@@ -83,12 +87,8 @@ if ~exist(absorption_mask,'file')
end
-% get the latest version of indexter output
-filename = fullfile(parameters.acq.dir, '4_grains', sprintf('phase_%02d', phaseID), 'index.mat');
-load(filename);
-% how many grains in this dataset?
-first = 1;
-last = length(grain);
+
+
% get reconstruction parameters
@@ -99,6 +99,8 @@ if ~strcmpi(check, 'y')
save(parameters_savefile,'parameters');
end
+first = 1;
+last = length(sample.phases{phaseID}.grains);
check = inputwdefault('Launch reconstruction? [y/n]', 'y');
if strcmpi(check, 'y')
diff --git a/zUtil_DataStructures/GtConflict.m b/zUtil_DataStructures/GtConflict.m
index df7f717701c29b0676d163655f2c24418c35f501..018d7809118bc56bb174100de633ea4e261299ba 100644
--- a/zUtil_DataStructures/GtConflict.m
+++ b/zUtil_DataStructures/GtConflict.m
@@ -1,9 +1,9 @@
classdef GtConflict
properties
- difspots = {};
+ difspots = NaN; %{} before...
maxnum = false;
- merge = {};
+ merge = NaN; %{} before...
allequals = false;
end
end
diff --git a/zUtil_DataStructures/GtLockDB.m b/zUtil_DataStructures/GtLockDB.m
index 6e07c61a6fff89c20da608bde8aeccea9aeaf2b8..bcb7d25ea46a911a23719acf584b0b7cf980b786 100644
--- a/zUtil_DataStructures/GtLockDB.m
+++ b/zUtil_DataStructures/GtLockDB.m
@@ -62,10 +62,10 @@ classdef GtLockDB < handle
if (obj.hasLock)
test = mym(sprintf('delete from %s where (filename) = ("%s")', obj.filetable, obj.filename));
if test
- disp('release file lock')
+ %disp('release file lock')
obj.hasLock = false;
else
- disp('release file lock failed');
+ disp('releasing file lock failed for some reason !!?');
end
end
end
diff --git a/zUtil_DataStructures/GtMergeTable.m b/zUtil_DataStructures/GtMergeTable.m
index 9f62e94bd7bf6e9201c15db525afb9f392df27f0..f30ba3b62973cd6654855131f5c8337b73fa2838 100644
--- a/zUtil_DataStructures/GtMergeTable.m
+++ b/zUtil_DataStructures/GtMergeTable.m
@@ -7,18 +7,9 @@ classdef GtMergeTable < handle
methods (Access = public)
- function obj = GtMergeTable(fileName, fieldNames)
- obj.fileLock = GtLock(fileName);
- obj.fieldNames = fieldNames;
- if ~exist(fileName,'file')
- fprintf('creating output file\n')
-
- for ii = 1 : length(fieldNames)
- table.(obj.fieldNames{ii}) = {};
- end
-
- save(fileName, '-struct', 'table');
- end
+ function obj = GtMergeTable(fileTable, fileName, fieldNames)
+ obj.fileLock = GtLockDB(fileTable,fileName);
+ obj.fieldNames = fieldNames
end
function fillTable(obj, tmp_array, fieldName)
diff --git a/zUtil_DataStructures/GtSample.m b/zUtil_DataStructures/GtSample.m
index 6e11ec8466735020adb026166a08e9f92cad9291..471f600db8784d720a23fb6029b002f15f548619 100644
--- a/zUtil_DataStructures/GtSample.m
+++ b/zUtil_DataStructures/GtSample.m
@@ -5,6 +5,8 @@ classdef GtSample < handle
volumeFile = '';
absVolFile = '';
+
+ fileTable = '';
end
methods (Access = public)
@@ -24,6 +26,9 @@ classdef GtSample < handle
for ii = 1: phases_num
obj.phases{ii} = GtPhase();
end
+ if (exist('fileTable', 'var'))
+ obj.fileTable = fileTable;
+ end
end
function merge(obj, other)
@@ -41,9 +46,11 @@ classdef GtSample < handle
for grainNum = 1:length(other.phases{phaseNum}.grains)
% Merge threshold
obj.mergeGrainField(other, phaseNum, grainNum, 'threshold', 0);
- obj.phases{phaseNum}.grains{grainNum}.selectedDiffspots = ...
- unique([obj.phases{phaseNum}.grains{grainNum}.selectedDiffspots ...
- other.phases{phaseNum}.grains{grainNum}.selectedDiffspots]);
+ if ~isempty(other.phases{phaseNum}.grains{grainNum}.selectedDiffspots)
+ obj.phases{phaseNum}.grains{grainNum}.selectedDiffspots = ...
+ other.phases{phaseNum}.grains{grainNum}.selectedDiffspots;
+ end
+ %removed : unique([obj.phases{phaseNum}.grains{grainNum}.selectedDiffspots ...
end
for grainNum = 1:length(other.phases{phaseNum}.summary)
obj.mergeSummaryField(other, phaseNum, grainNum, 'delete', false);
@@ -55,9 +62,9 @@ classdef GtSample < handle
obj.mergeSummaryField(other, phaseNum, grainNum, 'difspotID', []);
end
for grainNum = 1:length(other.phases{phaseNum}.conflicts)
- obj.mergeConflictsField(other, phaseNum, grainNum, 'difspots', {});
+ obj.mergeConflictsField(other, phaseNum, grainNum, 'difspots', []); %{}
obj.mergeConflictsField(other, phaseNum, grainNum, 'maxnum', false);
- obj.mergeConflictsField(other, phaseNum, grainNum, 'merge', {});
+ obj.mergeConflictsField(other, phaseNum, grainNum, 'merge', []); %{}
obj.mergeConflictsField(other, phaseNum, grainNum, 'allequals', false);
end
@@ -80,7 +87,7 @@ classdef GtSample < handle
end
end
- function mergeToFile(obj, fileName, fieldName)
+ function mergeToFile(obj, fileTable, fileName, fieldName)
% GTSAMPLE/MERGETOFILE This merges the current object into an existing
% object, which is loaded from a file.
%
@@ -91,8 +98,8 @@ classdef GtSample < handle
if (~exist('fieldName', 'var'))
fieldName = 'sample';
end
-
- lock = GtLock(fileName);
+
+ lock = GtLockDB(fileTable, fileName);
lock.acquire();
sample = load(fileName, fieldName);
@@ -201,14 +208,14 @@ classdef GtSample < handle
end
methods (Static, Access = public)
- function sample = loadFromFile(fileName, fieldName)
+ function sample = loadFromLockedFile(fileTable, fileName, fieldName)
% GTSAMPLE/LOADFROMFILE Synchronized loading from a file
if (~exist('fieldName', 'var'))
fieldName = 'sample';
end
- lock = GtLock(fileName);
+ lock = GtLockDB(fileTable, fileName);
lock.acquire();
sample = load(fileName, fieldName);
@@ -216,5 +223,17 @@ classdef GtSample < handle
lock.release();
end
+
+ function sample = loadFromFile(fileName, fieldName)
+ % GTSAMPLE/LOADFROMFILE Synchronized loading from a file
+
+ if (~exist('fieldName', 'var'))
+ fieldName = 'sample';
+ end
+
+ sample = load(fileName, fieldName);
+ sample = sample.(fieldName);
+
+ end
end
end