diff --git a/4_grains/gtLoadCluster.m b/4_grains/gtLoadCluster.m
index 4d6043350dc41e7b9da68a11cfe326cd117cc1d8..b8493056c0265a3b639baa78f5689e6a0a96afb6 100644
--- a/4_grains/gtLoadCluster.m
+++ b/4_grains/gtLoadCluster.m
@@ -1,17 +1,4 @@
-function cluster = gtLoadCluster(phase_id, cl_or_gr_ids, varargin)
-% GTLOADCLUSTER load the projection input of a grain cluster
-% cl = function cluster = gtLoadCluster(phase_id, cl_or_gr_ids, varargin)
-% INPUT:
-% phaseID = <int> phase ID
-% cl_or_gr_ids = <int> either the cluster_id (->sample) or
-% list of grain_ids composing the
-% cluster
-%
-% OPTIONAL INPUT (p/v pairs):
-% fields = <string> only load specific fields from
-% cluster structure ('ODF6D', 'SEG')
-% parameters = <struct> for security (make sure to load from right directory)
-%
+function cluster = gtLoadCluster(phase_id, grain_ids, varargin)
conf = struct('fields', {{}}, 'parameters', {[]});
conf = parse_pv_pairs(conf, varargin);
@@ -21,18 +8,12 @@ function cluster = gtLoadCluster(phase_id, cl_or_gr_ids, varargin)
phase_dir = fullfile(conf.parameters.acq.dir, '4_grains', sprintf('phase_%02d', phase_id));
end
- if numel(cl_or_gr_ids) == 1 %if only one element we assume it refers to a cluster
- sample = GtSample.loadFromFile;
- grain_ids_sorted = sample.phases{phase_id}.clusters(cl_or_gr_ids).included_ids;
- else
- grain_ids_sorted = sort(cl_or_gr_ids);
- if (any(grain_ids_sorted ~= cl_or_gr_ids))
- warning('gtLoadCluster:wrong_argumet', ...
- 'Some grain IDs were no sorted: %s', sprintf(' %d', cl_or_gr_ids));
- end
- end
-
+ grain_ids_sorted = sort(grain_ids);
+ if (any(grain_ids_sorted ~= grain_ids))
+ warning('gtLoadCluster:wrong_argumet', ...
+ 'Some grain IDs were no sorted: %s', sprintf(' %d', grain_ids));
+ end
str_ids = sprintf('_%04d', grain_ids_sorted);
cluster_file = fullfile(phase_dir, sprintf('grain_cluster%s.mat', str_ids));
diff --git a/4_grains/gtLoadClusterRec.m b/4_grains/gtLoadClusterRec.m
index 75bb4e456c95d3ff60d5db75e3f1421bb0f77580..f4128239cc00e31a8766e71db7e07ee1e1ff58b2 100644
--- a/4_grains/gtLoadClusterRec.m
+++ b/4_grains/gtLoadClusterRec.m
@@ -1,18 +1,4 @@
-function cluster_rec = gtLoadClusterRec(phase_id, cl_or_gr_ids, varargin)
-% GTLOADCLUSTERREC load the 6D reconstruction output of a grain cluster
-% cl = function cluster_rec = gtLoadClusterRec(phase_id, cl_or_gr_ids, varargin)
-% INPUT:
-% phaseID = <int> phase ID
-% cl_or_gr_ids = <int> either the cluster_id (->sample) or
-% list of grain_ids composing the
-% cluster
-%
-% OPTIONAL INPUT (p/v pairs):
-% fields = <string> only load specific fields from
-% cluster structure ('ODF6D', 'SEG')
-% parameters = <struct> for security (make sure to load from right directory)
-%
-
+function cluster_rec = gtLoadClusterRec(phase_id, grain_ids, varargin)
conf = struct('fields', {{}}, 'parameters', {[]});
conf = parse_pv_pairs(conf, varargin);
@@ -22,15 +8,11 @@ function cluster_rec = gtLoadClusterRec(phase_id, cl_or_gr_ids, varargin)
phase_dir = fullfile(conf.parameters.acq.dir, '4_grains', sprintf('phase_%02d', phase_id));
end
- if numel(cl_or_gr_ids) == 1 %only one element - it refers to a cluster
- sample = GtSample.loadFromFile;
- grain_ids_sorted = sample.phases{phase_id}.clusters(cl_or_gr_ids).included_ids;
- else
- grain_ids_sorted = sort(cl_or_gr_ids);
- if (any(grain_ids_sorted ~= cl_or_gr_ids))
- warning('gtLoadCluster:wrong_argumet', ...
- 'Some grain IDs were no sorted: %s', sprintf(' %d', cl_or_gr_ids));
- end
+ grain_ids_sorted = sort(grain_ids);
+
+ if (any(grain_ids_sorted ~= grain_ids))
+ warning('gtLoadCluster:wrong_argumet', ...
+ 'Some grain IDs were no sorted: %s', sprintf(' %d', grain_ids));
end
str_ids = sprintf('_%04d', grain_ids_sorted);
diff --git a/5_reconstruction/gtReconstructGrainTwinCluster.m b/5_reconstruction/gtReconstructGrainTwinCluster.m
index fb407da3de04996f70090d7f3d0a470d220737d7..72747aee40758c537c9445e19369e4e6b3afe81a 100644
--- a/5_reconstruction/gtReconstructGrainTwinCluster.m
+++ b/5_reconstruction/gtReconstructGrainTwinCluster.m
@@ -1,20 +1,7 @@
-function gtReconstructGrainTwinCluster(phase_id, cluster_id, workingdirectory, parameters, varargin)
+function gtReconstructGrainTwinCluster(grain_ids, phase_id, parameters, varargin)
% gtReconstructGrainOrientation 6D reconstructions on a GPU machine
-% gtReconstructGrainTwinCluster(phase_id, cluster_id, workingdirectory, parameters, varargin)
+% gtAstraReconstructGrain(grainIDs, phaseID, [parameters])
% -------------------------------------------------------
- cd(workingdirectory);
-
- if (isdeployed)
- global GT_DB %#ok<NUSED,TLEV>
- global GT_MATLAB_HOME %#ok<NUSED,TLEV>
- load('workspaceGlobal.mat');
- phase_id = str2double(phase_id);
- cluster_id = str2double(cluster_id);
- end
-
- sample = GtSample.loadFromFile;
- grain_ids = sample.phases{phase_id}.clusters(cluster_id).included_ids;
-
if (~exist('parameters', 'var') || isempty(parameters))
parameters = gtLoadParameters();
end
@@ -163,3 +150,4 @@ function gtReconstructGrainTwinCluster(phase_id, cluster_id, workingdirectory, p
save(grain_full_details_file, 'ODF6D', '-v7.3');
end
end
+
diff --git a/5_reconstruction/gtSetupReconstruction.m b/5_reconstruction/gtSetupReconstruction.m
index 9efebf03e76a1ea2322d45556a4560a6d3c0adc5..57f1f6448a309c57d508261ee257193b5bb167a2 100644
--- a/5_reconstruction/gtSetupReconstruction.m
+++ b/5_reconstruction/gtSetupReconstruction.m
@@ -1,19 +1,14 @@
-function gtSetupReconstruction(phaseID, varargin)
+function gtSetupReconstruction(phaseID, list)
% GTSETUPRECONSTRUCTION Simple helper function to launch reconstruction and segmentation of
% absorption volume - as well as reconstruction and segmentation of grain volumes
%
-% gtSetupReconstruction(phaseID, varargin)
+% gtSetupReconstruction(phaseID, list)
% ------------------------------
%
% INPUT:
% phaseID = number of the phase <double> {1}
+% list = vector of grainids, default value is {[1: num_grains]}
%
-% OPTIONAL INPUT:
-% grain_ids = vector of grain_ids, default value is {[1: num_grains]}
-% cluster_ids = vector of cluster_ids, default value is {[1: num_clusters]}
-% 'is_cluster
-% Version 005 12-10-2016 by W. Ludwig
-% Add possibility to launch grain-cluster reconstructions
% Version 004 25-05-2016 by W. Ludwig
% Add possibility to specify a list of grainids - which will be
% handled by OAR
@@ -28,12 +23,6 @@ function gtSetupReconstruction(phaseID, varargin)
% Move gtModifyStructure to before the abs reconstruction is done.
GPU_OK = gtCheckGpu();
-conf.grain_ids = [];
-conf.cluster_ids = [];
-
-if (~isempty(varargin))
- conf = parse_pv_pairs(conf, varargin);
-end
if (~GPU_OK)
disp('Not on a GPU machine, you won''t be able to reconstruct localy!');
@@ -68,7 +57,7 @@ gtSaveParameters(parameters);
nof_phases = numel(parameters.cryst);
-if (nof_phases > 1) && isempty(phaseID)
+if (nof_phases > 1)
phaseID = inputwdefaultnumeric('Enter phaseID', num2str(1));
end
phaseID_str = sprintf('%02d', phaseID);
@@ -139,21 +128,16 @@ else
end
end
-% If input parameter grain_ids is empty, we will use all grains by default
+% If input parameter list is empty, we will use all grains by default
+first = 1;
+last = sample.phases{phaseID}.getNumberOfGrains();
-
-if ~isempty(varargin)
- conf = parse_pv_pairs(conf, varargin);
+if (~exist('list', 'var') || isempty(list))
+ list = [first : last];
end
-if isempty(conf.grain_ids)
- first = 1;
- last = sample.phases{phaseID}.getNumberOfGrains();
- list = [first : last];
-end
-
-check = inputwdefault('Launch grain reconstruction? [y/n]', 'y');
+check = inputwdefault('Launch reconstruction? [y/n]', 'y');
rec_on_OAR = false;
if strcmpi(check, 'y')
if (GPU_OK)
@@ -164,35 +148,13 @@ if strcmpi(check, 'y')
end
if (rec_on_OAR)
launch_on_OAR('gtReconstructGrains', first, last, phaseID_str, ...
- parameters, 'njobs', 8, 'walltime', 3600 * 16, ...
- 'gpu', true, 'distribute', true, 'list', list);
+ parameters, 'njobs', 8, 'walltime', 3600 * 16, ...
+ 'gpu', true, 'distribute', true, 'list', list);
else
gtReconstructGrains(first, last, parameters.acq.dir, phaseID, parameters, 'list', list);
end
end
-if ~isempty(conf.cluster_ids)
- list = conf.cluster_ids;
- check = inputwdefault('Launch cluster reconstruction? [y/n]', 'y');
- rec_on_OAR = false;
- if strcmpi(check, 'y')
- if (GPU_OK)
- check2 = inputwdefault('Launch grain reconstruction via OAR? [y/n]', 'y');
- rec_on_OAR = strcmpi(check2, 'y');
- else
- rec_on_OAR = true;
- end
- if (rec_on_OAR)
- launch_on_OAR('gtReconstructGrainTwinClusters', first, last, phaseID_str, ...
- parameters, 'njobs', 8, 'walltime', 3600 * 16, ...
- 'gpu', true, 'distribute', true, 'list', list);
- else
- gtReconstructGrainTwinClusters(first, last, parameters.acq.dir, phaseID, parameters, 'list', list);
- end
-
- end
-end
-
if (~rec_on_OAR)
check = inputwdefault('Launch grain segmentation? [y/n]', 'y');
if strcmpi(check, 'y')
diff --git a/zUtil_Conf/batch-dev-conf.xml b/zUtil_Conf/batch-dev-conf.xml
index 1c8fd69ceb68eea2337149f616dc9906fc904c81..ee2084224625bb8690ede7a1f1e5c21eb0847320 100644
--- a/zUtil_Conf/batch-dev-conf.xml
+++ b/zUtil_Conf/batch-dev-conf.xml
@@ -47,9 +47,6 @@
<function name="gtReconstructGrains">
<path absolute="false">5_reconstruction/gtReconstructGrains.m</path>
</function>
- <function name="gtReconstructGrainTwinClusters">
- <path absolute="false">5_reconstruction/gtReconstructGrainTwinClusters.m</path>
- </function>
<function name="gtForwardSimulate_v2">
<path absolute="false">zUtil_ForwardSim/gtForwardSimulate_v2.m</path>
</function>