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Commit 3979e771 authored by Nicola Vigano's avatar Nicola Vigano
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Revert "Enable reconstruction of twinclusters on OAR, using gtSetupReconstruction" 

This reverts commit a3e9f983.
parent fabd60e3
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4_grains/gtLoadCluster.m
+ 6
− 25
View file @ 3979e771
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));
......
4_grains/gtLoadClusterRec.m
+ 6
− 24
View file @ 3979e771
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);
......
5_reconstruction/gtReconstructGrainTwinCluster.m
+ 3
− 15
View file @ 3979e771
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
5_reconstruction/gtSetupReconstruction.m
+ 12
− 50
View file @ 3979e771
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')
......
zUtil_Conf/batch-dev-conf.xml
+ 0
− 3
View file @ 3979e771
......@@ -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>
......
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