From 88e4b9108ba696a47b022f186269fc0fab74b7b7 Mon Sep 17 00:00:00 2001
From: Nicola Vigano <nicola.vigano@esrf.fr>
Date: Tue, 24 Feb 2015 19:18:54 +0100
Subject: [PATCH] Extended/Cluster: added support functions and moved
segmentation output to reconstruction file
Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>
---
4_grains/GtThreshold.m | 58 +++++++++++-------------------
4_grains/gtLoadCluster.m | 31 ++++++++++++++++
4_grains/gtLoadClusterRec.m | 31 ++++++++++++++++
4_grains/gtLoadGrain.m | 8 +++--
4_grains/gtLoadGrainRec.m | 8 +++--
4_grains/gtSaveCluster.m | 34 ++++++++++++++++++
4_grains/gtSaveClusterRec.m | 49 +++++++++++++++++++++++++
4_grains/gtSaveGrainRec.m | 9 +++--
5_reconstruction/GtAssembleVol3D.m | 18 +++++-----
9 files changed, 193 insertions(+), 53 deletions(-)
create mode 100644 4_grains/gtLoadCluster.m
create mode 100644 4_grains/gtLoadClusterRec.m
create mode 100644 4_grains/gtSaveCluster.m
create mode 100644 4_grains/gtSaveClusterRec.m
diff --git a/4_grains/GtThreshold.m b/4_grains/GtThreshold.m
index 9c750a2e..4bd2d5e3 100644
--- a/4_grains/GtThreshold.m
+++ b/4_grains/GtThreshold.m
@@ -119,7 +119,7 @@ classdef GtThreshold < handle
sample.phases{phaseID}.setBoundingBox(grainID, grain.segbb);
% Write to file
- obj.saveGrain(phaseID, grainID, grain);
+ obj.saveGrain(phaseID, grainID, grain, sample);
catch mexc
gtPrintException(mexc, ...
'Segmenting grain %d in phase %d failed', grainID, phaseID);
@@ -171,7 +171,7 @@ classdef GtThreshold < handle
grain_seg.segbb = round([(size(grain_rec.vol) -1), (size(grain_rec.vol) +1)] /2);
end
- obj.saveGrain(phaseID, grainID, grain_seg);
+ obj.saveGrain(phaseID, grainID, grain_seg, sample);
fprintf('Done.\n');
end
@@ -200,7 +200,7 @@ classdef GtThreshold < handle
end
sample.phases{phaseID}.setBoundingBox(grainID, grain.segbb);
- obj.saveGrain(phaseID, grainID, grain);
+ obj.saveGrain(phaseID, grainID, grain, sample);
fprintf('\b\b: Done.\n');
fprintf('Writing to sample.mat..')
@@ -263,65 +263,47 @@ classdef GtThreshold < handle
% grain = loadGrain(obj, phaseID, grainID)
grain_out = gtLoadGrain(phaseID, grainID, 'fields', {'id'});
- grain_rec = gtLoadGrainRec(phaseID, grainID);
is_6D = isfield(obj.param.rec, 'grains') ...
&& strcmpi(obj.param.rec.grains.algorithm(1:2), '6D');
- if (is_6D)
- file_ext_rec_path = fullfile(obj.param.acq.dir, ...
- '4_grains', sprintf('phase_%02d', phaseID), ...
- sprintf('grain_extended_details_%04d.mat', grainID));
+ is_extended = sample.phases{phaseID}.getUseExtended(grainID);
- if (sample.phases{phaseID}.getUseExtended(grainID))
- grain_rec = load(file_ext_rec_path, 'ODF6D');
- end
+ grain_rec = gtLoadGrainRec(phaseID, grainID, ...
+ 'is_extended', is_6D && is_extended);
+ if (is_6D)
grain_out.vol = grain_rec.ODF6D.intensity;
grain_out.shift = grain_rec.ODF6D.shift;
else
grain_out.vol = grain_rec.VOL3D.intensity;
grain_out.shift = grain_rec.VOL3D.shift;
end
-
- if (~isfield(grain_out, 'vol') || isempty(grain_out.vol))
- gtError('GtThreshold:wrong_argument', ...
- 'Volume to segment is empty!')
- end
end
- function saveGrain(~, phaseID, grainID, grain_seg)
+ function saveGrain(obj, phaseID, grainID, grain_seg, sample)
% GTTHRESHOLD/SAVEGRAIN
% saveGrain(obj, phaseID, grainID, grain)
- seg_struct = struct('SEG', grain_seg);
- gtSaveGrainRec(phaseID, grainID, seg_struct, 'fields', {'SEG'});
- end
+ is_6D = isfield(obj.param.rec, 'grains') ...
+ && strcmpi(obj.param.rec.grains.algorithm(1:2), '6D');
+ is_extended = sample.phases{phaseID}.getUseExtended(grainID);
- function cluster = loadCluster(obj, phase_id, grain_ids)
- str_ids = sprintf('_%04d', grain_ids);
- file_cluster_rec_path = fullfile(obj.param.acq.dir, ...
- '4_grains', sprintf('phase_%02d', phase_id), ...
- sprintf('grain_cluster_details%s.mat', str_ids));
- cluster_rec = load(file_cluster_rec_path);
+ grain_rec = struct('SEG', grain_seg);
+ gtSaveGrainRec(phaseID, grainID, grain_rec, 'fields', {'SEG'}, ...
+ 'is_extended', is_6D && is_extended);
+ end
+ function cluster = loadCluster(~, phase_id, grain_ids)
+ cluster_rec = gtLoadClusterRec(phase_id, grain_ids);
cluster = struct( ...
'id', grain_ids(1), ...
'vol', cluster_rec.ODF6D.intensity, ...
'shift', cluster_rec.ODF6D.shift );
end
- function saveCluster(obj, phase_id, grain_ids, cluster)
- str_ids = sprintf('_%04d', grain_ids);
- file_cluster_rec_path = fullfile(obj.param.acq.dir, ...
- '4_grains', sprintf('phase_%02d', phase_id), ...
- sprintf('grain_cluster_details%s.mat', str_ids));
- cluster_rec = load(file_cluster_rec_path);
-
- cluster_rec.SEG = struct( ...
- 'seg', cluster.seg, 'segbb', cluster.segbb, ...
- 'threshold', cluster.threshold, 'Area', cluster.Area, ...
- 'seed', cluster.seed );
- save(file_cluster_rec_path, '-struct', 'cluster_rec', '-v7.3');
+ function saveCluster(~, phase_id, grain_ids, cluster_seg)
+ cluster_rec = struct('SEG', cluster_seg);
+ gtSaveClusterRec(phase_id, grain_ids, cluster_rec, 'fields', {'SEG'});
end
function is_iterative = checkIsIterative(obj)
diff --git a/4_grains/gtLoadCluster.m b/4_grains/gtLoadCluster.m
new file mode 100644
index 00000000..c3b3af7d
--- /dev/null
+++ b/4_grains/gtLoadCluster.m
@@ -0,0 +1,31 @@
+function cluster = gtLoadCluster(phase_id, grain_ids, varargin)
+ conf = struct('fields', {{}}, 'parameters', {[]});
+ conf = parse_pv_pairs(conf, varargin);
+
+ if (isempty(conf.parameters))
+ phase_dir = fullfile('4_grains', sprintf('phase_%02d', phase_id));
+ else
+ phase_dir = fullfile(conf.parameters.acq.dir, '4_grains', sprintf('phase_%02d', phase_id));
+ end
+
+ grain_ids_sorted = sort(grain_ids);
+ grain_ids_unique = unique(grain_ids_sorted);
+
+ if (numel(grain_ids) ~= numel(grain_ids_unique))
+ warning('gtLoadCluster:wrong_argumet', ...
+ 'Some redundant grain IDs were given: %s', sprintf(' %d', grain_ids));
+ end
+ 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_unique);
+ cluster_file = fullfile(phase_dir, sprintf('grain_cluster%s.mat', str_ids));
+
+ if (isempty(conf.fields))
+ cluster = load(cluster_file);
+ else
+ cluster = load(cluster_file, conf.fields{:});
+ end
+end
diff --git a/4_grains/gtLoadClusterRec.m b/4_grains/gtLoadClusterRec.m
new file mode 100644
index 00000000..9d7b00b7
--- /dev/null
+++ b/4_grains/gtLoadClusterRec.m
@@ -0,0 +1,31 @@
+function cluster_rec = gtLoadClusterRec(phase_id, grain_ids, varargin)
+ conf = struct('fields', {{}}, 'parameters', {[]});
+ conf = parse_pv_pairs(conf, varargin);
+
+ if (isempty(conf.parameters))
+ phase_dir = fullfile('4_grains', sprintf('phase_%02d', phase_id));
+ else
+ phase_dir = fullfile(conf.parameters.acq.dir, '4_grains', sprintf('phase_%02d', phase_id));
+ end
+
+ grain_ids_sorted = sort(grain_ids);
+ grain_ids_unique = unique(grain_ids_sorted);
+
+ if (numel(grain_ids) ~= numel(grain_ids_unique))
+ warning('gtLoadCluster:wrong_argumet', ...
+ 'Some redundant grain IDs were given: %s', sprintf(' %d', grain_ids));
+ end
+ 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_unique);
+ cluster_file = fullfile(phase_dir, sprintf('grain_cluster_details%s.mat', str_ids));
+
+ if (isempty(conf.fields))
+ cluster_rec = load(cluster_file);
+ else
+ cluster_rec = load(cluster_file, conf.fields{:});
+ end
+end
diff --git a/4_grains/gtLoadGrain.m b/4_grains/gtLoadGrain.m
index 2e2a2dc2..a677ed91 100644
--- a/4_grains/gtLoadGrain.m
+++ b/4_grains/gtLoadGrain.m
@@ -1,5 +1,5 @@
function grain = gtLoadGrain(phase_id, grain_id, varargin)
- conf = struct('fields', {{}}, 'parameters', {[]});
+ conf = struct('fields', {{}}, 'parameters', {[]}, 'is_extended', {false});
conf = parse_pv_pairs(conf, varargin);
if (isempty(conf.parameters))
@@ -9,7 +9,11 @@ function grain = gtLoadGrain(phase_id, grain_id, varargin)
end
for ii = numel(grain_id):-1:1
- grain_file = fullfile(phase_dir, sprintf('grain_%04d.mat', grain_id(ii)));
+ if (conf.is_extended)
+ grain_file = fullfile(phase_dir, sprintf('grain_extended_%04d.mat', grain_id(ii)));
+ else
+ grain_file = fullfile(phase_dir, sprintf('grain_%04d.mat', grain_id(ii)));
+ end
if (isempty(conf.fields))
grain(ii) = load(grain_file);
diff --git a/4_grains/gtLoadGrainRec.m b/4_grains/gtLoadGrainRec.m
index 9dfe5f40..317fa2dc 100644
--- a/4_grains/gtLoadGrainRec.m
+++ b/4_grains/gtLoadGrainRec.m
@@ -1,5 +1,5 @@
function grain_det = gtLoadGrainRec(phase_id, grain_id, varargin)
- conf = struct('fields', {{}}, 'parameters', {[]});
+ conf = struct('fields', {{}}, 'parameters', {[]}, 'is_extended', {false});
conf = parse_pv_pairs(conf, varargin);
if (isempty(conf.parameters))
@@ -9,7 +9,11 @@ function grain_det = gtLoadGrainRec(phase_id, grain_id, varargin)
end
for ii = numel(grain_id):-1:1
- grain_file = fullfile(phase_dir, sprintf('grain_details_%04d.mat', grain_id(ii)));
+ if (conf.is_extended)
+ grain_file = fullfile(phase_dir, sprintf('grain_extended_details_%04d.mat', grain_id(ii)));
+ else
+ grain_file = fullfile(phase_dir, sprintf('grain_details_%04d.mat', grain_id(ii)));
+ end
if (isempty(conf.fields))
grain_det(ii) = load(grain_file);
diff --git a/4_grains/gtSaveCluster.m b/4_grains/gtSaveCluster.m
new file mode 100644
index 00000000..1f4206ed
--- /dev/null
+++ b/4_grains/gtSaveCluster.m
@@ -0,0 +1,34 @@
+function gtSaveCluster(phase_id, grain_ids, cluster, varargin)
+ conf = struct('fields', {{}}, 'parameters', {[]});
+ conf = parse_pv_pairs(conf, varargin);
+
+ if (isempty(conf.parameters))
+ phase_dir = fullfile('4_grains', sprintf('phase_%02d', phase_id));
+ else
+ phase_dir = fullfile(conf.parameters.acq.dir, '4_grains', sprintf('phase_%02d', phase_id));
+ end
+
+ grain_ids_sorted = sort(grain_ids);
+ grain_ids_unique = unique(grain_ids_sorted);
+
+ if (numel(grain_ids) ~= numel(grain_ids_unique))
+ warning('gtLoadCluster:wrong_argumet', ...
+ 'Some redundant grain IDs were given: %s', sprintf(' %d', grain_ids));
+ end
+ 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_unique);
+ grain_file = fullfile(phase_dir, sprintf('grain_cluster%s.mat', str_ids));
+
+ if (isempty(conf.fields))
+ save(grain_file, '-struct', 'grain', '-v7.3');
+ else
+ mat_grain_file = matfile(grain_file, 'Writable', true);
+ for ii_f = 1:numel(conf.fields)
+ mat_grain_file.(conf.fields{ii_f}) = cluster.(conf.fields{ii_f});
+ end
+ end
+end
diff --git a/4_grains/gtSaveClusterRec.m b/4_grains/gtSaveClusterRec.m
new file mode 100644
index 00000000..47c8a1ba
--- /dev/null
+++ b/4_grains/gtSaveClusterRec.m
@@ -0,0 +1,49 @@
+function gtSaveClusterRec(phase_id, grain_ids, cluster_rec_in, varargin)
+ details_fields = {'VOL3D', 'ODF6D', 'ODFw', 'ODFuvw', 'SEG'};
+ conf = struct( ...
+ 'fields', {details_fields}, ...
+ 'parameters', {[]}, ...
+ 'clean', {false} );
+ conf = parse_pv_pairs(conf, varargin);
+
+ % Only allow for the possible fields
+ conf.fields = intersect(conf.fields, details_fields);
+
+ grain_ids_sorted = sort(grain_ids);
+ grain_ids_unique = unique(grain_ids_sorted);
+
+ if (numel(grain_ids) ~= numel(grain_ids_unique))
+ warning('gtLoadCluster:wrong_argumet', ...
+ 'Some redundant grain IDs were given: %s', sprintf(' %d', grain_ids));
+ end
+ if (any(grain_ids_sorted ~= grain_ids))
+ warning('gtLoadCluster:wrong_argumet', ...
+ 'Some grain IDs were no sorted: %s', sprintf(' %d', grain_ids));
+ end
+
+ if (isempty(conf.parameters))
+ phase_dir = fullfile('4_grains', sprintf('phase_%02d', phase_id));
+ else
+ phase_dir = fullfile(conf.parameters.acq.dir, '4_grains', sprintf('phase_%02d', phase_id));
+ end
+
+ str_ids = sprintf('_%04d', grain_ids_unique);
+ cluster_file = fullfile(phase_dir, sprintf('grain_cluster_details%s.mat', str_ids));
+
+ if (conf.clean)
+ if (exist(cluster_file, file))
+ cluster_rec_out = load(cluster_file);
+ else
+ cluster_rec_out = struct();
+ end
+ for ii_f = 1:numel(conf.fields)
+ cluster_rec_out.(conf.fields{ii_f}) = cluster_rec_in.(conf.fields{ii_f});
+ end
+ save(cluster_file, '-struct', 'gr_det', '-v7.3');
+ else
+ mat_cluster_rec_file = matfile(cluster_file, 'Writable', true);
+ for ii_f = 1:numel(conf.fields)
+ mat_cluster_rec_file.(conf.fields{ii_f}) = cluster_rec_in.(conf.fields{ii_f});
+ end
+ end
+end
diff --git a/4_grains/gtSaveGrainRec.m b/4_grains/gtSaveGrainRec.m
index 6b6363b0..e342be06 100644
--- a/4_grains/gtSaveGrainRec.m
+++ b/4_grains/gtSaveGrainRec.m
@@ -3,14 +3,19 @@ function gtSaveGrainRec(phase_id, grain_id, grain_det, varargin)
conf = struct( ...
'fields', {details_fields}, ...
'parameters', {[]}, ...
- 'clean', false );
+ 'is_extended', {false}, ...
+ 'clean', {false} );
conf = parse_pv_pairs(conf, varargin);
% Only allow for the possible fields
conf.fields = intersect(conf.fields, details_fields);
phase_dir = fullfile('4_grains', sprintf('phase_%02d', phase_id));
- grain_file = fullfile(phase_dir, sprintf('grain_details_%04d.mat', grain_id));
+ if (conf.is_extended)
+ grain_file = fullfile(phase_dir, sprintf('grain_extended_details_%04d.mat', grain_id));
+ else
+ grain_file = fullfile(phase_dir, sprintf('grain_details_%04d.mat', grain_id));
+ end
if (conf.clean)
if (exist(grain_file, file))
diff --git a/5_reconstruction/GtAssembleVol3D.m b/5_reconstruction/GtAssembleVol3D.m
index 0d2e992a..68aa88a0 100644
--- a/5_reconstruction/GtAssembleVol3D.m
+++ b/5_reconstruction/GtAssembleVol3D.m
@@ -528,16 +528,15 @@ classdef GtAssembleVol3D < handle
for ii = 1:clustersNum
str_ids = sprintf('_%04d', clusters(ii).included_ids);
try
- file_cluster_rec_path = fullfile(obj.parameters.acq.dir, ...
- '4_grains', sprintf('phase_%02d', phase_id), ...
- sprintf('grain_cluster_details%s.mat', str_ids));
- cluster_rec = load(file_cluster_rec_path);
+ cluster_rec = gtLoadClusterRec( ...
+ phase_id, clusters(ii).included_ids, ...
+ 'fields', {'SEG', 'ODF6D'});
if (rotate_vols)
- file_cluster_path = fullfile(obj.parameters.acq.dir, ...
- '4_grains', sprintf('phase_%02d', phase_id), ...
- sprintf('grain_cluster%s.mat', str_ids));
- cluster = load(file_cluster_path);
+ cluster = gtLoadCluster( ...
+ phase_id, clusters(ii).included_ids, ...
+ 'fields', {'proj'});
+
cluster.proj.centerpix = cluster.proj.centerpix * rot;
int_vol = gtRotateVolume(cluster_rec.ODF6D.intensity, rot);
@@ -610,11 +609,12 @@ classdef GtAssembleVol3D < handle
if (assemble_6D)
if (sample.phases{phase_id}.getUseExtended(grain_id))
vol6D = obj.localPar.cache.get('grain_ext_rec', {phase_id, grain_id}, 'ODF6D');
+ gr_seg = obj.localPar.cache.get('grain_ext_rec', {phase_id, grain_id}, 'SEG');
else
vol6D = obj.localPar.cache.get('grain_rec', {phase_id, grain_id}, 'ODF6D');
+ gr_seg = obj.localPar.cache.get('grain_rec', {phase_id, grain_id}, 'SEG');
end
end
- gr_seg = obj.localPar.cache.get('grain_rec', {phase_id, grain_id}, 'SEG');
if (rotate_vols)
gr_proj = obj.localPar.cache.get('grain', {phase_id, grain_id}, 'proj');
--
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