From 4eac6426e5abc99db7b37443983ec7ff3f55deb5 Mon Sep 17 00:00:00 2001
From: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>
Date: Thu, 18 Jan 2018 10:06:58 +0100
Subject: [PATCH] fixing grain Thresholing on OAR; couple of small fixes
Signed-off-by: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>
---
1_preprocessing/gtFillCrystFields.m | 6 +++---
1_preprocessing/gtFindRotationAxis.m | 2 ++
5_reconstruction/gtAstraReconstructGrain.m | 4 ++++
5_reconstruction/gtChangeThreshold3D.m | 17 +++++++++++++----
5_reconstruction/gtReconstructGrains.m | 8 ++++++--
5_reconstruction/gtSetupReconstruction.m | 13 +------------
6_rendering/gtDrawGrainUnitCells.m | 3 ++-
zUtil_Indexter/gtINDEXMatchGrains.m | 8 ++++++--
zUtil_Python/oar/oar_api.py | 1 +
9 files changed, 38 insertions(+), 24 deletions(-)
diff --git a/1_preprocessing/gtFillCrystFields.m b/1_preprocessing/gtFillCrystFields.m
index 6d6795c4..f02b8e0a 100644
--- a/1_preprocessing/gtFillCrystFields.m
+++ b/1_preprocessing/gtFillCrystFields.m
@@ -370,8 +370,8 @@ function cryst = sfUpdateReflections(cryst, energy)
cryst.thetasp = asind(0.5*lambda./cryst.dspacingsp);
% Update the intensity info: MISSING !
- cryst.int = ones(1, numel(cryst.dspacing);
- cryst.intsp = ones(1, numel(cryst.dspacingsp);
- cryst.usedfam = true(1, numel(cryst.dspacing);
+ cryst.int = ones(1, numel(cryst.dspacing));
+ cryst.intsp = ones(1, numel(cryst.dspacingsp));
+ cryst.usedfam = true(1, numel(cryst.dspacing));
end
diff --git a/1_preprocessing/gtFindRotationAxis.m b/1_preprocessing/gtFindRotationAxis.m
index af9de586..cdd5f02c 100644
--- a/1_preprocessing/gtFindRotationAxis.m
+++ b/1_preprocessing/gtFindRotationAxis.m
@@ -25,6 +25,7 @@ try
name_next = fullfile(raw_data_dir, sprintf('%s%04d.edf', acq.name, indx_next) );
if exist(name_next,'file')
+ sprintf('Using images AFTER scan for determination of rotation axis posistion\n')
% FIRST CHOICE: IMAGES AFTER SCAN
indx_curr = 2*acq.nproj;
@@ -32,6 +33,7 @@ try
name_ref0 = fullfile(raw_data_dir, sprintf('ref0000_%04d.edf', indx_curr) );
name_ref1 = name_ref0;
else
+ sprintf('Using images DURING scan for determination of rotation axis posistion\n')
% SECOND CHOICE: IMAGES DURING SCAN
% WL May 2009
% changed to use per default the images at end of scan - should be more accurate;
diff --git a/5_reconstruction/gtAstraReconstructGrain.m b/5_reconstruction/gtAstraReconstructGrain.m
index 67d20eee..559d0c31 100644
--- a/5_reconstruction/gtAstraReconstructGrain.m
+++ b/5_reconstruction/gtAstraReconstructGrain.m
@@ -31,6 +31,10 @@ function varargout = gtAstraReconstructGrain(grainID, phaseID, parameters)
gr_extra = gtLoadGrain(phaseID, grainID, 'fields', {'selected'});
gr.proj.selected = gr_extra.selected;
end
+ if isempty(find(gr.proj.selected))
+ warning('No projection has been selected - skipping grain')
+ return
+ end
gr.proj.num_iter = rec_opts.num_iter;
gr.proj.stack = gr.proj.stack(:, gr.proj.selected, :);
diff --git a/5_reconstruction/gtChangeThreshold3D.m b/5_reconstruction/gtChangeThreshold3D.m
index dcbe41bd..263a14aa 100644
--- a/5_reconstruction/gtChangeThreshold3D.m
+++ b/5_reconstruction/gtChangeThreshold3D.m
@@ -1,4 +1,4 @@
-function [varargout] = gtChangeThreshold3D(firstID, lastID, ~, phaseID, parameters, varargin)
+function [varargout] = gtChangeThreshold3D(firstID, lastID, ~, phaseID, ~, varargin)
% GTCHANGETHRESHOLD3D
% seg = gtChangeThreshold3D(firstID, lastID, ~, phaseID, varargin)
% ----------------------------------------------------------------
@@ -11,6 +11,9 @@ function [varargout] = gtChangeThreshold3D(firstID, lastID, ~, phaseID, paramete
% varargin = to modify parameters.rec
%
+ args = struct('list', [], 'verbose', false);
+ args = parse_pv_pairs(args, varargin);
+
if (isdeployed)
global GT_DB
global GT_MATLAB_HOME
@@ -23,14 +26,20 @@ function [varargout] = gtChangeThreshold3D(firstID, lastID, ~, phaseID, paramete
warning('OAR:unexpected_behavior', ...
'We should expect only strings from shell environment')
end
+
+ args.list = str2num(args.list); %#ok<ST2NM>
end
+ % This handles OAR's habbit of passing lists of IDs in a field called
+ % 'list'
+ args.grain_ids = args.list;
+ args = rmfield(args, 'list');
- args = [varargin, 'verbose', false];
+ args = [fieldnames(args), struct2cell(args)]';
thresh = GtThreshold(args{:});
- if (nargin >= 1)
+ if (nargout >= 1)
varargout{1} = thresh.batchThreshold(phaseID, firstID, lastID);
else
- thresh.batchThreshold(phaseID, firstID, lastID)
+ thresh.batchThreshold(phaseID, firstID, lastID);
end
end
diff --git a/5_reconstruction/gtReconstructGrains.m b/5_reconstruction/gtReconstructGrains.m
index e4542458..dfadeab7 100644
--- a/5_reconstruction/gtReconstructGrains.m
+++ b/5_reconstruction/gtReconstructGrains.m
@@ -96,8 +96,12 @@ function gtReconstructGrains(first, last, workingdirectory, phaseID, parameters,
gtReconstructGrainOrientation(gr_id, phaseID, parameters);
end
if (~isdeployed)
- t.singleGrainAutoThreshold(phaseID, gr_id);
- fprintf(repmat('\b', [1 num_chars]))
+ try
+ t.singleGrainAutoThreshold(phaseID, gr_id);
+ fprintf(repmat('\b', [1 num_chars]))
+ catch
+ sprintf('Segmentation of grain %d failed - check reconstruction!', gr_id)
+ end
end
end
fprintf('Done (in %f seconds).\n', toc(c))
diff --git a/5_reconstruction/gtSetupReconstruction.m b/5_reconstruction/gtSetupReconstruction.m
index a21f11b0..44fbba42 100644
--- a/5_reconstruction/gtSetupReconstruction.m
+++ b/5_reconstruction/gtSetupReconstruction.m
@@ -177,18 +177,7 @@ if (~isempty(conf.grain_ids))
launch_on_OAR('gtChangeThreshold3D', first, last, ...
phaseID_str, parameters, 'core', 4, 'distribute', true, 'list', conf.grain_ids);
else
- if isempty(conf.grain_ids)
- gtChangeThreshold3D(first, last, [], phase_id);
- else
- t=GtThreshold();
- for i = 1 : numel(conf.grain_ids)
- if sample.phases{phase_id}.getSelected(conf.grain_ids(i))
- t.singleGrainAutoThreshold(phase_id, conf.grain_ids(i));
- else
- sprintf('skipping deselected grain %d\n',conf.grain_ids(i))
- end
- end
- end
+ gtChangeThreshold3D(first, last, [], phase_id, [], 'list', conf.grain_ids);
end
end
end
diff --git a/6_rendering/gtDrawGrainUnitCells.m b/6_rendering/gtDrawGrainUnitCells.m
index 8a618b87..1e919eba 100644
--- a/6_rendering/gtDrawGrainUnitCells.m
+++ b/6_rendering/gtDrawGrainUnitCells.m
@@ -98,8 +98,9 @@ app.linecolor = app.linecolor(1:numel(grains));
parameters = [];
load('parameters.mat');
labgeo = parameters.labgeo;
+detgeo = parameters.detgeo;
if isempty(app.pxsize{1})
- app.pxsize{1} = (labgeo.pixelsizeu + labgeo.pixelsizev)/2;
+ app.pxsize{1} = (detgeo.pixelsizeu + detgeo.pixelsizev)/2;
end
if isempty(app.hf)
diff --git a/zUtil_Indexter/gtINDEXMatchGrains.m b/zUtil_Indexter/gtINDEXMatchGrains.m
index 6b2b5cac..2a282608 100644
--- a/zUtil_Indexter/gtINDEXMatchGrains.m
+++ b/zUtil_Indexter/gtINDEXMatchGrains.m
@@ -1,4 +1,4 @@
-function [match, dev, dcm, drotm, conflicts, toBeChecked] = gtINDEXMatchGrains(...
+function [match, dev, dcm, drotm, conflicts, toBeChecked, tol] = gtINDEXMatchGrains(...
grain1, grain2, ph1, dc, drot, tol)
% GTINDEXMATCHGRAINS Matches multiple indexed grains between two datasets;
% can also be used to find unmerged grains.
@@ -178,7 +178,7 @@ disp('Loading pixelsize and crystallographic info from parameters.mat ...')
parameters = [];
load parameters
cryst = parameters.cryst(ph1);
-pixsize = 0.5*(parameters.labgeo.pixelsizeu + parameters.labgeo.pixelsizev);
+pixsize = 0.5*(parameters.detgeo.pixelsizeu + parameters.detgeo.pixelsizev);
match = NaN(nof_grains1,2);
@@ -224,6 +224,10 @@ dev.rot = NaN(3,3,nof_grains1);
% Extension to Rodrigues fundamental zone
% Rext = 0;
Rext = tol.Rdist;
+spacegroup = cryst.spacegroup;
+fzone_acc = gtCrystRodriguesFundZone(spacegroup,0);
+fzone_ext = gtCrystRodriguesFundZone(spacegroup,Rext);
+
if (any(gtIndexAllGrainValues(grain1,'R_onedge',[],1,[])) || ~isempty(drot))
diff --git a/zUtil_Python/oar/oar_api.py b/zUtil_Python/oar/oar_api.py
index 1c9bb50f..a3c6b683 100755
--- a/zUtil_Python/oar/oar_api.py
+++ b/zUtil_Python/oar/oar_api.py
@@ -17,6 +17,7 @@ except ImportError as exc:
from yaml import YamlLoader
try:
+ raise ImportError('requests has been disabled')
import requests
from requests.exceptions import ConnectionError, HTTPError
from urllib2 import URLError
--
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