From eb8b0547136b71f8dba6786ff49369c507f24075 Mon Sep 17 00:00:00 2001
From: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>
Date: Fri, 9 Jun 2017 11:57:58 +0200
Subject: [PATCH] minor fixes
Signed-off-by: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>
---
.../gt6DCreateProjDataFromExtendedGrain.m | 5 +++--
zUtil_EDF/edf_read.m | 13 +++++++------
zUtil_ForwardSim/gtFwdSimBuildDifstackBlobs.m | 6 +++---
zUtil_ForwardSim/gtFwdSimCheckSpotInRawImages.m | 4 ++--
4 files changed, 15 insertions(+), 13 deletions(-)
diff --git a/zUtil_Deformation/gt6DCreateProjDataFromExtendedGrain.m b/zUtil_Deformation/gt6DCreateProjDataFromExtendedGrain.m
index 6eb4bdd2..d9d7cd12 100644
--- a/zUtil_Deformation/gt6DCreateProjDataFromExtendedGrain.m
+++ b/zUtil_Deformation/gt6DCreateProjDataFromExtendedGrain.m
@@ -18,7 +18,8 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
'rspace_oversize', 1.1, ...
'ospace_lims', [], ...
'include_all', false, ...
- 'save', false );
+ 'save', false, ...
+ 'psf', []);
conf = parse_pv_pairs(conf, varargin);
if (~isstruct(gr_id))
@@ -299,7 +300,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
proj.vol_size_x = vol_size(2);
proj.vol_size_y = vol_size(1);
proj.vol_size_z = vol_size(3);
-
+ proj.psf = conf.psf;
refor.proj(conf.det_index) = proj;
refor.bb_ors = ors;
diff --git a/zUtil_EDF/edf_read.m b/zUtil_EDF/edf_read.m
index c59b684e..6bc03922 100644
--- a/zUtil_EDF/edf_read.m
+++ b/zUtil_EDF/edf_read.m
@@ -30,7 +30,7 @@ function [img, varargout] = edf_read(filename, GT_bb, dispmes, info, varargin)
dispmes = ~strcmp(dispmes, 'nodisp');
end
- conf = struct('verbose', dispmes, 'convert', true);
+ conf = struct('verbose', dispmes, 'convert', true, 'permute', true);
conf = parse_pv_pairs(conf, varargin);
% Check file
@@ -102,11 +102,12 @@ function [img, varargout] = edf_read(filename, GT_bb, dispmes, info, varargin)
%%% Let's reshape to the real format of the matrix
img = reshape(img, dim_1, dim_2, info.dim_3);
-
- if (info.dim_3 > 1) % 3D volume
- img = permute(img, [2 1 3]); % reorganise dimensions
- else % 2D image
- img = transpose(img);
+ if conf.permute
+ if (info.dim_3 > 1) % 3D volume
+ img = permute(img, [2 1 3]); % reorganise dimensions
+ else % 2D image
+ img = transpose(img);
+ end
end
if (~isa(img, 'double') && conf.convert)
diff --git a/zUtil_ForwardSim/gtFwdSimBuildDifstackBlobs.m b/zUtil_ForwardSim/gtFwdSimBuildDifstackBlobs.m
index 2e3fed20..6006d2b9 100644
--- a/zUtil_ForwardSim/gtFwdSimBuildDifstackBlobs.m
+++ b/zUtil_ForwardSim/gtFwdSimBuildDifstackBlobs.m
@@ -27,9 +27,9 @@ function bl = gtFwdSimBuildDifstackBlobs(blobids, parameters, stackUSize, stackV
blob_bb = blob_bb([2 1 3 5 4 6]);
bl(ii).mbbsize = blob_bb(4:6);
- bl(ii).mbbu = [blob_bb(1), blob_bb(1) + blob_bb(4) + 1];
- bl(ii).mbbv = [blob_bb(2), blob_bb(2) + blob_bb(5) + 1];
- bl(ii).mbbw = [blob_bb(3), blob_bb(3) + blob_bb(6) + 1];
+ bl(ii).mbbu = [blob_bb(1), blob_bb(1) + blob_bb(4) - 1];
+ bl(ii).mbbv = [blob_bb(2), blob_bb(2) + blob_bb(5) - 1];
+ bl(ii).mbbw = [blob_bb(3), blob_bb(3) + blob_bb(6) - 1];
% Essentially zero pads the blob to make it fit into ASTRA's
% diffraction stack
diff --git a/zUtil_ForwardSim/gtFwdSimCheckSpotInRawImages.m b/zUtil_ForwardSim/gtFwdSimCheckSpotInRawImages.m
index abb183cf..d9c74f6a 100644
--- a/zUtil_ForwardSim/gtFwdSimCheckSpotInRawImages.m
+++ b/zUtil_ForwardSim/gtFwdSimCheckSpotInRawImages.m
@@ -16,8 +16,8 @@ function [found_intensity, spotInfo] = gtFwdSimCheckSpotInRawImages(uvw, spotsCo
% completeness) is empty, use the same size as the difspot average size +
% 5 percent
if isempty(parameters.fsim.bb_size)
- bbhsize = floor(spotsCommProps.Xsize*1.05);
- bbvsize = floor(spotsCommProps.Ysize*1.05);
+ bbhsize = spotsCommProps.stackUSize;
+ bbvsize = spotsCommProps.stackVSize;
else
bbhsize = parameters.fsim.bb_size(1);
bbvsize = parameters.fsim.bb_size(2);
--
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