From 2b9c8172ea459851f5045fbffbe85a9eeb53ce68 Mon Sep 17 00:00:00 2001
From: Laura Nervo <lnervo@esrf.fr>
Date: Mon, 9 Jan 2012 15:36:44 +0000
Subject: [PATCH] Add fed structure in parameters.mat and modify
zUtil_Parameters's functions
History:
sed -i -e "s/ 1x1>/>/g" `grep " 1x1>" */*.m | awk -F":" '{print $1}' | sort -busi` | grep ">"
sed -i -e "s/ 1x1/>/g" `grep " 1x1" */*.m | awk -F":" '{print $1}' | sort -busi` | grep "> {"
sed -i -e "s/}>/}/g" `grep "}>" */*.m | awk -F":" '{print $1}' | sort -busi` | grep "> {"
sed -i -e "s/gtPlaceDifspotinFull_ln/gtPlaceDifspotinFull/g" `grep "gtPlaceDifspotinFull_ln" */*.m | awk -F":" '{print $1}' | sort -busi` | grep "gtPlaceDifspotinFull"
sed -i -e "s/))/)/g" `grep "disp(sprintf" */*.m | grep "))" | awk -F":" '{print $1}' | sort -busi` | grep "disp(sprintf("
sed -i -e "s/disp(sprintf(/fprintf(/g" `grep "disp(sprintf" */*.m | awk -F":" '{print $1}' | sort -busi` | grep "fprintf("
sed -i -e "s/ );/);/g" `grep "fprintf" */*.m | awk -F":" '{print $1}' | sort -busi` | grep "fprintf(" | grep ");"
Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>
git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@117 4c865b51-4357-4376-afb4-474e03ccb993
---
1_preprocessing/gtSetup.m | 11 +
7_fed/AndyFunctions/gtFEDCondor.m | 192 ++++---
7_fed/AndyFunctions/gtFEDCondor_ln.m | 176 ------
.../gtFedLoadGrainFromIndexter.m | 90 +--
7_fed/AndyFunctions/gtFedLoadRealBlobs.m | 33 +-
7_fed/AndyFunctions/gtFedLoadRealGrain.m | 81 +--
7_fed/AndyFunctions/gtFedSetupT0.m | 19 +-
7_fed/Ccode_SpreadInt/gtFedInitialize.m | 2 +-
7_fed/gtFedGenerateRandomGrain.m | 32 +-
7_fed/gtFedLoadGrainFromIndexter_ln.m | 146 -----
7_fed/gtFedLoadGrainWoIndexter.m | 15 +-
7_fed/gtFedParameters.m | 2 +
7_fed/gtFedSetParameters.m | 6 +-
7_fed/gtFedSetupT0.m | 12 +-
7_fed/gtFedShowDifBlob.m | 14 +-
7_fed/gtFedTestLoadData.m | 8 +-
7_fed/gtGrainPredict.m | 32 +-
zUtil_Parameters/build_list.m | 11 +
zUtil_Parameters/build_list_v2.m | 14 +
zUtil_Parameters/build_parameters.m | 543 ------------------
zUtil_Parameters/make_parameters.m | 2 +-
21 files changed, 332 insertions(+), 1109 deletions(-)
delete mode 100644 7_fed/AndyFunctions/gtFEDCondor_ln.m
delete mode 100644 7_fed/gtFedLoadGrainFromIndexter_ln.m
delete mode 100644 zUtil_Parameters/build_parameters.m
diff --git a/1_preprocessing/gtSetup.m b/1_preprocessing/gtSetup.m
index 6ef24f54..1d7e32e0 100644
--- a/1_preprocessing/gtSetup.m
+++ b/1_preprocessing/gtSetup.m
@@ -8,6 +8,9 @@ function gtSetup()
% '()' at the end of functions/methods
% add 'clear' statements to free memory
%
+% Version 006 06-01-2012 by LNervo
+% Add fed structure
+%
% Version 005 01-12-2011 by LNervo
% Adapt to new parameters file template
% Cryst1 is made of cryst1, xop1, reflections1
@@ -583,6 +586,14 @@ parameters.rec.use_extspots = false;
parameters.rec.percentile1 = 90;
parameters.rec.percentile2 = 20;
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% FED part
+parameters.fed.dir = parameters.acq.dir;
+parameters.fed.dct_vol = [parameters.acq.dir '/dct_vol.edf'];
+parameters.fed.dct_offset = [0 0 0];
+parameters.fed.renumber_list = [];
+
+
disp('Saving parameters.mat in the analysis directory...')
save([parameters.acq.dir '/' 'parameters.mat'],'parameters');
disp(' ')
diff --git a/7_fed/AndyFunctions/gtFEDCondor.m b/7_fed/AndyFunctions/gtFEDCondor.m
index 869dae29..4639c68e 100644
--- a/7_fed/AndyFunctions/gtFEDCondor.m
+++ b/7_fed/AndyFunctions/gtFEDCondor.m
@@ -1,10 +1,24 @@
-
-
-function gtFEDCondor(first, last, workingdirectory)
-% cleaned FED "do all" function for condor
-
-
-disp('gtFEDCondor.m')
+function gtFEDCondor(first, last, workingdirectory, varargin)
+% GTFEDCONDOR Run the FED code
+% gtFEDCondor(first, last, [workingdirectory],[varargin])
+% -------------------------------------------------------
+% cleaned FED "do all" function for OAR
+%
+% INPUT:
+% first = first grain to be processed
+% last = last grain to be processed
+% workingdirectory = current directory <string> {pwd}
+%
+% OPTIONAL INPUT:
+% vertical = set up the vertical detector case <logical> {0}
+% gv_name = grain volume name <string> {'5_reconstruction/dct.edf'}
+% saveflag = save data on disk <logical> {1}
+%
+
+app.vertical = false;
+app.gv_name = '5_reconstruction/dct.edf';
+app.saveflag = true; % want to save data
+app=parse_pv_pairs(app,varargin);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% get parameters
@@ -17,108 +31,122 @@ end
if isdeployed
first=str2double(first);
last=str2double(last);
-end
+end
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% load data files
cd(workingdirectory);
parameters=[];
grain=[];
-load('parameters.mat'); % parameters
-load('grain.mat') % grain
-
-% create FED folder in FED analysis directory if needed
-if ~exist(sprintf('%s/7_FED', parameters.FED.dir), 'dir')
- mkdir(sprintf('%s/7_FED', parameters.FED.dir))
+if exist('parameters.mat','file')
+ load('parameters.mat'); % parameters
+else
+ disp('Attention! the parameters file does not exist. Check the current directory')
+ return
+end
+if exist('grain.mat','file')
+ load('grain.mat') % grain
+else
+ disp('grain.mat not found')
+ disp('Copy the grain.mat from the forward scan if it''s the case and restart the function')
+ return
+end
+if exist(app.gv_name,'file')
+ parameters.fed.dct_vol=app.gv_name;
+ save('parameters.mat','parameters');
end
-saveflag=1; % want to save data
-
+% load volume
+if ~exist(parameters.fed.dct_vol,'file')
+ file=inputwdefault('Insert the path of the grain volume .edf file:',name);
+ dct_vol=edf_read(file);
+ parameters.fed.dct_vol=file;
+ save('parameters.mat','parameters');
+else
+ dct_vol=edf_read(parameters.fed.dct_vol);
+end
+% apply dataset specific shift
+dct_vol=gtPlaceSubVolume(zeros(size(dct_vol)), dct_vol, parameters.fed.dct_offset);
+size(dct_vol)
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% loop through grains
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
for grainid = first:last
-
- if 0 % setup grain
-
% create grain folder if needed
-if ~exist(sprintf('%s/7_FED/grain%d_', parameters.FED.dir, grainid), 'dir')
- mkdir(sprintf('%s/7_FED/grain%d_', parameters.FED.dir, grainid))
-end
-
-% setup fedgrain from indexter grain output
-% save into the above grain folder
-[fedpars, fedgrain]=gtFedLoadGrainFromIndexter(grainid, grain, saveflag);
-
-
-% load volume
-dct_vol=edf_read(parameters.FED.dct_vol);
-% apply dataset specific shift
-dct_vol=gtPlaceSubVolume(zeros(size(dct_vol)), dct_vol, parameters.FED.dct_offset);
-
-% setup FED grain
-% may need to select the right grain in the original volume
-
-
-[fedpars, gv]=gtFedLoadRealGrain(grainid, dct_vol, saveflag);
-
-
-% load blobs
-[gv, bl, bluvol] = gtFedLoadRealBlobs(grainid, saveflag);
-
- else
- % just load the grain
- disp('just loading gv/bl/fedgrain - not doing gtFedLoad...')
- load(sprintf('%s/7_FED/grain%d_/gv', parameters.FED.dir, grainid))
- load(sprintf('%s/7_FED/grain%d_/bl', parameters.FED.dir, grainid))
- load(sprintf('%s/7_FED/grain%d_/fedgrain', parameters.FED.dir, grainid))
- fedpars=fedgrain.fedpars;
+ [s,msg]=mkdir(sprintf('%s/7_fed/grain%d_', parameters.fed.dir, grainid));disp(msg)
+
+
+ if app.vertical==true
+
+ grainFed=load(sprintf('gr%d_fed.mat',grainid),'gr');
+ grainFed=grainFed.gr;
+
+ bbox=load('bbox.mat');
+ bbox=bbox.bbox;
+ % setup fedgrain with grainFed
+ [fedgrain,fedpars,grainFed]=gtFedLoadGrainWoIndexter(grainFed, bbox, 'save_flag',app.saveflag);
+
+ elseif app.vertical==false
+
+ % setup fedgrain from indexter grain output
+ % save into the above grain folder
+ [fedpars, fedgrain]=gtFedLoadGrainFromIndexter(grainid, grain, app.saveflag);
end
-
-
-
-% run the solver
-
-% do the 3 steps
-for fedstep=1:3
-% setup the TO matrices
-[fedpars, gv] = gtFedSetupT0(grainid, fedstep)
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ % setup FED grain
+ % may need to select the right grain in the original volume
+ [fedpars, gv]=gtFedLoadRealGrain(grainid, dct_vol, app.saveflag);
+
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ % load blobs
+ [gv, bl, bluvol] = gtFedLoadRealBlobs(grainid, app.saveflag);
+
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ % run the solver
-% run the solver for this step
-[gv,bl,err]=gtFedSolve(gv,bl,[],[],[],fedpars);
+ % do the 3 steps
+ for fedstep=1:3
+
+ % setup the TO matrices
+ [fedpars, gv] = gtFedSetupT0(grainid, fedstep);
+ % run the solver for this step
+ %[gv,bl,err]=gtFedSolve(grainid);
+ [gv,bl,err]=gtFedSolve(gv,bl,[],[],[],fedpars);
+ % shift the error info for later analysis
+ system(sprintf('mv %s/7_fed/grain%d_/err.mat %s/7_fed/grain%d_/err%d.mat', parameters.fed.dir, grainid, parameters.fed.dir, grainid, fedstep));
-% shift the error info for later analysis
- system(sprintf('mv %s/7_FED/grain%d_/err.mat %s/7_FED/grain%d_/err%d.mat', parameters.FED.dir, grainid, parameters.FED.dir, grainid, fedstep));
+ % make and save omega images
+ bl=gtFedMakeOmegaImages(bl, 0);
+ for i=1:length(bl)
+ bl(i).imfed_omega_save(:,:,fedstep)=bl(i).imfed_omega;
+ end
+ save(sprintf('%s/7_fed/grain%d_/bl.mat', parameters.fed.dir, grainid), 'bl', '-v7.3')
- % make and save omega images
- bl=gtFedMakeOmegaImages(bl, 0);
- for i=1:length(bl)
- bl(i).imfed_omega_save(:,:,fedstep)=bl(i).imfed_omega;
- end
- save(sprintf('%s/7_FED/grain%d_/bl.mat', parameters.FED.dir, grainid), 'bl', '-v7.3')
-
- % save d field of gv
- for i=1:length(gv)
- gv(i).d_save(:,fedstep)=gv(i).d;
- end
- save(sprintf('%s/7_FED/grain%d_/gv.mat', parameters.FED.dir, grainid), 'gv', '-v7.3')
+ % save d field of gv
+ for i=1:length(gv)
+ gv(i).d_save(:,fedstep)=gv(i).d;
+ end
+ save(sprintf('%s/7_fed/grain%d_/gv.mat', parameters.fed.dir, grainid), 'gv', '-v7.3')
- disp(sprintf('@@@@@@@@@@@@@@@@@@@@@ done step %d for grain %d @@@@@@@@@@@@@@@@@@@@@2', fedstep, grainid))
-end
+ fprintf('@@@@@@@@@@@@@@@@@@@@@ done step %d for grain %d @@@@@@@@@@@@@@@@@@@@@@', fedstep, grainid)
+ end
-%compress bl for space saving...
-bl=gtFedCompressBl(bl);
-save(sprintf('%s/7_FED/grain%d_/bl.mat', parameters.FED.dir, grainid), 'bl', '-v7.3')
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ % compress bl for space saving...
+ bl=gtFedCompressBl(bl);
+ save(sprintf('%s/7_fed/grain%d_/bl.mat', parameters.fed.dir, grainid), 'bl', '-v7.3')
-disp(sprintf('grain %d : bl variable compressed to save diskspace', grainid))
+ fprintf('grain %d : bl variable compressed to save diskspace', grainid)
-disp(sprintf('%%%%%%%%%%%% grain %d finished :-) %%%%%%%%%%%', grainid))
+ fprintf('%%%%%%%%%%%% grain %d finished :-) %%%%%%%%%%%', grainid)
end % loop through grains
diff --git a/7_fed/AndyFunctions/gtFEDCondor_ln.m b/7_fed/AndyFunctions/gtFEDCondor_ln.m
deleted file mode 100644
index 2a17d0e2..00000000
--- a/7_fed/AndyFunctions/gtFEDCondor_ln.m
+++ /dev/null
@@ -1,176 +0,0 @@
-function gtFEDCondor_ln(first, last, workingdirectory, varargin)
-% gtFEDCondor(first, last, [workingdirectory],[varargin])
-% cleaned FED "do all" function for condor
-%
-% INPUT :
-% first = first grain to be processed
-% last = last grain to be processed
-% workingdirectory = current directory <string> {pwd}
-%
-% OPTIONAL :
-% vertical = set up the vertical detector case <logical 1x1> {0}
-% gv_name = grain volume name <string> {'dct.edf'}
-% saveflag = save data on disk <logical 1x1> {1}
-%
-
-app.vertical=false;
-app.gv_name='dct.edf';
-app.saveflag=true; % want to save data
-app=parse_pv_pairs(app,varargin);
-
-disp('### Running gtFEDCondor_ln... ###')
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% get parameters
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-% special case for running interactively in current directory
-if ~exist('workingdirectory','var')
- workingdirectory=pwd;
-end
-if isdeployed
- first=str2double(first);
- last=str2double(last);
-end
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% load data files
-cd(workingdirectory);
-parameters=[];
-grain=[];
-if exist('parameters.mat','file')
- load('parameters.mat'); % parameters
-else
- disp('Attention! the parameters file does not exist. Check the current directory')
- return
-end
-if exist('grain.mat','file')
- load('grain.mat') % grain
-else
- disp('grain.mat not found')
- disp('Copy the grain.mat from the forward scan if it''s the case and restart the function')
- return
-end
-
-parameters
-grain
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% create FED folder in FED analysis directory if needed
-
-if ~isfield(parameters, 'FED')
- if ~isfield(parameters.FED, 'dir')
- parameters.FED.dir=parameters.acq.dir;
- end
- if ~isfield(parameters.FED, 'dct_vol')
- parameters.FED.dct_vol=[parameters.FED.dir '/' app.gv_name];
- end
- if ~isfield(parameters.FED, 'dct_offset')
- parameters.FED.dct_offset=[0 0 0];
- end
- save parameters parameters
-end
-
-if ~exist(sprintf('%s/7_FED', parameters.FED.dir), 'dir')
- mkdir(sprintf('%s/7_FED', parameters.FED.dir))
-end
-
-
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% loop through grains
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-for grainid = first:last
-
- % create grain folder if needed
- if ~exist(sprintf('%s/7_FED/grain%d_', parameters.FED.dir, grainid), 'dir')
- mkdir(sprintf('%s/7_FED/grain%d_', parameters.FED.dir, grainid))
- end
-
- if app.vertical
-
- grainFed=load(sprintf('gr%d_fed.mat',grainid),'gr');
- grainFed=grainFed.gr;
-
- bbox=load('bbox.mat');
- bbox=bbox.bbox;
- % setup fedgrain with grainFed
- [fedgrain,fedpars,grainFed]=gtFedLoadGrainWoIndexter(grainFed, bbox, 'save_flag',app.saveflag);
-
- else
-
- % setup fedgrain from indexter grain output
- % save into the above grain folder
- [fedpars, fedgrain]=gtFedLoadGrainFromIndexter(grainid, grain, app.saveflag);
- end
-
-
- % load volume
- if ~exist(parameters.FED.dct_vol,'file')
- file=inputwdefault('Insert the path of the direct beam scan dct.edf file:',name);
- dct_vol=edf_read(file);
- else
- dct_vol=edf_read(parameters.FED.dct_vol);
- end
- % apply dataset specific shift
- dct_vol=gtPlaceSubVolume(zeros(size(dct_vol)), dct_vol, parameters.FED.dct_offset);
- size(dct_vol)
-
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- % setup FED grain
- % may need to select the right grain in the original volume
- [fedpars, gv]=gtFedLoadRealGrain(grainid, dct_vol, saveflag);
-
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- % load blobs
- [gv, bl, bluvol] = gtFedLoadRealBlobs(grainid, saveflag);
-
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- % run the solver
-
- % do the 3 steps
- for fedstep=1:3
-
- % setup the TO matrices
- [fedpars, gv] = gtFedSetupT0(grainid, fedstep)
-
- % run the solver for this step
- %[gv,bl,err]=gtFedSolve(grainid);
- [gv,bl,err]=gtFedSolve(gv,bl,[],[],[],fedpars);
-
- % shift the error info for later analysis
- system(sprintf('mv %s/7_FED/grain%d_/err.mat %s/7_FED/grain%d_/err%d.mat', parameters.FED.dir, grainid, parameters.FED.dir, grainid, fedstep));
-
-
- % make and save omega images
- bl=gtFedMakeOmegaImages(bl, 0);
- for i=1:length(bl)
- bl(i).imfed_omega_save(:,:,fedstep)=bl(i).imfed_omega;
- end
- save(sprintf('%s/7_FED/grain%d_/bl.mat', parameters.FED.dir, grainid), 'bl', '-v7.3')
-
- % save d field of gv
- for i=1:length(gv)
- gv(i).d_save(:,fedstep)=gv(i).d;
- end
- save(sprintf('%s/7_FED/grain%d_/gv.mat', parameters.FED.dir, grainid), 'gv', '-v7.3')
-
- disp(sprintf('@@@@@@@@@@@@@@@@@@@@@ done step %d for grain %d @@@@@@@@@@@@@@@@@@@@@@', fedstep, grainid))
- end
-
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- % compress bl for space saving...
- bl=gtFedCompressBl(bl);
- save(sprintf('%s/7_FED/grain%d_/bl.mat', parameters.FED.dir, grainid), 'bl', '-v7.3')
-
- disp(sprintf('grain %d : bl variable compressed to save diskspace', grainid))
-
- disp(sprintf('%%%%%%%%%%%% grain %d finished :-) %%%%%%%%%%%', grainid))
-
-
-end % loop through grains
-
-
diff --git a/7_fed/AndyFunctions/gtFedLoadGrainFromIndexter.m b/7_fed/AndyFunctions/gtFedLoadGrainFromIndexter.m
index 76a957a0..327f5693 100644
--- a/7_fed/AndyFunctions/gtFedLoadGrainFromIndexter.m
+++ b/7_fed/AndyFunctions/gtFedLoadGrainFromIndexter.m
@@ -1,30 +1,31 @@
function [fedpars, fedgrain]=gtFedLoadGrainFromIndexter(grainid, indexter_grain, varargin)
-
+%% [fedpars, fedgrain]=gtFedLoadGrainFromIndexter(grainid, indexter_grain, varargin)
+%
% create a file called fedgrain.mat - equivilent to the random grain in the
% simulated data code.
% nothing more than the indexter data "unpacked" into single blobs rather
% than pairs.
% setup fedpars.mat at the same time
-
+%
% general comment - at the moment fedgrain and fedpars are saved together
% in one variable (fedgrain). This can perhaps be cleaned.
-
+%
% improve, automate and clean so that it can be run form condor without
% fucking around...
-
+%
% fedpars.mat is grain specific - therefore it should go in the grain
% folder. For the moment, let's introduce a folder structure called
-% 7_FED/grain%d_/ and put fedpars / bl etc in there
-
-% add a path to the dct volume in parameters.FED.final_dct_volume
-% also add parameters.FED.volume_offset to allow for sample movements
+% 7_fed/grain%d_/ and put fedpars / bl etc in there
+%
+% add a path to the dct volume in parameters.fed.final_dct_volume
+% also add parameters.fed.volume_offset to allow for sample movements
% (see fed_real_data_scheme script)
-
+%
% deal with renumbering in a sequence of datasets - ie in this scan it
% might be grain X, but in the reference dataset and the dct volume it
% might be grain Y.
-
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% are we saving?
if length(varargin)==1
save_flag=varargin{1};
@@ -33,9 +34,10 @@ else
disp('gtFedLoadGrainFromIndexter is not saving fedpars.mat, fedgrain.mat')
end
-
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% load DCT parameters
-load parameters
+parameters=[];
+load('parameters.mat');
% indexter output is passed in as indexter_grain
%%%%%%%%%%%%%%%%%%%%%%%% INDEXTER OUTPUT INTO FEDGRAIN %%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -48,13 +50,13 @@ fedgrain.R_vector = a.R_vector;
%%%%%%%%%%%%%%%%%%% GRAIN ID RENUMBERING IF PART OF SEQUENCE %%%%%%%%%%%%%%%%%%%%%%
% may need to consider renumbering
fedgrain.grainID=grainid;
-if isfield(parameters.FED, 'renumber_list')
- list=parameters.FED.renumber_list;
+if ~isempty(parameters.fed.renumber_list)
+ list=parameters.fed.renumber_list;
% list: [referenceID, this dataset ID]
ndx=find(list(:,2)==grainid);
if isempty(ndx)
disp('problem - this grain is not linked to a grain in the reference dataset')
- error
+ return
end
fedgrain.reference_grainid=list(ndx, 1);
else
@@ -63,9 +65,9 @@ end
%%%%%%%%%%%%%%%%%%%%%%%% SETUP FEDPARS %%%%%%%%%%%%%%%%%%%%%%%%%%%%
% How many blobs?
-nbl = 2*fedgrain.nof_pairs;
+nbl = 2*fedgrain.nof_pairs;
-% FED parameters definition
+%.fed parameters definition
fedpars = gtFedParameters();
% add parameters / could be interactive or use defaults
@@ -74,47 +76,47 @@ fedpars = gtFedSetParameters(fedpars, nbl, 'defaults');
% add GrainID
fedpars.grainID=grainid;
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% load general info from parameters.acq into fedpars
-disp('copy experiment geometry from parameters.acq to fedpars')
-fedpars.detpos=parameters.acq.detpos0;
-fedpars.detdiru=parameters.acq.detdiru0;
-fedpars.detdirv=parameters.acq.detdirv0;
-fedpars.rotdir=parameters.acq.rotdir0;
-fedpars.detucen=parameters.acq.detucen0;
-fedpars.detvcen=parameters.acq.detvcen0;
-fedpars.beamdir=parameters.acq.beamdir0;
-
-
+disp('copy experiment geometry from parameters to fedpars')
+% fedpars = gtAddMatFile(fedpars,gtGetGeometry(parameters,'geo',true),true,true,true);
+fedpars = gtAddMatFile(fedpars,gtGetGeometry(parameters,'opt',true),true,true,true);
%%%%%%%%%%%%%%%%%%%%%%%% INDEXTER OUTPUT INTO FEDGRAIN %%%%%%%%%%%%%%%%%%%%%%%%%%%%
% unpack variables, expanding pairs
-fedgrain.pairid = zeros(1, nbl);
+fedgrain.pairid = zeros(1, nbl);
fedgrain.difspots = zeros(1, nbl);
fedgrain.thetatype = zeros(1, nbl);
-fedgrain.hkl = zeros(nbl, size(a.hkl, 2));
-fedgrain.pl0 = zeros(nbl, 3);
-fedgrain.theta = zeros(1, nbl);
-fedgrain.eta = zeros(1, nbl);
-fedgrain.omega = zeros(1, nbl);
+fedgrain.hkl = zeros(nbl, size(a.hkl, 2));
+fedgrain.pl0 = zeros(nbl, 3);
+fedgrain.theta = zeros(1, nbl);
+fedgrain.eta = zeros(1, nbl);
+fedgrain.omega = zeros(1, nbl);
% expand pairs
fedgrain.pairid(1:2:end) = a.pairid;
fedgrain.pairid(2:2:end) = a.pairid;
-fedgrain.difspots(1:2:end)=a.difspots(1:fedgrain.nof_pairs);
-fedgrain.difspots(2:2:end)=a.difspots((fedgrain.nof_pairs+1):end);
+fedgrain.difspots(1:2:end) = a.difspots(1:fedgrain.nof_pairs);
+fedgrain.difspots(2:2:end) = a.difspots((fedgrain.nof_pairs+1):end);
fedgrain.thetatype(1:2:end) = a.thetatype;
fedgrain.thetatype(2:2:end) = a.thetatype;
-fedgrain.hkl(1:2:end, :)=a.hkl;
-fedgrain.hkl(2:2:end, :)=a.hkl;
+
+fedgrain.hkl(1:2:end, :) = a.hkl;
+fedgrain.hkl(2:2:end, :) = a.hkl;
+
fedgrain.pl0(1:2:end, :) = a.pl;
fedgrain.pl0(2:2:end, :) = -a.pl;
+
fedgrain.theta(1:2:end) = a.theta;
fedgrain.theta(2:2:end) = a.theta;
-fedgrain.sinth0=sind(fedgrain.theta);
+
+fedgrain.sinth0 = sind(fedgrain.theta);
+
fedgrain.eta(1:2:end) = a.eta;
fedgrain.eta(2:2:end) = mod(180-a.eta, 360);
+
fedgrain.omega(1:2:end) = a.omega;
fedgrain.omega(2:2:end) = a.omega+180;
@@ -122,21 +124,21 @@ warning('USING MEASURED DIFF ANGLES, SHOULD BE THEORETICAL!!!')
% here we should determine the specific hkls, and predict theta, eta and
% omega and pl0 based on these and the grain R-vector
-%warning('HARD CODING MAX_ELEMENTS_GRAIN...')
-%fedpars.max_elements_grain=2000
+warning('HARD CODING MAX_ELEMENTS_GRAIN...')
+fedpars.max_elements_grain=2000;
% combine fedgrain and fedpars - as fedpars can be grain specific
fedgrain.fedpars=fedpars;
if ~save_flag
- a=inputwdefault('save fedgrain.mat (which includes fedgrain.fedpars)?', 'y');
+ a=inputwdefault('save fedgrain.mat (which includes fedgrain.fedpars)? [y/n]', 'y');
if strcmpi(a, 'y')
- save(sprintf('%s/7_FED/grain%d_/fedgrain.mat', parameters.FED.dir, grainid), 'fedgrain')
+ save(sprintf('%s/7_fed/grain%d_/fedgrain.mat', parameters.fed.dir, grainid), 'fedgrain')
else
disp('not saving... you can do it yourself')
end
else
% new directory structure
-save(sprintf('%s/7_FED/grain%d_/fedgrain.mat', parameters.FED.dir, grainid), 'fedgrain')
+ save(sprintf('%s/7_fed/grain%d_/fedgrain.mat', parameters.fed.dir, grainid), 'fedgrain')
end
-disp('gtFedLoadGrainFromIndexter finished')
\ No newline at end of file
+end % end function
\ No newline at end of file
diff --git a/7_fed/AndyFunctions/gtFedLoadRealBlobs.m b/7_fed/AndyFunctions/gtFedLoadRealBlobs.m
index c47e9340..1c483cd9 100644
--- a/7_fed/AndyFunctions/gtFedLoadRealBlobs.m
+++ b/7_fed/AndyFunctions/gtFedLoadRealBlobs.m
@@ -27,11 +27,13 @@ else
save_flag=0;
end
-
-load parameters
+parameters=[];
+fedgrain=[];
+gv=[];
+load('parameters.mat');
% specific to this grain
-load(sprintf('%s/7_FED/grain%d_/fedgrain.mat', parameters.FED.dir, grainid));
-load(sprintf('%s/7_FED/grain%d_/gv.mat', parameters.FED.dir, grainid));
+load(sprintf('%s/7_fed/grain%d_/fedgrain.mat', parameters.fed.dir, grainid));
+load(sprintf('%s/7_fed/grain%d_/gv.mat', parameters.fed.dir, grainid));
gtDBConnect
@@ -52,6 +54,7 @@ lastimage=(parameters.acq.nproj*2)-1;
% Sample geometry and origin of SAMPLE coord. system:
sam=gtSampleGeoInSampleSystem;
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% matrices for computing rotation tensors / arbitary geometry unpacking
% arbitary geometry information will all come from fedpars.
@@ -138,7 +141,10 @@ for i=1:nbl
bl(i).difspotID=fedgrain.difspots(i);
[vol,bb] = gtDBBrowseDiffractionVolume(parameters.acq.name, bl(i).difspotID);
- if strcmp(parameters.acq.name, 'al_plast_dct1_b_grid_') | strcmp(parameters.acq.name, 'al_plast_dct1_b_nogrid_763V_') | strcmp(parameters.acq.name, 'al_plast_dct1_b_nogrid_1000V_19N_')
+ if strcmp(parameters.acq.name, 'al_plast_dct1_b_grid_') || ...
+ strcmp(parameters.acq.name, 'al_plast_dct1_b_nogrid_763V_') || ...
+ strcmp(parameters.acq.name, 'al_plast_dct1_b_nogrid_1000V_19N_')
+
disp('... apply fix for renumbered datasets')
[tmp1, tmp2]=mym(sprintf('select startimage, endimage from %sdifspot where difspotid=%d', parameters.acq.name, bl(i).difspotID));
bb(3)=tmp1;
@@ -253,7 +259,7 @@ for i=1:nbl
bl(i).addbl(2)+1:bl(i).addbl(2)+bb(5),...
bl(i).addbl(3)+1:bl(i).addbl(3)+bb(6)) = vol;
mask=imdilate(mask>0, ones(10,10,5));
- catch
+ catch Mexc
disp('problem with bounding box / mask for this blob')
mask=ones(size(bl(i).intm));
end
@@ -310,7 +316,7 @@ for i=1:nbl
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- disp(sprintf('done blob %d ...', i))
+ disp(['done blob ' num2str(i) '...'])
end
% repack fedpars into fedgrain
@@ -318,9 +324,9 @@ fedgrain.fedpars=fedpars;
% save updated gv and bl
if save_flag
- save(sprintf('%s/7_FED/grain%d_/bl.mat', parameters.FED.dir, grainid), 'bl', '-v7.3')
- save(sprintf('%s/7_FED/grain%d_/gv.mat', parameters.FED.dir, grainid), 'gv', '-v7.3')
- disp(sprintf('saving updated gv and bl'))
+ save(sprintf('%s/7_fed/grain%d_/bl.mat', parameters.fed.dir, grainid), 'bl', '-v7.3')
+ save(sprintf('%s/7_fed/grain%d_/gv.mat', parameters.fed.dir, grainid), 'gv', '-v7.3')
+ disp('saving updated gv and bl')
end
@@ -351,8 +357,9 @@ end
% save updated gv and bl
if save_flag
- save(sprintf('%s/7_FED/grain%d_/bl.mat', parameters.FED.dir, grainid), 'bl', '-v7.3')
- save(sprintf('%s/7_FED/grain%d_/gv.mat', parameters.FED.dir, grainid), 'gv', '-v7.3')
- disp(sprintf('saving updated gv and bl'))
+ save(sprintf('%s/7_fed/grain%d_/bl.mat', parameters.fed.dir, grainid), 'bl', '-v7.3')
+ save(sprintf('%s/7_fed/grain%d_/gv.mat', parameters.fed.dir, grainid), 'gv', '-v7.3')
+ disp('saving updated gv and bl')
end
+end
\ No newline at end of file
diff --git a/7_fed/AndyFunctions/gtFedLoadRealGrain.m b/7_fed/AndyFunctions/gtFedLoadRealGrain.m
index a779bc24..bd224412 100644
--- a/7_fed/AndyFunctions/gtFedLoadRealGrain.m
+++ b/7_fed/AndyFunctions/gtFedLoadRealGrain.m
@@ -8,12 +8,12 @@ function [fedpars, gv]=gtFedLoadRealGrain(grainid, dct_vol, varargin)
% for smoothness - this function is always launched in the folder of the
% dataste (parameters.acq.dir) and all paths to files are handled nicely.
%
-% will automatically select the gvsize (element size) to give a reasonable number of elements (<~2000)
-% this can be forced by setting parameters.FED.auto_gvsize=0, in which case
+% will automatically select the gvsize (element size) to give a reasonable number of elements (<~2000)
+% this can be forced by setting parameters.fed.auto_gvsize=0, in which case
% gvsize will default to whatever is set in fedpars.
%
% need to apply some renumbering if there is a sequence of datasets. Add
-% this to parameters.FED.renumber_list
+% this to parameters.fed.renumber_list
%
@@ -23,10 +23,12 @@ else
save_flag=0;
end
+parameters=[];
+fedgrain=[];
% load variables
-load parameters
+load('parameters.mat');
% specific to this grain
-load(sprintf('%s/7_FED/grain%d_/fedgrain.mat', parameters.FED.dir, grainid));
+load(sprintf('%s/7_fed/grain%d_/fedgrain.mat', parameters.fed.dir, grainid));
% unpack fedpars for convenience
fedpars=fedgrain.fedpars;
@@ -34,7 +36,7 @@ fedpars=fedgrain.fedpars;
dct_vol=dct_vol==fedgrain.reference_grainid;
fedpars.grainvol=sum(dct_vol(:));
-% use pairs only
+% use pairs only
nbl=2*fedgrain.nof_pairs;
@@ -55,7 +57,7 @@ z1=find(profilez, 1, 'first');
z2=find(profilez, 1, 'last');
sizez=1+z2-z1;
-% get the Grain volume
+% get the Grain volume
grvol = dct_vol(x1:x2, y1:y2, z1:z2);
fedpars.grvol = grvol;
@@ -69,7 +71,7 @@ x2=x2-sam.rad;
y1=y1-sam.rad;
y2=y2-sam.rad;
-fedpars.grainsize = [sizex sizey sizez]; % size of grain volume
+fedpars.grainsize = [sizex sizey sizez]; % size of grain volume
fedpars.grainoff = [x1 y1 z1]; % coordinates of voxel (0,0,0) in the SAMPLE ref.
grainoff=fedpars.grainoff;
@@ -92,7 +94,7 @@ if fedpars.auto_gvsize
end
fedpars.gvsize=[elementsize elementsize elementsize];
gvsize=fedpars.gvsize;
- disp(sprintf('using gvsize = %d', elementsize));
+ fprintf('using gvsize = %d\n', elementsize);
else
disp('using gvsize specified in fedgrain.fedpars')
gvsize=fedpars.gvsize;
@@ -112,7 +114,7 @@ fedpars.grainenv = grenv;
% pad grain volume to multiple of element size
grvol_pad = false(grenv);
-grvol_pad(1:size(grvol,1),1:size(grvol,2),1:size(grvol,3)) = grvol;
+grvol_pad(1:size(grvol,1),1:size(grvol,2),1:size(grvol,3)) = grvol;
grvol = grvol_pad;
% save padded grainsize into fedpars variable - required?
@@ -125,40 +127,40 @@ fedpars.grainsize=size(grvol);
% calculate the true required number of elements (non-empty...)
% label the volume, then prepare gv structure
-grvol_labelled=zeros(size(grvol));
-% label this volume - this will have complete elements,
+grvol_labelled=zeros(size(grvol));
+% label this volume - this will have complete elements,
% which must then be masked with grvol to get the correct grain shape
disp('Dividing grain volume into elements...')
tic
count=0;
for i = 1:ngv(1)
- irangel = gvsize(1)*(i-1)+1;
- irangeh = min(gvsize(1)*i,size(grvol,1));
-
- for j = 1:ngv(2)
- jrangel = gvsize(2)*(j-1)+1;
- jrangeh = min(gvsize(2)*j,size(grvol,2));
-
- for k= 1:ngv(3)
- krangel = gvsize(3)*(k-1)+1;
- krangeh = min(gvsize(3)*k,size(grvol,3));
-
- subvol(:,:,:) = grvol(irangel:irangeh, jrangel:jrangeh, krangel:krangeh);
- if any(subvol(:))
- count=count+1;
- grvol_labelled(irangel:irangeh, jrangel:jrangeh, krangel:krangeh)=count;
- end
-
- end
- end
+ irangel = gvsize(1)*(i-1)+1;
+ irangeh = min(gvsize(1)*i,size(grvol,1));
+
+ for j = 1:ngv(2)
+ jrangel = gvsize(2)*(j-1)+1;
+ jrangeh = min(gvsize(2)*j,size(grvol,2));
+
+ for k= 1:ngv(3)
+ krangel = gvsize(3)*(k-1)+1;
+ krangeh = min(gvsize(3)*k,size(grvol,3));
+
+ subvol(:,:,:) = grvol(irangel:irangeh, jrangel:jrangeh, krangel:krangeh);
+ if any(subvol(:))
+ count=count+1;
+ grvol_labelled(irangel:irangeh, jrangel:jrangeh, krangel:krangeh)=count;
+ end
+
+ end
+ end
end
toc
% voxel to element map comes straight from this
vox2gvind = grvol_labelled.*grvol;
fedpars.vox2gvind = vox2gvind;
nv=count;
-disp(sprintf('...found %d elements in this grain', nv))
+fprintf('...found %d elements in this grain\n', nv)
%nv = ngv(1)*ngv(2)*ngv(3); % total number of vol elements
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -180,12 +182,12 @@ for i=1:nv
% position of the first voxel of element
[gv(i).cs1(1), gv(i).cs1(2), gv(i).cs1(3)] = ind2sub(size(grvol_labelled), voxindices(1));
cs1_ingrain=gv(i).cs1;
- % element index
+ % element index
gv(i).ind = ((gv(i).cs1-1)./gvsize)+1;
% position allowing for grain offset
gv(i).cs1=gv(i).cs1+grainoff;
% element centre
- gv(i).cs = gv(i).cs1 + 0.5*gvsize - 0.5;
+ gv(i).cs = gv(i).cs1 + 0.5*gvsize - 0.5;
% complete element?
voxindices=find(vox2gvind==i);
@@ -201,7 +203,7 @@ for i=1:nv
% complete element subvolume
gv(i).vol=true(gvsize);
else
- gv(i).complete = false;
+ gv(i).complete = false;
% get the element subvolume
voxindrel=sub2ind(gvsize, voxsubrel(:,1)+1, voxsubrel(:,2)+1, voxsubrel(:,3)+1);
gv(i).vol(voxindrel)=true;
@@ -220,15 +222,16 @@ fedgrain.fedpars=fedpars;
if ~save_flag
a=inputwdefault('save gv.mat and updated fedgrain.mat? y/n', 'y');
if strcmpi(a, 'y')
- save(sprintf('%s/7_FED/grain%d_/fedgrain.mat', parameters.FED.dir, grainid), 'fedgrain')
- save(sprintf('%s/7_FED/grain%d_/gv.mat', parameters.FED.dir, grainid), 'gv', '-v7.3')
+ save(sprintf('%s/7_fed/grain%d_/fedgrain.mat', parameters.fed.dir, grainid), 'fedgrain')
+ save(sprintf('%s/7_fed/grain%d_/gv.mat', parameters.fed.dir, grainid), 'gv', '-v7.3')
else
disp('not saving... you can do it yourself')
end
else
disp('auto-saving fedgrain and gv')
- save(sprintf('%s/7_FED/grain%d_/fedgrain.mat', parameters.FED.dir, grainid), 'fedgrain')
- save(sprintf('%s/7_FED/grain%d_/gv.mat', parameters.FED.dir, grainid), 'gv', '-v7.3')
+ save(sprintf('%s/7_fed/grain%d_/fedgrain.mat', parameters.fed.dir, grainid), 'fedgrain')
+ save(sprintf('%s/7_fed/grain%d_/gv.mat', parameters.fed.dir, grainid), 'gv', '-v7.3')
end
+end
diff --git a/7_fed/AndyFunctions/gtFedSetupT0.m b/7_fed/AndyFunctions/gtFedSetupT0.m
index eb663ae5..c011ee5c 100644
--- a/7_fed/AndyFunctions/gtFedSetupT0.m
+++ b/7_fed/AndyFunctions/gtFedSetupT0.m
@@ -21,15 +21,19 @@ else
phase=0;
end
+parameters=[];
+gv=[];
+bl=[];
+fedgrain=[];
% load variables
load parameters
-load(sprintf('%s/7_FED/grain%d_/gv.mat', parameters.FED.dir, grainid));
-load(sprintf('%s/7_FED/grain%d_/bl.mat', parameters.FED.dir, grainid));
-load(sprintf('%s/7_FED/grain%d_/fedgrain.mat', parameters.FED.dir, grainid));
+load(sprintf('%s/7_fed/grain%d_/gv.mat', parameters.fed.dir, grainid));
+load(sprintf('%s/7_fed/grain%d_/bl.mat', parameters.fed.dir, grainid));
+load(sprintf('%s/7_fed/grain%d_/fedgrain.mat', parameters.fed.dir, grainid));
fedpars=fedgrain.fedpars;
-if phase==0 | ~isfield(fedpars, 'strategy')
+if phase==0 || ~isfield(fedpars, 'strategy')
% get the relevent fedpars parameters from user
list{1,1}='niter'; list{1,2}='Number of iterations in this phase';
list{2,1}='crude_acceleration'; list{2,2}='Crude acceleration of forward projector?';
@@ -157,5 +161,8 @@ fedgrain.fedpars=fedpars;
% save updated structures
disp('saving updated fedgrain and gv')
-save(sprintf('%s/7_FED/grain%d_/fedgrain.mat', parameters.FED.dir, grainid), 'fedgrain')
-save(sprintf('%s/7_FED/grain%d_/gv.mat', parameters.FED.dir, grainid), 'gv', '-v7.3')
+save(sprintf('%s/7_fed/grain%d_/fedgrain.mat', parameters.fed.dir, grainid), 'fedgrain')
+save(sprintf('%s/7_fed/grain%d_/gv.mat', parameters.fed.dir, grainid), 'gv', '-v7.3')
+
+
+end
\ No newline at end of file
diff --git a/7_fed/Ccode_SpreadInt/gtFedInitialize.m b/7_fed/Ccode_SpreadInt/gtFedInitialize.m
index 5783cea1..d6b3debf 100644
--- a/7_fed/Ccode_SpreadInt/gtFedInitialize.m
+++ b/7_fed/Ccode_SpreadInt/gtFedInitialize.m
@@ -48,7 +48,7 @@ clear mexFedSpreadIntByVoxel
% mexFedSpreadIntByVoxel.o (object file) and
% mexFedSpreadIntByVoxel.mexa64 files will be (re)created
disp(' ')
-disp('Current folder has to be .../matlabDCT/zUtil_FED/Ccode_SpreadInt ')
+disp('Current folder has to be .../matlabDCT/7_fed/Ccode_SpreadInt ')
disp('Start compiling gtFedSpreadIntByVoxel function...')
tmp = system('mexFed.sh');
diff --git a/7_fed/gtFedGenerateRandomGrain.m b/7_fed/gtFedGenerateRandomGrain.m
index 89b2b56e..1d5d957d 100644
--- a/7_fed/gtFedGenerateRandomGrain.m
+++ b/7_fed/gtFedGenerateRandomGrain.m
@@ -8,7 +8,7 @@ function grain = gtFedGenerateRandomGrain(grain,vert,pars,varargin)
% INPUT:
%
% grain = grain of interest (<struct>)
-% vert = difspots image output from "gtPlaceDifspotinFull_ln" (<double MxM>)
+% vert = difspots image output from "gtPlaceDifspotinFull" (<double MxM>)
% M is the size of the image (typically 2048)
% pars = parameters file (<struct> {parameters.mat})
% varargin = optional arguments list given by pairs
@@ -18,30 +18,30 @@ function grain = gtFedGenerateRandomGrain(grain,vert,pars,varargin)
%
% Reflections = number N of first reflections to consider (<double Nx1> {[]})
% Beamchroma = beam chromaticity (<char 1x4 > {'mono'}, 'poly')
-% Beamenergymin = minimum beam energy (in keV) (<double 1x1> {5})
-% Beamenergymax = maximum beam energy (in keV) (<double 1x1> {25})
-% showfigure = show or not the figure (<logical 1x1> {0})
+% Beamenergymin = minimum beam energy (in keV) (<double> {5})
+% Beamenergymax = maximum beam energy (in keV) (<double> {25})
+% showfigure = show or not the figure (<logical> {0})
% color = show or not the prediction spot positions coloured as
-% omega (<logical 1x1> {0})
-% Dlimit = maximum strain value (<double 1x1 {0}>)
-% Gref = reference full deformation gradient tensor (<double 3x3 {zeros(3)}>)
-% debug = debug mode on/off (<logical 1x1 {0}>)
+% omega (<logical> {0})
+% Dlimit = maximum strain value (<double> {0})
+% Gref = reference full deformation gradient tensor (<double 3x3 {zeros(3)})
+% debug = debug mode on/off (<logical> {0})
% axis = plot axis, image reference and beam direction in the
% image (<logical> {0})
-% save = save or not the grain (<logical 1x1> {0})
+% save = save or not the grain (<logical> {0})
% Markersize = marker size (<double> {15})
% Grayscale = scale of grays (<double 1x2> {[-300 500]})
%
%
% OUTPUT:
%
-% grain = grain of interest (<struct 1x1>)
+% grain = grain of interest (<struct>)
% added fields:
-% - randomID <int32 1x1>
+% - randomID <int32>
% - pllab <double Nx3>
% - hklsp <double Nx3>
% - dvec <double Nx3>
-% - allblobs <struct 1x1>
+% - allblobs <struct>
%
% updated fields:
% - thetatype <double Nx1>
@@ -257,13 +257,13 @@ end
%% Detector geometry
disp('Getting the detector geometry...')
-detdiru = acq.detdiru0';
-detdirv = acq.detdirv0';
+detdiru = geo.detdiru0';
+detdirv = geo.detdirv0';
Qdet = gtFedDetectorProjectionTensor(detdiru,detdirv,1,1);
tn = cross(detdiru,detdirv);
-detpos = (acq.detpos0./acq.pixelsize)';
+detpos = (geo.detpos0./acq.pixelsize)';
%uvorig = [acq.rotx; acq.ydet/2];
-uvorig = [acq.detucen0, acq.detvcen0]';
+uvorig = [geo.detucen0, geo.detvcen0]';
csam=grain.center';
omstep=180/acq.nproj;
diff --git a/7_fed/gtFedLoadGrainFromIndexter_ln.m b/7_fed/gtFedLoadGrainFromIndexter_ln.m
deleted file mode 100644
index 1183a048..00000000
--- a/7_fed/gtFedLoadGrainFromIndexter_ln.m
+++ /dev/null
@@ -1,146 +0,0 @@
-function [fedpars, fedgrain]=gtFedLoadGrainFromIndexter_ln(grainid, indexter_grain, varargin)
-%% [fedpars, fedgrain]=gtFedLoadGrainFromIndexter_ln(grainid, indexter_grain, varargin)
-%
-% create a file called fedgrain.mat - equivilent to the random grain in the
-% simulated data code.
-% nothing more than the indexter data "unpacked" into single blobs rather
-% than pairs.
-% setup fedpars.mat at the same time
-%
-% general comment - at the moment fedgrain and fedpars are saved together
-% in one variable (fedgrain). This can perhaps be cleaned.
-%
-% improve, automate and clean so that it can be run form condor without
-% fucking around...
-%
-% fedpars.mat is grain specific - therefore it should go in the grain
-% folder. For the moment, let's introduce a folder structure called
-% 7_FED/grain%d_/ and put fedpars / bl etc in there
-%
-% add a path to the dct volume in parameters.FED.final_dct_volume
-% also add parameters.FED.volume_offset to allow for sample movements
-% (see fed_real_data_scheme script)
-%
-% deal with renumbering in a sequence of datasets - ie in this scan it
-% might be grain X, but in the reference dataset and the dct volume it
-% might be grain Y.
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% are we saving?
-if length(varargin)==1
- save_flag=varargin{1};
-else
- save_flag=0;
- disp('gtFedLoadGrainFromIndexter is not saving fedpars.mat, fedgrain.mat')
-end
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% load DCT parameters
-load('parameters.mat');
-% indexter output is passed in as indexter_grain
-
-%%%%%%%%%%%%%%%%%%%%%%%% INDEXTER OUTPUT INTO FEDGRAIN %%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% simplify/unpack blob data from indexter
-a=indexter_grain{grainid};
-fedgrain.nof_pairs = a.nof_pairs;
-fedgrain.R_vector = a.R_vector;
-
-
-%%%%%%%%%%%%%%%%%%% GRAIN ID RENUMBERING IF PART OF SEQUENCE %%%%%%%%%%%%%%%%%%%%%%
-% may need to consider renumbering
-fedgrain.grainID=grainid;
-if isfield(parameters.FED, 'renumber_list')
- list=parameters.FED.renumber_list;
- % list: [referenceID, this dataset ID]
- ndx=find(list(:,2)==grainid);
- if isempty(ndx)
- disp('problem - this grain is not linked to a grain in the reference dataset')
- return
- end
- fedgrain.reference_grainid=list(ndx, 1);
-else
- fedgrain.reference_grainid=grainid;
-end
-
-%%%%%%%%%%%%%%%%%%%%%%%% SETUP FEDPARS %%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% How many blobs?
-nbl = 2*fedgrain.nof_pairs;
-
-% FED parameters definition
-fedpars = gtFedParameters(nbl);
-
-% add parameters / could be interactive or use defaults
-fedpars = gtFedSetParameters(fedpars, nbl, 'defaults');
-
-% add GrainID
-fedpars.grainID=grainid;
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% load general info from parameters.acq into fedpars
-disp('copy experiment geometry from parameters.acq to fedpars')
-fedpars.detpos=parameters.acq.detpos0;
-fedpars.detdiru=parameters.acq.detdiru0;
-fedpars.detdirv=parameters.acq.detdirv0;
-fedpars.rotdir=parameters.acq.rotdir0;
-fedpars.detucen=parameters.acq.detucen0;
-fedpars.detvcen=parameters.acq.detvcen0;
-fedpars.beamdir=parameters.acq.beamdir0;
-
-
-
-%%%%%%%%%%%%%%%%%%%%%%%% INDEXTER OUTPUT INTO FEDGRAIN %%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% unpack variables, expanding pairs
-fedgrain.pairid = zeros(1, nbl);
-fedgrain.difspots = zeros(1, nbl);
-fedgrain.thetatype = zeros(1, nbl);
-fedgrain.hkl = zeros(nbl, size(a.hkl, 2));
-fedgrain.pl0 = zeros(nbl, 3);
-fedgrain.theta = zeros(1, nbl);
-fedgrain.eta = zeros(1, nbl);
-fedgrain.omega = zeros(1, nbl);
-
-% expand pairs
-fedgrain.pairid(1:2:end) = a.pairid;
-fedgrain.pairid(2:2:end) = a.pairid;
-
-fedgrain.difspots(1:2:end)=a.difspots(1:fedgrain.nof_pairs);
-fedgrain.difspots(2:2:end)=a.difspots((fedgrain.nof_pairs+1):end);
-
-fedgrain.thetatype(1:2:end) = a.thetatype;
-fedgrain.thetatype(2:2:end) = a.thetatype;
-fedgrain.hkl(1:2:end, :)=a.hkl;
-fedgrain.hkl(2:2:end, :)=a.hkl;
-fedgrain.pl0(1:2:end, :) = a.pl;
-fedgrain.pl0(2:2:end, :) = -a.pl;
-fedgrain.theta(1:2:end) = a.theta;
-fedgrain.theta(2:2:end) = a.theta;
-fedgrain.sinth0=sind(fedgrain.theta);
-fedgrain.eta(1:2:end) = a.eta;
-fedgrain.eta(2:2:end) = mod(180-a.eta, 360);
-fedgrain.omega(1:2:end) = a.omega;
-fedgrain.omega(2:2:end) = a.omega+180;
-
-warning('USING MEASURED DIFF ANGLES, SHOULD BE THEORETICAL!!!')
-% here we should determine the specific hkls, and predict theta, eta and
-% omega and pl0 based on these and the grain R-vector
-
-warning('HARD CODING MAX_ELEMENTS_GRAIN...')
-fedpars.max_elements_grain=2000;
-% combine fedgrain and fedpars - as fedpars can be grain specific
-fedgrain.fedpars=fedpars;
-
-if ~save_flag
- a=inputwdefault('save fedgrain.mat (which includes fedgrain.fedpars)?', 'y');
- if strcmpi(a, 'y')
- save(sprintf('%s/7_FED/grain%d_/fedgrain.mat', parameters.FED.dir, grainid), 'fedgrain')
- else
- disp('not saving... you can do it yourself')
- end
-else
- % new directory structure
- save(sprintf('%s/7_FED/grain%d_/fedgrain.mat', parameters.FED.dir, grainid), 'fedgrain')
-end
-
-disp('gtFedLoadGrainFromIndexter finished')
-
-end % end function
\ No newline at end of file
diff --git a/7_fed/gtFedLoadGrainWoIndexter.m b/7_fed/gtFedLoadGrainWoIndexter.m
index 100c612b..293ea49f 100644
--- a/7_fed/gtFedLoadGrainWoIndexter.m
+++ b/7_fed/gtFedLoadGrainWoIndexter.m
@@ -20,9 +20,9 @@ function [fedgrain,fedpars,gr]=gtFedLoadGrainWoIndexter(gr, bbox, varargin)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% are we saving?
-app.save_flag=false;
-app.debug=false;
-app.max_el=2000;
+app.save_flag = false;
+app.debug = false;
+app.max_el = 2000;
app=parse_pv_pairs(app,varargin);
if ~app.save_flag && app.debug
disp('gtFedLoadGrainWoIndexter is not saving fedpars.mat, fedgrain.mat')
@@ -30,6 +30,7 @@ end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% load DCT parameters
+parameters=[];
load('parameters.mat');
% indexter output is passed in as indexter_grain
@@ -157,9 +158,11 @@ fedgrain.fedpars=fedpars;
% saving...
if app.save_flag
% new directory structure
- save(sprintf('%s/7_FED/grain%d_/fedgrain.mat', parameters.acq.dir, gr.id), 'fedgrain')
+ save(sprintf('%s/7_fed/grain%d_/fedgrain.mat', parameters.acq.dir, gr.id), 'fedgrain')
end
-disp('### Exiting from gtFedLoadGrainFromIndexter... ###')
-disp(' ')
+if app.debug
+ disp('### Exiting from gtFedLoadGrainFromIndexter... ###')
+ disp(' ')
+end
end % end function
\ No newline at end of file
diff --git a/7_fed/gtFedParameters.m b/7_fed/gtFedParameters.m
index 8e8128f5..11a236cd 100644
--- a/7_fed/gtFedParameters.m
+++ b/7_fed/gtFedParameters.m
@@ -62,3 +62,5 @@ fedpars.centoffs_correction = false; % this should no longer exist - leave in j
% fedpars.strategy.s1.solver = 'Flow'; fedpars.strategy.s1.dindex = ...
% fedpars.strategy.s2.solver = 'LSQR'; fedpars.strategy.s2.dindex = ...
% etc.
+
+end
\ No newline at end of file
diff --git a/7_fed/gtFedSetParameters.m b/7_fed/gtFedSetParameters.m
index cd721310..4316595b 100644
--- a/7_fed/gtFedSetParameters.m
+++ b/7_fed/gtFedSetParameters.m
@@ -138,7 +138,7 @@ if ~defaults
% get rid of "excess" default phases
if fedpars.nphases<3
for i=fedpars.nphases+1:3
- fedpars.strategy=rmfield(fedpars.strategy, sprintf('s%d', i))
+ fedpars.strategy=rmfield(fedpars.strategy, sprintf('s%d', i)
end
end
@@ -154,8 +154,8 @@ if ~defaults
list{10,1}='fbbminsize'; list{10,2}='Minimum flow bounding box size';
for i=1:fedpars.nphases
- disp(sprintf('Now set the dynamic values for phase %d', i))
- fedpars.strategy.(sprintf('s%d', i))=gtModifyStructure(fedpars.strategy.(sprintf('s%d', i)), list);
+ fprintf('Now set the dynamic values for phase %d', i)
+ fedpars.strategy.(sprintf('s%d', i)=gtModifyStructure(fedpars.strategy.(sprintf('s%d', i), list);
end
end
diff --git a/7_fed/gtFedSetupT0.m b/7_fed/gtFedSetupT0.m
index d38a118c..1e9b7a54 100644
--- a/7_fed/gtFedSetupT0.m
+++ b/7_fed/gtFedSetupT0.m
@@ -19,7 +19,7 @@ end
load fedpars
-if (phase == 0) || (phase == ~isfield(fedpars, 'strategy'))
+if (phase == 0) || (phase == ~isfield(fedpars, 'strategy')
% get the relevent fedpars parameters from user
fedpars.dindex = inputwdefaultnumeric('enter the desired dindex vector [Rx Ry Rz e11 e22 e33 e23 e13 e12]:', '[1 1 1 0 0 0 0 0 0]');
fedpars.T0strategy = inputwdefault('enter the desired T0 strategy A/B :', 'B');
@@ -54,8 +54,8 @@ end
r = setdiff(fedpars.loadbl, fedpars.usebl);
for i = 1:length(r)
pair = floor((r(i)+1)/2);
- pairA = (2*(pair-1))+1;
- pairB = (2*(pair-1))+2;
+ pairA = (2*(pair-1)+1;
+ pairB = (2*(pair-1)+2;
fedpars.usebl(fedpars.usebl==pairA) = [];
fedpars.usebl(fedpars.usebl==pairB) = [];
end
@@ -102,7 +102,7 @@ for i=1:length(gv)
if strcmpi(fedpars.T0strategy, 'A')
% solve for T0 as normal
[Usvd,Ssvd,Vsvd] = svd(U0_allbl,0);
- gv(i).T0 = Vsvd*diag(1./diag(Ssvd))*Usvd';
+ gv(i).T0 = Vsvd*diag(1./diag(Ssvd)*Usvd';
% force lines of T0 to zeros
gv(i).T0(~fedpars.dindex, :) = 0;
@@ -110,7 +110,7 @@ for i=1:length(gv)
% remove terms from U0_allbl
U0_allbl(:, ~fedpars.dindex) = [];
[Usvd,Ssvd,Vsvd] = svd(U0_allbl,0);
- tmpT0 = Vsvd*diag(1./diag(Ssvd))*Usvd';
+ tmpT0 = Vsvd*diag(1./diag(Ssvd)*Usvd';
% restore to standard dimensions
gv(i).T0 = zeros(9, 3*nbl);
gv(i).T0(fedpars.dindex, :) = tmpT0;
@@ -135,7 +135,7 @@ for i=1:length(gv)
end
% save updated structures
-disp(sprintf('saving updated fedpars and gv in %s', fedpars.filename))
+fprintf('saving updated fedpars and gv in %s', fedpars.filename)
save(fedpars.filename, 'fedpars', 'gv', '-append')
diff --git a/7_fed/gtFedShowDifBlob.m b/7_fed/gtFedShowDifBlob.m
index e36ee0b0..70e25015 100644
--- a/7_fed/gtFedShowDifBlob.m
+++ b/7_fed/gtFedShowDifBlob.m
@@ -4,14 +4,14 @@ function gtFedShowDifBlob(nbl,bl,wint,cmap)
% vol=permute(vol,[2,1,3]);
%
%
-% vol_view(vol,'plane','zx','slicendx',bl(nbl).cent(3))
+% vol_view(vol,'plane','zx','slicendx',bl(nbl).cent(3)
% xlabel('u - horizontal') % vol_view will change it back
% ylabel('v - vertical')
%
-% disp(sprintf('vol=bl(%d).int(:,:,:);',nbl))
+% fprintf('vol=bl(%d).int(:,:,:);',nbl)
% disp('vol=permute(vol,[2,1,3]);');
-% %disp(sprintf('vol_view(vol,''plane'',''zx'',''slicendx'',%d)',bl(nbl).cent(3)-bl(nbl).bbw(1)))
-% disp(sprintf('vol_view(vol,''slicendx'',%d)',bl(nbl).cent(3)-bl(nbl).bbw(1)))
+% %fprintf('vol_view(vol,''plane'',''zx'',''slicendx'',%d)',bl(nbl).cent(3)-bl(nbl).bbw(1))
+% fprintf('vol_view(vol,''slicendx'',%d)',bl(nbl).cent(3)-bl(nbl).bbw(1))
% %disp('xlabel(''u - horizontal'')')
% %disp('ylabel(''v - vertical'')')
@@ -42,14 +42,14 @@ s = warning('query', 'all');
warning off
if cmap == 0
- h = dipshow(vol,'lin','name',sprintf('Blob #%d ',nbl));
+ h = dipshow(vol,'lin','name',sprintf('Blob #%d ',nbl);
else
- h = dipshow(vol,[0 max(vol(:))],'name',sprintf('Blob #%d ',nbl));
+ h = dipshow(vol,[0 max(vol(:)],'name',sprintf('Blob #%d ',nbl);
end
warning(s)
set(h,'numbertitle','off')
-dipshow(h,'ch_slice',round(bl(nbl).commbl(3)))
+dipshow(h,'ch_slice',round(bl(nbl).commbl(3))
diff --git a/7_fed/gtFedTestLoadData.m b/7_fed/gtFedTestLoadData.m
index 74d0dbb3..5d42bace 100644
--- a/7_fed/gtFedTestLoadData.m
+++ b/7_fed/gtFedTestLoadData.m
@@ -67,9 +67,9 @@ omstep = 180/parameters.acq.nproj;
beamdir = parameters.acq.beamdir0';
-detuvorig= [parameters.acq.detucen0; parameters.acq.detvcen0]; % in detector pixels
-detdiru = parameters.acq.detdiru0'; % unit vector
-detdirv = parameters.acq.detdirv0'; % unit vector
+detuvorig= [parameters.geo.detucen0; parameters.geo.detvcen0]; % in detector pixels
+detdiru = parameters.geo.detdiru0'; % unit vector
+detdirv = parameters.geo.detdirv0'; % unit vector
detnorm = cross(detdiru,detdirv); % unit vector
@@ -77,7 +77,7 @@ detnorm = cross(detdiru,detdirv); % unit vector
% originally in detector pixels !!!
% change to grain voxels !!!
% pixel sizes in mm-s !!!
-detpos = parameters.acq.detpos0'*parameters.acq.pixelsize/fedpars.voxelsize;
+detpos = parameters.geo.detpos0'*parameters.acq.pixelsize/fedpars.voxelsize;
rotdir = parameters.acq.rotdir0'; % unit vector
detscaleu = fedpars.voxelsize/parameters.acq.pixelsize; % detector scaling along u (grain voxel size / det. pixel size)
diff --git a/7_fed/gtGrainPredict.m b/7_fed/gtGrainPredict.m
index b570642a..740766e2 100644
--- a/7_fed/gtGrainPredict.m
+++ b/7_fed/gtGrainPredict.m
@@ -8,7 +8,7 @@ function grain = gtFedGenerateRandomGrain(grain,vert,pars,varargin)
% INPUT:
%
% grain = grain of interest (<struct>)
-% vert = difspots image output from "gtPlaceDifspotinFull_ln" (<double MxM>)
+% vert = difspots image output from "gtPlaceDifspotinFull" (<double MxM>)
% M is the size of the image (typically 2048)
% pars = parameters file (<struct> {parameters.mat})
% varargin = optional arguments list given by pairs
@@ -18,30 +18,30 @@ function grain = gtFedGenerateRandomGrain(grain,vert,pars,varargin)
%
% Reflections = number N of first reflections to consider (<double Nx1> {[]})
% Beamchroma = beam chromaticity (<char 1x4 > {'mono'}, 'poly')
-% Beamenergymin = minimum beam energy (in keV) (<double 1x1> {5})
-% Beamenergymax = maximum beam energy (in keV) (<double 1x1> {25})
-% showfigure = show or not the figure (<logical 1x1> {0})
+% Beamenergymin = minimum beam energy (in keV) (<double> {5})
+% Beamenergymax = maximum beam energy (in keV) (<double> {25})
+% showfigure = show or not the figure (<logical> {0})
% color = show or not the prediction spot positions coloured as
-% omega (<logical 1x1> {0})
-% Dlimit = maximum strain value (<double 1x1 {0}>)
-% Gref = reference full deformation gradient tensor (<double 3x3 {zeros(3)}>)
-% debug = debug mode on/off (<logical 1x1 {0}>)
+% omega (<logical> {0})
+% Dlimit = maximum strain value (<double> {0})
+% Gref = reference full deformation gradient tensor (<double 3x3 {zeros(3)})
+% debug = debug mode on/off (<logical> {0})
% axis = plot axis, image reference and beam direction in the
% image (<logical> {0})
-% save = save or not the grain (<logical 1x1> {0})
+% save = save or not the grain (<logical> {0})
% Markersize = marker size (<double> {15})
% Grayscale = scale of grays (<double 1x2> {[-300 500]})
%
%
% OUTPUT:
%
-% grain = grain of interest (<struct 1x1>)
+% grain = grain of interest (<struct>)
% added fields:
-% - randomID <int32 1x1>
+% - randomID <int32>
% - pllab <double Nx3>
% - hklsp <double Nx3>
% - dvec <double Nx3>
-% - allblobs <struct 1x1>
+% - allblobs <struct>
%
% updated fields:
% - thetatype <double Nx1>
@@ -251,13 +251,13 @@ end
%% Detector geometry
disp('Getting the detector geometry...')
-detdiru = acq.detdiru0';
-detdirv = acq.detdirv0';
+detdiru = geo.detdiru0';
+detdirv = geo.detdirv0';
Qdet = gtFedDetectorProjectionTensor(detdiru,detdirv,1,1);
tn = cross(detdiru,detdirv);
-detpos = (acq.detpos0./acq.pixelsize)';
+detpos = (geo.detpos0./acq.pixelsize)';
%uvorig = [acq.rotx; acq.ydet/2];
-uvorig = [acq.detucen0, acq.detvcen0]';
+uvorig = [geo.detucen0, geo.detvcen0]';
csam=grain.center';
omstep=180/acq.nproj;
diff --git a/zUtil_Parameters/build_list.m b/zUtil_Parameters/build_list.m
index c074f155..5154de92 100644
--- a/zUtil_Parameters/build_list.m
+++ b/zUtil_Parameters/build_list.m
@@ -22,6 +22,7 @@ function list = build_list(saveflag)
% match
% index
% rec
+% fed
%
% list.mat has the same fields as parameters.mat, except for index:
% acq, cryst, xop, geo, opt, database, prep, seg, match_calib, match, rec
@@ -367,6 +368,16 @@ list.rec{8,1} = 'percentile2'; list.rec{8,2} = 'Percentile thresho
list.rec{8,3} = 'double';
+list.fed{1,1} = 'dir'; list.fed{1,2} = 'Data analysis directory';
+list.fed{1,3} = 'char';
+list.fed{2,1} = 'dct_vol'; list.fed{2,2} = 'Dct reconstructed volume filename (.edf)';
+list.fed{2,3} = 'char';
+list.fed{3,1} = 'dct_offset'; list.fed{3,2} = 'Offset to be applied to the volume [x y z]';
+list.fed{3,3} = 'double';
+list.fed{4,1} = 'renumber_list'; list.fed{4,2} = 'Renumbering list for grainID';
+list.fed{4,3} = 'double';
+
+
if saveflag
fnames=gtLastFileName('template_list','new');
save(fnames,'list','-v7.3');
diff --git a/zUtil_Parameters/build_list_v2.m b/zUtil_Parameters/build_list_v2.m
index ce380ed1..a219c369 100644
--- a/zUtil_Parameters/build_list_v2.m
+++ b/zUtil_Parameters/build_list_v2.m
@@ -25,6 +25,7 @@ function list = build_list(varargin)
% match
% index
% rec
+% fed
%
% The list has the same fields as parameters.mat, except for index:
% list.mat
@@ -403,6 +404,19 @@ list.rec{10,1} = 'voxelsize'; list.rec{10,2} = 'Voxelsize (mm/
list.rec{10,3} = 'double';
+%fed
+list.fed{1,1} = 'dir'; list.fed{1,2} = 'Data analysis directory';
+list.fed{1,3} = 'char';
+list.fed{2,1} = 'dct_vol'; list.fed{2,2} = 'Dct reconstructed volume filename (.edf)';
+list.fed{2,3} = 'char';
+list.fed{3,1} = 'dct_offset'; list.fed{3,2} = 'Offset to be applied to the volume [x y z]';
+list.fed{3,3} = 'double';
+list.fed{4,1} = 'renumber_list'; list.fed{4,2} = 'Renumbering list for grainID';
+list.fed{4,3} = 'double';
+
+
+
+
if app.saveflag
fnames=gtLastFileName('template_list','new');
if isempty(strfind(version,'2011'))
diff --git a/zUtil_Parameters/build_parameters.m b/zUtil_Parameters/build_parameters.m
deleted file mode 100644
index c72e1e59..00000000
--- a/zUtil_Parameters/build_parameters.m
+++ /dev/null
@@ -1,543 +0,0 @@
-function list=build_parameters
-
-list=[];
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% ACQUISITION structure
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-acq.collection_dir = '';
-acq.name = '';
-acq.dir = '';
-acq.date = '';
-acq.xdet = NaN;
-acq.ydet = NaN;
-acq.nproj = NaN;
-acq.refon = NaN;
-acq.nref = NaN;
-acq.ndark = NaN;
-acq.pixelsize = NaN;
-acq.count_time = NaN;
-acq.energy = NaN;
-acq.dist = NaN;
-acq.sensortype = '';
-acq.type = '';
-acq.interlaced_turns = false;
-acq.mono_tune = false;
-acq.rotation_axis = '';
-acq.distortion = '';
-acq.flip_images = false;
-acq.no_direct_beam = false;
-acq.rotation_direction = '';
-acq.collection_dir_old = '';
-acq.rotu = NaN;
-acq.rotx = NaN;
-acq.bb = [NaN NaN NaN NaN];
-acq.bbdir = [NaN NaN NaN NaN];
-acq.maxradius = NaN;
-acq.pair_tablename = '';
-acq.calib_tablename = '';
-acq.orig_xdet = NaN;
-acq.orig_ydet = NaN;
-acq.roi_x_off = NaN;
-acq.roi_y_off = NaN;
-
-list.acq{1,1} = 'collection_dir'; list.acq{1,2} = 'Collection directory';
-list.acq{1,3} = 'char';
-list.acq{2,1} = 'name'; list.acq{2,2} = 'Name of the dataset';
-list.acq{2,3} = 'char';
-list.acq{3,1} = 'dir'; list.acq{3,2} = 'Directory in which to analyse the data';
-list.acq{3,3} = 'char';
-list.acq{4,1} = 'date'; list.acq{4,2} = 'Date?';
-list.acq{4,3} = 'char';
-list.acq{5,1} = 'xdet'; list.acq{5,2} = 'Detector size X (pixels)';
-list.acq{5,3} = 'double';
-list.acq{6,1} = 'ydet'; list.acq{6,2} = 'Detector size Y (pixels)';
-list.acq{6,3} = 'double';
-list.acq{7,1} = 'nproj'; list.acq{7,2} = 'Number of images in *180 DEGREES* of scan';
-list.acq{7,3} = 'double';
-list.acq{8,1} = 'refon'; list.acq{8,2} = 'References after how many images?';
-list.acq{8,3} = 'double';
-list.acq{9,1} = 'nref'; list.acq{9,2} = 'How many reference images in a group?';
-list.acq{9,3} = 'double';
-list.acq{10,1} = 'ndark'; list.acq{10,2} = 'How many dark images taken?';
-list.acq{10,3} = 'double';
-list.acq{11,1} = 'pixelsize'; list.acq{11,2} = 'Pixelsize (mm)';
-list.acq{11,3} = 'double';
-list.acq{12,1} = 'count_time'; list.acq{12,2} = 'image integration time (s)';
-list.acq{12,3} = 'double';
-list.acq{13,1} = 'energy'; list.acq{13,2} = 'Beam energy (keV)';
-list.acq{13,3} = 'double';
-list.acq{14,1} = 'dist'; list.acq{14,2} = 'Sample-detector distance (mm)';
-list.acq{14,3} = 'double';
-list.acq{15,1} = 'sensortype'; list.acq{15,2} = 'Camera type (frelon / kodak4mv1)?';
-list.acq{15,3} = 'char';
-list.acq{16,1} = 'type'; list.acq{16,2} = 'DCT scan type (360degree, 180degree, etc)';
-list.acq{16,3} = 'char';
-list.acq{17,1} = 'interlaced_turns'; list.acq{17,2} = 'Interlaced scan? 0 for normal scan, 1 for one extra turn, etc';
-list.acq{17,3} = 'double';
-list.acq{18,1} = 'mono_tune'; list.acq{18,2} = 'Monochromator was tuned after N reference groups, or 0 for not tuned';
-list.acq{18,3} = 'double';
-list.acq{19,1} = 'rotation_axis'; list.acq{19,2} = 'Rotation axis orientation (vertical / horizontal)';
-list.acq{19,3} = 'char';
-list.acq{20,1} = 'distortion'; list.acq{20,2} = 'Distortion correction file with path (or "none")';
-list.acq{20,3} = 'char';
-list.acq{21,1} = 'flip_images'; list.acq{21,2} = 'Flip images for future coordinate system - normally no';
-list.acq{21,3} = 'char';
-list.acq{22,1} = 'no_direct_beam'; list.acq{22,2} = 'Special scan with no direct beam (taper frelon, offset detector)?';
-list.acq{22,3} = 'double';
-list.acq{23,1} = 'rotation_direction'; list.acq{23,2} = 'Horizontal axis scan - rotate images "clockwise" or "counterclockwise"?';
-list.acq{23,3} = 'double';
-list.acq{24,1} = 'collection_dir_old'; list.acq{24,2} = 'Old collection directory';
-list.acq{24,3} = 'char';
-list.acq{25,1} = 'rotu'; list.acq{25,2} = '';
-list.acq{25,3} = 'char';
-list.acq{26,1} = 'rotx'; list.acq{26,2} = '';
-list.acq{26,3} = 'double';
-list.acq{27,1} = 'bb'; list.acq{27,2} = '';
-list.acq{27,3} = 'double';
-list.acq{28,1} = 'bbdir'; list.acq{28,2} = '';
-list.acq{28,3} = 'char';
-list.acq{29,1} = 'maxradius'; list.acq{29,2} = '';
-list.acq{29,3} = 'char';
-list.acq{30,1} = 'pair_tablename'; list.acq{30,2} = 'Table for spot pairs';
-list.acq{30,3} = 'char';
-list.acq{31,1} = 'calib_tablename'; list.acq{31,2} = 'Table for calibration of pair matching';
-list.acq{31,3} = 'double';
-list.acq{32,1} = 'orig_xdet'; list.acq{32,2} = 'Original detector width'
-list.acq{32,3} = 'double';
-list.acq{33,1} = 'orig_ydet'; list.acq{33,2} = 'Original detector height'
-list.acq{33,3} = 'double';
-list.acq{34,1} = 'roi_x_off'; list.acq{34,2} = 'Horizontal offset of ROI'
-list.acq{34,3} = 'double';
-list.acq{35,1} = 'roi_y_off'; list.acq{35,2} = 'Vertical offset of ROI'
-list.acq{35,3} = 'double';
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% CRYSTALLOGRAPHY structure
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-cryst.material = '';
-cryst.latticepar = [NaN NaN NaN NaN NaN NaN];
-cryst.spacegroup = NaN;
-cryst.hermann_mauguin = '';
-cryst.crystal_system = '';
-
-list.cryst{1,1} = 'material'; list.cryst{1,2} = 'Sample material';
-list.cryst{1,3} = 'char';
-list.cryst{2,1} = 'latticepar'; list.cryst{2,2} = 'Sample lattice parameters [a b c alpha beta gamma] (angstrom, deg)';
-list.cryst{2,3} = 'double';
-list.cryst{3,1} = 'spacegroup'; list.cryst{3,2} = 'Sample spacegroup';
-list.cryst{3,3} = 'double';
-list.cryst{4,1} = 'hermann_mauguin'; list.cryst{4,2} = 'Hermann Mauguin short symbol';
-list.cryst{4,3} = 'char';
-list.cryst{5,1} = 'crystal_system'; list.cryst{5,2} = 'Crystallographic unit-cell structure system';
-list.cryst{5,3} = 'char';
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% XOP structure
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-xop.No = NaN;
-xop.tt = NaN;
-xop.dspacing = NaN;
-xop.Int = NaN;
-xop.F = NaN;
-xop.h = NaN;
-xop.k = NaN;
-xop.l = NaN;
-xop.Mult = NaN;
-xop.hkl = [NaN NaN NaN];
-xop.name = '';
-xop.xop_dir = '';
-
-list.xop{1,1} = 'No'; list.xop{1,2} = 'Number of reflection'; list.xop{1,3} = 'int8';
-list.xop{2,1} = 'tt'; list.xop{2,2} = 'Twotheta angle'; list.xop{2,3} = 'single';
-list.xop{3,1} = 'dspacing'; list.xop{3,2} = 'd-spacing'; list.xop{3,3} = 'single';
-list.xop{4,1} = 'Int'; list.xop{4,2} = 'Intensity'; list.xop{4,3} = 'single';
-list.xop{5,1} = 'F'; list.xop{5,2} = 'Form factor'; list.xop{5,3} = 'single';
-list.xop{6,1} = 'h'; list.xop{6,2} = 'h'; list.xop{6,3} = 'int8';
-list.xop{7,1} = 'k'; list.xop{7,2} = 'k'; list.xop{7,3} = 'int8';
-list.xop{8,1} = 'l'; list.xop{8,2} = 'l'; list.xop{8,3} = 'int8';
-list.xop{9,1} = 'Mult'; list.xop{9,2} = 'Multiplicity'; list.xop{9,3} = 'int8';
-list.xop{10,1} = 'hkl'; list.xop{10,2} = 'hkl Miller indexes'; list.xop{10,3} = 'int8';
-list.xop{11,1} = 'name'; list.xop{11,2} = 'XOP/Diamond crystallographic file'; list.xop{11,3} = 'char';
-list.xop{12,1} = 'xop_dir'; list.xop{12,2} = 'Directory for the XOP input file'; list.xop{12,3} = 'char';
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% GEOMETRY structure
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-geo.detpos0 = [NaN NaN NaN];
-geo.detdiru0 = [NaN NaN NaN];
-geo.detdirv0 = [NaN NaN NaN];
-geo.beamdir0 = [NaN NaN NaN];
-geo.rotdir0 = [NaN NaN NaN];
-geo.detucen0 = NaN;
-geo.detvcen0 = NaN;
-geo.detdir0 = [NaN NaN NaN];
-geo.detanglemin = NaN;
-geo.detanglemax = NaN;
-
-list.geo{1,1} = 'detpos0'; list.geo{1,2} = 'Detector position'; list.geo{1,3} = 'double';
-list.geo{2,1} = 'detdiru0'; list.geo{2,2} = 'Detector u-direction'; list.geo{2,3} = 'double';
-list.geo{3,1} = 'detdirv0'; list.geo{3,2} = 'Detector v-direction'; list.geo{3,3} = 'double';
-list.geo{4,1} = 'beamdir0'; list.geo{4,2} = 'Beam direction'; list.geo{4,3} = 'double';
-list.geo{5,1} = 'rotdir0'; list.geo{5,2} = 'Rotation axis direction'; list.geo{5,3} = 'double';
-list.geo{6,1} = 'detucen0'; list.geo{6,2} = 'Detector u-centre'; list.geo{6,3} = 'double';
-list.geo{7,1} = 'detvcen0'; list.geo{7,2} = 'Detector v-centre'; list.geo{7,3} = 'double';
-list.geo{8,1} = 'detdir0'; list.geo{8,2} = 'Detector normal direction'; list.geo{8,3} = 'double';
-list.geo{9,1} = 'detanglemin'; list.geo{9,2} = 'Detector minimum 2Theta angle'; list.geo{9,3} = 'double';
-list.geo{10,1} = 'detanglemax'; list.geo{10,2} = 'Detector maximum 2Theta angle'; list.geo{10,3} = 'double';
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% OPTIMIZED GEOMETRY parameters
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-opt.detpos = [NaN NaN NaN];
-opt.detdiru = [NaN NaN NaN];
-opt.detdirv = [NaN NaN NaN];
-opt.beamdir = [NaN NaN NaN];
-opt.rotdir = [NaN NaN NaN];
-opt.detucen = NaN;
-opt.detvcen = NaN;
-opt.detdir = [NaN NaN NaN];
-
-list.opt{1,1} = 'detpos'; list.opt{1,2} = 'Detector position'; list.opt{1,3} = 'double';
-list.opt{2,1} = 'detdiru'; list.opt{2,2} = 'Detector u-direction'; list.opt{2,3} = 'double';
-list.opt{3,1} = 'detdirv'; list.opt{3,2} = 'Detector v-direction'; list.opt{3,3} = 'double';
-list.opt{4,1} = 'beamdir'; list.opt{4,2} = 'Beam direction'; list.opt{4,3} = 'double';
-list.opt{5,1} = 'rotdir'; list.opt{5,2} = 'Rotation axis direction'; list.opt{5,3} = 'double';
-list.opt{6,1} = 'detucen'; list.opt{6,2} = 'Detector u-centre'; list.opt{6,3} = 'double';
-list.opt{7,1} = 'detvcen'; list.opt{7,2} = 'Detector v-centre'; list.opt{7,3} = 'double';
-list.opt{8,1} = 'detdir'; list.opt{8,2} = 'Detector normal direction'; list.opt{8,3} = 'double';
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% DATABASE structure
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-database.name = '';
-database.host = '';
-database.user = '';
-database.password = '';
-
-list.database{1,1} = 'name'; list.database{1,2} = 'Database name'; list.database{1,3} = 'char';
-list.database{2,1} = 'host'; list.database{2,2} = 'Database host'; list.database{2,3} = 'char';
-list.database{3,1} = 'user'; list.database{3,2} = 'Database user'; list.database{3,3} = 'char';
-list.database{4,1} = 'password'; list.database{4,2} = 'Database password'; list.database{4,3} = 'char';
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% PREPROCESSING structure
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-prep.normalisation = '';
-prep.absint = NaN;
-prep.absrange = NaN;
-prep.fullint = NaN;
-prep.fullrange = NaN;
-prep.margin = NaN;
-prep.intensity = NaN;
-prep.filtsize = [NaN NaN];
-prep.drifts_pad = '';
-prep.renumbered = false;
-prep.bb = [NaN NaN NaN NaN];
-prep.correct_drift = '';
-prep.udrift = NaN;
-prep.udriftabs = NaN;
-prep.vdrift = NaN;
-
-list.prep{1,1} = 'normalisation'; list.prep{1,2} = ''; list.prep{1,3} = 'char';
-list.prep{2,1} = 'absint'; list.prep{2,2} = ''; list.prep{2,3} = 'double';
-list.prep{3,1} = 'absrange'; list.prep{3,2} = ''; list.prep{3,3} = 'double';
-list.prep{4,1} = 'fullint'; list.prep{4,2} = ''; list.prep{4,3} = 'double';
-list.prep{5,1} = 'fullrange'; list.prep{5,2} = ''; list.prep{5,3} = 'double';
-list.prep{6,1} = 'margin'; list.prep{6,2} = ''; list.prep{6,3} = 'double';
-list.prep{7,1} = 'intensity'; list.prep{7,2} = ''; list.prep{7,3} = 'double';
-list.prep{8,1} = 'filtsize'; list.prep{8,2} = ''; list.prep{8,3} = 'double';
-list.prep{9,1} = 'drifts_pad'; list.prep{9,2} = ''; list.prep{9,3} = 'char';
-list.prep{10,1} = 'renumbered'; list.prep{10,2} = ''; list.prep{10,3} = 'logical';
-list.prep{11,1} = 'bb'; list.prep{11,2} = ''; list.prep{11,3} = 'double';
-list.prep{12,1} = 'correct_drift'; list.prep{12,2} = ''; list.prep{12,3} = 'char';
-list.prep{13,1} = 'udrift'; list.prep{13,2} = ''; list.prep{13,3} = 'double';
-list.prep{14,1} = 'udriftabs'; list.prep{14,2} = ''; list.prep{14,3} = 'double';
-list.prep{15,1} = 'vdrift'; list.prep{15,2} = ''; list.prep{15,3} = 'double';
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% SEGMENTATION structure
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-seg.th2 = NaN;
-seg.th1 = NaN;
-seg.th_grow_low = NaN;
-seg.th_grow_high = NaN;
-seg.minsize = NaN;
-seg.minint = NaN;
-seg.icut = NaN;
-seg.ExtLimImInt = NaN;
-seg.ExtLimTailInt = NaN;
-seg.DifSpotMask = '';
-seg.dbfields = '';
-seg.bb = [NaN NaN NaN NaN];
-seg.background_subtract = false;
-seg.overlaps_removed = false;
-
-list.seg{1,1} = 'th2'; list.seg{1,2} = '';
-list.seg{1,3} = 'double';
-list.seg{2,1} = 'th1'; list.seg{2,2} = 'Threshold for finding seeds';
-list.seg{2,3} = 'double';
-list.seg{3,1} = 'th_grow_low'; list.seg{3,2} = 'Lower limit of threshold for growing seeds';
-list.seg{3,3} = 'double';
-list.seg{4,1} = 'th_grow_high'; list.seg{4,2} = 'Upper limit of threshold for growing seeds';
-list.seg{4,3} = 'double';
-list.seg{5,1} = 'minsize'; list.seg{5,2} = '';
-list.seg{5,3} = 'double';
-list.seg{6,1} = 'minint'; list.seg{6,2} = '';
-list.seg{6,3} = 'double';
-list.seg{7,1} = 'icut'; list.seg{7,2} = '';
-list.seg{7,3} = 'double';
-list.seg{8,1} = 'ExtLimImInt'; list.seg{8,2} = 'First and last image in the stack with this minimum relative intensity';
-list.seg{8,3} = 'double';
-list.seg{9,1} = 'ExtLimTailInt'; list.seg{9,2} = 'Size of tails cut off the summed intensity curve through the image stack';
-list.seg{9,3} = 'double';
-list.seg{10,1} = 'DifSpotMask'; list.seg{10,2} = 'Mask used to create difspot.edf from blob';
-list.seg{10,3} = 'char';
-list.seg{11,1} = 'dbfields'; list.seg{11,2} = 'Database ''difspot'' table fields list';
-list.seg{11,3} = 'char';
-list.seg{12,1} = 'bb'; list.seg{12,2} = 'Bounding Box';
-list.seg{12,3} = 'double';
-list.seg{13,1} = 'background_subtract'; list.seg{13,2} = 'Subtraction of the background';
-list.seg{13,3} = 'double';
-list.seg{14,1} = 'overlaps_removed'; list.seg{14,2} = 'Removing of overlaps';
-list.seg{14,3} = 'logical';
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% MATCHING - CALIBRATION structure
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%match_calib = gtMatchDefaultParametersCalib;
-match_calib.thr_ang = NaN;
-match_calib.thr_ang_scale = NaN;
-match_calib.thr_max_offset = NaN;
-match_calib.thr_ext_offset = NaN;
-match_calib.thr_genim_offset = NaN;
-match_calib.corr_rot_to_det = NaN;
-match_calib.thr_for_corr = NaN;
-match_calib.thr_goodness = NaN;
-match_calib.thr_intint = NaN;
-match_calib.thr_area = NaN;
-match_calib.thr_bbsize = NaN;
-match_calib.minsizeX = NaN;
-match_calib.minsizeY = NaN;
-match_calib.tiltY = NaN;
-match_calib.tiltZ = NaN;
-match_calib.centmode = NaN;
-match_calib.addconstr = NaN;
-match_calib.theta_bounds = NaN;
-
-list.match_calib{1,1} = 'thr_ang'; list.match_calib{1,2} = ''; list.match_calib{1,3} = 'double';
-list.match_calib{2,1} = 'thr_ang_scale'; list.match_calib{2,2} = ''; list.match_calib{2,3} = 'double';
-list.match_calib{3,1} = 'thr_max_offset'; list.match_calib{3,2} = ''; list.match_calib{3,3} = 'double';
-list.match_calib{4,1} = 'thr_ext_offset'; list.match_calib{4,2} = ''; list.match_calib{4,3} = 'double';
-list.match_calib{5,1} = 'thr_genim_offset'; list.match_calib{5,2} = ''; list.match_calib{5,3} = 'double';
-list.match_calib{6,1} = 'corr_rot_to_det'; list.match_calib{6,2} = ''; list.match_calib{6,3} = 'double';
-list.match_calib{7,1} = 'thr_for_corr'; list.match_calib{7,2} = ''; list.match_calib{7,3} = 'double';
-list.match_calib{8,1} = 'thr_goodness'; list.match_calib{8,2} = ''; list.match_calib{8,3} = 'double';
-list.match_calib{9,1} = 'thr_intint'; list.match_calib{9,2} = ''; list.match_calib{9,3} = 'double';
-list.match_calib{10,1} = 'thr_area'; list.match_calib{10,2} = ''; list.match_calib{10,3} = 'double';
-list.match_calib{11,1} = 'thr_bbsize'; list.match_calib{11,2} = ''; list.match_calib{11,3} = 'double';
-list.match_calib{12,1} = 'minsizeX'; list.match_calib{12,2} = ''; list.match_calib{12,3} = 'double';
-list.match_calib{13,1} = 'minsizeY'; list.match_calib{13,2} = ''; list.match_calib{13,3} = 'double';
-list.match_calib{14,1} = 'tiltY'; list.match_calib{14,2} = ''; list.match_calib{14,3} = 'double';
-list.match_calib{15,1} = 'tiltZ'; list.match_calib{15,2} = ''; list.match_calib{15,3} = 'double';
-list.match_calib{16,1} = 'centmode'; list.match_calib{16,2} = ''; list.match_calib{16,3} = 'double';
-list.match_calib{17,1} = 'addconstr'; list.match_calib{17,2} = ''; list.match_calib{17,3} = 'double';
-list.match_calib{18,1} = 'theta_bounds'; list.match_calib{18,2} = ''; list.match_calib{18,3} = 'double';
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% MATCHING structure
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%match = gtMatchDefaultParameters;
-match.thr_ang = NaN;
-match.thr_ang_scale = NaN;
-match.thr_max_offset = NaN;
-match.thr_ext_offset = NaN;
-match.thr_genim_offset = NaN;
-match.corr_rot_to_det = NaN;
-match.thr_for_corr = NaN;
-match.thr_goodness = NaN;
-match.thr_intint = NaN;
-match.thr_area = NaN;
-match.thr_bbsize = NaN;
-match.minsizeX = NaN;
-match.minsizeY = NaN;
-match.tiltY = NaN;
-match.tiltZ = NaN;
-match.centmode = NaN;
-match.addconstr = NaN;
-
-list.match{1,1} = 'thr_ang'; list.match{1,2} = ''; list.match{1,3} = 'double';
-list.match{2,1} = 'thr_ang_scale'; list.match{2,2} = ''; list.match{2,3} = 'double';
-list.match{3,1} = 'thr_max_offset'; list.match{3,2} = ''; list.match{3,3} = 'double';
-list.match{4,1} = 'thr_ext_offset'; list.match{4,2} = ''; list.match{4,3} = 'double';
-list.match{5,1} = 'thr_genim_offset'; list.match{5,2} = ''; list.match{5,3} = 'double';
-list.match{6,1} = 'corr_rot_to_det'; list.match{6,2} = ''; list.match{6,3} = 'double';
-list.match{7,1} = 'thr_for_corr'; list.match{7,2} = ''; list.match{7,3} = 'double';
-list.match{8,1} = 'thr_goodness'; list.match{8,2} = ''; list.match{8,3} = 'double';
-list.match{9,1} = 'thr_intint'; list.match{9,2} = ''; list.match{9,3} = 'double';
-list.match{10,1} = 'thr_area'; list.match{10,2} = ''; list.match{10,3} = 'double';
-list.match{11,1} = 'thr_bbsize'; list.match{11,2} = ''; list.match{11,3} = 'double';
-list.match{12,1} = 'minsizeX'; list.match{12,2} = ''; list.match{12,3} = 'double';
-list.match{13,1} = 'minsizeY'; list.match{13,2} = ''; list.match{13,3} = 'double';
-list.match{14,1} = 'tiltY'; list.match{14,2} = ''; list.match{14,3} = 'double';
-list.match{15,1} = 'tiltZ'; list.match{15,2} = ''; list.match{15,3} = 'double';
-list.match{16,1} = 'centmode'; list.match{16,2} = ''; list.match{16,3} = 'double';
-list.match{17,1} = 'addconstr'; list.match{17,2} = ''; list.match{17,3} = 'double';
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% INDEXING structure
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%index.strategy = gtIndexDefaultStrategy;
-index.strategy.iter = NaN;
-index.strategy.r = NaN;
-index.strategy.s = NaN;
-
-list.index.strategy{1,1} = 'iter'; list.index.strategy{1,2} = 'Number of iterations';
-list.index.strategy{1,3} = 'double';
-list.index.strategy{2,1} = 'r'; list.index.strategy{2,2} = 'Tolerance for marking outliers in final grain sets (in std)';
-list.index.strategy{2,3} = 'double';
-list.index.strategy{3,1} = 's'; list.index.strategy{3,2} = 'Tolerance for marking outliers in final grain sets (in std)';
-list.index.strategy{3,3} = 'double';
-
-% Tolerances for building grains in the first iteration:
-index.strategy.b.beg.ang = NaN;
-index.strategy.b.beg.int = NaN;
-index.strategy.b.beg.bbxs = NaN;
-index.strategy.b.beg.bbys = NaN;
-index.strategy.b.beg.distsf = NaN;
-index.strategy.b.beg.distmax = NaN;
-index.strategy.b.beg.ming = NaN;
-index.strategy.b.beg.geo = NaN;
-
-list.index.strategy.b.beg{1,1} = 'ang'; list.index.strategy.b.beg{1,2} = 'angular difference in degrees';
-list.index.strategy.b.beg{1,3} = 'double';
-list.index.strategy.b.beg{2,1} = 'int'; list.index.strategy.b.beg{2,2} = 'max. intensity ratio';
-list.index.strategy.b.beg{2,3} = 'double';
-list.index.strategy.b.beg{3,1} = 'bbxs'; list.index.strategy.b.beg{3,2} = 'max. bbox x size ratio';
-list.index.strategy.b.beg{3,3} = 'double';
-list.index.strategy.b.beg{4,1} = 'bbys'; list.index.strategy.b.beg{4,2} = 'max. bbox y size ratio';
-list.index.strategy.b.beg{4,3} = 'double';
-list.index.strategy.b.beg{5,1} = 'distsf'; list.index.strategy.b.beg{5,2} = 'size factor for maximum distance';
-list.index.strategy.b.beg{5,3} = 'double';
-list.index.strategy.b.beg{6,1} = 'distmax'; list.index.strategy.b.beg{6,2} = 'max. absolut distance';
-list.index.strategy.b.beg{6,3} = 'double';
-list.index.strategy.b.beg{7,1} = 'ming'; list.index.strategy.b.beg{7,2} = 'min. no. of Friedel pairs in a grain';
-list.index.strategy.b.beg{7,3} = 'double';
-list.index.strategy.b.beg{8,1} = 'geo'; list.index.strategy.b.beg{8,2} = 'safety margin around sample volume';
-list.index.strategy.b.beg{8,3} = 'double';
-
-% Tolerances for building grains in the last iteration:
-index.strategy.b.end.ang = NaN;
-index.strategy.b.end.int = NaN;
-index.strategy.b.end.bbxs = NaN;
-index.strategy.b.end.bbys = NaN;
-index.strategy.b.end.distsf = NaN;
-index.strategy.b.end.distmax = NaN;
-index.strategy.b.end.ming = NaN;
-index.strategy.b.end.geo = NaN;
-
-list.index.strategy.b.end{1,1} = 'ang'; list.index.strategy.b.end{1,2} = 'angular difference in degrees';
-list.index.strategy.b.end{1,3} = 'double';
-list.index.strategy.b.end{2,1} = 'int'; list.index.strategy.b.end{2,2} = 'max. intensity ratio';
-list.index.strategy.b.end{2,3} = 'double';
-list.index.strategy.b.end{3,1} = 'bbxs'; list.index.strategy.b.end{3,2} = 'max. bbox x size ratio';
-list.index.strategy.b.end{3,3} = 'double';
-list.index.strategy.b.end{4,1} = 'bbys'; list.index.strategy.b.end{4,2} = 'max. bbox y size ratio';
-list.index.strategy.b.end{4,3} = 'double';
-list.index.strategy.b.end{5,1} = 'distsf'; list.index.strategy.b.end{5,2} = 'size factor for maximum distance';
-list.index.strategy.b.end{5,3} = 'double';
-list.index.strategy.b.end{6,1} = 'distmax'; list.index.strategy.b.end{6,2} = 'max. absolut distance';
-list.index.strategy.b.end{6,3} = 'double';
-list.index.strategy.b.end{7,1} = 'ming'; list.index.strategy.b.end{7,2} = 'min. no. of Friedel pairs in a grain';
-list.index.strategy.b.end{7,3} = 'double';
-list.index.strategy.b.end{8,1} = 'geo'; list.index.strategy.b.end{8,2} = 'safety margin around sample volume';
-list.index.strategy.b.end{8,3} = 'double';
-
-
-% Tolerances for merging grains in the first iteration:
-index.strategy.m.beg.bbxs = NaN;
-index.strategy.m.beg.bbys = NaN;
-index.strategy.m.beg.distsf = NaN;
-index.strategy.m.beg.int = NaN;
-
-list.index.strategy.m.beg{1,1} = 'bbxs'; list.index.strategy.m.beg{1,2} = 'max. bbox x size ratio';
-list.index.strategy.m.beg{1,3} = 'double';
-list.index.strategy.m.beg{2,1} = 'bbys'; list.index.strategy.m.beg{2,2} = 'max. bbox y size ratio';
-list.index.strategy.m.beg{2,3} = 'double';
-list.index.strategy.m.beg{3,1} = 'distsf'; list.index.strategy.m.beg{3,2} = 'size factor for maximum distance';
-list.index.strategy.m.beg{3,3} = 'double';
-list.index.strategy.m.beg{4,1} = 'int'; list.index.strategy.m.beg{4,2} = 'max. intensity ratio';
-list.index.strategy.m.beg{4,3} = 'double';
-
-% Tolerances for merging grains in the last iteration:
-index.strategy.m.end.bbxs = NaN;
-index.strategy.m.end.bbys = NaN;
-index.strategy.m.end.distsf = NaN;
-index.strategy.m.end.int = NaN;
-
-list.index.strategy.m.end{1,1} = 'bbxs'; list.index.strategy.m.end{1,2} = 'max. bbox x size ratio';
-list.index.strategy.m.end{1,3} = 'double';
-list.index.strategy.m.end{2,1} = 'bbys'; list.index.strategy.m.end{2,2} = 'max. bbox y size ratio';
-list.index.strategy.m.end{2,3} = 'double';
-list.index.strategy.m.end{3,1} = 'distsf'; list.index.strategy.m.end{3,2} = 'size factor for maximum distance';
-list.index.strategy.m.end{3,3} = 'double';
-list.index.strategy.m.end{4,1} = 'int'; list.index.strategy.m.end{4,2} = 'max. intensity ratio';
-list.index.strategy.m.end{4,3} = 'double';
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% RECONSTRUCTION structure
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-rec.ROI = '';
-rec.select_projections_auto = false;
-rec.do_forward_simulation = false;
-rec.do_reconstruction = false;
-rec.update_db = false;
-rec.show_results = false;
-rec.use_extspots = false;
-rec.percentile1 = NaN;
-rec.percentile2 = NaN;
-
-list.rec{1,1} = 'ROI'; list.rec{1,2} = 'Region Of Interest'; list.rec{1,3} = 'char';
-list.rec{2,1} = 'select_projections_auto'; list.rec{2,2} = ''; list.rec{2,3} = 'double';
-list.rec{3,1} = 'do_forward_simulation'; list.rec{3,2} = 'Do forward simulation'; list.rec{3,3} = 'double';
-list.rec{4,1} = 'update_db'; list.rec{4,2} = 'Do reconstruction'; list.rec{4,3} = 'double';
-list.rec{5,1} = 'show_results'; list.rec{5,2} = 'Update database'; list.rec{5,3} = 'double';
-list.rec{6,1} = 'use_extspots'; list.rec{6,2} = 'Show results'; list.rec{6,3} = 'double';
-list.rec{7,1} = 'percentile1'; list.rec{7,2} = 'Use extension spots'; list.rec{7,3} = 'double';
-list.rec{8,1} = 'percentile2'; list.rec{8,2} = ''; list.rec{8,3} = 'double';
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% BUILDING TOGETHER
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-parameters.acq = acq;
-parameters.cryst = cryst;
-parameters.xop = xop;
-parameters.geo = geo;
-parameters.opt = opt;
-parameters.prep = prep;
-parameters.seg = seg;
-parameters.match_calib = match_calib;
-parameters.match = match;
-parameters.index = index;
-parameters.rec = rec;
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% SAVING
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-save('/data/id11/graintracking/HowTo/template_parameters.mat','parameters','-v7.3');
-save('/data/id11/graintracking/HowTo/template_list.mat','list','-v7.3');
-
-disp('Saved parameters template in /data/id11/graintracking/HowTo/template_parameters.mat')
-disp('Saved parameters fields list in /data/id11/graintracking/HowTo/template_list.mat')
-
diff --git a/zUtil_Parameters/make_parameters.m b/zUtil_Parameters/make_parameters.m
index c2f22fad..bb571fe4 100644
--- a/zUtil_Parameters/make_parameters.m
+++ b/zUtil_Parameters/make_parameters.m
@@ -18,7 +18,7 @@ function [parameters, list] = make_parameters(version)
%
%
% FUNCTIONS CALLED:
-%[use]- complete_structure
+%[use]- build_list
%[use]- build_structure_v0
disp('Getting the field list of parameters...')
--
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