diff --git a/1_preprocessing/gtSetup_Utils/gtLoadAcquisitionXML.m b/1_preprocessing/gtSetup_Utils/gtLoadAcquisitionXML.m
index 9cfd857c776096d14253e1664afaf2c106b5abed..415a4cf79e4a91abc24261cc723d47e6b8b7cd17 100644
--- a/1_preprocessing/gtSetup_Utils/gtLoadAcquisitionXML.m
+++ b/1_preprocessing/gtSetup_Utils/gtLoadAcquisitionXML.m
@@ -1,7 +1,7 @@
-function params = gtLoadAcquisitionXML(parameters, list, xmlfname, interactive)
+function params_acq = gtLoadAcquisitionXML(acq, list_acq, xmlfname, interactive)
% FUNCTION gtLoadAcquisitionXML
-% params = gtLoadAcquisitionXML(parameters, list, xmlfname, interactive)
-% ----------------------------------------------------------------------
+% params_acq = gtLoadAcquisitionXML(acq, list_acq, xmlfname, interactive)
+% -----------------------------------------------------------------------
%
% Version 002 02/05/2012 by LNervo
% Add acq.beamchroma default value to 'mono'
@@ -17,24 +17,22 @@ function params = gtLoadAcquisitionXML(parameters, list, xmlfname, interactive)
tmpxml = xml_read(xmlfname);
tmpxml = tmpxml.acquisition;
- parameters.acq.name = tmpxml.scanName; % shouldn't change!
- parameters.acq.date = tmpxml.date;
- parameters.acq.xdet = tmpxml.projectionSize.DIM_2;
- parameters.acq.ydet = tmpxml.projectionSize.DIM_1;
- parameters.acq.nproj = tmpxml.tomo_N/2;
- parameters.acq.refon = tmpxml.ref_On;
- parameters.acq.nref = tmpxml.ref_N;
- parameters.acq.ndark = tmpxml.dark_N;
- parameters.acq.pixelsize = tmpxml.pixelSize/1000; % mm
- parameters.acq.count_time = tmpxml.ccdtime;
- parameters.acq.energy = tmpxml.energy;
- parameters.acq.dist = tmpxml.distance; % mm
- parameters.acq.sensortype = tmpxml.cameraName;
- parameters.acq.type = [num2str(tmpxml.scanRange) 'degree'];
- parameters.acq.orig_xdet = 2048;
- parameters.acq.orig_ydet = 2048;
- parameters.acq.roi_x_off = tmpxml.projectionSize.ROW_BEG;
- parameters.acq.roi_y_off = tmpxml.projectionSize.COL_BEG;
+ acq.name = tmpxml.scanName; % shouldn't change!
+ acq.date = tmpxml.date;
+ acq.xdet = tmpxml.projectionSize.DIM_2;
+ acq.ydet = tmpxml.projectionSize.DIM_1;
+ acq.nproj = tmpxml.tomo_N/2;
+ acq.refon = tmpxml.ref_On;
+ acq.nref = tmpxml.ref_N;
+ acq.ndark = tmpxml.dark_N;
+ acq.pixelsize = tmpxml.pixelSize/1000; % mm
+ acq.count_time = tmpxml.ccdtime;
+ acq.energy = tmpxml.energy;
+ acq.dist = tmpxml.distance; % mm
+ acq.sensortype = tmpxml.cameraName;
+ acq.type = [num2str(tmpxml.scanRange) 'degree'];
+ acq.roi_x_off = tmpxml.projectionSize.ROW_BEG;
+ acq.roi_y_off = tmpxml.projectionSize.COL_BEG;
else %if .xml not found
if interactive
disp('No .xml file found! Are you sure you are correctly in the acquistion directory?')
@@ -46,61 +44,62 @@ function params = gtLoadAcquisitionXML(parameters, list, xmlfname, interactive)
end
end
% guess some default values
- parameters.acq.date = date();
- parameters.acq.xdet = 2048;
- parameters.acq.ydet = 2048;
- parameters.acq.nproj = 7200;
- parameters.acq.refon = 200;
- parameters.acq.nref = 5;
- parameters.acq.ndark = 11;
- parameters.acq.pixelsize = 0.0014;
- parameters.acq.count_time = 2;
- parameters.acq.energy = 20;
- parameters.acq.dist = 5;
- parameters.acq.sensortype = 'frelon';
- parameters.acq.type = '360degree';
- parameters.acq.orig_xdet = 2048;
- parameters.acq.orig_ydet = 2048;
- parameters.acq.roi_x_off = 0;
- parameters.acq.roi_y_off = 0;
+ acq.date = date();
+ acq.xdet = 2048;
+ acq.ydet = 2048;
+ acq.nproj = 7200;
+ acq.refon = 200;
+ acq.nref = 5;
+ acq.ndark = 11;
+ acq.pixelsize = 0.0014;
+ acq.count_time = 2;
+ acq.energy = 20;
+ acq.dist = 5;
+ acq.sensortype = 'frelon';
+ acq.type = '360degree';
+ acq.roi_x_off = 0;
+ acq.roi_y_off = 0;
clear check
end
-
+
+
+ acq.orig_xdet = 2048;
+ acq.orig_ydet = 2048;
% interlacing parameters
% try to guess whether the scan is interlaced
- if exist([parameters.acq.name '0_0000.edf'], 'file')
- parameters.acq.interlaced_turns = true; % assume one extra turn is reasonable guess
+ if exist([acq.name '0_0000.edf'], 'file')
+ acq.interlaced_turns = true; % assume one extra turn is reasonable guess
disp('This looks like an interlaced scan! Doubling nproj...')
- parameters.acq.nproj = parameters.acq.nproj*2;
+ acq.nproj = acq.nproj*2;
else
- parameters.acq.interlaced_turns = false;
+ acq.interlaced_turns = false;
end
% mono tuned during scan?
- parameters.acq.mono_tune = false;
+ acq.mono_tune = false;
% if we have a horizontal rotation axis we turn the images during the copying process
- parameters.acq.rotation_axis = 'vertical';
- parameters.acq.distortion = 'none';
+ acq.rotation_axis = 'vertical';
+ acq.distortion = 'none';
% deal with flips and rotations
% subsequently, deal with flips and rotations, scans without direct beam
- parameters.acq.flip_images = false;
- parameters.acq.no_direct_beam = false;
+ acq.flip_images = false;
+ acq.no_direct_beam = false;
% rotate images to the gt coordinate system !!! Help !!!
- parameters.acq.rotation_direction = 'clockwise';
+ acq.rotation_direction = 'clockwise';
- parameters.acq.rotu = parameters.acq.xdet/2+0.5; % Images will be shifted in gtCreateFullLive to have rotation axis in center...
- parameters.acq.rotx = parameters.acq.rotu;
- parameters.acq.maxradius = max(parameters.acq.xdet,parameters.acq.ydet)/2*sqrt(2);
- parameters.acq.beamchroma = 'mono';
+ acq.rotu = acq.xdet/2+0.5; % Images will be shifted in gtCreateFullLive to have rotation axis in center...
+ acq.rotx = acq.rotu;
+ acq.maxradius = max(acq.xdet,acq.ydet)/2*sqrt(2);
+ acq.beamchroma = 'mono';
% if it is 360degree data, we need a pair table
- if strcmpi(parameters.acq.type, '360degree')
+ if strcmpi(acq.type, '360degree')
% pair tablename can be derived from the scan name
- parameters.acq.pair_tablename = [parameters.acq.name 'spotpairs'];
- parameters.acq.calib_tablename = [parameters.acq.name 'paircalib'];
+ acq.pair_tablename = [acq.name 'spotpairs'];
+ acq.calib_tablename = [acq.name 'paircalib'];
end
if interactive
@@ -111,10 +110,10 @@ function params = gtLoadAcquisitionXML(parameters, list, xmlfname, interactive)
else
header='Check all values. All "(?)" should be removed:';
end
- parameters.acq = gtModifyStructure(parameters.acq, list.acq(:,1:2), header);
+ acq = gtModifyStructure(acq, list_acq(:,1:2), header);
end
- params = parameters;
+ params_acq = acq;
end % end of function
diff --git a/3_pairmatchingGUI/gtMatchDefaultParametersGUI.m b/3_pairmatchingGUI/gtMatchDefaultParametersGUI.m
index 6155e81067e49e0e68a1f3494894337ff9c869ab..1ab81846486f336c89901a2c46f57d6435dbd035 100644
--- a/3_pairmatchingGUI/gtMatchDefaultParametersGUI.m
+++ b/3_pairmatchingGUI/gtMatchDefaultParametersGUI.m
@@ -1,11 +1,8 @@
-%
-% FUNCTION par_match = gtMatchDefaultParametersGUI()
-%
-% Stores and provides the default parameters for Friedel pair matching.
-%
-%
-
function par_match = gtMatchDefaultParametersGUI()
+% GTMATCHDEFAULTPARAMETERSGUI Stores and provides the default parameters for Friedel pair matching.
+% par_match = gtMatchDefaultParametersGUI()
+% -----------------------------------------
+%
par_match.thr_theta = 0.2;
par_match.thr_theta_scale = 0;
@@ -26,4 +23,4 @@ par_match.thr_meanerror = Inf;
par_match.thetalimits = [0 90];
-end
\ No newline at end of file
+end % end of function
\ No newline at end of file
diff --git a/zUtil_Cryst/gtLoadReflections.m b/zUtil_Cryst/gtLoadReflections.m
index eeab3fac98fbd64a148e9404998851d1ca21dafc..3b2401a15b757a02c3bfc17aed403d803a0a5172 100644
--- a/zUtil_Cryst/gtLoadReflections.m
+++ b/zUtil_Cryst/gtLoadReflections.m
@@ -125,16 +125,12 @@ if isreflections
title = lower(title);
title = strrep(title,'.','');
title = regexprep(title,'[^a-zA-Z]','');
- %title = regexprep(title,'theta','tt');
title = regexprep(title,'theta','twotheta');
if length(title)==1
title = regexprep(title,'m','mult');
- %title = regexprep(title,'^f','F');
title = regexprep(title,'^f','formfactor');
end
title = strtrim(title);
- %title = strrep(title,'dspacing','d0');
- %title = strrep(title,'dspc','d0');
title = strrep(title,'dspc','dspacing');
if ~strcmpi(title,'no')
reflections.(title)=C{i};
@@ -142,9 +138,7 @@ if isreflections
end
reflections.hkl=[reflections.h reflections.k reflections.l];
- reflections=rmfield(reflections,'h');
- reflections=rmfield(reflections,'k');
- reflections=rmfield(reflections,'l');
+ reflections=rmfield(reflections,{'h','k','l'});
xop = reflections;
ind=strfind(file,filesep);
diff --git a/zUtil_Parameters/build_list_v2.m b/zUtil_Parameters/build_list_v2.m
index 8ab5cf149c37bb196ac8d48f3bd8a044d0f93a6e..fa363968f74dba861e3180810237c17775f0b505 100644
--- a/zUtil_Parameters/build_list_v2.m
+++ b/zUtil_Parameters/build_list_v2.m
@@ -265,9 +265,9 @@ list.labgeo{23,1} = 'reflabY'; list.labgeo{23,2} = '';
list.labgeo{23,3} = 'char';
list.labgeo{24,1} = 'reflabZ'; list.labgeo{24,2} = '';
list.labgeo{24,3} = 'char';
-list.labgeo{25,1} = 'detsizeu'; list.labgeo{25,2} = '';
+list.labgeo{25,1} = 'detsizeu'; list.labgeo{25,2} = 'Number of pixels along the u direction';
list.labgeo{25,3} = 'double'; % scalar
-list.labgeo{26,1} = 'detsizev'; list.labgeo{26,2} = '';
+list.labgeo{26,1} = 'detsizev'; list.labgeo{26,2} = 'Number of pixels along the v direction';
list.labgeo{26,3} = 'double'; % scalar
list.labgeo{27,1} = 'rotcomp'; list.labgeo{27,2} = 'Rotation matrix components [computed]';
list.labgeo{27,3} = 'struct';