Add h5 files and correct h5scan script
This commit is contained in:
@@ -1,102 +1,61 @@
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function [cntrs,tp] = h5scan(pth,smp,ds,sn,varargin)
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% function [cntrs,tp] = h5scan(pth,smp,ds,sn,varargin)
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function [cntrs,tp] = h5scan(ds,sn)
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if ~isstr(ds), ds = sprintf('%.4d',ds); end;
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i = cellfun(@(x) isa(x,'detector'),varargin);
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if any(i), det = varargin{i}; varargin = varargin(~i); else, det = []; end;
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if ~isstr(ds), ds = sprintf('%.4d',ds); end;
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f = sprintf('%s.h5',ds);
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h = h5info(f,sprintf('/%d.1/measurement',sn));
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fid = H5F.open(f);
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for i = 1:length(h.Links)
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nm = h.Links(i).Name;
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try
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id = H5D.open(fid,h.Links(i).Value{1});
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cntrs.(nm) = H5D.read(id);
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H5D.close(id);
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if ~isempty(det) & strcmp(nm,det.name), cntrs.(nm) = integrate(det,double(cntrs.(nm))); end;
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end
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[~,tp.(nm)] = fileparts(h.Links(i).Value{1});
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end
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try
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h = h5info(f,sprintf('/%d.2/measurement',sn));
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catch
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h = [];
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end
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if ~isempty(h)
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for i = 1:length(h.Links)
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nm = h.Links(i).Name;
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try
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id = H5D.open(fid,h.Links(i).Value{1});
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cntrs.part2.(nm) = H5D.read(id);
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H5D.close(id);
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end
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[~,tp.part2.(nm)] = fileparts(h.Links(i).Value{1});
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end
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end
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f = sprintf('%s/%s/%s_%s/%s_%s.h5',pth,smp,smp,ds,smp,ds);
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h = h5info(f,sprintf('/%d.1/measurement',sn));
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fid = H5F.open(f);
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for i = 1:length(h.Links),
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nm = h.Links(i).Name;
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try,
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id = H5D.open(fid,h.Links(i).Value{1});
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cntrs.(nm) = H5D.read(id);
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H5D.close(id);
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if ~isempty(det) & strcmp(nm,det.name), cntrs.(nm) = integrate(det,double(cntrs.(nm))); end;
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catch,
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warning('solving problem with %s\n',nm);
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cntrs.(nm) = vrtlds(sprintf('%s/%s/%s_%s/scan%.4d/',pth,smp,smp,ds,sn),nm,det);
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end;
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[~,tp.(nm)] = fileparts(h.Links(i).Value{1});
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end;
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try,
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h = h5info(f,sprintf('/%d.2/measurement',sn));
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catch,
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h = [];
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end;
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if ~isempty(h),
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for i = 1:length(h.Links),
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nm = h.Links(i).Name;
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try,
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id = H5D.open(fid,h.Links(i).Value{1});
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cntrs.part2.(nm) = H5D.read(id);
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H5D.close(id);
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catch,
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warning('solving problem with %s\n',nm);
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cntrs.part2.(nm) = vrtlds(sprintf('%s/%s/%s_%s/scan%.4d/',pth,smp,smp,ds,sn),nm,det);
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end;
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[~,tp.part2.(nm)] = fileparts(h.Links(i).Value{1});
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end;
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end;
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if length(varargin),
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fn = sprintf('/%d.1/instrument/positioners/',sn);
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h = h5info(f,fn);
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[~,k,m] = intersect({h.Datasets.Name},varargin,'stable');
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h.Datasets = h.Datasets(k);
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for i = 1:length(h.Datasets),
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id = H5D.open(fid,[fn h.Datasets(i).Name]);
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cntrs.(h.Datasets(i).Name) = H5D.read(id);
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H5D.close(id);
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end;
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end;
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H5F.close(fid);
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H5F.close(fid);
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%%%%%%%%%%%%%%%%%%%%%%%%%%
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%%%%%%%%%%%%%%%%%%%%%%%%%%
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function A = vrtlds(f,nm,det)
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n = 0; A = [];
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fn = sprintf('%s/%s_%.4d.h5',f,nm,n);
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function A = vrtlds(f,nm,det)
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%try,
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n = 0; A = [];
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fn = sprintf('%s/%s_%.4d.h5',f,nm,n);
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while exist(fn) == 2,
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fid = H5F.open(fn); n = n+1;
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id = H5D.open(fid,sprintf('/entry_0000/ESRF-ID31/%s/data',nm));
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if 2 < nargin & strcmp(nm,'p3') & ~isempty(det),
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fprintf('integrating %s\n',fn);
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if isempty(A),
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A = integrate(det,double(H5D.read(id)),1);
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else,
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tmp = integrate(det,double(H5D.read(id)),1); A.y = cat(2,A.y,tmp.y); A.y0 = cat(2,A.y0,tmp.y0);
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end;
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else,
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fprintf('loading %s\n',fn);
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A = cat(3,A,H5D.read(id));
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end;
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H5D.close(id); H5F.close(fid);
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fn = sprintf('%s/%s_%.4d.h5',f,nm,n);
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end;
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%catch,
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% A = [];
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%end;
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% fid = H5F.open...
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% id = H5D.open...
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% sid = H5D.get_space(id);
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% [ndims,h5_dims]=H5S.get_simple_extent_dims(sid)
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% Read a 2x3 hyperslab of data from a dataset, starting in the 4th row and 5th column of the example dataset.
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% Create a property list identifier, then open the HDF5 file and the dataset /g1/g1.1/dset1.1.1.
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% fid = H5F.open('example.h5');
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% id = H5D.open(fid,'/g1/g1.1/dset1.1.1');
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% dims = ([500 1679 1475];
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% msid = H5S.create_simple(3,dims,[]);
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% sid = H5D.get_space(id);
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% offset = [n*500 0 0];
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% block = dims; % d1: 500 or min(d1tot-n*500,500)
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% H5S.select_hyperslab(sid,'H5S_SELECT_SET',offset,[],[],block);
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% data = H5D.read(id,'H5ML_DEFAULT',msid,sid,'H5P_DEFAULT');
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% H5D.close(id);
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% H5F.close(fid);
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while exist(fn) == 2
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fid = H5F.open(fn); n = n+1;
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id = H5D.open(fid,sprintf('/entry_0000/ESRF-ID31/%s/data',nm));
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if 2 < nargin & strcmp(nm,'p3') & ~isempty(det)
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fprintf('integrating %s\n',fn);
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if isempty(A)
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A = integrate(det,double(H5D.read(id)),1);
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else
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tmp = integrate(det,double(H5D.read(id)),1); A.y = cat(2,A.y,tmp.y); A.y0 = cat(2,A.y0,tmp.y0);
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end
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else
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fprintf('loading %s\n',fn);
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A = cat(3,A,H5D.read(id));
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end
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H5D.close(id); H5F.close(fid);
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fn = sprintf('%s/%s_%.4d.h5',f,nm,n);
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end
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end
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end
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