Add h5 files and correct h5scan script

matlab/src/h5scan.m

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

matlab/test_id31_1_metrology.m

@@ -46,9 +46,9 @@ Hm = [ 0  1  0 -l2  0;
 
 %% Angular alignment
 % Load Data
-data_it0 = h5scan(data_dir, 'alignment', 'h1rx_h1ry', 1);
-data_it1 = h5scan(data_dir, 'alignment', 'h1rx_h1ry_0002', 3);
-data_it2 = h5scan(data_dir, 'alignment', 'h1rx_h1ry_0002', 5);
+data_it0 = h5scan('alignment_h1rx_h1ry', 1);
+data_it1 = h5scan('alignment_h1rx_h1ry_0002', 3);
+data_it2 = h5scan('alignment_h1rx_h1ry_0002', 5);
 
 % Offset wrong points
 i_it0 = find(abs(data_it0.Rx_int_filtered(2:end)-data_it0.Rx_int_filtered(1:end-1))>1e-5);
@@ -81,8 +81,8 @@ ylim([-100, 800]);
 
 %% Eccentricity alignment
 % Load Data
-data_it0 = h5scan(data_dir, 'alignment', 'h1rx_h1ry_0002', 5);
-data_it1 = h5scan(data_dir, 'alignment', 'h1dx_h1dy', 1);
+data_it0 = h5scan('alignment_h1rx_h1ry_0002', 5);
+data_it1 = h5scan('alignment_h1dx_h1dy', 1);
 
 % Offset wrong points
 i_it0 = find(abs(data_it0.Dy_int_filtered(2:end)-data_it0.Dy_int_filtered(1:end-1))>1e-5);
@@ -110,7 +110,7 @@ ylim([-8, 14]);
 % This is estimated by moving the spheres using the micro-hexapod
 
 % Dx
-data_dx = h5scan(data_dir, 'metrology_acceptance_new_align', 'dx', 1);
+data_dx = h5scan('metrology_acceptance_new_align_dx', 1);
 
 dx_acceptance = zeros(5,1);
 
@@ -126,7 +126,7 @@ for i = [1:size(dx_acceptance, 1)]
 end
 
 % Dy
-data_dy = h5scan(data_dir, 'metrology_acceptance_new_align', 'dy', 1);
+data_dy = h5scan('metrology_acceptance_new_align_dy', 1);
 
 dy_acceptance = zeros(5,1);
 
@@ -142,7 +142,7 @@ for i = [1:size(dy_acceptance, 1)]
 end
 
 % Dz
-data_dz = h5scan(data_dir, 'metrology_acceptance_new_align', 'dz', 1);
+data_dz = h5scan('metrology_acceptance_new_align_dz', 1);
 
 dz_acceptance = zeros(5,1);
 
@@ -186,7 +186,7 @@ leg = legend('location', 'northeast', 'FontSize', 8, 'NumColumns', 1);
 leg.ItemTokenSize(1) = 15;
 
 %% X-Y scan with the micro-hexapod, and record of the vertical interferometer
-data = h5scan(data_dir, 'metrology_acceptance', 'after_int_align_meshXY', 1);
+data = h5scan('metrology_acceptance_after_int_align_meshXY', 1);
 
 x = 1e3*detrend(data.h1tx, 0); % [um]
 y = 1e3*detrend(data.h1ty, 0); % [um]

matlab/test_id31_2_open_loop_plant.m

@@ -198,10 +198,10 @@ linkaxes([ax1,ax2],'x');
 xlim([1, 1e3]);
 
 %% Load Data
-data_1_dx = h5scan(data_dir, 'align_int_enc_Rz', 'tx_first_scan', 2);
-data_1_dy = h5scan(data_dir, 'align_int_enc_Rz', 'tx_first_scan', 3);
-data_2_dx = h5scan(data_dir, 'align_int_enc_Rz', 'verif-after-correct-offset', 1);
-data_2_dy = h5scan(data_dir, 'align_int_enc_Rz', 'verif-after-correct-offset', 2);
+data_1_dx = h5scan('align_int_enc_Rz_tx_first_scan', 2);
+data_1_dy = h5scan('align_int_enc_Rz_tx_first_scan', 3);
+data_2_dx = h5scan('align_int_enc_Rz_verif-after-correct-offset', 1);
+data_2_dy = h5scan('align_int_enc_Rz_verif-after-correct-offset', 2);
 
 % Estimation of Rz misalignment
 p1 = polyfit(data_1_dx.Dx_int_filtered, data_1_dx.Dy_int_filtered, 1);