Add h5 files and correct h5scan script

figs/inkscape/convert_svg.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+# Directory containing SVG files
+INPUT_DIR="."
+
+# Loop through all SVG files in the directory
+for svg_file in "$INPUT_DIR"/*.svg; do
+    # Check if there are SVG files in the directory
+    if [ -f "$svg_file" ]; then
+        # Output PDF file name
+        pdf_file="../${svg_file%.svg}.pdf"
+        png_file="../${svg_file%.svg}"
+        
+        # Convert SVG to PDF using Inkscape
+        inkscape "$svg_file" --export-filename="$pdf_file" && \
+            pdftocairo -png -singlefile -cropbox "$pdf_file" "$png_file"
+    fi
+done

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);
+    f = sprintf('%s.h5',ds);
-if any(i), det = varargin{i}; varargin = varargin(~i); else, det = []; end;
+    h = h5info(f,sprintf('/%d.1/measurement',sn));
-if ~isstr(ds), ds = sprintf('%.4d',ds); end;
+    fid = H5F.open(f);
-
+    for i = 1:length(h.Links)
-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,
+        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,
+        end
-    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;
+    end
-try,
+    try
         h = h5info(f,sprintf('/%d.2/measurement',sn));
-catch,
+    catch
         h = [];
-end;
+    end
-if ~isempty(h),
+    if ~isempty(h)
-  for i = 1:length(h.Links),
+        for i = 1:length(h.Links)
             nm = h.Links(i).Name;
-    try,
+            try
                 id = H5D.open(fid,h.Links(i).Value{1});
                 cntrs.part2.(nm) = H5D.read(id);
                 H5D.close(id);
-    catch,
+            end
-      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
-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)
+    function A = vrtlds(f,nm,det)
-%try,
         n = 0; A = [];
         fn = sprintf('%s/%s_%.4d.h5',f,nm,n);
-  while exist(fn) == 2,
+
+        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),
+            if 2 < nargin & strcmp(nm,'p3') & ~isempty(det)
                 fprintf('integrating %s\n',fn);
-      if isempty(A),
+                if isempty(A)
                     A = integrate(det,double(H5D.read(id)),1);
-      else,
+                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;
+                end
-    else,
+            else
                 fprintf('loading %s\n',fn);
                 A = cat(3,A,H5D.read(id));
-    end;
+            end
             H5D.close(id); H5F.close(fid);
             fn = sprintf('%s/%s_%.4d.h5',f,nm,n);
-  end;
+        end
-%catch,
+    end
-%  A = [];
+end
-%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);

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_it0 = h5scan('alignment_h1rx_h1ry', 1);
-data_it1 = h5scan(data_dir, 'alignment', 'h1rx_h1ry_0002', 3);
+data_it1 = h5scan('alignment_h1rx_h1ry_0002', 3);
-data_it2 = h5scan(data_dir, 'alignment', 'h1rx_h1ry_0002', 5);
+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_it0 = h5scan('alignment_h1rx_h1ry_0002', 5);
-data_it1 = h5scan(data_dir, 'alignment', 'h1dx_h1dy', 1);
+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_dx = h5scan('align_int_enc_Rz_tx_first_scan', 2);
-data_1_dy = h5scan(data_dir, 'align_int_enc_Rz', 'tx_first_scan', 3);
+data_1_dy = h5scan('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_dx = h5scan('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_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);

test-bench-id31.org

@@ -685,9 +685,9 @@ The remaining errors after alignment are in the order of $\pm5\,\mu\text{rad}$ i
 #+begin_src matlab
 %% Angular alignment
 % Load Data
-data_it0 = h5scan(data_dir, 'alignment', 'h1rx_h1ry', 1);
+data_it0 = h5scan('alignment_h1rx_h1ry', 1);
-data_it1 = h5scan(data_dir, 'alignment', 'h1rx_h1ry_0002', 3);
+data_it1 = h5scan('alignment_h1rx_h1ry_0002', 3);
-data_it2 = h5scan(data_dir, 'alignment', 'h1rx_h1ry_0002', 5);
+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);
@@ -728,8 +728,8 @@ exportFig('figs/test_id31_metrology_align_rx_ry.pdf', 'width', 'half', 'height',
 #+begin_src matlab
 %% Eccentricity alignment
 % Load Data
-data_it0 = h5scan(data_dir, 'alignment', 'h1rx_h1ry_0002', 5);
+data_it0 = h5scan('alignment_h1rx_h1ry_0002', 5);
-data_it1 = h5scan(data_dir, 'alignment', 'h1dx_h1dy', 1);
+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);
@@ -793,7 +793,7 @@ The obtained lateral acceptance for pure displacements in any direction is estim
 % 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);
 
@@ -809,7 +809,7 @@ 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);
 
@@ -825,7 +825,7 @@ 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);
 
@@ -920,7 +920,7 @@ exportFig('figs/test_id31_interf_noise.pdf', 'width', 'half', 'height', 'normal'
 
 #+begin_src matlab
 %% 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]
@@ -1305,10 +1305,10 @@ Results shown in Figure ref:fig:test_id31_Rz_align_correct are indeed indicating
 
 #+begin_src matlab
 %% Load Data
-data_1_dx = h5scan(data_dir, 'align_int_enc_Rz', 'tx_first_scan', 2);
+data_1_dx = h5scan('align_int_enc_Rz_tx_first_scan', 2);
-data_1_dy = h5scan(data_dir, 'align_int_enc_Rz', 'tx_first_scan', 3);
+data_1_dy = h5scan('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_dx = h5scan('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_2_dy = h5scan('align_int_enc_Rz_verif-after-correct-offset', 2);
 #+end_src
 
 #+begin_src matlab
@@ -5208,108 +5208,67 @@ specs_ry_rms = 0.25; % [urad RMS]
 :header-args:matlab+: :comments none :mkdirp yes :eval no
 :END:
 #+begin_src matlab
-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);
+    f = sprintf('%s.h5',ds);
-if any(i), det = varargin{i}; varargin = varargin(~i); else, det = []; end;
+    h = h5info(f,sprintf('/%d.1/measurement',sn));
-if ~isstr(ds), ds = sprintf('%.4d',ds); end;
+    fid = H5F.open(f);
-
+    for i = 1:length(h.Links)
-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,
+        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,
+        end
-    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;
+    end
-try,
+    try
         h = h5info(f,sprintf('/%d.2/measurement',sn));
-catch,
+    catch
         h = [];
-end;
+    end
-if ~isempty(h),
+    if ~isempty(h)
-  for i = 1:length(h.Links),
+        for i = 1:length(h.Links)
             nm = h.Links(i).Name;
-    try,
+            try
                 id = H5D.open(fid,h.Links(i).Value{1});
                 cntrs.part2.(nm) = H5D.read(id);
                 H5D.close(id);
-    catch,
+            end
-      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
-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)
+    function A = vrtlds(f,nm,det)
-%try,
         n = 0; A = [];
         fn = sprintf('%s/%s_%.4d.h5',f,nm,n);
-  while exist(fn) == 2,
+
+        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),
+            if 2 < nargin & strcmp(nm,'p3') & ~isempty(det)
                 fprintf('integrating %s\n',fn);
-      if isempty(A),
+                if isempty(A)
                     A = integrate(det,double(H5D.read(id)),1);
-      else,
+                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;
+                end
-    else,
+            else
                 fprintf('loading %s\n',fn);
                 A = cat(3,A,H5D.read(id));
-    end;
+            end
             H5D.close(id); H5F.close(fid);
             fn = sprintf('%s/%s_%.4d.h5',f,nm,n);
-  end;
+        end
-%catch,
+    end
-%  A = [];
+end
-%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);
 #+end_src
 
 *** =sphereFit= - Fit sphere from x,y,z points