figs/inkscape/convert_svg.sh

@@ -1,18 +0,0 @@
-#!/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

@@ -1,61 +1,102 @@
-% 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;
 
-    f = sprintf('%s.h5',ds);
+i = cellfun(@(x) isa(x,'detector'),varargin);
-    h = h5info(f,sprintf('/%d.1/measurement',sn));
+if any(i), det = varargin{i}; varargin = varargin(~i); else, det = []; end;
-    fid = H5F.open(f);
+if ~isstr(ds), ds = sprintf('%.4d',ds); end;
-    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
 
-    H5F.close(fid);
+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);
 
-    function A = vrtlds(f,nm,det)
+%%%%%%%%%%%%%%%%%%%%%%%%%%
-        n = 0; A = [];
-        fn = sprintf('%s/%s_%.4d.h5',f,nm,n);
 
-        while exist(fn) == 2
+function A = vrtlds(f,nm,det)
-            fid = H5F.open(fn); n = n+1;
+%try,
-            id = H5D.open(fid,sprintf('/entry_0000/ESRF-ID31/%s/data',nm));
+  n = 0; A = [];
-            if 2 < nargin & strcmp(nm,'p3') & ~isempty(det)
+  fn = sprintf('%s/%s_%.4d.h5',f,nm,n);
-                fprintf('integrating %s\n',fn);
+  while exist(fn) == 2,
-                if isempty(A)
+    fid = H5F.open(fn); n = n+1;
-                    A = integrate(det,double(H5D.read(id)),1);
+    id = H5D.open(fid,sprintf('/entry_0000/ESRF-ID31/%s/data',nm));
-                else
+    if 2 < nargin & strcmp(nm,'p3') & ~isempty(det),
-                    tmp = integrate(det,double(H5D.read(id)),1); A.y = cat(2,A.y,tmp.y); A.y0 = cat(2,A.y0,tmp.y0);
+      fprintf('integrating %s\n',fn);
-                end
+      if isempty(A),
-            else
+        A = integrate(det,double(H5D.read(id)),1);
-                fprintf('loading %s\n',fn);
+      else,
-                A = cat(3,A,H5D.read(id));
+        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;
-            H5D.close(id); H5F.close(fid);
+    else,
-            fn = sprintf('%s/%s_%.4d.h5',f,nm,n);
+      fprintf('loading %s\n',fn);
-        end
+      A = cat(3,A,H5D.read(id));
-    end
+    end;
-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);

matlab/test_id31_1_metrology.m

@@ -46,9 +46,9 @@ Hm = [ 0  1  0 -l2  0;
 
 %% Angular alignment
 % Load Data
-data_it0 = h5scan('alignment_h1rx_h1ry', 1);
+data_it0 = h5scan(data_dir, 'alignment', 'h1rx_h1ry', 1);
-data_it1 = h5scan('alignment_h1rx_h1ry_0002', 3);
+data_it1 = h5scan(data_dir, 'alignment', 'h1rx_h1ry_0002', 3);
-data_it2 = h5scan('alignment_h1rx_h1ry_0002', 5);
+data_it2 = h5scan(data_dir, '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('alignment_h1rx_h1ry_0002', 5);
+data_it0 = h5scan(data_dir, 'alignment', 'h1rx_h1ry_0002', 5);
-data_it1 = h5scan('alignment_h1dx_h1dy', 1);
+data_it1 = h5scan(data_dir, '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('metrology_acceptance_new_align_dx', 1);
+data_dx = h5scan(data_dir, '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('metrology_acceptance_new_align_dy', 1);
+data_dy = h5scan(data_dir, '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('metrology_acceptance_new_align_dz', 1);
+data_dz = h5scan(data_dir, '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('metrology_acceptance_after_int_align_meshXY', 1);
+data = h5scan(data_dir, '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('align_int_enc_Rz_tx_first_scan', 2);
+data_1_dx = h5scan(data_dir, 'align_int_enc_Rz', 'tx_first_scan', 2);
-data_1_dy = h5scan('align_int_enc_Rz_tx_first_scan', 3);
+data_1_dy = h5scan(data_dir, 'align_int_enc_Rz', 'tx_first_scan', 3);
-data_2_dx = h5scan('align_int_enc_Rz_verif-after-correct-offset', 1);
+data_2_dx = h5scan(data_dir, 'align_int_enc_Rz', 'verif-after-correct-offset', 1);
-data_2_dy = h5scan('align_int_enc_Rz_verif-after-correct-offset', 2);
+data_2_dy = h5scan(data_dir, '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('alignment_h1rx_h1ry', 1);
+data_it0 = h5scan(data_dir, 'alignment', 'h1rx_h1ry', 1);
-data_it1 = h5scan('alignment_h1rx_h1ry_0002', 3);
+data_it1 = h5scan(data_dir, 'alignment', 'h1rx_h1ry_0002', 3);
-data_it2 = h5scan('alignment_h1rx_h1ry_0002', 5);
+data_it2 = h5scan(data_dir, '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('alignment_h1rx_h1ry_0002', 5);
+data_it0 = h5scan(data_dir, 'alignment', 'h1rx_h1ry_0002', 5);
-data_it1 = h5scan('alignment_h1dx_h1dy', 1);
+data_it1 = h5scan(data_dir, '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('metrology_acceptance_new_align_dx', 1);
+data_dx = h5scan(data_dir, '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('metrology_acceptance_new_align_dy', 1);
+data_dy = h5scan(data_dir, '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('metrology_acceptance_new_align_dz', 1);
+data_dz = h5scan(data_dir, '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('metrology_acceptance_after_int_align_meshXY', 1);
+data = h5scan(data_dir, '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('align_int_enc_Rz_tx_first_scan', 2);
+data_1_dx = h5scan(data_dir, 'align_int_enc_Rz', 'tx_first_scan', 2);
-data_1_dy = h5scan('align_int_enc_Rz_tx_first_scan', 3);
+data_1_dy = h5scan(data_dir, 'align_int_enc_Rz', 'tx_first_scan', 3);
-data_2_dx = h5scan('align_int_enc_Rz_verif-after-correct-offset', 1);
+data_2_dx = h5scan(data_dir, 'align_int_enc_Rz', 'verif-after-correct-offset', 1);
-data_2_dy = h5scan('align_int_enc_Rz_verif-after-correct-offset', 2);
+data_2_dy = h5scan(data_dir, 'align_int_enc_Rz', 'verif-after-correct-offset', 2);
 #+end_src
 
 #+begin_src matlab
@@ -5208,67 +5208,108 @@ 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;
 
-    f = sprintf('%s.h5',ds);
+i = cellfun(@(x) isa(x,'detector'),varargin);
-    h = h5info(f,sprintf('/%d.1/measurement',sn));
+if any(i), det = varargin{i}; varargin = varargin(~i); else, det = []; end;
-    fid = H5F.open(f);
+if ~isstr(ds), ds = sprintf('%.4d',ds); end;
-    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
 
-    H5F.close(fid);
+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);
 
-    function A = vrtlds(f,nm,det)
+%%%%%%%%%%%%%%%%%%%%%%%%%%
-        n = 0; A = [];
-        fn = sprintf('%s/%s_%.4d.h5',f,nm,n);
 
-        while exist(fn) == 2
+function A = vrtlds(f,nm,det)
-            fid = H5F.open(fn); n = n+1;
+%try,
-            id = H5D.open(fid,sprintf('/entry_0000/ESRF-ID31/%s/data',nm));
+  n = 0; A = [];
-            if 2 < nargin & strcmp(nm,'p3') & ~isempty(det)
+  fn = sprintf('%s/%s_%.4d.h5',f,nm,n);
-                fprintf('integrating %s\n',fn);
+  while exist(fn) == 2,
-                if isempty(A)
+    fid = H5F.open(fn); n = n+1;
-                    A = integrate(det,double(H5D.read(id)),1);
+    id = H5D.open(fid,sprintf('/entry_0000/ESRF-ID31/%s/data',nm));
-                else
+    if 2 < nargin & strcmp(nm,'p3') & ~isempty(det),
-                    tmp = integrate(det,double(H5D.read(id)),1); A.y = cat(2,A.y,tmp.y); A.y0 = cat(2,A.y0,tmp.y0);
+      fprintf('integrating %s\n',fn);
-                end
+      if isempty(A),
-            else
+        A = integrate(det,double(H5D.read(id)),1);
-                fprintf('loading %s\n',fn);
+      else,
-                A = cat(3,A,H5D.read(id));
+        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;
-            H5D.close(id); H5F.close(fid);
+    else,
-            fn = sprintf('%s/%s_%.4d.h5',f,nm,n);
+      fprintf('loading %s\n',fn);
-        end
+      A = cat(3,A,H5D.read(id));
-    end
+    end;
-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);
 #+end_src
 
 *** =sphereFit= - Fit sphere from x,y,z points