cleaned up initial params and added h5export

Author: larsloetgering

@ptyLab/h5exportRaw.m

@@ -0,0 +1,10 @@
+function h5exportRaw(obj, file_name)
+
+hdf5write(file_name, ...
+         '/ptychogram', obj.ptychogram,... 
+         '/encoder', obj.positions0*obj.dxo,...
+         '/dxd', obj.dxd,...
+         '/zo', obj.zo,...
+         '/wavelength', 2.48e-9);
+
+end

@ptyLab/initialParams.m

@@ -6,6 +6,7 @@
 p.addParameter('absObjectSwitch', false) % impose object being real and positiv
 p.addParameter('absObjectStepSize', 0.05) % step size for absObjectSwitch
 p.addParameter('batchSize', 10)         % fft-block size for parallel engines
+p.addParameter('backgroundModeSwitch',false) % contrains mode for background 
 p.addParameter('betaObject',0.25)       % mPIE feedback parameter (object)
 p.addParameter('betaProbe',0.25)        % mPIE feedback parameter (probe)
 p.addParameter('comStabilizationSwitch', true)% if true, the probe is centered
@@ -19,6 +20,7 @@
 p.addParameter('initialProbe','circ')   % choose initial probe ('obes', 'rand')
 p.addParameter('intensityConstraint','standard') % ('standard', 'sigmoid')
 p.addParameter('makeGIF', false) % probe orthogonalization frequency
+p.addParameter('modulusEnforcedProbeSwitch', false) % activates MEP update
 p.addParameter('npsm',1)                % number of probe state mixtures
 p.addParameter('nosm',1)                % number of object state mixtures
 p.addParameter('numIterations',1)       % number of iterations
@@ -27,7 +29,9 @@
 p.addParameter('orthogonalizationFrequency', 10) % probe orthogonalization frequency
 p.addParameter('positionOrder','random')% position order for sequential solvers ('sequential' or 'random')
 p.addParameter('probePowerCorrectionSwitch', true)  % switch to indicate if probe power correction is applied
+p.addParameter('probeSmoothenessSwitch', false) % imposes probe smootheness
 p.addParameter('saveMemory', true)      % if true, then the algorithm is run with low memory consumption (e.g. detector error is not saved)
+p.addParameter('showObjectSpectrum',false) % show Fourier transform of object
 p.addParameter('singleSwitch', true)    % if true, data is converted to single to save memory and processing time
 p.addParameter('smoothenessSwitch', false)  % if true, apply smoothness constraint to object
 p.addParameter('objectTVregSwitch', false) % TV regularization
@@ -46,17 +50,21 @@
 % algorithmic parameters
 obj.params.absorbingProbeBoundary = p.Results.absorbingProbeBoundary;
 obj.params.absObjectSwitch = p.Results.absObjectSwitch;
-obj.params.positionOrder = p.Results.positionOrder;
+obj.params.backgroundModeSwitch = p.Results.backgroundModeSwitch;
+obj.params.batchSize = p.Results.batchSize;
+obj.params.comStabilizationSwitch = p.Results.comStabilizationSwitch;
+obj.params.gpuSwitch = p.Results.gpuSwitch;
 obj.params.intensityConstraint = p.Results.intensityConstraint;
+obj.params.modulusEnforcedProbeSwitch = p.Results.modulusEnforcedProbeSwitch;
+obj.params.positionOrder = p.Results.positionOrder;
 obj.params.probePowerCorrectionSwitch = p.Results.probePowerCorrectionSwitch;
+obj.params.probeSmoothenessSwitch = p.Results.probeSmoothenessSwitch;
 obj.params.smoothenessSwitch = p.Results.smoothenessSwitch;
-obj.params.comStabilizationSwitch = p.Results.comStabilizationSwitch;
-obj.params.gpuSwitch = p.Results.gpuSwitch;
 obj.params.saveMemory = p.Results.saveMemory;
+obj.params.objectTVregSwitch = p.Results.objectTVregSwitch;
 obj.params.orthogonalizationFrequency = p.Results.orthogonalizationFrequency;
-obj.params.batchSize = p.Results.batchSize;
 obj.params.zPIEgradientStepSize = p.Results.zPIEgradientStepSize;
-obj.params.objectTVregSwitch = p.Results.objectTVregSwitch;
+
 % general parameters
 obj.params.npsm = p.Results.npsm;
 obj.params.nosm = p.Results.nosm;
@@ -65,6 +73,9 @@
 obj.params.deleteFrames = p.Results.deleteFrames;
 obj.params.FourierMaskSwitch = p.Results.FourierMaskSwitch;
 
+% monitoring
+obj.monitor.showObjectSpectrum = p.Results.showObjectSpectrum;
+
 % reconstruction
 obj.params.numIterations = p.Results.numIterations;
 obj.params.figureUpdateFrequency = p.Results.figureUpdateFrequency;

@ptyLab/showPtychogram.m

@@ -7,16 +7,15 @@ function showPtychogram(obj, varargin)
 
 if isfield(obj.params, 'fftshiftSwitch')
     if obj.params.fftshiftSwitch
-        sliceViewer( fftshift(log10(obj.ptychogram + 1)), 'Colormap', cmap );
+        sliceViewer( gather(fftshift(log10(obj.ptychogram + 1))), 'Colormap', cmap );
     else
-        sliceViewer( log10(obj.ptychogram + 1), 'Colormap', cmap );
+        sliceViewer( gather(log10(obj.ptychogram + 1)), 'Colormap', cmap );
     end
 else
-    sliceViewer( log10(obj.ptychogram + 1), 'Colormap', cmap );
+    sliceViewer( gather(log10(obj.ptychogram + 1)), 'Colormap', cmap );
 end
 
 title('ptychogram')
-
 screen_size = get(0,'screensize');
 h = gcf;
 h.Position(1:2) = round( min(screen_size(3:4)))/4*[1,1];

tutorials/1_getting_started/1_preprocess_and_reconstruct/preprocess.asv

@@ -0,0 +1,98 @@
+% preprocessing
+
+clear
+restoredefaultpath
+tic
+
+set(0,'DefaultFigureWindowStyle','normal')
+set(0, 'DefaultAxesFontSize', 18);
+set(0, 'DefaultFigureColor', 'w');
+set(0,'defaultAxesFontName', 'serif')
+
+% add toolbox folders
+directory_info = dir();
+toolboxFolder = erase( directory_info(1).folder, 'tutorials\1_getting_started\1_preprocess_and_reconstruct');
+
+%%
+cd(toolboxFolder);
+addpath(genpath(toolboxFolder))
+
+obj = ptyLab;
+obj.export.exportPath = 'C:\Users\Lars Loetgering\Documents\ptyLabExport';
+% change this depending on computer used for preprocessing
+obj.export.filePath = 'C:\Users\Lars Loetgering\Documents\fracPtyRaw\ptyLab_data\ptyLab_helical_beam.h5';
+obj.export.fileName = 'recent'; % this can be defined and determines output file name
+obj.params.verboseLevel = 'low';
+
+%% read hdf5 file
+
+tic
+disp('read h5 file data')
+obj.ptychogram = single(h5read(obj.export.filePath,'/ptychogram'));
+obj.params.encoder = h5read(obj.export.filePath,'/encoder');
+obj.dxd = h5read(obj.export.filePath,'/dxd');
+obj.zo = h5read(obj.export.filePath,'/zo');
+obj.wavelength = h5read(obj.export.filePath,'/wavelength');
+obj.numFrames = size(obj.ptychogram,3);
+toc
+
+%% sampling
+
+% detector coordinates
+obj.Nd = size(obj.ptychogram, 1);
+obj.Ld = obj.Nd * obj.dxd;
+obj.xd = (-obj.Nd/2:obj.Nd/2-1) * obj.dxd;
+[obj.Xd, obj.Yd] = meshgrid(obj.xd);    % 2D coordinates in detector plane
+
+% object coordinates
+obj.dxo = obj.wavelength * obj.zo / obj.Ld;   % Fraunhofer/Fresnel
+obj.No = 2^11;
+obj.Lo = obj.No * obj.dxo;
+obj.xo = (-obj.No/2:obj.No/2-1) * obj.dxo;
+[obj.Xo, obj.Yo] = meshgrid(obj.xo);
+
+% probe coordinates
+obj.dxp = obj.dxo;
+obj.Np = obj.Nd;
+obj.Lp = obj.Np * obj.dxp;
+obj.xp = (-obj.Np/2:obj.Np/2-1)*obj.dxp;
+[obj.Xp, obj.Yp] = meshgrid(obj.xp);
+
+%% convert positions
+
+% convert positions into pixels
+obj.positions0 = round( (obj.params.encoder) / obj.dxo );
+% center within object grid
+obj.positions0  = obj.positions0 - floor(mean(obj.positions0, 1))  + obj.No/2 - round(obj.Np/2);
+% take only the frames needed (if numFrames smaller than the number of positions in the file)
+obj.positions0  = obj.positions0(1:obj.numFrames,:);
+
+% show positions
+figure(3)
+plot(obj.positions0 (:,2), obj.positions0(:,1),'o-')
+axis equal,axis image
+set(gcf, 'color', 'w')
+
+%% set entrance pupil diameter
+
+obj.entrancePupilDiameter = obj.Lp/3; % rough beam size estimate
+obj.propagator.type = 'Fraunhofer';
+
+%% save memory by converting to single precision
+% (saves roughly a factor of 1.5 to 2 in memory and reconstruction speed)
+
+obj.params.singleSwitch = true;
+if obj.params.singleSwitch
+    obj.convert2single;
+end
+
+%% export data
+obj.export.format = 'mat';
+exportBool = true;
+if exportBool
+    obj.export.exportID = [obj.export.fileName];
+    obj.exportObj
+end
+obj.showPtychogram
+toc
+

tutorials/1_getting_started/1_preprocess_and_reconstruct/preprocess.m

@@ -12,6 +12,8 @@
 % add toolbox folders
 directory_info = dir();
 toolboxFolder = erase( directory_info(1).folder, 'tutorials\1_getting_started\1_preprocess_and_reconstruct');
+
+%%
 cd(toolboxFolder);
 addpath(genpath(toolboxFolder))
 
@@ -26,7 +28,7 @@
 
 tic
 disp('read h5 file data')
-obj.ptychogram = h5read(obj.export.filePath,'/ptychogram');
+obj.ptychogram = single(h5read(obj.export.filePath,'/ptychogram'));
 obj.params.encoder = h5read(obj.export.filePath,'/encoder');
 obj.dxd = h5read(obj.export.filePath,'/dxd');
 obj.zo = h5read(obj.export.filePath,'/zo');
@@ -91,5 +93,8 @@
     obj.export.exportID = [obj.export.fileName];
     obj.exportObj
 end
+
+%% show raw data
+obj.showPtychogram
 toc