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-rw-r--r-- | demos/exportDemoRD2Data.m | 35 | ||||
-rw-r--r-- | src/Python/test/readhd5.py | 28 |
2 files changed, 63 insertions, 0 deletions
diff --git a/demos/exportDemoRD2Data.m b/demos/exportDemoRD2Data.m new file mode 100644 index 0000000..028353b --- /dev/null +++ b/demos/exportDemoRD2Data.m @@ -0,0 +1,35 @@ +clear all +close all +%% +% % adding paths +addpath('../data/'); +addpath('../main_func/'); addpath('../main_func/regularizers_CPU/'); +addpath('../supp/'); + +load('DendrRawData.mat') % load raw data of 3D dendritic set +angles_rad = angles*(pi/180); % conversion to radians +size_det = size(data_raw3D,1); % detectors dim +angSize = size(data_raw3D, 2); % angles dim +slices_tot = size(data_raw3D, 3); % no of slices +recon_size = 950; % reconstruction size + +Sino3D = zeros(size_det, angSize, slices_tot, 'single'); % log-corrected sino +% normalizing the data +for jj = 1:slices_tot + sino = data_raw3D(:,:,jj); + for ii = 1:angSize + Sino3D(:,ii,jj) = log((flats_ar(:,jj)-darks_ar(:,jj))./(single(sino(:,ii)) - darks_ar(:,jj))); + end +end + +Sino3D = Sino3D.*1000; +Weights3D = single(data_raw3D); % weights for PW model +clear data_raw3D + +hdf5write('DendrData.h5', '/Weights3D', Weights3D) +hdf5write('DendrData.h5', '/Sino3D', Sino3D, 'WriteMode', 'append') +hdf5write('DendrData.h5', '/angles_rad', angles_rad, 'WriteMode', 'append') +hdf5write('DendrData.h5', '/size_det', size_det, 'WriteMode', 'append') +hdf5write('DendrData.h5', '/angSize', angSize, 'WriteMode', 'append') +hdf5write('DendrData.h5', '/slices_tot', slices_tot, 'WriteMode', 'append') +hdf5write('DendrData.h5', '/recon_size', recon_size, 'WriteMode', 'append')
\ No newline at end of file diff --git a/src/Python/test/readhd5.py b/src/Python/test/readhd5.py new file mode 100644 index 0000000..1e19e14 --- /dev/null +++ b/src/Python/test/readhd5.py @@ -0,0 +1,28 @@ +# -*- coding: utf-8 -*- +""" +Created on Wed Aug 23 16:34:49 2017 + +@author: ofn77899 +""" + +import h5py +import numpy + +def getEntry(nx, location): + for item in nx[location].keys(): + print (item) + +filename = r'C:\Users\ofn77899\Documents\GitHub\CCPi-FISTA_reconstruction\Demos\DendrData.h5' +nx = h5py.File(filename, "r") +#getEntry(nx, '/') +# I have exported the entries as children of / +entries = [entry for entry in nx['/'].keys()] +print (entries) + +Sino3D = numpy.asarray(nx.get('/Sino3D')) +Weights3D = numpy.asarray(nx.get('/Weights3D')) +angSize = numpy.asarray(nx.get('/angSize'), dtype=int)[0] +angles_rad = numpy.asarray(nx.get('/angles_rad')) +recon_size = numpy.asarray(nx.get('/recon_size'), dtype=int)[0] +size_det = numpy.asarray(nx.get('/size_det'), dtype=int)[0] +slices_tot = numpy.asarray(nx.get('/slices_tot'), dtype=int)[0]
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