From 7abea9ef222c1c63267945d210cd9a4ec39ee184 Mon Sep 17 00:00:00 2001 From: Edoardo Pasca Date: Wed, 21 Mar 2018 17:51:37 +0000 Subject: reasonable long run --- Wrappers/Python/wip/test_reader_reconstr.py | 139 ++++++++++++++-------------- 1 file changed, 67 insertions(+), 72 deletions(-) diff --git a/Wrappers/Python/wip/test_reader_reconstr.py b/Wrappers/Python/wip/test_reader_reconstr.py index 33ab461..79afd61 100755 --- a/Wrappers/Python/wip/test_reader_reconstr.py +++ b/Wrappers/Python/wip/test_reader_reconstr.py @@ -19,28 +19,7 @@ import numpy import matplotlib.pyplot as plt import os - -def add_dimension(data, fill_with, axis, start=True): - delta = data.shape[data.get_dimension_axis(axis)] - fill_with.shape[fill_with.get_dimension_axis(axis)] - command = 'data.array[' - i = 0 - for k,v in data.dimension_labels.items(): - if axis == v: - if start: - command = command + str(delta) + ":" - else: - l = data.get_dimension_size(axis) - delta - command = command + "0:" + str(l) - else: - command = command + ":" - - if i < data.number_of_dimensions -1: - command = command + ',' - i += 1 - command = command + "] = fill_with.array[:]" - #print (command) - exec(command) - #return command +import pickle def avg_img(image): @@ -51,48 +30,6 @@ def avg_img(image): avg += image[i] / l return avg -def setupCCPiGeometries(voxel_num_x, voxel_num_y, voxel_num_z, angles, counter): - vg = ImageGeometry(voxel_num_x=voxel_num_x,voxel_num_y=voxel_num_y, voxel_num_z=voxel_num_z) - Phantom_ccpi = ImageData(geometry=vg, - dimension_labels=['horizontal_x','horizontal_y','vertical']) - #.subset(['horizontal_x','horizontal_y','vertical']) - # ask the ccpi code what dimensions it would like - - voxel_per_pixel = 1 - geoms = pbalg.pb_setup_geometry_from_image(Phantom_ccpi.as_array(), - angles, - voxel_per_pixel ) - - pg = AcquisitionGeometry('parallel', - '3D', - angles, - geoms['n_h'], 1, - geoms['n_v'], 1 #2D in 3D is a slice 1 pixel thick - ) - - center_of_rotation = Phantom_ccpi.get_dimension_size('horizontal_x') / 2 - ad = AcquisitionData(geometry=pg,dimension_labels=['angle','vertical','horizontal']) - geoms_i = pbalg.pb_setup_geometry_from_acquisition(ad.as_array(), - angles, - center_of_rotation, - voxel_per_pixel ) - - #print (counter) - counter+=1 - #print (geoms , geoms_i) - if counter < 4: - if (not ( geoms_i == geoms )): - print ("not equal and {0}".format(counter)) - X = max(geoms['output_volume_x'], geoms_i['output_volume_x']) - Y = max(geoms['output_volume_y'], geoms_i['output_volume_y']) - Z = max(geoms['output_volume_z'], geoms_i['output_volume_z']) - return setupCCPiGeometries(X,Y,Z,angles, counter) - else: - print ("return geoms {0}".format(geoms)) - return geoms - else: - print ("return geoms_i {0}".format(geoms_i)) - return geoms_i reader = NexusReader(os.path.join(".." ,".." ,".." , "data" , "24737_fd.nxs" )) @@ -141,12 +78,14 @@ x_init = ImageData(geometry=vg, dimension_labels=['horizontal_x','horizontal_y', #%% print ("run FISTA") # Run FISTA for least squares without regularization -opt = {'tol': 1e-4, 'iter': 10} +opt = {'tol': 1e-4, 'iter': 500} x_fista0, it0, timing0, criter0 = FISTA(x_init, f, None, opt=opt) +pickle.dump(x_fista0, open("fista0.pkl", "wb")) + plt.imshow(x_fista0.subset(horizontal_x=80).array) plt.title('FISTA0') -plt.show() +#plt.show() # Now least squares plus 1-norm regularization lam = 0.1 @@ -154,23 +93,25 @@ g0 = Norm1(lam) # Run FISTA for least squares plus 1-norm function. x_fista1, it1, timing1, criter1 = FISTA(x_init, f, g0,opt=opt) +pickle.dump(x_fista1, open("fista1.pkl", "wb")) plt.imshow(x_fista0.subset(horizontal_x=80).array) plt.title('FISTA1') -plt.show() +#plt.show() plt.semilogy(criter1) -plt.show() +#plt.show() # Run FBPD=Forward Backward Primal Dual method on least squares plus 1-norm x_fbpd1, it_fbpd1, timing_fbpd1, criter_fbpd1 = FBPD(x_init,None,f,g0,opt=opt) +pickle.dump(x_fbpd1, open("fbpd1.pkl", "wb")) plt.imshow(x_fbpd1.subset(horizontal_x=80).array) plt.title('FBPD1') -plt.show() +#plt.show() plt.semilogy(criter_fbpd1) -plt.show() +#plt.show() # Now FBPD for least squares plus TV #lamtv = 1 @@ -187,12 +128,66 @@ plt.show() # Run CGLS, which should agree with the FISTA0 x_CGLS, it_CGLS, timing_CGLS, criter_CGLS = CGLS(x_init, Cop, padded_data, opt=opt) - +pickle.dump(x_CGLS, open("cgls.pkl", "wb")) plt.imshow(x_CGLS.subset(horizontal_x=80).array) plt.title('CGLS') plt.title('CGLS recon, compare FISTA0') -plt.show() +#plt.show() plt.semilogy(criter_CGLS) plt.title('CGLS criterion') +#plt.show() + + +clims = (0,1) +cols = 5 +rows = 1 +current = 1 +fig = plt.figure() +# projections row + +current = current +a=fig.add_subplot(rows,cols,current) +a.set_title('FISTA0') +imgplot = plt.imshow(x_fista0.subset(horizontal_x=80).as_array()) + +current = current + 1 +a=fig.add_subplot(rows,cols,current) +a.set_title('FISTA1') +imgplot = plt.imshow(x_fista1.subset(horizontal_x=80).as_array()) + +current = current + 1 +a=fig.add_subplot(rows,cols,current) +a.set_title('FBPD1') +imgplot = plt.imshow(x_fbpd1.subset(horizontal_x=80).as_array()) + +current = current + 1 +a=fig.add_subplot(rows,cols,current) +a.set_title('CGLS') +imgplot = plt.imshow(x_CGLS.subset(horizontal_x=80).as_array()) + +current = current + 1 +a=fig.add_subplot(rows,cols,current) +a.set_title('criteria') +imgplot = plt.loglog(criter0 , label='FISTA0') +imgplot = plt.loglog(criter1 , label='FISTA1') +imgplot = plt.loglog(criter_fbpd1, label='FBPD1') +imgplot = plt.loglog(criter_CGLS, label='CGLS') +#imgplot = plt.loglog(criter_fbpdtv, label='FBPD TV') +a.legend(loc='right') + +plt.show() + + +#%% +fig = plt.figure() +# projections row +b=fig.add_subplot(1,1,1) +b.set_title('criteria') +imgplot = plt.loglog(criter0 , label='FISTA0') +imgplot = plt.loglog(criter1 , label='FISTA1') +imgplot = plt.loglog(criter_fbpd1, label='FBPD1') +imgplot = plt.loglog(criter_CGLS, label='CGLS') +#imgplot = plt.loglog(criter_fbpdtv, label='FBPD TV') +b.legend(loc='right') plt.show() \ No newline at end of file -- cgit v1.2.3