def get_airlab_transformed_coms():
shared_landmarks = get_shared_landmarks_between_dk52_and_atlas()
atlas_com_dict = get_atlas_com()
DK52_com_dict = get_dk52_com()
atlas_com = np.array([atlas_com_dict[landmark] for landmark in shared_landmarks])
DK52_com_shared = {}
for landmark in shared_landmarks:
DK52_com_shared[landmark] = DK52_com_dict[landmark]
prep_list = get_prep_list_for_rough_alignment_test()
air_lab_transformed_list = []
air_lab_aligned_list = []
for prepi in prep_list:
airlab_aligned_coms = {}
transform = get_tranformation(prepi)
airlab_transformed_coms = {}
for name, com in DK52_com_shared.items():
com = np.array(com, dtype=float)/np.array([0.325,0.325,20])
airlab_transformed_coms[name] = (transform.forward_point(com)*np.array([0.325,0.325,20])).tolist()
aligned_com,_ = get_and_apply_transform(np.array(list(airlab_transformed_coms.values())),atlas_com)
for i in range(len(aligned_com)):
name = list(airlab_transformed_coms.keys())[i]
airlab_aligned_coms[name] = aligned_com[i]
air_lab_transformed_list.append(airlab_transformed_coms)
air_lab_aligned_list.append(airlab_aligned_coms)
return air_lab_transformed_list,air_lab_aligned_list
def get_transformed_coms():
prep_list_for_rough_alignment = get_prep_list_for_rough_alignment_test()
atlas_com = get_atlas_com()
transformed_coms = []
for prepi in prep_list_for_rough_alignment:
DK52_com_aligned_to_prep = get_DK52_com_aligned_to_prepi(prepi)
DK52_com_aligned_to_atlas,_= get_and_apply_transform(DK52_com_aligned_to_prep,atlas_com)
transformed_coms.append(DK52_com_aligned_to_atlas)
transformed_coms = np.array(transformed_coms)
return transformed_coms
def get_demons_diagonastics():
prep_list_for_rough_alignment = get_prep_list_for_rough_alignment_test()
atlas_com_aligned_to_DK52 = get_atlas_com_aligned_to_DK52()
reference_coms = []
transformed_coms = []
for prepi in prep_list_for_rough_alignment:
print('loading demons transformation for prep: ' + prepi)
demons_transform = get_demons_transform(prepi)
reference_com = get_reference_com(prepi)
transformed_com = transform_point_demons(demons_transform,
atlas_com_aligned_to_DK52)
transformed_coms.append(transformed_com)
reference_coms.append(reference_com)
transformed_coms = np.array(transformed_coms)
reference_coms = np.array(reference_coms)
return reference_coms, transformed_coms, atlas_com_aligned_to_DK52
def get_itk_demons_transformed_coms():
shared_landmarks = get_shared_landmarks_between_dk52_and_atlas()
atlas_com_dict = get_atlas_com()
DK52_com_dict = get_dk52_com()
atlas_com = np.array([atlas_com_dict[landmark] for landmark in shared_landmarks])
DK52_com = np.array([DK52_com_dict[landmark] for landmark in shared_landmarks])
prep_list = get_prep_list_for_rough_alignment_test()
itk_transformed_coms = []
itk_aligned_coms = []
for prepi in prep_list:
demons_transform = get_demons_transform(prepi)
DK52_com_transformed = transform_point_demons(demons_transform,DK52_com)
DK52_com_aligned,_ = get_and_apply_transform(DK52_com_transformed,atlas_com)
DK52_com_transformed = dict(zip(shared_landmarks,DK52_com_transformed))
DK52_com_aligned = dict(zip(shared_landmarks,DK52_com_aligned))
itk_transformed_coms.append(DK52_com_transformed)
itk_aligned_coms.append(DK52_com_aligned)
return itk_transformed_coms,itk_aligned_coms
def get_kui_transformed():
prep_list = get_prep_list_for_rough_alignment_test()
kui_transformed_com = []
for prepi in prep_list:
kui_transformed_com.append(get_transformed_com_dict(prepi))
return kui_transformed_com
air_lab_aligned_list.append(airlab_aligned_coms)
return air_lab_transformed_list,air_lab_aligned_list
if __name__ == '__main__':
atlas_com_dict = get_atlas_com()
dk52_com = get_dk52_com()
prep_coms = get_prep_coms()
affine_transformed_coms_itk,affine_aligned_coms_itk = get_itk_affine_transformed_coms()
demons_transformed_coms_itk,demons_aligned_coms_itk = get_itk_demons_transformed_coms()
transformed_coms_airlab,aligned_coms_airlab = get_airlab_transformed_coms()
kui_airlab_aligned_coms = get_kui_airlab()
kui_transformed_com = get_kui_transformed()
atlas_prep_list = ['Atlas' for _ in range(5)]
dk52_prep_list = ["DK52" for _ in range(5)]
figs = []
prep_list = get_prep_list_for_rough_alignment_test()
# compare_two_com_dict(dk52_com,prep_coms[0],['DK52' , 'DK39'])
# compare_two_com_dict(kui_transformed_com[0],prep_coms[0],['DK52 kui airlab' , 'DK39'])
# compare_two_com_dict(transformed_coms_airlab[0],prep_coms[0],['DK52 beth airlab' , 'DK39'])
# compare_two_com_dict(affine_transformed_coms_itk[0],prep_coms[0],['DK52 kui airlab' , 'DK39'])
print('plotting DK52 annotation against atlas')
fig = get_fig_two_com_dict(dk52_com,atlas_com_dict,['DK52' , 'Atlas'])
figs.append(ploty_to_matplot(fig))
print('plotting DK52 to annotation before image to image alignment')
figs.append(get_fig_offset_from_coms_to_a_reference(prep_coms,dk52_com,
get_prep_list_for_rough_alignment_test,get_all_landmarks_in_specimens,
'DK52 to brain preps before alignment'))
fig = get_fig_corresponding_coms_in_dict_to_reference(prep_coms,dk52_com,prep_list,dk52_prep_list)
figs.append(ploty_to_matplot(fig))
print('plotting DK52 after affine transform from itk')