#Right
#s_cst_ext_file = '/home/bao/tiensy/Lauren_registration/data_compare_mapping/pairwise_reg_cstext2cstext/CST_ROI_trkvis_Right/' + source_sub + '_' + target_sub + '/out_reg/iteration_4/' + source_sub + '_cst_R_tvis_ext_reg.trk'
#t_cst_ext_file = '/home/bao/tiensy/Lauren_registration/data_compare_mapping/pairwise_reg_cstext2cstext/CST_ROI_trkvis_Right/' + source_sub + '_' + target_sub + '/out_reg/iteration_4/' + target_sub + '_cst_R_tvis_ext_reg.trk'
#out_file = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/Lauren_pair_CSText2CSText/Lauren_pair_CSText2CSText_f300_l75_1NN/map_1nn_pairwise_reg_CST_R_ext_' + source_sub + '_aligned_to_CST_R_ext_' + target_sub + '_Lauren_f300_l75.txt'
s_cst_ext_file = '/home/bao/tiensy/Lauren_registration/data_compare_mapping/pairwise_reg_cstext2cstext/CST_ROI_trkvis_Right/' + source_sub + '_' + target_sub + '/out_reg_f100_l25/iteration_4/' + source_sub + '_cst_R_tvis_ext_reg.trk'
t_cst_ext_file = '/home/bao/tiensy/Lauren_registration/data_compare_mapping/pairwise_reg_cstext2cstext/CST_ROI_trkvis_Right/' + source_sub + '_' + target_sub + '/out_reg_f100_l25/iteration_4/' + target_sub + '_cst_R_tvis_ext_reg.trk'
out_file = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/Lauren_pair_CSText2CSText/Lauren_pair_CSText2CSText_f100_l25_1NN/map_1nn_pairwise_reg_CST_R_ext_' + source_sub + '_aligned_to_CST_R_ext_' + target_sub + '_Lauren_f100_l25.txt'
s_cst_idx_file = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/ROI_seg_tvis/ROI_seg_tvis_native/' + source_sub + '_corticospinal_R_tvis.pkl'
t_cst_idx_file = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/ROI_seg_tvis/ROI_seg_tvis_native/' + target_sub + '_corticospinal_R_tvis.pkl'
'''
source_ext = load_whole_tract(s_cst_ext_file)
target_ext = load_whole_tract(t_cst_ext_file)
s_cst_idx = load_pickle(s_cst_idx_file)
source = source_ext[:len(s_cst_idx)]
t_cst_idx = load_pickle(t_cst_idx_file)
target = target_ext[:len(t_cst_idx)]
#print len(source), len(target)
tractography1 = source
tractography2 = target_ext
map_all = mapping_nn(tractography1, tractography2)
ROIs = ROIs_subject[source]
#convert from LPS in TrackVis software to LAS in dpy format
ROIs = [[r[0],128.-r[1],r[2]] for r in ROIs]
'''
'''
#trackvis tractography native space
tracks_ind_file = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/ROI_seg_tvis_native/' + source + '_corticospinal_R_tvis_native.pkl'
tract_file = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/' + source + '_tracks_dti_tvis.trk'
tracks = load_whole_tract_trk(tract_file)
'''
#trackvis tractography-MNI space ROI segmentation
tract_file = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/tvis_tractography/' + source + '_tracks_dti_tvis_linear.dpy'
tracks = load_whole_tract(tract_file)
from intersect_roi import *
ROIs = ROIs_subject[source]
print ROIs
#common = intersec_ROIs_dpy(tracks, ROIs, Rs, vis = True)
common = intersec_ROIs(tracks, ROIs, Rs, vis = True)
print "\t Total ", len(tracks), " and the number of fibers cross the ROIs ", len(common)
tracks_ind_file = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/ROI_seg_tvis_MNI/' + source + '_corticospinal_L_tvis_MNI.pkl'
save_pickle(tracks_ind_file, common)
print "Saved file", tracks_ind_file
vis = False
save = True
for s_id in np.arange(len(source_ids)):
print '-----------------------------------------------------------------------------------------'
print 'Source: ', source_ids[s_id]
source = str(source_ids[s_id])
flirt_filename = '/home/bao/Personal/PhD_at_Trento/Research/ALS_Nivedita_Bao/Code/data/' + source+'/DIFF2DEPI_EKJ_64dirs_14/DTI/flirt.mat'
fa_filename= '/home/bao/Personal/PhD_at_Trento/Research/ALS_Nivedita_Bao/Segmentation_CST_francesca/' + source + '/DTI/dti_fa_brain.nii.gz'
tracks_filename = '/home/bao/Personal/PhD_at_Trento/Research/ALS_Nivedita_Bao/Segmentation_CST_francesca/' + source + '/DTI/dti.trk'
linear_filename = '/home/bao/Personal/PhD_at_Trento/Research/ALS_Nivedita_Bao/Segmentation_CST_francesca/' + source + '/DTI/dti_linear.dpy'
warp_tracks_linearly(flirt_filename,fa_filename, tracks_filename,linear_filename)
print 'Saved ', linear_filename
tract_linear = load_whole_tract(linear_filename)
if save:
from common_functions import save_tract_trk
fa_warped = '/home/bao/Personal/PhD_at_Trento/Research/ALS_Nivedita_Bao/Code/data/' + source+'/DIFF2DEPI_EKJ_64dirs_14/DTI/fa_warped.nii.gz'
fname_out = '/home/bao/Personal/PhD_at_Trento/Research/ALS_Nivedita_Bao/Segmentation_CST_francesca/' + source + '/DTI/dti_linear.trk'
save_tract_trk(tract_linear, fa_warped, fname_out )
print 'Saved ', fname_out
if vis:
tract = load_whole_tract(tracks_filename)
from dipy.viz import fvtk
from common_functions import visualize_tract
ren = fvtk.ren()
visualize_tract(ren, tract,color=fvtk.red)
visualize_tract(ren, tract_linear,color=fvtk.blue)
fvtk.show(ren)
'''
#Right
s_cst_ext_file = '/home/nilab/tiensy/Tractography_Mapping/data/trackvis_tractography/Elef_pair_CSText2CSText/CST_R_ext_' + source_sub + '_aligned_to_CST_R_ext_' + target_sub + '_elef_rand_50_fiberpoint_40.dpy'
out_file = '/home/nilab/tiensy/Tractography_Mapping/data/trackvis_tractography/Elef_pair_CSText2CSText/Elef_pair_CSText2CSText_1NN/map_1nn_pairwise_reg_CST_R_ext_' + source_sub + '_aligned_to_CST_R_ext_' + target_sub + '_elef_rand_50_fiberpoint_40.txt'
s_cst_idx_file = '/home/nilab/tiensy/Tractography_Mapping/data/trackvis_tractography/ROI_seg_tvis/ROI_seg_tvis_native/' + source_sub + '_corticospinal_R_tvis.pkl'
t_file = '/home/nilab/tiensy/Tractography_Mapping/data/trackvis_tractography/tvis_tractography/' + target_sub + '_tracks_dti_tvis.trk'
t_cst_idx_file = '/home/nilab/tiensy/Tractography_Mapping/data/trackvis_tractography/ROI_seg_tvis/ROI_seg_tvis_native/' + target_sub + '_corticospinal_R_tvis.pkl'
t_cst_ext_idx_file = '/home/nilab/tiensy/Tractography_Mapping/data/trackvis_tractography/50_SFF_in_ext/ROI_seg_native/' + target_sub + '_cst_R_tvis_ext.pkl'
'''
s_cst_idx = load_pickle(s_cst_idx_file)
source_ext = load_whole_tract(s_cst_ext_file)
source = source_ext[:len(s_cst_idx)]
target = load_tract(t_file, t_cst_ext_idx_file)
#print len(source), len(target)
tractography1 = source
tractography2 = target
map_all = mapping_nn(tractography1, tractography2)
if save:
#print 'Saving 1-NN Eleftherios tract based method: ', out_file
