# run "%qui qt" magic command from Ipython prompt for interactive mode
import pandas as pd
from mayavi import mlab
from atlaselectrophysiology import rendering
import ibllib.atlas as atlas
# the csv file is available here:
# https://github.com/int-brain-lab/ibllib-matlab/blob/master/needles/maps/first_pass_map.csv
output_video = '/home/olivier/Videos/first_pass.webm'
csv_file = "/home/olivier/Documents/MATLAB/ibllib-matlab/needles/maps/first_pass_map.csv"
# start of the code
brain_atlas = atlas.AllenAtlas(25)
brain_atlas = atlas.NeedlesAtlas(25)
df_map = pd.read_csv(csv_file)
fig = rendering.figure()
plt_trj = []
for index, rec in df_map.iterrows():
ins = atlas.Insertion.from_dict({'x': rec.ml_um, 'y': rec.ap_um, 'z': rec.dv_um,
'phi': rec.phi, 'theta': rec.theta, 'depth': rec.depth_um})
mlapdv = brain_atlas.xyz2ccf(ins.xyz)
plt = mlab.plot3d(mlapdv[:, 1], mlapdv[:, 2], mlapdv[:, 0],
line_width=3, color=(1, .6, .6), tube_radius=15)
plt_trj.append(plt)
##
# environment installation guide https://github.com/int-brain-lab/iblenv
# run "%qui qt" magic command from Ipython prompt for interactive mode
from mayavi import mlab
from one.api import ONE
from atlaselectrophysiology import rendering
import ibllib.atlas as atlas
one = ONE(base_url="https://alyx.internationalbrainlab.org")
fig = rendering.figure()
subject = 'KS003'
trajs = one.alyx.rest('trajectories', 'list', subject=subject)
ba_allen = atlas.AllenAtlas(25)
ba_needles = atlas.NeedlesAtlas(25)
plt_trj = []
for index, trj in enumerate(trajs):
if trj['coordinate_system'] == 'IBL-Allen':
brain_atlas = ba_allen
elif trj['coordinate_system'] == 'Needles-Allen':
brain_atlas = ba_needles
ins = atlas.Insertion.from_dict(trj, brain_atlas=brain_atlas)
ins = atlas.Insertion.from_dict(trj, brain_atlas=ba_allen)
mlapdv = brain_atlas.xyz2ccf(ins.xyz)
if trj['provenance'] == 'Micro-manipulator':
color = (0., 1., 0.) # Green
elif trj['provenance'] == 'Histology track':
color = (1., 0., 0.) # Red