def vis_sources_by_pval(padj, all_coord, short_label):
'''
1. visualize the sources (brain regions) based on the FDR-adjusted p values
display both the source objects and the brain object
'''
# Define the default camera state used for each subplot
CAM_STATE = dict(
azimuth=0, # azimuth angle
elevation=90, # elevation angle
scale_factor=180 # distance to the camera
)
S_KW = dict(camera_state=CAM_STATE)
# Create the scene
CBAR_STATE = dict(cbtxtsz=12,
txtsz=13.,
width=.5,
cbtxtsh=2.,
rect=(1., -2., 1., 4.))
sc = SceneObj(bgcolor='black', size=(1600, 1000))
# mask = padj<=0.05 # significant regions with true label
data0, max_p, min_p = get_log_pval(padj)
b_obj = BrainObj('white', hemisphere='both', translucent=True)
b_obj.animate(iterations=10, step=30, interval=1)
s_obj = SourceObj(
's1',
all_coord, #all_coord,
# mask = mask,
# mask_color='white',
# mask_radius = 15,
color=padj * 100,
data=data0,
text=short_label,
text_size=10,
text_bold=True,
text_color='yellow',
symbol='disc',
visible=True,
radius_min=10,
radius_max=40,
alpha=0.65)
s_obj_1.set_visible_sources('left')
s_obj.color_sources(data=data0, cmap='jet', clim=(min_p, max_p))
cb_data = ColorbarObj(s_obj,
cblabel='Log FDR-adjusted p value',
border=False,
**CBAR_STATE)
sc.add_to_subplot(b_obj, row=0, col=0, rotate='front')
sc.add_to_subplot(s_obj, row=0, col=0)
sc.add_to_subplot(cb_data, row=0, col=1, width_max=90)
# recording animation and save it
sc.record_animation('output/animate_pvalue_projection.gif', n_pic=10)
sc.preview()
s_obj_1 = SourceObj('iEEG', xyz1, data=data1, cmap=cmap)
s_obj_1.color_sources(data=data1)
s_obj_2 = SourceObj('iEEG', xyz2, data=data2, cmap=cmap)
s_obj_2.color_sources(data=data2)
s_obj_3 = SourceObj('iEEG', xyz3, data=data3, cmap=cmap)
s_obj_3.color_sources(data=data3)
s_obj_4 = SourceObj('iEEG', xyz4, data=data4, cmap=cmap)
s_obj_4.color_sources(data=data4)
s_obj_all = s_obj_1 + s_obj_2 + s_obj_3 + s_obj_4
b_obj_proj_left = BrainObj(template_brain,
hemisphere='both',
translucent=False)
b_obj_proj_left.project_sources(s_obj_all, clim=(0, 4), cmap=cmap)
sc.add_to_subplot(b_obj_proj_left,
row=0,
col=0,
rotate='right',
use_this_cam=True)
# b_obj_proj_left = BrainObj(template_brain, hemisphere='left', translucent=False)
# b_obj_proj_left.project_sources(s_obj_all, clim=(0, 4), cmap=cmap)
# sc.add_to_subplot(b_obj_proj_left, row=0, col=1, rotate='right', use_this_cam=True)
#
# b_obj_proj_right = BrainObj(template_brain, hemisphere='right', translucent=False)
# b_obj_proj_right.project_sources(s_obj_all, clim=(0, 4), cmap=cmap)
# sc.add_to_subplot(b_obj_proj_right, row=0, col=2, rotate='right', use_this_cam=True)
sc.record_animation(os.path.join(n_f_dir, 'intact_largest.gif'), n_pic=40)
sc.preview()
def generate_img(l_file,
r_file,
activated_areas,
brain_name,
out_file,
views,
add_hemispheres,
is_estimate=False,
cmap='copper',
vmin=0.,
vmax=0.01,
save_gif=False):
"""Generate .png and .gif animation of rotating brains
"""
sc = SceneObj(size=(1000 * (len(views) // 2 +
(1 if add_hemispheres else 0)),
1000 * (len(views) > 1)),
bgcolor='black')
KW = dict(title_size=14., zoom=2.) # zoom not working
CBAR_STATE = dict(cbtxtsz=12,
txtsz=10.,
width=.1,
cbtxtsh=3.,
rect=(-.3, -2., 1., 4.))
# PLOT OBJECTS
for i, rot in enumerate(views):
# cannot use the same object
b_obj = create_brain_obj(l_file,
r_file,
activated_areas,
brain_name,
cmap=cmap,
vmin=vmin,
vmax=vmax)
sc.add_to_subplot(b_obj,
row=i // 2,
col=i % 2,
rotate=rot,
title=rot,
**KW)
# Get the colorbar of the brain object and add it to the scene
# Identical brain ==> same colorbar
if add_hemispheres:
# add left brain
b_obj = create_brain_obj(l_file,
r_file,
activated_areas,
brain_name,
hemisphere='right',
cmap=cmap,
vmin=vmin,
vmax=vmax)
sc.add_to_subplot(b_obj,
row=i // 2 + 1,
col=0,
rotate='left',
title='right half',
**KW)
b_obj = create_brain_obj(l_file,
r_file,
activated_areas,
brain_name,
hemisphere='left',
cmap=cmap,
vmin=vmin,
vmax=vmax)
sc.add_to_subplot(b_obj,
row=i // 2 + 1,
col=1,
rotate='right',
title='left half',
**KW)
if is_estimate:
# cmap needs to be set for all objects
cb_parr = ColorbarObj(b_obj,
cblabel='Data to parcellates',
**CBAR_STATE)
# not working properly and can't find a way to rotate that bar
# sc.add_to_subplot(cb_parr, row=0, col=2, row_span=i//2+1, width_max=200)
# gif and png
# sc.preview()
if save_gif:
sc.record_animation(out_file + ('_est' if is_estimate else '') +
"_areas.gif")
sc.screenshot(saveas=out_file + ('_est' if is_estimate else '') +
"_areas.png")
return sc.render()