Skip to content

Commit

Permalink
drop confmap for the moment
Browse files Browse the repository at this point in the history
  • Loading branch information
@Shotgunosine
Shotgunosine committed Dec 19, 2023
1 parent 7a186b6 commit 024080b
Show file tree
Hide file tree
Showing 3 changed files with 117 additions and 113 deletions.
223 changes: 112 additions & 111 deletions contarg/normgrid.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,6 @@
from matplotlib.cm import ScalarMappable
import matplotlib as mpl
import seaborn as sns
from confmap.confmap import BFF
from sklearn.decomposition import PCA
from mixedvines.mixedvine import MixedVine
from mixedvines.copula import GaussianCopula
Expand Down Expand Up @@ -881,122 +880,124 @@ def calc_stimgrid(subject, src_surf_dir, surf_info_dir,

# make flattend cortical fig
if make_plots:
cm = BFF(surfaces.l.pial.points, surfaces.l.pial.tris)
cm.layout(normalize=False)
lp_triangulation = tri.Triangulation(cm.image.vertices[:,0], cm.image.vertices[:,1], triangles=cm.image.faces, mask=~lp_tri_stim_mask)

cm_maybe_gyrus_points = cm.image.vertices[maybe_gyrus_idxs]
cm_maybe_sw_points = cm.image.vertices[maybe_sw_idxs]
cm_sulc_near_0 = cm.image.vertices[stim_roi.idxs][(l_sulc[stim_roi.idxs] > -2) & (l_sulc[stim_roi.idxs] < 2)]

pca = PCA(2, random_state=0)
_ = pca.fit(cm.image.vertices[np.unique(lp_triangulation.get_masked_triangles())][:, :2])
flat_verts = pca.transform(cm.image.vertices[:, :2])

cm_roi_points = cm.image.vertices[np.unique(lp_triangulation.get_masked_triangles())]
oref_points = np.array([
[cm_roi_points[:,0].min(), (cm_roi_points[:,1].max() + cm_roi_points[:,1].min())/2],
[cm_roi_points[:,0].max(), (cm_roi_points[:,1].max() + cm_roi_points[:,1].min())/2],
[ (cm_roi_points[:,0].max() + cm_roi_points[:,0].min())/2, cm_roi_points[:,1].min()],
[ (cm_roi_points[:,0].max() + cm_roi_points[:,0].min())/2, cm_roi_points[:,1].max()],
])
tref_points = pca.transform(oref_points)
flat_maybe_gyrus_points = pca.transform(cm.image.vertices[maybe_gyrus_idxs, :2])
flat_sulc_near_0 = pca.transform(cm.image.vertices[stim_roi.idxs][(l_sulc[stim_roi.idxs] > -2) & (l_sulc[stim_roi.idxs] < 2), :2])
flat_maybe_sw_points = pca.transform(cm.image.vertices[sw_idxs, :2])
# print(tref_points)
# print(angle_between(tref_points[5], oref_points[5,1:]))
# print(180 - angle_between(tref_points[5], oref_points[5,1:]))
# ztheta = np.pi - angle_between(tref_points[5], oref_points[5,1:]) * (np.pi / 180)
# rot_mat = np.array([
# [np.cos(ztheta), -np.sin(ztheta)],
# [np.sin(ztheta), np.cos(ztheta)],
pass
# TODO figure out confmap dependency mess
# cm = BFF(surfaces.l.pial.points, surfaces.l.pial.tris)
# cm.layout(normalize=False)
# lp_triangulation = tri.Triangulation(cm.image.vertices[:,0], cm.image.vertices[:,1], triangles=cm.image.faces, mask=~lp_tri_stim_mask)
#
# cm_maybe_gyrus_points = cm.image.vertices[maybe_gyrus_idxs]
# cm_maybe_sw_points = cm.image.vertices[maybe_sw_idxs]
# cm_sulc_near_0 = cm.image.vertices[stim_roi.idxs][(l_sulc[stim_roi.idxs] > -2) & (l_sulc[stim_roi.idxs] < 2)]
#
# pca = PCA(2, random_state=0)
# _ = pca.fit(cm.image.vertices[np.unique(lp_triangulation.get_masked_triangles())][:, :2])
# flat_verts = pca.transform(cm.image.vertices[:, :2])
#
# cm_roi_points = cm.image.vertices[np.unique(lp_triangulation.get_masked_triangles())]
# oref_points = np.array([
# [cm_roi_points[:,0].min(), (cm_roi_points[:,1].max() + cm_roi_points[:,1].min())/2],
# [cm_roi_points[:,0].max(), (cm_roi_points[:,1].max() + cm_roi_points[:,1].min())/2],
# [ (cm_roi_points[:,0].max() + cm_roi_points[:,0].min())/2, cm_roi_points[:,1].min()],
# [ (cm_roi_points[:,0].max() + cm_roi_points[:,0].min())/2, cm_roi_points[:,1].max()],
# ])
# rot_mat
# tref_points = np.matmul(rot_mat, tref_points.T).T
# flat_verts = np.matmul(rot_mat, flat_verts.T).T
# tref_points = pca.transform(oref_points)
# flat_maybe_gyrus_points = pca.transform(cm.image.vertices[maybe_gyrus_idxs, :2])
# flat_sulc_near_0 = pca.transform(cm.image.vertices[stim_roi.idxs][(l_sulc[stim_roi.idxs] > -2) & (l_sulc[stim_roi.idxs] < 2), :2])
# flat_maybe_sw_points = pca.transform(cm.image.vertices[sw_idxs, :2])
# # print(tref_points)
# # print(angle_between(tref_points[5], oref_points[5,1:]))
# # print(180 - angle_between(tref_points[5], oref_points[5,1:]))
# # ztheta = np.pi - angle_between(tref_points[5], oref_points[5,1:]) * (np.pi / 180)
# # rot_mat = np.array([
# # [np.cos(ztheta), -np.sin(ztheta)],
# # [np.sin(ztheta), np.cos(ztheta)],
# # ])
# # rot_mat
# # tref_points = np.matmul(rot_mat, tref_points.T).T
# # flat_verts = np.matmul(rot_mat, flat_verts.T).T
# # # print(tref_points)
# # flip_mat = np.array([[1,0], [0,1]])
# # if tref_points[5,1] < 0:
# # flip_mat[1,1] = -1
# # tref_points = np.matmul(flip_mat, tref_points.T).T
# # flat_verts = np.matmul(flip_mat, flat_verts.T).T
# flip_mat = np.array([[1,0], [0,1]])
# if tref_points[1,0] < tref_points[0,0]:
# flip_mat[0,0] = -1
# tref_points = np.matmul(flip_mat, tref_points.T).T
# flat_verts = np.matmul(flip_mat, flat_verts.T).T
# flat_maybe_gyrus_points = np.matmul(flip_mat, flat_maybe_gyrus_points.T).T
# flat_sulc_near_0 = np.matmul(flip_mat, flat_sulc_near_0.T).T
# flat_maybe_sw_points = np.matmul(flip_mat, flat_maybe_sw_points.T).T
#
# flip_mat = np.array([[1,0], [0,1]])
# if tref_points[5,1] < 0:
# if tref_points[3,1] < tref_points[2,1]:
# flip_mat[1,1] = -1
# tref_points = np.matmul(flip_mat, tref_points.T).T
# flat_verts = np.matmul(flip_mat, flat_verts.T).T
flip_mat = np.array([[1,0], [0,1]])
if tref_points[1,0] < tref_points[0,0]:
flip_mat[0,0] = -1
tref_points = np.matmul(flip_mat, tref_points.T).T
flat_verts = np.matmul(flip_mat, flat_verts.T).T
flat_maybe_gyrus_points = np.matmul(flip_mat, flat_maybe_gyrus_points.T).T
flat_sulc_near_0 = np.matmul(flip_mat, flat_sulc_near_0.T).T
flat_maybe_sw_points = np.matmul(flip_mat, flat_maybe_sw_points.T).T

flip_mat = np.array([[1,0], [0,1]])
if tref_points[3,1] < tref_points[2,1]:
flip_mat[1,1] = -1
tref_points = np.matmul(flip_mat, tref_points.T).T
flat_verts = np.matmul(flip_mat, flat_verts.T).T
flat_maybe_gyrus_points = np.matmul(flip_mat, flat_maybe_gyrus_points.T).T
flat_sulc_near_0 = np.matmul(flip_mat, flat_sulc_near_0.T).T
flat_maybe_sw_points = np.matmul(flip_mat, flat_maybe_sw_points.T).T

norm = Normalize(vmin=-10, vmax=10)
colors = mpl.colormaps.get_cmap('RdBu_r')(norm(-l_sulc[lp_triangulation.get_masked_triangles()].mean(1)))
mappable = ScalarMappable(cmap='RdBu_r', norm=norm)

fig, ax = plt.subplots(1)
triplot = ax.tripcolor(
flat_verts[:,0],
flat_verts[:,1],
-l_sulc[lp_triangulation.get_masked_triangles()].mean(1),
triangles=lp_triangulation.get_masked_triangles(),
cmap='RdBu_r',
linewidth=1,
vmin=-10,
vmax=10,
alpha=0.8,
)
flat_roi_points = flat_verts[np.unique(lp_triangulation.get_masked_triangles())]

print(tref_points)

ax.axis('off')
ax.set_xlim((flat_roi_points[:, 0].min(), flat_roi_points[:, 0].max()))
ax.set_ylim((flat_roi_points[:, 1].min(), flat_roi_points[:, 1].max()))


ax.scatter(flat_maybe_gyrus_points[:,0],
flat_maybe_gyrus_points[:,1],
color='red',
alpha=1,
s=20,
label='Gyrus'
)
ax.scatter(flat_sulc_near_0[:,0],
flat_sulc_near_0[:,1],
color='black',
alpha=1,
s=30,
label='Old SW'
)
ax.scatter(flat_maybe_sw_points[:,0],
flat_maybe_sw_points[:,1],
color='mediumpurple',
alpha=1,
s=20,
label='New SW'
)

ax.plot(tref_points[:2,0], tref_points[:2, 1], color='black', label='Orig x dir', linestyle="dotted", alpha=0.7)
ax.scatter(*tref_points[0], color='black', alpha=0.5)
ax.plot(tref_points[2:,0], tref_points[2:, 1], color='black', label='Orig y dir', linestyle="dashed", alpha=0.7)
ax.scatter(*tref_points[2], color='black', alpha=0.5)

ax.set_xlim((flat_roi_points[:, 0].min(), flat_roi_points[:, 0].max()))
ax.set_ylim((flat_roi_points[:, 1].min(), flat_roi_points[:, 1].max()))


ax.legend()
fig.savefig(grid_out_figs / 'flat_cortex.png')
# flat_maybe_gyrus_points = np.matmul(flip_mat, flat_maybe_gyrus_points.T).T
# flat_sulc_near_0 = np.matmul(flip_mat, flat_sulc_near_0.T).T
# flat_maybe_sw_points = np.matmul(flip_mat, flat_maybe_sw_points.T).T
#
# norm = Normalize(vmin=-10, vmax=10)
# colors = mpl.colormaps.get_cmap('RdBu_r')(norm(-l_sulc[lp_triangulation.get_masked_triangles()].mean(1)))
# mappable = ScalarMappable(cmap='RdBu_r', norm=norm)
#
# fig, ax = plt.subplots(1)
# triplot = ax.tripcolor(
# flat_verts[:,0],
# flat_verts[:,1],
# -l_sulc[lp_triangulation.get_masked_triangles()].mean(1),
# triangles=lp_triangulation.get_masked_triangles(),
# cmap='RdBu_r',
# linewidth=1,
# vmin=-10,
# vmax=10,
# alpha=0.8,
# )
# flat_roi_points = flat_verts[np.unique(lp_triangulation.get_masked_triangles())]
#
# print(tref_points)
#
# ax.axis('off')
# ax.set_xlim((flat_roi_points[:, 0].min(), flat_roi_points[:, 0].max()))
# ax.set_ylim((flat_roi_points[:, 1].min(), flat_roi_points[:, 1].max()))
#
#
# ax.scatter(flat_maybe_gyrus_points[:,0],
# flat_maybe_gyrus_points[:,1],
# color='red',
# alpha=1,
# s=20,
# label='Gyrus'
# )
# ax.scatter(flat_sulc_near_0[:,0],
# flat_sulc_near_0[:,1],
# color='black',
# alpha=1,
# s=30,
# label='Old SW'
# )
# ax.scatter(flat_maybe_sw_points[:,0],
# flat_maybe_sw_points[:,1],
# color='mediumpurple',
# alpha=1,
# s=20,
# label='New SW'
# )
#
# ax.plot(tref_points[:2,0], tref_points[:2, 1], color='black', label='Orig x dir', linestyle="dotted", alpha=0.7)
# ax.scatter(*tref_points[0], color='black', alpha=0.5)
# ax.plot(tref_points[2:,0], tref_points[2:, 1], color='black', label='Orig y dir', linestyle="dashed", alpha=0.7)
# ax.scatter(*tref_points[2], color='black', alpha=0.5)
#
# ax.set_xlim((flat_roi_points[:, 0].min(), flat_roi_points[:, 0].max()))
# ax.set_ylim((flat_roi_points[:, 1].min(), flat_roi_points[:, 1].max()))
#
#
# ax.legend()
# fig.savefig(grid_out_figs / 'flat_cortex.png')
return stimgrid


Expand Down
5 changes: 4 additions & 1 deletion environment.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,4 +34,7 @@ dependencies:
- pip:
- fmm3dpy==1.0.0
- charm_gems==1.3
- mixedvines
- mixedvines
- pybids==0.16.1
- fmm3dpy==1.0.0
- confmap
2 changes: 1 addition & 1 deletion pyproject.toml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ dependencies = [
'templateflow >= 23.0.0',
'kneed >= 0.8.2',
'networkx >= 2.8.5',
'statsmodels >= 0.14.0'
'statsmodels >= 0.14.0',
]

[project.optional-dependencies]
Expand Down

0 comments on commit 024080b

Please sign in to comment.