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added create figure #4

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added create figure #4

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143 changes: 130 additions & 13 deletions plotting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,12 @@ def plot_surf_stat_map(coords, faces, stat_map=None,
threshold=None, bg_map=None,
bg_on_stat=False,
alpha='auto',
vmax=None, symmetric_cbar="auto",
vmin=None, vmax=None,
cbar='sequential', # or'diverging'
symmetric_cbar="auto",
figsize=None,
labels=None, label_cpal=None,
labels=None, label_col=None, label_cpal=None,
mask=None, mask_lenient=None,
**kwargs):

import numpy as np
Expand Down Expand Up @@ -53,6 +56,16 @@ def plot_surf_stat_map(coords, faces, stat_map=None,
antialiased=False,
color='white')

# where mask is indices of nodes to include:
if mask is not None:
cmask = np.zeros(len(coords))
cmask[mask] = 1
cutoff = 2 # include triangles in cortex only if ALL nodes in mask
if mask_lenient: # include triangles in cortex if ANY are in mask
cutoff = 0
fmask = np.where(cmask[faces].sum(axis=1) > cutoff)[0]


# If depth_map and/or stat_map are provided, map these onto the surface
# set_facecolors function of Poly3DCollection is used as passing the
# facecolors argument to plot_trisurf does not seem to work
Expand All @@ -78,11 +91,18 @@ def plot_surf_stat_map(coords, faces, stat_map=None,
stat_map_data = stat_map
stat_map_faces = np.mean(stat_map_data[faces], axis=1)

# Call _get_plot_stat_map_params to derive symmetric vmin and vmax
# And colorbar limits depending on symmetric_cbar settings
cbar_vmin, cbar_vmax, vmin, vmax = \
_get_plot_stat_map_params(stat_map_faces, vmax,
symmetric_cbar, kwargs)
if cbar is 'diverging':
print cbar
# Call _get_plot_stat_map_params to derive symmetric vmin and vmax
# And colorbar limits depending on symmetric_cbar settings
cbar_vmin, cbar_vmax, vmin, vmax = \
_get_plot_stat_map_params(stat_map_faces, vmax,
symmetric_cbar, kwargs)
if cbar is 'sequential':
if vmin is None:
vmin = stat_map_data.min()
if vmax is None:
vmax = stat_map_data.max()

if threshold is not None:
kept_indices = np.where(abs(stat_map_faces) >= threshold)[0]
Expand All @@ -96,9 +116,16 @@ def plot_surf_stat_map(coords, faces, stat_map=None,
stat_map_faces = stat_map_faces - vmin
stat_map_faces = stat_map_faces / (vmax-vmin)
if bg_on_stat:
face_colors = cmap(stat_map_faces) * face_colors
if mask is not None:
face_colors[fmask] = cmap(stat_map_faces)[fmask] * face_colors[fmask]
else:
face_colors = cmap(stat_map_faces) * face_colors
else:
face_colors = cmap(stat_map_faces)
if mask is not None:
face_colors[fmask] = cmap(stat_map_faces)[fmask]

else:
face_colors = cmap(stat_map_faces)

if labels is not None:
'''
Expand All @@ -111,6 +138,8 @@ def plot_surf_stat_map(coords, faces, stat_map=None,
valid color names from http://xkcd.com/color/rgb/
'''
if label_cpal is not None:
if label_col is not None:
raise ValueError("Don't use label_cpal and label_col together.")
if type(label_cpal) == str:
cpal = sns.color_palette(label_cpal, len(labels))
if type(label_cpal) == list:
Expand All @@ -121,12 +150,18 @@ def plot_surf_stat_map(coords, faces, stat_map=None,
except:
cpal = sns.xkcd_palette(label_cpal)




for n_label, label in enumerate(labels):
for n_face, face in enumerate(faces):
count = len(set(face).intersection(set(label)))
if (count > 0) & (count < 3):
if label_cpal is None:
face_colors[n_face,0:3] = sns.xkcd_palette(["black"])[0]
if label_col is not None:
face_colors[n_face,0:3] = sns.xkcd_palette([label_col])[0]
else:
face_colors[n_face,0:3] = sns.xkcd_palette(["black"])[0]
else:
face_colors[n_face,0:3] = cpal[n_label]

Expand Down Expand Up @@ -290,14 +325,96 @@ def crop_img(fig, margin=10):

kept = {'rows':[], 'cols':[]}
for row in range(img.shape[0]):
if len(set(np.ndarray.flatten(img[row,:,:]))) > 3:
if len(set(np.ndarray.flatten(img[row,:,:]))) > 1:
kept['rows'].append(row)
for col in range(img.shape[1]):
if len(set(np.ndarray.flatten(img[:,col,:]))) > 3:
if len(set(np.ndarray.flatten(img[:,col,:]))) > 1:
kept['cols'].append(col)

if margin:
return img[min(kept['rows'])-margin:max(kept['rows'])+margin,
min(kept['cols'])-margin:max(kept['cols'])+margin]
else:
return img[kept['rows']][:,kept['cols']]
return img[kept['rows']][:,kept['cols']]




def create_fig(data=None, labels=None, label_col=None,
hemi=None, surf='pial',
sulc=True, alpha='auto',
cmap='cubehelix', cpal='bright', cbar=False,
dmin=None, dmax=None,
mask=None):

import nibabel as nib, numpy as np
import matplotlib.pyplot as plt, matplotlib as mpl
from IPython.core.display import Image, display
import os

fsDir = '/afs/cbs.mpg.de/projects/mar004_lsd-lemon-preproc/freesurfer'
surf_f = '%s/fsaverage5/surf/%s.%s' % (fsDir, hemi, surf)
coords = nib.freesurfer.io.read_geometry(surf_f)[0]
faces = nib.freesurfer.io.read_geometry(surf_f)[1]
if sulc:
sulc_f = '%s/fsaverage5/surf/%s.sulc' % (fsDir, hemi)
sulc = nib.freesurfer.io.read_morph_data(sulc_f)
sulc_bool = True
else:
sulc = None
sulc_bool = False

# create images
imgs = []
for azim in [0, 180]:

if data is not None:
if dmin is None:
dmin = data[np.nonzero(data)].min()
if dmax is None:
dmax = data.max()
fig = plot_surf_stat_map(coords, faces, stat_map=data,
elev=0, azim=azim,
cmap=cmap,
bg_map=sulc,bg_on_stat=sulc_bool,
vmin=dmin, vmax=dmax,
labels=labels, label_col=label_col,
alpha=alpha,
mask=mask, mask_lenient=False)
#label_cpal=cpal)
else:
fig = plot_surf_label(coords, faces,
labels=labels,
elev=0, azim=azim,
bg_map=sulc,
cpal=cpal,
bg_on_labels=sulc_bool,
alpha=alpha)

# crop image
imgs.append((crop_img(fig, margin=15)),)
plt.close(fig)

# create figure with color bar
fig = plt.figure()
fig.set_size_inches(8, 4)

ax1 = plt.subplot2grid((4,60), (0,0), colspan = 26, rowspan =4)
plt.imshow(imgs[0])
ax1.set_axis_off()

ax2 = plt.subplot2grid((4,60), (0,28), colspan = 26, rowspan =4)
plt.imshow(imgs[1])
ax2.set_axis_off()

if cbar==True and data is not None:
cax = plt.subplot2grid((4,60), (1,59), colspan = 1, rowspan =2)
cmap = plt.cm.get_cmap(cmap)
norm = mpl.colors.Normalize(vmin=dmin, vmax=dmax)
cb = mpl.colorbar.ColorbarBase(cax, cmap=cmap, norm=norm)
cb.set_ticks([dmin, dmax])

fig.savefig('./tempimage')
plt.close(fig)
display(Image(filename='./tempimage.png', width=800))
os.remove('./tempimage.png')