def save_fa_overlay(faDir, ccDir, figDir, slist, orientationList):
brainFiles = [fn.split('_')[0] for fn in os.listdir(ccDir)]
f = plt.figure();
for bfn in brainFiles:
vcc = ConnectedComponent(fn=ccDir+bfn+'_concomp.npy')
fax = fa.FAXML(faDir+bfn+'_fa.xml')
fas = fa.FAData(faDir+bfn+'_fa.raw',fax.getShape())
cc3d = vcc.get_3d_cc(fax.getShape())
for view,s,xyz in zip(np.arange(len(slist)),slist,orientationList):
show_overlay(fas.data,cc3d,np.Inf,s,xyz,.5)
plt.savefig(figDir+bfn+'_ccfaOverlay_view'+repr(view)+'.pdf',)
plt.clf()
plt.close(f)
def main():
parser = argparse.ArgumentParser(description='Draw the FA map of a brain.')
parser.add_argument('faxmlfile', action="store")
parser.add_argument('farawfile', action="store")
parser.add_argument('--dimensions',
action="store",
default="xy",
help="xy, xz, or yz")
parser.add_argument('--zero_threshold',
action="store",
type=float,
default=0.2)
parser.add_argument('slice', action="store")
result = parser.parse_args()
# Read the XML file and then the data
try:
fax = fa.FAXML(result.faxmlfile)
fas = fa.FAData(result.farawfile, fax.getShape())
except:
print "Failed to parse FA files at: ", result.faxmlfile, result.faxmlfile
assert 0
# cut out the specified slice
if result.dimensions == "xy":
graphdata = fas.data[:, :, result.slice]
elif result.dimensions == "yz":
graphdata = fas.data[result.slice, :, :]
elif result.dimensions == "xz":
graphdata = fas.data[:, result.slice, :]
else:
print "Choose xy, xz, or yz as dimension or leave blank for xy default"
vec_func1 = np.vectorize(lambda x: 0.0 if math.isnan(x) else x)
vec_func2 = np.vectorize(
lambda x: int(math.fabs(x) / result.zero_threshold))
fgraphdata = vec_func1(graphdata)
igraphdata = vec_func2(fgraphdata)
matplotlib.pyplot.pcolor(igraphdata)
matplotlib.pyplot.show()
def save_overlay(faDir, mprDir, ccDir, figDir, slist, orientationList):
brainFiles = [fn.split('_')[0] for fn in os.listdir(ccDir)]
f = plt.figure(figsize=(14,9));
for bfn in brainFiles:
vcc = ConnectedComponent(fn=ccDir+bfn+'_concomp.npy')
fax = fa.FAXML(faDir+bfn+'_fa.xml')
fas = fa.FAData(faDir+bfn+'_fa.raw',fax.getShape())
mpx = mprage.MPRAGEXML(mprDir+'mprage_'+bfn+'_ss_crop.xml')
mpd = mprage.MPRAGEData(mprDir+'mprage_'+bfn+'_ss_crop.raw',mpx.getShape())
cc3d = vcc.get_3d_cc(fax.getShape())
for view,s,xyz in zip(np.arange(len(slist)),slist,orientationList):
plt.clf()
plt.subplot(221);
plt.title('FA Overlay')
show_overlay(fas.data,cc3d,np.Inf,s,xyz,.5)
plt.subplot(222);
plt.title('FA Original; '+bfn+', '+xyz+'-slice '+repr(s))
plt.imshow(get_slice(fas.data,s,xyz),cmap=plt.cm.gray)
plt.colorbar()
plt.subplot(223); plt.title('MPRAGE Overlay')
show_overlay(mpd.data,cc3d,np.Inf,s,xyz,.5)
plt.subplot(224);
plt.title('MPRAGE Original')
plt.imshow(get_slice(mpd.data,s,xyz),cmap=plt.cm.gray)
plt.colorbar()
#plt.tight_layout()
plt.savefig(figDir+bfn+'_ccfaOverlay_view'+repr(view)+'.pdf')
plt.close(f)
def show_figure(bfn):
faDir = "/mnt/braingraph1data/projects/will/mar12data/fa/"
ccDir = '/data/biggraphs/connectedcomp/'
global xyz
global sl
global sslice
fafn = faDir + bfn + "_fa"
faXML = fa.FAXML(fafn + '.xml')
faData = fa.FAData(fafn + '.raw', faXML.getShape())
vcc = lcc.ConnectedComponent(fn=ccDir + bfn + '_concomp.npy')
cc3d = vcc.get_3d_cc(faXML.getShape())
sl = 100
xyz = 'xy'
fig = figure()
ax = subplot(111)
subplots_adjust(left=0.25, bottom=0.25)
def draw_brain(sl, xyz):
ax = subplot(111)
ax.clear()
lcc.show_overlay(faData.data, cc3d, ncc=15, s=sl, xyz=xyz)
draw()
draw_brain(sl, xyz)
axcolor = 'lightgoldenrodyellow'
axslice = axes([0.25, 0.1, 0.65, 0.03], axisbg=axcolor)
sslice = Slider(axslice, 'Slice', 0, cc3d.shape[0] - 1, valinit=sl)
def update_slice(val):
global xyz
global sl
sl = val
draw_brain(sl, xyz)
sslice.on_changed(update_slice)
rax = axes([0.025, 0.5, 0.15, 0.15], axisbg=axcolor)
radio = RadioButtons(rax, ('xy', 'xz', 'yz'), active=0)
def xyzproj(newxyz):
print newxyz
global xyz
global sl
global sslice
xyz = newxyz
dimDict = {'xy': 2, 'xz': 1, 'yz': 0}
sl = int(cc3d.shape[dimDict[xyz]] / 2)
sslice.valmax = cc3d.shape[dimDict[xyz]]
sslice.set_val(sl)
draw()
draw_brain(sl, xyz)
radio.on_clicked(xyzproj)
show()