def display(data=None, orient='LPS', overlay=None, colormap=cm.gray, pixdim=None):
"mri=img.decimate(nim, 5)"
"ex. slice.plot(mri)"
import sys
print sys.argv
if data == None:
try:
fn=sys.argv[1]
from mri import img
data = img.read(fn)
except AttributeError:
print 'not passing data arg'
print('lets plot random data')
from numpy import random
data = random.randn(10,10,10)
try:
data.qform
print 'think its a nifti volume'
nim = data
mrdata = nim.data
print shape(mrdata)
pixdim = nim.voxdim[::-1]
except AttributeError:
if pixdim != None:
print 'using user supplied pixeldimensions', pixdim
else:
print 'probably not a nifti volume. using voxel units instead of actual distance units'
pixdim = [1.0,1.0,1.0]; #unitless
mrdata = data
fig = figure()
subplots_adjust(left=.15, bottom=.15,right=1, top=.95,wspace=.25, hspace=.35)
ax1 = fig.add_subplot(221);#axis('off')
#colorbar(fig,ax=ax1)
xlabel('Anterior (A->P 1st Dim)');ylabel('Right (R->L 2nd Dim)')
ax2 = fig.add_subplot(222);#axis('off')
xlabel('Inferior (I->S Dim)');ylabel('Anterior (A->P 1st Dim)')
ax3 = fig.add_subplot(223);#axis('off')
xlabel('Infererior (I->S 3rd dim)');ylabel('Right (R->L 2nd Dim)')
coord = fig.add_subplot(224);axis('off')
tracker = IndexTracker(mrdata, ax1, ax2, ax3, colormap, pixdim, overlay, coord)
fig.canvas.mpl_connect('scroll_event', tracker.onscroll)
cid = connect('button_press_event', tracker.click)
show()
return tracker
def __init__(self, data=None, orient="LPS", overlay=None, colormap=cm.gray, pixdim=None):
##
import sys
print sys.argv
if data == None:
try:
fn = sys.argv[1]
from mri import img
data = img.read(fn)
except AttributeError:
print "not passing data arg"
pass
try:
data.qform
print "think its a nifti volume"
nim = data
mrdata = nim.data
print shape(mrdata)
pixdim = nim.voxdim[::-1]
except AttributeError:
if pixdim != None:
print "using user supplied pixeldimensions", pixdim
else:
print "probably not a nifti volume. using voxel units instead of actual distance units"
pixdim = [1.0, 1.0, 1.0]
# unitless
mrdata = data
##
self.win = gtk.Window()
# win.connect("destroy", lambda x: gtk.main_quit())
self.win.connect("delete-event", self.hideinsteadofdelete)
self.win.set_default_size(600, 600)
self.win.set_title("Embedding in GTK")
vbox = gtk.VBox()
self.win.add(vbox)
fig = figure() # figsize=(5,4), dpi=100)
# subplots_adjust(left=.15, bottom=.15,right=1, top=.95,wspace=.25, hspace=.35)
# a = fig.add_subplot(111)
# t = arange(0.0,3.0,0.01)
# s = sin(2*pi*t)
# a.plot(t,s)
# a.plot(data)
ax1 = fig.add_subplot(221)
# axis('off')
# colorbar(fig,ax=ax1)
xlabel("Anterior (A->P 1st Dim)")
ylabel("Right (R->L 2nd Dim)")
ax2 = fig.add_subplot(222)
# axis('off')
xlabel("Inferior (I->S Dim)")
ylabel("Anterior (A->P 1st Dim)")
ax3 = fig.add_subplot(223)
# axis('off')
xlabel("Infererior (I->S 3rd dim)")
ylabel("Right (R->L 2nd Dim)")
coord = fig.add_subplot(224)
axis("off")
tracker = IndexTracker(mrdata, ax1, ax2, ax3, colormap, pixdim, overlay, coord)
# fig.canvas.mpl_connect('scroll_event', tracker.onscroll)
cid = connect("button_press_event", tracker.click)
print ("something")
sw = gtk.ScrolledWindow()
vbox.pack_start(sw)
# self.win.add (sw)
## A scrolled window border goes outside the scrollbars and viewport
sw.set_border_width(10)
# policy: ALWAYS, AUTOMATIC, NEVER
sw.set_policy(hscrollbar_policy=gtk.POLICY_AUTOMATIC, vscrollbar_policy=gtk.POLICY_ALWAYS)
canvas = FigureCanvas(fig) # a gtk.DrawingArea
##vbox.pack_start(canvas)
canvas.set_size_request(300, 200)
sw.add_with_viewport(canvas)
canvas.draw()
# manager = get_current_fig_manager()
## you can also access the window or vbox attributes this way
# toolbar = manager.toolbar
##vbox.pack_start(canvas)
# toolbar = NavigationToolbar(canvas, self.win)
##vbox.pack_start(toolbar, False, False)
# show()
# print tracker
#
# fig.show()
self.win.show_all()