def externalUpdate(self, new_img):
old_vox = self.image.vox_coords
if len(new_img.shape) > 3:
self.image = SlicerImage(new_img.subImage(0))
else:
self.image = SlicerImage(new_img)
self.image.vox_coords = old_vox
if iscomplex(self.image[:]):
self.image.prefilter = abs_xform
self.setNorm()
self.setUpAxesSize()
self.updateSlices(self.image.zyx_coords())
def initoverlay(self, action):
image_filter = gtk.FileFilter()
image_filter.add_pattern("*.hdr")
image_filter.add_pattern("*.nii")
image_filter.set_name("Recon Images")
fname = ask_fname(self,
"Choose file to overlay...",
action="open",
filter=image_filter)
if not fname:
return
img = readImage(fname, vrange=(0, 0))
self.overlay_img = SlicerImage(img)
img_dims = N.take(
N.array(self.image.shape) * self.image.dr, self.image.slicing())
ovl_dims = N.take(
N.array(self.overlay_img.shape) * self.overlay_img.dr,
self.overlay_img.slicing())
if not (img_dims == ovl_dims).all():
print img_dims, ovl_dims
print "Overlay failed because physical dimensions do not align..."
print "base image dimensions (zyx): [%3.1f %3.1f %3.1f] (mm)" % tuple(
img_dims)
print "overlay image dimenensions (zyx: [%3.1f %3.1f %3.1f] (mm)" % tuple(
ovl_dims)
return
self.setNorm()
(ax, cor, sag) = self.overlay_img.slicing()
self.ax_overlay = OverLay(self.ax_plot,
ax,
norm=self.overlay_norm,
interpolation=self.ax_plot.interpolation)
self.cor_overlay = OverLay(self.cor_plot,
cor,
norm=self.overlay_norm,
interpolation=self.cor_plot.interpolation)
self.sag_overlay = OverLay(self.sag_plot,
sag,
norm=self.overlay_norm,
interpolation=self.sag_plot.interpolation)
self.overlays = [self.ax_overlay, self.cor_overlay, self.sag_overlay]
self.updateSlices(self.image.zyx_coords(),
sliceplots=self.overlays,
image=self.overlay_img,
norm=self.overlay_norm)
def __init__(self, image, title="spmclone", parent=None):
gtk.Window.__init__(self)
children = self.get_children()
if children:
self.remove(children[0])
self.hide_all()
table = gtk.Table(4, 2)
# super dumb way of storing the image object with its original
# class identification
self.img_obj = image
self.image = len(image.shape) > 3 \
and SlicerImage(image.subImage(0)) \
or SlicerImage(image)
if iscomplex(self.image[:]):
self.image.prefilter = abs_xform
self.overlay_img = None
self.zoom = 0
self.slice_patches = None
self.setNorm()
self.dimlengths = self.image.dr * N.array(self.image.shape)
zyx_lim = self.image.extents()
# I'm using [ax,cor,sag] such that this list informs each
# sliceplot what dimension it slices in the image array
# (eg for coronal data, the coronal plot slices the 0th dim)
ax, cor, sag = self.image.slicing()
origin = [0, 0, 0]
# Make the ortho plots ---
self.ax_plot = SlicePlot(self.image.data_xform(ax, origin),
0,
0,
ax,
norm=self.norm,
extent=(zyx_lim[2] + zyx_lim[1]))
self.cor_plot = SlicePlot(self.image.data_xform(cor, origin),
0,
0,
cor,
norm=self.norm,
extent=(zyx_lim[2] + zyx_lim[0]))
self.sag_plot = SlicePlot(self.image.data_xform(sag, origin),
0,
0,
sag,
norm=self.norm,
extent=(zyx_lim[1] + zyx_lim[0]))
# Although it doesn't matter 99% of the time, this list is
# expected to be ordered this way
self.sliceplots = [self.ax_plot, self.cor_plot, self.sag_plot]
# menu bar
merge = gtk.UIManager()
merge.insert_action_group(self._create_action_group(), 0)
mergeid = merge.add_ui_from_string(ui_info)
self.menubar = merge.get_widget("/MenuBar")
table.attach(self.menubar, 0, 2, 0, 1)
self.menubar.set_size_request(600, 30)
table.attach(self.cor_plot, 0, 1, 1, 2)
self.cor_plot.set_size_request(250, 250)
table.attach(self.sag_plot, 1, 2, 1, 2)
self.sag_plot.set_size_request(250, 250)
table.attach(self.ax_plot, 0, 1, 2, 3)
self.ax_plot.set_size_request(250, 250)
self.displaybox = DisplayInfo(self.image)
self.displaybox.attach_toggle(self.crosshair_hider)
self.displaybox.attach_imginterp(self.interp_handler)
self.displaybox.attach_imgframe(self.zoom_handler)
self.displaybox.attach_imgspace(self.rediculous_handler)
table.attach(self.displaybox, 1, 2, 3, 4)
self.displaybox.set_size_request(300, 300)
self.statusbox = DisplayStatus(
tuple(self.image.vox_coords.tolist()),
tuple(self.image.zyx_coords().tolist()),
self.image[tuple(self.image.vox_coords)])
table.attach(self.statusbox, 0, 1, 3, 4)
self.statusbox.set_size_request(300, 300)
self.connect("configure_event", self.resize_handler)
#table.set_row_spacing(1,25)
# heights = 800
# 250 plot 1
# 250 plot 2
# 370 info stuff
# 30 menubar
self.connect_crosshair_id = []
self.connectCrosshairEvents()
self.set_data("ui-manager", merge)
self.add_accel_group(merge.get_accel_group())
self.set_default_size(600, 730)
self.set_border_width(3)
self.set_title(title)
self.add(table)
self.show_all()
#self.setUpAxesSize()
#P.show()
if parent:
self.set_screen(parent.get_screen())
self.destroy_handle = self.connect(
'destroy', lambda x: parent._plotter_died())
else:
self.connect("destroy", lambda x: gtk.main_quit())
gtk.main()
