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 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 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()
class spmclone(gtk.Window):
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()
#-------------------------------------------------------------------------
def setNorm(self):
"sets the whitepoint and blackpoint (uses raw data, not scaled)"
x = N.sort(self.image[:].flatten())
npts = x.shape[0]
p01 = x[int(round(.01 * npts))]
p99 = x[int(round(.99 * npts))]
self.norm = P.normalize(vmin=p01, vmax=p99)
#self.norm = P.normalize(-.1, 1.1)
if hasattr(self, "overlay_img") and self.overlay_img:
p01 = P.prctile(self.overlay_img[:], 1.0)
p99 = P.prctile(self.overlay_img[:], 99.)
self.overlay_norm = P.normalize(vmin=p01, vmax=p99)
#-------------------------------------------------------------------------
def xy(self, slice_idx):
(ax, cor, sag) = self.image.slicing()
x, y = {
ax: (2, 1), # x,y
cor: (2, 0), # x,z
sag: (1, 0), # y,z
}.get(slice_idx)
return x, y
#-------------------------------------------------------------------------
def updateSlices(self, zyx, sliceplots=None, image=None, norm=None):
if not sliceplots:
sliceplots = self.sliceplots
if not image:
image = self.image
if not norm:
norm = self.norm
for sliceplot in sliceplots:
idx = sliceplot.slice_idx
sliceplot.setData(image.data_xform(idx, zyx), norm=norm)
if self.slice_patches is not None:
p_idx = int(self.image.vox_coords[idx])
sliceplot.showPatches(self.slice_patches[idx][p_idx])
#-------------------------------------------------------------------------
def updateCrosshairs(self):
for s, sliceplot in enumerate(self.sliceplots):
idx = sliceplot.slice_idx
zyx = self.image.zyx_coords().tolist()
zyx.pop(s)
ud, lr = zyx
sliceplot.setCrosshairs(lr, ud)
#-------------------------------------------------------------------------
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 setUpAxesSize(self):
"Scale the axes appropriately for the image dimensions"
# assume that image resolution is isotropic in dim2 and dim1
# (not necessarily in dim0)
# want the isotropic resolution plot to be 215x215 pixels
#xy_imgsize = 215. # this should be more like 85% of the dim0 sliceplot
ref_size = self.dimlengths[-1]
slicing = self.image.slicing()
idx = slicing.index(0)
xy_imgsize = .85 * min(*self.sliceplots[idx].get_width_height())
for sliceplot in self.sliceplots:
dims_copy = self.dimlengths.tolist()
ax = sliceplot.getAxes()
s_idx = sliceplot.slice_idx
dims_copy.remove(self.dimlengths[s_idx])
slice_y, slice_x = self.image.is_xpose(s_idx) and \
dims_copy[::-1] or dims_copy
height = xy_imgsize * slice_y / ref_size
width = xy_imgsize * slice_x / ref_size
canvas_x, canvas_y = sliceplot.get_width_height()
w = width / canvas_x
h = height / canvas_y
l = (1.0 - width / canvas_x) / 2.
b = (1.0 - height / canvas_y) / 2.
ax.set_position([l, b, w, h])
sliceplot.draw_idle()
#-------------------------------------------------------------------------
def connectCrosshairEvents(self, mode="enable"):
if mode == "enable":
self._dragging = False
for sliceplot in self.sliceplots:
self.connect_crosshair_id.append(
sliceplot.mpl_connect("button_press_event",
self.SPMouseDown))
self.connect_crosshair_id.append(
sliceplot.mpl_connect("button_release_event",
self.SPMouseUp))
self.connect_crosshair_id.append(
sliceplot.mpl_connect("motion_notify_event",
self.SPMouseMotion))
sliceplot.toggleCrosshairs(mode=True)
else:
if len(self.connect_crosshair_id):
for id, sliceplot in enumerate(self.sliceplots):
sliceplot.mpl_disconnect(self.connect_crosshair_id[id])
sliceplot.mpl_disconnect(self.connect_crosshair_id[id + 1])
sliceplot.mpl_disconnect(self.connect_crosshair_id[id + 2])
sliceplot.toggleCrosshairs(mode=False)
self.connect_crosshair_id = []
#-------------------------------------------------------------------------
def SPMouseDown(self, event):
# for a new mouse down event, reset the mouse positions
self._mouse_lr = self._mouse_ud = None
self._dragging = event.inaxes
self.updateCoords(event)
#-------------------------------------------------------------------------
def SPMouseUp(self, event):
# if not dragging, no business being here!
if self._dragging:
self.updateCoords(event)
self._dragging = False
#-------------------------------------------------------------------------
def SPMouseMotion(self, event):
if self._dragging:
self.updateCoords(event)
#-------------------------------------------------------------------------
def updateCoords(self, event):
"Update all the necessary sliceplot data based on a mouse click."
# The tasks here are:
# 1 find zyx_coords of mouse click and translate to vox_coords
# 2 update the transverse sliceplots based on vox_coords
# 2a update the transverse overlays if present
# 3 update crosshairs on all sliceplots
# 4 update voxel space and zyx space texts
sliceplot = event.canvas
# using terminology up-down, left-right to avoid confusion with y,x
ud, lr = sliceplot.getEventCoords(event)
if self._mouse_lr == lr and self._mouse_ud == ud:
return
if lr is None or ud is None:
return
self._mouse_lr, self._mouse_ud = (lr, ud)
# trans_sliceplots are the transverse plots that get
# updated from where the mouse clicked
(ax, cor, sag) = self.image.slicing()
trans_sliceplots = {
self.sliceplots[ax]: (self.sliceplots[sag], self.sliceplots[cor]),
self.sliceplots[cor]: (self.sliceplots[sag], self.sliceplots[ax]),
self.sliceplots[sag]: (self.sliceplots[cor], self.sliceplots[ax]),
}.get(sliceplot)
trans_idx = (trans_sliceplots[0].slice_idx,
trans_sliceplots[1].slice_idx)
# where do left-right and up-down cut across in zyx space?
trans_ax = self.image.transverse_slicing(sliceplot.slice_idx)
zyx_clicked = self.image.zyx_coords()
zyx_clicked[trans_ax[0]] = lr
zyx_clicked[trans_ax[1]] = ud
vox = self.image.zyx2vox(zyx_clicked)
self.image.vox_coords[trans_idx[0]] = vox[trans_idx[0]]
self.image.vox_coords[trans_idx[1]] = vox[trans_idx[1]]
self.updateSlices(zyx_clicked, sliceplots=trans_sliceplots)
if self.overlay_img:
# basically do the same thing over again wrt the overlay dims
(ax_o, cor_o, sag_o) = self.overlay_img.slicing()
trans_overlays = {
self.sliceplots[ax]:
(self.overlays[sag_o], self.overlays[cor_o]),
self.sliceplots[cor]:
(self.overlays[sag_o], self.overlays[ax_o]),
self.sliceplots[sag]:
(self.overlays[cor_o], self.overlays[ax_o]),
}.get(sliceplot)
trans_idx = (trans_overlays[0].slice_idx,
trans_overlays[1].slice_idx)
vox = self.overlay_img.zyx2vox(zyx_clicked)
self.overlay_img.vox_coords[trans_idx[0]] = vox[trans_idx[0]]
self.overlay_img.vox_coords[trans_idx[1]] = vox[trans_idx[1]]
self.updateSlices(zyx_clicked,
sliceplots=trans_overlays,
image=self.overlay_img,
norm=self.overlay_norm)
self.updateCrosshairs()
# make text to update the statusbox label's
self.statusbox.set_vox_text(self.image.vox_coords[::-1].tolist())
self.statusbox.set_zyx_text(self.image.zyx_coords()[::-1].tolist())
point = tuple(self.image.vox_coords)
self.statusbox.set_intensity_text(self.image[point])
#-------------------------------------------------------------------------
def rediculous_handler(self, cbox):
#mode = cbox.get_active()==0 and "enable" or "disable"
#self.connectCrosshairEvents(mode=mode)
print "You've hit a useless button!"
return
#-------------------------------------------------------------------------
def interp_handler(self, cbox):
interp_method = interp_lookup[cbox.get_active()]
for sliceplot in self.sliceplots:
sliceplot.setInterpo(interp_method)
#-------------------------------------------------------------------------
def crosshair_hider(self, toggle):
hidden = (not toggle.get_active())
for sliceplot in self.sliceplots:
sliceplot.toggleCrosshairs(mode=hidden)
#-------------------------------------------------------------------------
def zoom_handler(self, cbox):
"Changes the view range of the sliceplots to be NxN mm"
self.zoom = {
0: 0,
1: 160,
2: 80,
3: 40,
4: 20,
5: 10,
}.get(cbox.get_active(), 0)
r_center = self.image.zyx_coords()
if self.zoom:
r_neg = r_center - N.array([self.zoom / 2.] * 3)
r_pos = r_center + N.array([self.zoom / 2.] * 3)
zyx_lim = zip(r_neg, r_pos)
self.dimlengths = N.array([self.zoom] * 3)
else:
self.dimlengths = self.image.dr * N.array(self.image.shape)
zyx_lim = self.image.extents()
for plot in self.sliceplots:
x, y = self.image.transverse_slicing(plot.slice_idx)
plot.setXYlim(zyx_lim[x], zyx_lim[y])
plot.setCrosshairs(r_center[x], r_center[y])
self.updateSlices(self.image.zyx_coords())
self.setUpAxesSize()
#-------------------------------------------------------------------------
def resize_handler(self, window, event):
#print "got resize signal"
self.setUpAxesSize()
#-------------------------------------------------------------------------
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 launch_overlay_toolbox(self, action):
if self.overlay_img is not None:
if not hasattr(self, "overlay_tools") or not self.overlay_tools:
self.overlay_tools = OverlayToolWin(self.overlays, self)
else:
self.overlay_tools.present()
#-------------------------------------------------------------------------
def killoverlay(self, action):
if self.overlay_img is not None:
for overlay in self.overlays:
overlay.removeSelf()
if hasattr(self, "overlay_tools") and self.overlay_tools:
self.overlay_tools.destroy()
del self.overlay_tools
self.overlay_img = None
self.overlay_norm = None
#-------------------------------------------------------------------------
def load_new_image(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 open...",
action="open",
filter=image_filter)
if not fname:
return
try:
img = readImage(fname, "nifti")
except:
img = readImage(fname, "analyze")
self.killoverlay(None)
self.__init__(img)
#-------------------------------------------------------------------------
def launch_sliceview(self, action):
from recon.visualization.sliceview import sliceview
sliceview(self.image, parent=self)
#-------------------------------------------------------------------------
def launch_recon_gui(self, action):
from recon.visualization.recon_gui import recon_gui
recon_gui(image=self.img_obj, parent=self)
#-------------------------------------------------------------------------
def _plotter_died(self):
pass
#-------------------------------------------------------------------------
def _create_action_group(self):
entries = (
("FileMenu", None, "_File"),
("Open Image", gtk.STOCK_OPEN, "_Open Image", "<control>O",
"Opens and plots a new image", self.load_new_image),
("Quit", gtk.STOCK_QUIT, "_Quit", "<control>Q", "Quits",
lambda action: self.destroy()),
("ToolsMenu", None, "_Tools"),
("Load Overlay", None, "_Load Overlay", "",
"Load an image to overlay", self.initoverlay),
("Unload Overlay", None, "_Unload Overlay", "",
"Unload the overlay", self.killoverlay),
("Overlay Adjustment Toolbox", None, "_Overlay Adjustment Toolbox",
"", "launch overlay toolbox", self.launch_overlay_toolbox),
("Plot In Sliceview", None, "_Plot In Sliceview", "",
"opens image in sliceview", self.launch_sliceview),
("Run Recon GUI", None, "_Run Recon GUI", "", "opens gui",
self.launch_recon_gui),
)
action_group = gtk.ActionGroup("WindowActions")
action_group.add_actions(entries)
return action_group
class spmclone (gtk.Window):
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()
#-------------------------------------------------------------------------
def setNorm(self):
"sets the whitepoint and blackpoint (uses raw data, not scaled)"
x = N.sort(self.image[:].flatten())
npts = x.shape[0]
p01 = x[int(round(.01*npts))]
p99 = x[int(round(.99*npts))]
self.norm = P.normalize(vmin = p01, vmax = p99)
#self.norm = P.normalize(-.1, 1.1)
if hasattr(self, "overlay_img") and self.overlay_img:
p01 = P.prctile(self.overlay_img[:], 1.0)
p99 = P.prctile(self.overlay_img[:], 99.)
self.overlay_norm = P.normalize(vmin = p01, vmax = p99)
#-------------------------------------------------------------------------
def xy(self, slice_idx):
(ax, cor, sag) = self.image.slicing()
x,y = {
ax: (2, 1), # x,y
cor: (2, 0), # x,z
sag: (1, 0), # y,z
}.get(slice_idx)
return x,y
#-------------------------------------------------------------------------
def updateSlices(self, zyx, sliceplots=None, image=None, norm=None):
if not sliceplots:
sliceplots = self.sliceplots
if not image:
image = self.image
if not norm:
norm = self.norm
for sliceplot in sliceplots:
idx = sliceplot.slice_idx
sliceplot.setData(image.data_xform(idx, zyx), norm=norm)
if self.slice_patches is not None:
p_idx = int(self.image.vox_coords[idx])
sliceplot.showPatches(self.slice_patches[idx][p_idx])
#-------------------------------------------------------------------------
def updateCrosshairs(self):
for s,sliceplot in enumerate(self.sliceplots):
idx = sliceplot.slice_idx
zyx = self.image.zyx_coords().tolist()
zyx.pop(s)
ud,lr = zyx
sliceplot.setCrosshairs(lr,ud)
#-------------------------------------------------------------------------
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 setUpAxesSize(self):
"Scale the axes appropriately for the image dimensions"
# assume that image resolution is isotropic in dim2 and dim1
# (not necessarily in dim0)
# want the isotropic resolution plot to be 215x215 pixels
#xy_imgsize = 215. # this should be more like 85% of the dim0 sliceplot
ref_size = self.dimlengths[-1]
slicing = self.image.slicing()
idx = slicing.index(0)
xy_imgsize = .85 * min(*self.sliceplots[idx].get_width_height())
for sliceplot in self.sliceplots:
dims_copy = self.dimlengths.tolist()
ax = sliceplot.getAxes()
s_idx = sliceplot.slice_idx
dims_copy.remove(self.dimlengths[s_idx])
slice_y, slice_x = self.image.is_xpose(s_idx) and \
dims_copy[::-1] or dims_copy
height = xy_imgsize*slice_y/ref_size
width = xy_imgsize*slice_x/ref_size
canvas_x, canvas_y = sliceplot.get_width_height()
w = width/canvas_x
h = height/canvas_y
l = (1.0 - width/canvas_x)/2.
b = (1.0 - height/canvas_y)/2.
ax.set_position([l,b,w,h])
sliceplot.draw_idle()
#-------------------------------------------------------------------------
def connectCrosshairEvents(self, mode="enable"):
if mode=="enable":
self._dragging = False
for sliceplot in self.sliceplots:
self.connect_crosshair_id.append(sliceplot.mpl_connect(
"button_press_event", self.SPMouseDown))
self.connect_crosshair_id.append(sliceplot.mpl_connect(
"button_release_event", self.SPMouseUp))
self.connect_crosshair_id.append(sliceplot.mpl_connect(
"motion_notify_event", self.SPMouseMotion))
sliceplot.toggleCrosshairs(mode=True)
else:
if len(self.connect_crosshair_id):
for id,sliceplot in enumerate(self.sliceplots):
sliceplot.mpl_disconnect(self.connect_crosshair_id[id])
sliceplot.mpl_disconnect(self.connect_crosshair_id[id+1])
sliceplot.mpl_disconnect(self.connect_crosshair_id[id+2])
sliceplot.toggleCrosshairs(mode=False)
self.connect_crosshair_id = []
#-------------------------------------------------------------------------
def SPMouseDown(self, event):
# for a new mouse down event, reset the mouse positions
self._mouse_lr = self._mouse_ud = None
self._dragging = event.inaxes
self.updateCoords(event)
#-------------------------------------------------------------------------
def SPMouseUp(self, event):
# if not dragging, no business being here!
if self._dragging:
self.updateCoords(event)
self._dragging = False
#-------------------------------------------------------------------------
def SPMouseMotion(self, event):
if self._dragging:
self.updateCoords(event)
#-------------------------------------------------------------------------
def updateCoords(self, event):
"Update all the necessary sliceplot data based on a mouse click."
# The tasks here are:
# 1 find zyx_coords of mouse click and translate to vox_coords
# 2 update the transverse sliceplots based on vox_coords
# 2a update the transverse overlays if present
# 3 update crosshairs on all sliceplots
# 4 update voxel space and zyx space texts
sliceplot = event.canvas
# using terminology up-down, left-right to avoid confusion with y,x
ud,lr = sliceplot.getEventCoords(event)
if self._mouse_lr == lr and self._mouse_ud == ud:
return
if lr is None or ud is None:
return
self._mouse_lr, self._mouse_ud = (lr, ud)
# trans_sliceplots are the transverse plots that get
# updated from where the mouse clicked
(ax, cor, sag) = self.image.slicing()
trans_sliceplots = {
self.sliceplots[ax]: (self.sliceplots[sag], self.sliceplots[cor]),
self.sliceplots[cor]: (self.sliceplots[sag], self.sliceplots[ax]),
self.sliceplots[sag]: (self.sliceplots[cor], self.sliceplots[ax]),
}.get(sliceplot)
trans_idx = (trans_sliceplots[0].slice_idx,
trans_sliceplots[1].slice_idx)
# where do left-right and up-down cut across in zyx space?
trans_ax = self.image.transverse_slicing(sliceplot.slice_idx)
zyx_clicked = self.image.zyx_coords()
zyx_clicked[trans_ax[0]] = lr
zyx_clicked[trans_ax[1]] = ud
vox = self.image.zyx2vox(zyx_clicked)
self.image.vox_coords[trans_idx[0]] = vox[trans_idx[0]]
self.image.vox_coords[trans_idx[1]] = vox[trans_idx[1]]
self.updateSlices(zyx_clicked, sliceplots=trans_sliceplots)
if self.overlay_img:
# basically do the same thing over again wrt the overlay dims
(ax_o, cor_o, sag_o) = self.overlay_img.slicing()
trans_overlays = {
self.sliceplots[ax]: (self.overlays[sag_o], self.overlays[cor_o]),
self.sliceplots[cor]: (self.overlays[sag_o], self.overlays[ax_o]),
self.sliceplots[sag]: (self.overlays[cor_o], self.overlays[ax_o]),
}.get(sliceplot)
trans_idx = (trans_overlays[0].slice_idx,
trans_overlays[1].slice_idx)
vox = self.overlay_img.zyx2vox(zyx_clicked)
self.overlay_img.vox_coords[trans_idx[0]] = vox[trans_idx[0]]
self.overlay_img.vox_coords[trans_idx[1]] = vox[trans_idx[1]]
self.updateSlices(zyx_clicked, sliceplots=trans_overlays,
image=self.overlay_img,
norm=self.overlay_norm)
self.updateCrosshairs()
# make text to update the statusbox label's
self.statusbox.set_vox_text(self.image.vox_coords[::-1].tolist())
self.statusbox.set_zyx_text(self.image.zyx_coords()[::-1].tolist())
point = tuple(self.image.vox_coords)
self.statusbox.set_intensity_text(self.image[point])
#-------------------------------------------------------------------------
def rediculous_handler(self, cbox):
#mode = cbox.get_active()==0 and "enable" or "disable"
#self.connectCrosshairEvents(mode=mode)
print "You've hit a useless button!"
return
#-------------------------------------------------------------------------
def interp_handler(self, cbox):
interp_method = interp_lookup[cbox.get_active()]
for sliceplot in self.sliceplots:
sliceplot.setInterpo(interp_method)
#-------------------------------------------------------------------------
def crosshair_hider(self, toggle):
hidden = (not toggle.get_active())
for sliceplot in self.sliceplots:
sliceplot.toggleCrosshairs(mode=hidden)
#-------------------------------------------------------------------------
def zoom_handler(self, cbox):
"Changes the view range of the sliceplots to be NxN mm"
self.zoom = {
0: 0,
1: 160,
2: 80,
3: 40,
4: 20,
5: 10,
}.get(cbox.get_active(), 0)
r_center = self.image.zyx_coords()
if self.zoom:
r_neg = r_center - N.array([self.zoom/2.]*3)
r_pos = r_center + N.array([self.zoom/2.]*3)
zyx_lim = zip(r_neg, r_pos)
self.dimlengths = N.array([self.zoom]*3)
else:
self.dimlengths = self.image.dr * N.array(self.image.shape)
zyx_lim = self.image.extents()
for plot in self.sliceplots:
x,y = self.image.transverse_slicing(plot.slice_idx)
plot.setXYlim(zyx_lim[x], zyx_lim[y])
plot.setCrosshairs(r_center[x], r_center[y])
self.updateSlices(self.image.zyx_coords())
self.setUpAxesSize()
#-------------------------------------------------------------------------
def resize_handler(self, window, event):
#print "got resize signal"
self.setUpAxesSize()
#-------------------------------------------------------------------------
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 launch_overlay_toolbox(self, action):
if self.overlay_img is not None:
if not hasattr(self, "overlay_tools") or not self.overlay_tools:
self.overlay_tools = OverlayToolWin(self.overlays, self)
else:
self.overlay_tools.present()
#-------------------------------------------------------------------------
def killoverlay(self, action):
if self.overlay_img is not None:
for overlay in self.overlays:
overlay.removeSelf()
if hasattr(self, "overlay_tools") and self.overlay_tools:
self.overlay_tools.destroy()
del self.overlay_tools
self.overlay_img = None
self.overlay_norm = None
#-------------------------------------------------------------------------
def load_new_image(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 open...", action="open",
filter=image_filter)
if not fname:
return
try:
img = readImage(fname, "nifti")
except:
img = readImage(fname, "analyze")
self.killoverlay(None)
self.__init__(img)
#-------------------------------------------------------------------------
def launch_sliceview(self, action):
from recon.visualization.sliceview import sliceview
sliceview(self.image, parent=self)
#-------------------------------------------------------------------------
def launch_recon_gui(self, action):
from recon.visualization.recon_gui import recon_gui
recon_gui(image=self.img_obj, parent=self)
#-------------------------------------------------------------------------
def _plotter_died(self):
pass
#-------------------------------------------------------------------------
def _create_action_group(self):
entries = (
( "FileMenu", None, "_File" ),
( "Open Image", gtk.STOCK_OPEN, "_Open Image", "<control>O",
"Opens and plots a new image", self.load_new_image ),
( "Quit", gtk.STOCK_QUIT,
"_Quit", "<control>Q",
"Quits",
lambda action: self.destroy() ),
( "ToolsMenu", None, "_Tools" ),
( "Load Overlay", None, "_Load Overlay", "",
"Load an image to overlay", self.initoverlay ),
( "Unload Overlay", None, "_Unload Overlay", "",
"Unload the overlay", self.killoverlay ),
( "Overlay Adjustment Toolbox", None,
"_Overlay Adjustment Toolbox", "",
"launch overlay toolbox", self.launch_overlay_toolbox ),
( "Plot In Sliceview", None,
"_Plot In Sliceview", "", "opens image in sliceview",
self.launch_sliceview ),
( "Run Recon GUI", None, "_Run Recon GUI", "", "opens gui",
self.launch_recon_gui ),
)
action_group = gtk.ActionGroup("WindowActions")
action_group.add_actions(entries)
return action_group
