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 load_any_image(self, action):
"called when open button/menu item is hit"
fid_filter = gtk.FileFilter()
fid_filter.add_pattern('fid')
fid_filter.set_name('FID Images')
dat_filter = gtk.FileFilter()
dat_filter.add_pattern('*.dat')
dat_filter.set_name('DAT Images')
ana_nii_filter = gtk.FileFilter()
ana_nii_filter.add_pattern('*.hdr')
ana_nii_filter.add_pattern('*.nii')
ana_nii_filter.set_name('ANALYZE/NIFTI Images')
fname = ask_fname(self,
'Choose file to load...',
action='open',
filter=[fid_filter, dat_filter, ana_nii_filter])
if not fname:
return
# cook any fid filename found
if fname[-8:] == '.fid/fid':
fname = os.path.split(fname)[0]
self.image = readImage(fname, vrange=(0, 1))
self._initialize_undo_buffer()
self.pathentry.set_text(fname.split('/')[-1])
self.update_plotter()
def load_any_image(self, action):
"called when open button/menu item is hit"
fid_filter = gtk.FileFilter()
fid_filter.add_pattern("fid")
fid_filter.set_name("FID Images")
dat_filter = gtk.FileFilter()
dat_filter.add_pattern("*.dat")
dat_filter.set_name("DAT Images")
ana_nii_filter = gtk.FileFilter()
ana_nii_filter.add_pattern("*.hdr")
ana_nii_filter.add_pattern("*.nii")
ana_nii_filter.set_name("ANALYZE/NIFTI Images")
fname = ask_fname(
self, "Choose file to load...", action="open", filter=[fid_filter, dat_filter, ana_nii_filter]
)
if not fname:
return
# cook any fid filename found
if fname[-8:] == ".fid/fid":
fname = os.path.split(fname)[0]
self.image = readImage(fname, vrange=(0, 1))
self._initialize_undo_buffer()
self.pathentry.set_text(fname.split("/")[-1])
self.update_plotter()
def reload_image(self, button):
"called when reload (refresh) button is hit"
if not self.image:
return
path = self.image.path
self.image = readImage(path, vrange=(0, 1))
self._initialize_undo_buffer()
self.update_plotter()
def reload_image(self, button):
"called when reload (refresh) button is hit"
if not self.image:
return
path = self.image.path
self.image = readImage(path, vrange=(0, 1))
self._initialize_undo_buffer()
self.update_plotter()
def load_data_prepd(fname, sl=0, N1=64):
img = imageio.readImage(fname, N1=N1)
cdata = np.empty((img.n_chan, img.n_pe, img.N1), 'F')
cdata[:] = img.cdata[:,0,sl,:,:]
del img.n_chan
del img.cdata
img.setData(cdata)
return img
def load_data_prepd(fname, sl=0, N1=64):
img = imageio.readImage(fname, N1=N1)
cdata = np.empty((img.n_chan, img.n_pe, img.N1), 'F')
cdata[:] = img.cdata[:, 0, sl, :, :]
del img.n_chan
del img.cdata
img.setData(cdata)
return img
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 setUp(self):
pwd = os.path.split(__file__)[0]
kernfile = os.path.join(pwd, 'fmap_based_kernel_long')
self.ref_kernel = np.fromstring(
open(kernfile, 'rb').read(), np.complex128)
self.ref_kernel.shape = (20, 64, 64, 64)
fmapfile = os.path.join(pwd, "test_fmap.nii")
fmapIm = readImage(fmapfile)
self.fmap, self.chi = (fmapIm[0].astype(np.float64),
fmapIm[1].astype(np.float64))
def setUp(self):
pwd = os.path.split(__file__)[0]
kernfile = os.path.join(pwd, 'fmap_based_kernel_long')
self.ref_kernel = np.fromstring(open(kernfile, 'rb').read(),
np.complex128)
self.ref_kernel.shape = (20,64,64,64)
fmapfile = os.path.join(pwd, "test_fmap.nii")
fmapIm = readImage(fmapfile)
self.fmap,self.chi = (fmapIm[0].astype(np.float64),
fmapIm[1].astype(np.float64))
def run(self, plotter="slice"):
opts, args = self.parse_args()
if not args:
self.print_help()
sys.exit(0)
image = readImage(args[0])
if plotter is "slice":
ViewImage(title=args[0]).run(image)
else:
ViewOrtho(title=args[0]).run(image)
def run(self):
opts, args = self.parse_args()
if args:
vrange = parseVolRangeOption(opts.vol_range, self)
try:
image = readImage(args[0], vrange=vrange)
except:
image = None
print 'Could not find image %s, try loading manually'%args[0]
else:
image = None
recon_gui(image=image, logfile=opts.log_file)
def run(self):
opts, args = self.parse_args()
if args:
vrange = parseVolRangeOption(opts.vol_range, self)
try:
image = readImage(args[0], vrange=vrange)
except:
image = None
print 'Could not find image %s, try loading manually' % args[0]
else:
image = None
recon_gui(image=image, logfile=opts.log_file)
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 run(self):
return readImage(self.filename,
self.format,
datatype=self.datatype,
vrange=self.vrange) #, N1=128)
#-------------------------------------------------------------------------
def _takedown(self, foo):
self.padre.overlay_tools = None
foo.destroy()
#-------------------------------------------------------------------------
def alpha_handler(self, adj):
for overlay in self.overlay_ref:
overlay.setAlpha(self.alphaslider.get_value())
#-------------------------------------------------------------------------
def cmap_handler(self, cbox):
cmap = cmap_lookup[cbox.get_active()]
for overlay in self.overlay_ref:
overlay.setCmap(cmap)
#-------------------------------------------------------------------------
def interpo_handler(self, cbox):
interpo = interp_lookup[cbox.get_active()]
for overlay in self.overlay_ref:
overlay.setInterpo(interpo)
##############################################################################
if __name__ == "__main__":
fname = sys.argv[1]
ftype = len(sys.argv) > 2 and sys.argv[2] or "analyze"
img = readImage(fname, ftype)
spmclone(img)
def run(self):
return readImage(self.filename, self.format,
datatype=self.datatype, vrange=self.vrange) #, N1=128)
#-------------------------------------------------------------------------
def _takedown(self, foo):
self.padre.overlay_tools = None
foo.destroy()
#-------------------------------------------------------------------------
def alpha_handler(self, adj):
for overlay in self.overlay_ref:
overlay.setAlpha(self.alphaslider.get_value())
#-------------------------------------------------------------------------
def cmap_handler(self, cbox):
cmap = cmap_lookup[cbox.get_active()]
for overlay in self.overlay_ref:
overlay.setCmap(cmap)
#-------------------------------------------------------------------------
def interpo_handler(self, cbox):
interpo = interp_lookup[cbox.get_active()]
for overlay in self.overlay_ref:
overlay.setInterpo(interpo)
##############################################################################
if __name__ == "__main__":
fname = sys.argv[1]
ftype = len(sys.argv) > 2 and sys.argv[2] or "analyze"
img = readImage(fname, ftype)
spmclone(img)