def axes(*args, **kwargs):
"""
Add an axis at positon rect specified by
axes() by itself creates a default full window axis
axes(rect, axisbg='w') where rect=[left, bottom, width, height] in
normalized (0,1) units background is the background color for
the axis, default white
axes(h, axisbg='w') where h is an axes instance makes h the
current axis An Axes instance is returned
axisbg is a color format string which sets the background color of
the axes (default white)
"""
nargs = len(args)
if args==0: return subplot(111)
if nargs>1:
error_msg('Only one non keyword arg to axes allowed')
arg = args[0]
if isinstance(arg, Axes):
Gcf().get_current_figwin().set_current_axes(arg)
return arg
else:
rect = arg
return Gcf().get_current_figwin().add_axes(
rect=rect, **kwargs)
def add_segment(self, button):
if not self.imageData:
error_msg("Cannot create surface. Image data of surface renderer is not set.")
return
if self.nsurf==0:
self.__adjust_scrollbar_threshold_for_data()
self.nsurf +=1
intensity = self.__calculate_intensity_threshold()
if intensity is None: return
name = self.__create_segment_name(self.nsurf)
if (not name) or name=="":
return
tree_iter = self.tree_surf.append(None)
self.tree_surf.set(tree_iter, 0,self.nsurf, 1, name)
self.__update_treeview_visibility()
self.paramd[self.nsurf] = SurfParams(self.imageData, intensity, self.lastColor)
params = self.paramd[self.nsurf]
if self.nsurf==1:
self.picker_surface_id = params.uuid
params.label = name
params.intensity = intensity
params.set_color(self.lastColor, self.lastColorName)
params.update_properties()
self.render()
def axes(*args, **kwargs):
"""
Add an axis at positon rect specified by
axes() by itself creates a default full window axis
axes(rect, axisbg='w') where rect=[left, bottom, width, height] in
normalized (0,1) units background is the background color for
the axis, default white
axes(h, axisbg='w') where h is an axes instance makes h the
current axis An Axes instance is returned
axisbg is a color format string which sets the background color of
the axes (default white)
"""
nargs = len(args)
if args == 0: return subplot(111)
if nargs > 1:
error_msg('Only one non keyword arg to axes allowed')
arg = args[0]
if isinstance(arg, Axes):
Gcf().get_current_figwin().set_current_axes(arg)
return arg
else:
rect = arg
return Gcf().get_current_figwin().add_axes(rect=rect, **kwargs)
def add_roi(self,*args):
dialog = gtk.FileSelection('Choose filename for ROI mask')
dialog.set_filename(shared.get_last_dir())
dialog.show()
response = dialog.run()
if response==gtk.RESPONSE_OK:
fname = dialog.get_filename()
dialog.destroy()
try:
#Actually add ROI
self.nroi+=1
tree_iter = self.tree_roi.append(None)
self.tree_roi.set(tree_iter,0,self.nroi,1,os.path.split(fname)[1],2,fname,3,True)
self.__update_treeview_visibility()
roi_image_reader = vtkNiftiImageReader()
roi_image_reader.SetFileName(fname)
roi_image_reader.Update()
roi_id = self.tree_roi.get(tree_iter,0)
self.paramd[roi_id] = RoiParams(roi_image_reader.GetOutput())
#self.paramd[roi_id].update_pipeline()
#print self.paramd[roi_id].intensity
shared.set_file_selection(fname)
except IOError:
error_msg(
'Could not load ROI mask from %s' % fname,
)
finally:
self.__update_treeview_visibility()
else: dialog.destroy()
self.render()
def load_image(self, *args):
if debug:
print "loc3djr_maintoolbar.load_image()"
debug = False
reader = None
pars = None
if debug:
reader = vtk.vtkImageReader2()
reader.SetDataScalarTypeToUnsignedShort()
reader.SetDataByteOrderToLittleEndian()
reader.SetFileNameSliceOffset(120)
reader.SetDataExtent(0, 511, 0, 511, 0, 106)
reader.SetFilePrefix('/home/jdhunter/seizure/data/ThompsonK/CT/raw/1.2.840.113619.2.55.1.1762864819.1957.1074338393.')
reader.SetFilePattern( '%s%d.raw')
reader.SetDataSpacing(25.0/512, 25.0/512, 0.125 )
reader.Update()
else:
dlg = widgets['dlgReader']
response = dlg.run()
if response == gtk.RESPONSE_OK:
try: reader = widgets.reader
except AttributeError:
pars = widgets.get_params()
pars = widgets.validate(pars)
if pars is None:
error_msg('Could not validate the parameters', dlg)
return
reader = widgets.get_reader(pars)
pars = widgets.get_params()
pars = widgets.validate(pars)
dlg.hide()
if debug:
print "reader=", reader
if not reader:
if debug:
print "hit cancel, see if we can survive"
else:
imageData = reader.GetOutput()
if debug:
print "pars=", pars
print "loc3djr_maintoolbar.load_image(): reader.GetOutput() is " , imageData
print "load_image(): imageData.SetSpacing(", reader.GetDataSpacing(), " )"
imageData.SetSpacing(reader.GetDataSpacing())
if debug:
print "calling EventHandler().notify('set image data', imageData)"
EventHandler().notify('set image data', imageData)
if type(reader) == vtkNiftiImageReader:
if debug:
print "calling EventHandler().setNifti()"
#XXX EventHandler().setNifti(reader.GetFilename())
EventHandler().setNifti(reader.GetQForm())
def hist(x, bins=10, noplot=0, normed=0):
"""
Compute the histogram of x. bins is either an integer number of
bins or a sequence giving the bins. x are the data to be binned.
if noplot is True, just compute the histogram and return the
number of observations and the bins as an (n, bins) tuple.
If noplot is False, compute the histogram and plot it, returning
n, bins, patches
If normed is true, the first element of the return tuple will be the
counts normalized to form a probability distribtion, ie,
n/(len(x)*dbin)
"""
n,bins = mlab.hist(x, bins, normed)
width = bins[1]-bins[0]
if noplot: return n, bins
else:
try:
patches = gca().bar(bins, n, width=width)
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def errorbar(x, y, e, u=None, fmt='b-'):
"""
Plot x versus y with error bars in e. if u is not None, then u
gives the upper error bars and e gives the lower error bars.
Otherwise e the error bars are symmetrix about y and given in the
array e.
fmt is the plot format symbol for y
Return value is a length 2 tuple. The first element is a list of
y symbol lines. The second element is a list of error bar lines.
"""
l0 = plot(x, y, fmt)
e = to_arrays(Float, e)
if u is None: u = e
upper = y + u
lower = y - e
width = (max(x) - min(x)) * 0.005
a = gca()
try:
l1 = a.vlines(x, y, lower)
l2 = a.vlines(x, y, upper)
l3 = a.hlines(upper, x - width, x + width)
l4 = a.hlines(lower, x - width, x + width)
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def errorbar(x, y, e, u=None, fmt='b-'):
"""
Plot x versus y with error bars in e. if u is not None, then u
gives the upper error bars and e gives the lower error bars.
Otherwise e the error bars are symmetrix about y and given in the
array e.
fmt is the plot format symbol for y
Return value is a length 2 tuple. The first element is a list of
y symbol lines. The second element is a list of error bar lines.
"""
l0 = plot(x,y,fmt)
e = to_arrays(Float, e)
if u is None: u = e
upper = y+u
lower = y-e
width = (max(x)-min(x))*0.005
a = gca()
try:
l1 = a.vlines(x, y, lower)
l2 = a.vlines(x, y, upper)
l3 = a.hlines(upper, x-width, x+width)
l4 = a.hlines(lower, x-width, x+width)
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def hist(x, bins=10, noplot=0, normed=0):
"""
Compute the histogram of x. bins is either an integer number of
bins or a sequence giving the bins. x are the data to be binned.
if noplot is True, just compute the histogram and return the
number of observations and the bins as an (n, bins) tuple.
If noplot is False, compute the histogram and plot it, returning
n, bins, patches
If normed is true, the first element of the return tuple will be the
counts normalized to form a probability distribtion, ie,
n/(len(x)*dbin)
"""
n, bins = mlab.hist(x, bins, normed)
width = bins[1] - bins[0]
if noplot: return n, bins
else:
try:
patches = gca().bar(bins, n, width=width)
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def load_image(self, *args):
print "loc3djr_maintoolbar.load_image()"
debug = False
reader = None
pars = None
if debug:
reader = vtk.vtkImageReader2()
reader.SetDataScalarTypeToUnsignedShort()
reader.SetDataByteOrderToLittleEndian()
reader.SetFileNameSliceOffset(120)
reader.SetDataExtent(0, 511, 0, 511, 0, 106)
reader.SetFilePrefix(
'/home/jdhunter/seizure/data/ThompsonK/CT/raw/1.2.840.113619.2.55.1.1762864819.1957.1074338393.'
)
reader.SetFilePattern('%s%d.raw')
reader.SetDataSpacing(25.0 / 512, 25.0 / 512, 0.125)
reader.Update()
else:
dlg = widgets['dlgReader']
response = dlg.run()
if response == gtk.RESPONSE_OK:
try:
reader = widgets.reader
except AttributeError:
pars = widgets.get_params()
pars = widgets.validate(pars)
if pars is None:
error_msg('Could not validate the parameters', dlg)
return
reader = widgets.get_reader(pars)
pars = widgets.get_params()
pars = widgets.validate(pars)
dlg.hide()
print "reader=", reader
if not reader:
print "hit cancel, see if we can survive"
else:
imageData = reader.GetOutput()
print "pars=", pars
print "loc3djr_maintoolbar.load_image(): reader.GetOutput() is ", imageData
print "load_image(): imageData.SetSpacing(", reader.GetDataSpacing(
), " )"
imageData.SetSpacing(reader.GetDataSpacing())
print "calling EventHandler().notify('set image data', imageData)"
EventHandler().notify('set image data', imageData)
if type(reader) == vtkNiftiImageReader:
print "calling EventHandler().setNifti()"
#XXX EventHandler().setNifti(reader.GetFilename())
EventHandler().setNifti(reader.GetQForm())
def take_all_shots(self, *args):
"""For each PyLocatorRenderWindow in list, take a SS"""
if len(self._sts)==0:
error_msg("Cannot take screenshots: \nNo instances registered.")
return False
fn_pattern = self.entryFn.get_text()
mag = self.sbMag.get_value()
for st in self._sts:
st.take_screenshot(fn_pattern, mag)
def take_shot(self, button, idx):
"""For one PyLocatorRenderWindow, take a SS"""
#print "take_shot", args
if len(self._sts)==0:
error_msg("Cannot take screenshots: \nNo instances registered.")
return False
fn_pattern = self.entryFn.get_text()
mag = self.sbMag.get_value()
self._sts[idx].take_screenshot(fn_pattern, mag)
def ok_clicked(w):
fname = dialog.get_filename()
shared.set_file_selection(fname)
try: EventHandler().save_registration_as(fname)
except IOError:
error_msg('Could not save data to %s' % fname,
)
else:
self.fileName = fname
dialog.destroy()
def ok_clicked(w):
fname = dialog.get_filename()
shared.set_file_selection(fname)
try:
EventHandler().save_registration_as(fname)
except IOError:
error_msg('Could not save data to %s' % fname, )
else:
self.fileName = fname
dialog.destroy()
def propose_fn(self,*args):
mri_fn = shared.lastSel
if len(mri_fn) == 0:
error_msg("Cannot propose filename: \nFilename of MRI unknown")
return False
for suff in [".nii.gz",".nii"]:
if mri_fn.endswith(suff):
mri_fn = mri_fn[:-len(suff)]
self.entryFn.set_text(mri_fn+"_pylocator%03i.png")
return True
def plot(*args, **kwargs):
"""
plot lines. *args is a variable length argument, allowing for
multiple x, y pairs with an optional format string. For
example, all of the following are legal
plot(x,y) # plot Numeric arrays y vs x
plot(x,y, 'bo') # plot Numeric arrays y vs x with blue circles
plot(y) # plot y using x = arange(len(y))
plot(y, 'r+') # ditto with red plusses
An arbitrary number of x, y, fmt groups can be specified, as in
a.plot(x1, y1, 'g^', x2, y2, 'l-')
Return value is a list of lines that were added
The following line styles are supported:
- : solid line
-- : dashed line
-. : dash-dot line
: : dotted line
| : verical lines
. : points
, : pixels
o : circle symbols
^ : triangle up symbols
v : triangle down symbols
< : triangle left symbols
> : triangle right symbols
s : square symbols
+ : plus symbols
The following color strings are supported
b : blue
g : green
r : red
c : cyan
m : magenta
y : yellow
k : black
w : white
Line styles and colors are combined in a single format string
"""
try:
lines = gca().plot(*args, **kwargs)
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
def plot(*args, **kwargs):
"""
plot lines. *args is a variable length argument, allowing for
multiple x, y pairs with an optional format string. For
example, all of the following are legal
plot(x,y) # plot Numeric arrays y vs x
plot(x,y, 'bo') # plot Numeric arrays y vs x with blue circles
plot(y) # plot y using x = arange(len(y))
plot(y, 'r+') # ditto with red plusses
An arbitrary number of x, y, fmt groups can be specified, as in
a.plot(x1, y1, 'g^', x2, y2, 'l-')
Return value is a list of lines that were added
The following line styles are supported:
- : solid line
-- : dashed line
-. : dash-dot line
: : dotted line
| : verical lines
. : points
, : pixels
o : circle symbols
^ : triangle up symbols
v : triangle down symbols
< : triangle left symbols
> : triangle right symbols
s : square symbols
+ : plus symbols
The following color strings are supported
b : blue
g : green
r : red
c : cyan
m : magenta
y : yellow
k : black
w : white
Line styles and colors are combined in a single format string
"""
try: lines = gca().plot(*args, **kwargs)
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
def figure(num=1):
"""
Create a new figure and return a handle to it
If figure(num) already exists, make it active and return the
handle to it.
"""
if num == 0:
error_msg('Figure number can not be 0.\n' + \
'Hey, give me a break, this is matlab compatability')
return
return Gcf(num).get_current_figwin().figure
def figure(num=1):
"""
Create a new figure and return a handle to it
If figure(num) already exists, make it active and return the
handle to it.
"""
if num==0:
error_msg('Figure number can not be 0.\n' + \
'Hey, give me a break, this is matlab compatability')
return
return Gcf(num).get_current_figwin().figure
def load_params_from_file(self, fname):
dialog = self['dlgReader']
try: s = file(fname, 'r').read()
except IOError:
error_msg('Could not open %s for reading' % fname, dialog)
return 0
p = Params()
p.from_string(s)
widgets.set_params(p)
widgets['entryInfoFile'].set_text(fname)
return 1
def bar(*args, **kwargs):
"""
bar(self, x, y, width=0.8)
Make a bar plot with rectangles at x, x+width, 0, y
x and y are Numeric arrays
Return value is a list of Rectangle patch instances
"""
try: patches = gca().bar(*args, **kwargs)
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def load_params_from_file(self, fname):
dialog = self['dlgReader']
try:
s = file(fname, 'r').read()
except IOError:
error_msg('Could not open %s for reading' % fname, dialog)
return 0
p = Params()
p.from_string(s)
widgets.set_params(p)
widgets['entryInfoFile'].set_text(fname)
return 1
def vlines(*args, **kwargs):
"""
lines = vlines(x, ymin, ymax, color='k'):
Plot vertical lines at each x from ymin to ymax. ymin or ymax
can be scalars or len(x) numpy arrays. If they are scalars,
then the respective values are constant, else the heights of
the lines are determined by ymin and ymax
Returns a list of lines that were added
"""
try: lines = gca().vlines(*args, **kwargs)
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def bar(*args, **kwargs):
"""
bar(self, x, y, width=0.8)
Make a bar plot with rectangles at x, x+width, 0, y
x and y are Numeric arrays
Return value is a list of Rectangle patch instances
"""
try:
patches = gca().bar(*args, **kwargs)
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def coplanar(self):
numSelected = EventHandler().get_num_selected()
if numSelected !=3:
error_msg("You must first select exactly 3 markers",
)
return
# SetNormal is missing from the 4.2 python API so this is
# a long winded way of setting the pw to intersect 3
# selected markers
m1, m2, m3 = EventHandler().get_selected()
p1 = m1.get_center()
p2 = m2.get_center()
p3 = m3.get_center()
pw = pwo.get_pw()
planeO = vtk.vtkPlaneSource()
planeO.SetOrigin(pw.GetOrigin())
planeO.SetPoint1(pw.GetPoint1())
planeO.SetPoint2(pw.GetPoint2())
planeO.Update()
planeN = vtk.vtkPlaneSource()
planeN.SetOrigin(p1)
planeN.SetPoint1(p2)
planeN.SetPoint2(p3)
planeN.Update()
normal = planeN.GetNormal()
planeO.SetNormal(normal)
planeO.SetCenter(
(p1[0] + p2[0] + p3[0])/3,
(p1[1] + p2[1] + p3[1])/3,
(p1[2] + p2[2] + p3[2])/3,
)
planeO.Update()
pwxyz = pwo.get_pwxyz()
pw.SetOrigin(planeO.GetOrigin())
pw.SetPoint1(planeO.GetPoint1())
pw.SetPoint2(planeO.GetPoint2())
pw.UpdatePlacement()
pwo.update_plane()
pwo.Render()
pwxyz.Render()
def hlines(*args, **kwargs):
"""
lines = hlines(self, y, xmin, xmax, fmt='k-')
plot horizontal lines at each y from xmin to xmax. xmin or
xmax can be scalars or len(x) numpy arrays. If they are
scalars, then the respective values are constant, else the
widths of the lines are determined by xmin and xmax
Returns a list of line instances that were added
"""
try: lines = gca().hlines(*args, **kwargs)
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def vlines(*args, **kwargs):
"""
lines = vlines(x, ymin, ymax, color='k'):
Plot vertical lines at each x from ymin to ymax. ymin or ymax
can be scalars or len(x) numpy arrays. If they are scalars,
then the respective values are constant, else the heights of
the lines are determined by ymin and ymax
Returns a list of lines that were added
"""
try:
lines = gca().vlines(*args, **kwargs)
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def hlines(*args, **kwargs):
"""
lines = hlines(self, y, xmin, xmax, fmt='k-')
plot horizontal lines at each y from xmin to xmax. xmin or
xmax can be scalars or len(x) numpy arrays. If they are
scalars, then the respective values are constant, else the
widths of the lines are determined by xmin and xmax
Returns a list of line instances that were added
"""
try:
lines = gca().hlines(*args, **kwargs)
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def on_buttonDir_clicked(button=None):
dialog = gtk.FileSelection('Choose image file directory')
dialog.set_filename(shared.get_last_dir())
dialog.set_transient_for(widgets['dlgReader'])
dialog.set_filename(widgets['entryDir'].get_text())
response = dialog.run()
if response == gtk.RESPONSE_OK:
dir = dialog.get_filename()
if os.path.isdir(dir):
widgets['entryDir'].set_text(dir)
shared.set_file_selection(dir)
dialog.destroy()
else:
error_msg('%s is not a directory' % dir, dialog)
else:
dialog.destroy()
def scatter(*args, **kwargs):
"""
scatter(self, x, y, s=None, c='b'):
Make a scatter plot of x versus y. s is a size (in data
coords) and can be either a scalar or an array of the same
length as x or y. c is a color and can be a single color
format string or an length(x) array of intensities which will
be mapped by the colormap jet.
If size is None a default size will be used
"""
try: patches = gca().scatter(*args, **kwargs)
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def on_buttonDir_clicked(button=None):
dialog = gtk.FileSelection('Choose image file directory')
dialog.set_filename(shared.get_last_dir())
dialog.set_transient_for(widgets['dlgReader'])
dialog.set_filename(widgets['entryDir'].get_text())
response = dialog.run()
if response == gtk.RESPONSE_OK:
dir = dialog.get_filename()
if os.path.isdir(dir):
widgets['entryDir'].set_text(dir)
shared.set_file_selection(dir)
dialog.destroy()
else:
error_msg('%s is not a directory' % dir, dialog)
else:
dialog.destroy()
def show_correlation_props(self, button):
dialog = gtk.FileSelection('Choose filename for correlation data')
dialog.set_filename(shared.get_last_dir())
dialog.show()
response = dialog.run()
if response==gtk.RESPONSE_OK:
fname = dialog.get_filename()
dialog.destroy()
try: EventHandler().load_correlation_from(fname)
except IOError:
error_msg(
'Could not load correlation from %s' % fname,
)
else:
shared.set_file_selection(fname)
self.fileName = fname
else: dialog.destroy()
def scatter(*args, **kwargs):
"""
scatter(self, x, y, s=None, c='b'):
Make a scatter plot of x versus y. s is a size (in data
coords) and can be either a scalar or an array of the same
length as x or y. c is a color and can be a single color
format string or an length(x) array of intensities which will
be mapped by the colormap jet.
If size is None a default size will be used
"""
try:
patches = gca().scatter(*args, **kwargs)
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def show_correlation_props(self, button):
dialog = gtk.FileSelection('Choose filename for correlation data')
dialog.set_filename(shared.get_last_dir())
dialog.show()
response = dialog.run()
if response == gtk.RESPONSE_OK:
fname = dialog.get_filename()
dialog.destroy()
try:
EventHandler().load_correlation_from(fname)
except IOError:
error_msg('Could not load correlation from %s' % fname, )
else:
shared.set_file_selection(fname)
self.fileName = fname
else:
dialog.destroy()
def axis(*v):
"""
axis() returns the current axis as a length a length 4 vector
axis(v) where v= [xmin xmax ymin ymax] sets the min and max of the
x and y axis limits
"""
try: v[0]
except IndexError:
xlim = gca().get_xlim()
ylim = gca().get_ylim()
return [xlim[0], xlim[1], ylim[0], ylim[1]]
v = v[0]
if len(v) != 4:
error_msg('v must contain [xmin xmax ymin ymax]')
return
gca().set_xlim([v[0], v[1]])
gca().set_ylim([v[2], v[3]])
draw_if_interactive()
def add_segment(self, button):
'render, man'
val = self.get_intensity()
if val is None: return
name = self.entryName.get_text()
if not len(name):
error_msg('You must enter a name in the Intensity tab')
return
if not self.paramd.has_key(name):
self.paramd[name] = SurfParams(self.sr.renderer, self.sr.interactor)
params = self.paramd[name]
params.label = name
params.intensity = val
params.color = self.lastColor
params.set_image_data(self.sr.imageData)
params.update_properties()
self.update_segments_frame()
self.update_pipeline_frame()
self.update_picker_frame()
def axis(*v):
"""
axis() returns the current axis as a length a length 4 vector
axis(v) where v= [xmin xmax ymin ymax] sets the min and max of the
x and y axis limits
"""
try:
v[0]
except IndexError:
xlim = gca().get_xlim()
ylim = gca().get_ylim()
return [xlim[0], xlim[1], ylim[0], ylim[1]]
v = v[0]
if len(v) != 4:
error_msg('v must contain [xmin xmax ymin ymax]')
return
gca().set_xlim([v[0], v[1]])
gca().set_ylim([v[2], v[3]])
draw_if_interactive()
def save_params_to_file(self, fname):
"""
Pickle the params to file fname. If successful return 1
"""
dialog = self['dlgReader']
pars = widgets.get_params()
pars = widgets.validate(pars)
if pars is None:
error_msg('Invalid parameters')
return 0
try: fh = file(fname, 'w')
except IOError:
error_msg('Could not open %s for writing' % fname, dialog)
return 0
fh.write(str(pars))
widgets['entryInfoFile'].set_text(fname)
return 1
def save_params_to_file(self, fname):
"""
Pickle the params to file fname. If successful return 1
"""
dialog = self['dlgReader']
pars = widgets.get_params()
pars = widgets.validate(pars)
if pars is None:
error_msg('Invalid parameters')
return 0
try:
fh = file(fname, 'w')
except IOError:
error_msg('Could not open %s for writing' % fname, dialog)
return 0
fh.write(str(pars))
widgets['entryInfoFile'].set_text(fname)
return 1
def subplot(*args):
"""
Create a subplot command, creating axes with
subplot(numRows, numCols, plotNum)
where plotNum=1 is the first plot number and increasing plotNums
fill rows first. max(plotNum)==numRows*numCols
You can leave out the commas if numRows<=numCols<=plotNum<10, as
in
subplot(211) # 2 rows, 1 column, first (upper) plot
subplot(111) is the default axis
"""
try:
Gcf().get_current_figwin().add_subplot(*args)
a = gca()
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def set(h, s, val):
"""
Set handle h property in string s to value val
h can be a handle or vector of handles.
h is an instance (or vector of instances) of a class, eg a Line2D
or an Axes or AxisText. if s is 'somename', this function calls
o.set_somename(val)
for every instance in o in h
"""
if not iterable(h): h = [h]
else: h = flatten(h)
for o in h:
try:
func = 'o.set_%s(val)' % s
eval(func, {}, {'o': o, 'val': val})
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def add_segment(self, button):
'render, man'
val = self.get_intensity()
if val is None: return
name = self.entryName.get_text()
if not len(name):
error_msg('You must enter a name in the Intensity tab')
return
if not self.paramd.has_key(name):
self.paramd[name] = SurfParams(self.sr.renderer,
self.sr.interactor)
params = self.paramd[name]
params.label = name
params.intensity = val
params.color = self.lastColor
params.set_image_data(self.sr.imageData)
params.update_properties()
self.update_segments_frame()
self.update_pipeline_frame()
self.update_picker_frame()
def set(h, s, val):
"""
Set handle h property in string s to value val
h can be a handle or vector of handles.
h is an instance (or vector of instances) of a class, eg a Line2D
or an Axes or AxisText. if s is 'somename', this function calls
o.set_somename(val)
for every instance in o in h
"""
if not iterable(h): h = [h]
else: h = flatten(h)
for o in h:
try:
func = 'o.set_%s(val)' % s
eval(func, {}, {'o': o, 'val' : val})
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def subplot(*args):
"""
Create a subplot command, creating axes with
subplot(numRows, numCols, plotNum)
where plotNum=1 is the first plot number and increasing plotNums
fill rows first. max(plotNum)==numRows*numCols
You can leave out the commas if numRows<=numCols<=plotNum<10, as
in
subplot(211) # 2 rows, 1 column, first (upper) plot
subplot(111) is the default axis
"""
try:
Gcf().get_current_figwin().add_subplot(*args)
a = gca()
except ValueError, msg:
msg = raise_msg_to_str(msg)
error_msg(msg)
raise RuntimeError, msg
def validate(self, o):
dlg = self['dlgReader']
if o.readerClass != 'vtkNiftiImageReader':
if len(o.pattern) == 0:
msg = 'You must supply a number pattern for entry %s.\n' % \
self['labelPattern'].get_label() + 'Consider "%d"'
return error_msg(msg, dlg)
if o.pattern[0] != '%':
msg = '%s format string must begin with a %%.\n' % \
self['labelPattern'].get_label() + 'Consider "%d"'
return error_msg(msg, dlg)
if widgets['radiobuttonDimOther'].get_active():
dim1, dim2 = o.dimensions
val = dim1 = str2posint_or_err(dim1, 'Other: dimension 1', dlg)
if val is None: return None
val = dim2 = str2posint_or_err(dim2, 'Other: dimension 2', dlg)
if val is None: return None
o.dimensions = dim1, dim2
val = o.first = str2int_or_err(o.first, widgets['labelFirst'], dlg)
if val is None:
return None
val = o.last = str2posint_or_err(o.last, widgets['labelLast'], dlg)
if val is None: return None
if o.readerClass != 'vtkNiftiImageReader':
fnames = self.get_file_names(o)
for fname in fnames:
if debug:
print "validate(): doing fname ", fname
if not os.path.exists(fname):
return error_msg('Could not find file %s' % fname, dlg)
if o.readerClass == 'vtkBMPReader':
reader = vtk.vtkBMPReader()
b = reader.CanReadFile(fname)
if not b:
return error_msg(
'Could not read file %s with reader %s' %
(fname, o.readerClass), dlg)
else:
if len(o.extension) > 0:
fname = os.path.join(o.dir, o.pattern + "." + o.extension)
if not os.path.exists(fname):
return error_msg('Could not find file %s' % fname, dlg)
else:
fname = o.pattern
files = os.listdir(o.dir)
match = False
for file in files:
file = file.split(".")
if len(file) > 1:
if file[0] == fname:
if file[1] in ["nii", "img", "hdr"]:
match = True
break
if not match:
return error_msg(
'Could not find file %s with extension nii, img, hdr [.gz]'
% fname, dlg)
# Depth Field Of View
val = o.dfov = str2posnum_or_err(o.dfov, widgets['labelDFOV'], dlg)
if debug:
print "dfov=", val
if val is None: return None
# Spacing between slices
val = o.spacing = str2posnum_or_err(o.spacing, widgets['labelSpacing'],
dlg)
if debug:
print "spacing=", val
if val is None: return None
# Size of header
if o.header == '': o.header = 0
else:
val = o.header = str2int_or_err(o.header, widgets['labelHeader'],
dlg)
if val is None: return None
if debug:
print "header=", val
# Data mask
if o.mask is not None:
if o.mask == '': o.mask = None
else:
val = o.mask = str2int_or_err(o.mask, widgets['labelMask'],
dlg)
if val is None: return None
if debug:
print "mask=", val
return o
def set_current_axes(self, a):
if a not in self.axes.values():
error_msg('Axes is not in current figure')
self.currentAxis = a
def validate(self, o):
dlg = self['dlgReader']
if o.readerClass!='vtkNiftiImageReader':
if len(o.pattern)==0:
msg = 'You must supply a number pattern for entry %s.\n' % \
self['labelPattern'].get_label() + 'Consider "%d"'
return error_msg(msg, dlg)
if o.pattern[0]!='%':
msg = '%s format string must begin with a %%.\n' % \
self['labelPattern'].get_label() + 'Consider "%d"'
return error_msg(msg, dlg)
if widgets['radiobuttonDimOther'].get_active():
dim1, dim2 = o.dimensions
val = dim1 = str2posint_or_err(dim1, 'Other: dimension 1', dlg)
if val is None: return None
val = dim2 = str2posint_or_err(dim2, 'Other: dimension 2', dlg)
if val is None: return None
o.dimensions = dim1, dim2
val = o.first = str2int_or_err(o.first, widgets['labelFirst'], dlg)
if val is None:
return None
val = o.last = str2posint_or_err(o.last, widgets['labelLast'], dlg)
if val is None: return None
if o.readerClass!='vtkNiftiImageReader':
fnames = self.get_file_names(o)
for fname in fnames:
print "validate(): doing fname ", fname
if not os.path.exists(fname):
return error_msg('Could not find file %s' % fname, dlg)
if o.readerClass=='vtkBMPReader':
reader = vtk.vtkBMPReader()
b = reader.CanReadFile(fname)
if not b:
return error_msg('Could not read file %s with reader %s'
% (fname, o.readerClass), dlg)
else:
if len(o.extension) > 0:
fname=os.path.join(o.dir,o.pattern+"."+o.extension)
if not os.path.exists(fname):
return error_msg('Could not find file %s' % fname, dlg)
else:
fname=o.pattern
files=os.listdir(o.dir)
match=False
for file in files:
file=file.split(".")
if len(file)>1:
if file[0]==fname:
if file[1] in ["nii","img","hdr"]:
match=True
break
if not match:
return error_msg('Could not find file %s with extension nii, img, hdr [.gz]' % fname, dlg)
# Depth Field Of View
val = o.dfov = str2posnum_or_err(o.dfov, widgets['labelDFOV'], dlg)
print "dfov=", val
if val is None: return None
# Spacing between slices
val = o.spacing = str2posnum_or_err(
o.spacing, widgets['labelSpacing'], dlg)
print "spacing=", val
if val is None: return None
# Size of header
if o.header=='': o.header = 0
else:
val = o.header = str2int_or_err(
o.header, widgets['labelHeader'], dlg)
if val is None: return None
print "header=", val
# Data mask
if o.mask is not None:
if o.mask=='': o.mask = None
else:
val = o.mask = str2int_or_err(
o.mask, widgets['labelMask'], dlg)
if val is None: return None
print "mask=", val
return o
def checkPickerName():
if self.pickerName is None:
error_msg("You must select the pick segment in the Picker tab")
return False
return True
def checkPickerName():
if self.pickerName is None:
error_msg('You must select the pick segment in the Picker tab')
return False
return True
def set_current_axes(self, a):
if a not in self.axes.values():
error_msg('Axes is not in current figure')
self.currentAxis = a
def checkPickerId():
if not self.picker_id:
error_msg('Cannot insert marker. Choose surface first.')
return False
return True