diff --git a/fsl.py b/fsl.py
index 7b7f3a5e2c563b90bd1b6af1a24ac4aa760d25de..b0854b773a75931f4283a30c29358f16b6bebaa9 100755
--- a/fsl.py
+++ b/fsl.py
@@ -151,15 +151,15 @@ def buildGUI(fslTool, toolCtx, fslEnvActive):
actions.append((
wx.ID_HELP,
'{} Help'.format(fslTool.toolName),
- lambda ev: webpage.openFSLHelp(fslTool.helpPage)))
+ lambda *ev: webpage.openFSLHelp(fslTool.helpPage)))
for (name, func) in fslTool.actions:
- actions.append((-1, name, lambda ev: func(frame, ctx)))
+ actions.append((wx.ID_ANY, name, lambda ev, f=func: f(frame, ctx)))
actions.append((
wx.ID_EXIT,
'Exit',
- lambda ev: frame.Close()))
+ lambda *ev: frame.Close()))
for wxId, name, func in actions:
menuItem = fslMenu.Append(wxId, name)
diff --git a/fsl/data/fslimage.py b/fsl/data/fslimage.py
index 3828be36b40ea38407d089ac0746d295316e7069..45d000ec99876d160875a7c7b64cfa19dc4b7a24 100644
--- a/fsl/data/fslimage.py
+++ b/fsl/data/fslimage.py
@@ -77,8 +77,8 @@ class Image(object):
lo, hi = sorted(tx[:, axis])
- lo = lo - self.pixdim[axis] * 0.5
- hi = hi + self.pixdim[axis] * 0.5
+ lo = float(lo - self.pixdim[axis] * 0.5)
+ hi = float(hi + self.pixdim[axis] * 0.5)
return (lo, hi)
@@ -87,7 +87,9 @@ class Image(object):
"""
Transforms the given set of points in voxel coordinates to
points in world coordinates, according to the affine
- transformation specified in the image file. Parameters:
+ transformation specified in the image file. The returned array
+ is either a numpy.float64 array, or a single integer value,
+ depending on the input. Parameters:
- p: N*A array, where N is the number of points, and A
is the number of axes to consider (default: 3)
@@ -101,31 +103,39 @@ class Image(object):
"""
voxp = self._transform(p, self.worldToVoxMat, axes)
- voxp = np.array(voxp, dtype=np.int64)
-
- return voxp
+
+ if voxp.size == 1: return int(voxp[0])
+ else: return voxp
def voxToWorld(self, p, axes=None):
"""
Transforms the given set of points in world coordinates to
points in voxel coordinates, according to the affine
- transformation specified in the image file. See the
- worldToVox docstring for more details.
-
- """
- return self._transform(p, self.voxToWorldMat, axes)
+ transformation specified in the image file. The returned
+ array is either a numpy.float64 array, or a single float
+ value, depending on the input. See the worldToVox
+ docstring for more details.
+ """
+
+ worldp = self._transform(p, self.voxToWorldMat, axes)
+
+ if worldp.size == 1:
+ #print 'casting to float!'
+ return float(worldp)
+ else: return worldp
def _transform(self, p, a, axes):
"""
Transforms the given set of points p according to the given
- affine transformation a. See the worldToVox docstring for
- more details.
+ affine transformation a. The transformed points are returned
+ as a numpy.float64 array. See the worldToVox docstring for
+ more details.
"""
p = self._fillPoints(p, axes)
- t = np.zeros((len(p), 3), dtype=p.dtype)
+ t = np.zeros((len(p), 3), dtype=np.float64)
x = p[:, 0]
y = p[:, 1]
@@ -148,6 +158,7 @@ class Image(object):
"""
if not isinstance(p, collections.Iterable): p = [p]
+
p = np.array(p)
if axes is None: return p
diff --git a/fsl/fslview/imagelistpanel.py b/fsl/fslview/imagelistpanel.py
index 389bd00835a2c372f9f22212d8301f6c391235c6..ca1d53b092eac426b9a3ec3e5f1534bd033dcf5c 100644
--- a/fsl/fslview/imagelistpanel.py
+++ b/fsl/fslview/imagelistpanel.py
@@ -112,11 +112,12 @@ class ImageListPanel(wx.Panel):
except: lastDir = os.getcwd()
wildcard = imagefile.wildcard()
-
+
+ # wx wildcard handling is buggy, so i'm disabling it for now
dlg = wx.FileDialog(self.GetParent(),
message='Open image file',
defaultDir=lastDir,
- wildcard=wildcard,
+# wildcard=wildcard,
style=wx.FD_OPEN)
if dlg.ShowModal() != wx.ID_OK: return
diff --git a/fsl/fslview/orthopanel.py b/fsl/fslview/orthopanel.py
index 0c774506846048b1d40870ac0574904eea610e2b..de806cd8620d751800330c23aeb4ffbc50b26298 100644
--- a/fsl/fslview/orthopanel.py
+++ b/fsl/fslview/orthopanel.py
@@ -152,3 +152,16 @@ class OrthoFrame(wx.Frame):
wx.Frame.__init__(self, parent, title=title)
self.panel = OrthoPanel(self, imageList)
self.Layout()
+
+
+class OrthoDialog(wx.Dialog):
+ """
+ Convenience class for displaying an OrthoPanel in a (possibly modal)
+ dialog window.
+ """
+
+ def __init__(self, parent, imageList, title=None):
+
+ wx.Dialog.__init__(self, parent, title=title)
+ self.panel = OrthoPanel(self, imageList)
+ self.Layout()
diff --git a/fsl/fslview/slicecanvas.py b/fsl/fslview/slicecanvas.py
index 5071bbde76093f56c070841e1c165c4c148b3d6d..05e60d3570d3713554cb6d3483d0c77fbe2aa2af 100644
--- a/fsl/fslview/slicecanvas.py
+++ b/fsl/fslview/slicecanvas.py
@@ -120,17 +120,20 @@ class GLImageData(object):
yidxs = np.arange(self.ydim, dtype=np.float32)
yidxs, xidxs = np.meshgrid(yidxs, xidxs, indexing='ij')
- # And put them into a single array (the image.voxToWorld
- # method needs xyz coordinates, hence the N*3 shape here)
- positionData = np.zeros((self.xdim * self.ydim, 3), dtype=np.float32)
- positionData[:, xax] = xidxs.ravel(order='C')
- positionData[:, yax] = yidxs.ravel(order='C')
+ # And put them into a single array
+ positionData = np.vstack((
+ xidxs.ravel(order='C'),
+ yidxs.ravel(order='C'))).transpose()
# Then we transform them from voxel
- # coordinates to world coordinates
- positionData = image.voxToWorld(positionData)[:, (xax, yax)]
-
- # GL buffers for the geometry and position data
+ # coordinates to world coordinates,
+ # making sure that they are of type
+ # float32
+ positionData = image.voxToWorld(positionData, axes=(xax, yax))
+ positionData = np.array(positionData, dtype=np.float32)
+
+ # Define GL buffers for the geometry and position
+ # data containing the data we just created above
geomData = geomData .ravel(order='C')
positionData = positionData.ravel(order='C')
geomBuffer = vbo.VBO(geomData, gl.GL_STATIC_DRAW)
@@ -461,6 +464,13 @@ class SliceCanvas(wxgl.GLCanvas):
self._ypos = None
self._zpos = None
+ self.xmin = 0
+ self.ymin = 0
+ self.zmin = 0
+ self.xmax = 1
+ self.ymax = 1
+ self.zmax = 1
+
# This flag is set by the _initGLData method
# when it has finished initialising the OpenGL
# shaders
diff --git a/fsl/tools/bet.py b/fsl/tools/bet.py
index 39dc18f89960d823f14b62693c6228c08a501cd2..849379a63f809760b2ec325b0bf83e7a058f84d3 100644
--- a/fsl/tools/bet.py
+++ b/fsl/tools/bet.py
@@ -140,7 +140,7 @@ class Options(props.HasProperties):
cmd.append('-r')
cmd.append('{}'.format(self.headRadius))
- if all((self.xCoordinate > 0.0,
+ if any((self.xCoordinate > 0.0,
self.yCoordinate > 0.0,
self.zCoordinate > 0.0)):
cmd.append('-c')
@@ -193,40 +193,11 @@ def selectHeadCentre(opts, button):
image = fslimage.Image(opts.inputImage)
imageList = fslimage.ImageList([image])
parent = button.GetTopLevelParent()
- frame = orthopanel.OrthoFrame(parent, imageList, opts.inputImage)
+ frame = orthopanel.OrthoDialog(parent, imageList, opts.inputImage)
panel = frame.panel
- voxCoords = [opts.xCoordinate, opts.yCoordinate, opts.zCoordinate]
- worldCoords = image.voxToWorld([voxCoords])[0]
-
- panel.setLocation(*worldCoords)
-
# Whenever the x/y/z coordinates change on
- # the Options object,update the orthopanel
- # location
- def updateViewX(val, *a): panel.setXLocation(image.voxToWorld(val, axes=0))
- def updateViewY(val, *a): panel.setYLocation(image.voxToWorld(val, axes=1))
- def updateViewZ(val, *a): panel.setZLocation(image.voxToWorld(val, axes=2))
-
- optListeners = (
- ('xCoordinate', 'updateViewX_{}'.format(id(panel)), updateViewX),
- ('yCoordinate', 'updateViewY_{}'.format(id(panel)), updateViewY),
- ('zCoordinate', 'updateViewZ_{}'.format(id(panel)), updateViewZ))
-
- for listener in optListeners:
- opts.addListener(*listener)
-
- def rmListeners(ev):
- for listener in optListeners:
- prop = listener[0]
- name = listener[1]
- opts.removeListener(prop, name)
-
- # Remove the listeners when the dialog is closed
- frame.Bind(wx.EVT_WINDOW_DESTROY, rmListeners)
-
- # And whenever the x/y/z coordinates change
- # on the dialog, update the option values.
+ # the ortho panel, update the option values.
def updateOpts(ev):
x = image.worldToVox(ev.x, axes=0)
y = image.worldToVox(ev.y, axes=1)
@@ -247,10 +218,18 @@ def selectHeadCentre(opts, button):
panel.Bind(orthopanel.EVT_LOCATION_EVENT, updateOpts)
+ # Set the initial location on the orthopanel.
+ # TODO this ain't working, as it needs to be
+ # done after the frame has been displayed, i.e
+ # via wx.CallAfter or similar.
+ voxCoords = [opts.xCoordinate, opts.yCoordinate, opts.zCoordinate]
+ worldCoords = image.voxToWorld([voxCoords])[0]
+ panel.setLocation(*worldCoords)
+
# Position the dialog by the button that was clicked
pos = button.GetScreenPosition()
frame.SetPosition(pos)
- frame.Show()
+ frame.ShowModal()
betView = props.NotebookGroup((
@@ -297,10 +276,15 @@ def runBet(parent, opts):
if exitCode != 0: return
- image = nb.load(imagefile.addExt(opts.outputImage))
- frame = orthopanel.OrthoFrame(window,
- image.get_data(),
- title=opts.outputImage)
+ inImage = fslimage.Image(opts.inputImage)
+ outImage = fslimage.Image(opts.outputImage)
+ imageList = fslimage.ImageList([inImage, outImage])
+
+ outImage.display.cmap = 'Reds'
+ outImage.display.displayMin = 1
+ outImage.display.rangeClip = True
+
+ frame = orthopanel.OrthoFrame(parent, imageList, opts.outputImage)
frame.Show()
runwindow.checkAndRun('BET', opts, parent, Options.genBetCmd,
diff --git a/fsl/tools/fslview.py b/fsl/tools/fslview.py
index c5b9cd167511525f5e7da6ca8bae2fe390456ff2..11fd296ba8fc03d1bed1dbd6e1b0901a4ec79e41 100644
--- a/fsl/tools/fslview.py
+++ b/fsl/tools/fslview.py
@@ -30,6 +30,7 @@ class FslViewPanel(wx.Panel):
self.sizer.Add(self.listPanel, flag=wx.EXPAND)
self.Layout()
+ self.Fit()
def fslviewArguments(parser):