From a1698720c40dccd48f6b1b8300248980892faa9c Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Fri, 13 Feb 2015 14:31:15 +0000
Subject: [PATCH] Atlas panel is slightly functional. User can choose which
atlases to display information for, and can show/hide label masks for
individual regions
Fixes to GLVolume/GLMask colour map creation in situations where the
image data only has a single value.
---
fsl/data/atlases.py | 53 +++++--
fsl/data/image.py | 26 +++-
fsl/data/strings.py | 5 +-
fsl/fslview/controls/atlaspanel.py | 200 ++++++++++++++++++++++---
fsl/fslview/displaycontext/maskopts.py | 2 +-
fsl/fslview/gl/glmask.py | 13 +-
fsl/fslview/gl/glvolume.py | 5 +-
fsl/fslview/layouts.py | 1 +
fsl/fslview/views/canvaspanel.py | 13 ++
9 files changed, 267 insertions(+), 51 deletions(-)
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index b03012ed7..9a4287f80 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -10,6 +10,8 @@
Instances of the :class:`Atlas` class is a
+MNI152
+
<atlas>
<header>
@@ -75,7 +77,18 @@ def listAtlases():
atlasFiles = glob.glob(op.join(ATLAS_DIR, '*.xml'))
atlasDescs = map(AtlasDescription, atlasFiles)
- return {d.key: d for d in atlasDescs}
+ return {d.atlasID: d for d in atlasDescs}
+
+
+def loadAtlas(atlasDesc, loadSummary=False):
+
+ if loadSummary or atlasDesc.atlasType == 'label':
+ return LabelAtlas(atlasDesc)
+
+ if atlasDesc.atlasType == 'probabilistic':
+ return ProbabilisticAtlas(atlasDesc)
+ else:
+ raise ValueError('Unknown atlas type: {}'.format(atlasDesc.atlasType))
class AtlasDescription(object):
@@ -92,9 +105,13 @@ class AtlasDescription(object):
header = root.find('header')
data = root.find('data')
- self.key = op.splitext(op.basename(filename))[0]
+ self.atlasID = op.splitext(op.basename(filename))[0]
self.name = header.find('name').text
- self.atlasType = header.find('type').text
+ self.atlasType = header.find('type').text.lower()
+
+ # Spelling error in some of the atlas.xml files.
+ if self.atlasType == 'probabalistic':
+ self.atlasType = 'probabilistic'
images = header.findall('images')
self.images = []
@@ -141,11 +158,12 @@ class AtlasDescription(object):
# Load the appropriate transformation matrix
# and transform all those voxel coordinates
xform = fslimage.Image(self.images[0], loadData=False).voxToWorldMat
- coords = transform.transform(coords, xform)
+ coords = transform.transform(coords, xform.T)
# Update the coordinates
# in our label objects
for i, label in enumerate(self.labels):
+
label.x, label.y, label.z = coords[i]
@@ -164,34 +182,39 @@ class Atlas(fslimage.Image):
if imgRes < minImageRes:
minImageRes = imgRes
imageIdx = i
-
+
if isLabel: imageFile = atlasDesc.summaryImages[imageIdx]
else: imageFile = atlasDesc.images[ imageIdx]
fslimage.Image.__init__(self, imageFile)
+ self.desc = atlasDesc
+
-class LabelAtlas(fslimage.Image):
+class LabelAtlas(Atlas):
def __init__(self, atlasDesc):
Atlas.__init__(self, atlasDesc, isLabel=True)
- def label(self, voxelLoc):
+ def label(self, worldLoc):
+
+ voxelLoc = transform.transform([worldLoc], self.worldToVoxMat.T)[0]
+
val = self.data[voxelLoc[0], voxelLoc[1], voxelLoc[2]]
- if self.atlasDesc.atlasType == 'Label':
- return self.atlasDesc.label[val]
+ if self.desc.atlasType == 'label':
+ return val
- elif self.atlasDesc.atlasType == 'Probabilistic':
- return self.atlasDesc.label[val - 1]
+ elif self.desc.atlasType == 'probabilistic':
+ return val - 1
-class ProbabilisticAtlas(fslimage.Image):
+class ProbabilisticAtlas(Atlas):
def __init__(self, atlasDesc):
Atlas.__init__(self, atlasDesc, isLabel=False)
- def proportions(self, voxelLoc):
- props = self.data[voxelLoc[0], voxelLoc[1], voxelLoc[2], :]
- return zip(self.atlasDesc.labels, props)
+ def proportions(self, worldLoc):
+ voxelLoc = transform.transform([worldLoc], self.worldToVoxMat.T)[0]
+ return self.data[voxelLoc[0], voxelLoc[1], voxelLoc[2], :]
diff --git a/fsl/data/image.py b/fsl/data/image.py
index f5c8d04c6..5a7b68a08 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -252,7 +252,6 @@ class Image(props.HasProperties):
def getXFormCode(self):
"""This method returns the code contained in the NIFTI1 header,
indicating the space to which the (transformed) image is oriented.
-
"""
sform_code = self.nibImage.get_header()['sform_code']
@@ -272,13 +271,13 @@ class Image(props.HasProperties):
This method returns one of the following values, indicating the
direction in which coordinates along the specified axis increase:
- - :attr:`~fsl.data.image.ORIENT_L2R`: Left to right
- - :attr:`~fsl.data.image.ORIENT_R2L`: Right to left
- - :attr:`~fsl.data.image.ORIENT_A2P`: Anterior to posterior
- - :attr:`~fsl.data.image.ORIENT_P2A`: Posterior to anterior
- - :attr:`~fsl.data.image.ORIENT_I2S`: Inferior to superior
- - :attr:`~fsl.data.image.ORIENT_S2I`: Superior to inferior
- - :attr:`~fsl.data.image.ORIENT_UNKNOWN`: Orientation is unknown
+ - :attr:`~fsl.data.constants.ORIENT_L2R`: Left to right
+ - :attr:`~fsl.data.constants.ORIENT_R2L`: Right to left
+ - :attr:`~fsl.data.constants.ORIENT_A2P`: Anterior to posterior
+ - :attr:`~fsl.data.constants.ORIENT_P2A`: Posterior to anterior
+ - :attr:`~fsl.data.constants.ORIENT_I2S`: Inferior to superior
+ - :attr:`~fsl.data.constants.ORIENT_S2I`: Superior to inferior
+ - :attr:`~fsl.data.constants.ORIENT_UNKNOWN`: Orientation is unknown
The returned value is dictated by the XForm code contained in the
image file header (see the :meth:`getXFormCode` method). Basically,
@@ -385,6 +384,16 @@ class ImageList(props.HasProperties):
return iio.addImages(self, fromDir, addToEnd)
+ def find(self, name):
+ """Returns the first image with the given name, or ``None`` if
+ there is no image with said name.
+ """
+ for image in self.images:
+ if image.name == name:
+ return image
+ return None
+
+
# Wrappers around the images list property, allowing this
# ImageList object to be used as if it is actually a list.
def __len__( self): return self.images.__len__()
@@ -400,6 +409,7 @@ class ImageList(props.HasProperties):
def extend( self, iterable): return self.images.extend(iterable)
def pop( self, index=-1): return self.images.pop(index)
def move( self, from_, to): return self.images.move(from_, to)
+ def remove( self, item): return self.images.remove(item)
def insert( self, index, item): return self.images.insert(index,
item)
def insertAll( self, index, items): return self.images.insertAll(index,
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index 25ca89ef9..13044da23 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -29,7 +29,9 @@ messages = TypeDict({
'actions.loadcolourmap.invalidname' : 'Please use only letters, '
'numbers, and underscores.',
'actions.loadcolourmap.installerror' : 'An error occurred while '
- 'installing the colour map',
+ 'installing the colour map',
+
+ 'atlaspanel.unknownLocation' : 'Unknown location'
})
@@ -59,6 +61,7 @@ actions = TypeDict({
'CanvasPanel.toggleImageList' : 'Show/hide image list',
'CanvasPanel.toggleDisplayProperties' : 'Show/hide display properties',
'CanvasPanel.toggleLocationPanel' : 'Show/hide location panel',
+ 'CanvasPanel.toggleAtlasPanel' : 'Show/hide atlas panel',
'CanvasPanel.toggleCanvasProperties' : 'Show/hide canvas properties',
diff --git a/fsl/fslview/controls/atlaspanel.py b/fsl/fslview/controls/atlaspanel.py
index e5e5dc4ea..0dcaf6e72 100644
--- a/fsl/fslview/controls/atlaspanel.py
+++ b/fsl/fslview/controls/atlaspanel.py
@@ -7,15 +7,18 @@
import logging
-import wx
+import wx
+import wx.html as wxhtml
+import numpy as np
import pwidgets.elistbox as elistbox
import pwidgets.notebook as notebook
import fsl.utils.transform as transform
+import fsl.data.image as fslimage
import fsl.data.atlases as atlases
import fsl.data.strings as strings
-import fsl.fslview.widgets.swappanel as swappanel
+import fsl.data.constants as constants
import fsl.fslview.panel as fslpanel
@@ -24,25 +27,29 @@ log = logging.getLogger(__name__)
class AtlasListWidget(wx.Panel):
- def __init__(self, parent, atlasDesc, imageList, displayCtx, listBox):
+ def __init__(self, parent, atlasDesc, atlasPanel):
wx.Panel.__init__(self, parent)
- self.atlasDesc = atlasDesc
-
- self.enableBox = wx.CheckBox(self)
+ self.atlasDesc = atlasDesc
+ self.atlasPanel = atlasPanel
+ self.enableBox = wx.CheckBox(self)
self.sizer = wx.BoxSizer(wx.HORIZONTAL)
self.sizer.Add(self.enableBox, flag=wx.EXPAND)
+ self.enableBox.Bind(wx.EVT_CHECKBOX, self.onEnable)
-class AtlasPanel(fslpanel.FSLViewPanel):
+ def onEnable(self, ev):
+
+ if self.enableBox.GetValue():
+ self.atlasPanel.enableAtlasInfo(self.atlasDesc.atlasID)
+ else:
+ self.atlasPanel.disableAtlasInfo(self.atlasDesc.atlasID)
+
- # actions
- def addSummaryOverlay( self): pass
- def addProbabilisticOverlay(self): pass
- def addLabelOverlay( self): pass
+class AtlasPanel(fslpanel.FSLViewPanel):
def __init__(self, parent, imageList, displayCtx):
@@ -58,13 +65,12 @@ class AtlasPanel(fslpanel.FSLViewPanel):
# Info panel, containing atlas-based regional
# proportions/labels for the current location
- self.infoPanel = wx.TextCtrl(self.notebook, style=(wx.TE_MULTILINE |
- wx.TE_READONLY))
+ self.infoPanel = wxhtml.HtmlWindow(self.notebook)
# Atlas list, containing a list of atlases
# that the user can choose from
self.atlasList = elistbox.EditableListBox(
- self.atlasListPanel,
+ self.notebook,
style=(elistbox.ELB_NO_ADD |
elistbox.ELB_NO_REMOVE |
elistbox.ELB_NO_MOVE))
@@ -73,9 +79,163 @@ class AtlasPanel(fslpanel.FSLViewPanel):
# allowing the user to add/remove overlays
self.overlayPanel = wx.Panel(self.notebook)
- self.notebook.Add(self.infoPanel,
- strings.labels['AtlasPanel.infoPanel'])
- self.notebook.Add(self.atlasListPanel,
- strings.labels['AtlasPanel.atlasListPanel'])
- self.notebook.Add(self.overlayPanel,
- strings.labels['AtlasPanel.overlayPanel'])
+ self.notebook.AddPage(self.infoPanel,
+ strings.labels['AtlasPanel.infoPanel'])
+ self.notebook.AddPage(self.atlasList,
+ strings.labels['AtlasPanel.atlasListPanel'])
+ self.notebook.AddPage(self.overlayPanel,
+ strings.labels['AtlasPanel.overlayPanel'])
+
+ # The info panel contains clickable links
+ # for the currently displayed regions -
+ # when a link is clicked, the location
+ # is centred at the corresponding region
+ self.infoPanel.Bind(wxhtml.EVT_HTML_LINK_CLICKED,
+ self._infoPanelLinkClicked)
+
+
+ # Set up the list of atlases to choose from
+ self.atlasDescs = atlases.listAtlases()
+ self.enabledAtlases = {}
+
+ listItems = sorted(self.atlasDescs.items(), key=lambda (a, d): d.name)
+
+ for i, (atlasID, desc) in enumerate(listItems):
+
+ self.atlasList.Append(desc.name, atlasID)
+ widget = AtlasListWidget(self.atlasList, desc, self)
+ self.atlasList.SetItemWidget(i, widget)
+
+ displayCtx.addListener('location', self._name, self._locationChanged)
+
+
+ def _infoPanelLinkClicked(self, ev):
+
+ atlasID, labelIndex = ev.GetLinkInfo().GetHref().split()
+ labelIndex = int(labelIndex)
+ atlas = self.enabledAtlases[atlasID]
+ label = atlas.desc.labels[labelIndex]
+
+ log.debug('{}/{} clicked'.format(atlasID, label.name))
+
+ if isinstance(atlas, atlases.ProbabilisticAtlas):
+ pass
+
+ elif isinstance(atlas, atlases.LabelAtlas):
+ self.toggleLabelOverlay(atlasID, labelIndex)
+
+
+
+ def enableAtlasInfo(self, atlasID):
+
+ desc = self.atlasDescs[atlasID]
+ atlasImage = atlases.loadAtlas(desc)
+
+ self.enabledAtlases[atlasID] = atlasImage
+
+ self._locationChanged()
+
+
+ def disableAtlasInfo(self, atlasID):
+
+ self.enabledAtlases.pop(atlasID, None)
+ self._locationChanged()
+
+
+ def toggleSummaryOverlay(self, atlasID):
+ pass
+
+
+ def toggleProbabilisticOverlay(self, atlasID, labelIndex):
+ pass
+
+
+ def toggleLabelOverlay(self, atlasID, labelIndex):
+
+ desc = self.atlasDescs[atlasID]
+ overlayName = '{}/{}'.format(atlasID, desc.labels[labelIndex].name)
+ overlay = self._imageList.find(overlayName)
+
+ if overlay is not None:
+ self._imageList.remove(overlay)
+
+ log.debug('Removing overlay {}'.format(overlayName))
+
+ else:
+ atlas = self.enabledAtlases.get(atlasID, None)
+ if atlas is None:
+ atlas = atlases.loadAtlas(self.atlasDescs[atlasID], True)
+
+ if desc.atlasType == 'probabilistic': labelVal = labelIndex + 1
+ elif desc.atlasType == 'label': labelVal = labelIndex
+
+ mask = np.zeros(atlas.shape, dtype=np.uint8)
+ mask[atlas.data == labelIndex] = labelVal
+
+ overlay = fslimage.Image(
+ mask,
+ atlas.voxToWorldMat,
+ name=overlayName)
+ overlay.imageType = 'mask'
+
+ log.debug('Adding overlay {}'.format(overlayName))
+
+ self._imageList.append(overlay)
+
+ display = self._displayCtx.getDisplayProperties(overlay)
+ display.getDisplayOpts().colour = np.random.random(3)
+
+
+
+
+
+ def _locationChanged(self, *a):
+ image = self._displayCtx.getSelectedImage()
+ display = self._displayCtx.getDisplayProperties(image)
+ loc = self._displayCtx.location
+ text = self.infoPanel
+
+ loc = transform.transform([loc], display.displayToWorldMat)[0]
+
+ if image.getXFormCode() != constants.NIFTI_XFORM_MNI_152:
+ text.SetPage(strings.messages['atlaspanel.unknownLocation'])
+ return
+
+ lines = []
+
+ labelTemplate = """{}
+ (<a href="{} {}">Show/Hide</a>)
+ """
+ probTemplate = """
+ {:0.2f}% {}
+ (<a href="{} {}">Show/Hide</a>)
+ """
+
+ for atlasID, atlas in self.enabledAtlases.items():
+
+ lines.append('<b>{}</b>'.format(atlas.desc.name))
+
+ if isinstance(atlas, atlases.ProbabilisticAtlas):
+ proportions = atlas.proportions(loc)
+
+ for label, prop in zip(atlas.desc.labels, proportions):
+ if prop == 0.0:
+ continue
+ lines.append(probTemplate.format(prop,
+ label.name,
+ atlasID,
+ label.index,
+ atlasID,
+ label.index))
+
+ elif isinstance(atlas, atlases.LabelAtlas):
+
+ labelVal = atlas.label(loc)
+ label = atlas.desc.labels[labelVal]
+ lines.append(labelTemplate.format(label.name,
+ atlasID,
+ label.index,
+ atlasID,
+ label.index))
+
+ text.SetPage('<br>'.join(lines))
diff --git a/fsl/fslview/displaycontext/maskopts.py b/fsl/fslview/displaycontext/maskopts.py
index daabf5076..864004543 100644
--- a/fsl/fslview/displaycontext/maskopts.py
+++ b/fsl/fslview/displaycontext/maskopts.py
@@ -45,5 +45,5 @@ class MaskOpts(fsldisplay.DisplayOpts):
self.threshold.setMin( 0, self.dataMin - 0.5 * dRangeLen)
self.threshold.setMax( 0, self.dataMax + 0.5 * dRangeLen)
- self.threshold.setRange(0, self.dataMin, self.dataMax)
+ self.threshold.setRange(0, 0.1, self.dataMax + 0.1)
self.setConstraint('threshold', 'minDistance', dMinDistance)
diff --git a/fsl/fslview/gl/glmask.py b/fsl/fslview/gl/glmask.py
index a2502b593..36231c7c0 100644
--- a/fsl/fslview/gl/glmask.py
+++ b/fsl/fslview/gl/glmask.py
@@ -52,7 +52,7 @@ class GLMask(glvolume.GLVolume):
self.setAxes(self.xax, self.yax)
def colourUpdate(*a):
- self.refreshColourTexture(self.colourResolution)
+ self.refreshColourTexture()
lnrName = '{}_{}'.format(type(self).__name__, id(self))
@@ -109,17 +109,20 @@ class GLMask(glvolume.GLVolume):
# or above the current display range will be mapped
# to texture coordinate values less than 0.0 or greater
# than 1.0 respectively.
+ if imax == imin: scale = 1
+ else: scale = imax - imin
+
cmapXform = np.identity(4, dtype=np.float32)
- cmapXform[0, 0] = 1.0 / (imax - imin)
+ cmapXform[0, 0] = 1.0 / scale
cmapXform[3, 0] = -imin * cmapXform[0, 0]
self.colourMapXform = cmapXform
if opts.invert:
- colourmap = np.tile([[0.0, 0.0, 0.0, 0.0]], (2, 1))
+ colourmap = np.tile([[0.0, 0.0, 0.0, 0.0]], (16, 1))
border = np.array(opts.colour, dtype=np.float32)
else:
- colourmap = np.tile([[opts.colour]], (2, 1))
+ colourmap = np.tile([[opts.colour]], (16, 1))
border = np.array([0.0, 0.0, 0.0, 0.0], dtype=np.float32)
colourmap = np.floor(colourmap * 255)
@@ -145,7 +148,7 @@ class GLMask(glvolume.GLVolume):
gl.glTexImage1D(gl.GL_TEXTURE_1D,
0,
gl.GL_RGBA8,
- 2,
+ 16,
0,
gl.GL_RGBA,
gl.GL_UNSIGNED_BYTE,
diff --git a/fsl/fslview/gl/glvolume.py b/fsl/fslview/gl/glvolume.py
index 2ae2f42cf..9cad22cc8 100644
--- a/fsl/fslview/gl/glvolume.py
+++ b/fsl/fslview/gl/glvolume.py
@@ -249,8 +249,11 @@ class GLVolume(globject.GLImageObject):
# or above the current display range will be mapped
# to texture coordinate values less than 0.0 or greater
# than 1.0 respectively.
+ if imax == imin: scale = 1
+ else: scale = imax - imin
+
cmapXform = np.identity(4, dtype=np.float32)
- cmapXform[0, 0] = 1.0 / (imax - imin)
+ cmapXform[0, 0] = 1.0 / scale
cmapXform[3, 0] = -imin * cmapXform[0, 0]
self.colourMapXform = cmapXform
diff --git a/fsl/fslview/layouts.py b/fsl/fslview/layouts.py
index c5caa7aaa..c11f70bb7 100644
--- a/fsl/fslview/layouts.py
+++ b/fsl/fslview/layouts.py
@@ -103,6 +103,7 @@ CanvasPanelActionLayout = props.HGroup(
actionButton('toggleImageList', CanvasPanel),
actionButton('toggleDisplayProperties', CanvasPanel),
actionButton('toggleLocationPanel', CanvasPanel),
+ actionButton('toggleAtlasPanel', CanvasPanel),
actionButton('toggleCanvasProperties', CanvasPanel)),
wrap=True,
showLabels=False)
diff --git a/fsl/fslview/views/canvaspanel.py b/fsl/fslview/views/canvaspanel.py
index ec7cd847e..10f103d39 100644
--- a/fsl/fslview/views/canvaspanel.py
+++ b/fsl/fslview/views/canvaspanel.py
@@ -30,6 +30,7 @@ import fsl.fslview.displaycontext as displayctx
import fsl.fslview.controls.imagelistpanel as imagelistpanel
import fsl.fslview.controls.imagedisplaypanel as imagedisplaypanel
import fsl.fslview.controls.locationpanel as locationpanel
+import fsl.fslview.controls.atlaspanel as atlaspanel
import fsl.fslview.widgets.togglepanel as togp
import colourbarpanel
@@ -183,6 +184,7 @@ class CanvasPanel(fslpanel.FSLViewPanel):
'screenshot' : self.screenshot,
'toggleColourBar' : self.toggleColourBar,
'toggleImageList' : self.toggleImageList,
+ 'toggleAtlasPanel' : self.toggleAtlasPanel,
'toggleDisplayProperties' : self.toggleDisplayProperties,
'toggleLocationPanel' : self.toggleLocationPanel,
'toggleCanvasProperties' : self.toggleCanvasProperties}
@@ -245,6 +247,9 @@ class CanvasPanel(fslpanel.FSLViewPanel):
self.__listLocContainer, imageList, displayCtx)
self.__locationPanel = locationpanel.LocationPanel(
+ self.__listLocContainer, imageList, displayCtx)
+
+ self.__atlasPanel = atlaspanel.AtlasPanel(
self.__listLocContainer, imageList, displayCtx)
self.__displayPropsPanel = imagedisplaypanel.ImageDisplayPanel(
@@ -259,6 +264,9 @@ class CanvasPanel(fslpanel.FSLViewPanel):
self.__listLocSizer.Add(self.__locationPanel,
flag=wx.EXPAND,
proportion=1)
+ self.__listLocSizer.Add(self.__atlasPanel,
+ flag=wx.EXPAND,
+ proportion=1)
self.__dispSetSizer = wx.BoxSizer(wx.HORIZONTAL)
self.__dispSetContainer.SetSizer(self.__dispSetSizer)
@@ -289,6 +297,7 @@ class CanvasPanel(fslpanel.FSLViewPanel):
self.__locationPanel .Show(False)
self.__canvasPropsPanel .Show(False)
self.__displayPropsPanel.Show(False)
+ self.__atlasPanel .Show(False)
# Use a different listener name so that subclasses
# can register on the same properties with self._name
@@ -398,6 +407,10 @@ class CanvasPanel(fslpanel.FSLViewPanel):
def toggleLocationPanel(self, *a):
self.__locationPanel.Show(not self.__locationPanel.IsShown())
self.__layout()
+
+ def toggleAtlasPanel(self, *a):
+ self.__atlasPanel.Show(not self.__atlasPanel.IsShown())
+ self.__layout()
def toggleDisplayProperties(self, *a):
self.__displayPropsPanel.Show(not self.__displayPropsPanel.IsShown())
--
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