diff --git a/fsl/data/melodicimage.py b/fsl/data/melodicimage.py
index f3b628810e332213a8ec3487a71773c983063b80..258e5663288956e718205404ddd67ce72bc71e28 100644
--- a/fsl/data/melodicimage.py
+++ b/fsl/data/melodicimage.py
@@ -79,9 +79,11 @@ class MelodicImage(fslimage.Image):
*args,
**kwargs)
- self.__meldir = dirname
- self.__melmix = melresults.getComponentTimeSeries( dirname)
- self.__melFTmix = melresults.getComponentPowerSpectra(dirname)
+ self.__meldir = dirname
+ self.__melmix = melresults.getComponentTimeSeries( dirname)
+ self.__melFTmix = melresults.getComponentPowerSpectra(dirname)
+ self.__melICClass = melresults.MelodicClassification(
+ self.numComponents())
# Automatically set the
# TR value if possible
@@ -92,6 +94,8 @@ class MelodicImage(fslimage.Image):
if dataImage.is4DImage():
self.tr = dataImage.pixdim[3]
+ # TODO load classifications if present
+
def getComponentTimeSeries(self, component):
"""Returns the time course for the specified (0-indexed) component. """
@@ -125,3 +129,7 @@ class MelodicImage(fslimage.Image):
:func:`.melodicresults.getDataFile` function.
"""
return melresults.getDataFile(self.__meldir)
+
+
+ def getICClassification(self):
+ return self.__melICClass
diff --git a/fsl/data/melodicresults.py b/fsl/data/melodicresults.py
index 105c1ae28aa31dbbbd7f6ae5064dc033aa007dce..85a538198513cd4a1a44841fc2d6eb0922335cac 100644
--- a/fsl/data/melodicresults.py
+++ b/fsl/data/melodicresults.py
@@ -179,3 +179,82 @@ def getComponentPowerSpectra(meldir):
"""
ftmixfile = getFTMixFile(meldir)
return np.loadtxt(ftmixfile)
+
+
+
+class MelodicClassification(object):
+ """
+ """
+
+ def __init__(self, ncomps):
+ """Create a ``MelodicClassification`` instance.
+ """
+
+ self.__ncomps = ncomps
+
+ self.__componentLabels = [[] for i in range(ncomps)]
+ self.__labelComponents = {}
+
+
+ def load(self, filename):
+ pass
+
+
+ def save(self, filename):
+ pass
+
+
+ def getLabels(self, component):
+ return list(self.__componentLabels[component])
+
+
+ def addLabel(self, component, label):
+
+ cmpLabels = self.__componentLabels[component]
+ labelCmps = self.__labelComponents.get(label, [])
+
+ if label in cmpLabels:
+ return
+
+ cmpLabels[component].append(label)
+ labelCmps[label] .append(component)
+
+ self.__componentLabels[component] = cmpLabels
+ self.__labelComponents[label] = labelCmps
+
+
+ def removeLabel(self, component, label):
+
+ if label not in self.__componentLabels[component]:
+ return
+
+ self.__componentLabels[component].remove(label)
+ self.__labelComponents[label] .remove(component)
+
+
+ def clearLabels(self, component):
+
+ labels = self.getLabels(component)
+
+ for l in labels:
+ self.removeLabel(component, l)
+
+
+ def getComponents(self, label):
+ return list(self.__labelComponents.get(label, []))
+
+
+ def addComponent(self, label, component):
+ self.addLabel(component, label)
+
+
+ def removeComponent(self, label, component):
+ self.removeLabel(component, label)
+
+
+ def clearComponents(self, label):
+
+ components = self.getComponents(label)
+
+ for c in components:
+ self.removeComponent(label, c)
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index 14621ff482b00e3cb434a23b05ff8195ba7a644c..3a761984607d6bc13514c56cbe9211fc7240c6a2 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -122,6 +122,9 @@ messages = TypeDict({
'OrthoEditProfile.displaySpaceChange' : 'Setting {} as the display '
'space reference image - this '
'is necessary for editing.',
+
+
+ 'MelodicClassificationPanel.disabled' : 'Choose a melodic image.',
})
@@ -173,6 +176,8 @@ titles = TypeDict({
'OverlayInfoPanel' : 'Overlay information',
'ShellPanel' : 'Python shell',
+ 'MelodicClassificationPanel' : 'Melodic IC classification',
+
'LookupTablePanel.loadLut' : 'Select a lookup table file',
'LookupTablePanel.labelExists' : 'Label already exists',
})
@@ -188,17 +193,18 @@ actions = TypeDict({
'FSLEyesFrame.closeViewPanel' : 'Close',
- 'CanvasPanel.screenshot' : 'Take screenshot',
- 'CanvasPanel.showCommandLineArgs' : 'Show command line for scene',
- 'CanvasPanel.toggleColourBar' : 'Colour bar',
- 'CanvasPanel.toggleOverlayList' : 'Overlay list',
- 'CanvasPanel.toggleDisplayProperties' : 'Overlay display properties',
- 'CanvasPanel.toggleLocationPanel' : 'Location panel',
- 'CanvasPanel.toggleAtlasPanel' : 'Atlas panel',
- 'CanvasPanel.toggleLookupTablePanel' : 'Lookup tables',
- 'CanvasPanel.toggleClusterPanel' : 'Cluster browser',
- 'CanvasPanel.toggleOverlayInfo' : 'Overlay information',
- 'CanvasPanel.toggleShell' : 'Python shell',
+ 'CanvasPanel.screenshot' : 'Take screenshot',
+ 'CanvasPanel.showCommandLineArgs' : 'Show command line for scene',
+ 'CanvasPanel.toggleColourBar' : 'Colour bar',
+ 'CanvasPanel.toggleOverlayList' : 'Overlay list',
+ 'CanvasPanel.toggleDisplayProperties' : 'Overlay display properties',
+ 'CanvasPanel.toggleLocationPanel' : 'Location panel',
+ 'CanvasPanel.toggleAtlasPanel' : 'Atlas panel',
+ 'CanvasPanel.toggleLookupTablePanel' : 'Lookup tables',
+ 'CanvasPanel.toggleClusterPanel' : 'Cluster browser',
+ 'CanvasPanel.toggleOverlayInfo' : 'Overlay information',
+ 'CanvasPanel.toggleClassificationPanel' : 'Melodic IC classification',
+ 'CanvasPanel.toggleShell' : 'Python shell',
'OrthoPanel.toggleOrthoToolBar' : 'View properties',
'OrthoPanel.toggleEditToolBar' : 'Edit toolbar',
diff --git a/fsl/fsleyes/controls/melodicclassificationpanel.py b/fsl/fsleyes/controls/melodicclassificationpanel.py
new file mode 100644
index 0000000000000000000000000000000000000000..861c96c44493cfa9c749f00ee21a2854165ccaf8
--- /dev/null
+++ b/fsl/fsleyes/controls/melodicclassificationpanel.py
@@ -0,0 +1,174 @@
+#!/usr/bin/env python
+#
+# melodicclassificationpanel.py - The MelodicClassificationPanel class.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""This module provides the :class:`MelodicClassificationPanel` class, a
+*FSLeyes control* panel which allows the user to classify the components
+of a :class:`.MelodicImage`.
+"""
+
+import wx
+
+
+import pwidgets.widgetgrid as widgetgrid
+import pwidgets.texttag as texttag
+import pwidgets.notebook as notebook
+
+import fsl.data.strings as strings
+import fsl.data.melodicimage as fslmelimage
+import fsl.fsleyes.panel as fslpanel
+
+
+class MelodicClassificationPanel(fslpanel.FSLEyesPanel):
+ """The ``MelodicClassificationPanel``
+ """
+
+ #
+ # Choose label colours
+ # Load/save from/to file
+ #
+ def __init__(self, parent, overlayList, displayCtx):
+ """Create a ``MelodicClassificationPanel``.
+
+ :arg parent: The :mod:`wx` parent object.
+
+ :arg overlayList: The :class:`.OverlayList`.
+
+ :arg displayCtx: The :class:`.DisplayContext` instance.
+ """
+ fslpanel.FSLEyesPanel.__init__(self, parent, overlayList, displayCtx)
+
+ self.__disabledText = wx.StaticText(
+ self,
+ style=(wx.ALIGN_CENTRE_HORIZONTAL |
+ wx.ALIGN_CENTRE_VERTICAL))
+
+ self.__notebook = notebook.Notebook(self)
+ self.__componentGrid = ComponentGrid( self.__notebook)
+ self.__labelGrid = LabelGrid( self.__notebook)
+
+ self.__notebook.AddPage(self.__componentGrid, 'Components')
+ self.__notebook.AddPage(self.__labelGrid, 'Labels')
+
+ self.__mainSizer = wx.BoxSizer(wx.HORIZONTAL)
+ self.__mainSizer.Add(self.__notebook, flag=wx.EXPAND, proportion=1)
+
+ # TODO Things which you don't want shown when
+ # a melodic image is not selected should
+ # be added to __mainSizer. Things which
+ # you always want displayed should be
+ # added to __sizer (but need to be laid
+ # out w.r.t. __disabledText/__mainSizer)
+
+ self.__sizer = wx.BoxSizer(wx.HORIZONTAL)
+ self.__sizer.Add(self.__disabledText, flag=wx.EXPAND, proportion=1)
+ self.__sizer.Add(self.__mainSizer, flag=wx.EXPAND, proportion=1)
+
+ self.SetSizer(self.__sizer)
+
+ overlayList.addListener('overlays',
+ self._name,
+ self.__selectedOverlayChanged)
+ displayCtx .addListener('selectedOverlay',
+ self._name,
+ self.__selectedOverlayChanged)
+
+ self.__overlay = None
+ self.__selectedOverlayChanged()
+
+
+ def destroy(self):
+ """
+ """
+ self._displayCtx .removeListener('selectedOverlay', self._name)
+ self._overlayList.removeListener('overlays', self._name)
+ fslpanel.FSLEyesPanel.destroy(self)
+
+
+ def __enable(self, enable=True, message=''):
+ """
+ """
+
+ self.__disabledText.SetLabel(message)
+
+ self.__sizer.Show(self.__disabledText, not enable)
+ self.__sizer.Show(self.__mainSizer, enable)
+
+ self.Layout()
+
+
+ def __selectedOverlayChanged(self, *a):
+
+ overlay = self._displayCtx.getSelectedOverlay()
+
+ if (overlay is None) or \
+ not isinstance(overlay, fslmelimage.MelodicImage):
+ self.__enable(False, strings.messages[self, 'disabled'])
+ return
+
+ self.__overlay = overlay
+
+ self.__componentGrid.setOverlay(overlay)
+ self.__labelGrid .setOverlay(overlay)
+
+ self.__enable(True)
+
+
+class ComponentGrid(wx.Panel):
+
+ def __init__(self, parent):
+ wx.Panel.__init__(self, parent)
+
+ self.__grid = widgetgrid.WidgetGrid(self)
+ self.__sizer = wx.BoxSizer(wx.HORIZONTAL)
+
+ self.__grid.ShowRowLabels(False)
+ self.__grid.ShowColLabels(True)
+
+ self.__sizer.Add(self.__grid, flag=wx.EXPAND, proportion=1)
+
+ self.SetSizer(self.__sizer)
+
+
+ def setOverlay(self, overlay):
+
+ numComps = overlay.numComponents()
+
+ self.__grid.ClearGrid()
+ self.__grid.SetGridSize(numComps, 2, growCols=[1])
+
+ self.__grid.SetColLabel(0, 'Component #')
+ self.__grid.SetColLabel(1, 'Labels')
+
+ for i in range(numComps):
+
+ tags = texttag.TextTagPanel(self.__grid,
+ style=(texttag.TTP_ALLOW_NEW_TAGS |
+ texttag.TTP_ADD_NEW_TAGS |
+ texttag.TTP_NO_DUPLICATES))
+
+ self.__grid.SetText( i, 0, str(i))
+ self.__grid.SetWidget(i, 1, tags)
+
+ self.Layout()
+
+
+
+class LabelGrid(wx.Panel):
+
+ def __init__(self, parent):
+
+ wx.Panel.__init__(self, parent)
+
+ self.__grid = widgetgrid.WidgetGrid(self)
+ self.__sizer = wx.BoxSizer(wx.HORIZONTAL)
+
+ self.__sizer.Add(self.__grid, flag=wx.EXPAND, proportion=1)
+
+ self.SetSizer(self.__sizer)
+
+
+ def setOverlay(self, overlay):
+ pass
diff --git a/fsl/fsleyes/views/canvaspanel.py b/fsl/fsleyes/views/canvaspanel.py
index 4ca4ad4068d0bdd2d7ecd5ff81c84f746edc768e..3822151e78eae02c5f4eae506c3f5640583641dd 100644
--- a/fsl/fsleyes/views/canvaspanel.py
+++ b/fsl/fsleyes/views/canvaspanel.py
@@ -21,23 +21,23 @@ import matplotlib.image as mplimg
import props
-import fsl.fsleyes.fsleyes_parseargs as fsleyes_parseargs
-import fsl.utils.dialog as fsldlg
-import fsl.utils.settings as fslsettings
-import fsl.data.image as fslimage
-import fsl.data.strings as strings
-import fsl.fsleyes.displaycontext as displayctx
-import fsl.fsleyes.controls.overlaylistpanel as overlaylistpanel
-import fsl.fsleyes.controls.overlayinfopanel as overlayinfopanel
-import fsl.fsleyes.controls.atlaspanel as atlaspanel
-import fsl.fsleyes.controls.overlaydisplaytoolbar as overlaydisplaytoolbar
-import fsl.fsleyes.controls.locationpanel as locationpanel
-import fsl.fsleyes.controls.clusterpanel as clusterpanel
-import fsl.fsleyes.controls.lookuptablepanel as lookuptablepanel
-import fsl.fsleyes.controls.shellpanel as shellpanel
-
-import colourbarpanel
-import viewpanel
+import fsl.fsleyes.fsleyes_parseargs as fsleyes_parseargs
+import fsl.utils.dialog as fsldlg
+import fsl.utils.settings as fslsettings
+import fsl.data.image as fslimage
+import fsl.data.strings as strings
+import fsl.fsleyes.displaycontext as displayctx
+import fsl.fsleyes.controls.overlaylistpanel as overlaylistpanel
+import fsl.fsleyes.controls.overlayinfopanel as overlayinfopanel
+import fsl.fsleyes.controls.atlaspanel as atlaspanel
+import fsl.fsleyes.controls.overlaydisplaytoolbar as overlaydisplaytoolbar
+import fsl.fsleyes.controls.locationpanel as locationpanel
+import fsl.fsleyes.controls.clusterpanel as clusterpanel
+import fsl.fsleyes.controls.lookuptablepanel as lookuptablepanel
+import fsl.fsleyes.controls.melodicclassificationpanel as melclasspanel
+import fsl.fsleyes.controls.shellpanel as shellpanel
+import colourbarpanel
+import viewpanel
log = logging.getLogger(__name__)
@@ -84,16 +84,18 @@ class CanvasPanel(viewpanel.ViewPanel):
:mod:`control <.controls>` panels:
- =========================== ===========================================
- ``toggleOverlayList`` Toggles an :class:`.OverlayListPanel`.
- ``toggleOverlayInfo`` Toggles an :class:`.OverlayInfoPanel`.
- ``toggleAtlasPanel`` Toggles an :class:`.AtlasPanel`.
- ``toggleDisplayProperties`` Toggles an :class:`.OverlayDisplayToolBar`.
- ``toggleLocationPanel`` Toggles a :class:`.LocationPanel`.
- ``toggleClusterPanel`` Toggles a :class:`.ClusterPanel`.
- ``toggleLookupTablePanel`` Toggles a :class:`.LookupTablePanel`.
- ``toggleShell`` Toggles a :class:`.ShellPanel`.
- =========================== ===========================================
+ ============================== ===========================================
+ ``toggleOverlayList`` Toggles an :class:`.OverlayListPanel`.
+ ``toggleOverlayInfo`` Toggles an :class:`.OverlayInfoPanel`.
+ ``toggleAtlasPanel`` Toggles an :class:`.AtlasPanel`.
+ ``toggleDisplayProperties`` Toggles an :class:`.OverlayDisplayToolBar`.
+ ``toggleLocationPanel`` Toggles a :class:`.LocationPanel`.
+ ``toggleClusterPanel`` Toggles a :class:`.ClusterPanel`.
+ ``toggleLookupTablePanel`` Toggles a :class:`.LookupTablePanel`.
+ ``toggleClassificationPanel`` Toggles a
+ :class:`.MelodicClassificationPanel`.
+ ``toggleShell`` Toggles a :class:`.ShellPanel`.
+ ============================== ===========================================
A couple of other actions are also provided, with the same names as their
@@ -246,29 +248,32 @@ class CanvasPanel(viewpanel.ViewPanel):
extraActions = {}
actionz = [
- ('screenshot', self.screenshot),
- ('showCommandLineArgs', self.showCommandLineArgs),
- ('toggleOverlayList', lambda *a: self.togglePanel(
+ ('screenshot', self.screenshot),
+ ('showCommandLineArgs', self.showCommandLineArgs),
+ ('toggleOverlayList', lambda *a: self.togglePanel(
overlaylistpanel.OverlayListPanel,
location=wx.BOTTOM)),
- ('toggleOverlayInfo', lambda *a: self.togglePanel(
+ ('toggleOverlayInfo', lambda *a: self.togglePanel(
overlayinfopanel.OverlayInfoPanel,
- location=wx.RIGHT)),
- ('toggleAtlasPanel', lambda *a: self.togglePanel(
+ location=wx.LEFT)),
+ ('toggleAtlasPanel', lambda *a: self.togglePanel(
atlaspanel.AtlasPanel,
location=wx.BOTTOM)),
- ('toggleDisplayProperties', lambda *a: self.togglePanel(
+ ('toggleDisplayProperties', lambda *a: self.togglePanel(
overlaydisplaytoolbar.OverlayDisplayToolBar,
viewPanel=self)),
- ('toggleLocationPanel', lambda *a: self.togglePanel(
+ ('toggleLocationPanel', lambda *a: self.togglePanel(
locationpanel.LocationPanel,
location=wx.BOTTOM)),
- ('toggleClusterPanel', lambda *a: self.togglePanel(
+ ('toggleClusterPanel', lambda *a: self.togglePanel(
clusterpanel.ClusterPanel,
location=wx.TOP)),
- ('toggleLookupTablePanel', lambda *a: self.togglePanel(
+ ('toggleLookupTablePanel', lambda *a: self.togglePanel(
lookuptablepanel.LookupTablePanel,
- location=wx.TOP))]
+ location=wx.TOP)),
+ ('toggleClassificationPanel', lambda *a: self.togglePanel(
+ melclasspanel.MelodicClassificationPanel,
+ location=wx.RIGHT))]
actionz += extraActions.items()