From 731437527f9ef0e43c96e4ffdfa231cc792e2bcb Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Tue, 27 Oct 2015 09:00:31 +0000
Subject: [PATCH] Basic (buggy) support for MelodicImage overlays in
TimeSeriesPanel. Things are going to change.
---
fsl/data/melodicimage.py | 40 ++++++-
fsl/data/melodicresults.py | 87 ++++++++++++--
fsl/fsleyes/controls/timeserieslistpanel.py | 25 ++--
fsl/fsleyes/overlay.py | 20 +++-
fsl/fsleyes/views/plotpanel.py | 3 +-
fsl/fsleyes/views/timeseriespanel.py | 122 +++++++++++---------
6 files changed, 215 insertions(+), 82 deletions(-)
diff --git a/fsl/data/melodicimage.py b/fsl/data/melodicimage.py
index d0c4b5f8a..6bdc25480 100644
--- a/fsl/data/melodicimage.py
+++ b/fsl/data/melodicimage.py
@@ -8,6 +8,7 @@
"""This module provides the :class:`MelodicImage` class, an :class:`.Image`
sub-class which encapsulates data from a MELODIC analysis.
"""
+import os.path as op
import image as fslimage
import melodicresults as melresults
@@ -17,7 +18,42 @@ class MelodicImage(fslimage.Image):
"""
"""
- def __init__(self, path):
+ def __init__(self, image, *args, **kwargs):
"""
"""
- pass
+
+
+ if op.isdir(image):
+
+ dirname = image
+ filename = 'melodic_IC'
+
+
+ else:
+ dirname = op.dirname( image)
+ filename = op.basename(image)
+
+ dirname = dirname.rstrip(op.sep)
+
+ if not melresults.isMelodicDir(dirname):
+ raise ValueError('{} does not appear to be a '
+ 'MELODIC directory'.format(dirname))
+
+ if not filename.startswith('melodic_IC'):
+ raise ValueError('{} does not appear to be a MELODIC '
+ 'component file'.format(filename))
+
+ fslimage.Image.__init__(self,
+ op.join(dirname, filename),
+ *args,
+ **kwargs)
+
+ self.__melmix = melresults.getComponentTimeSeries(dirname)
+
+
+ def getComponentTimeSeries(self, component):
+ return self.__melmix[:, component]
+
+
+ def numComponents(self):
+ return self.shape[3]
diff --git a/fsl/data/melodicresults.py b/fsl/data/melodicresults.py
index 492a76e62..d05a25ab3 100644
--- a/fsl/data/melodicresults.py
+++ b/fsl/data/melodicresults.py
@@ -13,21 +13,90 @@ following functions are provided:
.. autosummary::
nosignatures:
- isMELODICDir
- getMELODICDir
-
+ isMelodicDir
+ getMelodicDir
getICFile
-
getNumComponents
getComponentTimeSeries
"""
-def isMELODICDir(path):
+import os
+import os.path as op
+import numpy as np
+
+import fsl.data.image as fslimage
+
+
+def isMelodicDir(path):
+ """
+ """
+
+ # Must be named *.ica or *.gica
+ meldir = getMelodicDir(path)
+
+ if meldir is None:
+ return False
+
+ # Must contain an image file called melodic_IC
+ try:
+ fslimage.addExt(op.join(meldir, 'melodic_IC'), mustExist=True)
+ except ValueError:
+ return False
+
+ # Must contain a file called melodic_mix
+ if not op.exists(op.join(meldir, 'melodic_mix')):
+ return False
+
+ return True
+
+
+def getMelodicDir(path):
+ """
+ """
+
+ # TODO This code is identical to featresults.getFEATDir.
+ # Can you generalise it and put it somewhere in fsl.utils?
+
+ sufs = ['.ica', '.gica']
+ idxs = [(path.rfind(s), s) for s in sufs]
+ idx, suf = max(idxs, key=lambda (i, s): i)
+
+ if idx == -1:
+ return None
+
+ idx += len(suf)
+ path = path[:idx]
+
+ if path.endswith(suf) or path.endswith('{}{}'.format(suf, op.sep)):
+ return path
+
+ return None
+
+
+def getICFile(meldir):
+ """
+ """
+ return fslimage.addExt(op.join(meldir, 'melodic_IC'))
+
+
+def getMixFile(meldir):
+ """
+ """
+ return op.join(meldir, 'melodic_mix')
+
+
+def getNumComponents(meldir):
+ """
+ """
+
+ icImg = fslimage.Image(getICFile(meldir), loadData=False)
+ return icImg.shape[3]
+
+
+def getComponentTimeSeries(meldir):
"""
"""
- # A MELODIC directory:
- # - Must be called *.ica
- # - Must contain melodic_IC.nii.gz
- # - Must contain melodic_mix
+ mixfile = getMixFile(meldir)
+ return np.loadtxt(mixfile)
diff --git a/fsl/fsleyes/controls/timeserieslistpanel.py b/fsl/fsleyes/controls/timeserieslistpanel.py
index 7d94536c8..a4da0a512 100644
--- a/fsl/fsleyes/controls/timeserieslistpanel.py
+++ b/fsl/fsleyes/controls/timeserieslistpanel.py
@@ -15,12 +15,12 @@ import copy
import wx
import numpy as np
-import props
-import pwidgets.elistbox as elistbox
-import fsl.fsleyes.panel as fslpanel
-import fsl.fsleyes.tooltips as fsltooltips
-import fsl.data.strings as strings
-import fsl.fsleyes.colourmaps as fslcm
+import props
+import pwidgets.elistbox as elistbox
+import fsl.fsleyes.panel as fslpanel
+import fsl.fsleyes.tooltips as fsltooltips
+import fsl.data.strings as strings
+import fsl.fsleyes.colourmaps as fslcm
class TimeSeriesListPanel(fslpanel.FSLEyesPanel):
@@ -114,12 +114,17 @@ class TimeSeriesListPanel(fslpanel.FSLEyesPanel):
"""Creates a label to use for the given :class:`.TimeSeries` instance.
"""
+ import fsl.fsleyes.views.timeseriespanel as tsp
+
display = self._displayCtx.getDisplay(ts.overlay)
- return '{} [{} {} {}]'.format(display.name,
- ts.coords[0],
- ts.coords[1],
- ts.coords[2])
+ if isinstance(ts, tsp.MelodicTimeSeries):
+ return '{} [component {}]'.format(display.name, ts.coords)
+ else:
+ return '{} [{} {} {}]'.format(display.name,
+ ts.coords[0],
+ ts.coords[1],
+ ts.coords[2])
def __makeFEATModelTSLabel(self, parentTs, modelTs):
diff --git a/fsl/fsleyes/overlay.py b/fsl/fsleyes/overlay.py
index c6d6fbf24..2ee9a540e 100644
--- a/fsl/fsleyes/overlay.py
+++ b/fsl/fsleyes/overlay.py
@@ -191,19 +191,24 @@ def guessDataSourceType(filename):
is unrecognised, the first tuple value will be ``None``.
"""
- import fsl.data.image as fslimage
- import fsl.data.model as fslmodel
- import fsl.data.featimage as fslfeatimage
- import fsl.data.featresults as featresults
+ import fsl.data.image as fslimage
+ import fsl.data.model as fslmodel
+ import fsl.data.featimage as fslfeatimage
+ import fsl.data.melodicimage as fslmelimage
+ import fsl.data.melodicresults as melresults
+ import fsl.data.featresults as featresults
+
+ filename = op.abspath(filename)
if filename.endswith('.vtk'):
return fslmodel.Model, filename
else:
-
if op.isdir(filename):
if featresults.isFEATDir(filename):
return fslfeatimage.FEATImage, filename
+ elif melresults.isMelodicDir(filename):
+ return fslmelimage.MelodicImage, filename
else:
filename = fslimage.addExt(filename, False)
@@ -212,6 +217,8 @@ def guessDataSourceType(filename):
if featresults.isFEATDir(filename):
return fslfeatimage.FEATImage, filename
+ elif melresults.isMelodicDir(filename):
+ return fslmelimage.MelodicImage, filename
else:
return fslimage.Image, filename
@@ -288,7 +295,8 @@ def loadOverlays(paths, loadFunc='default', errorFunc='default', saveDir=True):
e = str(e)
msg = strings.messages['overlay.loadOverlays.error'].format(s, e)
title = strings.titles[ 'overlay.loadOverlays.error']
- log.debug('Error loading overlay ({}), ({})'.format(s, e))
+ log.debug('Error loading overlay ({}), ({})'.format(s, e),
+ exc_info=True)
wx.MessageBox(msg, title, wx.ICON_ERROR | wx.OK)
# If loadFunc or errorFunc are explicitly set to
diff --git a/fsl/fsleyes/views/plotpanel.py b/fsl/fsleyes/views/plotpanel.py
index d8079e8f0..c69b7c484 100644
--- a/fsl/fsleyes/views/plotpanel.py
+++ b/fsl/fsleyes/views/plotpanel.py
@@ -488,7 +488,8 @@ class PlotPanel(viewpanel.ViewPanel):
if ds.alpha == 0:
return (0, 0), (0, 0)
- log.debug('Drawing plot for {}'.format(ds.overlay))
+ log.debug('Drawing {} for {}'.format(type(ds).__name__,
+ ds.overlay))
xdata, ydata = ds.getData()
diff --git a/fsl/fsleyes/views/timeseriespanel.py b/fsl/fsleyes/views/timeseriespanel.py
index 7a39d1217..79bfcf41d 100644
--- a/fsl/fsleyes/views/timeseriespanel.py
+++ b/fsl/fsleyes/views/timeseriespanel.py
@@ -23,6 +23,7 @@ details):
TimeSeries
FEATTimeSeries
+ MelodicTimeSeries
"""
@@ -37,6 +38,7 @@ import props
import plotpanel
import fsl.data.featimage as fslfeatimage
+import fsl.data.melodicimage as fslmelimage
import fsl.data.image as fslimage
import fsl.fsleyes.displaycontext as fsldisplay
import fsl.fsleyes.colourmaps as fslcmaps
@@ -66,8 +68,9 @@ class TimeSeries(plotpanel.DataSeries):
plotpanel.DataSeries.__init__(self, overlay)
self.tsPanel = tsPanel
- self.coords = map(int, coords)
- self.data = overlay.data[coords[0], coords[1], coords[2], :]
+ self.coords = None
+ self.data = None
+ self.update(coords)
def __copy__(self):
@@ -91,15 +94,15 @@ class TimeSeries(plotpanel.DataSeries):
destroyed/recreated whenever the
:attr:`.DisplayContext.location` changes.
"""
-
- coords = map(int, coords)
- if coords == self.coords:
- return False
-
+
self.coords = coords
- self.data = self.overlay.data[coords[0], coords[1], coords[2], :]
+ self.data = self._getData(coords)
return True
+
+ def _getData(self, coords):
+ return self.overlay.data[coords[0], coords[1], coords[2], :]
+
def getData(self, xdata=None, ydata=None):
"""Overrides :meth:`.DataSeries.getData` Returns the data associated
@@ -648,6 +651,17 @@ class FEATModelFitTimeSeries(TimeSeries):
self.data = self.overlay.fit(contrast, xyz, fitType == 'full')
+
+class MelodicTimeSeries(TimeSeries):
+
+ def __init__(self, tsPanel, overlay, component):
+ TimeSeries.__init__(self, tsPanel, overlay, component)
+
+
+ def _getData(self, component):
+ return self.overlay.getComponentTimeSeries(component)
+
+
class TimeSeriesPanel(plotpanel.PlotPanel):
"""A :class:`.PlotPanel` which plots time series data from
:class:`.Image` overlays.
@@ -707,12 +721,12 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
The ``TimeSeriesPanel`` has some extra functionality for
- :class:`.FEATImage` overlays. For these overlays, a :class:`FEATTimeSeries`
- instance is plotted, instead of a regular :class:`TimeSeries` instance. The
- ``FEATTimeSeries`` class, in turn, has the ability to generate more
- ``TimeSeries`` instances which represent various aspects of the FEAT model
- fit. See the :class:`FEATTimeSeries` and the
- :class:`.TimeSeriesControlPanel` classes for more details.
+ :class:`.FEATImage` overlays. For these overlays, a
+ :class:`.FEATTimeSeries` instance is plotted, instead of a regular
+ :class:`.TimeSeries` instance. The ``FEATTimeSeries`` class, in turn, has
+ the ability to generate more ``TimeSeries`` instances which represent
+ various aspects of the FEAT model fit. See the :class:`.FEATTimeSeries`
+ and the :class:`.TimeSeriesControlPanel` classes for more details.
"""
@@ -844,7 +858,7 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
def getCurrent(self):
- """Returns the :class:`TimeSeries` instance for the current time
+ """Returns the :class:`.TimeSeries` instance for the current time
course. If :attr:`showCurrent` is ``False``, or the currently
selected overlay is not a :class:`.Image` (see
:attr:`.DisplayContext.selectedOverlay`) this method will return
@@ -881,34 +895,25 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
overlays = [o for o in self._overlayList
if o is not currOverlay]
- # Remove overlays for which the
- # current location is out of bounds
- locs = map(self.__getTimeSeriesLocation, overlays)
- locovl = filter(lambda (l, o): l is not None,
- zip(locs, overlays))
-
- if len(locovl) > 0:
- locs, overlays = zip(*locovl)
-
- tss = map(self.__genTimeSeries, overlays, locs)
+ tss = map(self.__genTimeSeries, overlays)
- extras.extend([ts for ts in tss if ts is not None])
+ extras.extend([ts for ts in tss if ts is not None])
- for ts in tss:
- ts.alpha = 1
- ts.lineWidth = 0.5
-
- # Use a random colour for each overlay,
- # but use the same random colour each time
- colour = self.__overlayColours.get(
- ts.overlay,
- fslcmaps.randomBrightColour())
+ for ts in tss:
+ ts.alpha = 1
+ ts.lineWidth = 0.5
+
+ # Use a random colour for each overlay,
+ # but use the same random colour each time
+ colour = self.__overlayColours.get(
+ ts.overlay,
+ fslcmaps.randomBrightColour())
- ts.colour = colour
- self.__overlayColours[ts.overlay] = colour
+ ts.colour = colour
+ self.__overlayColours[ts.overlay] = colour
- if isinstance(ts, FEATTimeSeries):
- extras.extend(ts.getModelTimeSeries())
+ if isinstance(ts, FEATTimeSeries):
+ extras.extend(ts.getModelTimeSeries())
self.drawDataSeries(extras)
else:
@@ -918,9 +923,9 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
def __currentSettingsChanged(self, *a):
"""Called when the settings controlling the display of the current time
course(s) changes. If the current time course is a
- :class:`FEATTimeSeries`, the display settings are propagated to all of
+ :class:`.FEATTimeSeries`, the display settings are propagated to all of
its associated time courses (see the
- :meth:`FEATTimeSeries.getModelTimeSeries` method).
+ :meth:`.FEATTimeSeries.getModelTimeSeries` method).
"""
if self.__currentTs is None:
return
@@ -948,7 +953,7 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
def __overlaysChanged(self, *a):
"""Called when the :class:`.OverlayList` changes. Makes sure
- that there are no :class:`TimeSeries` instances in the
+ that there are no :class:`.TimeSeries` instances in the
:attr:`.PlotPanel.dataSeries` list which refer to overlays that
no longer exist.
"""
@@ -962,7 +967,7 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
def __bindCurrentProps(self, ts, bind=True):
- """Binds or unbinds the properties of the given :class:`TimeSeries`
+ """Binds or unbinds the properties of the given :class:`.TimeSeries`
instance with the current display settings (e.g.
:attr:`currentColour`, :attr:`currentAlpha`, etc).
"""
@@ -992,6 +997,9 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
not overlay.is4DImage():
return None
+ if isinstance(overlay, fslmelimage.MelodicImage):
+ return opts.volume
+
vox = opts.transformCoords([[x, y, z]], 'display', 'voxel')[0]
vox = np.round(vox)
@@ -1006,15 +1014,25 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
return vox
- def __genTimeSeries(self, overlay, vox):
- """Creates and returns a :class:`TimeSeries` or :class:`FEATTimeSeries`
- instance for the specified voxel of the specified overlay.
+ def __genTimeSeries(self, overlay):
+ """Creates and returns a :class:`.TimeSeries` or
+ :class:`.FEATTimeSeries` instance for the specified voxel of the
+ specified overlay.
"""
+ loc = self.__getTimeSeriesLocation(overlay)
+
+ if loc is None:
+ return None
+
if isinstance(overlay, fslfeatimage.FEATImage):
- ts = FEATTimeSeries(self, overlay, vox)
+ ts = FEATTimeSeries(self, overlay, loc)
+
+ elif isinstance(overlay, fslmelimage.MelodicImage):
+ ts = MelodicTimeSeries(self, overlay, loc)
+
else:
- ts = TimeSeries(self, overlay, vox)
+ ts = TimeSeries(self, overlay, loc)
ts.colour = self.currentColour
ts.alpha = self.currentAlpha
@@ -1043,18 +1061,14 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
return
overlay = self._displayCtx.getSelectedOverlay()
- vox = self.__getTimeSeriesLocation(overlay)
-
- if vox is None:
- return
if overlay is prevOverlay:
self.__currentOverlay = prevOverlay
self.__currentTs = prevTs
- prevTs.update(vox)
+ prevTs.update(self.__getTimeSeriesLocation(overlay))
else:
- ts = self.__genTimeSeries(overlay, vox)
+ ts = self.__genTimeSeries(overlay)
self.__currentTs = ts
self.__currentOverlay = overlay
--
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