diff --git a/fsl/data/featresults.py b/fsl/data/featresults.py
index 719092a03771d78867d36c69ae7d241fa2231b59..138c0379e11563504f39f4aac6ece0cb44db0036 100644
--- a/fsl/data/featresults.py
+++ b/fsl/data/featresults.py
@@ -134,7 +134,7 @@ def loadDesign(featdir):
if line.strip() == '/Matrix':
break
- matrix = np.loadtxt(f)
+ matrix = np.loadtxt(f, ndmin=2)
if matrix is None or matrix.size == 0:
raise RuntimeError('{} does not appear to be a '
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 31988dc6ed7cfa5d770a1cde2152b00804bf0d89..3dda62827dec53ca10ec928cf5cbaea68875a5f0 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -333,9 +333,14 @@ class Image(props.HasProperties):
return int(code)
- def getWorldOrientation(self, axis, code=None):
- """Returns a code representing the orientation of the specified axis
- in world space.
+ def getOrientation(self, axis, xform):
+ """Returns a code representing the orientation of the specified data
+ axis in the coordinate system defined by the given transformation
+ matrix.
+
+ :arg xform: A transformation matrix which is assumed to transform
+ coordinates from the image world coordinate system to
+ some other coordinate system.
This method returns one of the following values, indicating the
direction in which coordinates along the specified axis increase:
@@ -357,45 +362,16 @@ class Image(props.HasProperties):
increases from inferior to superior).
"""
- if self.getXFormCode(code) == constants.NIFTI_XFORM_UNKNOWN:
- return constants.ORIENT_UNKNOWN
-
- if axis == 0: return constants.ORIENT_L2R
- elif axis == 1: return constants.ORIENT_P2A
- elif axis == 2: return constants.ORIENT_I2S
-
- else: return constants.ORIENT_UNKNOWN
-
-
- def getVoxelOrientation(self, axis, code=None):
- """Returns a code representing the (estimated) orientation of the
- specified data axis.
-
- :arg code: May be either ``qform`` or ``sform``, specifying which
- transformation to use.
-
- See the :meth:`getWorldOrientation` method for a description
- of the return value.
- """
-
- if self.getXFormCode(code) == constants.NIFTI_XFORM_UNKNOWN:
- return constants.ORIENT_UNKNOWN
-
- if code is None: xform = self.nibImage.get_affine()
- elif code == 'sform': xform = self.nibImage.get_sform()
- elif code == 'qform': xform = self.nibImage.get_qform()
- else: raise ValueError('code must be None, qform, or sform')
+ if self.getXFormCode() == constants.NIFTI_XFORM_UNKNOWN:
+ return constants.ORIENT_UNKNOWN
- # the aff2axcodes returns one code for each
- # axis in the image array (i.e. in voxel space),
- # which denotes the real world direction
import nibabel as nib
code = nib.orientations.aff2axcodes(
xform,
((constants.ORIENT_R2L, constants.ORIENT_L2R),
(constants.ORIENT_A2P, constants.ORIENT_P2A),
(constants.ORIENT_S2I, constants.ORIENT_I2S)))[axis]
-
+
return code
diff --git a/fsl/data/melodicimage.py b/fsl/data/melodicimage.py
index 6bdc254805eb25fd0fe3e967901f081e6ae5b08b..3a2087da9a028717e832374be773ff89d3d07dfc 100644
--- a/fsl/data/melodicimage.py
+++ b/fsl/data/melodicimage.py
@@ -8,30 +8,58 @@
"""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 props
+
import image as fslimage
import melodicresults as melresults
class MelodicImage(fslimage.Image):
+ """The ``MelodicImage`` class is an :class:`.Image` which encapsulates
+ the results of a FSL MELODIC analysis. A ``MelodicImage`` corresponds to
+ the spatial component map file, generally called ``melodic_IC.nii.gz``.
+
+ The ``MelodicImage`` class provides a few MELODIC-specific attributes and
+ methods:
+
+ .. autosummary::
+
+ tr
+ getComponentTimeSeries
+ numComponents
+ getTopLevelAnalysisDir
+ getDataFile
"""
+
+
+ tr = props.Real(default=1.0)
+ """The TR time of the raw data from which this ``MelodicImage`` was
+ generated. If it is possible to do so, this is automatically initialised
+ from the data file (see the :meth:`getDataFile` method).
"""
+
- def __init__(self, image, *args, **kwargs):
- """
- """
+ def __init__(self, path, *args, **kwargs):
+ """Create a ``MelodicImage``.
+ :arg path: A path specifying the ``melodic_IC`` image file, or the
+ ``.ica`` directory.
- if op.isdir(image):
+ All other arguments are passed through to the :meth:`.Image.__init__`
+ method.
+ """
- dirname = image
+ if op.isdir(path):
+ dirname = path
filename = 'melodic_IC'
-
else:
- dirname = op.dirname( image)
- filename = op.basename(image)
+ dirname = op.dirname( path)
+ filename = op.basename(path)
dirname = dirname.rstrip(op.sep)
@@ -48,12 +76,41 @@ class MelodicImage(fslimage.Image):
*args,
**kwargs)
+ self.__meldir = dirname
self.__melmix = melresults.getComponentTimeSeries(dirname)
+ # Automatically set the
+ # TR value if possible
+ dataFile = self.getDataFile()
+
+ if dataFile is not None:
+ dataImage = fslimage.Image(dataFile, loadData=False)
+ if dataImage.is4DImage():
+ self.tr = dataImage.pixdim[3]
+
def getComponentTimeSeries(self, component):
+ """Returns the time course for the specified (0-indexed) component. """
return self.__melmix[:, component]
def numComponents(self):
+ """Returns the number of components in this ``MelodicImage``. """
return self.shape[3]
+
+
+ def getTopLevelAnalysisDir(self):
+ """Returns the top level analysis, if the melodic analysis for this
+ ``MelodicImage`` is contained within another analysis. Otherwise,
+ returnsa ``None``. See the
+ :func:`.melodicresults.getTopLevelAnalysisDir` function.
+ """
+ return melresults.getTopLevelAnalysisDir(self.__meldir)
+
+
+ def getDataFile(self):
+ """Returns the file name of the data image from which this
+ ``MelodicImage`` was generated, if possible. See the
+ :func:`.melodicresults.getDataFile` function.
+ """
+ return melresults.getDataFile(self.__meldir)
diff --git a/fsl/data/melodicresults.py b/fsl/data/melodicresults.py
index d05a25ab309e369353cd1b637cb884e1194f67f2..c31811723bd78e2ce8036072d3c5d3f0e19734d5 100644
--- a/fsl/data/melodicresults.py
+++ b/fsl/data/melodicresults.py
@@ -15,49 +15,46 @@ following functions are provided:
isMelodicDir
getMelodicDir
+ getTopLevelAnalysisDir
+ getDataFile
getICFile
+ getMixFile
getNumComponents
getComponentTimeSeries
"""
-import os
import os.path as op
import numpy as np
-import fsl.data.image as fslimage
+import fsl.data.image as fslimage
+import fsl.data.featresults as featresults
def isMelodicDir(path):
- """
+ """Returns ``True`` if the given path looks like it is contained within
+ a MELODIC directory, ``False`` otherwise.
"""
# 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
+ return getMelodicDir(path) is not None
def getMelodicDir(path):
- """
+ """Returns the MELODIC directory in which the given path is contained,
+ or ``None`` if it is not contained within a MELODIC directory. A melodic
+ directory:
+
+ - Must be named ``*.ica`` or ``*.gica``
+ - Must contain a file called ``melodic_IC.nii.gz``
+ - Must contain a file called ``melodic_mix``.
"""
# TODO This code is identical to featresults.getFEATDir.
# Can you generalise it and put it somewhere in fsl.utils?
+ path = op.abspath(path)
+
sufs = ['.ica', '.gica']
idxs = [(path.rfind(s), s) for s in sufs]
idx, suf = max(idxs, key=lambda (i, s): i)
@@ -66,28 +63,92 @@ def getMelodicDir(path):
return None
idx += len(suf)
- path = path[:idx]
+ path = path[:idx].rstrip(op.sep)
- if path.endswith(suf) or path.endswith('{}{}'.format(suf, op.sep)):
- return path
+ if not path.endswith(suf):
+ return None
+
+ # Must contain an image file called melodic_IC
+ try:
+ fslimage.addExt(op.join(path, 'melodic_IC'), mustExist=True)
+ except ValueError:
+ return None
+
+ # Must contain a file called melodic_mix
+ if not op.exists(op.join(path, 'melodic_mix')):
+ return None
- return None
+ return path
-def getICFile(meldir):
+def getTopLevelAnalysisDir(path):
+ """If the given path is a MELODIC directory, and it is contained within
+ a FEAT directory, or another MELODIC directory, the path to the latter
+ directory is returned. Otherwise, ``None`` is returned.
"""
+
+ meldir = getMelodicDir(path)
+ sufs = ['.feat', '.gfeat', '.ica', '.gica']
+
+ if meldir is None:
+ return None
+
+ if featresults.isFEATDir(meldir):
+ return featresults.getFEATDir(meldir)
+
+ parentDir = op.dirname(meldir)
+ parentDir = parentDir.rstrip(op.sep)
+
+ if not any([parentDir.endswith(s) for s in sufs]):
+ return None
+
+ # Must contain a file called filtered_func_data.nii.gz
+ dataFile = op.join(parentDir, 'filtered_func_data')
+
+ try:
+ dataFile = fslimage.addExt(dataFile, mustExist=True)
+ except ValueError:
+ return None
+
+ return parentDir
+
+
+def getDataFile(meldir):
+ """If the given melodic directory is contained within another analysis
+ directory, the path to the data file is returned. Otherwise ``None`` is
+ returned.
"""
+
+ topDir = getTopLevelAnalysisDir(meldir)
+
+ if topDir is None:
+ return None
+
+ dataFile = op.join(topDir, 'filtered_func_data')
+
+ try:
+ return fslimage.addExt(dataFile, mustExist=True)
+ except ValueError:
+ return None
+
+
+def getICFile(meldir):
+ """Returns the path to the melodic IC image. """
return fslimage.addExt(op.join(meldir, 'melodic_IC'))
def getMixFile(meldir):
- """
- """
+ """Returns the path to the melodic mix file. """
return op.join(meldir, 'melodic_mix')
+def getReportFile(meldir):
+ pass
+
+
def getNumComponents(meldir):
- """
+ """Returns the number of components generated in the melodic analysis
+ contained in the given directrory.
"""
icImg = fslimage.Image(getICFile(meldir), loadData=False)
@@ -95,7 +156,8 @@ def getNumComponents(meldir):
def getComponentTimeSeries(meldir):
- """
+ """Returns a ``numpy`` array containing the melodic mix for the given
+ directory.
"""
mixfile = getMixFile(meldir)
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index 27ec5ed61ebbe336a80ad5fae945d5651d4660c7..a3846b2c83f02d6e3ac6394ebd5567a5fcff6ce7 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -325,13 +325,17 @@ labels = TypeDict({
'OverlayInfoPanel.Image.transform' : 'Transform/space',
'OverlayInfoPanel.Image.orient' : 'Orientation',
- 'OverlayInfoPanel.Image' : 'NIFTI1 image',
- 'OverlayInfoPanel.FEATImage' : 'NIFTI1 image (FEAT analysis)',
- 'OverlayInfoPanel.FEATImage.featInfo' : 'FEAT information',
- 'OverlayInfoPanel.Model' : 'VTK model',
- 'OverlayInfoPanel.Model.numVertices' : 'Number of vertices',
- 'OverlayInfoPanel.Model.numIndices' : 'Number of indices',
- 'OverlayInfoPanel.dataSource' : 'Data source',
+ 'OverlayInfoPanel.Image' : 'NIFTI1 image',
+ 'OverlayInfoPanel.FEATImage' : 'NIFTI1 image '
+ '(FEAT analysis)',
+ 'OverlayInfoPanel.FEATImage.featInfo' : 'FEAT information',
+ 'OverlayInfoPanel.MelodicImage' : 'NIFTI1 image '
+ '(MELODIC analysis)',
+ 'OverlayInfoPanel.MelodicImage.melodicInfo' : 'MELODIC information',
+ 'OverlayInfoPanel.Model' : 'VTK model',
+ 'OverlayInfoPanel.Model.numVertices' : 'Number of vertices',
+ 'OverlayInfoPanel.Model.numIndices' : 'Number of indices',
+ 'OverlayInfoPanel.dataSource' : 'Data source',
})
@@ -612,12 +616,9 @@ nifti = TypeDict({
'voxOrient.0' : 'X voxel orientation',
'voxOrient.1' : 'Y voxel orientation',
'voxOrient.2' : 'Z voxel orientation',
- 'sformOrient.0' : 'X sform orientation',
- 'sformOrient.1' : 'Y sform orientation',
- 'sformOrient.2' : 'Z sform orientation',
- 'qformOrient.0' : 'X qform orientation',
- 'qformOrient.1' : 'Y qform orientation',
- 'qformOrient.2' : 'Z qform orientation',
+ 'worldOrient.0' : 'X world orientation',
+ 'worldOrient.1' : 'Y world orientation',
+ 'worldOrient.2' : 'Z world orientation',
'qform' : 'QForm matrix',
'sform' : 'SForm matrix',
@@ -708,4 +709,14 @@ feat = TypeDict({
'numPoints' : 'Number of volumes',
'numEVs' : 'Number of EVs',
'numContrasts' : 'Number of contrasts',
+ 'report' : 'Link to report',
+})
+
+
+melodic = TypeDict({
+ 'dataFile' : 'Data file',
+ 'partOfAnalysis' : 'Part of analysis',
+ 'numComponents' : 'Number of ICs',
+ 'tr' : 'TR time',
+ 'report' : 'Link to report',
})
diff --git a/fsl/fsleyes/colourmaps.py b/fsl/fsleyes/colourmaps.py
index 46e1a2f1b07ceb429367d8cfc18b728280ac1d5f..0589151de45b3242394a6b55c768d8af5991bd9c 100644
--- a/fsl/fsleyes/colourmaps.py
+++ b/fsl/fsleyes/colourmaps.py
@@ -626,7 +626,7 @@ def randomBrightColour():
def randomDarkColour():
"""Generates a random saturated and darkened RGB colour."""
- return applyBricon(randomBrightColour(), 0.25, 0.5)
+ return applyBricon(randomBrightColour(), 0.35, 0.5)
def complementaryColour(rgb):
diff --git a/fsl/fsleyes/controls/overlayinfopanel.py b/fsl/fsleyes/controls/overlayinfopanel.py
index 8f15f85342208b794a0aca449b20e9df794764a2..7d340e1718408977a36cd0bf239d9da1fa3df3ea 100644
--- a/fsl/fsleyes/controls/overlayinfopanel.py
+++ b/fsl/fsleyes/controls/overlayinfopanel.py
@@ -14,9 +14,11 @@ import collections
import wx
import wx.html as wxhtml
-import fsl.data.strings as strings
-import fsl.data.constants as constants
-import fsl.fsleyes.panel as fslpanel
+import numpy as np
+
+import fsl.data.strings as strings
+import fsl.data.constants as constants
+import fsl.fsleyes.panel as fslpanel
class OverlayInfoPanel(fslpanel.FSLEyesPanel):
@@ -30,14 +32,15 @@ class OverlayInfoPanel(fslpanel.FSLEyesPanel):
:scale: 50%
:align: center
- Slightly different informtion is shown depending on the overlay type,
+ Slightly different information is shown depending on the overlay type,
and is generated by the following methods:
- =================== ==========================
- :class:`.Image` :meth:`__getImageInfo`
- :class:`.FEATImage` :meth:`__getFEATImageInfo`
- :class:`.Model` :meth:`__getModelInfo`
- =================== ==========================
+ ====================== =============================
+ :class:`.Image` :meth:`__getImageInfo`
+ :class:`.FEATImage` :meth:`__getFEATImageInfo`
+ :class:`.MelodicImage` :meth:`__getMelodicImageInfo`
+ :class:`.Model` :meth:`__getModelInfo`
+ ====================== =============================
"""
@@ -177,8 +180,10 @@ class OverlayInfoPanel(fslpanel.FSLEyesPanel):
info = OverlayInfo('{} - {}'.format(
display.name, strings.labels[self, overlay]))
+
img = overlay.nibImage
hdr = img.get_header()
+ opts = display.getDisplayOpts()
voxUnits, timeUnits = hdr.get_xyzt_units()
qformCode = int(hdr['qform_code'])
@@ -239,7 +244,8 @@ class OverlayInfoPanel(fslpanel.FSLEyesPanel):
section=xformSect)
for i in range(3):
- orient = overlay.getVoxelOrientation(i)
+ xform = opts.getTransform('world', 'id')
+ orient = overlay.getOrientation(i, xform)
orient = '{} - {}'.format(
strings.anatomy['Image', 'lowlong', orient],
strings.anatomy['Image', 'highlong', orient])
@@ -248,23 +254,15 @@ class OverlayInfoPanel(fslpanel.FSLEyesPanel):
section=orientSect)
for i in range(3):
- orient = overlay.getWorldOrientation(i, code='sform')
+ xform = np.eye(4)
+ orient = overlay.getOrientation(i, xform)
orient = '{} - {}'.format(
strings.anatomy['Image', 'lowlong', orient],
strings.anatomy['Image', 'highlong', orient])
- info.addInfo(strings.nifti['sformOrient.{}'.format(i)],
+ info.addInfo(strings.nifti['worldOrient.{}'.format(i)],
orient,
section=orientSect)
- for i in range(3):
- orient = overlay.getWorldOrientation(i, code='qform')
- orient = '{} - {}'.format(
- strings.anatomy['Image', 'lowlong', orient],
- strings.anatomy['Image', 'highlong', orient])
- info.addInfo(strings.nifti['qformOrient.{}'.format(i)],
- orient,
- section=orientSect)
-
return info
@@ -293,6 +291,33 @@ class OverlayInfoPanel(fslpanel.FSLEyesPanel):
return info
+
+ def __getMelodicImageInfo(self, overlay, display):
+ """Creates and returns an :class:`OverlayInfo` object containing
+ information about the given :class:`.MelodicImage` overlay.
+
+ :arg overlay: A :class:`.MelodicImage` instance.
+ :arg display: The :class:`.Display` instance assocated with the
+ ``MelodicImage``.
+ """
+
+ info = self.__getImageInfo(overlay, display)
+
+ melInfo = collections.OrderedDict([
+ ('tr', overlay.tr),
+ ('dataFile', overlay.getDataFile()),
+ ('partOfAnalysis', overlay.getTopLevelAnalysisDir()),
+ ('numComponents', overlay.numComponents()),
+ ])
+
+ secName = strings.labels[self, overlay, 'melodicInfo']
+ info.addSection(secName)
+
+ for k, v in melInfo.items():
+ info.addInfo(strings.melodic[k], v, section=secName)
+
+ return info
+
def __getModelInfo(self, overlay, display):
"""Creates and returns an :class:`OverlayInfo` object containing
diff --git a/fsl/fsleyes/controls/timeserieslistpanel.py b/fsl/fsleyes/controls/timeserieslistpanel.py
index c3d500fb48be3bc98aa70c8d1b0947d43b7ea45d..c211d35b9c7f7d5c0d98ebf94ddf4c53ac4b15c4 100644
--- a/fsl/fsleyes/controls/timeserieslistpanel.py
+++ b/fsl/fsleyes/controls/timeserieslistpanel.py
@@ -183,7 +183,7 @@ class TimeSeriesListPanel(fslpanel.FSLEyesPanel):
copy.setData(*ts.getData())
# This is hacky, and is here in order to
- # make the __onLIstSelect method work.
+ # make the __onListSelect method work.
if isinstance(ts, timeseries.MelodicTimeSeries):
copy.tsLoc = 'volume'
copy.coord = ts.getComponent()
diff --git a/fsl/fsleyes/overlay.py b/fsl/fsleyes/overlay.py
index 62d6c1890340963d47df8ff687d053a4a68d9d83..053801d5f8db5d2e1667920a47045449a2a696af 100644
--- a/fsl/fsleyes/overlay.py
+++ b/fsl/fsleyes/overlay.py
@@ -182,12 +182,12 @@ class OverlayList(props.HasProperties):
return self.overlays.insertAll(index, items)
-def guessDataSourceType(filename):
+def guessDataSourceType(path):
"""A convenience function which, given the name of a file or directory,
figures out a suitable overlay type.
Returns a tuple containing two values - a type which should be able to
- load the filename, and the filename, possibly adjusted. If the file type
+ load the path, and the path itself, possibly adjusted. If the type
is unrecognised, the first tuple value will be ``None``.
"""
@@ -198,30 +198,53 @@ def guessDataSourceType(filename):
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:
-
- try: filename = fslimage.addExt(filename, True)
- except ValueError: return None, filename
+ path = op.abspath(path)
+
+ # VTK files are easy
+ if path.endswith('.vtk'):
+ return fslmodel.Model, path
+
+ # Now, we check to see if the given
+ # path is part of a FEAT or MELODIC
+ # analysis. The way we go about this is
+ # a bit silly, but is necessary due to
+ # the fact thet a melodic analysis can
+ # be contained within a feat analysis
+ # (or another melodic analysis). So we
+ # check for all analysis types and, if
+ # more than one analysis type matches,
+ # we return the one with the longest
+ # path name.
+ analyses = [
+ (fslfeatimage.FEATImage, featresults.getFEATDir( path)),
+ (fslmelimage .MelodicImage, melresults .getMelodicDir(path))]
+
+ # Remove the analysis types that didn't match
+ # (the get*Dir function returned None)
+ analyses = [(t, d) for (t, d) in analyses if d is not None]
+
+ # If we have one or more matches for
+ # an analysis directory, we return
+ # the one with the longest path
+ if len(analyses) > 0:
+
+ dirlens = map(len, [d for (t, d) in analyses])
+ maxidx = dirlens.index(max(dirlens))
+
+ return analyses[maxidx]
- if featresults.isFEATDir(filename):
- return fslfeatimage.FEATImage, filename
- elif melresults.isMelodicDir(filename):
- return fslmelimage.MelodicImage, filename
- else:
- return fslimage.Image, filename
+ # If the path is not an analysis directory,
+ # see if it is a regular nifti image
+ try:
+ path = fslimage.addExt(path, mustExist=True)
+ return fslimage.Image, path
+
+ except ValueError:
+ pass
- return None, filename
+ # Otherwise, I don't
+ # know what to do
+ return None, path
def makeWildcard():
diff --git a/fsl/fsleyes/plotting/timeseries.py b/fsl/fsleyes/plotting/timeseries.py
index 8d484aa16aed370f6a7cdb12149774f16aeff847..64c1631098279f21448f5f4de1bc096b6ba16545 100644
--- a/fsl/fsleyes/plotting/timeseries.py
+++ b/fsl/fsleyes/plotting/timeseries.py
@@ -71,8 +71,7 @@ class TimeSeries(dataseries.DataSeries):
def getData(self, xdata=None, ydata=None):
"""Overrides :meth:`.DataSeries.getData`. Returns the data associated
- with this ``TimeSeries`` instance, pre-processed according to the
- current :class:`.TimeSeriesPanel` settings.
+ with this ``TimeSeries`` instance.
The ``xdata`` and ``ydata`` arguments may be used by sub-classes to
override the x/y data in the event that they have already performed
@@ -88,22 +87,7 @@ class TimeSeries(dataseries.DataSeries):
xdata = np.array(xdata, dtype=np.float32)
ydata = np.array(ydata, dtype=np.float32)
-
- if self.tsPanel.usePixdim:
- xdata *= self.overlay.pixdim[3]
- if self.tsPanel.plotMode == 'demean':
- ydata = ydata - ydata.mean()
-
- elif self.tsPanel.plotMode == 'normalise':
- ymin = ydata.min()
- ymax = ydata.max()
- ydata = 2 * (ydata - ymin) / (ymax - ymin) - 1
-
- elif self.tsPanel.plotMode == 'percentChange':
- mean = ydata.mean()
- ydata = 100 * (ydata / mean) - 100
-
return xdata, ydata
@@ -499,7 +483,7 @@ class FEATTimeSeries(VoxelTimeSeries):
copenum)
- def __plotPEFitChanged(self, evnum):
+ def __plotPEFitChanged(self, *a):
"""Called when the :attr:`plotPEFits` setting changes.
If necessary, creates and caches one or more
diff --git a/fsl/fsleyes/profiles/orthoviewprofile.py b/fsl/fsleyes/profiles/orthoviewprofile.py
index aa90f209924d48c1d611facc11e10abbf9f67e58..8554f225965a2f1a92cab803f5d9f42fa22834d7 100644
--- a/fsl/fsleyes/profiles/orthoviewprofile.py
+++ b/fsl/fsleyes/profiles/orthoviewprofile.py
@@ -24,24 +24,27 @@ class OrthoViewProfile(profiles.Profile):
allow the user to navigate through the ``OrthoPanel`` display of the
overlays in the :class:`.OverlayList`.
- ``OrthoViewProfile`` defines three *modes* (see the :class:`.Profile`
- class documentation):
+ ``OrthoViewProfile`` defines the following *modes* (see the
+ :class:`.Profile` class documentation):
- ======== ==============================================================
- ``nav`` The user can change the currently displayed location. This is
- accomplished by updating the :attr:`.DisplayContext.location`
- property on left mouse drags.
+ ========== ==============================================================
+ ``nav`` The user can change the currently displayed location. This is
+ accomplished by updating the :attr:`.DisplayContext.location`
+ property on left mouse drags.
- ``zoom`` The user can zoom in/out of a canvas with the mouse wheel, and
- draw a rectangle on a canvas in which to zoom. This is
- accomplished by updating the :attr:`.SliceCanvasOpts.zoom`
- property on mouse wheel changes, and displaying a
- :class:`~.annotations.Rect` annotation on left mouse drags.
+ ``zoom`` The user can zoom in/out of a canvas with the mouse wheel, and
+ draw a rectangle on a canvas in which to zoom. This is
+ accomplished by updating the :attr:`.SliceCanvasOpts.zoom`
+ property on mouse wheel changes, and displaying a
+ :class:`~.annotations.Rect` annotation on left mouse drags.
- ``pan`` The user can pan around a canvas (if the canvas is zoomed in).
- This is accomplished by calling the
- :meth:`.SliceCanvas.panDisplayBy` on left mouse drags.
- ======== ==============================================================
+ ``pan`` The user can pan around a canvas (if the canvas is zoomed in).
+ This is accomplished by calling the
+ :meth:`.SliceCanvas.panDisplayBy` on left mouse drags.
+
+ ``bricon`` The user can drag the mouse along a canvas to change the
+ brightness/contrast of the currently selected overlay.
+ ========== ==============================================================
The ``OrthoViewProfile`` class also defines a few actions:
@@ -86,7 +89,7 @@ class OrthoViewProfile(profiles.Profile):
if extraModes is None: extraModes = []
if extraActions is None: extraActions = {}
- modes = ['nav', 'pan', 'zoom']
+ modes = ['nav', 'pan', 'zoom', 'bricon']
actionz = {
'resetZoom' : self.resetZoom,
'centreCursor' : self.centreCursor,
@@ -309,7 +312,7 @@ class OrthoViewProfile(profiles.Profile):
if zoom == 0:
return
- self._zoomModeMouseWheel(canvas, zoom)
+ self._zoomModeMouseWheel(None, canvas, zoom)
def _zoomModeLeftMouseDrag(self, ev, canvas, mousePos, canvasPos):
@@ -424,3 +427,33 @@ class OrthoViewProfile(profiles.Profile):
else: return
canvas.panDisplayBy(xoff, yoff)
+
+
+ def _briconModeLeftMouseDrag(self, ev, canvas, mousePos, canvasPos):
+ """Handles left mouse drags in ``bricon`` mode.
+
+ The brightness and contrast of the currently selected overlay are
+ adjusted according to the location of the mouse, relative to the
+ canvas.
+ """
+
+ overlay = self._displayCtx.getSelectedOverlay()
+
+ if overlay is None:
+ return
+
+ display = self._displayCtx.getDisplay(overlay)
+ w, h = canvas.GetSize().Get()
+ x, y = mousePos
+
+ brightness = float(x) / w
+ contrast = float(y) / h
+
+ log.debug('Adjusting bricon for {} '
+ '(brightness: {}, contrast: {})'.format(
+ overlay.name,
+ brightness,
+ contrast))
+
+ display.brightness = 100 * brightness
+ display.contrast = 100 * contrast
diff --git a/fsl/fsleyes/profiles/profilemap.py b/fsl/fsleyes/profiles/profilemap.py
index 36554a6af266991408f34656dcfcbb50e4ee59c5..747841b8e67671b4928d1c8da420249bf104faab 100644
--- a/fsl/fsleyes/profiles/profilemap.py
+++ b/fsl/fsleyes/profiles/profilemap.py
@@ -68,7 +68,8 @@ tempModeMap = {
(('nav', wx.WXK_CONTROL), 'zoom'),
(('pan', wx.WXK_CONTROL), 'zoom'),
(('nav', wx.WXK_ALT), 'pan'),
- (('zoom', wx.WXK_ALT), 'pan'))),
+ (('zoom', wx.WXK_ALT), 'pan'),
+ (('nav', wx.WXK_SHIFT), 'bricon'))),
# OrthoEditProfile inherits all of the
# settings for OrthoViewProfile above,
diff --git a/fsl/fsleyes/splash.py b/fsl/fsleyes/splash.py
index 3a4faef6ccd4600f327e5912381ae9da1ef64dcf..a3b8b8a6bc4492f64a85aaf442bcbb615827559e 100644
--- a/fsl/fsleyes/splash.py
+++ b/fsl/fsleyes/splash.py
@@ -50,7 +50,7 @@ class FSLEyesSplash(wx.Frame):
splashimg = splashbmp.ConvertToImage()
self.__splashPanel = imagepanel.ImagePanel(self, splashimg)
- self.__statusBar = wx.StaticText(self, style=wx.ELLIPSIZE_MIDDLE)
+ self.__statusBar = wx.StaticText(self, style=wx.ST_ELLIPSIZE_MIDDLE)
self.__statusBar.SetLabel(strings.messages[self, 'default'])
diff --git a/fsl/fsleyes/views/canvaspanel.py b/fsl/fsleyes/views/canvaspanel.py
index 6e95555ef665d4d8015325f7b61c49493826ae47..4ca4ad4068d0bdd2d7ecd5ff81c84f746edc768e 100644
--- a/fsl/fsleyes/views/canvaspanel.py
+++ b/fsl/fsleyes/views/canvaspanel.py
@@ -36,8 +36,8 @@ 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 colourbarpanel
+import viewpanel
log = logging.getLogger(__name__)
@@ -64,10 +64,16 @@ class CanvasPanel(viewpanel.ViewPanel):
Sub-classes of the ``CanvasPanel`` must do the following:
1. Add their content to the panel that is accessible via the
- :meth:`getCanvasPanel` method (see the note on
+ :meth:`getContentPanel` method (see the note on
:ref:`adding content <canvaspanel-adding-content>`).
2. Override the :meth:`getGLCanvases` method.
+
+ 3. Call the :meth:`centrePanelLayout` method in their ``__init__``
+ method.
+
+ 4. Override the :meth:`centrePanelLayout` method if any custom layout is
+ necessary.
**Actions**
@@ -104,14 +110,14 @@ class CanvasPanel(viewpanel.ViewPanel):
.. _canvaspanel-adding-content:
+
**Adding content**
- To support colour bar functionality, the ``CanvasPanel`` uses a hierarchy
- of ``wx.Panel`` instances, depicted in the following containment
- hierarchy diagram:
-
+ To support colour bar and screenshot functionality, the ``CanvasPanel``
+ uses a hierarchy of ``wx.Panel`` instances, depicted in the following
+ containment hierarchy diagram:
.. graphviz::
@@ -127,23 +133,49 @@ class CanvasPanel(viewpanel.ViewPanel):
rankdir="BT";
1 [label="CanvasPanel"];
- 2 [label="Canvas container"];
- 3 [label="ColourBarPanel"];
- 4 [label="Centre panel"];
- 5 [label="Content added by sub-classes"];
+ 2 [label="Centre panel"];
+ 3 [label="Custom content (for complex layouts)"];
+ 4 [label="Container panel"];
+ 5 [label="ColourBarPanel"];
+ 6 [label="Content panel"];
+ 7 [label="Content added by sub-classes"];
2 -> 1;
3 -> 2;
4 -> 2;
5 -> 4;
+ 6 -> 4;
+ 7 -> 6;
}
As depicted in the diagram, sub-classes need to add their content to the
- *centre panel*. This panel is accessible via the :meth:`getCanvasPanel`
- method. The *container panel* is what gets passed to the
+ *content panel*. This panel is accessible via the :meth:`getContentPanel`
+ method.
+
+
+ The *centre panel* is what gets passed to the
:meth:`.ViewPanel.setCentrePanel` method, and is accessible via the
- :meth:`getCanvasContainer` method, if necessary.
+ :meth:`getCentrePanel` method, if necessary. The *container panel* is
+ also available, via the :meth:`getContainerPanel`. Everything in the
+ container panel will appear in screenshots (see the :meth:`screenshot`
+ method).
+
+
+ The :meth:`centrePanelLayout` method lays out the centre panel, using the
+ :meth:`layoutContainerPanel` method to lay out the colour bar and the
+ content panel. The ``centrePanelLayout`` method simply adds the canvas
+ container directly to the centre panel. Sub-classes which have more
+ advanced layout requirements (e.g. the :class:`.LightBoxPanel` needs a
+ scrollbar) may override the :meth:`centrePanelLayout` method to implement
+ their own layout. These sub-class implementations must:
+
+ 1. Call the :meth:`layoutContainerPanel` method.
+
+ 2. Add the container panel (accessed via :meth:`getContainerPanel`)
+ to the centre panel (accessed via :meth:`getCentrePanel`).
+
+ 3. Add any other custom content to the centre panel.
"""
@@ -274,10 +306,11 @@ class CanvasPanel(viewpanel.ViewPanel):
self.disableProperty('syncOverlayOrder')
self.disableProperty('syncOverlayDisplay')
- self.__canvasContainer = wx.Panel(self)
- self.__canvasPanel = wx.Panel(self.__canvasContainer)
+ self.__centrePanel = wx.Panel(self)
+ self.__containerPanel = wx.Panel(self.__centrePanel)
+ self.__contentPanel = wx.Panel(self.__containerPanel)
- self.setCentrePanel(self.__canvasContainer)
+ self.setCentrePanel(self.__centrePanel)
# Stores a reference to a wx.Timer
# when movie mode is enabled
@@ -291,17 +324,18 @@ class CanvasPanel(viewpanel.ViewPanel):
self.__movieRateChanged)
# Canvas/colour bar layout is managed in
- # the _layout/_toggleColourBar methods
- self.__canvasSizer = None
- self.__colourBar = None
+ # the layoutColourBarAndCanvas method
+ self.__colourBar = None
# Use a different listener name so that subclasses
# can register on the same properties with self._name
lName = 'CanvasPanel_{}'.format(self._name)
- self.__opts.addListener('colourBarLocation', lName, self.__layout)
- self.__opts.addListener('showColourBar', lName, self.__layout)
-
- self.__layout()
+ self.__opts.addListener('colourBarLocation',
+ lName,
+ self.__colourBarPropsChanged)
+ self.__opts.addListener('showColourBar',
+ lName,
+ self.__colourBarPropsChanged)
def destroy(self):
@@ -337,20 +371,28 @@ class CanvasPanel(viewpanel.ViewPanel):
return self.__opts
- def getCanvasPanel(self):
+ def getCentrePanel(self):
+ """Returns the ``wx.Panel`` which is passed to
+ :meth:`.ViewPanel.setCentrePanel`. See the note on
+ :ref:`adding content <canvaspanel-adding-content>`.
+ """
+ return self.__centrePanel
+
+
+ def getContentPanel(self):
"""Returns the ``wx.Panel`` to which sub-classes must add their content.
See the note on :ref:`adding content <canvaspanel-adding-content>`.
"""
- return self.__canvasPanel
+ return self.__contentPanel
- def getCanvasContainer(self):
+ def getContainerPanel(self):
"""Returns the ``wx.Panel`` which contains the
- :class:`.ColourBarPanel` if it is being displayed, and the canvas
+ :class:`.ColourBarPanel` if it is being displayed, and the content
panel. See the note on
:ref:`adding content <canvaspanel-adding-content>`.
"""
- return self.__canvasContainer
+ return self.__containerPanel
def getGLCanvases(self):
@@ -375,11 +417,27 @@ class CanvasPanel(viewpanel.ViewPanel):
return None
- def __layout(self, *a):
- """Called when any colour bar display properties are changed (see
- :class:`.SceneOpts`). Lays out the container panel, which contains
- the :class:`.ColourBarPanel` and all content added by the
- ``CanvasPanel`` sub-class implementation.
+ def centrePanelLayout(self):
+ """Lays out the centre panel. This method may be overridden by
+ sub-classes which need more advanced layout logic. See the note on
+ :ref:`adding content <canvaspanel-adding-content>`
+ """
+
+ self.layoutContainerPanel()
+
+ sizer = wx.BoxSizer(wx.HORIZONTAL)
+ sizer.Add(self.__containerPanel, flag=wx.EXPAND, proportion=1)
+ self.__centrePanel.SetSizer(sizer)
+
+ self.PostSizeEvent()
+
+
+ def layoutContainerPanel(self):
+ """Creates a ``wx.Sizer``, and uses it to lay out the colour bar panel
+ and canvas panel. The sizer object is returned.
+
+ This method is used by the default :meth:`centrePanelLayout` method,
+ and is available for custom sub-class implementations to use.
"""
if not self.__opts.showColourBar:
@@ -391,19 +449,15 @@ class CanvasPanel(viewpanel.ViewPanel):
self.__colourBar.destroy()
self.__colourBar.Destroy()
self.__colourBar = None
-
- self.__canvasSizer = wx.BoxSizer(wx.HORIZONTAL)
- self.__canvasSizer.Add(self.__canvasPanel,
- flag=wx.EXPAND,
- proportion=1)
- self.__canvasContainer.SetSizer(self.__canvasSizer)
- self.PostSizeEvent()
+ sizer = wx.BoxSizer(wx.HORIZONTAL)
+ sizer.Add(self.__contentPanel, flag=wx.EXPAND, proportion=1)
+ self.__containerPanel.SetSizer(sizer)
return
if self.__colourBar is None:
self.__colourBar = colourbarpanel.ColourBarPanel(
- self.__canvasContainer, self._overlayList, self._displayCtx)
+ self.__containerPanel, self._overlayList, self._displayCtx)
self.__opts.bindProps('colourBarLabelSide',
self.__colourBar,
@@ -415,23 +469,18 @@ class CanvasPanel(viewpanel.ViewPanel):
self.__colourBar.orientation = 'vertical'
if self.__opts.colourBarLocation in ('top', 'bottom'):
- self.__canvasSizer = wx.BoxSizer(wx.VERTICAL)
+ sizer = wx.BoxSizer(wx.VERTICAL)
else:
- self.__canvasSizer = wx.BoxSizer(wx.HORIZONTAL)
-
- self.__canvasContainer.SetSizer(self.__canvasSizer)
+ sizer = wx.BoxSizer(wx.HORIZONTAL)
if self.__opts.colourBarLocation in ('top', 'left'):
- self.__canvasSizer.Add(self.__colourBar, flag=wx.EXPAND)
- self.__canvasSizer.Add(self.__canvasPanel, flag=wx.EXPAND,
- proportion=1)
+ sizer.Add(self.__colourBar, flag=wx.EXPAND)
+ sizer.Add(self.__contentPanel, flag=wx.EXPAND, proportion=1)
else:
- self.__canvasSizer.Add(self.__canvasPanel, flag=wx.EXPAND,
- proportion=1)
- self.__canvasSizer.Add(self.__colourBar, flag=wx.EXPAND)
+ sizer.Add(self.__contentPanel, flag=wx.EXPAND, proportion=1)
+ sizer.Add(self.__colourBar, flag=wx.EXPAND)
- # Force the canvas panel to resize itself
- self.PostSizeEvent()
+ self.__containerPanel.SetSizer(sizer)
def __movieModeChanged(self, *a):
@@ -455,6 +504,13 @@ class CanvasPanel(viewpanel.ViewPanel):
self.__movieTimer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.__movieUpdate)
self.__movieTimer.Start(rate)
+
+
+ def __colourBarPropsChanged(self, *a):
+ """Called when any colour bar display properties are changed (see
+ :class:`.SceneOpts`). Calls :meth:`canvasPanelLayout`.
+ """
+ self.centrePanelLayout()
def __movieRateChanged(self, *a):
@@ -653,7 +709,7 @@ def _screenshot(overlayList, displayCtx, canvasPanel):
# direct parent of the colour bar
# canvas, and an ancestor of the
# other GL canvases
- parent = canvasPanel.getCanvasContainer()
+ parent = canvasPanel.getContainerPanel()
width, height = parent.GetClientSize().Get()
windowDC = wx.WindowDC(parent)
memoryDC = wx.MemoryDC()
@@ -679,6 +735,9 @@ def _screenshot(overlayList, displayCtx, canvasPanel):
rgb = bmp.ConvertToImage().GetData()
rgb = np.fromstring(rgb, dtype=np.uint8)
+ log.debug('Creating bitmap {} * {} for {} screenshot'.format(
+ width, height, type(canvasPanel).__name__))
+
data[:, :, :3] = rgb.reshape(height, width, 3)
# Patch in bitmaps for every GL canvas
@@ -689,6 +748,11 @@ def _screenshot(overlayList, displayCtx, canvasPanel):
if glCanvas is None:
continue
+ # Hidden wx objects will
+ # still return a size
+ if not glCanvas.IsShown():
+ continue
+
pos = relativePosition(glCanvas, parent)
size = glCanvas.GetClientSize().Get()
@@ -710,6 +774,9 @@ def _screenshot(overlayList, displayCtx, canvasPanel):
w = xend - xstart
h = yend - ystart
bmp = bmp[:h, :w, :]
+
+ log.debug('Patching {} in at [{} - {}], [{} - {}]'.format(
+ type(glCanvas).__name__, xstart, xend, ystart, yend))
data[ystart:yend, xstart:xend] = bmp
diff --git a/fsl/fsleyes/views/lightboxpanel.py b/fsl/fsleyes/views/lightboxpanel.py
index 0d3de04f3e24cb7b70e36179650bff1d5b8d9e2e..7ac448133b5a65dfbbb221ac93bab5c4ddb434fb 100644
--- a/fsl/fsleyes/views/lightboxpanel.py
+++ b/fsl/fsleyes/views/lightboxpanel.py
@@ -86,11 +86,11 @@ class LightBoxPanel(canvaspanel.CanvasPanel):
actionz)
self.__scrollbar = wx.ScrollBar(
- self.getCanvasPanel(),
+ self.getCentrePanel(),
style=wx.SB_VERTICAL)
self.__lbCanvas = lightboxcanvas.WXGLLightBoxCanvas(
- self.getCanvasPanel(),
+ self.getContentPanel(),
overlayList,
displayCtx)
@@ -117,10 +117,9 @@ class LightBoxPanel(canvaspanel.CanvasPanel):
sceneOpts.bindProps('zrange', self.__lbCanvas)
self.__canvasSizer = wx.BoxSizer(wx.HORIZONTAL)
- self.getCanvasPanel().SetSizer(self.__canvasSizer)
+ self.getContentPanel().SetSizer(self.__canvasSizer)
- self.__canvasSizer.Add(self.__lbCanvas, flag=wx.EXPAND, proportion=1)
- self.__canvasSizer.Add(self.__scrollbar, flag=wx.EXPAND)
+ self.__canvasSizer.Add(self.__lbCanvas, flag=wx.EXPAND, proportion=1)
# When the display context location changes,
# make sure the location is shown on the canvas
@@ -162,8 +161,9 @@ class LightBoxPanel(canvaspanel.CanvasPanel):
self.__onLightBoxChange()
self.__onZoom()
+
self.__selectedOverlayChanged()
- self.Layout()
+ self.centrePanelLayout()
self.initProfile()
# The ViewPanel AuiManager seems to
@@ -204,6 +204,25 @@ class LightBoxPanel(canvaspanel.CanvasPanel):
"""Returns a reference to the :class:`.LightBoxCanvas` instance. """
return self.__lbCanvas
+
+ def centrePanelLayout(self):
+ """Overrides :meth:`.CanvasPanel.centrePanelLayout`. Adds the
+ scrollbar to the centre panel.
+ """
+
+ self.layoutContainerPanel()
+
+ centrePanel = self.getCentrePanel()
+ containerPanel = self.getContainerPanel()
+ sizer = wx.BoxSizer(wx.HORIZONTAL)
+
+ centrePanel.SetSizer(sizer)
+
+ sizer.Add(containerPanel, flag=wx.EXPAND, proportion=1)
+ sizer.Add(self.__scrollbar, flag=wx.EXPAND)
+
+ self.PostSizeEvent()
+
def __selectedOverlayChanged(self, *a):
"""Called when the :attr:`.DisplayContext.selectedOverlay` changes.
diff --git a/fsl/fsleyes/views/orthopanel.py b/fsl/fsleyes/views/orthopanel.py
index 5ae778dac51596a86598ae20ea6aa8ac5f54b167..25ca142f550b4effa1afd5c67b9266b4161f80eb 100644
--- a/fsl/fsleyes/views/orthopanel.py
+++ b/fsl/fsleyes/views/orthopanel.py
@@ -148,19 +148,19 @@ class OrthoPanel(canvaspanel.CanvasPanel):
sceneOpts,
actionz)
- canvasPanel = self.getCanvasPanel()
+ contentPanel = self.getContentPanel()
# The canvases themselves - each one displays a
# slice along each of the three world axes
- self.__xcanvas = slicecanvas.WXGLSliceCanvas(canvasPanel,
+ self.__xcanvas = slicecanvas.WXGLSliceCanvas(contentPanel,
overlayList,
displayCtx,
zax=0)
- self.__ycanvas = slicecanvas.WXGLSliceCanvas(canvasPanel,
+ self.__ycanvas = slicecanvas.WXGLSliceCanvas(contentPanel,
overlayList,
displayCtx,
zax=1)
- self.__zcanvas = slicecanvas.WXGLSliceCanvas(canvasPanel,
+ self.__zcanvas = slicecanvas.WXGLSliceCanvas(contentPanel,
overlayList,
displayCtx,
zax=2)
@@ -172,9 +172,9 @@ class OrthoPanel(canvaspanel.CanvasPanel):
self.__zLabels = {}
for side in ('left', 'right', 'top', 'bottom'):
- self.__xLabels[side] = wx.StaticText(canvasPanel)
- self.__yLabels[side] = wx.StaticText(canvasPanel)
- self.__zLabels[side] = wx.StaticText(canvasPanel)
+ self.__xLabels[side] = wx.StaticText(contentPanel)
+ self.__yLabels[side] = wx.StaticText(contentPanel)
+ self.__zLabels[side] = wx.StaticText(contentPanel)
self.__xcanvas.bindProps('showCursor', sceneOpts)
self.__ycanvas.bindProps('showCursor', sceneOpts)
@@ -236,13 +236,14 @@ class OrthoPanel(canvaspanel.CanvasPanel):
# the slice canvases when the canvas
# panel is resized, so aspect ratio
# is maintained
- canvasPanel.Bind(wx.EVT_SIZE, self.__onResize)
+ contentPanel.Bind(wx.EVT_SIZE, self.__onResize)
# Initialise the panel
self.__refreshLayout()
self.__bgColourChanged()
self.__overlayListChanged()
self.__locationChanged()
+ self.centrePanelLayout()
self.initProfile()
# The ViewPanel AuiManager seems to
@@ -328,8 +329,8 @@ class OrthoPanel(canvaspanel.CanvasPanel):
bg = [int(round(c * 255)) for c in bg]
fg = [int(round(c * 255)) for c in fg]
- self.getCanvasPanel().SetBackgroundColour(bg)
- self.getCanvasPanel().SetForegroundColour(fg)
+ self.getContentPanel().SetBackgroundColour(bg)
+ self.getContentPanel().SetForegroundColour(fg)
self.__xcanvas.SetBackgroundColour(bg)
self.__ycanvas.SetBackgroundColour(bg)
@@ -358,16 +359,12 @@ class OrthoPanel(canvaspanel.CanvasPanel):
self.__zLabels.values()
if overlay is not None:
- opts = self._displayCtx.getOpts(overlay)
+ opts = self._displayCtx.getOpts(overlay)
+ xform = opts.getTransform('world', 'display')
- if opts.transform in ('pixdim', 'id'):
- xorient = overlay.getVoxelOrientation(0)
- yorient = overlay.getVoxelOrientation(1)
- zorient = overlay.getVoxelOrientation(2)
- else:
- xorient = overlay.getWorldOrientation(0)
- yorient = overlay.getWorldOrientation(1)
- zorient = overlay.getWorldOrientation(2)
+ xorient = overlay.getOrientation(0, xform)
+ yorient = overlay.getOrientation(1, xform)
+ zorient = overlay.getOrientation(2, xform)
if constants.ORIENT_UNKNOWN in (xorient, yorient, zorient):
@@ -428,13 +425,10 @@ class OrthoPanel(canvaspanel.CanvasPanel):
# Update anatomy labels when
# overlay bounds change
- if i == self._displayCtx.selectedOverlay:
- opts.addListener('bounds',
- self._name,
- self.__refreshLabels,
- overwrite=True)
- else:
- opts.removeListener('bounds', self._name)
+ opts.addListener('bounds',
+ self._name,
+ self.__refreshLabels,
+ overwrite=True)
# anatomical orientation may have changed with an image change
self.__refreshLabels()
@@ -479,23 +473,17 @@ class OrthoPanel(canvaspanel.CanvasPanel):
self.PostSizeEvent()
return
- opts = self._displayCtx.getOpts(overlay)
- # The image is being displayed as it is stored on
- # disk - the image.getOrientation method calculates
- # and returns labels for each voxelwise axis.
- if opts.transform in ('pixdim', 'id'):
- xorient = overlay.getVoxelOrientation(0)
- yorient = overlay.getVoxelOrientation(1)
- zorient = overlay.getVoxelOrientation(2)
+ log.debug('Refreshing orientation labels '
+ 'according to {}'.format(overlay.name))
- # The overlay is being displayed in 'real world' space -
- # the definition of this space may be present in the
- # overlay meta data
- else:
- xorient = overlay.getWorldOrientation(0)
- yorient = overlay.getWorldOrientation(1)
- zorient = overlay.getWorldOrientation(2)
+ # Figure out the orientation of the
+ # image in the display coordinate system
+ opts = self._displayCtx.getOpts(overlay)
+ xform = opts.getTransform('world', 'display')
+ xorient = overlay.getOrientation(0, xform)
+ yorient = overlay.getOrientation(1, xform)
+ zorient = overlay.getOrientation(2, xform)
xlo = strings.anatomy['Image', 'lowshort', xorient]
ylo = strings.anatomy['Image', 'lowshort', yorient]
@@ -504,6 +492,10 @@ class OrthoPanel(canvaspanel.CanvasPanel):
yhi = strings.anatomy['Image', 'highshort', yorient]
zhi = strings.anatomy['Image', 'highshort', zorient]
+ log.debug('X orientation: {} - {}'.format(xlo, xhi))
+ log.debug('Y orientation: {} - {}'.format(ylo, yhi))
+ log.debug('Z orientation: {} - {}'.format(zlo, zhi))
+
bg = sceneOpts.bgColour
fg = colourmaps.complementaryColour(bg)
bg = [int(round(c * 255)) for c in bg]
@@ -513,16 +505,16 @@ class OrthoPanel(canvaspanel.CanvasPanel):
self.__xLabels['left'] .SetLabel(ylo)
self.__xLabels['right'] .SetLabel(yhi)
- self.__xLabels['top'] .SetLabel(zlo)
- self.__xLabels['bottom'].SetLabel(zhi)
+ self.__xLabels['bottom'].SetLabel(zlo)
+ self.__xLabels['top'] .SetLabel(zhi)
self.__yLabels['left'] .SetLabel(xlo)
self.__yLabels['right'] .SetLabel(xhi)
- self.__yLabels['top'] .SetLabel(zlo)
- self.__yLabels['bottom'].SetLabel(zhi)
+ self.__yLabels['bottom'].SetLabel(zlo)
+ self.__yLabels['top'] .SetLabel(zhi)
self.__zLabels['left'] .SetLabel(xlo)
self.__zLabels['right'] .SetLabel(xhi)
- self.__zLabels['top'] .SetLabel(ylo)
- self.__zLabels['bottom'].SetLabel(yhi)
+ self.__zLabels['bottom'].SetLabel(ylo)
+ self.__zLabels['top'] .SetLabel(yhi)
self.PostSizeEvent()
@@ -539,7 +531,7 @@ class OrthoPanel(canvaspanel.CanvasPanel):
opts = self.getSceneOptions()
layout = opts.layout
- width, height = self.getCanvasPanel().GetClientSize().Get()
+ width, height = self.getContentPanel().GetClientSize().Get()
show = [opts.showXCanvas, opts.showYCanvas, opts.showZCanvas]
canvases = [self.__xcanvas, self.__ycanvas, self.__zcanvas]
@@ -765,7 +757,7 @@ class OrthoPanel(canvaspanel.CanvasPanel):
for w in widgets:
self.__canvasSizer.Add(w, flag=flag)
- self.getCanvasPanel().SetSizer(self.__canvasSizer)
+ self.getContentPanel().SetSizer(self.__canvasSizer)
# Calculate/ adjust the appropriate sizes
# for each canvas, such that they are scaled
@@ -775,7 +767,7 @@ class OrthoPanel(canvaspanel.CanvasPanel):
self.__calcCanvasSizes()
self.Layout()
- self.getCanvasPanel().Layout()
+ self.getContentPanel().Layout()
self.Refresh()
diff --git a/fsl/fsleyes/views/plotpanel.py b/fsl/fsleyes/views/plotpanel.py
index 0a64d0e59dd5dcafbdf053cb7f0783f3806eb696..e80aa4b782ebd24f5dc04a026b658effb3eac796 100644
--- a/fsl/fsleyes/views/plotpanel.py
+++ b/fsl/fsleyes/views/plotpanel.py
@@ -355,13 +355,16 @@ class PlotPanel(viewpanel.ViewPanel):
self.Refresh()
- def drawDataSeries(self, extraSeries=None, **plotArgs):
+ def drawDataSeries(self, extraSeries=None, preproc=None, **plotArgs):
"""Plots all of the :class:`.DataSeries` instances in the
:attr:`dataSeries` list
:arg extraSeries: A sequence of additional ``DataSeries`` to be
plotted.
+ :arg preproc: An optional preprocessing function - passed to the
+ :meth:`__drawOneDataSeries` method.
+
:arg plotArgs: Passed through to the :meth:`__drawOneDataSeries`
method.
"""
@@ -397,7 +400,7 @@ class PlotPanel(viewpanel.ViewPanel):
ylims = []
for ds in toPlot:
- xlim, ylim = self.__drawOneDataSeries(ds, **plotArgs)
+ xlim, ylim = self.__drawOneDataSeries(ds, preproc, **plotArgs)
xlims.append(xlim)
ylims.append(ylim)
@@ -474,16 +477,26 @@ class PlotPanel(viewpanel.ViewPanel):
self.Refresh()
- def __drawOneDataSeries(self, ds, **plotArgs):
+ def __drawOneDataSeries(self, ds, preproc=None, **plotArgs):
"""Plots a single :class:`.DataSeries` instance. This method is called
by the :meth:`drawDataSeries` method.
:arg ds: The ``DataSeries`` instance.
+ :arg preproc: An optional preprocessing function which must accept
+ the ``DataSeries`` instance as its sole argument, and
+ must return the ``(xdata, ydata)`` with any required
+ processing applied. The default preprocessing function
+ returns the result of a call to
+ :meth:`.DataSeries.getData`.
+
:arg plotArgs: May be used to customise the plot - these
arguments are all passed through to the
``Axis.plot`` function.
"""
+
+ if preproc is None:
+ preproc = lambda s: s.getData()
if ds.alpha == 0:
return (0, 0), (0, 0)
@@ -491,7 +504,7 @@ class PlotPanel(viewpanel.ViewPanel):
log.debug('Drawing {} for {}'.format(type(ds).__name__,
ds.overlay))
- xdata, ydata = ds.getData()
+ xdata, ydata = preproc(ds)
if len(xdata) != len(ydata) or len(xdata) == 0:
return (0, 0), (0, 0)
diff --git a/fsl/fsleyes/views/timeseriespanel.py b/fsl/fsleyes/views/timeseriespanel.py
index 5a879e526528b542ece4f59efe961faa81221d1b..d83221c9a1eee94064fc5a21b1cc3f4fa1f6351a 100644
--- a/fsl/fsleyes/views/timeseriespanel.py
+++ b/fsl/fsleyes/views/timeseriespanel.py
@@ -20,7 +20,7 @@ import fsl.data.featimage as fslfeatimage
import fsl.data.melodicimage as fslmelimage
import fsl.data.image as fslimage
import fsl.fsleyes.colourmaps as fslcmaps
-import fsl.fsleyes.plotting.timeseries as timeseries
+import fsl.fsleyes.plotting as plotting
import fsl.fsleyes.controls.timeseriescontrolpanel as timeseriescontrolpanel
import fsl.fsleyes.controls.timeserieslistpanel as timeserieslistpanel
@@ -281,14 +281,15 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
tss = [ts for ts in tss if ts is not None]
for i, ts in enumerate(list(tss)):
- if isinstance(ts, timeseries.FEATTimeSeries):
+ if isinstance(ts, plotting.FEATTimeSeries):
tss.pop(i)
tss = tss[:i] + ts.getModelTimeSeries() + tss[i:]
for ts in tss:
ts.label = ts.makeLabel()
- self.drawDataSeries(extraSeries=tss)
+ self.drawDataSeries(extraSeries=tss,
+ preproc=self.__prepareTimeSeriesData)
def getTimeSeries(self, overlay):
@@ -298,6 +299,39 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
return self.__currentTss.get(overlay)
+ def __prepareTimeSeriesData(self, ts):
+ """Given a :class:`.TimeSeries` instance, scales and normalises
+ the x and y data according to the current values of the
+ :attr:`usePixdim` and :attr:`plotMode` properties.
+
+ This method is used as a preprocessing function for all
+ :class:`.TimeSeries` instances that are plotted - see the
+ :meth:`.PlotPanel.drawDataSeries` method.
+ """
+
+ xdata, ydata = ts.getData()
+
+ if self.usePixdim:
+ if isinstance(ts.overlay, fslmelimage.MelodicImage):
+ xdata *= ts.overlay.tr
+ else:
+ xdata *= ts.overlay.pixdim[3]
+
+ if self.plotMode == 'demean':
+ ydata = ydata - ydata.mean()
+
+ elif self.plotMode == 'normalise':
+ ymin = ydata.min()
+ ymax = ydata.max()
+ ydata = 2 * (ydata - ymin) / (ymax - ymin) - 1
+
+ elif self.plotMode == 'percentChange':
+ mean = ydata.mean()
+ ydata = 100 * (ydata / mean) - 100
+
+ return xdata, ydata
+
+
def __overlayListChanged(self, *a):
"""Called when the :class:`.OverlayList` changes. Makes sure that
there are no :class:`.TimeSeries` instances in the
@@ -402,18 +436,18 @@ class TimeSeriesPanel(plotpanel.PlotPanel):
return None, None, None
if isinstance(overlay, fslfeatimage.FEATImage):
- ts = timeseries.FEATTimeSeries(self, overlay, self._displayCtx)
+ ts = plotting.FEATTimeSeries(self, overlay, self._displayCtx)
targets = [self._displayCtx]
propNames = ['location']
elif isinstance(overlay, fslmelimage.MelodicImage) and \
self.plotMelodicICs:
- ts = timeseries.MelodicTimeSeries(self, overlay, self._displayCtx)
+ ts = plotting.MelodicTimeSeries(self, overlay, self._displayCtx)
targets = [self._displayCtx.getOpts(overlay)]
propNames = ['volume']
else:
- ts = timeseries.VoxelTimeSeries(self, overlay, self._displayCtx)
+ ts = plotting.VoxelTimeSeries(self, overlay, self._displayCtx)
targets = [self._displayCtx]
propNames = ['location']
diff --git a/fsl/tools/render.py b/fsl/tools/render.py
index e346114e1992714d70b9885373b980a8a68c20fb..f586153e2bc5b3bd8d5f948a815e5afdcb51fdd8 100644
--- a/fsl/tools/render.py
+++ b/fsl/tools/render.py
@@ -77,22 +77,10 @@ def buildLabelBitmaps(overlayList,
display = displayCtx.getDisplay(overlay)
opts = display.getDisplayOpts()
-
- # The overlay is being displayed as it is stored on
- # disk - the image.getOrientation method calculates
- # and returns labels for each voxelwise axis.
- if opts.transform in ('pixdim', 'id'):
- xorient = overlay.getVoxelOrientation(0)
- yorient = overlay.getVoxelOrientation(1)
- zorient = overlay.getVoxelOrientation(2)
-
- # The overlay is being displayed in 'real world' space -
- # the definition of this space may be present in the
- # overlay meta data
- else:
- xorient = overlay.getWorldOrientation(0)
- yorient = overlay.getWorldOrientation(1)
- zorient = overlay.getWorldOrientation(2)
+ xform = opts.getTransform('world', 'display')
+ xorient = overlay.getOrientation(0, xform)
+ yorient = overlay.getOrientation(1, xform)
+ zorient = overlay.getOrientation(2, xform)
if constants.ORIENT_UNKNOWN in [xorient, yorient, zorient]:
fgColour = 'red'
diff --git a/fsl/utils/dialog.py b/fsl/utils/dialog.py
index ec53c566a417f0247b094f7cdd24e0e30867d8bd..8cc91ac0b27cf11adc5f5a99277eb58e7940214f 100644
--- a/fsl/utils/dialog.py
+++ b/fsl/utils/dialog.py
@@ -132,12 +132,19 @@ class SimpleMessageDialog(wx.Dialog):
self.SetClientSize(( width, height))
self.Layout()
+ self.__message.Layout()
if self.__style & SMD_KEEP_CENTERED:
self.CentreOnParent()
+ # This ridiculousness seems to be
+ # necessary to force a repaint on
+ # all platforms (OSX, GTK, GTK/SSH)
+ wx.Yield()
self.Refresh()
self.Update()
+ self.__message.Refresh()
+ self.__message.Update()
wx.Yield()