From eb1b217b94578e061bb47ba0a5517aff49019e8a Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Sun, 6 Dec 2015 15:10:50 +0000
Subject: [PATCH] The melodic classification panel 'load labels' button can be
used to load a melodic overlay.
---
fsl/data/melodicresults.py | 33 ++
fsl/data/strings.py | 39 ++-
.../controls/melodicclassificationpanel.py | 290 ++++++++++++++----
3 files changed, 302 insertions(+), 60 deletions(-)
diff --git a/fsl/data/melodicresults.py b/fsl/data/melodicresults.py
index 6de7dc48f..ab159fbb6 100644
--- a/fsl/data/melodicresults.py
+++ b/fsl/data/melodicresults.py
@@ -113,6 +113,11 @@ def getDataFile(meldir):
return None
+def getMeanFile(meldir):
+ """Return a path to the mean image of the meloidic input data. """
+ return fslimage.addExt(op.join(meldir, 'mean'))
+
+
def getICFile(meldir):
"""Returns the path to the melodic IC image. """
return fslimage.addExt(op.join(meldir, 'melodic_IC'))
@@ -406,6 +411,7 @@ def loadMelodicLabelFile(filename):
to be of the format generated by FIX or Melview; such a file should
have a structure resembling the following::
+
filtered_func_data.ica
1, Signal, False
2, Unclassified Noise, True
@@ -417,6 +423,7 @@ def loadMelodicLabelFile(filename):
8, Signal, False
[2, 5, 6, 7]
+
The first line of the file contains the name of the melodic directory.
Then, one line is present for each component, containing the following,
separated by commas:
@@ -427,10 +434,29 @@ def loadMelodicLabelFile(filename):
- ``'True'`` if the component has been classified as *bad*,
``'False'`` otherwise.
+
The last line of the file contains the index (starting from 1) of all
*bad* components, i.e. those components which are not classified as
signal or unknown.
+
+ :arg filename: Name of the label file to load.
+
+ :returns: A tuple containing the path to the melodic directory
+ as specified in the label file, and a list of lists, one
+ list per component, with each list containing the labels for
+ the corresponding component.
+
+
+ .. note:: This function will also parse files which only contain a
+ bad component list, e.g.::
+
+ [2, 5, 6, 7]
+
+ In this case, the returned melodic directory path will be
+ ``None``.
"""
+
+ filename = op.abspath(filename)
with open(filename, 'rt') as f:
lines = f.readlines()
@@ -462,6 +488,13 @@ def loadMelodicLabelFile(filename):
melDir = lines[0]
noisyComps = map(int, lines[-1][1:-1].split(', '))
+ # The melodic directory path should
+ # either be an absolute path, or
+ # be specified relative to the location
+ # of the label file.
+ if not op.isabs(melDir):
+ melDir = op.join(op.dirname(filename), melDir)
+
# Parse the labels for every component
# We dot not add the labels as we go
# as, if something is wrong with the
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index ca43e65ff..1691e050f 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -141,12 +141,35 @@ messages = TypeDict({
'is necessary for editing.',
- 'MelodicClassificationPanel.disabled' : 'Choose a melodic image.',
+ 'MelodicClassificationPanel.disabled' : 'Choose a melodic image.',
+ 'MelodicClassificationPanel.loadError' : 'An error occurred while '
+ 'loading the file {}.'
+ '\n\nDetails: {}',
+ 'MelodicClassificationPanel.noMelDir' : 'The label file {} does not '
+ 'specify a path to a Melodic '
+ 'directory!',
+ 'MelodicClassificationPanel.saveError' : 'An error occurred while '
+ 'saving the file {}.'
+ '\n\nDetails: {}',
+ 'MelodicClassificationPanel.wrongNComps' : 'The mumber of components in '
+ 'the label file {} is greater '
+ 'than the number of components '
+ 'in the overlay {}!',
+ 'MelodicClassificationPanel.diffMelDir' : 'The label file {} does not '
+ 'refer to the melodic '
+ 'directory of the selected '
+ 'overlay ({}). What do you '
+ 'want to do?',
+
+ 'MelodicClassificationPanel.diffMelDir.labels' : 'Load the overlay in '
+ 'the label file',
+ 'MelodicClassificationPanel.diffMelDir.overlay' : 'Apply the labels to '
+ 'the current overlay'
+
- 'MelodicClassificationPanel.loadError' : 'An error occurred while loading '
- 'the file {}.\n\nDetails: {}',
- 'MelodicClassificationPanel.saveError' : 'An error occurred while saving '
- 'the file {}.\n\nDetails: {}',
+ 'An error occurred while '
+ 'saving the file {}.'
+ '\n\nDetails: {}',
})
@@ -387,9 +410,9 @@ labels = TypeDict({
'MelodicClassificationPanel.componentTab' : 'Components',
'MelodicClassificationPanel.labelTab' : 'Labels',
- 'MelodicClassificationPanel.loadButton' : 'Load from file',
- 'MelodicClassificationPanel.saveButton' : 'Save to file',
- 'MelodicClassificationPanel.clearButton' : 'Clear all labels',
+ 'MelodicClassificationPanel.loadButton' : 'Load labels',
+ 'MelodicClassificationPanel.saveButton' : 'Save labels',
+ 'MelodicClassificationPanel.clearButton' : 'Clear labels',
'ComponentGrid.componentColumn' : 'IC #',
'ComponentGrid.labelColumn' : 'Labels',
diff --git a/fsl/fsleyes/controls/melodicclassificationpanel.py b/fsl/fsleyes/controls/melodicclassificationpanel.py
index 380d75769..af2b2a90e 100644
--- a/fsl/fsleyes/controls/melodicclassificationpanel.py
+++ b/fsl/fsleyes/controls/melodicclassificationpanel.py
@@ -10,16 +10,22 @@ of a :class:`.MelodicImage`.
"""
+import os
+import os.path as op
import logging
import wx
import pwidgets.notebook as notebook
+import fsl.utils.settings as fslsettings
import fsl.data.strings as strings
+import fsl.data.image as fslimage
+import fsl.data.melodicresults as fslmelresults
import fsl.data.melodicimage as fslmelimage
import fsl.fsleyes.colourmaps as fslcm
import fsl.fsleyes.panel as fslpanel
+import fsl.fsleyes.autodisplay as autodisplay
import melodicclassificationgrid as melodicgrid
@@ -30,25 +36,7 @@ class MelodicClassificationPanel(fslpanel.FSLEyesPanel):
"""The ``MelodicClassificationPanel``
"""
- #
- # File format:
- # First line: ica directory name
- # Lines 2-(N+1): One line for each component
- # Last line: List of bad components
- #
- # A component line:
- # Component index, Label1, Label2, True|False
- #
- #
- #
- # Save to a FSLeyes label file:
- #
- # Save to a FIX/MELview file:
- # - Component has 'Signal' label
- # - Component has 'Unknown' label
- # - All other labels are output as 'Unclassified Noise'
- # (these are added to the list on the last line of the file)
- #
+
def __init__(self, parent, overlayList, displayCtx):
"""Create a ``MelodicClassificationPanel``.
@@ -109,10 +97,10 @@ class MelodicClassificationPanel(fslpanel.FSLEyesPanel):
self.__btnSizer .Add(self.__clearButton, flag=wx.EXPAND, proportion=1)
self.__mainSizer.Add(self.__notebook, flag=wx.EXPAND, proportion=1)
- self.__mainSizer.Add(self.__btnSizer, flag=wx.EXPAND)
self.__sizer .Add(self.__disabledText, flag=wx.EXPAND, proportion=1)
self.__sizer .Add(self.__mainSizer, flag=wx.EXPAND, proportion=1)
+ self.__sizer .Add(self.__btnSizer, flag=wx.EXPAND)
self.SetSizer(self.__sizer)
@@ -152,6 +140,9 @@ class MelodicClassificationPanel(fslpanel.FSLEyesPanel):
self.__sizer.Show(self.__disabledText, not enable)
self.__sizer.Show(self.__mainSizer, enable)
+ self.__saveButton .Enable(enable)
+ self.__clearButton.Enable(enable)
+
self.Layout()
@@ -173,35 +164,131 @@ class MelodicClassificationPanel(fslpanel.FSLEyesPanel):
def __onLoadButton(self, ev):
- """
+ """Called when the *Load labels* button is pushed. Prompts the user
+ to select a label file to load, then does the following:
+
+ 1. If the selected label file refers to the currently selected
+ melodic_IC overlay, the labels are applied to the overlay.
+
+ 2. If the selected label file refers to a different melodic_IC
+ overlay, the user is asked whether they want to load the
+ different melodic_IC file (the default), or whether they
+ want the labels applied to the existing overlay.
+
+ 3. If the selected label file does not refer to any overlay
+ (it only contains the bad component list), the user is asked
+ whether they want the labels applied to the current melodic_IC
+ overlay.
+
+ If the number of labels in the file is less than the number of
+ melodic_IC components, thew remaining components are labelled
+ as unknown. If the number of labels in the file is greater than
+ the number of melodic_IC components, an error is shown, and
+ nothing is done.
"""
- lut = self.__lut
- overlay = self._displayCtx.getSelectedOverlay()
- melclass = overlay.getICClassification()
- dlg = wx.FileDialog(
+ # The aim of the code beneath this function
+ # is to load a set of component labels, and
+ # to figure out which overlay they should
+ # be added to. When it has done this, it
+ # calls this function.
+ def applyLabels(labelFile, overlay, allLabels):
+
+ lut = self.__lut
+ melclass = overlay.getICClassification()
+
+ ncomps = overlay.numComponents()
+ nlabels = len(allLabels)
+
+ # Error: number of labels in the
+ # file is greater than the number
+ # of components in the overlay.
+ if ncomps < nlabels:
+ msg = strings.messages[self, 'wrongNComps'].format(
+ labelFile, overlay.dataSource)
+ title = strings.titles[ self, 'loadError']
+ wx.MessageBox(msg, title, wx.ICON_ERROR | wx.OK)
+ return
+
+ # Number of labels in the file is
+ # less than number of components
+ # in the overlay - we pad the
+ # labels with 'Unknown'
+ elif ncomps > nlabels:
+ for i in range(nlabels, ncomps):
+ allLabels.append(['Unknown'])
+
+ # Disable notification while applying
+ # labels so the component/label grids
+ # don't confuse themselves. We'll
+ # manually refresh them below.
+ melclass.disableNotification('labels')
+ lut .disableNotification('labels')
+
+ melclass.clear()
+
+ for comp, lbls in enumerate(allLabels):
+ for lbl in lbls:
+ melclass.addLabel(comp, lbl)
+
+ # Make sure a colour in the melodic
+ # lookup table exists for all labels
+ for comp, labels in enumerate(melclass.labels):
+ for label in labels:
+
+ label = melclass.getDisplayLabel(label)
+ lutLabel = lut.getByName(label)
+
+ if lutLabel is None:
+ log.debug('New melodic classification '
+ 'label: {}'.format(label))
+ lut.new(label)
+
+ melclass.enableNotification('labels')
+ lut .enableNotification('labels')
+
+ # If we have just loaded a MelodicImage,
+ # make sure it is selected. If we loaded
+ # labels for an existing MelodicImage,
+ # this will have no effect.
+ self._displayCtx.disableListener('selectedOverlay', self._name)
+ self._displayCtx.selectOverlay(overlay)
+ self._displayCtx.enableListener('selectedOverlay', self._name)
+ self.__selectedOverlayChanged()
+
+ # If the current overlay is a MelodicImage,
+ # the open file dialog starting point will
+ # be the melodic directory.
+ overlay = self._displayCtx.getSelectedOverlay()
+ selectedIsMelodic = isinstance(overlay, fslmelimage.MelodicImage)
+
+ if selectedIsMelodic:
+ loadDir = overlay.getMelodicDir()
+
+ # Otherwise it will be the most
+ # recent overlay load directory.
+ else:
+ loadDir = fslsettings.read('loadOverlayLastDir', os.getcwd())
+
+ # Ask the user to select a label file
+ dlg = wx.FileDialog(
self,
message=strings.titles[self, 'loadDialog'],
- defaultDir=overlay.getMelodicDir(),
+ defaultDir=loadDir,
style=wx.FD_OPEN)
+ # User cancelled the dialog
if dlg.ShowModal() != wx.ID_OK:
return
+ # Load the specified label file
filename = dlg.GetPath()
-
- # Disable notification during the load,
- # so the component/label grids don't
- # confuse themselves. We'll manually
- # refresh them below.
- melclass.disableNotification('labels')
- lut .disableNotification('labels')
-
try:
- melclass.clear()
- melclass.load(filename)
-
+ melDir, allLabels = fslmelresults.loadMelodicLabelFile(filename)
+
+ # Problem loading the file
except Exception as e:
+
e = str(e)
msg = strings.messages[self, 'loadError'].format(filename, e)
title = strings.titles[ self, 'loadError']
@@ -209,24 +296,123 @@ class MelodicClassificationPanel(fslpanel.FSLEyesPanel):
'({}), ({})'.format(filename, e), exc_info=True)
wx.MessageBox(msg, title, wx.ICON_ERROR | wx.OK)
- # Make sure a colour in the melodic
- # lookup table exists for all labels
- for comp, labels in enumerate(melclass.labels):
- for label in labels:
+ return
+
+ # Ok we've got the labels, now
+ # we need to figure out which
+ # overlay to add them to.
- label = melclass.getDisplayLabel(label)
- lutLabel = lut.getByName(label)
-
- if lutLabel is None:
- log.debug('New melodic classification '
- 'label: {}'.format(label))
- lut.new(label)
+ # If the label file does not refer
+ # to a Melodic directory, and the
+ # current overlay is a melodic
+ # image, apply the labels to the image.
+ if selectedIsMelodic and (melDir is None):
+ applyLabels(filename, overlay, allLabels)
+ return
- melclass.enableNotification('labels')
- lut .enableNotification('labels')
+ # If the label file refers to a
+ # Melodic directory, and the
+ # current overlay is a melodic
+ # image.
+ if selectedIsMelodic and (melDir is not None):
- lut .notify('labels')
- melclass.notify('labels')
+ overlayDir = overlay.getMelodicDir()
+
+ # And both the current overlay and
+ # the label file refer to the same
+ # melodic directory, then we apply
+ # the labels to the curent overlay.
+ if op.abspath(melDir) == op.abspath(overlayDir):
+
+ applyLabels(filename, overlay, allLabels)
+ return
+
+ # Otherwise, if the overlay and the
+ # label file refer to different
+ # melodic directories...
+
+ # Ask the user whether they want to
+ dlg = wx.MessageDialog(
+ self,
+ strings.messages[self, 'diffMelDir'].format(
+ melDir, overlayDir),
+ style=wx.ICON_QUESTION | wx.YES_NO | wx.CANCEL)
+ dlg.SetYesNoLabels(
+ strings.messages[self, 'diffMelDir.labels'],
+ strings.messages[self, 'diffMelDir.overlay'])
+
+ response = dlg.ShowModal()
+
+ # User cancelled the dialog
+ if response == wx.ID_CANCEL:
+ return
+
+ # User chose to load the melodic
+ # image specified in the label
+ # file. We'll carry on with this
+ # processing below.
+ elif response == wx.ID_YES:
+ pass
+
+ # Apply the labels to the current
+ # overlay, even though they are
+ # from different analyses.
+ else:
+ applyLabels(filename, overlay, allLabels)
+ return
+
+ # If we've reached this far, we are
+ # going to attempt to identify the
+ # melodic image associated with the
+ # label file, load that image, and
+ # then apply the labels.
+
+ # The label file does not
+ # specify a melodic directory
+ if melDir is None:
+
+ msg = strings.messages[self, 'noMelDir'].format(filename)
+ title = strings.titles[ self, 'loadError']
+ wx.MessageBox(msg, title, wx.ICON_ERROR | wx.OK)
+ return
+
+ # Try loading the melodic_IC image
+ # specified in the label file. We'll
+ # load the mean image as well, as an
+ # underlay.
+ try:
+ overlay = fslmelimage.MelodicImage( melDir)
+ mean = fslmelresults.getMeanFile(melDir)
+ mean = fslimage.Image( mean)
+
+ log.debug('Adding {} and {} to overlay list'.format(overlay, mean))
+
+ self._overlayList.disableListener('overlays', self._name)
+ self._displayCtx .disableListener('selectedOverlay', self._name)
+ self._overlayList.extend([mean, overlay])
+ self._overlayList.enableListener('overlays', self._name)
+ self._displayCtx .enableListener('selectedOverlay', self._name)
+
+ if self._displayCtx.autoDisplay:
+ for o in [overlay, mean]:
+ autodisplay.autoDisplay(o,
+ self._overlayList,
+ self._displayCtx)
+
+ fslsettings.write('loadOverlayLastDir', op.abspath(melDir))
+
+ except Exception as e:
+
+ e = str(e)
+ msg = strings.messages[self, 'loadError'].format(filename, e)
+ title = strings.titles[ self, 'loadError']
+ log.debug('Error loading classification file '
+ '({}), ({})'.format(filename, e), exc_info=True)
+ wx.MessageBox(msg, title, wx.ICON_ERROR | wx.OK)
+
+ # Apply the loaded labels
+ # to the loaded overlay.
+ applyLabels(filename, overlay, allLabels)
def __onSaveButton(self, ev):
--
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