diff --git a/fsl/data/image.py b/fsl/data/image.py
index f27dfdb404a63b25ddad4bdd7e43fc52ea17fcd8..249b7a56cbfa63f11e96a3e35fd11f9027687b0c 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -277,23 +277,29 @@ class Image(props.HasProperties):
return len(self.shape) > 3 and self.shape[3] > 1
- def getXFormCode(self):
+ def getXFormCode(self, code=None):
"""This method returns the code contained in the NIFTI1 header,
indicating the space to which the (transformed) image is oriented.
+
+ The ``code`` parameter may be either ``sform`` (the default) or
+ ``qform`` in which case the corresponding matrix is used.
"""
- sform_code = self.nibImage.get_header()['sform_code']
- # Invalid values
- if sform_code > 4: code = constants.NIFTI_XFORM_UNKNOWN
- elif sform_code < 0: code = constants.NIFTI_XFORM_UNKNOWN
+ if code is None: code = 'sform_code'
+ elif code == 'sform' : code = 'sform_code'
+ elif code == 'qform' : code = 'qform_code'
+ else: raise ValueError('code must be None, sform, or qform')
- # All is well
- else: code = sform_code
+ code = self.nibImage.get_header()[code]
+ # Invalid values
+ if code > 4: code = constants.NIFTI_XFORM_UNKNOWN
+ elif code < 0: code = constants.NIFTI_XFORM_UNKNOWN
+
return int(code)
- def getWorldOrientation(self, axis):
+ def getWorldOrientation(self, axis, code=None):
"""Returns a code representing the orientation of the specified axis
in world space.
@@ -316,17 +322,17 @@ class Image(props.HasProperties):
to superior).
"""
- if self.getXFormCode() == constants.NIFTI_XFORM_UNKNOWN:
- return -1
+ 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 -1
+ else: return constants.ORIENT_UNKNOWN
- def getVoxelOrientation(self, axis):
+ def getVoxelOrientation(self, axis, code=None):
"""Returns a code representing the (estimated) orientation of the
specified voxelwise axis.
@@ -334,17 +340,23 @@ class Image(props.HasProperties):
of the return value.
"""
- if self.getXFormCode() == constants.NIFTI_XFORM_UNKNOWN:
- return -1
+ 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')
# the aff2axcodes returns one code for each
# axis in the image array (i.e. in voxel space),
# which denotes the real world direction
code = nib.orientations.aff2axcodes(
- self.nibImage.get_affine(),
+ xform,
((constants.ORIENT_R2L, constants.ORIENT_L2R),
(constants.ORIENT_A2P, constants.ORIENT_P2A),
(constants.ORIENT_S2I, constants.ORIENT_I2S)))[axis]
+
return code
@@ -354,8 +366,8 @@ class Image(props.HasProperties):
# so i'm just providing '*.gz'for now
ALLOWED_EXTENSIONS = ['.nii.gz', '.nii', '.img', '.hdr', '.img.gz', '.gz']
"""The file extensions which we understand. This list is used as the default
-if if the ``allowedExts`` parameter is not passed to any of the functions in
-this module.
+if if the ``allowedExts`` parameter is not passed to any of the functions
+below.
"""
EXTENSION_DESCRIPTIONS = ['Compressed NIFTI1 images',
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index 98b961fe5da7e42803d5dad576afae651d5de3d1..0a84a375a3bc23c78c6d9e6a0f8a59ed101fd5ee 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -145,6 +145,7 @@ titles = TypeDict({
'HistogramListPanel' : 'Histogram list',
'HistogramControlPanel' : 'Histogram control',
'ClusterPanel' : 'Cluster browser',
+ 'OverlayInfoPanel' : 'Overlay information',
'LookupTablePanel.loadLut' : 'Select a lookup table file',
'LookupTablePanel.labelExists' : 'Label already exists',
@@ -170,6 +171,7 @@ actions = TypeDict({
'CanvasPanel.toggleAtlasPanel' : 'Atlas panel',
'CanvasPanel.toggleLookupTablePanel' : 'Lookup tables',
'CanvasPanel.toggleClusterPanel' : 'Cluster browser',
+ 'CanvasPanel.toggleOverlayInfo' : 'Overlay information',
'OrthoPanel.toggleOrthoToolBar' : 'View properties',
'OrthoPanel.toggleProfileToolBar' : 'Mode controls',
@@ -292,7 +294,10 @@ labels = TypeDict({
'CanvasSettingsPanel.scene' : 'Scene settings',
'CanvasSettingsPanel.ortho' : 'Ortho view settings',
'CanvasSettingsPanel.lightbox' : 'Lightbox settings',
-
+
+ 'OverlayInfoPanel.Image.dimensions' : 'Dimensions',
+ 'OverlayInfoPanel.Image.transform' : 'Transform/space',
+ 'OverlayInfoPanel.Image.orient' : 'Orientation',
})
@@ -548,3 +553,66 @@ anatomy = TypeDict({
('Image', 'space', constants.NIFTI_XFORM_TALAIRACH) : 'Talairach',
('Image', 'space', constants.NIFTI_XFORM_MNI_152) : 'MNI152',
})
+
+
+nifti = TypeDict({
+
+ 'dimensions' : 'Number of dimensions',
+ 'dataSource' : 'Data source',
+
+ 'datatype' : 'Data type',
+ 'vox_units' : 'XYZ units',
+ 'time_units' : 'Time units',
+ 'descrip' : 'Description',
+ 'qform_code' : 'QForm code',
+ 'sform_code' : 'SForm code',
+
+ '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',
+
+ 'qform' : 'QForm matrix',
+ 'sform' : 'SForm matrix',
+
+ 'dim1' : 'dim1',
+ 'dim2' : 'dim2',
+ 'dim3' : 'dim3',
+ 'dim4' : 'dim4',
+ 'dim5' : 'dim5',
+ 'dim6' : 'dim6',
+ 'dim7' : 'dim7',
+
+ 'pixdim1' : 'pixdim1',
+ 'pixdim2' : 'pixdim2',
+ 'pixdim3' : 'pixdim3',
+ 'pixdim4' : 'pixdim4',
+ 'pixdim5' : 'pixdim5',
+ 'pixdim6' : 'pixdim6',
+ 'pixdim7' : 'pixdim7',
+
+ ('datatype', 0) : 'UNKNOWN',
+ ('datatype', 1) : 'BINARY',
+ ('datatype', 2) : 'UINT8',
+ ('datatype', 4) : 'INT16',
+ ('datatype', 8) : 'INT32',
+ ('datatype', 16) : 'FLOAT32',
+ ('datatype', 32) : 'COMPLEX64',
+ ('datatype', 64) : 'DOUBLE64',
+ ('datatype', 128) : 'RGB',
+ ('datatype', 255) : 'ALL',
+ ('datatype', 256) : 'INT8',
+ ('datatype', 512) : 'UINT16',
+ ('datatype', 768) : 'UINT32',
+ ('datatype', 1024) : 'INT64',
+ ('datatype', 1280) : 'UINT64',
+ ('datatype', 1536) : 'FLOAT128',
+ ('datatype', 1792) : 'COMPLEX128',
+ ('datatype', 2048) : 'COMPLEX256',
+ ('datatype', 2304) : 'RGBA32',
+})
diff --git a/fsl/fslview/actions/__init__.py b/fsl/fslview/actions/__init__.py
index 7ace0c048452fb7dfff0d4981693ea9967290302..9f4249cec40e65d5418ea772915a9152b7662559 100644
--- a/fsl/fslview/actions/__init__.py
+++ b/fsl/fslview/actions/__init__.py
@@ -22,6 +22,7 @@ or more actions. As the :class:`.FSLViewPanel` class derives from
import logging
+import collections
import props
@@ -210,7 +211,7 @@ class ActionProvider(props.SyncableHasProperties):
if actions is None:
actions = {}
- self.__actions = {}
+ self.__actions = collections.OrderedDict()
for name, func in actions.items():
act = Action(overlayList, displayCtx, action=func)
@@ -246,7 +247,7 @@ class ActionProvider(props.SyncableHasProperties):
"""Return a dictionary containing ``{name -> Action}`` mappings for
all defined actions.
"""
- return dict(self.__actions)
+ return collections.OrderedDict(self.__actions)
def isEnabled(self, name):
diff --git a/fsl/fslview/controls/__init__.py b/fsl/fslview/controls/__init__.py
index a9471fdad551b58a595041c24ae62fc14f19f333..39ad296b6424c216047f0c963f55f8e7251e4225 100644
--- a/fsl/fslview/controls/__init__.py
+++ b/fsl/fslview/controls/__init__.py
@@ -16,6 +16,7 @@ from histogramlistpanel import HistogramListPanel
from histogramcontrolpanel import HistogramControlPanel
from clusterpanel import ClusterPanel
from canvassettingspanel import CanvasSettingsPanel
+from overlayinfopanel import OverlayInfoPanel
from orthotoolbar import OrthoToolBar
from orthoprofiletoolbar import OrthoProfileToolBar
diff --git a/fsl/fslview/controls/overlayinfopanel.py b/fsl/fslview/controls/overlayinfopanel.py
new file mode 100644
index 0000000000000000000000000000000000000000..b0edb0b4b611c48d7b15577c120644b0e1bef1ee
--- /dev/null
+++ b/fsl/fslview/controls/overlayinfopanel.py
@@ -0,0 +1,233 @@
+#!/usr/bin/env python
+#
+# overlayinfopanel.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import collections
+
+import wx
+import wx.html as wxhtml
+
+import fsl.data.strings as strings
+import fsl.fslview.panel as fslpanel
+
+
+class OverlayInfo(object):
+ """A little class which encapsulates human-readable information about
+ one overlay. ``OverlayInfo`` objects are created and returned by the
+ ``OverlayInfoPanel.__get*Info`` methods.
+ """
+
+ def __init__(self, title):
+
+ self.title = title
+ self.info = []
+ self.sections = collections.OrderedDict()
+
+
+ def addSection(self, section):
+ self.sections[section] = []
+
+
+ def addInfo(self, name, info, section=None):
+ if section is None: self.info .append((name, info))
+ else: self.sections[section].append((name, info))
+
+
+
+class OverlayInfoPanel(fslpanel.FSLViewPanel):
+
+
+ def __init__(self, parent, overlayList, displayCtx):
+
+ fslpanel.FSLViewPanel.__init__(self, parent, overlayList, displayCtx)
+
+ self.__info = wxhtml.HtmlWindow(self)
+ self.__sizer = wx.BoxSizer(wx.HORIZONTAL)
+ self.__sizer.Add(self.__info, flag=wx.EXPAND, proportion=1)
+
+ self.SetSizer(self.__sizer)
+
+ displayCtx .addListener('selectedOverlay',
+ self._name,
+ self.__selectedOverlayChanged)
+ overlayList.addListener('overlays',
+ self._name,
+ self.__selectedOverlayChanged)
+
+ self.__currentOverlay = None
+ self.__currentDisplay = None
+ self.__selectedOverlayChanged()
+ self.Layout()
+
+ def destroy(self):
+ self._displayCtx .removeListener('selectedOverlay', self._name)
+ self._overlayList.removeListener('overlays', self._name)
+
+ if self.__currentDisplay is not None:
+ self.__currentDisplay.removeListener('name', self._name)
+
+ self.__currentOverlay = None
+ self.__currentDisplay = None
+
+ fslpanel.FSLViewPanel.destroy(self)
+
+
+ def __selectedOverlayChanged(self, *a):
+
+ overlay = self._displayCtx.getSelectedOverlay()
+
+ if overlay == self.__currentOverlay:
+ return
+
+ if self.__currentDisplay is not None:
+ self.__currentDisplay.removeListener('name', self._name)
+
+ self.__currenOverlay = None
+ self.__currenDisplay = None
+
+ if overlay is not None:
+ self.__currentOverlay = overlay
+ self.__currentDisplay = self._displayCtx.getDisplay(overlay)
+
+ self.__currentDisplay.addListener('name',
+ self._name,
+ self.__overlayNameChanged)
+
+ self.__updateInformation()
+
+
+ def __overlayNameChanged(self, *a):
+ self.__updateInformation()
+
+
+ def __updateInformation(self):
+
+ overlay = self.__currentOverlay
+ display = self.__currentDisplay
+ infoFunc = '_{}__get{}Info'.format(type(self) .__name__,
+ type(overlay).__name__)
+ infoFunc = getattr(self, infoFunc, None)
+
+ if infoFunc is None:
+ self.__info.SetPage('')
+ return
+
+ info = infoFunc(overlay, display)
+
+ self.__info.SetPage(self.__formatOverlayInfo(info))
+
+
+ def __formatOverlayInfo(self, info):
+ lines = [info.title]
+ lines += map(str, info.info)
+
+ for sec in info.sections.keys():
+ lines += [sec]
+ lines += map(str, info.sections[sec])
+
+ return '<br>'.join(lines)
+
+
+ def __getImageInfo(self, overlay, display):
+
+ info = OverlayInfo(display.name)
+ img = overlay.nibImage
+ hdr = img.get_header()
+
+ voxUnits, timeUnits = hdr.get_xyzt_units()
+
+ dimSect = strings.labels[self, overlay, 'dimensions']
+ xformSect = strings.labels[self, overlay, 'transform']
+ orientSect = strings.labels[self, overlay, 'orient']
+
+ info.addSection(dimSect)
+ info.addSection(xformSect)
+ info.addSection(orientSect)
+
+ info.addInfo(strings.nifti['dataSource'], overlay.dataSource)
+ info.addInfo(strings.nifti['datatype'],
+ strings.nifti['datatype', int(hdr['datatype'])])
+ info.addInfo(strings.nifti['descrip'], hdr['descrip'])
+
+ info.addInfo(strings.nifti['vox_units'], voxUnits, section=dimSect)
+ info.addInfo(strings.nifti['time_units'], timeUnits, section=dimSect)
+
+ info.addInfo(strings.nifti['dimensions'],
+ '{}D'.format(len(overlay.shape)),
+ section=dimSect)
+
+ for i in range(len(overlay.shape)):
+ info.addInfo(strings.nifti['dim{}'.format(i + 1)],
+ str(overlay.shape[i]),
+ section=dimSect)
+
+ for i in range(len(overlay.shape)):
+
+ pixdim = hdr['pixdim'][i + 1]
+
+ if i < 3: pixdim = '{} {}'.format(pixdim, voxUnits)
+ elif i == 3: pixdim = '{} {}'.format(pixdim, timeUnits)
+
+ info.addInfo(
+ strings.nifti['pixdim{}'.format(i + 1)],
+ pixdim,
+ section=dimSect)
+
+ info.addInfo(strings.nifti['qform_code'],
+ strings.anatomy['Image', 'space', int(hdr['qform_code'])],
+ section=xformSect)
+ info.addInfo(strings.nifti['sform_code'],
+ strings.anatomy['Image', 'space', int(hdr['sform_code'])],
+ section=xformSect)
+
+ # TODO matrix formatting (you'll need to use
+ # HTML, or maybe get the formatOverlayInfo
+ # method to support different types)
+ info.addInfo(strings.nifti['qform'],
+ str(img.get_qform()),
+ section=xformSect)
+ info.addInfo(strings.nifti['sform'],
+ str(img.get_sform()),
+ section=xformSect)
+
+ for i in range(3):
+ orient = overlay.getVoxelOrientation(i)
+ orient = '{} - {}'.format(
+ strings.anatomy['Image', 'lowlong', orient],
+ strings.anatomy['Image', 'highlong', orient])
+ info.addInfo(strings.nifti['voxOrient.{}'.format(i)],
+ orient,
+ section=orientSect)
+
+ for i in range(3):
+ orient = overlay.getWorldOrientation(i, code='sform')
+ orient = '{} - {}'.format(
+ strings.anatomy['Image', 'lowlong', orient],
+ strings.anatomy['Image', 'highlong', orient])
+ info.addInfo(strings.nifti['sformOrient.{}'.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
+
+
+ def __getFEATImageInfo(self, overlay, display):
+ return self.__getImageInfo(overlay)
+
+
+ def __getModelInfo(self, overlay, display):
+ info = OverlayInfo(display.name)
+
+ return info
diff --git a/fsl/fslview/views/canvaspanel.py b/fsl/fslview/views/canvaspanel.py
index 0c7f9d3f226dfaf79c47730f56e82dd876fa0bc8..521d31ef213a7908c523285a26e0bc16cea3983b 100644
--- a/fsl/fslview/views/canvaspanel.py
+++ b/fsl/fslview/views/canvaspanel.py
@@ -12,6 +12,7 @@ class for all panels which display image data (e.g. the
"""
import logging
+import collections
import wx
@@ -57,22 +58,24 @@ class CanvasPanel(viewpanel.ViewPanel):
if extraActions is None:
extraActions = {}
- actionz = dict({
- 'screenshot' : self.screenshot,
- 'showCommandLineArgs' : self.showCommandLineArgs,
- 'toggleOverlayList' : lambda *a: self.togglePanel(
- fslcontrols.OverlayListPanel),
- 'toggleAtlasPanel' : lambda *a: self.togglePanel(
- fslcontrols.AtlasPanel),
- 'toggleDisplayProperties' : lambda *a: self.togglePanel(
- fslcontrols.OverlayDisplayToolBar, False, self),
- 'toggleLocationPanel' : lambda *a: self.togglePanel(
- fslcontrols.LocationPanel),
- 'toggleClusterPanel' : lambda *a: self.togglePanel(
- fslcontrols.ClusterPanel),
- 'toggleLookupTablePanel' : lambda *a: self.togglePanel(
- fslcontrols.LookupTablePanel),
- }.items() + extraActions.items())
+ actionz = [
+ ('screenshot', self.screenshot),
+ ('showCommandLineArgs', self.showCommandLineArgs),
+ ('toggleOverlayList', lambda *a: self.togglePanel(
+ fslcontrols.OverlayListPanel)),
+ ('toggleOverlayInfo', lambda *a: self.togglePanel(
+ fslcontrols.OverlayInfoPanel)),
+ ('toggleAtlasPanel', lambda *a: self.togglePanel(
+ fslcontrols.AtlasPanel)),
+ ('toggleDisplayProperties', lambda *a: self.togglePanel(
+ fslcontrols.OverlayDisplayToolBar, False, self)),
+ ('toggleLocationPanel', lambda *a: self.togglePanel(
+ fslcontrols.LocationPanel)),
+ ('toggleClusterPanel', lambda *a: self.togglePanel(
+ fslcontrols.ClusterPanel)),
+ ('toggleLookupTablePanel', lambda *a: self.togglePanel(
+ fslcontrols.LookupTablePanel))]
+ actionz = collections.OrderedDict(actionz + extraActions.items())
viewpanel.ViewPanel.__init__(
self, parent, overlayList, displayCtx, actionz)