Merge branch 'rel/0.31.2' into 'v0.31'

Rel/0.31.2

See merge request fsl/fsleyes/fsleyes!164

.ci/test_template.sh

@@ -68,24 +68,24 @@ if [ "$TEST_STYLE"x != "x" ]; then exit 0; fi
 # Run the tests
 export MPLBACKEND=wxagg
 export FSLEYES_TEST_GL=2.1
-((xvfb-run -a -s "-screen 0 640x480x24" pytest --cov-report= --cov-append -m "not (clitest or overlayclitest)" && echo "0" > status) || echo "1" > status) || true
+((xvfb-run -a -s "-screen 0 1920x1200x24" pytest --cov-report= --cov-append -m "not (clitest or overlayclitest)" && echo "0" > status) || echo "1" > status) || true
 status=`cat status`
 failed=$status
 sleep 5
 
-((xvfb-run -a -s "-screen 0 640x480x24" pytest --cov-report= --cov-append -m "clitest" && echo "0" > status) || echo "1" > status) || true
+((xvfb-run -a -s "-screen 0 1920x1200x24" pytest --cov-report= --cov-append -m "clitest" && echo "0" > status) || echo "1" > status) || true
 status=`cat status`
 failed=`echo "$status + $failed" | bc`
 sleep 5
 
-((xvfb-run -a -s "-screen 0 640x480x24" pytest --cov-report= --cov-append -m "overlayclitest" && echo "0" > status) || echo "1" > status) || true
+((xvfb-run -a -s "-screen 0 1920x1200x24" pytest --cov-report= --cov-append -m "overlayclitest" && echo "0" > status) || echo "1" > status) || true
 status=`cat status`
 failed=`echo "$status + $failed" | bc`
 sleep 5
 
 # test overlay types for GL14 as well
 export FSLEYES_TEST_GL=1.4
-((xvfb-run -a -s "-screen 0 640x480x24" pytest --cov-report= --cov-append -m "overlayclitest" && echo "0" > status) || echo "1" > status) || true
+((xvfb-run -a -s "-screen 0 1920x1200x24" pytest --cov-report= --cov-append -m "overlayclitest" && echo "0" > status) || echo "1" > status) || true
 status=`cat status`
 failed=`echo "$status + $failed" | bc`
 

.gitlab-ci.yml

@@ -163,27 +163,27 @@ variables:
     - bash ./.ci/test_template.sh
 
 
-test:3.5:
+test:3.6:
   stage: test
-  image: pauldmccarthy/fsleyes-py35-wxpy4-gtk2
+  image: pauldmccarthy/fsleyes-py36-wxpy4-gtk3
   <<: *test_template
 
 
-test:3.6:
+test:3.7:
   stage: test
-  image: pauldmccarthy/fsleyes-py36-wxpy4-gtk2
+  image: pauldmccarthy/fsleyes-py37-wxpy4-gtk3
   <<: *test_template
 
 
-test:3.7:
+test:3.8:
   stage: test
-  image: pauldmccarthy/fsleyes-py37-wxpy4-gtk2
+  image: pauldmccarthy/fsleyes-py38-wxpy4-gtk3
   <<: *test_template
 
 
 test:build-pypi-dist:
   stage: test
-  image: pauldmccarthy/fsleyes-py35-wxpy4-gtk2
+  image: pauldmccarthy/fsleyes-py36-wxpy4-gtk3
   <<: *except_releases
 
   tags:
@@ -201,7 +201,7 @@ test:build-pypi-dist:
 
 style:
   stage: style
-  image: pauldmccarthy/fsleyes-py35-wxpy4-gtk2
+  image: pauldmccarthy/fsleyes-py36-wxpy4-gtk3
   <<: *test_template
   variables:
     TEST_STYLE: "true"
@@ -219,7 +219,7 @@ style:
     - docker
 
   stage: doc
-  image: python:3.5
+  image: python:3.6
 
 
 build-userdoc:
@@ -256,7 +256,7 @@ build-pypi-dist:
   <<: *check_version
 
   stage: build
-  image: pauldmccarthy/fsleyes-py35-wxpy4-gtk2
+  image: pauldmccarthy/fsleyes-py36-wxpy4-gtk3
 
   tags:
     - docker
@@ -281,7 +281,7 @@ deploy-doc:
   <<: *setup_ssh
   stage: deploy
   when:  manual
-  image: python:3.5
+  image: python:3.6
 
   tags:
     - docker
@@ -299,7 +299,7 @@ deploy-pypi:
   <<: *setup_ssh
   stage: deploy
   when:  manual
-  image: python:3.5
+  image: python:3.6
 
   tags:
     - docker

CHANGELOG.rst

@@ -9,6 +9,28 @@ This document contains the ``fsleyes`` release history in reverse
 chronological order.
 
 
+0.31.2 (Tuesday October 22nd 2019)
+----------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* FSLeyes is now more lenient towards NIfTI images with extreme qform affines.
+* Various changes to improve GTK3 compatibility.
+* Various changes to reduce warnings and unnecessary output messages.
+
+
+Fixed
+^^^^^
+
+
+* Image texture data is now prepared off the main thread; this was the
+  behaviour before version 0.30.0, but was accidentally disabled for that
+  release.
+
+
 0.31.1 (Tuesday October 8th 2019)
 ---------------------------------
 

fsleyes/__init__.py

@@ -337,6 +337,18 @@ def _hacksAndWorkarounds():
     if fslplatform.frozen:
         os.environ.pop('MPLCONFIGDIR', None)
 
+    # nibabel rejects NIfTI images where the
+    # quaternion vector has a length greater
+    # than 1. This is fine, as it is mandated
+    # by the NIfTI spec. But FSL is much more
+    # lenient than nibabel, and nibabel can
+    # also reject some qforms due to float32
+    # imprecision. So here we're increasing
+    # the tolerance of nibabel to strange
+    # qforms.
+    import nibabel as nib
+    nib.Nifti1Header.quaternion_threshold = -1e5
+
     # OSX sometimes sets the local environment
     # variables to non-standard values, which
     # breaks the python locale module.

fsleyes/actions/applyflirtxfm.py

@@ -29,7 +29,7 @@ import numpy as np
 import wx
 
 import fsl.data.image      as fslimage
-import fsl.utils.transform as transform
+import fsl.transform.flirt as flirt
 import fsleyes.strings     as strings
 from . import                 base
 
@@ -87,7 +87,7 @@ def calculateTransform(overlay, overlayList, displayCtx, matFile, refFile):
     """Calculates a source voxel -> reference world transformation matrix
     from the given FLIRT transform and refernece image files.
 
-    See the :func:`fsl.utils.transform.flirtMatrixToSform` function.
+    See the :func:`fsl.transform.flirt.flirtMatrixToSform` function.
 
     :arg overlay:     The :class:`.Image` overlay - the source image of the
                       FLIRT transformation.
@@ -110,7 +110,7 @@ def calculateTransform(overlay, overlayList, displayCtx, matFile, refFile):
 
     flirtMat = np.loadtxt(matFile)
 
-    return transform.flirtMatrixToSform(flirtMat, overlay, refImg)
+    return flirt.flirtMatrixToSform(flirtMat, overlay, refImg)
 
 
 def promptForFlirtFiles(parent, overlay, overlayList, displayCtx, save=False):
@@ -260,8 +260,8 @@ def guessFlirtFiles(path):
         mat = op.join(regDir, mat)
         ref = op.join(regDir, ref)
 
-        try:    ref = fslimage.addExt(ref)
-        except: continue
+        try:              ref = fslimage.addExt(ref)
+        except Exception: continue
 
         if op.exists(mat):
             matFile = mat

fsleyes/actions/base.py

@@ -145,6 +145,14 @@ class Action(props.HasProperties):
         return self.__displayCtx
 
 
+    @property
+    def instance(self):
+        """Return the instance which owns this ``Action``, if relevant.
+        Returns ``None`` otherwise.
+        """
+        return self.__instance
+
+
     def __call__(self, *args, **kwargs):
         """Calls this action. An :exc:`ActionDisabledError` will be raised
         if :attr:`enabled` is ``False``.

fsleyes/actions/moviegif.py

@@ -19,7 +19,7 @@ import          PIL
 import          wx
 
 import fsl.utils.idle                 as idle
-import fsl.utils.transform            as transform
+import fsl.transform.affine           as affine
 import fsl.utils.settings             as fslsettings
 import fsleyes_widgets.utils.progress as progress
 from   fsleyes_widgets import            isalive
@@ -261,7 +261,7 @@ def makeGif(overlayList,
             # normalise the rotmat for this
             # frame to the rms difference
             # from the starting rotmat
-            frame = transform.rmsdev(ctx.startFrame, frame)
+            frame = affine.rmsdev(ctx.startFrame, frame)
 
             # Keep capturing frames until we
             # have performed a full 360 degree

fsleyes/actions/saveflirtxfm.py

@@ -15,7 +15,7 @@ import logging
 import numpy as np
 
 import fsl.data.image               as fslimage
-import fsl.utils.transform          as transform
+import fsl.transform.affine         as affine
 import fsleyes_widgets.utils.status as status
 import fsleyes.strings              as strings
 from . import                          base
@@ -95,4 +95,4 @@ def calculateTransform(overlay,
     if refImg is None:
         refImg = fslimage.Image(refFile, loadData=False)
 
-    return transform.sformToFlirtMatrix(overlay, refImg, srcXform)
+    return affine.sformToFlirtMatrix(overlay, refImg, srcXform)

fsleyes/actions/saveoverlay.py

@@ -46,7 +46,8 @@ class SaveOverlayAction(base.Action):
         :arg frame:       The :class:`.FSLeyesFrame`.
         """
         base.Action.__init__(self, overlayList, displayCtx, self.__saveOverlay)
-        self.__name = '{}_{}'.format(type(self).__name__, id(self))
+        self.__name       = '{}_{}'.format(type(self).__name__, id(self))
+        self.__registered = None
 
         displayCtx .addListener('selectedOverlay',
                                 self.__name,
@@ -64,6 +65,11 @@ class SaveOverlayAction(base.Action):
         """
         self.displayCtx .removeListener('selectedOverlay', self.__name)
         self.overlayList.removeListener('overlays',        self.__name)
+
+        if self.__registered is not None:
+            self.__registered.deregister(self.__name, 'saveState')
+            self.__registered = None
+
         base.Action.destroy(self)
 
 
@@ -82,19 +88,17 @@ class SaveOverlayAction(base.Action):
                         isinstance(overlay, fslimage.Image) and
                         (not overlay.saveState))
 
-        for ovl in self.overlayList:
-
-            if not isinstance(ovl, fslimage.Image):
-                continue
-
-            ovl.deregister(self.__name, 'saveState')
-
-            # Register a listener on the saved property
-            # of the currently selected image, so we can
-            # enable the save action when the image
-            # becomes 'unsaved', and vice versa.
-            if ovl is overlay:
-                ovl.register(self.__name,
+        if self.__registered is not None:
+            self.__registered.deregister(self.__name, 'saveState')
+            self.__registered = None
+
+        # Register a listener on the saved property
+        # of the currently selected image, so we can
+        # enable the save action when the image
+        # becomes 'unsaved', and vice versa.
+        if self.enabled:
+            self.__registered = overlay
+            overlay.register(self.__name,
                              self.__overlaySaveStateChanged,
                              'saveState')
 
@@ -108,28 +112,17 @@ class SaveOverlayAction(base.Action):
         see the :meth:`__selectedOverlayChanged` method.
         """
 
-        overlay = self.displayCtx.getSelectedOverlay()
-
-        if overlay is None:
-            self.enabled = False
-
-        elif not isinstance(overlay, fslimage.Image):
-            self.enabled = False
-        else:
-            self.enabled = not overlay.saveState
+        overlay = self.__registered
+        self.enabled = (overlay is not None) and (not overlay.saveState)
 
 
     def __saveOverlay(self):
         """Called when this :class:`.Action` is executed. Calls
-        :func:`saveOverlay` with the currentyl selected overlay.
+        :func:`saveOverlay` with the currently selected overlay.
         """
 
-        overlay = self.displayCtx.getSelectedOverlay()
-
-        if (overlay is not None)               and \
-           isinstance(overlay, fslimage.Image) and \
-           (not overlay.saveState):
-
+        overlay = self.__registered
+        if overlay is not None:
             display = self.displayCtx.getDisplay(overlay)
             saveOverlay(overlay, display)
 

fsleyes/actions/screenshot.py

@@ -82,7 +82,7 @@ class ScreenshotAction(base.Action):
         # it is available
         if 'png' in fmts:
             fmts = [('png', fmts['png'])] + \
-                   [(k, v) for k, v in fmts.items() if k is not 'png']
+                   [(k, v) for k, v in fmts.items() if k != 'png']
         else:
             fmts = list(fmts.items())
 

fsleyes/controls/atlasinfopanel.py

@@ -73,6 +73,7 @@ class AtlasInfoPanel(fslpanel.FSLeyesPanel):
         self.__infoPanel      = wxhtml.HtmlWindow(self.__contentPanel)
         self.__atlasList      = elistbox.EditableListBox(
             self.__contentPanel,
+            vgap=5,
             style=(elistbox.ELB_NO_ADD    |
                    elistbox.ELB_NO_REMOVE |
                    elistbox.ELB_NO_MOVE))
@@ -166,7 +167,7 @@ class AtlasInfoPanel(fslpanel.FSLeyesPanel):
 
         def onLoad(atlas):
 
-            if not self or self.destroyed():
+            if not self or self.destroyed:
                 return
 
             self.__enabledAtlases[atlasID] = atlas
@@ -499,6 +500,8 @@ class AtlasListWidget(wx.CheckBox):
 
         self.Bind(wx.EVT_CHECKBOX, self.__onEnable)
 
+        self.SetMinSize(self.GetBestSize())
+
 
     def __onEnable(self, ev):
         """Called when this ``AtlasListWidget`` is clicked. Toggles

fsleyes/controls/atlasmanagementpanel.py

@@ -55,6 +55,7 @@ class AtlasManagementPanel(fslpanel.FSLeyesPanel):
             labels=names,
             clientData=descs,
             tooltips=paths,
+            vgap=5,
             style=(elistbox.ELB_NO_MOVE |
                    elistbox.ELB_TOOLTIP_DOWN))
 

fsleyes/controls/atlasoverlaypanel.py

@@ -101,6 +101,7 @@ class AtlasOverlayPanel(fslpanel.FSLeyesPanel):
                                                    style=wx.SP_LIVE_UPDATE)
         self.__atlasList       = elistbox.EditableListBox(
             self.__contentPanel,
+            vgap=5,
             style=(elistbox.ELB_NO_ADD    |
                    elistbox.ELB_NO_REMOVE |
                    elistbox.ELB_NO_MOVE))
@@ -385,6 +386,7 @@ class AtlasOverlayPanel(fslpanel.FSLeyesPanel):
             # widgets asynchronously on the wx idle loop.
             regionList = elistbox.EditableListBox(
                 self.__regionPanel,
+                vgap=5,
                 style=(elistbox.ELB_NO_ADD    |
                        elistbox.ELB_NO_REMOVE |
                        elistbox.ELB_NO_MOVE))
@@ -546,7 +548,7 @@ class OverlayListWidget(wx.Panel):
 
             if not self or \
                not self.__atlasOvlPanel or \
-               self.__atlasOvlPanel .destroyed():
+               self.__atlasOvlPanel.destroyed:
                 return
 
             self.__atlasPanel.enableAtlasPanel()

fsleyes/controls/atlaspanel.py

@@ -322,7 +322,7 @@ class AtlasPanel(ctrlpanel.ControlPanel):
 
                 # The atlas panel may be destroyed
                 # before the atlas is loaded.
-                if not self or self.destroyed():
+                if not self or self.destroyed:
                     return
 
                 self.__loadedAtlases[atlasID, summary, res] = atlas

fsleyes/controls/colourbar.py

@@ -39,7 +39,7 @@ def colourBarMinorAxisSize(fontSize):
     # Fix the minor axis of the colour bar,
     # according to the font size, and a
     # constant size for the colour bar
-    return 2 * fontSize + 40
+    return round(2 * fontSize + 40)
 
 
 class ColourBar(props.HasProperties, notifier.Notifier):

fsleyes/controls/controlpanel.py

@@ -83,7 +83,7 @@ class SettingsPanel(ControlPanel):
 
         ControlPanel.__init__(self, *args, **kwargs)
 
-        self.__widgets = widgetlist.WidgetList(self)
+        self.__widgets = widgetlist.WidgetList(self, minHeight=24)
         self.__sizer   = wx.BoxSizer(wx.VERTICAL)
 
         self.SetSizer(self.__sizer)

fsleyes/controls/displayspacewarning.py

@@ -79,6 +79,8 @@ class DisplaySpaceWarning(fslpanel.FSLeyesPanel):
         self.__sizer    .Add(self.__realSizer, flag=wx.EXPAND)
 
         self.SetSizer(self.__sizer)
+        self.Fit()
+        self.__size = self.GetBestSize()
 
         self.__changeDS .Bind(wx.EVT_BUTTON, self.__onChangeDS)
 
@@ -117,6 +119,9 @@ class DisplaySpaceWarning(fslpanel.FSLeyesPanel):
         message is shown.
         """
 
+        if self.destroyed:
+            return
+
         parent       = self.GetParent()
         condition    = self.__warnCondition
         displayCtx   = self.displayCtx
@@ -144,10 +149,16 @@ class DisplaySpaceWarning(fslpanel.FSLeyesPanel):
         else:
             show = False
 
+        if show: size = self.__size
+        else:    size = (0, 0)
+
         if show:
             log.debug('Showing display space warning ({} / {})'.format(
                 displaySpace, condition))
 
+        self.SetMinSize(   size)
+        self.CacheBestSize(size)
+
         self.__sizer.Show(self.__realSizer, show)
         self.Layout()
         self.Fit()

fsleyes/controls/edittransformpanel.py

@@ -18,7 +18,7 @@ import numpy as np
 
 import fsl.data.image                       as fslimage
 import fsl.utils.idle                       as idle
-import fsl.utils.transform                  as transform
+import fsl.transform.affine                 as affine
 
 import fsleyes_props                        as props
 import fsleyes_widgets.floatslider          as fslider
@@ -457,12 +457,12 @@ class EditTransformPanel(ctrlpanel.ControlPanel):
             # of the image in world coordinates
             # to define the origin of rotation.
             shape  = self.__overlay.shape
-            lo, hi = transform.axisBounds(shape, self.__overlay.voxToWorldMat)
+            lo, hi = affine.axisBounds(shape, self.__overlay.voxToWorldMat)
             origin = [l + (h - l) / 2.0 for h, l in zip(hi, lo)]
         else:
             origin = self.displayCtx.worldLocation
 
-        return transform.compose(scales, offsets, rotations, origin)
+        return affine.compose(scales, offsets, rotations, origin)
 
 
     def __xformChanged(self, ev=None):
@@ -481,7 +481,7 @@ class EditTransformPanel(ctrlpanel.ControlPanel):
         else:                         v2wXform = self.__extraXform
 
         xform = self.__getCurrentXform()
-        xform = transform.concat(xform, v2wXform)
+        xform = affine.concat(xform, v2wXform)
 
         self.__formatXform(xform, self.__newXform)
 
@@ -491,7 +491,7 @@ class EditTransformPanel(ctrlpanel.ControlPanel):
         # the voxToWorldMat entirely. So we include
         # a worldToVoxMat transform to trick the
         # NiftiOpts code.
-        opts.displayXform = transform.concat(xform, overlay.worldToVoxMat)
+        opts.displayXform = affine.concat(xform, overlay.worldToVoxMat)
 
 
     def __onApply(self, ev):
@@ -511,7 +511,7 @@ class EditTransformPanel(ctrlpanel.ControlPanel):
         newXform = self.__getCurrentXform()
         opts     = self.displayCtx.getOpts(overlay)
 
-        xform = transform.concat(newXform, v2wXform)
+        xform = affine.concat(newXform, v2wXform)
 
         with props.suppress(opts, 'displayXform'):
             opts.displayXform     = np.eye(4)
@@ -622,7 +622,7 @@ class EditTransformPanel(ctrlpanel.ControlPanel):
         else:                         v2wXform = self.__extraXform
 
         newXform = self.__getCurrentXform()
-        v2wXform = transform.concat(newXform, v2wXform)
+        v2wXform = affine.concat(newXform, v2wXform)
 
         if affType == 'flirt':
             xform = saveflirtxfm.calculateTransform(

fsleyes/controls/filetreepanel.py

@@ -355,9 +355,9 @@ class FileTypePanel(elb.EditableListBox):
         :arg ftpanel: The :class:`.FileTreePanel`
         """
         elb.EditableListBox.__init__(
-            self, parent, style=(elb.ELB_NO_ADD    |
-                                 elb.ELB_NO_REMOVE |
-                                 elb.ELB_NO_MOVE))
+            self, parent, vgap=5, style=(elb.ELB_NO_ADD    |
+                                         elb.ELB_NO_REMOVE |
+                                         elb.ELB_NO_MOVE))
 
         self.__ftpanel = ftpanel
 
@@ -378,6 +378,7 @@ class FileTypePanel(elb.EditableListBox):
 
         for ftype in filetypes:
             toggle = wx.CheckBox(self)
+            toggle.SetMinSize(toggle.GetBestSize())
             self.Append(ftype, extraWidget=toggle)
             toggle.Bind(wx.EVT_CHECKBOX, self.__onToggle)
 

fsleyes/controls/locationpanel.py

@@ -17,7 +17,7 @@ import wx.html as wxhtml
 
 import numpy as np
 
-import fsl.utils.transform            as transform
+import fsl.transform.affine           as affine
 import fsl.utils.settings             as fslsettings
 import fsl.data.image                 as fslimage
 import fsl.data.mesh                  as fslmesh
@@ -408,7 +408,7 @@ class LocationInfoPanel(fslpanel.FSLeyesPanel):
             if w > width:  width  = w
             if h > height: height = h
 
-        return width + 5, height + 5
+        return width + 5, height
 
 
     def __selectedOverlayChanged(self, *a):
@@ -657,7 +657,7 @@ class LocationInfoPanel(fslpanel.FSLeyesPanel):
             shape    = refImage.shape[:3]
             vlo      = [0, 0, 0]
             vhi      = np.array(shape) - 1
-            wlo, whi = transform.axisBounds(shape, v2w)
+            wlo, whi = affine.axisBounds(shape, v2w)
             wstep    = refImage.pixdim[:3]
         else:
             vlo     = [0, 0, 0]
@@ -701,7 +701,7 @@ class LocationInfoPanel(fslpanel.FSLeyesPanel):
                   between the three location properties.
         """
 
-        if not self or self.destroyed():
+        if not self or self.destroyed:
             return
 
         if len(self.overlayList) == 0:       return