Merge branch 'rel/0.33.2' into 'v0.33'

Rel/0.33.2

See merge request fsl/fsleyes/fsleyes!209

CHANGELOG.rst

@@ -9,6 +9,41 @@ This document contains the ``fsleyes`` release history in reverse
 chronological order.
 
 
+0.33.2 (Tuesday 23rd June 2020)
+-------------------------------
+
+
+Added
+^^^^^
+
+
+* Added some more line styles to the plotting panels (!206).
+* Added a new "accessible" lookup table, courtesy of Paul Tol
+  (https://personal.sron.nl/~pault/) (!206).
+
+
+Changed
+^^^^^^^
+
+
+* Increased the default plotting line width (!206).
+* The default plot colours are now from a pre-generated accessible palette,
+  rather than being randomly generated (!206).
+* The default plot line style is also rotated, in addition the plot colour
+  (!206).
+* Adjusted the histogram panel so that, when plotting a probability histogram,
+  the values are normalised by bin-width (!203).
+* A minor adjustment to the default font, to improve readability on some
+  platforms (!202).
+
+
+Fixed
+^^^^^
+
+
+* Fixed an issue with FSLeyes not shutting down cleanly (!204).
+
+
 0.33.1 (Monday 8th June 2020)
 -----------------------------
 

apidoc/conf.py

@@ -371,12 +371,13 @@ latex_elements = {
 # special-members flag)
 autoclass_content = 'class'
 
-# Document private members and special members (e.g. __init__)
-autodoc_default_flags = ['private-members', 'special-members']
 
-# Documentation for python modules is in the same order
-# as the source code.
-autodoc_member_order = 'bysource'
+autodoc_default_options = {
+    'special-members' : True,
+    'private-members' : True,
+    'undoc-members'   : True,
+    'member-order'    : 'bysource',
+}
 
 def autodoc_skip_member(app, what, name, obj, skip, options):
 

assets/luts/order.txt

@@ -5,3 +5,4 @@ freesurfercolorlut         FreeSurferColorLut
 mgh-cma-freesurfer         MGH/CMA/Freesurfer
 melodic-classes            Melodic IC classification
 random_big                 Random (big)
+paul_tol_accessible        Accessible

assets/luts/paul_tol_accessible.lut

+# The "bright" colour-blind accessible colour palette,
+# devised by Paul Tol (https://personal.sron.nl/~pault/).
+1 0.266667 0.466667 0.666667 Blue
+2 0.400000 0.800000 0.933333 Cyan
+3 0.133333 0.533333 0.200000 Green
+4 0.800000 0.733333 0.266667 Yellow
+5 0.933333 0.400000 0.466667 Red
+6 0.666667 0.200000 0.466667 Purple
+7 0.666667 0.666667 0.666667 Grey

fsleyes/actions/addmaskdataseries.py

@@ -133,9 +133,9 @@ class AddMaskDataSeriesAction(base.Action):
         xdata = np.arange(len(ydata))
 
         ds.colour    = self.__plotPanel.getOverlayPlotColour(overlay)
+        ds.lineStyle = self.__plotPanel.getOverlayPlotStyle(overlay)
+        ds.lineWidth = 2
         ds.alpha     = 1
-        ds.lineWidth = 1
-        ds.lineStyle = '-'
         ds.label     = '{} [mask: {}]'.format(overlay.name, maskimg.name)
 
         # We have to run the data through

fsleyes/actions/addroihistogram.py

@@ -135,9 +135,9 @@ class AddROIHistogramAction(base.Action):
                                              self.displayCtx,
                                              self.__plotPanel)
         ds.colour    = self.__plotPanel.getOverlayPlotColour(overlay)
+        ds.lineStyle = self.__plotPanel.getOverlayPlotStyle(overlay)
+        ds.lineWidth = 2
         ds.alpha     = 1
-        ds.lineWidth = 1
-        ds.lineStyle = '-'
         ds.label     = '{} [mask: {}]'.format(overlay.name, maskimg.name)
 
         # We have to run the data through

fsleyes/colourmaps.py

@@ -855,7 +855,10 @@ def fileType(fname):
         return 'vest'
 
     with open(fname, 'rt') as f:
-        line = f.readline().strip()
+        for line in f:
+            line = f.readline().strip()
+            if (line != '') and (not line.startswith('#')):
+                break
 
     tkns = list(line.split())
 

fsleyes/frame.py

@@ -164,7 +164,7 @@ class FSLeyesFrame(wx.Frame):
             fontSize = 10
 
         font.SetPointSize(fontSize)
-        font.SetWeight(wx.FONTWEIGHT_LIGHT)
+        font.SetWeight(wx.FONTWEIGHT_NORMAL)
         self.SetFont(font)
 
         self.__overlayList = overlayList

fsleyes/gl/__init__.py

@@ -615,6 +615,7 @@ class GLContext(object):
             # created, we no longer need
             # references to the wx objects
             app           = self.__app
+            self.__parent.Close()
             self.__parent = None
             self.__canvas = None
             self.__app    = None

fsleyes/plotting/dataseries.py

@@ -71,8 +71,18 @@ class DataSeries(props.HasProperties):
     """Line width. """
 
 
-    lineStyle = props.Choice(('-', '--', '-.', ':'))
-    """Line style. """
+    lineStyle = props.Choice(('-',
+                              '--',
+                              '-.',
+                              ':',
+                              (0, (5, 7)),
+                              (0, (1, 7)),
+                              (0, (4, 10, 1, 10)),
+                              (0, (4, 1, 1, 1, 1, 1)),
+                              (0, (4, 1, 4, 1, 1, 1))))
+    """Line style. See
+    https://matplotlib.org/gallery/lines_bars_and_markers/linestyles.html
+    """
 
 
     def __init__(self, overlay, overlayList, displayCtx, plotPanel):

fsleyes/plotting/histogramseries.py

@@ -222,6 +222,13 @@ class HistogramSeries(dataseries.DataSeries):
         return self.__xdata, self.__ydata
 
 
+    @property
+    def binWidth(self):
+        """Returns the width of one bin for this :class:`HistogramSeries`. """
+        lo, hi = self.dataRange.x
+        return (hi - lo) / self.nbins
+
+
     def getVertexData(self):
         """Returns a ``numpy`` array of shape ``(N, 2)``, which contains a
         set of "vertices" which can be used to display the histogram data
@@ -241,7 +248,8 @@ class HistogramSeries(dataseries.DataSeries):
         return verts
 
 
-    def getNumHistogramValues(self):
+    @property
+    def numHistogramValues(self):
         """Returns the number of values which were used in calculating the
         histogram.
         """

fsleyes/profiles/histogramprofile.py

@@ -427,7 +427,9 @@ class RangePolygon(patches.Polygon):
             # post-processing normally performed
             # by the HistogramPanel to the data.
             if hsPanel.histType == 'probability':
-                vertices[:, 1] /= hs.getNumHistogramValues()
+                nvals    = hs.numHistogramValues
+                binWidth = hs.binWidth
+                vertices[:, 1] /= (nvals * binWidth)
 
         # Nothing to plot, or we shouldn't
         # be plotting the range overlay
@@ -457,7 +459,9 @@ class RangePolygon(patches.Polygon):
             yval = float(histy[xidx])
 
             if hsPanel.histType == 'probability':
-                yval /= hs.getNumHistogramValues()
+                nvals    = hs.numHistogramValues
+                binWidth = hs.binWidth
+                yval /= (nvals * binWidth)
 
             vertices = np.array([[lo, 0], [lo, yval], [hi, yval], [hi, 0]])
 

fsleyes/strings.py

@@ -1329,10 +1329,17 @@ choices = TypeDict({
     'HistogramPanel.plotType' : {'centre'      : 'Bin centres',
                                  'edge'        : 'Bin edges'},
 
-    'DataSeries.lineStyle' : {'-'  : 'Solid line',
-                              '--' : 'Dashed line',
-                              '-.' : 'Dash-dot line',
-                              ':'  : 'Dotted line'},
+    'DataSeries.lineStyle' : {
+        '-'                      : 'Solid line',
+        '--'                     : 'Dashed line',
+        '-.'                     : 'Dash-dot line',
+        ':'                      : 'Dotted line',
+        (0, (5, 7))              : 'Loose dashed line',
+        (0, (1, 7))              : 'Loose dotted line',
+        (0, (4, 10, 1, 10))      : 'Loose dash-dot line',
+        (0, (4, 1, 1, 1, 1, 1))  : 'Dash-dot-dot line',
+        (0, (4, 1, 4, 1, 1, 1))  : 'Dash-dash-dot line',
+    },
 
     'TimeSeriesPanel.plotMode' : {'normal'        : 'Normal - no '
                                                     'scaling/offsets',

fsleyes/version.py

@@ -14,7 +14,7 @@ version number. See also the :mod:`fsl.version` module.
 """
 
 
-__version__ = '0.33.1'
+__version__ = '0.33.2'
 """Current version number, as a string. The FSLeyes version number consists
 of three numbers, separated by a period, which roughly obeys the Semantic
 Versioning conventions (http://semver.org/).

fsleyes/views/histogrampanel.py

@@ -254,9 +254,9 @@ class HistogramPanel(plotpanel.OverlayPlotPanel):
 
         hs = hsType(overlay, self.overlayList, self.displayCtx, self)
         hs.colour      = self.getOverlayPlotColour(overlay)
+        hs.lineStyle   = self.getOverlayPlotStyle(overlay)
+        hs.lineWidth   = 2
         hs.alpha       = 1
-        hs.lineWidth   = 1
-        hs.lineStyle   = '-'
 
         return hs, [], []
 
@@ -310,9 +310,16 @@ class HistogramPanel(plotpanel.OverlayPlotPanel):
             return xdata, ydata
 
         # Or a HistogramSeries instance
-        nvals = hs.getNumHistogramValues()
-        if   self.histType == 'count':       return xdata, ydata
-        elif self.histType == 'probability': return xdata, ydata / nvals
+        if self.histType == 'count':
+            return xdata, ydata
+
+        # Normalise by bin width to produce a
+        # probability density function, so it
+        # will look approximately the same,
+        # regardless of the current nbins setting
+        elif self.histType == 'probability':
+            nvals = hs.numHistogramValues
+            return xdata, ydata / (nvals * hs.binWidth)
 
 
     def __selectedOverlayChanged(self, *a):

fsleyes/views/plotpanel.py

@@ -831,6 +831,7 @@ class PlotPanel(viewpanel.ViewPanel):
                 labels,
                 loc='upper right',
                 fontsize=10,
+                handlelength=3,
                 fancybox=True)
             legend.get_frame().set_alpha(0.6)
 
@@ -1131,8 +1132,17 @@ class OverlayPlotPanel(PlotPanel):
     the same (initial) colour is used for the same overlay, across multiple
     plots.
 
-    Sub-classes should use the :meth:`getOverlayPlotColour` method to retrieve
-    the initial colour to use for a given overlay.
+    See also :attr:`plotStyles`.
+
+    Sub-classes should use the :meth:`getOverlayPlotColour` and
+    :meth:`getOverlayPlotStyle`methods to retrieve the initial colour and
+    linestyle to use for a given overlay.
+    """
+
+
+    plotStyles = {}
+    """This dictionary is used to store a collection of ``{overlay : colour}``
+    mappings - it is used in conjunction with :attr:`plotColours`.
     """
 
 
@@ -1182,6 +1192,15 @@ class OverlayPlotPanel(PlotPanel):
         self.__refreshProps  = {}
         self.__refreshCounts = {}
 
+        # Pre-generated default colours and line
+        # styles to use - see plotColours, plotStyles,
+        # getOverlayPlotColour, and getOverlayPlotStyle
+        lut    = fslcm.getLookupTable('paul_tol_accessible')
+        styles = plotting.DataSeries.lineStyle.getChoices()
+        limit  = min(len(lut), len(styles))
+        self.__defaultColours = [l.colour for l in lut[   :limit]]
+        self.__defaultStyles  = [s        for s in styles[:limit]]
+
         self            .addListener('dataSeries',
                                      self.__name,
                                      self.__dataSeriesChanged)
@@ -1276,12 +1295,36 @@ class OverlayPlotPanel(PlotPanel):
         colour = self.plotColours.get(overlay)
 
         if colour is None:
-            colour = fslcm.randomDarkColour()
+            idx    = len(self.plotColours) % len(self.__defaultColours)
+            colour = self.__defaultColours[idx]
             self.plotColours[overlay] = colour
 
         return colour
 
 
+    def getOverlayPlotStyle(self, overlay):
+        """Returns an initial line style to use for plots associated with the
+        given overlay. If a colour is present in the  :attr:`plotStyles`
+        dictionary, it is returned. Otherwise a line style is generated,
+        added to ``plotStyles``, and returned.
+
+        The format of the returned line style is suitable for use with the
+        ``linestyle`` argument of the ``matplotlib`` ``plot``functions.
+        """
+
+        if isinstance(overlay, fsloverlay.ProxyImage):
+            overlay = overlay.getBase()
+
+        style = self.plotStyles.get(overlay)
+
+        if style is None:
+            idx   = len(self.plotStyles) % len(self.__defaultStyles)
+            style = self.__defaultStyles[idx]
+            self.plotStyles[overlay] = style
+
+        return style
+
+
     @actions.action
     def addDataSeries(self):
         """Every :class:`.DataSeries` which is currently plotted, and has not
@@ -1374,7 +1417,9 @@ class OverlayPlotPanel(PlotPanel):
 
         .. note:: Sub-class implementations should set the
                   :attr:`.DataSeries.colour` property to that returned by
-                  the :meth:`getOverlayPlotColour` method.
+                  the :meth:`getOverlayPlotColour` method, and the
+                  :attr:`.DataSeries.lineStyle` property to that returned by
+                  the :meth:`getOverlayPlotStyle` method
 
 
         Different ``DataSeries`` types need to be re-drawn when different

fsleyes/views/powerspectrumpanel.py

@@ -207,9 +207,9 @@ class PowerSpectrumPanel(plotpanel.OverlayPlotPanel):
             return None, None, None
 
         ps.colour    = self.getOverlayPlotColour(overlay)
+        ps.lineStyle = self.getOverlayPlotStyle(overlay)
+        ps.lineWidth = 2
         ps.alpha     = 1.0
-        ps.lineWidth = 1
-        ps.lineStyle = '-'
 
         return ps, targets, propNames
 

fsleyes/views/timeseriespanel.py

@@ -344,9 +344,9 @@ class TimeSeriesPanel(plotpanel.OverlayPlotPanel):
             return None, None, None
 
         ts.colour    = self.getOverlayPlotColour(overlay)
+        ts.lineStyle = self.getOverlayPlotStyle(overlay)
+        ts.lineWidth = 2
         ts.alpha     = 1
-        ts.lineWidth = 1
-        ts.lineStyle = '-'
 
         return ts, targets, propNames
 

tests/test_histogramseries.py

@@ -100,7 +100,7 @@ def test_HistogramSeries():
     gotx, goty = hs.getData()
 
     assert hs.nbins == nbins
-    assert hs.getNumHistogramValues() == nvals
+    assert hs.numHistogramValues == nvals
     assert np.all(np.isclose(hx, gotx))
     assert np.all(np.isclose(hy, goty))