fix viewer errors

relion/viewers/viewer_base.py

@@ -277,7 +277,7 @@ def _getZoom(self):
             zoom = 100
         return zoom
 
-    def _showImagesInClasses(self):
+    def _showImagesInClasses(self, param=None):
         """ Read Relion _data.star images file and
         generate a new metadata with the Xmipp classification standard:
         a 'classes' block and a 'class00000?_images' block per class.
@@ -297,7 +297,7 @@ def _showImagesInClasses(self):
 
         return views
 
-    def _showClassesOnly(self):
+    def _showClassesOnly(self, param=None):
         views = []
         viewParams = {showj.MODE: showj.MODE_GALLERY,
                       showj.RENDER: 'rlnReferenceImage',
@@ -317,7 +317,7 @@ def _showClassesOnly(self):
     # showImagesAngularAssignment
     # =============================================================================
     @protected_show
-    def _showImagesAngularAssignment(self):
+    def _showImagesAngularAssignment(self, param=None):
         views = []
 
         for it in self._iterations:
@@ -332,7 +332,7 @@ def _showImagesAngularAssignment(self):
         return views
 
     @protected_show
-    def _showOptimiserFile(self):
+    def _showOptimiserFile(self, param=None):
         views = []
 
         for it in self._iterations:
@@ -348,7 +348,7 @@ def _showOptimiserFile(self):
     # =============================================================================
     # showLLRelion
     # =============================================================================
-    def _showLL(self):
+    def _showLL(self, param=None):
         views = []
         for it in self._iterations:
             fn = self.protocol._getIterData(it)
@@ -359,7 +359,7 @@ def _showLL(self):
     # =============================================================================
     # ShowPMax
     # =============================================================================
-    def _showPMax(self):
+    def _showPMax(self, param=None):
         labels = ['rlnIterationNumber', 'rlnAveragePmax',
                   'rlnLogLikelihood']
         tablePMax = Table(columns=labels)
@@ -389,7 +389,7 @@ def _showPMax(self):
     # =============================================================================
     # Get classes info per iteration
     # =============================================================================
-    def _plotClassDistribution(self):
+    def _plotClassDistribution(self, param=None):
         labels = ["rlnClassDistribution", "rlnAccuracyRotations"]
         if Plugin.IS_GT30():
             labels.append("rlnAccuracyTranslationsAngst")
@@ -470,7 +470,7 @@ def map_index_to_rgb_color(ind):
     # =============================================================================
     # ShowChanges
     # =============================================================================
-    def _showChanges(self):
+    def _showChanges(self, param=None):
         labels = ['rlnIterationNumber'] + self.protocol.CHANGE_LABELS
         tableChanges = Table(columns=labels)
 
@@ -497,7 +497,7 @@ def _showChanges(self):
     # ShowVolumes
     # =============================================================================
     @protected_show
-    def _showVolumes(self):
+    def _showVolumes(self, param=None):
         if self.displayVol == VOLUME_CHIMERA:
             return self._showVolumesChimera()
         elif self.displayVol == VOLUME_SLICES:
@@ -546,7 +546,7 @@ def _showVolumesChimera(self):
     # showAngularDistribution
     # =============================================================================
     @protected_show
-    def _showAngularDistribution(self):
+    def _showAngularDistribution(self, param=None):
         views = []
 
         if self.displayAngDist == ANGDIST_CHIMERA:
@@ -635,7 +635,7 @@ def _createAngDist2D(self, it):
     def _getFigure(self):
         return None if self.figure == 0 else 'active'
 
-    def _showSSNR(self):
+    def _showSSNR(self, param=None):
         prefixes = self._getPrefixes()
         nrefs = len(self._refsList)
         n = nrefs * len(prefixes)
@@ -678,7 +678,7 @@ def _plotSSNR(self, a, fn, table, label):
     # =============================================================================
     # plotFSC
     # =============================================================================
-    def _showFSC(self):
+    def _showFSC(self, param=None):
         print("Showing FSC for iterations: ", self._iterations)
         threshold = self.resolutionThresholdFSC.get()
 

relion/viewers/viewer_ctfrefine.py

@@ -239,7 +239,7 @@ def show(self, event=None):
         self.plotter.getColorBar(sc2)
         self.plotter.show()
 
-    def _displayBeamTilt(self):
+    def _displayBeamTilt(self, param=None):
         phaseDifferenceFn = self.protocol.fileWithPhaseDifferenceName()
         modelFitFn = self.protocol.fileWithModelFitterName()
 
@@ -267,7 +267,7 @@ def createScipionPartView(self, filename):
                           env=self._env,
                           viewParams=viewParams)
 
-    def _displayParticles(self):
+    def _displayParticles(self, param=None):
         views = []
         fn = self.protocol.outputParticles.getFileName()
         v = self.createScipionPartView(fn)

relion/viewers/viewer_postprocess.py

@@ -114,7 +114,7 @@ def _showVolumesChimera(self, volPath):
         view = ChimeraClientView(volPath)
         return [view]
 
-    def _showVolume(self):
+    def _showVolume(self, param=None):
         volPath = self.protocol._getExtraPath('postprocess.mrc:mrc')
 
         if self.displayVol == VOLUME_CHIMERA:
@@ -123,7 +123,7 @@ def _showVolume(self):
         elif self.displayVol == VOLUME_SLICES:
             return self._showVolumeShowj(volPath)
 
-    def _showMaskedVolume(self):
+    def _showMaskedVolume(self, param=None):
         volPath = self.protocol._getExtraPath('postprocess_masked.mrc:mrc')
 
         if self.displayMaskedVol == VOLUME_CHIMERA:
@@ -138,7 +138,7 @@ def _showMaskedVolume(self):
     def _getFigure(self):
         return None if self.figure == 0 else 'active'
 
-    def _showFSC(self):
+    def _showFSC(self, param=None):
         threshold = self.resolutionThresholdFSC.get()
 
         fscViewer = FscViewer(project=self.protocol.getProject(),
@@ -172,7 +172,7 @@ def _plotFSC(self, a, model_star, label, legend=None):
     # =========================================================================
     # plotGuinier
     # =========================================================================
-    def _showGuinier(self):
+    def _showGuinier(self, param=None):
         xplotter = RelionPlotter(windowTitle='Guinier Plot')
         a = xplotter.createSubPlot("", 'Angstroms^-2', 'log(Amplitude)',
                                    yformat=False)

setup.py

@@ -65,7 +65,7 @@
     # For a discussion on single-sourcing the version across setup.py and the
     # project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    version='3.0.0a2',  # Required
+    version='3.0.0a4',  # Required
 
     # This is a one-line description or tagline of what your project does. This
     # corresponds to the "Summary" metadata field: