From ebd0769e5cf7486eff5b1c423fbfad53bf196c66 Mon Sep 17 00:00:00 2001 From: Grigory Sharov Date: Sun, 17 May 2020 18:03:18 +0100 Subject: [PATCH] fix viewer errors --- relion/viewers/viewer_base.py | 24 ++++++++++++------------ relion/viewers/viewer_ctfrefine.py | 4 ++-- relion/viewers/viewer_postprocess.py | 8 ++++---- setup.py | 2 +- 4 files changed, 19 insertions(+), 19 deletions(-) diff --git a/relion/viewers/viewer_base.py b/relion/viewers/viewer_base.py index 9a926e9d..76cb049a 100644 --- a/relion/viewers/viewer_base.py +++ b/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() diff --git a/relion/viewers/viewer_ctfrefine.py b/relion/viewers/viewer_ctfrefine.py index 6c173d3d..4cd9da87 100644 --- a/relion/viewers/viewer_ctfrefine.py +++ b/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) diff --git a/relion/viewers/viewer_postprocess.py b/relion/viewers/viewer_postprocess.py index afaf9818..3bc5f9b6 100644 --- a/relion/viewers/viewer_postprocess.py +++ b/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) diff --git a/setup.py b/setup.py index feeca675..11e2c46a 100644 --- a/setup.py +++ b/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: