rotational_spectra

xmipp3/protocols/protocol_rotational_spectra.py → xmipp3/legacy/protocols/protocol_rotational_spectra.py

@@ -1,4 +1,3 @@
-# **************************************************************************
 # *
 # * Authors:     Josue Gomez Blanco ([email protected])
 # *

xmipp3/protocols.conf

@@ -70,7 +70,6 @@ Protocols SPA = [
 			{"tag": "section", "text": "more", "openItem": "False", "children": [
 				{"tag": "protocol", "value": "XmippProtML2D", "text": "default"},
 				{"tag": "protocol", "value": "XmippProtKerdensom", "text": "default"},
-				{"tag": "protocol", "value": "XmippProtRotSpectra", "text": "default"}				
 			]}
 		]}
 	]},

xmipp3/protocols/__init__.py

@@ -96,7 +96,7 @@
 from .protocol_resolution_deepres import XmippProtDeepRes
 from .protocol_postProcessing_deepPostProcessing import XmippProtDeepVolPostProc
 from .protocol_rotate_volume import XmippProtRotateVolume
-from .protocol_rotational_spectra import XmippProtRotSpectra
+#from .protocol_rotational_spectra import XmippProtRotSpectra
 from .protocol_rotational_symmetry import XmippProtRotationalSymmetry
 from .protocol_screen_particles import XmippProtScreenParticles
 from .protocol_screen_deepConsensus import XmippProtScreenDeepConsensus, XmippProtDeepConsSubSet

xmipp3/tests/test_protocols_xmipp_2d.py

@@ -1141,33 +1141,6 @@ def _checkTranslationScaling(self, protAssign, protParticles, shiftsAppliedBefor
         [self.assertAlmostEqual(inT * scale, outT) for inT, outT in zip(inTranslation, outTranslation)]
 
 
-class TestXmippRotSpectra(TestXmippBase):
-    """This class check if the protocol to calculate the rotational spectra from particles in Xmipp works properly."""
-    @classmethod
-    def setUpClass(cls):
-        setupTestProject(cls)
-        TestXmippBase.setData('mda')
-        cls.protImport = cls.runImportParticles(cls.particlesFn, 3.5)
-        cls.align2D = cls.runCL2DAlign(cls.protImport.outputParticles)
-
-    def test_rotSpectra(self):
-        print("Run Rotational Spectra")
-        xmippProtRotSpectra = self.newProtocol(XmippProtRotSpectra, SomXdim=2, SomYdim=2)
-        xmippProtRotSpectra.inputParticles.set(self.align2D.outputParticles)
-        self.launchProtocol(xmippProtRotSpectra)        
-        self.assertIsNotNone(xmippProtRotSpectra.outputClasses, "There was a problem with Rotational Spectra")
-
-    def test_rotSpectraMask(self):
-        print("Run Rotational Spectra with Mask")
-        protMask = self.runCreateMask(3.5, 100)
-        xmippProtRotSpectra = self.newProtocol(XmippProtRotSpectra, useMask=True, SomXdim=2, SomYdim=2)
-        xmippProtRotSpectra.inputParticles.set(self.align2D.outputParticles)
-        xmippProtRotSpectra.useMask.set(True)
-        xmippProtRotSpectra.Mask.set(protMask.outputMask)
-        self.launchProtocol(xmippProtRotSpectra)
-        self.assertIsNotNone(xmippProtRotSpectra.outputClasses, "There was a problem with Rotational Spectra")
-
-
 class TestXmippKerdensom(TestXmippBase):
     """This class check if the protocol to calculate the kerdensom from particles in Xmipp works properly."""
     @classmethod

xmipp3/viewers/viewer.py

@@ -41,7 +41,7 @@
 from xmipp3.protocols import XmippProtKerdensom
 from xmipp3.protocols import XmippParticlePickingAutomatic
 from xmipp3.protocols import XmippProtParticlePickingPairs
-from xmipp3.protocols import XmippProtRotSpectra
+#from xmipp3.protocols import XmippProtRotSpectra
 from xmipp3.protocols import XmippProtScreenParticles
 from xmipp3.protocols import XmippProtCTFMicrographs
 from xmipp3.protocols import XmippProtValidateNonTilt
@@ -70,7 +70,6 @@ class XmippViewer(DataViewer):
                 XmippProtExtractParticlesPairs,
                 XmippProtKerdensom,
                 XmippProtParticlePickingPairs,
-                XmippProtRotSpectra,
                 XmippProtScreenParticles,
                 XmippProtCTFMicrographs,
                 XmippProtValidateNonTilt,
@@ -187,15 +186,6 @@ def _visualize(self, obj, **kwargs):
             #                                     ratio2Value=4.5)
             # self._views.append(MovieGainMonitorPlotter(movieGainMonitor))
 
-        elif issubclass(cls, XmippProtRotSpectra):
-            self._visualize(obj.outputClasses,
-                            viewParams={'columns': obj.SomXdim.get(),
-                                        RENDER: ' spectraPlot._filename average._filename',
-                                        ZOOM: 30,
-                                        VISIBLE: 'enabled id _size average._filename '
-                                                 'spectraPlot._filename',
-                                        'labels': 'id _size',
-                                        SORT_BY: 'id'})
 
         elif issubclass(cls, XmippProtKerdensom):
             self._visualize(obj.outputClasses, viewParams={'columns': obj.SomXdim.get(),

xmipp3/wizards.py

@@ -41,7 +41,7 @@
     XmippProtFilterParticles, XmippProtFilterVolumes, XmippProtMaskParticles,
     XmippProtMaskVolumes, XmippProtAlignVolume, XmippProtCL2D,
     XmippProtHelicalParameters, XmippProtConsensusPicking, XmippProtMonoRes,
-    XmippProtRotSpectra, XmippProtReconstructHighRes, XmippProtExtractUnit,
+    XmippProtReconstructHighRes, XmippProtExtractUnit,
     XmippProtShiftParticles, XmippProtVolumeDeformZernike3D, XmippProtStructureMapZernike3D,
     XmippProtSubtractProjection, XmippProtBoostParticles)
 
@@ -220,8 +220,7 @@ def show(self, form):
 
 
 class XmippParticleMaskRadiiWizard(ParticlesMaskRadiiWizard):
-    _targets = [(XmippProtMaskParticles, ['innerRadius', 'outerRadius']),
-                (XmippProtRotSpectra, ['spectraInnerRadius', 'spectraOuterRadius'])]
+    _targets = [(XmippProtMaskParticles, ['innerRadius', 'outerRadius'])]
 
     def _getParameters(self, protocol):