Merge pull request #224 from scipion-em/rc3.0.0b4

Rc3.0.0b4

relion/__init__.py

@@ -33,6 +33,7 @@
 
 _logo = "relion_logo.png"
 _references = ['Scheres2012a', 'Scheres2012b', 'Kimanius2016', 'Zivanov2018']
+_url = "https://github.com/scipion-em/scipion-em-relion"
 
 
 class Plugin(pwem.Plugin):

relion/convert/convert31.py

@@ -106,12 +106,20 @@ def update(self, ogId, **kwargs):
 
     def updateAll(self, **kwargs):
         """ Update all Optics Groups with these values. """
+        missing = {k: v for k, v in kwargs.items() if not self.hasColumn(k)}
+        existing  = {k: v for k, v in kwargs.items() if self.hasColumn(k)}
+
+        self.addColumns(**missing)
+
         for og in self:
-            self.update(og.rlnOpticsGroup, **kwargs)
+            self.update(og.rlnOpticsGroup, **existing)
 
     def add(self, newOg):
         self.__store(newOg)
 
+    def hasColumn(self, colName):
+        return hasattr(self.first(), colName)
+
     def addColumns(self, **kwargs):
         """ Add new columns with default values (type inferred from it). """
         items = self.first()._asdict().items()
@@ -395,7 +403,7 @@ def writeSetOfParticles(self, partsSet, starFile, **kwargs):
         extraLabels = kwargs.get('extraLabels', [])
         extraLabels.extend(PARTICLE_EXTRA_LABELS)
         if kwargs.get('fillRandomSubset'):
-            extraLabels.append('_rlnRandomSubset')
+            extraLabels.append('rlnRandomSubset')
 
         self._extraLabels = [l for l in extraLabels
                              if firstPart.hasAttribute('_%s' % l)]

relion/protocols/protocol_autopick_ref.py

@@ -219,15 +219,13 @@ def _defineParams(self, form):
                            'in the micrographs.')
 
         form.addParam('refsCtfCorrected', params.BooleanParam, default=True,
-                      condition=refCondition,
                       label='Are References CTF corrected?',
                       help='Set to Yes if the references were created with '
                            'CTF-correction inside RELION.\n'
                            'If set to Yes, the input micrographs should contain '
                            'the CTF information.')
 
         form.addParam('ignoreCTFUntilFirstPeak', params.BooleanParam,
-                      condition=refCondition,
                       default=False,
                       label='Ignore CTFs until first peak?',
                       help='Set this to Yes, only if this option was also used '
@@ -399,7 +397,7 @@ def getAutopickParams(self):
         else:  # 3D reference
             params += ' --ref ../../reference_3d.mrc'
             params += ' --sym %s' % self.symmetryGroup
-            params += ' --healpix_order %s' % self.angularSamplingDeg
+            params += ' --healpix_order %d' % (int(self.angularSamplingDeg.get()) + 1)
 
         ps = self.getInputReferences().getSamplingRate()
         params += ' --angpix_ref %0.5f' % ps
@@ -410,6 +408,9 @@ def getAutopickParams(self):
         if self.refsCtfCorrected:
             params += ' --ctf'
 
+        if self.ignoreCTFUntilFirstPeak:
+            params += ' --ctf_intact_first_peak'
+
         params += ' --ang %d' % self.angularSampling
         # Negative values for filters means no-filter
         if self.lowpassFilterRefs > 0:

relion/protocols/protocol_base.py

@@ -174,7 +174,6 @@ def _defineParams(self, form):
                            'of input particles will be put into the'
                            'star file that is generated.')
         form.addParam('maskDiameterA', IntParam, default=-1,
-                      condition='not doContinue',
                       label='Particle mask diameter (A)',
                       help='The experimental images will be masked with a '
                            'soft circular mask with this <diameter>. '
@@ -289,6 +288,7 @@ def _defineParams(self, form):
                                'when the mask contains only a relatively '
                                'small volume inside the box.')
             form.addParam('isMapAbsoluteGreyScale', BooleanParam, default=False,
+                          condition='not doContinue',
                           label="Is initial 3D map on absolute greyscale?",
                           help='The probabilities are based on squared differences,'
                                ' so that the absolute grey scale is important. \n'
@@ -317,7 +317,7 @@ def _defineParams(self, form):
             self.addSymmetry(form)
 
             form.addParam('initialLowPassFilterA', FloatParam, default=60,
-                          condition='not is2D',
+                          condition='not is2D and not doContinue',
                           label='Initial low-pass filter (A)',
                           help='It is recommended to strongly low-pass filter your '
                                'initial reference map. If it has not yet been '
@@ -477,14 +477,14 @@ def _defineParams(self, form):
                       label='Perform image alignment?', condition="isClassify",
                       help='If set to No, then rather than performing both alignment '
                            'and classification, only classification will be performed. '
-                           'This allows the use of very focused masks.This requires '
+                           'This allows the use of very focused masks. This requires '
                            'that the optimal orientations of all particles are already '
                            'calculated.')
         if self.IS_3D:
             form.addParam('angularSamplingDeg', EnumParam, default=2,
                           choices=ANGULAR_SAMPLING_LIST,
                           label='Initial angular sampling (deg)',
-                          condition='not isClassify or doImageAlignment',
+                          condition='doImageAlignment and (isClassify or not doContinue)',
                           help='There are only a few discrete angular samplings'
                                ' possible because we use the HealPix library to'
                                ' generate the sampling of the first two Euler '
@@ -505,7 +505,7 @@ def _defineParams(self, form):
                                'the sampling rate will be increased \n'
                                'automatically after that.')
         form.addParam('offsetSearchRangePix', FloatParam, default=5,
-                      condition='not isClassify or doImageAlignment',
+                      condition='doImageAlignment and (isClassify or not doContinue)',
                       label='Initial offset range (pix)',
                       help='Probabilities will be calculated only for '
                            'translations in a circle with this radius (in '
@@ -514,7 +514,7 @@ def _defineParams(self, form):
                            'translation for each image in the previous '
                            'iteration.')
         form.addParam('offsetSearchStepPix', FloatParam, default=1.0,
-                      condition='not isClassify or doImageAlignment',
+                      condition='doImageAlignment and (isClassify or not doContinue)',
                       label='Initial offset step (pix)',
                       help='Translations will be sampled with this step-size '
                            '(in pixels). Translational sampling is also done '
@@ -548,6 +548,7 @@ def _defineParams(self, form):
                                    'get higher weights than those further away.')
             else:
                 form.addParam('localSearchAutoSamplingDeg', EnumParam,
+                              condition='not doContinue',
                               default=4, choices=ANGULAR_SAMPLING_LIST,
                               label='Local search from auto-sampling (deg)',
                               help='In the automated procedure to increase the '
@@ -578,6 +579,7 @@ def _defineParams(self, form):
 
         if self.IS_CLASSIFY and self.IS_GT30():
             form.addParam('allowCoarserSampling', BooleanParam,
+                          condition='doImageAlignment',
                           default=False,
                           label='Allow coarser sampling?',
                           help='If set to Yes, the program will use '
@@ -614,6 +616,7 @@ def _defineParams(self, form):
 
     def addSymmetry(self, container):
         container.addParam('symmetryGroup', StringParam, default='c1',
+                           condition='not doContinue',
                            label="Symmetry",
                            help='See [[Relion Symmetry][http://www2.mrc-lmb.cam.ac.uk/'
                            'relion/index.php/Conventions_%26_File_formats#Symmetry]] '
@@ -930,7 +933,7 @@ def _setNormalArgs(self, args):
         args['--i'] = self._getFileName('input_star')
         args['--particle_diameter'] = maskDiameter
 
-        # Since Relion 3.1 --angpix is not longer a valid argument
+        # Since Relion 3.1 --angpix is no longer a valid argument
         if relion.Plugin.IS_30():
             args['--angpix'] = ps
 

relion/protocols/protocol_initialmodel.py

@@ -91,7 +91,6 @@ def _defineParams(self, form):
                       label="Input particles",
                       help='Select the input images from the project.')
         form.addParam('maskDiameterA', IntParam, default=-1,
-                      condition='not doContinue',
                       label='Particle mask diameter (A)',
                       help='The experimental images will be masked with a '
                            'soft circular mask with this <diameter>. '
@@ -155,6 +154,7 @@ def _defineParams(self, form):
 
         form.addSection('Optimisation')
         form.addParam('numberOfClasses', IntParam, default=1,
+                      condition='not doContinue',
                       label='Number of classes',
                       help='The number of classes (K) for a multi-reference '
                            'ab initio SGD refinement. These classes will be '
@@ -165,12 +165,14 @@ def _defineParams(self, form):
                            'iterations.')
 
         form.addParam('doFlattenSolvent', BooleanParam, default=True,
+                      condition='not doContinue',
                       label='Flatten and enforce non-negative solvent?',
                       help='If set to Yes, the job will apply a spherical '
                            'mask and enforce all values in the reference '
                            'to be non-negative.')
 
         form.addParam('symmetryGroup', StringParam, default='c1',
+                      condition='not doContinue',
                       label="Symmetry",
                       help='SGD sometimes works better in C1. If you make an '
                            'initial model in C1 but want to run Class3D/Refine3D '
@@ -208,6 +210,7 @@ def _defineParams(self, form):
         self._defineSGD3(form)
 
         form.addParam('sgdNoiseVar', IntParam, default=-1,
+                      condition='not doContinue',
                       expertLevel=LEVEL_ADVANCED,
                       label='Increased noise variance half-life',
                       help='When set to a positive value, the initial '

relion/tests/test_convert_relion.py

@@ -844,6 +844,10 @@ def test_fromStar(self):
         og = OpticsGroups.fromStar(partsStar)
         fog = og.first()
 
+        # test hasColumn method
+        for colName in ['rlnMtfFileName', 'rlnOpticsGroupName']:
+            self.assertTrue(og.hasColumn(colName))
+
         # acq = first.getAcquisition()
         self.assertEqual(fog.rlnMtfFileName, 'mtf_k2_200kV.star')
         self.assertEqual(fog.rlnOpticsGroupName, 'opticsGroup1')

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='3.0.0b3',  # Required
+    version='3.0.0b4',  # Required
 
     # This is a one-line description or tagline of what your project does. This
     # corresponds to the "Summary" metadata field: