Merge pull request #234 from scipion-em/devel

3.0.0b5

relion/convert/convert31.py

@@ -572,8 +572,8 @@ def rowToCtf(row, ctf):
         ctf.setResolution(row.rlnCtfMaxResolution or 0)
         ctf.setFitQuality(row.rlnCtfFigureOfMerit or 0)
 
-        if getattr(row, 'rlnCtfPhaseShift', False):
-            ctf.setPhaseShift(row.rlnCtfPhaseShift)
+        if getattr(row, 'rlnPhaseShift', False):
+            ctf.setPhaseShift(row.rlnPhaseShift)
         ctf.standardize()
 
         if hasattr(row, 'rlnCtfImage'):

relion/convert/convert_base.py

@@ -164,7 +164,7 @@ def _ctfToRow(self, ctf, row):
         phaseShift = ctf.getPhaseShift()
 
         if phaseShift is not None:
-            row['rlnCtfPhaseShift'] = phaseShift
+            row['rlnPhaseShift'] = phaseShift
 
 
 class ReaderBase:

relion/protocols/protocol_assign_optic_groups.py

@@ -191,11 +191,12 @@ def createOutputStep(self, inputId):
                        for row in micTable}
 
             # check if MTF file exists
-            for i in og:
-                if not pwutils.exists(i.rlnMtfFileName):
-                    self.warning("MTF file %s not found for %s" % (
-                        i.rlnMtfFileName, i.rlnOpticsGroupName
-                    ))
+            if og.hasColumn('rlnMtfFileName'):
+                for i in og:
+                    if not pwutils.exists(i.rlnMtfFileName):
+                        self.warning("MTF file %s not found for %s" % (
+                            i.rlnMtfFileName, i.rlnOpticsGroupName
+                        ))
 
             def updateItem(item, row):
                 micName = getMicName(item)

relion/protocols/protocol_bayesian_polishing.py

@@ -220,7 +220,8 @@ def convertInputStep(self, movId, partId, postId):
         moviesPixelSize = inputMovies.getSamplingRate()
         binningFactor = inputParts.getSamplingRate() / moviesPixelSize
 
-        writer = convert.createWriter()
+        og = convert.OpticsGroups.fromImages(inputMovies)
+        writer = convert.createWriter(optics=og)
         writer.writeSetOfMicrographs(inputMovies,
                                      self._getFileName('input_mics'),
                                      postprocessImageRow=self._updateMic)

relion/protocols/protocol_reconstruct.py

@@ -123,6 +123,9 @@ def _insertReconstructStep(self):
             if self.ctfIntactFirstPeak:
                 params += ' --ctf_intact_first_peak'
 
+            if imgSet.isPhaseFlipped():
+                params += ' --ctf_phase_flipped'
+
         if self.extraParams.hasValue():
             params += " " + self.extraParams.get()
 

relion/viewers/viewer_base.py

@@ -188,10 +188,11 @@ def _defineParams(self, form):
                            default=ANGDIST_2DPLOT,
                            display=params.EnumParam.DISPLAY_HLIST,
                            label='Display angular distribution',
-                           help='*2D plot*: display angular distribution as interative 2D in matplotlib.\n'
+                           help='*2D plot*: display angular distribution as interactive 2D in matplotlib.\n'
                                 '*chimera*: display angular distribution using Chimera with red spheres.')
             group.addParam('spheresScale', params.IntParam, default=-1,
                            expertLevel=LEVEL_ADVANCED,
+                           condition='displayAngDist == %d' % ANGDIST_CHIMERA,
                            label='Spheres distance',
                            help='If the value is -1 then the distance is set '
                                 'to 0.75 * xVolDim')
@@ -366,13 +367,15 @@ def _showPMax(self, paramName=None):
         tablePMax = Table(columns=labels)
 
         for it in self._getAllIters():
+            if it == 1:  # skip iter1 with Pmax=1
+                continue
             # always list all iterations
             prefix = self.protocol.PREFIXES[0]
             fn = self.protocol._getFileName(prefix + 'model', iter=it)
             table = Table(fileName=fn, tableName='model_general')
             row = table[0]
-            tablePMax.addRow(it, row.rlnAveragePmax,
-                             row.rlnLogLikelihood)
+            tablePMax.addRow(int(it), float(row.rlnAveragePmax),
+                             float(row.rlnLogLikelihood))
 
         fn = self.protocol._getFileName('all_avgPmax')
         with open(fn, 'w') as f:
@@ -382,7 +385,7 @@ def _showPMax(self, paramName=None):
         xplotter.createSubPlot("Avg PMax per Iterations", "Iterations",
                                "Avg PMax")
         xplotter.plotMd(tablePMax, 'rlnIterationNumber',
-                        'rlnAveragePmax', 'g')
+                        'rlnAveragePmax')
         xplotter.showLegend(['rlnAveragePmax'])
 
         return [self.createDataView(fn), xplotter]

relion/viewers/viewer_ctfrefine.py

@@ -67,6 +67,7 @@ def _defineParams(self, form):
         form.addSection(label="Results")
         form.addParam('useMatplotlib', params.BooleanParam, default=True,
                       label='Use matplotlib for display',
+                      condition="not {}".format(showDefocus),
                       help='If False, images will be displayed with ImageJ')
 
         form.addParam('displayAnisoMag', params.LabelParam,

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='3.0.0b4',  # Required
+    version='3.0.0b5',  # Required
 
     # This is a one-line description or tagline of what your project does. This
     # corresponds to the "Summary" metadata field: