3.0.0

README.rst

@@ -33,11 +33,15 @@ This plugin provide wrappers around several programs of `RELION <https://www3.mr
 .. |devel| image:: http://scipion-test.cnb.csic.es:9980/badges/relion_devel.svg
 .. |support| image:: http://scipion-test.cnb.csic.es:9980/badges/relion_support.svg
 
+**IMPORTANT!**
+
+    If you have imported movies with a gain file in **DM4** format, you need to **flip the gain reference upside-down** in the motion correction protocol! (`bug details <https://github.com/I2PC/xmippCore/issues/39>`_)
+
 
 Installation
 ------------
 
-You will need to use `3.0 <https://github.com/I2PC/scipion/releases/tag/V3.0.0>`_ version of Scipion to be able to run these protocols. To install the plugin, you have two options:
+You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:
 
 a) Stable version
 
@@ -59,16 +63,14 @@ b) Developer's version
 
       scipion installp -p path_to_scipion-em-relion --devel
 
-RELION sources will be downloaded and compiled automatically with the plugin, but you can also link an existing installation. Default installation path assumed is ``software/em/relion-3.1.0``, if you want to change it, set *RELION_HOME* in ``scipion.conf`` file to the folder where the RELION is installed. If you need to use CUDA different from the one used during Scipion installation (defined by *CUDA_LIB*), you can add *RELION_CUDA_LIB* variable to the config file. Moreover, if you have to use a MPI for Relion different from Scipion MPI, you can set *RELION_MPI_BIN* and *RELION_MPI_LIB* variables in the config file.
+RELION sources will be downloaded and compiled automatically with the plugin, but you can also link an existing installation. Default installation path assumed is ``software/em/relion-3.1.1``, if you want to change it, set *RELION_HOME* in ``scipion.conf`` file to the folder where the RELION is installed. If you need to use CUDA different from the one used during Scipion installation (defined by *CUDA_LIB*), you can add *RELION_CUDA_LIB* variable to the config file. Moreover, if you have to use a MPI for Relion different from Scipion MPI, you can set *RELION_MPI_BIN* and *RELION_MPI_LIB* variables in the config file.
 
 To check the installation, simply run one of the tests. A complete list of tests can be displayed by executing ``scipion test --show --grep relion``
 
 Supported versions
 ------------------
 
-3.1.0
-
-We are still working towards stable plugin release, so some things might not work yet. Handling optics groups needs more testing, you are welcome to be a volunteer.
+3.1.0, 3.1.1
 
 **IMPORTANT**: Relion-3.0 can be used with this plugin but we do not officially support it anymore, i.e. there will be no bugfixes for it.
 

relion/__init__.py

@@ -25,24 +25,25 @@
 # **************************************************************************
 
 import os
+
 import pyworkflow.utils as pwutils
 import pwem
 
 from .constants import *
 
-__version__ = '3.0.0b7'
+__version__ = '3.0.0'
 _logo = "relion_logo.png"
 _references = ['Scheres2012a', 'Scheres2012b', 'Kimanius2016', 'Zivanov2018']
 
 
 class Plugin(pwem.Plugin):
     _homeVar = RELION_HOME
-    _supportedVersions = [V3_0, V3_1]
+    _supportedVersions = [V3_0, V3_1, V3_1_1]
     _url = "https://github.com/scipion-em/scipion-em-relion"
 
     @classmethod
     def _defineVariables(cls):
-        cls._defineEmVar(RELION_HOME, 'relion-%s' % V3_1)
+        cls._defineEmVar(RELION_HOME, 'relion-%s' % V3_1_1)
         cls._defineVar(RELION_CUDA_LIB, pwem.Config.CUDA_LIB)
 
     @classmethod
@@ -59,7 +60,7 @@ def getEnviron(cls):
         if binPath not in environ['PATH']:
             environ.update({'PATH': binPath,
                             'LD_LIBRARY_PATH': libPath,
-                            #'SCIPION_MPI_FLAGS': os.environ.get('RELION_MPI_FLAGS', ''),
+                            # 'SCIPION_MPI_FLAGS': os.environ.get('RELION_MPI_FLAGS', ''),
                             }, position=pwutils.Environ.BEGIN)
 
         # Get Relion CUDA library path if defined
@@ -78,11 +79,6 @@ def getEnviron(cls):
     def IS_30(cls):
         return cls.getActiveVersion().startswith('3.0')
 
-    @classmethod
-    def IS_31(cls):
-        # avoid using this, IS_GT30 is preferred
-        return cls.getActiveVersion().startswith('3.1')
-
     @classmethod
     def IS_GT30(cls):
         return not cls.getActiveVersion().startswith('3.0')
@@ -101,5 +97,10 @@ def defineBinaries(cls, env):
         env.addPackage('relion', version='3.1.0',
                        url='https://github.com/3dem/relion/archive/3.1.0.tar.gz',
                        commands=relion_commands,
+                       updateCuda=True)
+
+        env.addPackage('relion', version='3.1.1',
+                       url='https://github.com/3dem/relion/archive/3.1.1.tar.gz',
+                       commands=relion_commands,
                        updateCuda=True,
                        default=True)

relion/constants.py

@@ -36,6 +36,7 @@
 # Supported versions:
 V3_0 = '3.0'
 V3_1 = '3.1.0'
+V3_1_1 = '3.1.1'
 
 MASK_FILL_ZERO = 0
 MASK_FILL_NOISE = 1
@@ -169,11 +170,10 @@
 
 
 PARTICLE_EXTRA_LABELS = [
-    'rlnBfactor',
     'rlnCtfBfactor',
     'rlnCtfScalefactor',
     'rlnPhaseShift',
-    'rlnParticleSelectZScore',
-    'rlnMovieFrameNumber',
-    'rlnGroupName'
+    'rlnGroupName',
+    'rlnGroupNumber',
+    'rlnRandomSubset'
 ]

relion/convert/__init__.py

@@ -24,12 +24,14 @@
 # *
 # **************************************************************************
 
+import math
+
 from .convert_utils import *
 from .convert_deprecated import *
 from .convert_coordinates import *
 from .dataimport import *
 import relion
-import math
+
 
 # Writing of star files will be handle by the Writer class
 # We have a new implementation of it for Relion > 3.1 since
@@ -74,7 +76,6 @@ def writeSetOfParticles(imgSet, starFile, **kwargs):
         blockName: The name of the data block (default particles)
         fillMagnification: If True set magnification values (default False)
         alignType:
-        fillRandomSubset:
         extraLabels:
         postprocessImageRow:
         format: string value to specify STAR format, if '30' it will use
@@ -107,6 +108,7 @@ class ClassesLoader:
     def __init__(self, protocol, alignType):
         self._protocol = protocol
         self._alignType = alignType
+        self._reader = None  # Will be created later
 
     def _loadClassesInfo(self, iteration):
         """ Read some information about the produced Relion 3D classes
@@ -144,27 +146,18 @@ def _updateParticle(self, item, row):
         item.setClassId(row.rlnClassNumber)
         self._reader.setParticleTransform(item, row)
 
-        # Try to create extra objects only once if item is reused
-        if not hasattr(item, '_rlnNormCorrection'):
-            item._rlnNormCorrection = Float()
-            item._rlnLogLikeliContribution = Float()
-            item._rlnMaxValueProbDistribution = Float()
-
-        item._rlnNormCorrection.set(row.rlnNormCorrection)
-        item._rlnLogLikeliContribution.set(row.rlnLogLikeliContribution)
-        item._rlnMaxValueProbDistribution.set(row.rlnMaxValueProbDistribution)
-
-        if hasattr(item, '_rlnGroupName'):
-            item._rlnGroupName.set(row.rlnGroupName)
-        elif hasattr(row, 'rlnGroupName'):
-            item._rlnGroupName = String(row.rlnGroupName)
+        if getattr(self, '__updatingFirst', True):
+            self._reader.createExtraLabels(item, row, PARTICLE_EXTRA_LABELS)
+            self.__updatingFirst = False
+        else:
+            self._reader.setExtraLabels(item, row)
 
     def _updateClass(self, item):
         classId = item.getObjId()
         if classId in self._classesInfo:
             index, fn, row = self._classesInfo[classId]
             item.setAlignment(self._alignType)
-            if self._alignType == pwem.ALIGN_PROJ:
+            if self._alignType == ALIGN_PROJ:
                 fn += ':mrc'  # mark reference as a MRC volume
             item.getRepresentative().setLocation(index, fn)
             item._rlnClassDistribution = Float(row.rlnClassDistribution)

relion/convert/convert30.py

@@ -70,6 +70,7 @@ def _writeSetOfMoviesOrMics(self, imgIterable,
         micRow[imgLabelName] = ''  # Just to add label, proper value later
         iterMics = iter(imgIterable)
         mic = next(iterMics)
+        self._setCtf = mic.hasCTF()
         self._micToRow(mic, micRow)
 
         micsTable = self._createTableFromDict(micRow)
@@ -87,6 +88,10 @@ def _writeSetOfMoviesOrMics(self, imgIterable,
     def _micToRow(self, mic, row):
         WriterBase._micToRow(self, mic, row)
 
+        # Set CTF values
+        if self._setCtf:
+            self._ctfToRow(mic.getCTF(), row)
+
         # Add now the Acquisition labels
         acq = mic.getAcquisition()
         row.update({
@@ -140,7 +145,7 @@ def setParticleTransform(self, particle, row):
             elif self._alignType == pwem.ALIGN_PROJ:
                 self.setParticleTransform = self.__setParticleTransformProj
             else:
-                raise Exception("Unexpected alignment type: %s"
+                raise TypeError("Unexpected alignment type: %s"
                                 % self._alignType)
 
         # Call again the modified function