release 3.2.0

CHANGES.txt

@@ -1,3 +1,8 @@
+v3.2.0:
+  - Wizard to apply operation in relion particles
+  - 3D Classification defines its possible outputs
+  - An initio fixed (not using optimization set)
+  - Other FSCs are plotted in the refine and postprocess protocols
 v3.1.6:
   - 3D Classification more completed/standard
   - 3D classes can be fed to mapback or others

reliontomo/__init__.py

@@ -30,7 +30,7 @@
 
 _logo = "relion_logo.png"
 _references = ['Scheres2012a', 'Scheres2012b', 'Kimanius2016', 'Zivanov2018']
-__version__ = '3.1.6'
+__version__ = '3.2.0'
 
 
 class Plugin(relion.Plugin):

reliontomo/constants.py

@@ -143,8 +143,19 @@
 OUT_PARTICLES_STAR = 'particles.star'
 TRAJECTORIES_STAR = 'trajectories.star'
 MANIFOLDS_STAR = 'manifolds.star'
+
+REFINE_FSC_REF_STAR = '_model.star'
+REFINE_STAR_FSC_TABLE = 'model_class_1'
+REFINE_STAR_FSC_COLUMNS = ['rlnGoldStandardFsc', 'rlnFourierCompleteness']
+
 POSTPROCESS_DIR = 'PostProcess'
 FSC_REF_STAR = join(POSTPROCESS_DIR, 'postprocess.star')
+POSTPROCESS_STAR_FSC_TABLE = 'fsc'
+POSTPROCESS_STAR_FSC_COLUMNS = ['rlnFourierShellCorrelationCorrected',
+                                'rlnFourierShellCorrelationUnmaskedMaps',
+                                'rlnFourierShellCorrelationMaskedMaps',
+                                'rlnCorrectedFourierShellCorrelationPhaseRandomizedMaskedMaps']
+
 RE4_INDIV_GEN_FILES = [OUT_TOMOS_STAR, OUT_PARTICLES_STAR, TRAJECTORIES_STAR, MANIFOLDS_STAR, FSC_REF_STAR]
 OPTIMISATION_SET_STAR = 'optimisation_set.star'
 PSUBTOMOS_SQLITE = 'pseudosubtomograms%s.sqlite'

reliontomo/convert/convert40_tomo.py

@@ -136,7 +136,7 @@ def pseudoSubtomograms2Star(self, pSubtomoSet, outStar, withPriors=False):
             partsWriter = Table.Writer(f)
             partsWriter.writeTableName(PARTICLES_TABLE)
             partsWriter.writeHeader(tomoTable.getColumns())
-            for pSubtomo in pSubtomoSet:
+            for pSubtomo in pSubtomoSet.iterSubtomos():
                 angles, shifts = getTransformInfoFromCoordOrSubtomo(pSubtomo, pSubtomo.getSamplingRate())
                 pSubtomoFile = pSubtomo.getFileName()
                 pSubtomoFile = pSubtomoFile.replace(':' + MRC, '') if pSubtomoFile else FILE_NOT_FOUND

reliontomo/protocols/protocol_3d_classify_subtomograms.py

@@ -54,6 +54,7 @@ class ProtRelion3DClassifySubtomograms(ProtRelionRefineSubtomograms):
     classesTable = Table()
     opticsTable = Table()
     particlesTable = Table()
+    _possibleOutputs = outputObjects
 
     def __init__(self, **kwargs):
         super().__init__(**kwargs)

reliontomo/protocols/protocol_base_refine.py

@@ -290,22 +290,26 @@ def convertInputStep(self):
     # -------------------------- INFO functions -------------------------------
 
     # --------------------------- UTILS functions -----------------------------
-    def _genBaseCommand(self):
+    def _genBaseCommand(self, useOptimizationSet=True ):
         cmd = ''
-        cmd += self._genIOBaseCmd()  # I/O args
+        cmd += self._genIOBaseCmd(useOptimizationSet=useOptimizationSet)  # I/O args
         cmd += self._genCTFBaseCmd()  # CTF args
         cmd += self._genOptimisationBaseCmd()  # Optimisation args
         cmd += self._genComputeBaseCmd()  # Compute args
         cmd += self._genAddiotionalBaseCmd()  # Additional args
         return cmd
 
-    def _genIOBaseCmd(self):
+    def _genIOBaseCmd(self, useOptimizationSet=True):
 
         inRelionParticles = self.getInputParticles()
 
-        # Use optimization set file
-        self.info("Using optimization_set: %s" % inRelionParticles.filesMaster)
-        cmd = '--ios %s ' % inRelionParticles.filesMaster
+        cmd = ''
+
+        if useOptimizationSet:
+            # Use optimization set file
+            self.info("Using optimization_set: %s" % inRelionParticles.filesMaster)
+            cmd += '--ios %s ' % inRelionParticles.filesMaster
+
 
         cmd += '--i %s ' % self.getOutStarFileName()
         cmd += '--o %s ' % (self._getExtraPath() + '/')  # If not, Relion will concatenate it directly as a prefix

reliontomo/protocols/protocol_base_relion.py

@@ -23,8 +23,9 @@
 # *
 # **************************************************************************
 from os.path import exists, join
+from emtable import Table
 
-from pwem.objects import VolumeMask
+from pwem.objects import VolumeMask, FSC
 from pwem.protocols import EMProtocol
 from pyworkflow.protocol import PointerParam
 from pyworkflow.utils import Message, createLink
@@ -105,3 +106,16 @@ def genRelionParticles(self, optimisationFileName=OPTIMISATION_SET_STAR, particl
 
         return psubtomoSet
 
+    def genFSCs(self, starFile, tableName, fscColumns):
+        fscSet = self._createSetOfFSCs()
+        table = Table(fileName=starFile, tableName=tableName)
+        resolution_inv = table.getColumnValues('rlnResolution')
+        for columnName in fscColumns:
+            columValues = table.getColumnValues(columnName)
+            fsc = FSC(objLabel=columnName[3:])
+            fsc.setData(resolution_inv, columValues)
+            fscSet.append(fsc)
+
+        fscSet.write()
+        return fscSet
+

reliontomo/protocols/protocol_de_novo_initial_model.py

@@ -102,7 +102,7 @@ def createOutputStep(self):
     # --------------------------- UTILS functions -----------------------------
     def _genInitModelCommand(self):
         # Common parameters from base protocol
-        cmd = self._genBaseCommand()
+        cmd = self._genBaseCommand(useOptimizationSet=False)
 
         # Initial model specific commands
         cmd += ' --denovo_3dref --grad --zero_mask --auto_sampling --pad 1 '

reliontomo/protocols/protocol_edit_particles_star.py

@@ -26,7 +26,8 @@
 # **************************************************************************
 from enum import Enum
 from pyworkflow import BETA
-from pyworkflow.protocol import BooleanParam, FloatParam, EnumParam
+from pyworkflow.protocol import BooleanParam, FloatParam, EnumParam, \
+    PointerParam
 from reliontomo import Plugin
 from reliontomo.constants import OUT_PARTICLES_STAR, COORD_X, COORD_Y, COORD_Z, SHIFTX_ANGST, SHIFTY_ANGST, \
     SHIFTZ_ANGST, ROT, TILT, PSI
@@ -73,6 +74,12 @@ def _defineParams(self, form):
                       default=False,
                       help='Perform centering of particles according to a position in the reference.')
         group = form.addGroup('Shift center', condition='doRecenter')
+        group.addParam('averageSubTomogram', PointerParam, pointerClass='AverageSubTomogram',
+                      label='Average of subtomogram (optional)', allowsNull=True,
+                      )
+        group.addParam('refMask', PointerParam, pointerClass='VolumeMask',
+                       label='Reference mask (optional)', allowsNull=True,
+                       )
         group.addParam('shiftX', FloatParam,
                        label='X (pix.)',
                        default=0,
@@ -216,3 +223,9 @@ def _genOperateCmd(self):
 
         return operateCmd
 
+    def getAverageSubTomogram(self):
+        return self.averageSubTomogram.get()
+
+    def getMask3D(self):
+        return self.refMask.get()
+

reliontomo/protocols/protocol_post_process.py

@@ -25,12 +25,14 @@
 # *
 # **************************************************************************
 from enum import Enum
-from pwem.objects import VolumeMask
+from pwem.objects import VolumeMask, FSC
 from pyworkflow import BETA
 from pyworkflow.protocol import PointerParam, BooleanParam, FloatParam, GE, LE, IntParam, FileParam
 from pyworkflow.utils import makePath
 from reliontomo import Plugin
-from reliontomo.constants import POST_PROCESS_MRC, POSTPROCESS_DIR
+from reliontomo.constants import POST_PROCESS_MRC, POSTPROCESS_DIR, \
+    POSTPROCESS_STAR_FSC_TABLE, \
+    POSTPROCESS_STAR_FSC_COLUMNS, FSC_REF_STAR
 from reliontomo.objects import RelionSetOfPseudoSubtomograms
 from reliontomo.protocols.protocol_base_relion import ProtRelionTomoBase
 
@@ -40,6 +42,7 @@
 class outputObjects(Enum):
     relionParticles = RelionSetOfPseudoSubtomograms
     postProcessVolume = VolumeMask
+    outputFSC = FSC
 
 
 class ProtRelionPostProcess(ProtRelionTomoBase):
@@ -154,8 +157,16 @@ def createOutputStep(self):
         inParticles = self.inReParticles.get()
         pSubtomoSet = self.genRelionParticles()
         postProccesMrc = self._genPostProcessOutputMrcFile(POST_PROCESS_MRC)
+
+        # Output FSC
+
+        fn = self._getExtraPath(FSC_REF_STAR)
+        setOfFSC = self.genFSCs(fn, POSTPROCESS_STAR_FSC_TABLE,
+                                POSTPROCESS_STAR_FSC_COLUMNS)
+
         self._defineOutputs(**{outputObjects.postProcessVolume.name: postProccesMrc,
-                               outputObjects.relionParticles.name: pSubtomoSet})
+                               outputObjects.relionParticles.name: pSubtomoSet,
+                               outputObjects.outputFSC.name: setOfFSC})
         self._defineSourceRelation(inParticles, postProccesMrc)
         self._defineSourceRelation(inParticles, pSubtomoSet)
 

reliontomo/protocols/protocol_refine_subtomograms.py

@@ -27,23 +27,25 @@
 from enum import Enum
 from emtable import Table
 from pwem.convert.headers import fixVolume
-from pwem.objects import FSC
+from pwem.objects import SetOfFSCs
 from pyworkflow import BETA
 from reliontomo.objects import RelionSetOfPseudoSubtomograms
 from reliontomo.protocols.protocol_base_refine import ProtRelionRefineBase
 from reliontomo import Plugin
 from os.path import getmtime
 from pyworkflow.protocol import PointerParam, LEVEL_ADVANCED, FloatParam, StringParam, BooleanParam, EnumParam
 from pyworkflow.utils import createLink
-from reliontomo.constants import ANGULAR_SAMPLING_LIST, SYMMETRY_HELP_MSG, OUT_PARTICLES_STAR
+from reliontomo.constants import ANGULAR_SAMPLING_LIST, SYMMETRY_HELP_MSG, \
+    OUT_PARTICLES_STAR, REFINE_FSC_REF_STAR, REFINE_STAR_FSC_TABLE, \
+    REFINE_STAR_FSC_COLUMNS
 from reliontomo.utils import getProgram
 from tomo.objects import AverageSubTomogram
 
 
 class outputObjects(Enum):
     relionParticles = RelionSetOfPseudoSubtomograms
     average = AverageSubTomogram
-    outputFSC = FSC
+    outputFSC = SetOfFSCs
 
 
 class ProtRelionRefineSubtomograms(ProtRelionRefineBase):
@@ -229,20 +231,18 @@ def createOutputStep(self):
         vol.setHalfMaps([half1, half2])
 
         # Output FSC
-        fsc = FSC(objLabel=self.getRunName())
-        fn = self._getExtraPath("_model.star")
-        table = Table(fileName=fn, tableName='model_class_1')
-        resolution_inv = table.getColumnValues('rlnResolution')
-        frc = table.getColumnValues('rlnGoldStandardFsc')
-        fsc.setData(resolution_inv, frc)
+        fn = self._getExtraPath(REFINE_FSC_REF_STAR)
+
+        setOfFSC = self.genFSCs(fn, REFINE_STAR_FSC_TABLE,
+                                REFINE_STAR_FSC_COLUMNS)
 
         outputDict = {outputObjects.relionParticles.name: relionParticles,
                       outputObjects.average.name: vol,
-                      outputObjects.outputFSC.name: fsc}
+                      outputObjects.outputFSC.name: setOfFSC}
         self._defineOutputs(**outputDict)
         self._defineSourceRelation(inParticles, relionParticles)
         self._defineSourceRelation(inParticles, vol)
-        self._defineSourceRelation(inParticles, fsc)
+        self._defineSourceRelation(inParticles, setOfFSC)
 
     # -------------------------- INFO functions -------------------------------