Merge branch 'devel' into co_fixes

xmipp3/protocols/protocol_compare_reprojections.py

@@ -31,7 +31,7 @@
 
 from pyworkflow import VERSION_1_1
 from pyworkflow.protocol.params import (PointerParam, StringParam, FloatParam, BooleanParam, IntParam)
-from pyworkflow.utils.path import cleanPath
+from pyworkflow.utils.path import cleanPath, cleanPattern
 from pwem.protocols import ProtAnalysis3D
 from pwem.objects import (SetOfClasses2D, Image, SetOfAverages, SetOfParticles)
 import pwem.emlib.metadata as md
@@ -133,7 +133,7 @@ def produceResiduals(self, fnAngles, Ts):
         xdim = self._getDimensions()
         args = "-i %s -o %s --ref %s --optimizeAngles --optimizeShift --max_shift %d --oprojections %s --sampling %f" \
                % (fnAngles, anglesOutFn, fnVol, floor(xdim*0.05), projectionsOutFn, Ts)
-        self.fnResiduals = self._getExtraPath("residuals.stk")
+        self.fnResiduals = self._getExtraPath("residuals.mrcs")
         if self.doEvaluateResiduals:
             args += " --oresiduals %s" % self.fnResiduals
 
@@ -143,13 +143,13 @@ def produceResiduals(self, fnAngles, Ts):
             args += "--optimizeGray --max_gray_scale 0.95 "
         self.runJob("xmipp_angular_continuous_assign2", args)
 
-        if self.doEvaluateResiduals:
-            self._computeResiduals(fnVol)
+#        if self.doEvaluateResiduals:
+#            self._computeResiduals(fnVol)
 
     def evaluateResiduals(self):
         # Evaluate each image
         fnAutoCorrelations = self._getExtraPath("autocorrelations.xmd")
-        stkAutoCorrelations = self._getExtraPath("autocorrelations.stk")
+        stkAutoCorrelations = self._getExtraPath("autocorrelations.mrcs")
         stkResiduals = self.fnResiduals
         anglesOutFn = self._getExtraPath("anglesCont.xmd")
         self.runJob("xmipp_image_residuals", " -i %s -o %s --save_metadata_stack %s"
@@ -277,6 +277,7 @@ def _computeResiduals(self, fnVol):
             cleanPath(fnNewParticles)
         if os.path.exists(mrcsresiduals):
             cleanPath(mrcsresiduals)
+        cleanPattern(self._getExtraPath("residual_part*.stk"))
 
     # --------------------------- INFO functions --------------------------------------------
     def _summary(self):

xmipp3/protocols/protocol_convert_pdb.py

@@ -70,7 +70,7 @@ def _defineParams(self, form):
         This definition is also used to generate automatically the GUI.
         """
         # Defining condition string for x, y, z coords
-        coordsCondition = 'setSize and not vol'
+        coordsCondition = 'setSize and not vol and not isinstance(pdbObj, SetOfAtomStructs)'
 
         # Defining parallel arguments
         form.addParallelSection(threads=4, mpi=1)
@@ -254,6 +254,9 @@ def _validate(self):
         if self.numberOfMpi > 1:
             errors.append('MPI cannot be selected, because Scipion is going to drop support for it. Select threads instead.')
 
+        if isinstance(self.pdbObj.get(), SetOfAtomStructs) and not self.size.hasValue():
+            errors.append('Please set size when using SetOfAtomStructs as input')
+
         return errors
 
     # --------------------------- UTLIS functions --------------------------------------------

xmipp3/protocols/protocol_extract_particles.py

@@ -570,6 +570,7 @@ def readPartsFromMics(self, micList, outputParts):
                         # adding the variance and Gini coeff. value of the mic zone
                         setXmippAttributes(p, row, md.MDL_SCORE_BY_VAR)
                         setXmippAttributes(p, row, md.MDL_SCORE_BY_GINI)
+                        setXmippAttributes(p, row, md.MDL_LOCAL_AVERAGE)
                         if row.containsLabel(md.MDL_ZSCORE_DEEPLEARNING1):
                             setXmippAttributes(p, row, md.MDL_ZSCORE_DEEPLEARNING1)
 

xmipp3/protocols/protocol_generate_reprojections.py

@@ -28,7 +28,7 @@
 import os
 
 from pyworkflow import VERSION_2_0
-from pyworkflow.protocol.params import PointerParam
+from pyworkflow.protocol.params import PointerParam, BooleanParam
 from pyworkflow.utils.path import cleanPath
 from pwem.protocols import ProtAnalysis3D
 from pwem.objects import Image
@@ -60,6 +60,9 @@ def _defineParams(self, form):
         form.addParam('inputVolume', PointerParam, label="Volume to compare images to", important=True,
                       pointerClass='Volume',
                       help='Volume to be used for class comparison')
+        form.addParam('ignoreCTF', BooleanParam, default=True, label='Ignore CTF',
+                      help='By ignoring the CTF you will create projections more similar to what a person expects, '
+                           'while by using the CTF you will create projections more similar to what the microscope sees')
         form.addParallelSection(threads=0, mpi=8)
 
     #--------------------------- INSERT steps functions --------------------------------------------
@@ -96,9 +99,10 @@ def produceProjections(self, fnAngles, Ts):
         fnVol = self._getTmpPath("volume.vol")
         anglesOutFn = self._getExtraPath("anglesCont.stk")
         projectionsOutFn = self._getExtraPath("projections.stk")
-        args = "-i %s -o %s --ref %s --oprojections %s --sampling %f " \
-             "--max_angular_change 90" % (fnAngles, anglesOutFn, fnVol,
-                                          projectionsOutFn, Ts)
+        args = "-i %s -o %s --ref %s --oprojections %s --sampling %f " %\
+             (fnAngles, anglesOutFn, fnVol, projectionsOutFn, Ts)
+        if self.ignoreCTF:
+            args += " --ignoreCTF "
         self.runJob("xmipp_angular_continuous_assign2", args)
         fnNewParticles = self._getExtraPath("images.stk")
         if os.path.exists(fnNewParticles):