Merge pull request #111 from scipion-em/devel

Release 3.3.1

CHANGES.txt

@@ -1,3 +1,23 @@
+v3.3.1:
+ Users:
+  - Small fixes regarding the register of the tilt series acquisition attributes.
+  - Fix the template matching output register reported by Ricardo Righetto (thanks!).
+  - Fix the classic subtomo refine transformation matrices assignment when generating the output.
+  - Fix the particles order in the registered output of protocol extract particles from TS.
+  - Protocol 'extract particles from TS' is now semi-streamified.
+  - Protocol 'tilt series alignment and tomo reconstruction':
+        * Fix the sampling rate of the set of tilt series interpolated.
+        * Fix the generation of tomograms when not requested.
+        * The interpolated tilt series is now generated applying the transformation matrix in Scipion convention to the
+          non-interpolated tilt series.
+        * Input and output convert steps improved.
+        * Remove form parameter 'Step between tilts' as it can now be read from the acquisition.
+        * Add param to correct the XDrift.
+        * Some other changes in the protocol form.
+  - Protocol 'average subtomograms' adapted to work with EMAN 3D particles generated from 3D particles (the ones
+    resulting when using the protocol 'extract particles from TS')
+ Developers:
+  - Test for TS alignment & tomo reconstruction updated to the new TCL.
 v3.3.0:
  Users:
   - Prevent viewers from locking the screen focus.

emantomo/__init__.py

@@ -22,7 +22,7 @@
 # *  e-mail address 'scipion@cnb.csic.es'
 # *
 # **************************************************************************
-__version__ = "3.3.0"
+__version__ = "3.3.1"
 _logo = "eman2_logo.png"
 _references = ['GALAZMONTOYA2015279', 'BELL201625']
 _url = "https://github.com/scipion-em/scipion-em-emantomo"

emantomo/convert/convert.py

@@ -449,12 +449,18 @@ def jsons2SetCoords3D(protocol, setTomograms, outPath):
     coord3DSet.setSamplingRate(setTomograms.getSamplingRate())
     first = True
     for tomo in setTomograms.iterItems():
-        outFile = '*%s_info.json' % pwutils.removeBaseExt(tomo.getFileName().split("__")[0])
+        # File search by tsId
+        outFile = '*%s_info.json' % tomo.getTsId()
         pattern = join(outPath, outFile)
         files = glob.glob(pattern)
 
         if not files or not isfile(files[0]):
-            continue
+            # File search by filename
+            outFile = '*%s_info.json' % pwutils.removeBaseExt(tomo.getFileName().split("__")[0])
+            pattern = join(outPath, outFile)
+            files = glob.glob(pattern)
+            if not files or not isfile(files[0]):
+                continue
 
         jsonFnbase = files[0]
         jsonBoxDict = loadJson(jsonFnbase)

emantomo/objects.py

@@ -73,6 +73,19 @@ def getProjsFrom2dStack(self, shrink=1):
                              (shrink * img.attrs['EMAN.ptcl_source_coord'][:-1]).tolist())
         return projsList
 
+    def get3dCoordsFrom3dStack(self, scaleFactor=1, invertZ=False):
+        """Generate a list of elements in which each element is a list containing the following data:
+        [xCoord, yCoord, zCoord] read from the HDF stack header.
+        """
+        coordsList = []
+        for particleId in range(len(self._imgObjList)):
+            img = self._imgObjList[str(particleId)]
+            coords = (scaleFactor * img.attrs['EMAN.ptcl_source_coord']).tolist()
+            if invertZ:
+                coords[-1] = -1 * coords[-1]
+            coordsList.append(coords)
+        return coordsList
+
     def getSamplingRate(self):
         """Reads the sampling rate from the HDF header"""
         return self._imgObjList['0'].attrs['EMAN.apix_x']

emantomo/protocols/protocol_average_subtomos.py

@@ -29,20 +29,21 @@
 import glob
 import os
 import shutil
-from os.path import join, basename
+from os.path import join, basename, abspath
 
 from pyworkflow import BETA
 
 from pwem.protocols import EMProtocol
 from pyworkflow.protocol import PointerParam, FloatParam, StringParam, BooleanParam, LEVEL_ADVANCED
-from pyworkflow.utils import Message, makePath, removeBaseExt, replaceExt
+from pyworkflow.utils import Message, makePath, removeBaseExt, replaceExt, createLink
 from ..constants import SPT_00_DIR, INPUT_PTCLS_LST, THREED_01, SYMMETRY_HELP_MSG, SUBTOMOGRAMS_DIR
 
 from ..convert import writeSetOfSubTomograms, refinement2Json
 import emantomo
 
 from tomo.protocols import ProtTomoBase
 from tomo.objects import AverageSubTomogram
+from ..objects import EmanParticle, EmanSetOfParticles
 
 
 class OutputsAverageSubtomos(enum.Enum):
@@ -118,7 +119,13 @@ def _initialize(self):
 
     def convertInputStep(self):
         inSubtomos = self.inputSetOfSubTomogram.get()
-        writeSetOfSubTomograms(inSubtomos, self.hdfSubtomosDir)
+        if type(inSubtomos) is EmanSetOfParticles:
+            # If True, the 3D particles HDF stacks will already exist because they have been extracted with EMAN pppt
+            hdfStacks = inSubtomos.getUniqueValues(EmanParticle.STACK_3D_HDF)
+            [createLink(abspath(hdfStack), self._getExtraPath(SUBTOMOGRAMS_DIR, basename(hdfStack))) for
+             hdfStack in hdfStacks]
+        else:
+            writeSetOfSubTomograms(inSubtomos, self.hdfSubtomosDir)
         refinement2Json(self, inSubtomos)
 
         # Generate a virtual stack of particle represented by a .lst file, as expected by EMAN

emantomo/protocols/protocol_base.py

@@ -24,6 +24,7 @@
 # *
 # **************************************************************************
 import glob
+import logging
 import re
 from os.path import join, abspath, basename
 
@@ -44,6 +45,9 @@
 from tomo.protocols import ProtTomoBase
 from tomo.utils import getNonInterpolatedTsFromRelations
 
+
+logger = logging.getLogger(__name__)
+
 IN_TS = 'inputTS'
 IN_COORDS = 'inputCoordinates'
 IN_CTF = 'inputCTF'
@@ -70,9 +74,7 @@ def convertTsStep(self, mdObj):
         # The converted TS must be unbinned, because EMAN will read the sampling rate from its header. This is why
         # the TS associated to the CTF is the one considered first. Later, when generating the json, the TS alignment
         # parameters are read from the introduced TS and the shifts are scaled to at the unbinned scale
-        # if mdObj.ctf:
-        #     inTsFName = mdObj.ctf.getTiltSeries().getFirstItem().getFileName()
-        # else:
+        logger.info(f'Converting TS {mdObj.tsId} into HDF...')
         inTsFName = mdObj.ts.getFirstItem().getFileName()
         sRate = mdObj.ts.getSamplingRate()
         self.convertOrLink(inTsFName, mdObj.tsId, TS_DIR, sRate)

emantomo/protocols/protocol_clip_tomograms.py

@@ -62,7 +62,7 @@ def _defineParams(self, form):
                       label="Input tomograms",
                       important=True)
 
-        line = form.addLine('New center coordinates [pix.] (opt.)',
+        line = form.addLine('New center coordinates [px] (opt.)',
                             help='For each empty coordinate, the correspònding original center coordinate '
                                  'will be used.')
         line.addParam('xc', IntParam,
@@ -75,7 +75,7 @@ def _defineParams(self, form):
                       label="cz",
                       allowsNull=True)
 
-        line = form.addLine('New dimensions [pix.] (opt.)',
+        line = form.addLine('New dimensions [px] (opt.)',
                             help='For each empty dimension, the original corresponding dimension will be used.')
         line.addParam('xDim', IntParam,
                       label="dx",