Merge pull request #46 from scipion-em/devel

3.1.2
scipion-em · Nov 17, 2023 · 90a1d1b · 90a1d1b
2 parents 8082c66 + 4f66405
commit 90a1d1b
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Showing 4 changed files with 22 additions and 18 deletions.
diff --git a/CHANGES.txt b/CHANGES.txt
@@ -1,3 +1,4 @@
+3.1.2: fix tlt and defocus files do not correspond to the tilt series
 3.1.1: fix reconstruction protocol trigger if no alignment exists
 3.1:
 - fix defocus shift: should be passed in a file for ctf correction, and as a param for reconstruction

diff --git a/novactf/__init__.py b/novactf/__init__.py
@@ -27,7 +27,7 @@
 import pwem
 
 
-__version__ = '3.1.1'
+__version__ = '3.1.2'
 _references = ["Turonova2017"]
 NOVACTF_HOME = 'NOVACTF_HOME'
 

diff --git a/novactf/protocols/protocol_tomoDefocus.py b/novactf/protocols/protocol_tomoDefocus.py
@@ -24,7 +24,6 @@
 # *
 # *****************************************************************************
 
-import os
 from glob import glob
 
 from pyworkflow import BETA
@@ -130,41 +129,44 @@ def _insertAllSteps(self):
     def convertInputStep(self, tsObjId):
         ts = self.getInputTs()[tsObjId]
         tsId = ts.getTsId()
+        self.info("Generating tlt file and defocus file for %s (id %s)" % (tsId, tsObjId))
 
         ctfTomoSeries = self.getCtfTomoSeriesFromTsId(tsId)
 
         tmpPrefix = self._getTmpPath(tsId)
         extraPrefix = self._getExtraPath(tsId)
 
+        # Create the folders for the tilt series
         path.makePath(tmpPrefix)
         path.makePath(extraPrefix)
 
-        firstItem = ts.getFirstItem()
-
         # Generate angle file
-        angleFilePath = os.path.join(tmpPrefix,
-                                     firstItem.parseFileName(extension=".tlt"))
+        angleFilePath = self.getTltFileName(tsId)
+
+        self.info("Generating %s" % angleFilePath)
         ts.generateTltFile(angleFilePath)
 
         # Generate defocus file
-        defocusFilePath = os.path.join(extraPrefix,
-                                       firstItem.parseFileName(extension=".defocus"))
+        defocusFilePath = self.getDefocusFileName(tsId)
+
         imodUtils.generateDefocusIMODFileFromObject(ctfTomoSeries, defocusFilePath)
 
+    def getTltFileName(self, tsId):
+        return self._getTmpPath(tsId, tsId + ".tlt")
+
+    def getDefocusFileName(self,tsId):
+        return self._getExtraPath(tsId, tsId + ".defocus")
+
     def computeDefocusStep(self, tsObjId):
         ts = self.getInputTs()[tsObjId]
         tsId = ts.getTsId()
 
-        tmpPrefix = self._getTmpPath(ts.getTsId())
-        extraPrefix = self._getExtraPath(tsId)
-
         firstItem = ts.getFirstItem()
 
         ih = ImageHandler()
         xDim, yDim, _, _ = ih.getDimensions(firstItem.getFileName() + ":mrc")
 
-        defocusFilePath = os.path.join(extraPrefix,
-                                       firstItem.parseFileName(extension=".defocus"))
+        defocusFilePath = self.getDefocusFileName(tsId)
 
         if self.tomoShift.get() > 0.01:
             defocusShift = self.tomoThickness.get() / 2 + self.tomoShift.get()
@@ -176,7 +178,7 @@ def computeDefocusStep(self, tsObjId):
             'InputProjections': firstItem.getFileName(),
             'FullImage': str(xDim) + "," + str(yDim),
             'Thickness': self.tomoThickness.get(),
-            'TiltFile': os.path.join(tmpPrefix, firstItem.parseFileName(extension=".tlt")),
+            'TiltFile': self.getTltFileName(tsId),
             'CorrectionType': "phaseflip" if self.correctionType.get() == 0 else "multiplication",
             'DefocusFileFormat': "imod",
             'CorrectAstigmatism': self.correctAstigmatism.get(),
@@ -217,7 +219,10 @@ def triggerReconstructionProtocolStep(self):
         project = manager.loadProject(self.getProject().getName())
 
         applyAlignment = self.getInputTs().getFirstItem().getFirstItem().hasTransform()
-        protTomoReconstruction = ProtNovaCtfTomoReconstruction(applyAlignment=applyAlignment)
+
+        label = self.getObjLabel() + " - REC"
+        protTomoReconstruction = ProtNovaCtfTomoReconstruction(applyAlignment=applyAlignment,
+                                                               objLabel=label)
         protTomoReconstruction.protTomoCtfDefocus.set(self)
         protTomoReconstruction.numberOfThreads.set(self.numberOfThreads.get())
         protTomoReconstruction.numberOfMpi.set(self.numberOfMpi.get())

diff --git a/novactf/protocols/protocol_tomoReconstruction.py b/novactf/protocols/protocol_tomoReconstruction.py
@@ -183,10 +183,8 @@ def processIntermediateStacksStep(self, tsObjId, counter):
 
         tsId = ts.getTsId()
         tmpPrefix = self._getTmpPath(tsId)
-        extraPrefixPreviousProt = self.protTomoCtfDefocus.get()._getExtraPath(tsId)
 
-        defocusFilePath = os.path.join(extraPrefixPreviousProt,
-                                       firstItem.parseFileName(extension=".defocus_"))
+        defocusFilePath = self.protTomoCtfDefocus.get().getDefocusFileName(tsId) + "_"
         tltFilePath = os.path.join(tmpPrefix, firstItem.parseFileName(extension=".tlt"))
         outputFilePath = os.path.join(tmpPrefix, firstItem.parseFileName(extension=".mrc_"))