Merge pull request #226 from scipion-em/oddevenfixes

Oddevenfixes

CHANGES.txt

@@ -1,3 +1,10 @@
+3.3.0:
+  - Fixing a bug with odd even in tomogram reconstruction
+  - Tolerating errors in alignment
+  - Making tomogram reconstruction error tolerant
+  - Making tilt series alignment error tolerant
+  - Adding possible outputs in xray eraser
+  - Removing visible parameters with the intepolation is not applied
 3.2.0:
   - add more possible outputs
   - fixing ctf after aretomo
@@ -79,4 +86,4 @@
   - fix betterradius param in gold eraser tab of the fid alignment
   - add missing pix size in fid align
   - fix minpacing in gold picker
-  - add missing taper arg for newstack
+  - add missing taper arg for newstack

imod/protocols/protocol_base.py

@@ -102,7 +102,7 @@ def wrapper(self, tsId, *args):
         return wrapper
 
     def convertInputStep(self, tsObjId, generateAngleFile=True,
-                         imodInterpolation=True, doSwap=False):
+                         imodInterpolation=True, doSwap=False, oddEven=False):
         """
 
         :param tsObjId: Tilt series identifier
@@ -140,18 +140,30 @@ def convertInputStep(self, tsObjId, generateAngleFile=True,
             # Use IMOD newstack interpolation
             if firstItem.hasTransform():
                 # Generate transformation matrices file
-                outputTmFileName = os.path.join(tmpPrefix,
-                                                firstItem.parseFileName(extension=".xf"))
+                outputTmFileName = os.path.join(tmpPrefix, firstItem.parseFileName(extension=".xf"))
                 utils.formatTransformFile(ts, outputTmFileName)
 
-                argsAlignment, paramsAlignment = self.getBasicNewstackParams(ts,
+                def applyNewStack(outputTsFileName, fnIn):
+
+                    argsAlignment, paramsAlignment = self.getBasicNewstackParams(ts,
                                                                              outputTsFileName,
+                                                                             inputTsFileName=fnIn,
                                                                              xfFile=outputTmFileName,
                                                                              firstItem=firstItem,
                                                                              doSwap=doSwap)
+                    Plugin.runImod(self, 'newstack', argsAlignment % paramsAlignment)
 
                 self.info("Interpolating tilt series %s with imod" % tsId)
-                Plugin.runImod(self, 'newstack', argsAlignment % paramsAlignment)
+                applyNewStack(outputTsFileName, None)
+
+                if oddEven:
+                    fnOdd = ts.getOddFileName()
+                    fnEven = ts.getEvenFileName()
+
+                    outputOddTsFileName = os.path.join(tmpPrefix, tsId+EXT_MRCS_TS_EVEN_NAME)
+                    outputEvenTsFileName = os.path.join(tmpPrefix, tsId+EXT_MRCS_TS_ODD_NAME)
+                    applyNewStack(outputOddTsFileName, fnOdd)
+                    applyNewStack(outputEvenTsFileName, fnEven)
 
             else:
                 self.info("Linking tilt series %s" % tsId)

imod/protocols/protocol_tomoReconstruction.py

@@ -32,7 +32,7 @@
 from tomo.objects import Tomogram
 
 from .. import Plugin
-from .protocol_base import ProtImodBase, EXT_MRC_ODD_NAME, EXT_MRC_EVEN_NAME
+from .protocol_base import ProtImodBase, EXT_MRC_ODD_NAME, EXT_MRC_EVEN_NAME, EXT_MRCS_TS_EVEN_NAME, EXT_MRCS_TS_ODD_NAME
 
 
 class ProtImodTomoReconstruction(ProtImodBase):
@@ -181,7 +181,10 @@ def _insertAllSteps(self):
     # --------------------------- STEPS functions -----------------------------
     def convertInputStep(self, tsObjId, **kwargs):
         # Considering swapXY is required to make tilt axis vertical
-        super().convertInputStep(tsObjId, doSwap=True)
+        oddEvenFlag = False
+        if self.inputSetOfTiltSeries.get().hasOddEven():
+            oddEvenFlag = True
+        super().convertInputStep(tsObjId, doSwap=True, oddEven=oddEvenFlag)
 
     @ProtImodBase.tryExceptDecorator
     def computeReconstructionStep(self, tsObjId):
@@ -244,13 +247,13 @@ def getArgs():
         oddEvenTmp = [[], []]
 
         if self.applyToOddEven(ts):
-            oddFn = firstItem.getOdd().split('@')[1]
+            oddFn = os.path.join(tmpPrefix, tsId+EXT_MRCS_TS_ODD_NAME)
             paramsTilt['InputProjections'] = oddFn
             oddEvenTmp[0] = os.path.join(tmpPrefix, firstItem.parseFileName(extension="_odd.rec"))
             paramsTilt['OutputFile'] = oddEvenTmp[0]
-
             Plugin.runImod(self, 'tilt', argsTilt % paramsTilt)
-            evenFn = firstItem.getEven().split('@')[1]
+
+            evenFn = os.path.join(tmpPrefix, tsId+EXT_MRCS_TS_EVEN_NAME)
             paramsTilt['InputProjections'] = evenFn
             oddEvenTmp[1] = os.path.join(tmpPrefix, firstItem.parseFileName(extension="_even.rec"))
             paramsTilt['OutputFile'] = oddEvenTmp[1]

imod/protocols/protocol_xCorrPrealignment.py

@@ -47,6 +47,7 @@ class ProtImodXcorrPrealignment(ProtImodBase):
 
     _label = 'Coarse prealignment'
     _devStatus = BETA
+    _possibleOutputs = {"TiltSeries": tomoObj.SetOfTiltSeries}
 
     # -------------------------- DEFINE param functions -----------------------
     def _defineParams(self, form):
@@ -83,6 +84,7 @@ def _defineParams(self, form):
 
         form.addParam('binning',
                       params.IntParam,
+                      condition='computeAlignment==0',
                       default=1,
                       label='Binning for the interpolated',
                       help='Binning to be applied to the interpolated '
@@ -91,7 +93,8 @@ def _defineParams(self, form):
                            'bigger than 1')
 
         form.addParam('Trimming parameters', params.LabelParam,
-                                 label='Tilt axis angle detected from import. In case another value is desired please adjust the number below')
+                      label='Tilt axis angle detected from import. In case another value is desired please adjust the '
+                            'number below')
 
         form.addParam('tiltAxisAngle',
                       params.FloatParam,
@@ -104,41 +107,40 @@ def _defineParams(self, form):
                            'system with no axis inversions')
 
         trimming = form.addGroup('Trimming parameters',
-                                  expertLevel=params.LEVEL_ADVANCED)
+                                 expertLevel=params.LEVEL_ADVANCED)
 
         xtrimming = trimming.addLine('Horizontal: Number of pixels to avoid from the',
-                                  expertLevel=params.LEVEL_ADVANCED,
-                                  help="Starting and ending X coordinates of a region to correlate, "
-                                       "based on the position of the region at zero tilt.")
+                                     expertLevel=params.LEVEL_ADVANCED,
+                                     help="Starting and ending X coordinates of a region to correlate, "
+                                          "based on the position of the region at zero tilt.")
 
         xtrimming.addParam('xmin',
-                       params.IntParam,
-                       label='left',
-                       allowsNull=True,
-                       expertLevel=params.LEVEL_ADVANCED)
+                           params.IntParam,
+                           label='left',
+                           allowsNull=True,
+                           expertLevel=params.LEVEL_ADVANCED)
 
         xtrimming.addParam('xmax',
-                          params.IntParam,
-                          label='right',
-                          allowsNull=True,
-                          expertLevel=params.LEVEL_ADVANCED)
+                           params.IntParam,
+                           label='right',
+                           allowsNull=True,
+                           expertLevel=params.LEVEL_ADVANCED)
 
         ytrimming = trimming.addLine('Vertical: Number of pixels to avoid from the',
-                                  expertLevel=params.LEVEL_ADVANCED,
-                                  help="Starting and ending Y coordinates of a region to correlate.")
+                                     expertLevel=params.LEVEL_ADVANCED,
+                                     help="Starting and ending Y coordinates of a region to correlate.")
 
         ytrimming.addParam('ymin',
-                          params.IntParam,
-                          label='top',
-                          allowsNull=True,
-                          expertLevel=params.LEVEL_ADVANCED)
+                           params.IntParam,
+                           label='top',
+                           allowsNull=True,
+                           expertLevel=params.LEVEL_ADVANCED)
 
         ytrimming.addParam('ymax',
-                          params.IntParam,
-                          label='botton',
-                          allowsNull=True,
-                          expertLevel=params.LEVEL_ADVANCED)
-
+                           params.IntParam,
+                           label='botton',
+                           allowsNull=True,
+                           expertLevel=params.LEVEL_ADVANCED)
 
         filtering = form.addGroup('Filtering parameters',
                                   expertLevel=params.LEVEL_ADVANCED)
@@ -243,8 +245,6 @@ def computeXcorrStep(self, tsObjId):
             'filterRadius2': self.filterRadius2.get()
         }
 
-
-
         argsXcorr = "-input %(input)s " \
                     "-output %(output)s " \
                     "-tiltfile %(tiltfile)s " \
@@ -267,11 +267,11 @@ def computeXcorrStep(self, tsObjId):
             if xmin is None:
                 xmin = 0
             if xmax is None:
-                xmax = xdim-1
+                xmax = xdim - 1
             if ymin is None:
                 ymin = 0
             if ymax is None:
-                ymax = ydim-1
+                ymax = ydim - 1
 
             argsXcorr += " -xminmax %i,%i " % (xmin, xmax)
             argsXcorr += " -yminmax %i,%i " % (ymin, ymax)