Merge pull request #122 from scipion-em/devel

Release 3.4.0
scipion-em · Aug 20, 2024 · ec8f7b4 · ec8f7b4
2 parents 7decbdc + ec6d3a0
commit ec8f7b4
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Showing 4 changed files with 25 additions and 19 deletions.
diff --git a/CHANGES.txt b/CHANGES.txt
@@ -1,3 +1,6 @@
+v3.3.4:
+ Users: hotfix - solved bug in the validation method of the classic initial volume protocol.
+ Developers: add odd dimensions checking to the classic initial volume.
 v3.3.3:
  Users: hotfix - solve problems when using the emantomo viewer with coordinates picked with crYOLO.
 v3.3.2:

diff --git a/emantomo/__init__.py b/emantomo/__init__.py
@@ -22,7 +22,7 @@
 # *  e-mail address '[email protected]'
 # *
 # **************************************************************************
-__version__ = "3.3.3"
+__version__ = "3.3.4"
 _logo = "eman2_logo.png"
 _references = ['GALAZMONTOYA2015279', 'BELL201625']
 _url = "https://github.com/scipion-em/scipion-em-emantomo"

diff --git a/emantomo/convert/convert.py b/emantomo/convert/convert.py
@@ -368,10 +368,11 @@ def jsonFilesFromSet(setScipion, path):
         tomo_files = []
         for file in setScipion.getFiles():
             fileBasename = pwutils.removeBaseExt(file)
+            parentDir = basename(dirname(file))
             if "__" in fileBasename:
-                fnInputCoor = '%s_info.json' % fileBasename.split("__")[0]
+                fnInputCoor = '%s-%s_info.json' % (parentDir, fileBasename.split("__")[0])
             else:
-                fnInputCoor = '%s_info.json' % fileBasename
+                fnInputCoor = '%s-%s_info.json' % (parentDir, fileBasename)
             pathInputCoor = pwutils.join(path, fnInputCoor)
             json_files.append(pathInputCoor)
             tomo_files.append(file)
@@ -389,24 +390,24 @@ def jsonFilesFromSet(setScipion, path):
 
 def setCoords3D2Jsons(json_files, setCoords, mode="w"):
     paths = []
-    TOMO_ID = Coordinate3D.TOMO_ID_ATTR
-    tomoIds = sorted(setCoords.getUniqueValues(TOMO_ID))
+    tomoIds = sorted(setCoords.getUniqueValues(Coordinate3D.TOMO_ID_ATTR))
     json_files = sorted(json_files)
     for tomoId, json_file in zip(tomoIds, json_files):
         coords = []
         groupIds = setCoords.getUniqueValues("_groupId", where='_tomoId="%s"' % tomoId)
         dict_eman = dict(zip(groupIds, range(len(groupIds))))
-        for coor in setCoords.iterCoordinates():
-            tomoName = pwutils.removeBaseExt(coor.getVolume().getFileName())
+        for coord in setCoords.iterCoordinates():
+
+            tomoName = pwutils.removeBaseExt(coord.getVolume().getFileName())
             if "__" in tomoName:
                 tomoName = '%s_info' % tomoName.split("__")[0]
             else:
                 tomoName += "_info"
             if tomoName in json_file:
-                coords.append([coor.getX(const.BOTTOM_LEFT_CORNER),
-                               coor.getY(const.BOTTOM_LEFT_CORNER),
-                               coor.getZ(const.BOTTOM_LEFT_CORNER),
-                               "manual", 0.0, dict_eman[coor.getGroupId()]])
+                coords.append([coord.getX(const.BOTTOM_LEFT_CORNER),
+                               coord.getY(const.BOTTOM_LEFT_CORNER),
+                               coord.getZ(const.BOTTOM_LEFT_CORNER),
+                               "manual", 0.0, dict_eman[coord.getGroupId()]])
 
         if coords:
             coordDict = {"boxes_3d": coords,

diff --git a/emantomo/protocols/protocol_tomo_initialmodel.py b/emantomo/protocols/protocol_tomo_initialmodel.py
@@ -25,8 +25,6 @@
 # **************************************************************************
 from enum import Enum
 from emantomo.constants import INIT_MODEL_DIR, INIR_MODEL_NAME_OLD, SYMMETRY_HELP_MSG
-from pwem.emlib.image import ImageHandler
-from pyworkflow import BETA
 from pyworkflow.protocol import params
 from pyworkflow.utils.path import makePath, replaceBaseExt
 from pwem.protocols import EMProtocol
@@ -261,17 +259,21 @@ def _validate(self):
         refVol = self.reference.get()
         if refVol:
             # Check the dimensions
-            ih = ImageHandler()
-            x, y, z, _ = ih.getDimensions(refVol.getFileName())
-            refVolDims = (x, y, z)
             inParticles = self.particles.get()
-            dimsDict = self._firstDim
+            dimsDict = inParticles._firstDim
             inParticlesDims = (dimsDict[0], dimsDict[1], dimsDict[2])
+            # Eman fails if the dimensions are odd numbers
+            for iDim in inParticlesDims:
+                if iDim % 2 != 0:
+                    errorMsg.append('The particles dimensions must be an even number')
+                    break
+            x, y, z = refVol.getDimensions()
+            refVolDims = (x, y, z)
             if refVolDims != inParticlesDims:
                 errorMsg.append(f'The dimensions of the reference volume {refVolDims} px and the particles '
                                 f'{inParticlesDims} px must be the same')
             # Check the sampling rate
-            tol = 1e-03
+            tol = 2e-03
             inParticlesSRate = inParticles.getSamplingRate()
             refVolSRate = refVol.getSamplingRate()
             if abs(inParticlesSRate - refVolSRate) >= tol:
@@ -281,7 +283,7 @@ def _validate(self):
             # Check the mask
             mask = self.mask.get()
             if mask:
-                x, y, z, _ = ih.getDimensions(refVol.getFileName())
+                x, y, z = mask.getDimensions()
                 maskDims = (x, y, z)
                 maskSRate = mask.getSamplingRate()
                 if inParticlesDims != maskDims: