Merge pull request #77 from scipion-em/jj_hot_fix_model_wf

Hotfix - problem with the common model wf steps with vesicle models
scipion-em · May 16, 2023 · b43dac6 · b43dac6
2 parents 576a522 + 600fefa
commit b43dac6
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Showing 3 changed files with 8 additions and 4 deletions.
diff --git a/CHANGES.txt b/CHANGES.txt
@@ -1,3 +1,6 @@
+V3.1.19:
+  - Hot fix: one of the steps of the common list from the model workflow is not included in the Dynamo side. The plugin
+    now offers the same behavior, so this kind of models do not fail now.
 V3.1.18
   - Model workflow able to generate correct (coordinates of a model) and failed (meshes whose model workflow failed
     and need to be fixed).

diff --git a/dynamo/__init__.py b/dynamo/__init__.py
@@ -31,7 +31,7 @@
 import pyworkflow.utils as pwutils
 from .constants import *
 
-__version__ = '3.1.18'
+__version__ = '3.1.19'
 _logo = "icon.png"
 _references = ['CASTANODIEZ2012139']
 

diff --git a/dynamo/protocols/protocol_model_workflow.py b/dynamo/protocols/protocol_model_workflow.py
@@ -222,14 +222,15 @@ def writeMatlabFile(self, tomoId, modelName, modelFile):
             codeFid.write(content)
         return codeFilePath
 
-    def _genCommonModelWfSteps(self):
+    def _genCommonModelWfSteps(self, isVesicle=False):
         """See
         https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Example_of_membrane_model_workflow_through_the_command_line"""
         contentMWf = "m.mesh_parameter = %i\n" % self.meshParameter.get()
         contentMWf += "m.crop_mesh_parameter = %i\n" % self.cropping.get()
         contentMWf += "m.mesh_maximum_triangles = %i\n" % self.maxTr.get()
         contentMWf = "m.subdivision_iterations=%i\n" % self.subDivision.get()
-        contentMWf += "m.controlUpdate()\n"
+        if not isVesicle:
+            contentMWf += "m.controlUpdate()\n"  # This step fails for vesicle model on the Dynamo side
         contentMWf += "m.createMesh()\n"
         if self.doRefineMesh.get():
             contentMWf += "m.refineMesh()\n"
@@ -243,7 +244,7 @@ def _genCommonModelWfSteps(self):
     def genVesicleCmdFileContents(self):
         # Let Dynamo approximate the geometry based on the points annotated in the boxing protocol
         contentMWf = "m.approximateGeometryFromPoints()\n"
-        contentMWf += self._genCommonModelWfSteps()
+        contentMWf += self._genCommonModelWfSteps(isVesicle=True)
         return contentMWf
 
     def genSCmdFileContents(self):