ctffind updated to 4.1.8 (output code bug was fixed)

config/templates/scipion.template

@@ -21,7 +21,7 @@ EM_ROOT = software/em
 
 BSOFT_HOME = %(EM_ROOT)s/bsoft-1.9.0
 CTFFIND_HOME = %(EM_ROOT)s/ctffind-3.6
-CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.5
+CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.8
 DOGPICKER_HOME = %(EM_ROOT)s/dogpicker-0.2.1
 EMAN2DIR = %(EM_ROOT)s/eman-2.12
 ETHAN_HOME = %(EM_ROOT)s/ethan-1.2

install/script.py

@@ -387,6 +387,9 @@
 env.addPackage('ctffind4', version='4.1.5',
                tar='ctffind_V4.1.5.tgz')
 
+env.addPackage('ctffind4', version='4.1.8',
+               tar='ctffind_V4.1.8.tgz')
+
 env.addPackage('summovie', version='1.0.2',
                tar='summovie_1.0.2.tgz')
 

pyworkflow/em/packages/grigoriefflab/grigoriefflab.py

@@ -53,7 +53,7 @@ def getSupportedVersions(var='FREALIGN'):
     if var == 'UNBLUR':
         return ['1.0_150529', '1.0.2']
     elif var == 'CTFFIND4':
-        return ['4.0.15', '4.1.5']
+        return ['4.0.15', '4.1.5', '4.1.8']
     else:  # FREALIGN
         return ['9.07']
 

pyworkflow/em/packages/grigoriefflab/protocol_ctffind.py

@@ -256,7 +256,7 @@ def _prepareCommand(self):
                 self._params['stepPhaseShift'] = self.stepPhaseShift.get()
             else:
                 self._params['phaseShift'] = "no"
-            if self.resamplePix:  # ctffind v4.1.5
+            if self.resamplePix:  # ctffind >= v4.1.5
                 self._params['resamplePix'] = "yes"
             else:
                 self._params['resamplePix'] = "no"
@@ -294,7 +294,7 @@ def _prepareRecalCommand(self, ctfModel):
                 self._params['stepPhaseShift'] = self.stepPhaseShift.get()
             else:
                 self._params['phaseShift'] = "no"
-            if self.resamplePix:  # ctffind v4.1.5
+            if self.resamplePix:  # ctffind >= v4.1.5
                 self._params['resamplePix'] = "yes"
             else:
                 self._params['resamplePix'] = "no"
@@ -335,7 +335,7 @@ def _argsCtffind4(self):
 %(maxDefocus)f
 %(step_focus)f"""
 
-        if getVersion('CTFFIND4') == '4.1.5':
+        if getVersion('CTFFIND4') in ['4.1.5', '4.1.8']:
             if self.findPhaseShift:
                 self._args += """
 no
@@ -402,7 +402,7 @@ def _getCTFModel(self, defocusU, defocusV, defocusAngle, psdFile):
 
     def _summary(self):
         summary = em.ProtCTFMicrographs._summary(self)
-        if self.useCtffind4:
+        if self.useCtffind4 and getVersion('CTFFIND4') == '4.1.5':
             summary.append("NOTE: ctffind4.1.5 finishes correctly (all output is generated properly),"
                            " but returns an error code. Disregard error messages until this is fixed."
                            "http://grigoriefflab.janelia.org/node/5421")