Merge pull request I2PC#332 from I2PC/v1.0

RELEASE V1.0.0  2016-02-20

CHANGELOG.md

@@ -1,5 +1,5 @@
 
-## v1.0.0 (2016-02-15) Augusto
+## v1.0.0 (2016-02-20) Augusto
 
 - Allows to combine several EM software packages (~ 100 protocols):
   - All protocols from Xmipp 

config/workflows/workflow_betagal1.json

@@ -32,7 +32,7 @@
         "alignFrame0": 0,
         "alignFrameN": 0,
         "doGPU": false,
-        "GPUCore": 1,
+        "GPUCore": 0,
         "winSize": 150,
         "sumFrame0": 0,
         "sumFrameN": 0,

pyworkflow/em/packages/grigoriefflab/bibtex.py

@@ -134,7 +134,18 @@
 keywords = "Electron microscopy, Maximum likelihood, Classification, Single particle, Protein structure "
 }
 
-
+@Article{Rohou2015,
+   Author="Rohou, A.  and Grigorieff, N. ",
+   Title="{{C}{T}{F}{F}{I}{N}{D}4: {F}ast and accurate defocus estimation from electron micrographs}",
+   Journal="J. Struct. Biol.",
+   Year="2015",
+   Volume="192",
+   Number="2",
+   Pages="216--221",
+   Month="Nov",
+   doi = "http://dx.doi.org/10.1016/j.jsb.2015.08.008",
+   url = "http://www.sciencedirect.com/science/article/pii/S1047847715300460"
+}
 """
 
 

pyworkflow/em/packages/grigoriefflab/convert.py

@@ -202,12 +202,13 @@ def readCtfModel(ctfModel, filename, ctf4=False):
         result =  parseCtffind4Output(filename)
         if result is None:
             setWrongDefocus(ctfModel)
-            ctfFit, ctfResolution = -999, -999 
+            ctfFit, ctfResolution, ctfPhaseShift = -999, -999, -999
         else:
-            defocusU, defocusV, defocusAngle, _, ctfFit, ctfResolution = result
+            defocusU, defocusV, defocusAngle, ctfPhaseShift, ctfFit, ctfResolution = result
             ctfModel.setStandardDefocus(defocusU, defocusV, defocusAngle)
         ctfModel._ctffind4_crossCorrelation = Float(ctfFit)
         ctfModel._ctffind4_ctfResolution = Float(ctfResolution)
+        ctfModel._ctffind4_ctfPhaseShift = Float(ctfPhaseShift)
 
 
 def geometryFromMatrix(matrix):

pyworkflow/em/packages/grigoriefflab/protocol_ctffind.py

@@ -50,16 +50,40 @@ class ProtCTFFind(em.ProtCTFMicrographs):
 
 
     def _defineProcessParams(self, form):
-        form.addParam('useCftfind4', params.BooleanParam, default=True,
+        form.addParam('useCtffind4', params.BooleanParam, default=True,
               label="Use ctffind4 to estimate the CTF?",
               help='If is true, the protocol will use ctffind4 instead of ctffind3')
         form.addParam('astigmatism', params.FloatParam, default=100.0,
-              label='Expected (tolerated) astigmatism', expertLevel=params.LEVEL_ADVANCED,
-              condition='useCftfind4', )
+              label='Expected (tolerated) astigmatism (A)',
+              expertLevel=params.LEVEL_ADVANCED,
+              help='Astigmatism values much larger than this will be penalised '
+                   '(Angstroms; set negative to remove this restraint)',
+              condition='useCtffind4')
         form.addParam('findPhaseShift', params.BooleanParam, default=False,
-              label="Find additional phase shift?", condition='useCftfind4',
-              expertLevel=params.LEVEL_ADVANCED,)
-
+              label="Find additional phase shift?", condition='useCtffind4',
+              help='If the data was collected with phase plate, this will find '
+                   'additional phase shift due to phase plate',
+              expertLevel=params.LEVEL_ADVANCED)
+
+        group = form.addGroup('Phase shift parameters')
+        group.addParam('minPhaseShift', params.FloatParam, default=0.0,
+              label="Minimum phase shift (rad)", condition='findPhaseShift',
+              help='Lower bound of the search for additional phase shift. '
+                   'Phase shift is of scattered electrons relative to '
+                   'unscattered electrons. In radians.',
+              expertLevel=params.LEVEL_ADVANCED)
+        group.addParam('maxPhaseShift', params.FloatParam, default=3.15,
+              label="Maximum phase shift (rad)", condition='findPhaseShift',
+              help='Upper bound of the search for additional phase shift. '
+                   'Phase shift is of scattered electrons relative to '
+                   'unscattered electrons. In radians. '
+                   'Please use value between 0.10 and 3.15',
+              expertLevel=params.LEVEL_ADVANCED)
+        group.addParam('stepPhaseShift', params.FloatParam, default=0.2,
+              label="Phase shift search step (rad)", condition='findPhaseShift',
+              help='Step size for phase shift search (radians)',
+              expertLevel=params.LEVEL_ADVANCED)
+
     #--------------------------- STEPS functions ---------------------------------------------------
     def _estimateCTF(self, micFn, micDir, micName):
         """ Run ctffind, 3 or 4, with required parameters """
@@ -71,7 +95,9 @@ def _estimateCTF(self, micFn, micDir, micName):
         if downFactor != 1:
             #Replace extension by 'mrc' cause there are some formats that cannot be written (such as dm3)
             import pyworkflow.em.packages.xmipp3 as xmipp3
-            self.runJob("xmipp_transform_downsample","-i %s -o %s --step %f --method fourier" % (micFn, micFnMrc, downFactor), env=xmipp3.getEnviron())
+            self.runJob("xmipp_transform_downsample",
+                        "-i %s -o %s --step %f --method fourier" % (micFn, micFnMrc, downFactor),
+                        env=xmipp3.getEnviron())
             self._params['scannedPixelSize'] = self.inputMicrographs.get().getScannedPixelSize() * downFactor
         else:
             micFnMrc = self._getTmpPath(pwutils.replaceBaseExt(micFn, "mrc"))
@@ -122,12 +148,7 @@ def _createNewCtfModel(self, mic):
         out = self._getCtfOutPath(micDir)
         psdFile = self._getPsdPath(micDir)
         ctfModel2 = em.CTFModel()
-
-        if not self.useCftfind4:
-            readCtfModel(ctfModel2, out)
-        else:
-            readCtfModel(ctfModel2, out, True)
-
+        readCtfModel(ctfModel2, out, ctf4=self.useCtffind4.get())
         ctfModel2.setPsdFile(psdFile)
         ctfModel2.setMicrograph(mic)
         return ctfModel2
@@ -144,12 +165,7 @@ def _createOutputStep(self):
             out = self._getCtfOutPath(micDir)
 
             ctfModel = em.CTFModel()
-
-            if not self.useCftfind4:
-                readCtfModel(ctfModel, out)
-            else:
-                readCtfModel(ctfModel, out, True)
-
+            readCtfModel(ctfModel, out, ctf4=self.useCtffind4.get())
             ctfModel.setPsdFile(psdFile)
             ctfModel.setMicrograph(mic)
 
@@ -164,16 +180,23 @@ def _createOutputStep(self):
     #--------------------------- INFO functions ----------------------------------------------------
     def _validate(self):
         errors = []
-        if self.useCftfind4:
-            ctffind = CTFFIND4_PATH
-        else:
-            ctffind = CTFFIND_PATH
+        ctffind = CTFFIND4_PATH if self.useCtffind4 else CTFFIND_PATH
         if not os.path.exists(ctffind):
             errors.append('Missing %s' % ctffind)
+
+        valueStep = round(self.stepPhaseShift.get(), 2)
+        valueMin = round(self.minPhaseShift.get(), 2)
+        valueMax = round(self.maxPhaseShift.get(), 2)
+
+        if not (self.minPhaseShift < self.maxPhaseShift and
+                valueStep <= (valueMax-valueMin) and
+                0.10 <= valueMax <= 3.15):
+            errors.append('Wrong values for phase shift search.')
+
         return errors
 
     def _citations(self):
-        return ['Mindell2003']
+        return ['Rohou2015'] if self.useCtffind4 else ['Mindell2003']
 
     def _methods(self):
         if self.inputMicrographs.get() is None:
@@ -194,12 +217,15 @@ def _prepareCommand(self):
             self._params['lowRes'] = 50
         self._params['highRes'] = sampling / self._params['highRes']
         self._params['step_focus'] = 500.0
-        if not self.useCftfind4:
+        if not self.useCtffind4:
             self._argsCtffind3()
         else:
             self._params['astigmatism'] = self.astigmatism.get()
             if self.findPhaseShift:
                 self._params['phaseShift'] = "yes"
+                self._params['minPhaseShift'] = self.minPhaseShift.get()
+                self._params['maxPhaseShift'] = self.maxPhaseShift.get()
+                self._params['stepPhaseShift'] = self.stepPhaseShift.get()
             else:
                 self._params['phaseShift'] = "no"
             self._argsCtffind4()
@@ -226,12 +252,15 @@ def _prepareRecalCommand(self, ctfModel):
         self._params['maxDefocus'] = max([float(line[0]), float(line[1])])
         self._params['windowSize'] = size
 
-        if not self.useCftfind4:
+        if not self.useCtffind4:
             self._argsCtffind3()
         else:
             self._params['astigmatism'] = self.astigmatism.get()
             if self.findPhaseShift:
                 self._params['phaseShift'] = "yes"
+                self._params['minPhaseShift'] = self.minPhaseShift.get()
+                self._params['maxPhaseShift'] = self.maxPhaseShift.get()
+                self._params['stepPhaseShift'] = self.stepPhaseShift.get()
             else:
                 self._params['phaseShift'] = "no"
             self._argsCtffind4()
@@ -248,7 +277,29 @@ def _argsCtffind3(self):
 
     def _argsCtffind4(self):
         self._program = 'export OMP_NUM_THREADS=1; ' + CTFFIND4_PATH
-        self._args = """ << eof
+        if self.findPhaseShift:
+            self._args = """ << eof
+%(micFn)s
+%(ctffindPSD)s
+%(sampling)f
+%(voltage)f
+%(sphericalAberration)f
+%(ampContrast)f
+%(windowSize)d
+%(lowRes)f
+%(highRes)f
+%(minDefocus)f
+%(maxDefocus)f
+%(step_focus)f
+%(astigmatism)f
+%(phaseShift)s
+%(minPhaseShift)f
+%(maxPhaseShift)f
+%(stepPhaseShift)f
+eof
+"""
+        else:
+            self._args = """ << eof
 %(micFn)s
 %(ctffindPSD)s
 %(sampling)f
@@ -276,7 +327,7 @@ def _parseOutput(self, filename):
         """ Try to find the output estimation parameters
         from filename. It search for a line containing: Final Values.
         """
-        if not self.useCftfind4:
+        if not self.useCtffind4:
             return parseCtffindOutput(filename)
         else:
             return parseCtffind4Output(filename)
@@ -287,3 +338,4 @@ def _getCTFModel(self, defocusU, defocusV, defocusAngle, psdFile):
         ctf.setPsdFile(psdFile)
 
         return ctf
+