Merge pull request #90 from scipion-em/devel

3.9.1

CHANGES.txt

@@ -1,3 +1,7 @@
+3.9.1
+  Users:
+   - Adding a main help to the protocols and some helps modified.
+   - Phase shift parameter are now in a line
 3.9:
   Users:
    - add ctffind5, rename config vars

cistem/__init__.py

@@ -32,7 +32,7 @@
 from .constants import *
 
 
-__version__ = '3.9'
+__version__ = '3.9.1'
 _logo = "cistem_logo.png"
 _references = ['Grant2018']
 

cistem/protocols/program_ctffind.py

@@ -111,8 +111,11 @@ def defineProcessParams(cls, form):
         line = group.addLine('Defocus search range (A)',
                              condition='not recalculate',
                              help='Select _minimum_ and _maximum_ values for '
-                                  'defocus search range (in A). Underfocus'
-                                  ' is represented by a positive number.')
+                                  'defocus search range (in A). Underfocus '
+                                  'is represented by a positive number. This '
+                                  'range is critical for the proper estimation. '
+                                  'Note that these number should be around the '
+                                  'nominal defocus of the acquisition.')
         line.addParam('minDefocus', params.FloatParam, default=5000.,
                       label='Min')
         line.addParam('maxDefocus', params.FloatParam, default=50000.,
@@ -158,24 +161,22 @@ def defineProcessParams(cls, form):
                            'with variable phase shift that must be '
                            'determined together with the defocus '
                            'parameters?')
-        form.addParam('minPhaseShift', params.FloatParam, default=0.,
-                      label="Minimum phase shift (deg)",
-                      condition='findPhaseShift',
-                      help='If finding an additional phase shift, '
-                           'this value sets the lower bound for the '
-                           'search.')
-        form.addParam('maxPhaseShift', params.FloatParam, default=180,
-                      label="Maximum phase shift (deg)",
-                      condition='findPhaseShift',
-                      help='If finding an additional phase shift, '
-                           'this value sets the upper bound for the '
-                           'search.')
-        form.addParam('stepPhaseShift', params.FloatParam, default=10,
-                      label="Phase shift search step (deg)",
-                      condition='findPhaseShift',
-                      help='If finding an additional phase shift, '
-                           'this value sets the step size for the '
-                           'search.')
+        line = form.addLine('Phase shift (deg)',
+                            condition='findPhaseShift',
+                            help="Select _minimum_ and _maximum_ values for "
+                                 " phase shift search range (in deg). Also "
+                                 "the search step should be provided. "
+                                 "The phase shift will be estimated in step from the "
+                                 "minumum to the maximum pprovided values")
+        line.addParam('minPhaseShift', params.FloatParam, default=0.,
+                      label="Min",
+                      condition='findPhaseShift')
+        line.addParam('maxPhaseShift', params.FloatParam, default=180.,
+                      label="Max",
+                      condition='findPhaseShift')
+        line.addParam('stepPhaseShift', params.FloatParam, default=10.,
+                      label="Step",
+                      condition='findPhaseShift')
 
         form.addParallelSection(threads=3)
 

cistem/protocols/protocol_ctffind.py

@@ -107,8 +107,8 @@ def _getErrorFromCtffindTxt(self, mic, e):
         file = self._getCtfOutPath(mic)
         with open(file, "r") as fh:
             for line in fh.readlines():
-                if line.startswith("Error"):
-                    return line.replace("Error:", "")
+                if "Error:" in line:
+                    return line.split("Error:")[-1]
         return e
 
     def _estimateCTF(self, mic, *args):

cistem/protocols/protocol_tomo_resample.py

@@ -40,7 +40,8 @@
 
 class CistemProtTomoResample(EMProtocol, ProtTomoBase):
     """
-    Resample tomograms by Fourier cropping/padding using cisTEM. This is equivalent to binning/unbinning operations but free of aliasing artifacts.
+    Resample tomograms by Fourier cropping/padding using cisTEM.
+    This is equivalent to binning/unbinning operations but free of aliasing artifacts.
 
     More info:
         https://cistem.org

cistem/protocols/protocol_ts_ctffind.py

@@ -46,15 +46,39 @@
 
 MRCS_EXT = ".mrcs"
 # create simple, lightweight data structures similar to a class, but without the overhead of defining a full class
-CistemTsCtfMd = namedtuple('CistemTsCtfMd', ['ts', 'tsFn', 'outputLog', 'outputPsd'])
+CistemTsCtfMd = namedtuple('CistemTsCtfMd',
+                           ['ts', 'tsFn', 'outputLog', 'outputPsd'])
 
 
 class TsCtffindOutputs(Enum):
     CTFs = SetOfCTFTomoSeries
 
 
 class CistemProtTsCtffind(EMProtocol):
-    """ CTF estimation on a set of tilt series using CTFFIND. """
+    """ The contrast transfer function (CTF) affects the relative signal-to-noise
+    ratio (SNR) of Fourier components of each image. Those Fourier components
+    where the CTF is near 0.0 have very low SNR compared to others. It is therefore
+    essential to obtain accurate estimates of the CTF for each image so that
+    data from multiple imges may be combined in an optimal manner during later
+    processing.\n
+
+    You can use CTFfind (Rohou & Grigorieff, 2015) to estimate CTF parameter values
+    for each image. The main parameter to be determined for each image is the
+    objective lens defocus (in Angstroms). Because in general lenses are astigmatic,
+    one actually needs to determine two defocus values (describing defocus along
+    the lens' major and minor axes) and the angle of astigmatism.\n
+
+    To estimate the values of these three defocus parameters for an image,
+    CTFfind computes a filtered version of the amplitude spectrum of the micrograph
+    and then fits a model of the CTF (Equation 6 of Rohou & Grigorieff) to this
+    filtered amplitude spectrum. It then returns the values of the defocus parameters
+    which maximize the quality of the fit, as well as an image of the filtered
+    amplitude spectrum, with the CTF model.\n
+
+    Another diagnostic output is a 1D plot of the experimental amplitude spectrum,
+    the CTF fit and the quality of fitting.
+    """
+
     _label = 'tilt-series ctffind'
     _devStatus = PROD
     _possibleOutputs = TsCtffindOutputs
@@ -72,7 +96,7 @@ def _defineParams(self, form, stream=False):
         form.addSection(label='Input')
         form.addParam('inputTiltSeries', params.PointerParam, important=True,
                       pointerClass='SetOfTiltSeries, SetOfCTFTomoSeries',
-                      label='Input tilt series')
+                      label='Tilt series')
         form.addHidden('recalculate', params.BooleanParam,
                        default=False,
                        condition='recalculate',
@@ -94,15 +118,19 @@ def _insertAllSteps(self):
         self._initialize()
         pIdList = []
         for mdObj in self.tsCtfMdList:
-            pidConvert = self._insertFunctionStep(self.convertInputStep, mdObj, prerequisites=[])
-            pidProcess = self._insertFunctionStep(self.processTiltSeriesStep, mdObj, prerequisites=pidConvert)
-            pidCreateOutput = self._insertFunctionStep(self.createOutputStep, mdObj, prerequisites=pidProcess)
+            pidConvert = self._insertFunctionStep(self.convertInputStep,
+                                                  mdObj, prerequisites=[])
+            pidProcess = self._insertFunctionStep(self.processTiltSeriesStep,
+                                                  mdObj, prerequisites=pidConvert)
+            pidCreateOutput = self._insertFunctionStep(self.createOutputStep,
+                                                       mdObj, prerequisites=pidProcess)
             pIdList.append(pidCreateOutput)
         self._insertFunctionStep(self.closeStep, prerequisites=pIdList)
 
     def _initialize(self):
         self.inTsSet = self._getInputTs()
-        self._params = createCtfParams(self.inTsSet, self.windowSize.get(), self.lowRes.get(), self.highRes.get(),
+        self._params = createCtfParams(self.inTsSet, self.windowSize.get(),
+                                       self.lowRes.get(), self.highRes.get(),
                                        self.minDefocus.get(), self.maxDefocus.get())
         self._ctfProgram = ProgramCtffind(self)
         for ts in self.inTsSet.iterItems():
@@ -143,7 +171,8 @@ def createOutputStep(self, mdObj):
         if outCtfSet:
             outCtfSet.enableAppend()
         else:
-            outCtfSet = SetOfCTFTomoSeries.create(self._getPath(), template='ctfTomoSeriess%s.sqlite')
+            outCtfSet = SetOfCTFTomoSeries.create(self._getPath(),
+                                                  template='ctfTomoSeriess%s.sqlite')
             outCtfSet.setSetOfTiltSeries(self.inTsSet)
             outCtfSet.setStreamState(Set.STREAM_OPEN)
             self._defineOutputs(**{self._possibleOutputs.CTFs.name: outCtfSet})
@@ -221,5 +250,3 @@ def getCtfParamsDict(self):
         """ Return a copy of the global params dict,
         to avoid overwriting values. """
         return self._params
-
-

cistem/protocols/protocol_ts_resample.py

@@ -42,7 +42,8 @@
 
 class CistemProtTsResample(EMProtocol, ProtTomoBase):
     """
-    Resample tilt series by Fourier cropping/padding using cisTEM. This is equivalent to binning/unbinning operations but free of aliasing artifacts.
+    Resample tilt series by Fourier cropping/padding using cisTEM.
+    This is equivalent to binning/unbinning operations but free of aliasing artifacts.
 
     More info:
         https://cistem.org
@@ -82,17 +83,17 @@ def _defineParams(self, form):
         form.addSection(label=pwutils.Message.LABEL_INPUT)
         form.addParam('inputSetOfTiltSeries', PointerParam,
                       pointerClass='SetOfTiltSeries',
-                      allowsNull=False,
-                      label='Input tilt series')
+                      important=True,
+                      label='Tilt series')
 
         form.addParam('newXsize', IntParam,
                       default=512, validators=[Positive],
-                      label='New X-Size',
-                      help='Volume will be rescaled to this size in X dimension (voxels)')
+                      label='New X-Size (px)',
+                      help='Images will be rescaled to this size in X dimension (pixels)')
         form.addParam('newYsize', IntParam,
                       default=512, validators=[Positive],
-                      label='New Y-Size',
-                      help='Volume will be rescaled to this size in Y dimension (voxels)')
+                      label='New Y-Size (px)',
+                      help='Images will be rescaled to this size in Y dimension (pixels)')
 
     # -------------------------- INSERT steps functions -----------------------
     def _insertAllSteps(self):

cistem/wizards.py

@@ -47,7 +47,7 @@ def _getProvider(self, protocol):
         _objs = self._getParameters(protocol)['input']
         return CtfWizard._getListProvider(self, _objs)
 
-    def show(self, form):
+    def show(self, form, *args):
         protocol = form.protocol
         params = self._getParameters(protocol)
         _value = params['value']