Merge pull request #1 from scipion-em/devel

remove unused code, add summary

CHANGES.txt

@@ -1,2 +1,3 @@
+1.0.2 - remove unused code
 1.0.0 - First plugin version
 

README.rst

@@ -4,12 +4,12 @@ SIDESPLITTER plugin
 
 This plugin provide wrappers around `SIDESPLITTER <https://github.com/StructuralBiology-ICLMedicine/SIDESPLITTER>`_ program for mitigating local overfitting.
 
-+------------------+------------------+
-| stable: |stable| | devel: | |devel| |
-+------------------+------------------+
++--------------+----------------+
+| prod: |prod| | devel: |devel| |
++--------------+----------------+
 
-.. |stable| image:: http://scipion-test.cnb.csic.es:9980/badges/sidesplitter_prod.svg
-.. |devel| image:: http://scipion-test.cnb.csic.es:9980/badges/sidesplitter_sdevel.svg
+.. |prod| image:: http://scipion-test.cnb.csic.es:9980/badges/cistem_prod.svg
+.. |devel| image:: http://scipion-test.cnb.csic.es:9980/badges/cistem_devel.svg
 
 
 Installation

setup.py

@@ -66,7 +66,7 @@
     # For a discussion on single-sourcing the version across setup.py and the
     # project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    version='1.0.1',  # Required
+    version='1.0.2',  # Required
 
     # This is a one-line description or tagline of what your project does. This
     # corresponds to the "Summary" metadata field:

sidesplitter/convert.py

@@ -24,38 +24,26 @@
 # *
 # **************************************************************************
 
-import os
-
-import pyworkflow.utils as pwutils
 from pwem.emlib.image import ImageHandler
 
 
 def getImageLocation(location):
     return ImageHandler.locationToXmipp(location)
 
 
-def convertMask(img, outputPath, newDim=None):
+def convertMask(img, outFn, newDim=None):
     """ Convert binary mask to a format read by Relion and truncate the
     values between 0-1 values, due to Relion only support masks with this
     values (0-1).
     Params:
         img: input image to be converted.
-        outputPath: it can be either a directory or a file path.
-            If it is a directory, the output name will be inferred from input
-            and put into that directory. If it is not a directory,
-            it is assumed is the output filename.
+        outFn: output file path.
     Return:
         new file name of the mask.
     """
 
     ih = ImageHandler()
     imgFn = getImageLocation(img.getLocation())
-
-    if os.path.isdir(outputPath):
-        outFn = os.path.join(outputPath, pwutils.replaceBaseExt(imgFn, 'mrc'))
-    else:
-        outFn = outputPath
-
     ih.truncateMask(imgFn, outFn, newDim=newDim)
 
     return outFn

sidesplitter/protocols/protocol_sidesplitter.py

@@ -32,7 +32,7 @@
 from pwem.objects import Volume
 from pwem.emlib.image import ImageHandler
 
-import sidesplitter
+from sidesplitter import Plugin
 from ..convert import convertMask
 
 
@@ -47,15 +47,8 @@ class ProtSideSplitter(ProtAnalysis3D):
     def _getInputPath(self, *paths):
         return self._getPath('input', *paths)
 
-    def _initialize(self):
-        """ This function is meant to be called after the
-        working dir for the protocol have been set.
-        (maybe after recovery from mapper)
-        """
-        self._createFilenameTemplates()
-
     def _createFilenameTemplates(self):
-        """ Centralize how files are called for iterations and references. """
+        """ Centralize how files are called. """
         myDict = {'half1': self._getInputPath("half1_unfil.mrc"),
                   'half2': self._getInputPath("half2_unfil.mrc"),
                   'mask': self._getInputPath("mask.mrc"),
@@ -93,15 +86,14 @@ def _defineParams(self, form):
     # --------------------------- INSERT steps functions ----------------------
 
     def _insertAllSteps(self):
-        objId = self.protRefine.get().getObjId()
-        self._initialize()
-        self._insertFunctionStep('convertInputStep', objId)
+        self._createFilenameTemplates()
+        self._insertFunctionStep('convertInputStep')
         self._insertFunctionStep('runSideSplitterStep')
         self._insertFunctionStep('createOutputStep')
 
     # --------------------------- STEPS functions -----------------------------
 
-    def convertInputStep(self, protId):
+    def convertInputStep(self):
         """ Convert input half-maps to mrc as expected by SIDESPLITTER."""
         pwutils.makePath(self._getInputPath())
 
@@ -121,11 +113,11 @@ def runSideSplitterStep(self):
         """ Call SIDESPLITTER with the appropriate parameters. """
         args = self._getArgs()
         param = ' '.join(['%s %s' % (k, str(v)) for k, v in args.items()])
-        program = sidesplitter.Plugin.getProgram()
+        program = Plugin.getProgram()
         cmd = 'export OMP_NUM_THREADS=%d; ' % self.numberOfThreads.get()
         cmd += program
 
-        self.runJob(cmd, param, env=sidesplitter.Plugin.getEnviron(),
+        self.runJob(cmd, param, env=Plugin.getEnviron(),
                     cwd=self._getExtraPath(),
                     numberOfThreads=1)
 
@@ -154,6 +146,11 @@ def createOutputStep(self):
     def _summary(self):
         summary = []
 
+        if hasattr(self, 'outputVolume1'):
+            summary.append("Created locally filtered half-maps.")
+        else:
+            summary.append("Output is not ready")
+
         return summary
 
     def _validate(self):
@@ -165,17 +162,17 @@ def _validate(self):
 
     def _getArgs(self):
         """ Prepare the args dictionary."""
-        args = {'--v1': self._getPaths(self._getFileName('half1')),
-                '--v2': self._getPaths(self._getFileName('half2'))}
+        args = {'--v1': self._getRelPath(self._getFileName('half1')),
+                '--v2': self._getRelPath(self._getFileName('half2'))}
 
         if self.mask.hasValue():
-            args.update({'--mask': self._getPaths(self._getFileName('mask'))})
+            args['--mask'] = self._getRelPath(self._getFileName('mask'))
 
         if self.doSNRWeighting:
-            args.update({'--spectrum': ' '})
+            args['--spectrum'] = ' '
 
         return args
 
-    def _getPaths(self, fn):
-        """ Return relative path to the input dir from cwd=extra. """
-        return pwutils.join("../input", os.path.basename(fn))
+    def _getRelPath(self, fn):
+        """ Return relative path from cwd=extra. """
+        return os.path.relpath(fn, self._getExtraPath())

sidesplitter/tests/test_protocol_sidesplitter.py

@@ -41,7 +41,7 @@
                                                  "ProtRelionRefine3D",
                                                  doRaise=True)
 except ImportError as e:
-    print("Relion plugin not found! You need to install to be able to run this test.")
+    print("Relion plugin not found! You need to install it to be able to run this test.")
 
 
 class TestSideSplitter(BaseTest):