Merge pull request #1141 from I2PC/release-1.1.facilities-dash_in_fil…

…ename_#1073

Release 1.1.facilities dash in filename #1073

pyworkflow/em/packages/xmipp3/protocol_movie_correlation.py

@@ -115,8 +115,8 @@ def _processMovie(self, movie):
         inputMd = os.path.join(movieFolder, 'input_movie.xmd')
         writeMovieMd(movie, inputMd, a0, aN, useAlignment=False)
 
-        args  = '-i %s ' % inputMd
-        args += '-o %s ' % self._getShiftsFile(movie)
+        args  = '-i "%s" ' % inputMd
+        args += '-o "%s" ' % self._getShiftsFile(movie)
         args += '--sampling %f ' % movie.getSamplingRate()
         args += '--max_freq %f ' % self.maxFreq
         args += '--Bspline %d ' % self.INTERP_MAP[self.splineOrder.get()]
@@ -157,10 +157,10 @@ def _processMovie(self, movie):
 
         if self.doSaveAveMic or self.doComputePSD:
             fnAvg = self._getExtraPath(self._getOutputMicName(movie))
-            args += ' --oavg %s' % fnAvg
+            args += ' --oavg "%s"' % fnAvg
 
         if self.doComputePSD:
-            fnInitial = os.path.join(movieFolder,"initialMic.mrc")
+            fnInitial = os.path.join(movieFolder, "initialMic.mrc")
             args  += ' --oavgInitial %s' % fnInitial
 
         if self.doSaveMovie:

pyworkflow/em/packages/xmipp3/protocol_movie_opticalflow.py

@@ -140,7 +140,7 @@ def _processMovie(self, movie):
         writeMovieMd(movie, inputMd, a0, aN, useAlignment=self.useAlignment)
 
         args = '-i %s ' % inputMd
-        args += '-o %s ' % self._getOutputShifts(movie)
+        args += '-o "%s" ' % self._getOutputShifts(movie)
         args += ' --frameRange %d %d ' % (0, aN - a0)
 
         if dark:
@@ -161,7 +161,7 @@ def _processMovie(self, movie):
         # We should save the movie either if the user selected it (default)
         # or if the PSD is going to be computed
         if self.doSaveAveMic or self.doComputePSD:
-            args += '--oavg %s ' % outMicFn
+            args += '--oavg "%s" ' % outMicFn
 
         if self.doComputePSD:
             args  += '--oavgInitial %s ' % aveMic

pyworkflow/em/protocol/protocol_align_movies.py

@@ -506,7 +506,7 @@ def averageMovie(self, movie, inputFn, outputMicFn, binFactor=1, roi=None,
         self.__runXmippProgram('xmipp_movie_alignment_correlation', args)
 
     def computePSD(self, inputMic, oroot, dim=400, overlap=0.7):
-        args = '--micrograph %s --oroot %s ' % (inputMic, oroot)
+        args = '--micrograph "%s" --oroot %s ' % (inputMic, oroot)
         args += '--dont_estimate_ctf --pieceDim %d --overlap %f' % (dim, overlap)
 
         self.__runXmippProgram('xmipp_ctf_estimate_from_micrograph', args)

pyworkflow/em/protocol/protocol_import/base.py

@@ -136,12 +136,6 @@ def _defineParams(self, form):
               label="File timeout (secs)",
               help="Interval of time (in seconds) after which, if a file \n"
                    "has not changed, we consider it as a new file. \n")
-
-        form.addParam('endTokenFile', params.StringParam, default=None,
-              condition='dataStreaming',
-              label="End token file",
-              help="Specify an ending file if you want to have more control\n"
-                   "about when to stop importing files.")
 
     def _defineImportParams(self, form):
         """ Override to add options related to the different types

pyworkflow/em/protocol/protocol_import/images.py

@@ -132,9 +132,16 @@ def importImagesStep(self, pattern, voltage, sphericalAberration,
         img.setAcquisition(acquisition)
         n = 1
         copyOrLink = self.getCopyOrLink()
+        alreadyWarned = False # Use this flag to warn only once
 
         for i, (fileName, fileId) in enumerate(self.iterFiles()):
             dst = self._getExtraPath(basename(fileName))
+            if ' ' in dst:
+                if not alreadyWarned:
+                    self.warning('Warning: your file names have white spaces!')
+                    self.warning('Removing white spaces from copies/symlinks.')
+                    alreadyWarned = True
+                dst = dst.replace(' ', '')
             copyOrLink(fileName, dst)
             # Handle special case of Imagic images, copying also .img or .hed
             self.handleImgHed(copyOrLink, fileName, dst)