flow improvements: add possible outputs and binThreads

xmipp3/protocols/protocol_align_volume.py

@@ -54,7 +54,10 @@ class XmippProtAlignVolume(ProtAlignVolume):
     _label = 'align volume'
     nVols = 0
     _devStatus = PROD
-
+    OUTPUT_NAME1 = "outputVolume"
+    OUTPUT_NAME2 = "outputVolumes"
+    _possibleOutputs = {OUTPUT_NAME1: Volume,
+                        OUTPUT_NAME2: SetOfVolumes}
 
     def __init__(self, **args):
         ProtAlignVolume.__init__(self, **args)

xmipp3/protocols/protocol_convert_pdb.py

@@ -74,6 +74,14 @@ def _defineParams(self, form):
 
         # Defining parallel arguments
         form.addParallelSection(threads=4, mpi=1)
+        form.addParam('binThreads', params.IntParam,
+                      label='threads',
+                      default=2,
+                      help='Number of threads used by Xmipp each time it is called in the protocol execution. For '
+                           'example, if 3 Scipion threads and 3 Xmipp threads are set, the pdbs will be '
+                           'processed in groups of 2 at the same time with a call of Xmipp with 3 threads each, so '
+                           '6 threads will be used at the same time. Beware the memory of your machine has '
+                           'memory enough to load together the number of pdbs specified by Scipion threads.')
 
         # Generating form
         form.addSection(label='Input')

xmipp3/protocols/protocol_preprocess/protocol_preprocess.py

@@ -124,11 +124,13 @@ class XmippProtPreprocessParticles(XmippProcessParticles):
         apply threshold, etc """
     _label = 'preprocess particles'
     _devStatus = PROD
+    _possibleOutputs = {"outputParticles": SetOfParticles}
+
     # Normalization enum constants
     NORM_OLD = 0
     NORM_NEW = 1
     NORM_RAMP =2
-    
+
     def __init__(self, **kwargs):
         XmippProcessParticles.__init__(self, **kwargs)
 

xmipp3/protocols/protocol_preprocess_micrographs.py

@@ -46,6 +46,8 @@ class XmippProtPreprocessMicrographs(ProtPreprocessMicrographs):
     You can crop borders, remove bad pixels, etc. """
     _label = 'preprocess micrographs'
 
+    _possibleOutputs = {OUTPUT_MICROGRAPHS: SetOfMicrographs}
+
 
     def __init__(self, **args):        
         ProtPreprocessMicrographs.__init__(self, **args)

xmipp3/protocols/protocol_volume_adjust_sub.py

@@ -42,6 +42,8 @@ class XmippProtVolAdjBase(EMProtocol):
     """ Helper class that contains some Protocol utilities methods
     used by both  XmippProtVolSubtraction and XmippProtVolAdjust."""
 
+    _possibleOutputs = {"outputVolume": Volume}
+
     # --------------------------- DEFINE param functions --------------------------------------------
     @classmethod
     def _defineParams(self, form):