Merge pull request #20 from chrisfilo/enh/saveworkflow

Enh/saveworkflow

Author: satra

CHANGES

@@ -3,6 +3,7 @@ Next release
 * ENH: New interfaces: nipy.Trim
 
 * ENH: Allow control over terminal output for commandline interfaces
+* ENH: Added preliminary support for generating Python code from Workflows.
 
 Release 0.7.0 (Dec 18, 2012)
 ============================

doc/users/index.rst

@@ -31,6 +31,7 @@
    function_interface
    mapnode_and_iterables
    model_specification
+   saving_workflows
 
 
 

doc/users/saving_workflows.rst

@@ -0,0 +1,105 @@
+.. _saving_workflows:
+
+===================================================
+Saving Workflows and Nodes to a file (experimental)
+===================================================
+
+On top of the standard way of saving (i.e. serializing) objects in Python 
+(see `pickle <http://docs.python.org/2/library/pickle.html>`_) Nipype 
+provides methods to turn Workflows and nodes into human readable code. 
+This is useful if you want to save a Workflow that you have generated 
+on the fly for future use.
+
+To generate Python code for a Workflow use the export method:
+
+.. testcode::
+
+	from nipype.interfaces.fsl import BET, ImageMaths
+	from nipype.pipeline.engine import Workflow, Node, MapNode, format_node
+	from nipype.interfaces.utility import Function, IdentityInterface
+	
+	bet = Node(BET(), name='bet')
+	bet.iterables = ('frac', [0.3, 0.4])
+	
+	bet2 = MapNode(BET(), name='bet2', iterfield=['infile'])
+	bet2.iterables = ('frac', [0.4, 0.5])
+	
+	maths = Node(ImageMaths(), name='maths')
+	
+	def testfunc(in1):
+	    """dummy func
+	    """
+	    out = in1 + 'foo' + "out1"
+	    return out
+	
+	funcnode = Node(Function(input_names=['a'], output_names=['output'], function=testfunc),
+	                name='testfunc')
+	funcnode.inputs.in1 = '-sub'
+	func = lambda x: x
+	
+	inode = Node(IdentityInterface(fields=['a']), name='inode')
+	
+	wf = Workflow('testsave')
+	wf.add_nodes([bet2])
+	wf.connect(bet, 'mask_file', maths, 'in_file')
+	wf.connect(bet2, ('mask_file', func), maths, 'in_file2')
+	wf.connect(inode, 'a', funcnode, 'in1')
+	wf.connect(funcnode, 'output', maths, 'op_string')
+	
+	wf.export()
+	
+This will create a file "outputtestsave.py" with the following content:
+
+.. testcode::
+
+	from nipype.pipeline.engine import Workflow, Node, MapNode
+	from nipype.interfaces.utility import IdentityInterface
+	from nipype.interfaces.utility import Function
+	from nipype.utils.misc import getsource
+	from nipype.interfaces.fsl.preprocess import BET
+	from nipype.interfaces.fsl.utils import ImageMaths
+	# Functions
+	func = lambda x: x
+	# Workflow
+	testsave = Workflow("testsave")
+	# Node: testsave.inode
+	inode = Node(IdentityInterface(fields=['a'], mandatory_inputs=True), name="inode")
+	# Node: testsave.testfunc
+	testfunc = Node(Function(input_names=['a'], output_names=['output']), name="testfunc")
+	def testfunc_1(in1):
+	    """dummy func
+	    """
+	    out = in1 + 'foo' + "out1"
+	    return out
+	
+	testfunc.inputs.function_str = getsource(testfunc_1)
+	testfunc.inputs.ignore_exception = False
+	testfunc.inputs.in1 = '-sub'
+	testsave.connect(inode, "a", testfunc, "in1")
+	# Node: testsave.bet2
+	bet2 = MapNode(BET(), iterfield=['infile'], name="bet2")
+	bet2.iterables = ('frac', [0.4, 0.5])
+	bet2.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
+	bet2.inputs.ignore_exception = False
+	bet2.inputs.output_type = 'NIFTI_GZ'
+	bet2.inputs.terminal_output = 'stream'
+	# Node: testsave.bet
+	bet = Node(BET(), name="bet")
+	bet.iterables = ('frac', [0.3, 0.4])
+	bet.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
+	bet.inputs.ignore_exception = False
+	bet.inputs.output_type = 'NIFTI_GZ'
+	bet.inputs.terminal_output = 'stream'
+	# Node: testsave.maths
+	maths = Node(ImageMaths(), name="maths")
+	maths.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
+	maths.inputs.ignore_exception = False
+	maths.inputs.output_type = 'NIFTI_GZ'
+	maths.inputs.terminal_output = 'stream'
+	testsave.connect(bet2, ('mask_file', func), maths, "in_file2")
+	testsave.connect(bet, "mask_file", maths, "in_file")
+	testsave.connect(testfunc, "output", maths, "op_string")
+	
+The file is ready to use and includes all the necessary imports.
+
+.. include:: ../links_names.txt

nipype/pipeline/engine.py

@@ -543,17 +543,22 @@ def write_hierarchical_dotfile(self, dotfilename=None, colored=True,
         else:
             logger.info(dotstr)
 
-    def export(self, prefix="output", format="python", include_config=False):
+    def export(self, filename=None, prefix="output", format="python", include_config=False):
         """Export object into a different format
 
         Parameters
         ----------
+        filename: string
+           file to save the code to; overrides prefix
 
         prefix: string
            prefix to use for output file
 
         format: string
            one of "python"
+           
+        include_config: boolean
+           whether to include node and workflow config values
         """
         formats = ["python"]
         if format not in formats:
@@ -606,7 +611,10 @@ def export(self, prefix="output", format="python", include_config=False):
             for function in functions:
                 functionlines.append(cPickle.loads(function).rstrip())
             all_lines = importlines + functionlines + lines
-            with open('%s%s.py' % (prefix, self.name), 'wt') as fp:
+            
+            if not filename:
+                filename = '%s%s.py' % (prefix, self.name)
+            with open(filename, 'wt') as fp:
                 #fp.writelines('\n'.join([line.replace('\n', '\\n') for line in all_lines]))
                 fp.writelines('\n'.join(all_lines))
         return all_lines