Updated keyword in result dictionary to runtime instead of cmd-level

Author: pintohutch

nipype/interfaces/afni/__init__.py

@@ -8,8 +8,8 @@
 
 from .base import Info
 from .preprocess import (To3D, Refit, Resample, TStat, Automask, Volreg, Merge,
-                         ZCutUp, Calc, TShift, Warp, Detrend, Despike, Copy,
-                         Fourier, Allineate, Maskave, SkullStrip, TCat, Fim,
+                         ZCutUp, Calc, TShift, Warp, Detrend, Despike, DegreeCentrality,
+                         Copy, Fourier, Allineate, Maskave, SkullStrip, TCat, Fim,
                          BlurInMask, Autobox, TCorrMap, Bandpass, Retroicor,
                          TCorrelate, TCorr1D, BrickStat, ROIStats, AutoTcorrelate,
                          AFNItoNIFTI, Eval, Means)

nipype/interfaces/afni/preprocess.py

@@ -180,6 +180,7 @@ class RefitInputSpec(CommandLineInputSpec):
                         ' template type, e.g. TLRC, MNI, ORIG')
 
 
+
 class Refit(CommandLine):
     """Changes some of the information inside a 3D dataset's header
 
@@ -506,6 +507,104 @@ class Despike(AFNICommand):
     output_spec = AFNICommandOutputSpec
 
 
+class CentralityInputSpec(AFNICommandInputSpec):
+    """
+    inherits the out_file parameter from AFNICommandOutputSpec base class
+    """
+
+    in_file = File(desc='input file to 3dDegreeCentrality',
+                   argstr='%s',
+                   position=-1,
+                   mandatory=True,
+                   exists=True,
+                   copyfile=False)
+
+    mask = File(desc='mask file to mask input data',
+                   argstr="-mask %s",
+                   exists=True)
+
+    thresh = traits.Float(desc='threshold to exclude connections where corr <= thresh',
+                          argstr='-thresh %f')
+
+    polort = traits.Int(desc='', argstr='-polort %d')
+
+    autoclip = traits.Bool(desc='Clip off low-intensity regions in the dataset',
+                           argstr='-autoclip')
+
+    automask = traits.Bool(desc='Mask the dataset to target brain-only voxels',
+                           argstr='-automask')
+
+
+class DegreeCentralityInputSpec(CentralityInputSpec):
+    """
+    inherits the out_file parameter from AFNICommandOutputSpec base class
+    """
+
+    in_file = File(desc='input file to 3dDegreeCentrality',
+                   argstr='%s',
+                   position=-1,
+                   mandatory=True,
+                   exists=True,
+                   copyfile=False)
+
+    mask = File(desc='mask file to mask input data',
+                   argstr="-mask %s",
+                   exists=True)
+
+    thresh = traits.Float(desc='threshold to exclude connections where corr <= thresh',
+                          argstr='-thresh %f')
+
+    sparsity = traits.Float(desc='only take the top percent of connections',
+                            argstr='-sparsity %f')
+
+    out_1d = traits.Str(desc='output filepath to text dump of correlation matrix',
+                        argstr='-out1D')
+
+    polort = traits.Int(desc='', argstr='-polort %d')
+
+    autoclip = traits.Bool(desc='Clip off low-intensity regions in the dataset',
+                           argstr='-autoclip')
+
+    automask = traits.Bool(desc='Mask the dataset to target brain-only voxels',
+                           argstr='-automask')
+
+
+class DegreeCentralityOutputSpec(AFNICommandOutputSpec):
+    """
+    inherits the out_file parameter from AFNICommandOutputSpec base class
+    """
+
+    one_d_file = File(desc='The text output of the similarity matrix computed'\
+                           'after thresholding with one-dimensional and '\
+                           'ijk voxel indices, correlations, image extents, '\
+                           'and affine matrix')
+
+
+class DegreeCentrality(AFNICommand):
+    """Performs degree centrality on a dataset using a given maskfile
+    via 3dDegreeCentrality
+
+    For complete details, see the `3dDegreeCentrality Documentation.
+    <http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dDegreeCentrality.html>
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces import afni as afni
+    >>> degree = afni.DegreeCentrality()
+    >>> degree.inputs.in_file = 'func_preproc.nii'
+    >>> degree.inputs.mask = 'mask.nii'
+    >>> degree.inputs.sparsity = 1 # keep the top one percent of connections
+    >>> degree.cmdline
+    '3dDegreeCentrality -sparsity 1 -mask mask.nii func_preproc.nii'
+    >>> res = degree.run() # doctest: +SKIP
+    """
+
+    _cmd = '3dDegreeCentrality'
+    input_spec = DegreeCentralityInputSpec
+    output_spec = DegreeCentralityOutputSpec
+
+
 class AutomaskInputSpec(AFNICommandInputSpec):
     in_file = File(desc='input file to 3dAutomask',
                    argstr='%s',

nipype/interfaces/base.py

@@ -1375,8 +1375,8 @@ def _process(drain=0):
         result['stderr'] = []
         result['merged'] = ''
 
-    setattr(runtime, 'cmd_memory', mem_mb/1024.0)
-    setattr(runtime, 'cmd_threads', num_threads)
+    setattr(runtime, 'runtime_memory', mem_mb/1024.0)
+    setattr(runtime, 'runtime_threads', num_threads)
     runtime.stderr = '\n'.join(result['stderr'])
     runtime.stdout = '\n'.join(result['stdout'])
     runtime.merged = result['merged']

nipype/pipeline/plugins/callback_log.py

@@ -10,24 +10,20 @@ def log_nodes_cb(node, status, result=None):
 
     # Check runtime profile stats
     if result is None:
-        node_mem = cmd_mem = run_seconds = cmd_threads = 'N/A'
+        runtime_memory = runtime_seconds = runtime_threads = 'N/A'
     else:
         try:
-            node_mem = result['node_memory']
+            runtime_memory = result['runtime_memory']
         except KeyError:
-            node_mem = 'Unknown'
+            runtime_memory = 'Unknown'
         try:
-            cmd_mem = result['cmd_memory']
+            runtime_seconds = result['runtime_seconds']
         except KeyError:
-            cmd_mem = 'Unknown'
+            runtime_seconds = 'Unknown'
         try:
-            run_seconds = result['run_seconds']
-        except KeyError:
-            run_seconds = 'Unknown'
-        try:
-            cmd_threads = result['cmd_threads']
+            runtime_threads = result['runtime_threads']
         except:
-            cmd_threads = 'Unknown'
+            runtime_threads = 'Unknown'
 
     # Check status and write to log
     # Start
@@ -44,10 +40,9 @@ def log_nodes_cb(node, status, result=None):
         node._id + '"' + ',"finish":' + '"' + str(datetime.datetime.now()) +  \
         '"' + ',"estimated_memory":' + '"'+ str(node._interface.estimated_memory) + '"'+ \
         ',"num_threads":' + '"'+ str(node._interface.num_threads) + '"'+ \
-        ',"cmd-level_threads":' + '"'+ str(cmd_threads) + '"'+ \
-        ',"node-level_memory":' + '"'+ str(node_mem) + '"'+ \
-        ',"cmd-level_memory":' + '"'+ str(cmd_mem) + '"' + \
-        ',"run_seconds":' + '"'+ str(run_seconds) + '"'+ '}'
+        ',"runtime_threads":' + '"'+ str(runtime_threads) + '"'+ \
+        ',"runtime_memory":' + '"'+ str(runtime_memory) + '"' + \
+        ',"runtime_seconds":' + '"'+ str(runtime_seconds) + '"'+ '}'
 
         logger.debug(message)
     # Other

nipype/pipeline/plugins/multiproc.py

@@ -40,10 +40,10 @@ def run_node(node, updatehash, runtime_profile=False):
             retval = node.run(updatehash=updatehash)
             run_secs = (datetime.datetime.now() - start).total_seconds()
             result['result'] = retval
-            result['run_seconds'] = run_secs
+            result['runtime_seconds'] = run_secs
             if hasattr(retval.runtime, 'get'):
-                result['cmd_memory'] = retval.runtime.get('cmd_memory')
-                result['cmd_threads'] = retval.runtime.get('cmd_threads')
+                result['runtime_memory'] = retval.runtime.get('runtime_memory')
+                result['runtime_threads'] = retval.runtime.get('runtime_threads')
         except:
             etype, eval, etr = sys.exc_info()
             result['traceback'] = format_exception(etype,eval,etr)