Merge pull request #663 from satra/fix/spm_mcr

Fix/spm mcr

Author: satra

CHANGES

@@ -25,8 +25,10 @@ Next release
         - FA created output files with erroneous extension
 
 * FIX: Deals properly with 3d files in SPM Realign
+* FIX: SPM with MCR fixed
 
 * API: 'name' is now a positional argument for Workflow, Node, and MapNode constructors
+* API: SPM now defaults to SPM8 or SPM12b job format
 
 Release 0.8.0 (May 8, 2013)
 ===========================

doc/users/index.rst

@@ -34,7 +34,7 @@
    joinnode_and_itersource
    model_specification
    saving_workflows
-
+   spmmcr
 
 
 

doc/users/spmmcr.rst

@@ -0,0 +1,24 @@
+.. _spmmcr:
+
+====================================
+Using SPM with MATLAB Common Runtime
+====================================
+
+In order to use the standalone MCR version of spm, you need to ensure that
+the following commands are executed at the beginning of your script:
+
+.. testcode::
+
+    from nipype import spm
+    matlab_cmd = '/path/to/run_spm8.sh /path/to/Compiler_Runtime/v713/ script'
+    spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
+
+you can test by calling:
+
+.. testcode::
+
+   spm.SPMCommand().version
+
+Information about the MCR version of SPM8 can be found at:
+
+http://en.wikibooks.org/wiki/SPM/Standalone

examples/fmri_spm.py

@@ -15,10 +15,14 @@
 
 Import necessary modules from nipype."""
 
+from nipype import spm, fsl
+
+# In order to use this example with SPM's matlab common runtime
+# matlab_cmd = ('/Users/satra/Downloads/spm8/run_spm8.sh '
+#               '/Applications/MATLAB/MATLAB_Compiler_Runtime/v713/ script')
+# spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
+
 import nipype.interfaces.io as nio           # Data i/o
-import nipype.interfaces.spm as spm          # spm
-import nipype.interfaces.matlab as mlab      # how to run matlab
-import nipype.interfaces.fsl as fsl          # fsl
 import nipype.interfaces.utility as util     # utility
 import nipype.pipeline.engine as pe          # pypeline engine
 import nipype.algorithms.rapidart as ra      # artifact detection
@@ -40,7 +44,8 @@
 fsl.FSLCommand.set_default_output_type('NIFTI')
 
 # Set the way matlab should be called
-mlab.MatlabCommand.set_default_matlab_cmd("matlab -nodesktop -nosplash")
+# import nipype.interfaces.matlab as mlab      # how to run matlab
+# mlab.MatlabCommand.set_default_matlab_cmd("matlab -nodesktop -nosplash")
 
 """The nipype tutorial contains data for two subjects.  Subject data
 is in two subdirectories, ``s1`` and ``s2``.  Each subject directory
@@ -382,7 +387,7 @@ def getstripdir(subject_id):
 """
 
 if __name__ == '__main__':
-    l1pipeline.run()
+    l1pipeline.run('MultiProc')
 #    l2pipeline.run()
 #    l1pipeline.write_graph()
 

nipype/interfaces/spm/base.py

@@ -1,6 +1,18 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""The spm module provides basic functions for interfacing with SPM  tools."""
+"""The spm module provides basic functions for interfacing with SPM  tools.
+
+In order to use the standalone MCR version of spm, you need to ensure that
+the following commands are executed at the beginning of your script::
+
+   from nipype import spm
+   matlab_cmd = '/path/to/run_spm8.sh /path/to/Compiler_Runtime/v713/ script'
+   spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
+
+you can test by calling::
+
+   spm.SPMCommand().version
+"""
 
 __docformat__ = 'restructuredtext'
 
@@ -111,7 +123,7 @@ class Info(object):
     """Handles SPM version information
     """
     @staticmethod
-    def version(matlab_cmd=None):
+    def version(matlab_cmd=None, paths=None, use_mcr=None):
         """Returns the path to the SPM directory in the Matlab path
         If path not found, returns None.
 
@@ -135,6 +147,15 @@ def version(matlab_cmd=None):
             except:
                 matlab_cmd = 'matlab -nodesktop -nosplash'
         mlab = MatlabCommand(matlab_cmd=matlab_cmd)
+        mlab.inputs.mfile = False
+        if paths:
+            mlab.inputs.paths = paths
+        if use_mcr:
+            mlab.inputs.nodesktop = Undefined
+            mlab.inputs.nosplash = Undefined
+            mlab.inputs.single_comp_thread = Undefined
+            mlab.inputs.mfile = True
+            mlab.inputs.uses_mcr = True
         mlab.inputs.script = """
 if isempty(which('spm')),
 throw(MException('SPMCheck:NotFound','SPM not in matlab path'));
@@ -144,7 +165,6 @@ def version(matlab_cmd=None):
 fprintf(1, 'NIPYPE path:%s|name:%s|release:%s', spm_path, name, version);
 exit;
         """
-        mlab.inputs.mfile = False
         try:
             out = mlab.run()
         except (IOError, RuntimeError), e:
@@ -178,6 +198,9 @@ class SPMCommandInputSpec(BaseInterfaceInputSpec):
     mfile = traits.Bool(True, desc='Run m-code using m-file',
                         usedefault=True)
     use_mcr = traits.Bool(desc='Run m-code using SPM MCR')
+    use_v8struct = traits.Bool(True, min_ver='8', usedefault=True,
+                               desc=('Generate SPM8 and higher compatible jobs')
+                               )
 
 
 class SPMCommand(BaseInterface):
@@ -215,17 +238,25 @@ def _matlab_cmd_update(self):
         # and can be set only during init
         self.mlab = MatlabCommand(matlab_cmd=self.inputs.matlab_cmd,
                                   mfile=self.inputs.mfile,
-                                  paths=self.inputs.paths,
-                                  uses_mcr=self.inputs.use_mcr)
+                                  paths=self.inputs.paths)
         self.mlab.inputs.script_file = 'pyscript_%s.m' % \
             self.__class__.__name__.split('.')[-1].lower()
         if isdefined(self.inputs.use_mcr) and self.inputs.use_mcr:
             self.mlab.inputs.nodesktop = Undefined
             self.mlab.inputs.nosplash = Undefined
+            self.mlab.inputs.single_comp_thread = Undefined
+            self.mlab.inputs.uses_mcr = True
+            self.mlab.inputs.mfile = True
 
     @property
     def version(self):
-        return Info.version()
+        version_dict = Info.version(matlab_cmd=self._matlab_cmd,
+                                    paths=self._paths,
+                                    use_mcr=self._use_mcr)
+        if version_dict:
+            return '.'.join((version_dict['name'].split('SPM')[-1],
+                             version_dict['release']))
+        return version_dict
 
     @property
     def jobtype(self):
@@ -300,9 +331,10 @@ def _reformat_dict_for_savemat(self, contents):
 
         Examples
         --------
-        >>> a = SPMCommand()._reformat_dict_for_savemat(dict(a=1,b=dict(c=2,d=3)))
-        >>> print a
-        [{'a': 1, 'b': [{'c': 2, 'd': 3}]}]
+        >>> a = SPMCommand()._reformat_dict_for_savemat(dict(a=1,
+        ...                                                  b=dict(c=2, d=3)))
+        >>> a == [{'a': 1, 'b': [{'c': 2, 'd': 3}]}]
+        True
 
         """
         newdict = {}
@@ -401,48 +433,46 @@ def _make_matlab_command(self, contents, postscript=None):
         mscript = """
         %% Generated by nipype.interfaces.spm
         if isempty(which('spm')),
-             throw(MException('SPMCheck:NotFound','SPM not in matlab path'));
+             throw(MException('SPMCheck:NotFound', 'SPM not in matlab path'));
         end
-        [name, ver] = spm('ver');
-        fprintf('SPM version: %s Release: %s\\n',name, ver);
-        fprintf('SPM path: %s\\n',which('spm'));
+        [name, version] = spm('ver');
+        fprintf('SPM version: %s Release: %s\\n',name, version);
+        fprintf('SPM path: %s\\n', which('spm'));
         spm('Defaults','fMRI');
 
-        if strcmp(spm('ver'),'SPM8'), spm_jobman('initcfg');end\n
+        if strcmp(name, 'SPM8') || strcmp(name, 'SPM12b'),
+           spm_jobman('initcfg');
+           spm_get_defaults('CmdLine', 1);
+        end\n
         """
         if self.mlab.inputs.mfile:
-            if self.jobname in ['st', 'smooth', 'preproc', 'preproc8',
-                                'fmri_spec', 'fmri_est', 'factorial_design',
-                                'defs', 'dicom']:
-                # parentheses
-                mscript += self._generate_job('jobs{1}.%s{1}.%s(1)' %
+            if isdefined(self.inputs.use_v8struct) and self.inputs.use_v8struct:
+                mscript += self._generate_job('jobs{1}.spm.%s.%s' %
                                               (self.jobtype, self.jobname),
                                               contents[0])
             else:
-                #curly brackets
-                mscript += self._generate_job('jobs{1}.%s{1}.%s{1}' %
-                                              (self.jobtype, self.jobname),
-                                              contents[0])
+                if self.jobname in ['st', 'smooth', 'preproc', 'preproc8',
+                                'fmri_spec', 'fmri_est', 'factorial_design',
+                                'defs']:
+                    # parentheses
+                    mscript += self._generate_job('jobs{1}.%s{1}.%s(1)' %
+                                                  (self.jobtype, self.jobname),
+                                                  contents[0])
+                else:
+                    #curly brackets
+                    mscript += self._generate_job('jobs{1}.%s{1}.%s{1}' %
+                                                  (self.jobtype, self.jobname),
+                                                  contents[0])
         else:
             jobdef = {'jobs': [{self.jobtype:
-                                  [{self.jobname:self.reformat_dict_for_savemat
-                                      (contents[0])}]}]}
+                                [{self.jobname:
+                                  self.reformat_dict_for_savemat(contents[0])}]
+                                }]}
             savemat(os.path.join(cwd, 'pyjobs_%s.mat' % self.jobname), jobdef)
             mscript += "load pyjobs_%s;\n\n" % self.jobname
         mscript += """
-        if strcmp(spm('ver'),'SPM8'),
-           jobs=spm_jobman('spm5tospm8',{jobs});
-        end
-        spm_jobman(\'run_nogui\',jobs);\n
+        spm_jobman(\'run\', jobs);\n
         """
         if postscript is not None:
             mscript += postscript
         return mscript
-
-    @property
-    def version(self):
-        version_dict = Info.version()
-        if version_dict:
-            return '.'.join((version_dict['name'].split('SPM')[-1],
-                             version_dict['release']))
-        return version_dict

nipype/interfaces/spm/preprocess.py

@@ -136,7 +136,7 @@ class RealignInputSpec(SPMCommandInputSpec):
     wrap = traits.List(traits.Int(), minlen=3, maxlen=3,
                         field='eoptions.wrap',
                         desc='Check if interpolation should wrap in [x,y,z]')
-    write_which = traits.ListInt([1, 1], field='roptions.which',
+    write_which = traits.ListInt([2, 1], field='roptions.which',
                               minlen=2, maxlen=2, usedefault=True,
                               desc='determines which images to reslice')
     write_interp = traits.Range(low=0, high=7, field='roptions.interp',
@@ -146,7 +146,7 @@ class RealignInputSpec(SPMCommandInputSpec):
                    desc='Check if interpolation should wrap in [x,y,z]')
     write_mask = traits.Bool(field='roptions.mask',
                              desc='True/False mask output image')
-    out_prefix = traits.String('r', field='prefix', usedefault=True,
+    out_prefix = traits.String('r', field='roptions.prefix', usedefault=True,
                                desc='realigned output prefix')
 
 

nipype/interfaces/spm/tests/test_base.py

@@ -134,6 +134,9 @@ class TestClass(spm.SPMCommand):
     dc = TestClass()  # dc = derived_class
     dc.inputs.test_in = True
     out = dc._make_matlab_command(dc._parse_inputs())
+    yield assert_equal, out.find('jobs{1}.spm.jobtype.jobname.testfield = 1;') > 0, 1
+    dc.inputs.use_v8struct = False
+    out = dc._make_matlab_command(dc._parse_inputs())
     yield assert_equal, out.find('jobs{1}.jobtype{1}.jobname{1}.testfield = 1;') > 0, 1
 
 def test_make_matlab_command():
@@ -145,5 +148,8 @@ class TestClass(spm.SPMCommand):
     filelist, outdir, cwd = create_files_in_directory()
     contents = {'contents': [1, 2, 3, 4]}
     script = dc._make_matlab_command([contents])
+    yield assert_true, 'jobs{1}.spm.jobtype.jobname.contents(3) = 3;' in script
+    dc.inputs.use_v8struct = False
+    script = dc._make_matlab_command([contents])
     yield assert_true, 'jobs{1}.jobtype{1}.jobname{1}.contents(3) = 3;' in script
     clean_directory(outdir, cwd)