sty: pep8

Author: satra

nipype/interfaces/spm/base.py

@@ -25,6 +25,7 @@
 from ... import logging
 logger = logging.getLogger('interface')
 
+
 def func_is_3d(in_file):
     """Checks if input functional files are 3d."""
 
@@ -33,41 +34,44 @@ def func_is_3d(in_file):
     else:
         img = load(in_file)
         shape = img.get_shape()
-        if len(shape) == 3 or (len(shape)==4 and shape[3]==1):
+        if len(shape) == 3 or (len(shape) == 4 and shape[3] == 1):
             return True
         else:
             return False
 
+
 def get_first_3dfile(in_files):
     if not func_is_3d(in_files):
         return None
     if isinstance(in_files[0], list):
         return in_files[0]
     return in_files
 
+
 def scans_for_fname(fname):
     """Reads a nifti file and converts it to a numpy array storing
     individual nifti volumes.
 
     Opens images so will fail if they are not found.
 
     """
-    if isinstance(fname,list):
-        scans = np.zeros((len(fname),),dtype=object)
-        for sno,f in enumerate(fname):
-            scans[sno] = '%s,1'%f
+    if isinstance(fname, list):
+        scans = np.zeros((len(fname),), dtype=object)
+        for sno, f in enumerate(fname):
+            scans[sno] = '%s,1' % f
         return scans
     img = load(fname)
     if len(img.get_shape()) == 3:
-        return np.array(('%s,1'%fname,),dtype=object)
+        return np.array(('%s,1' % fname,), dtype=object)
     else:
         n_scans = img.get_shape()[3]
-        scans = np.zeros((n_scans,),dtype=object)
+        scans = np.zeros((n_scans,), dtype=object)
         for sno in range(n_scans):
-            scans[sno] = '%s,%d'% (fname, sno+1)
+            scans[sno] = '%s,%d' % (fname, sno + 1)
         return scans
 
-def scans_for_fnames(fnames,keep4d=False,separate_sessions=False):
+
+def scans_for_fnames(fnames, keep4d=False, separate_sessions=False):
     """Converts a list of files to a concatenated numpy array for each
     volume.
 
@@ -84,14 +88,14 @@ def scans_for_fnames(fnames,keep4d=False,separate_sessions=False):
         if func_is_3d(fnames[0]):
             fnames = [fnames]
     if separate_sessions or keep4d:
-        flist = np.zeros((len(fnames),),dtype=object)
-    for i,f in enumerate(fnames):
+        flist = np.zeros((len(fnames),), dtype=object)
+    for i, f in enumerate(fnames):
         if separate_sessions:
             if keep4d:
-                if isinstance(f,list):
+                if isinstance(f, list):
                     flist[i] = np.array(f, dtype=object)
                 else:
-                    flist[i] = np.array([f],dtype=object)
+                    flist[i] = np.array([f], dtype=object)
             else:
                 flist[i] = scans_for_fname(f)
         else:
@@ -102,14 +106,15 @@ def scans_for_fnames(fnames,keep4d=False,separate_sessions=False):
                 if flist is None:
                     flist = scans
                 else:
-                    flist = np.concatenate((flist,scans))
+                    flist = np.concatenate((flist, scans))
     return flist
 
+
 class Info(object):
     """Handles SPM version information
     """
     @staticmethod
-    def version( matlab_cmd = None ):
+    def version(matlab_cmd=None):
         """Returns the path to the SPM directory in the Matlab path
         If path not found, returns None.
 
@@ -132,20 +137,20 @@ def version( matlab_cmd = None ):
                 matlab_cmd = os.environ['MATLABCMD']
             except:
                 matlab_cmd = 'matlab -nodesktop -nosplash'
-        mlab = MatlabCommand(matlab_cmd = matlab_cmd)
+        mlab = MatlabCommand(matlab_cmd=matlab_cmd)
         mlab.inputs.script = """
-        if isempty(which('spm')),
-        throw(MException('SPMCheck:NotFound','SPM not in matlab path'));
-        end;
-        spm_path = spm('dir');
-        [name, version] = spm('ver');
-        fprintf(1, 'NIPYPE path:%s|name:%s|release:%s', spm_path, name, version);
-        exit;
+if isempty(which('spm')),
+throw(MException('SPMCheck:NotFound','SPM not in matlab path'));
+end;
+spm_path = spm('dir');
+[name, version] = spm('ver');
+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:
+        except (IOError, RuntimeError), e:
             # if no Matlab at all -- exception could be raised
             # No Matlab -- no spm
             logger.debug(str(e))
@@ -158,12 +163,13 @@ def version( matlab_cmd = None ):
                 out_dict[key] = val
             return out_dict
 
+
 def no_spm():
     """ Checks if SPM is NOT installed
     used with nosetests skipif to skip tests
     that will fail if spm is not installed"""
 
-    if Info.version() == None or 'NIPYPE_NO_MATLAB' in os.environ:
+    if Info.version() is None or 'NIPYPE_NO_MATLAB' in os.environ:
         return True
     else:
         return False
@@ -173,9 +179,10 @@ class SPMCommandInputSpec(BaseInterfaceInputSpec):
     matlab_cmd = traits.Str(desc='matlab command to use')
     paths = InputMultiPath(Directory(), desc='Paths to add to matlabpath')
     mfile = traits.Bool(True, desc='Run m-code using m-file',
-                          usedefault=True)
+                        usedefault=True)
     use_mcr = traits.Bool(desc='Run m-code using SPM MCR')
 
+
 class SPMCommand(BaseInterface):
     """Extends `BaseInterface` class to implement SPM specific interfaces.
 
@@ -200,7 +207,7 @@ def __init__(self, **inputs):
         self._matlab_cmd_update()
 
     @classmethod
-    def set_mlab_paths(cls, matlab_cmd=None, paths = None, use_mcr=None):
+    def set_mlab_paths(cls, matlab_cmd=None, paths=None, use_mcr=None):
         cls._matlab_cmd = matlab_cmd
         cls._paths = paths
         cls._use_mcr = use_mcr
@@ -214,7 +221,7 @@ def _matlab_cmd_update(self):
                                   paths=self.inputs.paths,
                                   uses_mcr=self.inputs.use_mcr)
         self.mlab.inputs.script_file = 'pyscript_%s.m' % \
-        self.__class__.__name__.split('.')[-1].lower()
+            self.__class__.__name__.split('.')[-1].lower()
 
     @property
     def jobtype(self):
@@ -234,7 +241,8 @@ def _check_mlab_inputs(self):
 
     def _run_interface(self, runtime):
         """Executes the SPM function using MATLAB."""
-        self.mlab.inputs.script = self._make_matlab_command(deepcopy(self._parse_inputs()))
+        self.mlab.inputs.script = self._make_matlab_command(
+            deepcopy(self._parse_inputs()))
         results = self.mlab.run()
         runtime.returncode = results.runtime.returncode
         if self.mlab.inputs.uses_mcr:
@@ -250,7 +258,6 @@ def _list_outputs(self):
 
         raise NotImplementedError
 
-
     def _format_arg(self, opt, spec, val):
         """Convert input to appropriate format for SPM."""
         if spec.is_trait_type(traits.Bool):
@@ -260,7 +267,7 @@ def _format_arg(self, opt, spec, val):
 
     def _parse_inputs(self, skip=()):
         spmdict = {}
-        metadata=dict(field=lambda t : t is not None)
+        metadata = dict(field=lambda t: t is not None)
         for name, spec in self.inputs.traits(**metadata).items():
             if skip and name in skip:
                 continue
@@ -325,47 +332,47 @@ def _generate_job(self, prefix='', contents=None):
         if contents is None:
             return jobstring
         if isinstance(contents, list):
-            for i,value in enumerate(contents):
+            for i, value in enumerate(contents):
                 if prefix.endswith(")"):
-                    newprefix = "%s,%d)" % (prefix[:-1], i+1)
+                    newprefix = "%s,%d)" % (prefix[:-1], i + 1)
                 else:
-                    newprefix = "%s(%d)" % (prefix, i+1)
+                    newprefix = "%s(%d)" % (prefix, i + 1)
                 jobstring += self._generate_job(newprefix, value)
             return jobstring
         if isinstance(contents, dict):
-            for key,value in contents.items():
+            for key, value in contents.items():
                 newprefix = "%s.%s" % (prefix, key)
                 jobstring += self._generate_job(newprefix, value)
             return jobstring
         if isinstance(contents, np.ndarray):
             if contents.dtype == np.dtype(object):
                 if prefix:
-                    jobstring += "%s = {...\n"%(prefix)
+                    jobstring += "%s = {...\n" % (prefix)
                 else:
                     jobstring += "{...\n"
-                for i,val in enumerate(contents):
+                for i, val in enumerate(contents):
                     if isinstance(val, np.ndarray):
                         jobstring += self._generate_job(prefix=None,
                                                         contents=val)
-                    elif isinstance(val,str):
-                        jobstring += '\'%s\';...\n'%(val)
+                    elif isinstance(val, str):
+                        jobstring += '\'%s\';...\n' % (val)
                     else:
-                        jobstring += '%s;...\n'%str(val)
+                        jobstring += '%s;...\n' % str(val)
                 jobstring += '};\n'
             else:
-                for i,val in enumerate(contents):
+                for i, val in enumerate(contents):
                     for field in val.dtype.fields:
                         if prefix:
-                            newprefix = "%s(%d).%s"%(prefix, i+1, field)
+                            newprefix = "%s(%d).%s" % (prefix, i + 1, field)
                         else:
-                            newprefix = "(%d).%s"%(i+1, field)
+                            newprefix = "(%d).%s" % (i + 1, field)
                         jobstring += self._generate_job(newprefix,
                                                         val[field])
             return jobstring
         if isinstance(contents, str):
-            jobstring += "%s = '%s';\n" % (prefix,contents)
+            jobstring += "%s = '%s';\n" % (prefix, contents)
             return jobstring
-        jobstring += "%s = %s;\n" % (prefix,str(contents))
+        jobstring += "%s = %s;\n" % (prefix, str(contents))
         return jobstring
 
     def _make_matlab_command(self, contents, postscript=None):
@@ -387,7 +394,7 @@ def _make_matlab_command(self, contents, postscript=None):
 
         """
         cwd = os.getcwd()
-        mscript  = """
+        mscript = """
         %% Generated by nipype.interfaces.spm
         if isempty(which('spm')),
              throw(MException('SPMCheck:NotFound','SPM not in matlab path'));
@@ -400,19 +407,23 @@ def _make_matlab_command(self, contents, postscript=None):
         if strcmp(spm('ver'),'SPM8'), spm_jobman('initcfg');end\n
         """
         if self.mlab.inputs.mfile:
-            if self.jobname in ['st','smooth','preproc','preproc8','fmri_spec','fmri_est',
-                                'factorial_design', 'defs'] :
+            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])
+                                              (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])
+                                              (self.jobtype, self.jobname),
+                                              contents[0])
         else:
-            jobdef = {'jobs':[{self.jobtype:[{self.jobname:self.reformat_dict_for_savemat
-                                         (contents[0])}]}]}
-            savemat(os.path.join(cwd,'pyjobs_%s.mat'%self.jobname), jobdef)
+            jobdef = {'jobs': [{self.jobtype:
+                                  [{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'),