Test release + modif HDF5 transpose (#95)

* added transpose option for ImportHDF5

* version 0.2

ephypype/__init__.py

@@ -1,3 +1,3 @@
 from . import interfaces  # noqa
 from . import gather  # noqa
-__version__ = '0.1'
+__version__ = '0.2'

ephypype/import_data.py

@@ -48,7 +48,7 @@ def write_hdf5(filename, data, dataset_name='dataset', dtype='f'):
     hf.close()
 
 
-def _read_hdf5(filename, dataset_name='dataset'):
+def _read_hdf5(filename, dataset_name='dataset', transpose=False):
 
     """
     Read hdf5 file
@@ -58,7 +58,8 @@ def _read_hdf5(filename, dataset_name='dataset'):
             hdf5 filename
         dataset_name : str
             name of dataset to create
-
+        transpose: bool
+            if the data needs to be transpose or not
     Outputs
         data : array, shape (n_vertices, n_times)
             raw data for whose the dataset is created
@@ -67,6 +68,9 @@ def _read_hdf5(filename, dataset_name='dataset'):
     hf = h5py.File(filename, 'r')
     data = hf[dataset_name][()]
 
+    if transpose:
+        data = np.transpose(data)
+
     old_path, basename, ext = split_f(filename)
     npy_filename = os.path.abspath(basename + '.npy')
     print(npy_filename)

ephypype/nodes/import_data.py

@@ -90,6 +90,10 @@ class ImportHdf5InputSpec(BaseInterfaceInputSpec):
     data_field_name = traits.String('dataset', desc='Name of dataset',
                                     usedefault=True)
 
+    transpose = traits.Bool(
+        False, usedefault=True,
+        desc="If the matlab data have to be transposed once read")
+
 
 class ImportHdf5OutputSpec(TraitedSpec):
     """Output spec for ImportHdf5"""
@@ -113,6 +117,11 @@ class ImportHdf5(BaseInterface):
     data_field_name : string
         Name of the dataset
 
+    transpose:
+        type = Bool
+        default = False, usedefault = True,
+        desc = "If the matlab data have to be transposed once read")
+
     Outputs
     -------
     ts_file : str
@@ -126,7 +135,9 @@ def _run_interface(self, runtime):
 
         ts_hdf5_file = self.inputs.ts_hdf5_file
         data_field_name = self.inputs.data_field_name
-        self.ts_file = _read_hdf5(ts_hdf5_file, dataset_name=data_field_name)
+
+        self.ts_file = _read_hdf5(ts_hdf5_file, dataset_name=data_field_name,
+                                  transpose=self.inputs.transpose)
 
         return runtime