mihaic · Jul 20, 2016 · Jul 19, 2016 · Jul 20, 2016
diff --git a/brainiak/factor_analysis/__init__.py → brainiak/factoranalysis/__init__.py b/brainiak/factor_analysis/__init__.py → brainiak/factoranalysis/__init__.py
diff --git a/brainiak/factor_analysis/htfa.py → brainiak/factoranalysis/htfa.py b/brainiak/factor_analysis/htfa.py → brainiak/factoranalysis/htfa.py
diff --git a/brainiak/factor_analysis/tfa.py → brainiak/factoranalysis/tfa.py b/brainiak/factor_analysis/tfa.py → brainiak/factoranalysis/tfa.py
diff --git a/brainiak/factor_analysis/tfa_extension.cpp → brainiak/factoranalysis/tfa_extension.cpp b/brainiak/factor_analysis/tfa_extension.cpp → brainiak/factoranalysis/tfa_extension.cpp
diff --git a/brainiak/functional_alignment/__init__.py → brainiak/funcalign/__init__.py b/brainiak/functional_alignment/__init__.py → brainiak/funcalign/__init__.py
diff --git a/brainiak/functional_alignment/srm.py → brainiak/funcalign/srm.py b/brainiak/functional_alignment/srm.py → brainiak/funcalign/srm.py
diff --git a/examples/factor_analysis/README.rst → examples/factoranalysis/README.rst b/examples/factor_analysis/README.rst → examples/factoranalysis/README.rst
diff --git a/...ctor_analysis/get_tfa_input_from_nifti.py → ...actoranalysis/get_tfa_input_from_nifti.py b/...ctor_analysis/get_tfa_input_from_nifti.py → ...actoranalysis/get_tfa_input_from_nifti.py
diff --git a/...actor_analysis/latent_factor_from_htfa.py → ...factoranalysis/latent_factor_from_htfa.py b/...actor_analysis/latent_factor_from_htfa.py → ...factoranalysis/latent_factor_from_htfa.py
@@ -63,7 +63,7 @@
 n_voxel, n_tr = data[0].shape
 
 # Run HTFA with downloaded data
-from brainiak.factor_analysis.htfa import HTFA
+from brainiak.factoranalysis.htfa import HTFA
 # uncomment below line to get help message on HTFA
 #help(HTFA)
 

diff --git a/...factor_analysis/latent_factor_from_tfa.py → .../factoranalysis/latent_factor_from_tfa.py b/...factor_analysis/latent_factor_from_tfa.py → .../factoranalysis/latent_factor_from_tfa.py
@@ -47,7 +47,7 @@
 n_voxel, n_tr = data.shape
 
 # Run TFA with downloaded data
-from brainiak.factor_analysis.tfa import TFA
+from brainiak.factoranalysis.tfa import TFA
 # uncomment below line to get help message on TFA
 #help(TFA)
 

diff --git a/examples/factor_analysis/requirements.txt → examples/factoranalysis/requirements.txt b/examples/factor_analysis/requirements.txt → examples/factoranalysis/requirements.txt
diff --git a/examples/factor_analysis/run_mpi_htfa.sh → examples/factoranalysis/run_mpi_htfa.sh b/examples/factor_analysis/run_mpi_htfa.sh → examples/factoranalysis/run_mpi_htfa.sh
diff --git a/...les/functional_alignment/download-data.sh → examples/funcalign/download-data.sh b/...les/functional_alignment/download-data.sh → examples/funcalign/download-data.sh
diff --git a/...les/functional_alignment/requirements.txt → examples/funcalign/requirements.txt b/...les/functional_alignment/requirements.txt → examples/funcalign/requirements.txt
diff --git a/...gnment/srm_image_prediction_example.ipynb → ...calign/srm_image_prediction_example.ipynb b/...gnment/srm_image_prediction_example.ipynb → ...calign/srm_image_prediction_example.ipynb
@@ -38,8 +38,8 @@
    },
    "outputs": [],
    "source": [
-    "import brainiak.functional_alignment.srm\n",
-    "help(brainiak.functional_alignment.srm.SRM)"
+    "import brainiak.funcalign.srm\n",
+    "help(brainiak.funcalign.srm.SRM)"
    ]
   },
   {
@@ -114,7 +114,7 @@
    },
    "outputs": [],
    "source": [
-    "srm = brainiak.functional_alignment.srm.SRM(n_iter=10, features=50, verbose=False)\n",
+    "srm = brainiak.funcalign.srm.SRM(n_iter=10, features=50, verbose=False)\n",
     "srm.fit(movie_data)"
    ]
   },
@@ -334,7 +334,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.4.3"
+   "version": "3.5.1"
   }
  },
  "nbformat": 4,

diff --git a/...alignment/srm_image_prediction_example.py → ...funcalign/srm_image_prediction_example.py b/...alignment/srm_image_prediction_example.py → ...funcalign/srm_image_prediction_example.py
@@ -30,10 +30,9 @@
     movie_data[subject] = stats.zscore(movie_data[subject],axis=1,ddof=1)
 
 # Run SRM with the movie data
-import brainiak.functional_alignment.srm
-help(brainiak.functional_alignment.srm.SRM)
-srm = brainiak.functional_alignment.srm.SRM(n_iter=10, features=50,
-        verbose=True)
+import brainiak.funcalign.srm
+help(brainiak.funcalign.srm.SRM)
+srm = brainiak.funcalign.srm.SRM(n_iter=10, features=50, verbose=True)
 srm.fit(movie_data)
 
 # We define a function to present the output of the experiment.

diff --git a/setup.py b/setup.py
@@ -35,8 +35,8 @@ def __str__(self):
 
 ext_modules = [
     Extension(
-        'brainiak.factor_analysis.tfa_extension',
-        ['brainiak/factor_analysis/tfa_extension.cpp'],
+        'brainiak.factoranalysis.tfa_extension',
+        ['brainiak/factoranalysis/tfa_extension.cpp'],
         include_dirs=[
             # Path to pybind11 headers
             get_pybind_include(),

diff --git a/tests/factor_analysis/test_htfa.py → tests/factoranalysis/test_htfa.py b/tests/factor_analysis/test_htfa.py → tests/factoranalysis/test_htfa.py
@@ -14,13 +14,13 @@
 import pytest
 
 def test_R():
-    from brainiak.factor_analysis.htfa import HTFA
+    from brainiak.factoranalysis.htfa import HTFA
     with pytest.raises(TypeError) as excinfo:
         htfa = HTFA()
     assert "missing 1 required positional argument" in str(excinfo.value)
 
 def test_X():
-    from brainiak.factor_analysis.htfa import HTFA
+    from brainiak.factoranalysis.htfa import HTFA
     import numpy as np
 
     n_voxel = 100
@@ -104,7 +104,7 @@ def test_X():
 
 def test_can_run():
     import numpy as np
-    from brainiak.factor_analysis.htfa import HTFA
+    from brainiak.factoranalysis.htfa import HTFA
     from mpi4py import MPI
     comm = MPI.COMM_WORLD
     rank = comm.Get_rank()

diff --git a/tests/factor_analysis/test_tfa.py → tests/factoranalysis/test_tfa.py b/tests/factor_analysis/test_tfa.py → tests/factoranalysis/test_tfa.py
@@ -14,7 +14,7 @@
 import pytest
 
 def test_tfa():
-    from brainiak.factor_analysis.tfa import TFA
+    from brainiak.factoranalysis.tfa import TFA
     import numpy as np
 
     n_voxel = 100

diff --git a/tests/functional_alignment/test_srm.py → tests/funcalign/test_srm.py b/tests/functional_alignment/test_srm.py → tests/funcalign/test_srm.py
@@ -12,8 +12,8 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 def test_can_instantiate():
-    import brainiak.functional_alignment.srm
-    s = brainiak.functional_alignment.srm.SRM()
+    import brainiak.funcalign.srm
+    s = brainiak.funcalign.srm.SRM()
     assert s, "Invalid SRM instance!"
 
     import numpy as np
@@ -23,8 +23,8 @@ def test_can_instantiate():
     subjects = 2
     features = 3
 
-    s = brainiak.functional_alignment.srm.SRM(verbose=True, n_iter=5,
-                                             features=features)
+    s = brainiak.funcalign.srm.SRM(verbose=True, n_iter=5,
+                                   features=features)
     assert s, "Invalid SRM instance!"