diff --git a/brainiak/factor_analysis/__init__.py b/brainiak/factoranalysis/__init__.py similarity index 100% rename from brainiak/factor_analysis/__init__.py rename to brainiak/factoranalysis/__init__.py diff --git a/brainiak/factor_analysis/htfa.py b/brainiak/factoranalysis/htfa.py similarity index 100% rename from brainiak/factor_analysis/htfa.py rename to brainiak/factoranalysis/htfa.py diff --git a/brainiak/factor_analysis/tfa.py b/brainiak/factoranalysis/tfa.py similarity index 100% rename from brainiak/factor_analysis/tfa.py rename to brainiak/factoranalysis/tfa.py diff --git a/brainiak/factor_analysis/tfa_extension.cpp b/brainiak/factoranalysis/tfa_extension.cpp similarity index 100% rename from brainiak/factor_analysis/tfa_extension.cpp rename to brainiak/factoranalysis/tfa_extension.cpp diff --git a/brainiak/functional_alignment/__init__.py b/brainiak/funcalign/__init__.py similarity index 100% rename from brainiak/functional_alignment/__init__.py rename to brainiak/funcalign/__init__.py diff --git a/brainiak/functional_alignment/srm.py b/brainiak/funcalign/srm.py similarity index 100% rename from brainiak/functional_alignment/srm.py rename to brainiak/funcalign/srm.py diff --git a/examples/factor_analysis/README.rst b/examples/factoranalysis/README.rst similarity index 100% rename from examples/factor_analysis/README.rst rename to examples/factoranalysis/README.rst diff --git a/examples/factor_analysis/get_tfa_input_from_nifti.py b/examples/factoranalysis/get_tfa_input_from_nifti.py similarity index 100% rename from examples/factor_analysis/get_tfa_input_from_nifti.py rename to examples/factoranalysis/get_tfa_input_from_nifti.py diff --git a/examples/factor_analysis/latent_factor_from_htfa.py b/examples/factoranalysis/latent_factor_from_htfa.py similarity index 98% rename from examples/factor_analysis/latent_factor_from_htfa.py rename to examples/factoranalysis/latent_factor_from_htfa.py index 91bb9af3a..d1f3c09df 100644 --- a/examples/factor_analysis/latent_factor_from_htfa.py +++ b/examples/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/examples/factor_analysis/latent_factor_from_tfa.py b/examples/factoranalysis/latent_factor_from_tfa.py similarity index 97% rename from examples/factor_analysis/latent_factor_from_tfa.py rename to examples/factoranalysis/latent_factor_from_tfa.py index f34da9819..0aab25342 100644 --- a/examples/factor_analysis/latent_factor_from_tfa.py +++ b/examples/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 b/examples/factoranalysis/requirements.txt similarity index 100% rename from examples/factor_analysis/requirements.txt rename to examples/factoranalysis/requirements.txt diff --git a/examples/factor_analysis/run_mpi_htfa.sh b/examples/factoranalysis/run_mpi_htfa.sh similarity index 100% rename from examples/factor_analysis/run_mpi_htfa.sh rename to examples/factoranalysis/run_mpi_htfa.sh diff --git a/examples/functional_alignment/download-data.sh b/examples/funcalign/download-data.sh similarity index 100% rename from examples/functional_alignment/download-data.sh rename to examples/funcalign/download-data.sh diff --git a/examples/functional_alignment/requirements.txt b/examples/funcalign/requirements.txt similarity index 100% rename from examples/functional_alignment/requirements.txt rename to examples/funcalign/requirements.txt diff --git a/examples/functional_alignment/srm_image_prediction_example.ipynb b/examples/funcalign/srm_image_prediction_example.ipynb similarity index 97% rename from examples/functional_alignment/srm_image_prediction_example.ipynb rename to examples/funcalign/srm_image_prediction_example.ipynb index 556e18a95..16468eb36 100644 --- a/examples/functional_alignment/srm_image_prediction_example.ipynb +++ b/examples/funcalign/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/examples/functional_alignment/srm_image_prediction_example.py b/examples/funcalign/srm_image_prediction_example.py similarity index 96% rename from examples/functional_alignment/srm_image_prediction_example.py rename to examples/funcalign/srm_image_prediction_example.py index a5ec44661..6f9eaedc9 100644 --- a/examples/functional_alignment/srm_image_prediction_example.py +++ b/examples/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 index b3b3cf79a..328f3cf89 100644 --- 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 b/tests/factoranalysis/test_htfa.py similarity index 97% rename from tests/factor_analysis/test_htfa.py rename to tests/factoranalysis/test_htfa.py index 93d63c3c5..689813255 100644 --- a/tests/factor_analysis/test_htfa.py +++ b/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 b/tests/factoranalysis/test_tfa.py similarity index 98% rename from tests/factor_analysis/test_tfa.py rename to tests/factoranalysis/test_tfa.py index ea20a33f7..d97735b57 100644 --- a/tests/factor_analysis/test_tfa.py +++ b/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 b/tests/funcalign/test_srm.py similarity index 92% rename from tests/functional_alignment/test_srm.py rename to tests/funcalign/test_srm.py index d9e600143..7569ce026 100644 --- a/tests/functional_alignment/test_srm.py +++ b/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!"