'mipy' to 'dmipy' replace

dmipy/core/modeling_framework.py

@@ -25,10 +25,10 @@
     from pathos.helpers import cpu_count
 
 GRADIENT_TABLES_PATH = pkg_resources.resource_filename(
-    'mipy', 'data/gradient_tables'
+    'dmipy', 'data/gradient_tables'
 )
 SIGNAL_MODELS_PATH = pkg_resources.resource_filename(
-    'mipy', 'signal_models'
+    'dmipy', 'signal_models'
 )
 
 

dmipy/data/saved_acquisition_schemes.py

@@ -6,10 +6,10 @@
     acquisition_scheme_from_gradient_strengths)
 
 _GRADIENT_TABLES_PATH = pkg_resources.resource_filename(
-    'mipy', 'data/gradient_tables'
+    'dmipy', 'data/gradient_tables'
 )
 DATA_PATH = pkg_resources.resource_filename(
-    'mipy', 'data/'
+    'dmipy', 'data/'
 )
 
 

dmipy/data/saved_data.py

@@ -6,7 +6,7 @@
 import matplotlib.pyplot as plt
 from . import saved_acquisition_schemes
 DATA_PATH = pkg_resources.resource_filename(
-    'mipy', 'data/'
+    'dmipy', 'data/'
 )
 
 

dmipy/distributions/distributions.py

@@ -23,13 +23,13 @@
 
 SPHERICAL_INTEGRATOR = utils.SphericalIntegrator()
 GRADIENT_TABLES_PATH = pkg_resources.resource_filename(
-    'mipy', 'data/gradient_tables'
+    'dmipy', 'data/gradient_tables'
 )
 SIGNAL_MODELS_PATH = pkg_resources.resource_filename(
-    'mipy', 'signal_models'
+    'dmipy', 'signal_models'
 )
 DATA_PATH = pkg_resources.resource_filename(
-    'mipy', 'data'
+    'dmipy', 'data'
 )
 SPHERE_CARTESIAN = np.loadtxt(
     join(GRADIENT_TABLES_PATH, 'sphere_with_cap.txt')

dmipy/hcp_interface/downloader_aws.py

@@ -2,9 +2,11 @@
 import boto
 import pkg_resources
 import os
+import nibabel as nib
+
 
 HCP_DATA_PATH = pkg_resources.resource_filename(
-    'mipy', 'data/hcp/'
+    'dmipy', 'data/hcp/'
 )
 
 
@@ -48,6 +50,9 @@ def download_and_prepare_dmipy_example_dataset(self):
         if not os.path.exists(directory):
             os.makedirs(directory)
 
+        print ('Downloading data to {}'.format(directory))
+
+        counter = 0
         for key in self.s3_bucket.list("HCP_1200"):
             path = pathlib.Path(key.name)
             if (
@@ -61,34 +66,17 @@ def download_and_prepare_dmipy_example_dataset(self):
                     'data' in path.parts[-1] or
                     'nodif' in path.parts[-1]
                 ):
+                    print ('Downloading {}'.format(path.parts[-1]))
                     filepath = os.path.join(directory, path.parts[-1])
                     with open(filepath, 'wb') as f:
                         key.get_contents_to_file(f)
+                    counter += 1
+                    if counter == 4:
+                        break
 
-    def download_hcp_dataset(self, subject):
-        """
-        Parameters
-        ----------
-        subject: integer
-            the identification number of the HCP subject to download
-        """
-
-
-def download(aws_key, aws_secret, subject=100307):
-
-    for key in s3_bucket.list("HCP_1200"):
-        path = pathlib.Path(key.name)
-        if (
-            len(path.parts) == 5 and
-            subject == int(path.parts[1]) and
-            path.parts[-2] == "Diffusion"
-        ):
-            if (
-                'bval' in path.parts[-1] or
-                'bvec' in path.parts[-1] or
-                'data' in path.parts[-1] or
-                'nodif' in path.parts[-1]
-            ):
+        folder_name = "example_slice"
+        example_directory = os.path.join(HCP_DATA_PATH, folder_name)
+        if not os.path.exists(example_directory):
+            os.makedirs(example_directory)
 
-                with open(path.parts[-1], 'wb') as f:
-                    key.get_contents_to_file(f)
+        data = nib.load(os.path.join(directory, 'data.nii.gz')).get_data()

dmipy/optimizers/brute2fine.py

@@ -7,7 +7,7 @@
 numba, have_numba, _ = optional_package("numba")
 
 SPHERES_PATH = pkg_resources.resource_filename(
-    'mipy', 'data/spheres'
+    'dmipy', 'data/spheres'
 )
 
 

doc/conf.py

@@ -283,7 +283,7 @@ def setup(app):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'mipy', 'dmipy Documentation',
+  ('index', 'dmipy', 'dmipy Documentation',
    'Rutger Fick, Demian Wassermann', 'dmipy', 'One line description of project.',
    'Miscellaneous'),
 ]