add tests and documentation for nltools.prefs

docs/api.rst

@@ -63,12 +63,58 @@ methods in the current release of Neurolearn.
 .. automodule:: nltools.file_reader
     :members:
 
-:mod:`nltools.util`: Utilities
+:mod:`nltools.utils`: Utilities
 ==============================
 
 .. automodule:: nltools.utils
     :members:
 
+:mod:`nltools.prefs`: Preferences
+================================
+
+This module can be used to adjust the default MNI template settings that are used
+internally by all `Brain_Data` operations. By default all operations are performed in
+**MNI152 2mm space**. Thus any files loaded with be resampled to this space by default.You can control this on a per-file loading basis using the `mask` argument of `Brain_Data`, e.g.
+
+.. code-block::
+
+    from nltools.data import Brain_Data
+
+    # my_brain will be resampled to 2mm
+    brain = Brain_Data('my_brain.nii.gz') 
+
+    # my_brain will now be resampled to the same space as my_mask
+    brain = Brain_Data('my_brain.nii.gz', mask='my_mask.nii.gz') # will be resampled 
+
+Alternatively this module can be used to switch between 2mm or 3mm MNI spaces with and without ventricles:
+
+.. code-block::
+
+    from nltools.prefs import MNI_Template, resolve_mni_path
+    from nltools.data import Brain_Data
+
+    MNI_Template['resolution'] = '3mm'
+
+    # my_brain will be resampled to 3mm and future operation will be in 3mm space
+    brain = Brain_Data('my_brain.nii.gz') 
+
+    # get the template nifti files
+    resolve_mni_path(MNI_Template)
+
+    # will print like:
+    {
+        'resolution': '3mm',
+        'mask_type': 'with_ventricles',
+        'mask': '/Users/Esh/Documents/pypackages/nltools/nltools/resources/MNI152_T1_3mm_brain_mask.nii.gz',
+        'plot': '/Users/Esh/Documents/pypackages/nltools/nltools/resources/MNI152_T1_3mm.nii.gz',
+        'brain':
+        '/Users/Esh/Documents/pypackages/nltools/nltools/resources/MNI152_T1_3mm_brain.nii.gz'
+    }
+
+.. automodule:: nltools.prefs
+   :members:
+   :show-inheritance:
+
 :mod:`nltools.plotting`: Plotting Tools
 =======================================
 

docs/conf.py

@@ -15,6 +15,7 @@
 import sys
 import os
 import shlex
+import time
 
 sys.path.insert(0, os.path.abspath("sphinxext"))
 import sphinx_gallery
@@ -76,9 +77,9 @@
 master_doc = "index"
 
 # General information about the project.
-project = u"nltools"
-copyright = u"2020, Cosan Laboratory"
-author = u"Cosan Laboratory"
+project = "nltools"
+copyright = f"{time.strftime('%Y')}, Cosan Laboratory"
+author = "Cosan Laboratory"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -169,7 +170,7 @@
     "bootstrap_version": "3",
     "globaltoc_includehidden": "true",
     "source_link_position": "footer",
-    "globaltoc_depth": 1,
+    "globaltoc_depth": 2,
     "navbar_pagenav_name": "TOC",
     "navbar_links": [
         ("Installation", "install"),
@@ -315,7 +316,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "nltools", u"nltools Documentation", [author], 1)]
+man_pages = [(master_doc, "nltools", "nltools Documentation", [author], 1)]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -330,7 +331,7 @@
     (
         master_doc,
         "nltools",
-        u"nltools Documentation",
+        "nltools Documentation",
         author,
         "nltools",
         "One line description of project.",

nltools/__init__.py

@@ -10,6 +10,7 @@
     "mask",
     "prefs",
     "external",
+    "prefs",
     "__version__",
 ]
 

nltools/prefs.py

@@ -1,16 +1,8 @@
-"""
-NeuroLearn Preferences
-======================
-
-
-"""
-__all__ = ["MNI_Template", "resolve_mni_path"]
-__author__ = ["Luke Chang"]
-__license__ = "MIT"
-
 import os
 from nltools.utils import get_resource_path
 
+__all__ = ["MNI_Template", "resolve_mni_path"]
+
 MNI_Template = dict(
     resolution="2mm",
     mask_type="with_ventricles",

nltools/tests/test_prefs.py

@@ -0,0 +1,11 @@
+from nltools.prefs import MNI_Template
+from nltools.data import Brain_Data
+
+
+def test_change_mni_resolution():
+    assert MNI_Template["resolution"] == "2mm"
+    brain = Brain_Data()
+    assert brain.mask.affine[1, 1] == 2.0
+    MNI_Template["resolution"] = "3mm"
+    new_brain = Brain_Data()
+    assert new_brain.mask.affine[1, 1] == 3.0