misc edits to prepare for release

nimh-dsst · Aug 16, 2023 · b546bef · b546bef
1 parent 7bec6a2
commit b546bef
Show file tree

Hide file tree

Showing 14 changed files with 212 additions and 175 deletions.
diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@ methods. It includes containers for storing photostimulation-specific device par
 (either 2D or 3D), and time series data related to photostimulation.
 </div>
 
-<br>We release six <a href="https://pynwb.readthedocs.io/en/stable/">PyNWB</a> containers as part of this extension:
+<br>We release six <a href="https://pynwb.readthedocs.io/en/stable/">PyNWB</a> containers as part of this extension (we currently only have a Python implementation, rather than both Python and a MATLAB ones):
 
 * The `SpatialLightModulator` and `Laser` containers store metadata about the spatial light modulator and laser used in the photostimulation, respectively. These containers are then stored within the `PhotostimulationMethod` parent container, which stores the remaining photostimulation method-specifici metadata.
 * `HolographicPattern` stores the **holographic pattern** used in stimulation.
@@ -167,6 +167,10 @@ from the home folder. Similar to the specification docs, API documentation is st
 `./api_docs/build/index.html` to access the API documentation in a website format.
 
 
+## Credit
+
+Code by Carl Harris and Paul LaFosse (equal contribution). Collaboration between the NIMH's [Data Science and Sharing Team](https://cmn.nimh.nih.gov/dsst) and [Histed Lab](https://www.nimh.nih.gov/research/research-conducted-at-nimh/research-areas/clinics-and-labs/ncb).
+
 
 This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).
 
diff --git a/PKL_tests/file_classes_PKL.py → old/PKL_tests/file_classes_PKL.py b/PKL_tests/file_classes_PKL.py → old/PKL_tests/file_classes_PKL.py
diff --git a/PKL_tests/file_defined_namespace_PKL.py → old/PKL_tests/file_defined_namespace_PKL.py b/PKL_tests/file_defined_namespace_PKL.py → old/PKL_tests/file_defined_namespace_PKL.py
diff --git a/PKL_tests/test.extensions.yaml → old/PKL_tests/test.extensions.yaml b/PKL_tests/test.extensions.yaml → old/PKL_tests/test.extensions.yaml
diff --git a/PKL_tests/test.namespace.yaml → old/PKL_tests/test.namespace.yaml b/PKL_tests/test.namespace.yaml → old/PKL_tests/test.namespace.yaml
diff --git a/PKL_tests/test_file_PKL.py → old/PKL_tests/test_file_PKL.py b/PKL_tests/test_file_PKL.py → old/PKL_tests/test_file_PKL.py
diff --git a/PKL_tests/test_unit.py → old/PKL_tests/test_unit.py b/PKL_tests/test_unit.py → old/PKL_tests/test_unit.py
diff --git a/file_classes.py → old/file_classes.py b/file_classes.py → old/file_classes.py
diff --git a/file_defined_namespace.py → old/file_defined_namespace.py b/file_defined_namespace.py → old/file_defined_namespace.py
diff --git a/test_file.py → old/test_file.py b/test_file.py → old/test_file.py
diff --git a/test_local.py → old/test_local.py b/test_local.py → old/test_local.py
diff --git a/test_unit.py → old/test_unit.py b/test_unit.py → old/test_unit.py
diff --git a/src/pynwb/ndx_photostim/photostim.py b/src/pynwb/ndx_photostim/photostim.py
@@ -79,7 +79,7 @@ class PhotostimulationMethod(NWBContainer):
             {'name': 'stimulus_method', 'type': str,
              'doc': ("Scanning or scanless method for shaping optogenetic light "
                      "(ex., diffraction limited points,3D shot, disks, etc.)."),
-             'default': None},
+             'default': "point"},
             {'name': 'sweep_pattern', 'type': str,
              'doc': ("Sweeping pattern, if spatially modulated during stimulation (none, or other)."),
              'default': None},
@@ -205,9 +205,9 @@ def __init__(self, **kwargs):
             if args_to_set['dimension'] is None:
                 args_to_set['dimension'] = mask_dim
 
-            if len(np.setdiff1d(np.unique(args_to_set['image_mask_roi']), np.array([0, 1]))) > 0:
-                if len(np.setdiff1d(np.unique(args_to_set['image_mask_roi']), np.array([0., 1.]))) > 0:
-                    raise ValueError("'image_mask_roi' data must be either 0 (off) or 1 (on).")
+#             if len(np.setdiff1d(np.unique(args_to_set['image_mask_roi']), np.array([0, 1]))) > 0:
+#                 if len(np.setdiff1d(np.unique(args_to_set['image_mask_roi']), np.array([0., 1.]))) > 0:
+#                     raise ValueError("'image_mask_roi' data must be either 0 (off) or 1 (on).")
 
         for key, val in args_to_set.items():
             setattr(self, key, val)

diff --git a/tutorial.ipynb b/tutorial.ipynb