Merge branch 'master' into release-14.2

Author: zm711

CODE_OF_CONDUCT.md

@@ -1,46 +1,16 @@
-# Contributor Covenant Code of Conduct
+# [The NumFOCUS Code of Conduct](https://numfocus.org/code-of-conduct)
 
-## Our Pledge
+Neo subscribes to the NumFOCUS Code of Conduct.
 
-In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+## The Short Version
+Be kind to others. Do not insult or put down others. Behave professionally. Remember that harassment and sexist, racist, or exclusionary jokes are not appropriate for NumFOCUS.
 
-## Our Standards
+All communication should be appropriate for a professional audience including people of many different backgrounds. Sexual language and imagery is not appropriate.
 
-Examples of behavior that contributes to creating a positive environment include:
+NumFOCUS is dedicated to providing a harassment-free community for everyone, regardless of gender, sexual orientation, gender identity and expression, disability, physical appearance, body size, race, or religion. We do not tolerate harassment of community members in any form.
 
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
+Thank you for helping make this a welcoming, friendly community for all.
 
-Examples of unacceptable behavior by participants include:
+## The Complete Version
 
-* The use of sexualized language or imagery and unwelcome sexual attention or advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a professional setting
-
-## Our Responsibilities
-
-Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
-
-Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
-
-## Scope
-
-This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
-
-## Enforcement
-
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at [email protected]. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
-
-Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
-
-## Attribution
-
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
-
-[homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/4/
+The full version of the NumFOCUS Code of Conduct is available at the [NumFOCUS website](https://numfocus.org/code-of-conduct)

README.rst

@@ -27,6 +27,7 @@ Neo objects behave just like normal NumPy arrays, but with additional metadata,
 checks for dimensional consistency and automatic unit conversion.
 
 A project with similar aims but for neuroimaging file formats is `NiBabel`_.
+Neo is a `NumFocus Affiliated Project`_.
 
 Code status
 -----------
@@ -82,3 +83,4 @@ and by the European Union's Research and Innovation Program Horizon Europe Grant
 .. _`issue tracker`: https://github.c
 .. _tridesclous: https://github.com/tridesclous/tridesclous
 .. _ephyviewer: https://github.com/NeuralEnsemble/ephyviewer
+.. _`NumFocus Affiliated Project`: https://numfocus.org/sponsored-projects/affiliated-projects

doc/source/governance.rst

@@ -5,7 +5,8 @@ Governance
 Neo is a community-developed project,
 we welcome contributions from anyone who is interested in the project.
 The project maintainers are the members of the `Neo maintainers team`_.
-All contributors agree to abide by the Code of Conduct, see the file `CODE_OF_CONDUCT.md`_.
+All contributors agree to abide by the `NumFocus Code of Conduct`_,
+see the file `CODE_OF_CONDUCT.md`_.
 
 Contributions
 =============
@@ -49,3 +50,4 @@ The current maintainers are:
 .. _`@mdenker`: https://github.com/mdenker
 .. _`@alejoe91`: https://github.com/alejoe91
 .. _`@zm711`: https://github.com/zm711
+.. _`NumFocus Code of Conduct`: https://numfocus.org/code-of-conduct

neo/rawio/neuronexusrawio.py

@@ -132,10 +132,11 @@ def _parse_header(self):
         self._n_samples, self._n_channels = self.metadata["status"]["shape"]
         # Stored as a simple float32 binary file
         BINARY_DTYPE = "float32"
+        TIMESTAMP_DTYPE = "int64" # this is from the allego sample reader timestamps are np.int64
         binary_file = self.binary_file
         timestamp_file = self.timestamp_file
 
-        # the will cretae a memory map with teh generic mechanism
+        # the will cretae a memory map with the generic mechanism
         buffer_id = "0"
         self._buffer_descriptions = {0: {0: {}}}
         self._buffer_descriptions[0][0][buffer_id] = {
@@ -149,7 +150,7 @@ def _parse_header(self):
         # Make the memory map for timestamp
         self._timestamps = np.memmap(
             timestamp_file,
-            dtype=np.int64,  # this is from the allego sample reader timestamps are np.int64
+            dtype=TIMESTAMP_DTYPE,  
             mode="r",
             offset=0,  # headerless binary file
         )
@@ -167,24 +168,28 @@ def _parse_header(self):
         signal_channels = []
         channel_info = self.metadata["sapiens_base"]["biointerface_map"]
 
-        # as per dicussion with the Neo/SpikeInterface teams stream_id will become buffer_id
-        # and because all data is stored in the same buffer stream for the moment all channels
-        # will be in stream_id = 0. In the future this will be split into sub_streams based on
-        # type but for now it will be the end-users responsability for this.
-        stream_id = "0"  # hard-coded see note above
+        # NeuroNexus uses a single buffer for all file types. Now that we buffer API
+        # we divide each Allego signal into it's appropriate stream for the end-user
         buffer_id = "0"
         for channel_index, channel_name in enumerate(channel_info["chan_name"]):
             channel_id = channel_info["ntv_chan_name"][channel_index]
             # 'ai0' indicates analog data which is stored as microvolts
+            # sometimes also called the pri data for NeuroNexus terminology
             if channel_info["chan_type"][channel_index] == "ai0":
                 units = "uV"
+                stream_id = "ai-pri"
             # 'd' means digital. Per discussion with neuroconv users the use of
             # 'a.u.' makes the units clearer
-            elif channel_info["chan_type"][channel_index][0] == "d":
+            elif channel_info["chan_type"][channel_index][:2] == "di":
                 units = "a.u."
-            # aux channel
+                stream_id = "din"
+            elif channel_info["chan_type"][channel_index][:2] == "do":
+                # aux channel
+                units = "a.u."
+                stream_id = "dout"
             else:
                 units = "V"
+                stream_id = "aux"
 
             signal_channels.append(
                 (
@@ -212,7 +217,7 @@ def _parse_header(self):
         signal_streams["buffer_id"] = buffer_id
         self._stream_buffer_slice = {}
         for stream_index, stream_id in enumerate(stream_ids):
-            name = stream_id_to_stream_name.get(int(stream_id), "")
+            name = stream_id_to_stream_name.get(stream_id, "")
             signal_streams["name"][stream_index] = name
             chan_inds = np.flatnonzero(signal_channels["stream_id"] == stream_id)
             self._stream_buffer_slice[stream_id] = chan_inds
@@ -294,7 +299,10 @@ def _get_analogsignal_buffer_description(self, block_index, seg_index, buffer_id
         return self._buffer_descriptions[block_index][seg_index][buffer_id]
 
 
-# this is pretty useless right now, but I think after a
-# refactor with sub streams we could adapt this for the sub-streams
-# so let's leave this here for now :)
-stream_id_to_stream_name = {"0": "Neuronexus Allego Data"}
+# here we map the stream_id to the more descriptive stream_name
+stream_id_to_stream_name = {
+    "ai-pri": "NeuroNexus Allego Analog (pri) Data",
+    "din": "NeuroNexus Allego Digital-in (din) Data",
+    "dout": "NeuroNexus Allego Digital-out (dout) Data",
+    "aux": "NeuroNexus Allego Auxiliary (aux) Data",
+}