Heberto feedback

Author: zm711

neo/io/__init__.py

@@ -45,7 +45,7 @@
 * :attr:`NestIO`
 * :attr:`NeuralynxIO`
 * :attr:`NeuroExplorerIO`
-* :attr:`NeuronexusIO
+* :attr:`NeuroNexusIO
 * :attr:`NeuroScopeIO`
 * :attr:`NeuroshareIO`
 * :attr:`NixIO`
@@ -192,7 +192,7 @@
 
     .. autoattribute:: extensions
 
-.. autoclass:: neo.io.NeuronexusIO
+.. autoclass:: neo.io.NeuroNexusIO
     .. autoattribute:: extensions
 
 .. autoclass:: neo.io.NeuroScopeIO
@@ -330,7 +330,7 @@
 from neo.io.nestio import NestIO
 from neo.io.neuralynxio import NeuralynxIO
 from neo.io.neuroexplorerio import NeuroExplorerIO
-from neo.io.neuronexusio import NeuronexusIO
+from neo.io.neuronexusio import NeuroNexusIO
 from neo.io.neuroscopeio import NeuroScopeIO
 from neo.io.nixio import NixIO
 from neo.io.nixio_fr import NixIO as NixIOFr
@@ -387,7 +387,7 @@
     NestIO,
     NeuralynxIO,
     NeuroExplorerIO,
-    NeuronexusIO,
+    NeuroNexusIO,
     NeuroScopeIO,
     NeuroshareIO,
     NWBIO,

neo/io/neuronexusio.py

@@ -1,11 +1,11 @@
 from neo.io.basefromrawio import BaseFromRaw
-from neo.rawio.neuronexusrawio import NeuronexusRawIO
+from neo.rawio.neuronexusrawio import NeuroNexusRawIO
 
 
-class NeuronexusIO(NeuronexusRawIO, BaseFromRaw):
-    __doc__ = NeuronexusRawIO.__doc__
+class NeuroNexusIO(NeuroNexusRawIO, BaseFromRaw):
+    __doc__ = NeuroNexusRawIO.__doc__
     _prefered_signal_group_mode = "group-by-same-units"
 
     def __init__(self, filename):
-        NeuronexusRawIO.__init__(self, filename=filename)
+        NeuroNexusRawIO.__init__(self, filename=filename)
         BaseFromRaw.__init__(self, filename)

neo/rawio/__init__.py

@@ -29,7 +29,7 @@
 * :attr:`MicromedRawIO`
 * :attr:`NeuralynxRawIO`
 * :attr:`NeuroExplorerRawIO`
-* :attr:`NeuronexusRawIO
+* :attr:`NeuroNexusRawIO
 * :attr:`NeuroScopeRawIO`
 * :attr:`NIXRawIO`
 * :attr:`OpenEphysRawIO`
@@ -115,7 +115,7 @@
 
     .. autoattribute:: extensions
 
-.. autoclass:: neo.rawio.NeuronexusRawIO
+.. autoclass:: neo.rawio.NeuroNexusRawIO
 
     .. autoattributes:: extensions
 
@@ -202,7 +202,7 @@
 from neo.rawio.micromedrawio import MicromedRawIO
 from neo.rawio.neuralynxrawio import NeuralynxRawIO
 from neo.rawio.neuroexplorerrawio import NeuroExplorerRawIO
-from neo.rawio.neuronexusrawio import NeuronexusRawIO
+from neo.rawio.neuronexusrawio import NeuroNexusRawIO
 from neo.rawio.neuroscoperawio import NeuroScopeRawIO
 from neo.rawio.nixrawio import NIXRawIO
 from neo.rawio.openephysrawio import OpenEphysRawIO
@@ -237,7 +237,7 @@
     MedRawIO,
     NeuralynxRawIO,
     NeuroExplorerRawIO,
-    NeuronexusRawIO,
+    NeuroNexusRawIO,
     NeuroScopeRawIO,
     NIXRawIO,
     OpenEphysRawIO,

neo/rawio/neuronexusrawio.py

@@ -1,11 +1,11 @@
 """
-Neuronexus has their own file format based on their Allego Recording System
+NeuroNexus has their own file format based on their Allego Recording System
 https://www.neuronexus.com/webinar/allego-software-updates/
 
 The format involves 3 files:
   * The *.xdat.json metadata file
   * The *_data.xdat binary file of all raw data
-  * The *_timestamps.xdat binary file of the timeestamp data
+  * The *_timestamps.xdat binary file of the timestamp data
   
 Based on sample data is appears that the binary file is always a float32 format
 Other information can be found within the metadata json file
@@ -23,9 +23,11 @@
 like channel_names, channel_ids, channel_types.
 
 An additional note on channels. It appears that analog channels are called `pri` or
-`ai0` within the metadata where as digital channels are called `din0` or `dout0`.
+`ai0` within the metadata whereas digital channels are called `din0` or `dout0`.
 In this first implementation it is up to the user to do the appropriate channel slice
-to only get the data they want. 
+to only get the data they want. This is a buffer-based approach that Sam likes.
+Eventually we will try to divide these channels into streams (analog vs digital) or
+we can come up with a work around if users open an issue requesting this.
 
 Zach McKenzie
 
@@ -47,14 +49,14 @@
 from neo.core import NeoReadWriteError
 
 
-class NeuronexusRawIO(BaseRawIO):
+class NeuroNexusRawIO(BaseRawIO):
 
     extensions = ["xdat", "json"]
     rawmode = "one-file"
 
     def __init__(self, filename: str | Path = ""):
         """
-        The Allego Neuronexus reader for the `xdat` file format
+        The Allego NeuroNexus reader for the `xdat` file format
 
         Parameters
         ----------
@@ -66,12 +68,12 @@ def __init__(self, filename: str | Path = ""):
         * The format involves 3 files:
             * The *.xdat.json metadata file
             * The *_data.xdat binary file of all raw data
-            * The *_timestamps.xdat binary file of the timeestamp data
+            * The *_timestamps.xdat binary file of the timestamp data
         From the metadata the other two files are located within the same directory
         and loaded.
 
         * The metadata is stored as the metadata attribute for individuals hoping
-        to extract probe information, but neo itself does not load any of the probe
+        to extract probe information, but Neo itself does not load any of the probe
         information
 
         Examples
@@ -146,7 +148,11 @@ def _parse_header(self):
         # We can do a quick timestamp check to make sure it is the correct timestamp data for the
         # given metadata
         if self._timestamps[0] != self.metadata["status"]["timestamp_range"][0]:
-            raise NeoReadWriteError(f"The metadata indicates a different starting timestamp")
+            metadata_start = self.metadata["status"]["timestamp_range"][0]
+            data_start = self._teimstamps[0]
+            raise NeoReadWriteError(
+                f"The metadata indicates a different starting timestamp {metadata_start} than the data starting timestamp {data_start}"
+            )
 
         # organize the channels
         signal_channels = []
@@ -156,7 +162,7 @@ def _parse_header(self):
         # 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
+        stream_id = '0'  # hard-coded see note above
         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
@@ -272,4 +278,4 @@ def read_metadata(self, fname_metadata):
 # 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"}
+stream_id_to_stream_name = {'0': "Neuronexus Allego Data"}

neo/test/iotest/test_neuronexusio.py

@@ -4,15 +4,15 @@
 
 import unittest
 
-from neo.io import NeuronexusIO
+from neo.io import NeuroNexusIO
 from neo.test.iotest.common_io_test import BaseTestIO
 
 
-class TestNeuronexusIO(
+class TestNeuroNexusIO(
     BaseTestIO,
     unittest.TestCase,
 ):
-    ioclass = NeuronexusIO
+    ioclass = NeuroNexusIO
     entities_to_download = ["neuronexus"]
     entities_to_test = ["neuronexus/allego_1/allego_2__uid0701-13-04-49.xdat.json"]
 

neo/test/rawiotest/test_neuronexusrawio.py

@@ -1,15 +1,15 @@
 import unittest
 import numpy as np
 
-from neo.rawio.neuronexusrawio import NeuronexusRawIO
+from neo.rawio.neuronexusrawio import NeuroNexusRawIO
 from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
 
 
-class TestNeuronexusRawIO(
+class TestNeuroNexusRawIO(
     BaseTestRawIO,
     unittest.TestCase,
 ):
-    rawioclass = NeuronexusRawIO
+    rawioclass = NeuroNexusRawIO
     entities_to_download = ["neuronexus"]
     entities_to_test = [
         "neuronexus/allego_1/allego_2__uid0701-13-04-49.xdat.json"