From 034f96ec0aa04927649cdec88c58aaa74cd833c4 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Sat, 6 Apr 2024 11:14:21 -0400
Subject: [PATCH 01/15] initial fixes

---
 neo/rawio/intanrawio.py | 141 ++++++++++++++++++++++++++++++++--------
 1 file changed, 115 insertions(+), 26 deletions(-)

diff --git a/neo/rawio/intanrawio.py b/neo/rawio/intanrawio.py
index 756acb88a..819b701ab 100644
--- a/neo/rawio/intanrawio.py
+++ b/neo/rawio/intanrawio.py
@@ -95,10 +95,26 @@ def _parse_header(self):
             raise FileNotFoundError(f"{filename} does not exist")
 
         if self.filename.endswith(".rhs"):
-            self.file_format = "header-attached"
-            self._global_info, self._ordered_channels, data_dtype, header_size, self._block_size = read_rhs(
-                self.filename
-            )
+            if filename.name == "info.rhs":
+                if any((filename.parent / file).exists for file in one_file_per_signal_filenames):
+                    self.file_format = "one-file-per-signal"
+                    raw_file_paths_dict = create_one_file_per_signal_dict(dirname=filename.parent, rhs=True)
+                else:
+                    self.file_format = "one-file-per-channel"
+                    raw_file_paths_dict = create_one_file_per_channel_dict(dirname=filename.parent, rhs=True)
+            else:
+                self.file_format = "header-attached"
+
+            (
+                self._global_info,
+                self._ordered_channels,
+                data_dtype,
+                header_size,
+                self._block_size,
+                channel_number_dict,
+            ) = read_rhs(self.filename)
+
+
         # 3 possibilities for rhd files, one combines the header and the data in the same file with suffix `rhd` while
         # the other two separates the data from the header which is always called `info.rhd`
         # attached to the actual binary file with data
@@ -107,11 +123,11 @@ def _parse_header(self):
                 # first we have one-file-per-signal which is where one neo stream/file is saved as .dat files
                 if any((filename.parent / file).exists() for file in one_file_per_signal_filenames):
                     self.file_format = "one-file-per-signal"
-                    raw_file_paths_dict = create_one_file_per_signal_dict(filename.parent)
+                    raw_file_paths_dict = create_one_file_per_signal_dict(dirname=filename.parent)
                 # then there is one-file-per-channel where each channel in a neo stream is in its own .dat file
                 else:
                     self.file_format = "one-file-per-channel"
-                    raw_file_paths_dict = create_one_file_per_channel_dict(filename.parent)
+                    raw_file_paths_dict = create_one_file_per_channel_dict(dirname=filename.parent)
             # finally the format with the header-attached to the binary file as one giant file
             else:
                 self.file_format = "header-attached"
@@ -435,13 +451,15 @@ def read_variable_header(f, header):
 ]
 
 
-def read_rhs(filename):
+def read_rhs(filename, file_format: str):
     BLOCK_SIZE = 128  # sample per block
 
     with open(filename, mode="rb") as f:
         global_info = read_variable_header(f, rhs_global_header)
 
         channels_by_type = {k: [] for k in [0, 3, 4, 5, 6]}
+        if not file_format == "header-attached":
+            data_dtype = {k: [] for k in range(7)}  # 5 streams + 6 for timestamps for not header attached
         for g in range(global_info["nb_signal_group"]):
             group_info = read_variable_header(f, rhs_signal_group_header)
 
@@ -452,6 +470,10 @@ def read_rhs(filename):
                     if bool(chan_info["channel_enabled"]):
                         channels_by_type[chan_info["signal_type"]].append(chan_info)
 
+
+        # useful dictionary for knowing the number of channels for non-header attached formats
+        channel_number_dict = {i: len(channels_by_type[i]) for i in range(6)}
+
         header_size = f.tell()
 
     sr = global_info["sampling_rate"]
@@ -469,7 +491,14 @@ def read_rhs(filename):
         chan_info["offset"] = -32768 * 0.195
         chan_info["dtype"] = "uint16"
         ordered_channels.append(chan_info)
-        data_dtype += [(name, "uint16", BLOCK_SIZE)]
+        if file_format == "header-attached":
+            data_dtype += [(name, "uint16", BLOCK_SIZE)]
+        else:
+            data_dtype[0] = "int16" 
+
+
+    # TODO @Heberto I need to read about this section more.... I'm not
+    # sure how it works
 
     if bool(global_info["dc_amplifier_data_saved"]):
         for chan_info in channels_by_type[0]:
@@ -500,6 +529,9 @@ def read_rhs(filename):
         ordered_channels.append(chan_info_stim)
         data_dtype += [(name + "_STIM", "uint16", BLOCK_SIZE)]
 
+    # TODO @Heberto to update to version 3 we also likely need to add in the
+    # supply and aux voltages.
+
     # 3: Analog input channel.
     # 4: Analog output channel.
     for sig_type in [
@@ -514,23 +546,46 @@ def read_rhs(filename):
             chan_info["offset"] = -32768 * 0.0003125
             chan_info["dtype"] = "uint16"
             ordered_channels.append(chan_info)
-            data_dtype += [(name, "uint16", BLOCK_SIZE)]
+            if file_format == "header-attached":
+                data_dtype += [(name, "uint16", BLOCK_SIZE)]
+            else:
+                data_dtype[sig_type] = "unit16"
 
     # 5: Digital input channel.
     # 6: Digital output channel.
     for sig_type in [5, 6]:
-        # at the moment theses channel are not in sig channel list
-        # but they are in the raw memamp
         if len(channels_by_type[sig_type]) > 0:
-            name = {5: "DIGITAL-IN", 6: "DIGITAL-OUT"}[sig_type]
-            data_dtype += [(name, "uint16", BLOCK_SIZE)]
+            name = {4: "DIGITAL-IN", 5: "DIGITAL-OUT"}[sig_type]
+            chan_info = channels_by_type[sig_type][0]
+            # So currently until we have get_digitalsignal_chunk we need to do a tiny hack to
+            # make this memory map work correctly. So since our digital data is not organized
+            # by channel like analog/ADC are we have to overwrite the native name to create
+            # a single permanent name that we can find with channel id
+            chan_info["native_channel_name"] = name  # overwite to allow memmap to work
+            chan_info["sampling_rate"] = sr
+            chan_info["units"] = "TTL"  # arbitrary units TTL for logic
+            chan_info["gain"] = 1.0
+            chan_info["offset"] = 0.0
+            chan_info["dtype"] = "uint16"
+            ordered_channels.append(chan_info)
+            if file_format == "header-attached":
+                data_dtype += [(name, "uint16", BLOCK_SIZE)]
+            else:
+                data_dtype[sig_type] = "uint16"
 
-    if bool(global_info["notch_filter_mode"]) and global_info["major_version"] >= 3:
-        global_info["notch_filter_applied"] = True
+    if global_info["notch_filter_mode"] == 2 and global_info["major_version"] >= V("3.0"):
+        global_info["notch_filter"] = "60Hz"
+    elif global_info["notch_filter_mode"] == 1 and global_info["major_version"]>= V("3.0"):
+        global_info["notch_filter"] = "50Hz"
     else:
-        global_info["notch_filter_applied"] = False
+        global_info["notch_filter"] = False
 
-    return global_info, ordered_channels, data_dtype, header_size, BLOCK_SIZE
+    if not file_format == "header-attached":
+        # filter out dtypes without any values
+        data_dtype = {k: v for (k, v) in data_dtype.items() if len(v) > 0}
+        channel_number_dict = {k: v for (k, v) in channel_number_dict.items() if v > 0}
+
+    return global_info, ordered_channels, data_dtype, header_size, BLOCK_SIZE, channel_number_dict
 
 
 ###############
@@ -808,8 +863,11 @@ def read_rhd(filename, file_format: str):
     return global_info, ordered_channels, data_dtype, header_size, BLOCK_SIZE, channel_number_dict
 
 
-###########################
-# RHD Zone for Binary Files
+##########################################################################
+# RHX Zone for Binary Files
+# This zone gives the headerless binary files for both rhs and rhd header files
+# This occurs with the new rhx version of the intan recording software as an
+# optional software that can be turned
 
 # For One File Per Signal
 one_file_per_signal_filenames = [
@@ -822,13 +880,29 @@ def read_rhd(filename, file_format: str):
 ]
 
 
-def create_one_file_per_signal_dict(dirname):
-    """Function for One File Per Signal Type"""
+def create_one_file_per_signal_dict(dirname, rhs: bool=False):
+    """Function for One File Per Signal Type
+    
+    Parameters
+    ----------
+    dirname: pathlib.Path
+        The folder to explore
+    rhs: bool, default: False
+        Whether this is an rhd or an rhs file
+    """
+
+    # if rhs we have an extra stream to add
+    if rhs:
+        one_file_per_signal_filenames.insert(4, "analogout.dat")
+
     raw_file_paths_dict = {}
     for raw_index, raw_file in enumerate(one_file_per_signal_filenames):
         if Path(dirname / raw_file).is_file():
             raw_file_paths_dict[raw_index] = Path(dirname / raw_file)
-    raw_file_paths_dict[6] = Path(dirname / "time.dat")
+    if rhs:
+        raw_file_paths_dict[7] = Path(dirname / "time.dat")
+    else:
+        raw_file_paths_dict[6] = Path(dirname / "time.dat")
 
     return raw_file_paths_dict
 
@@ -838,19 +912,34 @@ def create_one_file_per_signal_dict(dirname):
     "amp",
     "aux",
     "vdd",
-    "board-ANALOG",
+    "board-ANALOG-IN",
     "board-DIGITAL-IN",
     "board-DIGITAL-OUT",
 ]
 
 
-def create_one_file_per_channel_dict(dirname):
-    """Utility function for One File Per Channel"""
+def create_one_file_per_channel_dict(dirname, rhs: bool=False):
+    """Utility function for One File Per Channel
+    
+    Parameters
+    ----------
+    dirname: pathlib.Path
+        The folder to explore
+    rhs: bool, default: False
+        Whether this is an rhd or an rhs file
+    """
+    # if rhs we have an extra stream to add
+    if rhs:
+        possible_raw_file_prefixes.insert(4, "board-ANALOG-OUT")
+
     file_names = dirname.glob("**/*.dat")
     files = [file for file in file_names if file.is_file()]
     raw_file_paths_dict = {}
     for raw_index, prefix in enumerate(possible_raw_file_prefixes):
         raw_file_paths_dict[raw_index] = [file for file in files if prefix in file.name]
-    raw_file_paths_dict[6] = [Path(dirname / "time.dat")]
+    if rhs:
+        raw_file_paths_dict[7] = [Path(dirname / "time.dat")]
+    else:
+        raw_file_paths_dict[6] = [Path(dirname / "time.dat")]
 
     return raw_file_paths_dict

From 35ba654778ab8ca967eab75564bfd69ed9ac9b64 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Sat, 6 Apr 2024 11:29:31 -0400
Subject: [PATCH 02/15] oops

---
 neo/rawio/intanrawio.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/neo/rawio/intanrawio.py b/neo/rawio/intanrawio.py
index 819b701ab..3d0bec073 100644
--- a/neo/rawio/intanrawio.py
+++ b/neo/rawio/intanrawio.py
@@ -112,7 +112,7 @@ def _parse_header(self):
                 header_size,
                 self._block_size,
                 channel_number_dict,
-            ) = read_rhs(self.filename)
+            ) = read_rhs(self.filename, self.file_format)
 
 
         # 3 possibilities for rhd files, one combines the header and the data in the same file with suffix `rhd` while

From 5b554017c21a4fef047acc8adf3aade066d4fc7c Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Mon, 8 Apr 2024 10:23:04 -0400
Subject: [PATCH 03/15] add in dtypes and channel numbers for rhs

---
 neo/rawio/intanrawio.py | 105 ++++++++++++++++++++++++++--------------
 1 file changed, 70 insertions(+), 35 deletions(-)

diff --git a/neo/rawio/intanrawio.py b/neo/rawio/intanrawio.py
index 3d0bec073..7ef734874 100644
--- a/neo/rawio/intanrawio.py
+++ b/neo/rawio/intanrawio.py
@@ -22,6 +22,7 @@
 import os
 from collections import OrderedDict
 from packaging.version import Version as V
+import warnings
 
 import numpy as np
 
@@ -114,7 +115,6 @@ def _parse_header(self):
                 channel_number_dict,
             ) = read_rhs(self.filename, self.file_format)
 
-
         # 3 possibilities for rhd files, one combines the header and the data in the same file with suffix `rhd` while
         # the other two separates the data from the header which is always called `info.rhd`
         # attached to the actual binary file with data
@@ -457,9 +457,12 @@ def read_rhs(filename, file_format: str):
     with open(filename, mode="rb") as f:
         global_info = read_variable_header(f, rhs_global_header)
 
+        # channels_by_type is simpler than data_dtype because 0 contains 0, 10 and 11 internally
         channels_by_type = {k: [] for k in [0, 3, 4, 5, 6]}
         if not file_format == "header-attached":
-            data_dtype = {k: [] for k in range(7)}  # 5 streams + 6 for timestamps for not header attached
+            # data_dtype for rhs is complicated. There is not 1, 2 (supply and aux),
+            # but there are dc-amp (10) and stim (11). we make timestamps (7)
+            data_dtype = {k: [] for k in [0, 3, 4, 5, 6, 7, 10, 11]}
         for g in range(global_info["nb_signal_group"]):
             group_info = read_variable_header(f, rhs_signal_group_header)
 
@@ -470,9 +473,8 @@ def read_rhs(filename, file_format: str):
                     if bool(chan_info["channel_enabled"]):
                         channels_by_type[chan_info["signal_type"]].append(chan_info)
 
-
         # useful dictionary for knowing the number of channels for non-header attached formats
-        channel_number_dict = {i: len(channels_by_type[i]) for i in range(6)}
+        channel_number_dict = {i: len(channels_by_type[i]) for i in [0, 3, 4, 5, 6]}
 
         header_size = f.tell()
 
@@ -480,7 +482,11 @@ def read_rhs(filename, file_format: str):
 
     # construct dtype by re-ordering channels by types
     ordered_channels = []
-    data_dtype = [("timestamp", "int32", BLOCK_SIZE)]
+    if file_format == "header-attached":
+        data_dtype = [("timestamp", "int32", BLOCK_SIZE)]
+    else:
+        data_dtype[7] = "int32"
+        channel_number_dict[7] = 1
 
     # 0: RHS2000 amplifier channel.
     for chan_info in channels_by_type[0]:
@@ -488,19 +494,23 @@ def read_rhs(filename, file_format: str):
         chan_info["sampling_rate"] = sr
         chan_info["units"] = "uV"
         chan_info["gain"] = 0.195
-        chan_info["offset"] = -32768 * 0.195
-        chan_info["dtype"] = "uint16"
+        if file_format == "header-attached":
+            chan_info["offset"] = -32768 * 0.195
+        else:
+            chan_info["offset"] = 0.0
+        if file_format == "header-attached":
+            chan_info["dtype"] = "uint16"
+        else:
+            chan_info["dtype"] = "int16"
         ordered_channels.append(chan_info)
         if file_format == "header-attached":
             data_dtype += [(name, "uint16", BLOCK_SIZE)]
         else:
-            data_dtype[0] = "int16" 
-
-
-    # TODO @Heberto I need to read about this section more.... I'm not
-    # sure how it works
+            data_dtype[0] = "int16"
 
     if bool(global_info["dc_amplifier_data_saved"]):
+        # if we have dc amp we need to grab the correct number of channels
+        channel_number_dict[10] = channel_number_dict[0]
         for chan_info in channels_by_type[0]:
             name = chan_info["native_channel_name"]
             chan_info_dc = dict(chan_info)
@@ -512,25 +522,35 @@ def read_rhs(filename, file_format: str):
             chan_info_dc["signal_type"] = 10  # put it in another group
             chan_info_dc["dtype"] = "uint16"
             ordered_channels.append(chan_info_dc)
-            data_dtype += [(name + "_DC", "uint16", BLOCK_SIZE)]
+            if file_format == "header-attached":
+                data_dtype += [(name + "_DC", "uint16", BLOCK_SIZE)]
+            else:
+                data_dtype[10] = "unit16"
+    # I can't seem to get stim files to generate for one-file-per-channel
+    # so let's skip for now and can be given on request
 
-    for chan_info in channels_by_type[0]:
-        name = chan_info["native_channel_name"]
-        chan_info_stim = dict(chan_info)
-        chan_info_stim["native_channel_name"] = name + "_STIM"
-        chan_info_stim["sampling_rate"] = sr
-        # stim channel are coplicated because they are coded
-        # with bits, they do not fit the gain/offset rawio strategy
-        chan_info_stim["units"] = ""
-        chan_info_stim["gain"] = 1.0
-        chan_info_stim["offset"] = 0.0
-        chan_info_stim["signal_type"] = 11  # put it in another group
-        chan_info_stim["dtype"] = "uint16"
-        ordered_channels.append(chan_info_stim)
-        data_dtype += [(name + "_STIM", "uint16", BLOCK_SIZE)]
-
-    # TODO @Heberto to update to version 3 we also likely need to add in the
-    # supply and aux voltages.
+    if file_format != "one-file-per-channel":
+        for chan_info in channels_by_type[0]:
+            name = chan_info["native_channel_name"]
+            chan_info_stim = dict(chan_info)
+            chan_info_stim["native_channel_name"] = name + "_STIM"
+            chan_info_stim["sampling_rate"] = sr
+            # stim channel are complicated because they are coded
+            # with bits, they do not fit the gain/offset rawio strategy
+            chan_info_stim["units"] = ""
+            chan_info_stim["gain"] = 1.0
+            chan_info_stim["offset"] = 0.0
+            chan_info_stim["signal_type"] = 11  # put it in another group
+            chan_info_stim["dtype"] = "uint16"
+            ordered_channels.append(chan_info_stim)
+            if file_format == "header-attached":
+                data_dtype += [(name + "_STIM", "uint16", BLOCK_SIZE)]
+            else:
+                data_dtype[11] == "unit16"
+    else:
+        warnings.warn('Stim not implemented for one-file-per-channel due to lack of test files')
+
+    # No supply or aux for rhs files (ie no stream 1 and 2)
 
     # 3: Analog input channel.
     # 4: Analog output channel.
@@ -575,7 +595,7 @@ def read_rhs(filename, file_format: str):
 
     if global_info["notch_filter_mode"] == 2 and global_info["major_version"] >= V("3.0"):
         global_info["notch_filter"] = "60Hz"
-    elif global_info["notch_filter_mode"] == 1 and global_info["major_version"]>= V("3.0"):
+    elif global_info["notch_filter_mode"] == 1 and global_info["major_version"] >= V("3.0"):
         global_info["notch_filter"] = "50Hz"
     else:
         global_info["notch_filter"] = False
@@ -880,9 +900,9 @@ def read_rhd(filename, file_format: str):
 ]
 
 
-def create_one_file_per_signal_dict(dirname, rhs: bool=False):
+def create_one_file_per_signal_dict(dirname, rhs: bool = False):
     """Function for One File Per Signal Type
-    
+
     Parameters
     ----------
     dirname: pathlib.Path
@@ -892,6 +912,7 @@ def create_one_file_per_signal_dict(dirname, rhs: bool=False):
     """
 
     # if rhs we have an extra stream to add
+
     if rhs:
         one_file_per_signal_filenames.insert(4, "analogout.dat")
 
@@ -904,6 +925,13 @@ def create_one_file_per_signal_dict(dirname, rhs: bool=False):
     else:
         raw_file_paths_dict[6] = Path(dirname / "time.dat")
 
+    if rhs:
+        # 10 and 11 are hardcoded in the rhs_reader above so hardcoded here too
+        if Path(dirname / "dcamplifier.dat").is_file():
+            raw_file_paths_dict[10] = Path(dirname / "dcamplifier.dat")
+        if Path(dirname / "stim.dat").is_file():
+            raw_file_paths_dict[11] = Path(dirname / "stim.dat")
+
     return raw_file_paths_dict
 
 
@@ -918,9 +946,9 @@ def create_one_file_per_signal_dict(dirname, rhs: bool=False):
 ]
 
 
-def create_one_file_per_channel_dict(dirname, rhs: bool=False):
+def create_one_file_per_channel_dict(dirname, rhs: bool = False):
     """Utility function for One File Per Channel
-    
+
     Parameters
     ----------
     dirname: pathlib.Path
@@ -942,4 +970,11 @@ def create_one_file_per_channel_dict(dirname, rhs: bool=False):
     else:
         raw_file_paths_dict[6] = [Path(dirname / "time.dat")]
 
+    if rhs:
+        # 10 and 11 are hardcoded in the rhs reader so hardcoded here
+        raw_file_paths_dict[10] = [file for file in files if "dc-" in file.name]
+        # we can find the files, but I can see how to read them out of header
+        # so for now we don't expose the stim files in one-file-per-channel
+        raw_file_paths_dict[11] = [file for file in files if "stim-" in file.name]
+
     return raw_file_paths_dict

From d55f3aa2ffc403475fd40bec467c0f07d968162c Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Tue, 9 Apr 2024 13:21:10 -0400
Subject: [PATCH 04/15] add test files in tests more fixes

---
 neo/rawio/intanrawio.py               | 22 ++++++++++++++++++----
 neo/test/iotest/test_intanio.py       |  2 ++
 neo/test/rawiotest/test_intanrawio.py |  2 ++
 3 files changed, 22 insertions(+), 4 deletions(-)

diff --git a/neo/rawio/intanrawio.py b/neo/rawio/intanrawio.py
index 7ef734874..a3f3591a0 100644
--- a/neo/rawio/intanrawio.py
+++ b/neo/rawio/intanrawio.py
@@ -211,7 +211,10 @@ def _parse_header(self):
         signal_streams = np.zeros(stream_ids.size, dtype=_signal_stream_dtype)
         signal_streams["id"] = stream_ids
         for stream_index, stream_id in enumerate(stream_ids):
-            signal_streams["name"][stream_index] = stream_type_to_name.get(int(stream_id), "")
+            if self.filename.endswith('.rhd'):
+                signal_streams["name"][stream_index] = stream_type_to_name_rhd.get(int(stream_id), "")
+            else:
+                signal_streams["name"][stream_index] = stream_type_to_name_rhs.get(int(stream_id), "")
 
         self._max_sampling_rate = np.max(signal_channels["sampling_rate"])
 
@@ -450,6 +453,16 @@ def read_variable_header(f, header):
     ("electrode_impedance_phase", "float32"),
 ]
 
+stream_type_to_name_rhs= {
+    0: "RHS2000 amplifier channel",
+    3: "USB board ADC input channel",
+    4: "USB board ADC output channel",
+    5: "USB board digital input channel",
+    6: "USB board digital output channel",
+    10: "DC Amplifier channel",
+    11: "Stim channel"
+}
+
 
 def read_rhs(filename, file_format: str):
     BLOCK_SIZE = 128  # sample per block
@@ -530,6 +543,7 @@ def read_rhs(filename, file_format: str):
     # so let's skip for now and can be given on request
 
     if file_format != "one-file-per-channel":
+        channel_number_dict[11] = channel_number_dict[0] # should be one stim / amplifier channel
         for chan_info in channels_by_type[0]:
             name = chan_info["native_channel_name"]
             chan_info_stim = dict(chan_info)
@@ -548,7 +562,7 @@ def read_rhs(filename, file_format: str):
             else:
                 data_dtype[11] == "unit16"
     else:
-        warnings.warn('Stim not implemented for one-file-per-channel due to lack of test files')
+        warnings.warn("Stim not implemented for `one-file-per-channel` due to lack of test files")
 
     # No supply or aux for rhs files (ie no stream 1 and 2)
 
@@ -575,7 +589,7 @@ def read_rhs(filename, file_format: str):
     # 6: Digital output channel.
     for sig_type in [5, 6]:
         if len(channels_by_type[sig_type]) > 0:
-            name = {4: "DIGITAL-IN", 5: "DIGITAL-OUT"}[sig_type]
+            name = {5: "DIGITAL-IN", 6: "DIGITAL-OUT"}[sig_type]
             chan_info = channels_by_type[sig_type][0]
             # So currently until we have get_digitalsignal_chunk we need to do a tiny hack to
             # make this memory map work correctly. So since our digital data is not organized
@@ -675,7 +689,7 @@ def read_rhs(filename, file_format: str):
     ("electrode_impedance_phase", "float32"),
 ]
 
-stream_type_to_name = {
+stream_type_to_name_rhd = {
     0: "RHD2000 amplifier channel",
     1: "RHD2000 auxiliary input channel",
     2: "RHD2000 supply voltage channel",
diff --git a/neo/test/iotest/test_intanio.py b/neo/test/iotest/test_intanio.py
index a91138384..211d600de 100644
--- a/neo/test/iotest/test_intanio.py
+++ b/neo/test/iotest/test_intanio.py
@@ -19,6 +19,8 @@ class TestIntanIO(
         "intan/intan_rhd_test_1.rhd",
         "intan/intan_fpc_test_231117_052630/info.rhd",
         "intan/intan_fps_test_231117_052500/info.rhd",
+        "intan/intan_fpc_rhs_test_240329_091536/info.rhs",
+        "intan/intan_fps_rhs_test_240329_091637/info.rhs",
     ]
 
 
diff --git a/neo/test/rawiotest/test_intanrawio.py b/neo/test/rawiotest/test_intanrawio.py
index 794480787..f2e39600d 100644
--- a/neo/test/rawiotest/test_intanrawio.py
+++ b/neo/test/rawiotest/test_intanrawio.py
@@ -16,6 +16,8 @@ class TestIntanRawIO(
         "intan/intan_rhd_test_1.rhd",
         "intan/intan_fpc_test_231117_052630/info.rhd",
         "intan/intan_fps_test_231117_052500/info.rhd",
+        "intan/intan_fpc_rhs_test_240329_091536/info.rhs",
+        "intan/intan_fps_rhs_test_240329_091637/info.rhs",
     ]
 
 

From f82eb61a210bce22ccf4644884eb5036af552d54 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Thu, 2 May 2024 16:44:32 -0400
Subject: [PATCH 05/15] Fix naming of test files

---
 neo/test/iotest/test_intanio.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/neo/test/iotest/test_intanio.py b/neo/test/iotest/test_intanio.py
index 211d600de..bd18359a2 100644
--- a/neo/test/iotest/test_intanio.py
+++ b/neo/test/iotest/test_intanio.py
@@ -19,8 +19,8 @@ class TestIntanIO(
         "intan/intan_rhd_test_1.rhd",
         "intan/intan_fpc_test_231117_052630/info.rhd",
         "intan/intan_fps_test_231117_052500/info.rhd",
-        "intan/intan_fpc_rhs_test_240329_091536/info.rhs",
-        "intan/intan_fps_rhs_test_240329_091637/info.rhs",
+        "intan/intan_fpc_rhs_test_240329_091537/info.rhs",
+        "intan/intan_fps_rhs_test_240329_091636/info.rhs",
     ]
 
 

From fbb2ebff130f40c5db58fc29f751fbcf3de2f2a8 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Thu, 2 May 2024 20:11:00 -0400
Subject: [PATCH 06/15] Update neo/test/rawiotest/test_intanrawio.py

---
 neo/test/rawiotest/test_intanrawio.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/neo/test/rawiotest/test_intanrawio.py b/neo/test/rawiotest/test_intanrawio.py
index f2e39600d..398aa3566 100644
--- a/neo/test/rawiotest/test_intanrawio.py
+++ b/neo/test/rawiotest/test_intanrawio.py
@@ -16,8 +16,8 @@ class TestIntanRawIO(
         "intan/intan_rhd_test_1.rhd",
         "intan/intan_fpc_test_231117_052630/info.rhd",
         "intan/intan_fps_test_231117_052500/info.rhd",
-        "intan/intan_fpc_rhs_test_240329_091536/info.rhs",
-        "intan/intan_fps_rhs_test_240329_091637/info.rhs",
+        "intan/intan_fpc_rhs_test_240329_091537/info.rhs",
+        "intan/intan_fps_rhs_test_240329_091636/info.rhs",
     ]
 
 

From 13ab6c5e96a914e33644a55b519a16ff7e6f8218 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Thu, 2 May 2024 20:21:02 -0400
Subject: [PATCH 07/15] Fix pointers to test files

---
 neo/test/iotest/test_intanio.py       | 2 +-
 neo/test/rawiotest/test_intanrawio.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/neo/test/iotest/test_intanio.py b/neo/test/iotest/test_intanio.py
index bd18359a2..7d15a5f99 100644
--- a/neo/test/iotest/test_intanio.py
+++ b/neo/test/iotest/test_intanio.py
@@ -19,7 +19,7 @@ class TestIntanIO(
         "intan/intan_rhd_test_1.rhd",
         "intan/intan_fpc_test_231117_052630/info.rhd",
         "intan/intan_fps_test_231117_052500/info.rhd",
-        "intan/intan_fpc_rhs_test_240329_091537/info.rhs",
+        "intan/intan_fpc_rhs_test_240329_091637/info.rhs",
         "intan/intan_fps_rhs_test_240329_091636/info.rhs",
     ]
 
diff --git a/neo/test/rawiotest/test_intanrawio.py b/neo/test/rawiotest/test_intanrawio.py
index 398aa3566..1666efc69 100644
--- a/neo/test/rawiotest/test_intanrawio.py
+++ b/neo/test/rawiotest/test_intanrawio.py
@@ -16,7 +16,7 @@ class TestIntanRawIO(
         "intan/intan_rhd_test_1.rhd",
         "intan/intan_fpc_test_231117_052630/info.rhd",
         "intan/intan_fps_test_231117_052500/info.rhd",
-        "intan/intan_fpc_rhs_test_240329_091537/info.rhs",
+        "intan/intan_fpc_rhs_test_240329_091637/info.rhs",
         "intan/intan_fps_rhs_test_240329_091636/info.rhs",
     ]
 

From e01f638b5800ceaa48bde1abd06eb037a2147700 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Thu, 2 May 2024 20:34:47 -0400
Subject: [PATCH 08/15] oops

---
 neo/rawio/intanrawio.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/neo/rawio/intanrawio.py b/neo/rawio/intanrawio.py
index a3f3591a0..b96a38514 100644
--- a/neo/rawio/intanrawio.py
+++ b/neo/rawio/intanrawio.py
@@ -97,7 +97,7 @@ def _parse_header(self):
 
         if self.filename.endswith(".rhs"):
             if filename.name == "info.rhs":
-                if any((filename.parent / file).exists for file in one_file_per_signal_filenames):
+                if any((filename.parent / file).exists() for file in one_file_per_signal_filenames):
                     self.file_format = "one-file-per-signal"
                     raw_file_paths_dict = create_one_file_per_signal_dict(dirname=filename.parent, rhs=True)
                 else:

From 78700d7c32b8a8b951e27e0f2ef386c9c9466cf5 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Thu, 2 May 2024 20:51:04 -0400
Subject: [PATCH 09/15] dtype fixes

---
 neo/rawio/intanrawio.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/neo/rawio/intanrawio.py b/neo/rawio/intanrawio.py
index b96a38514..7a766d79a 100644
--- a/neo/rawio/intanrawio.py
+++ b/neo/rawio/intanrawio.py
@@ -538,7 +538,7 @@ def read_rhs(filename, file_format: str):
             if file_format == "header-attached":
                 data_dtype += [(name + "_DC", "uint16", BLOCK_SIZE)]
             else:
-                data_dtype[10] = "unit16"
+                data_dtype[10] = "uint16"
     # I can't seem to get stim files to generate for one-file-per-channel
     # so let's skip for now and can be given on request
 
@@ -560,7 +560,7 @@ def read_rhs(filename, file_format: str):
             if file_format == "header-attached":
                 data_dtype += [(name + "_STIM", "uint16", BLOCK_SIZE)]
             else:
-                data_dtype[11] == "unit16"
+                data_dtype[11] == "uint16"
     else:
         warnings.warn("Stim not implemented for `one-file-per-channel` due to lack of test files")
 
@@ -583,7 +583,7 @@ def read_rhs(filename, file_format: str):
             if file_format == "header-attached":
                 data_dtype += [(name, "uint16", BLOCK_SIZE)]
             else:
-                data_dtype[sig_type] = "unit16"
+                data_dtype[sig_type] = "uint16"
 
     # 5: Digital input channel.
     # 6: Digital output channel.

From fa49d3952134e638a4c220d0e91f656261c75d78 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Fri, 3 May 2024 18:02:41 -0400
Subject: [PATCH 10/15] split rhs and rhd + fix timestamps

---
 neo/rawio/intanrawio.py | 176 +++++++++++++++++++++++++++-------------
 1 file changed, 121 insertions(+), 55 deletions(-)

diff --git a/neo/rawio/intanrawio.py b/neo/rawio/intanrawio.py
index 7da9397e7..6fe63c48e 100644
--- a/neo/rawio/intanrawio.py
+++ b/neo/rawio/intanrawio.py
@@ -98,12 +98,12 @@ def _parse_header(self):
 
         if self.filename.endswith(".rhs"):
             if filename.name == "info.rhs":
-                if any((filename.parent / file).exists() for file in one_file_per_signal_filenames):
+                if any((filename.parent / file).exists() for file in one_file_per_signal_filenames_rhs):
                     self.file_format = "one-file-per-signal"
-                    raw_file_paths_dict = create_one_file_per_signal_dict(dirname=filename.parent, rhs=True)
+                    raw_file_paths_dict = create_one_file_per_signal_dict_rhs(dirname=filename.parent)
                 else:
                     self.file_format = "one-file-per-channel"
-                    raw_file_paths_dict = create_one_file_per_channel_dict(dirname=filename.parent, rhs=True)
+                    raw_file_paths_dict = create_one_file_per_channel_dict_rhs(dirname=filename.parent)
             else:
                 self.file_format = "header-attached"
 
@@ -122,13 +122,13 @@ def _parse_header(self):
         elif self.filename.endswith(".rhd"):
             if filename.name == "info.rhd":
                 # first we have one-file-per-signal which is where one neo stream/file is saved as .dat files
-                if any((filename.parent / file).exists() for file in one_file_per_signal_filenames):
+                if any((filename.parent / file).exists() for file in one_file_per_signal_filenames_rhd):
                     self.file_format = "one-file-per-signal"
-                    raw_file_paths_dict = create_one_file_per_signal_dict(dirname=filename.parent)
+                    raw_file_paths_dict = create_one_file_per_signal_dict_rhd(dirname=filename.parent)
                 # then there is one-file-per-channel where each channel in a neo stream is in its own .dat file
                 else:
                     self.file_format = "one-file-per-channel"
-                    raw_file_paths_dict = create_one_file_per_channel_dict(dirname=filename.parent)
+                    raw_file_paths_dict = create_one_file_per_channel_dict_rhd(dirname=filename.parent)
             # finally the format with the header-attached to the binary file as one giant file
             else:
                 self.file_format = "header-attached"
@@ -175,7 +175,8 @@ def _parse_header(self):
         # check timestamp continuity
         if self.file_format == "header-attached":
             timestamp = self._raw_data["timestamp"].flatten()
-        # timestamps are always the last stream
+
+        # timestamps are always 6 for rhd and 7 for rhs
         elif self.file_format == "one-file-per-signal":
             time_stream_index = max(self._raw_data.keys())
             timestamp = self._raw_data[time_stream_index]
@@ -213,7 +214,7 @@ def _parse_header(self):
         signal_streams = np.zeros(stream_ids.size, dtype=_signal_stream_dtype)
         signal_streams["id"] = stream_ids
         for stream_index, stream_id in enumerate(stream_ids):
-            if self.filename.endswith('.rhd'):
+            if self.filename.endswith(".rhd"):
                 signal_streams["name"][stream_index] = stream_type_to_name_rhd.get(int(stream_id), "")
             else:
                 signal_streams["name"][stream_index] = stream_type_to_name_rhs.get(int(stream_id), "")
@@ -455,14 +456,14 @@ def read_variable_header(f, header):
     ("electrode_impedance_phase", "float32"),
 ]
 
-stream_type_to_name_rhs= {
+stream_type_to_name_rhs = {
     0: "RHS2000 amplifier channel",
     3: "USB board ADC input channel",
     4: "USB board ADC output channel",
     5: "USB board digital input channel",
     6: "USB board digital output channel",
     10: "DC Amplifier channel",
-    11: "Stim channel"
+    11: "Stim channel",
 }
 
 
@@ -501,8 +502,8 @@ def read_rhs(filename, file_format: str):
     if file_format == "header-attached":
         data_dtype = [("timestamp", "int32", BLOCK_SIZE)]
     else:
-        data_dtype[7] = "int32"
-        channel_number_dict[7] = 1
+        data_dtype[15] = "int32"
+        channel_number_dict[15] = 1
 
     # 0: RHS2000 amplifier channel.
     for chan_info in channels_by_type[0]:
@@ -546,7 +547,7 @@ def read_rhs(filename, file_format: str):
     # so let's skip for now and can be given on request
 
     if file_format != "one-file-per-channel":
-        channel_number_dict[11] = channel_number_dict[0] # should be one stim / amplifier channel
+        channel_number_dict[11] = channel_number_dict[0]  # should be one stim / amplifier channel
         for chan_info in channels_by_type[0]:
             name = chan_info["native_channel_name"]
             chan_info_stim = dict(chan_info)
@@ -902,12 +903,11 @@ def read_rhd(filename, file_format: str):
 
 ##########################################################################
 # RHX Zone for Binary Files
-# This zone gives the headerless binary files for both rhs and rhd header files
-# This occurs with the new rhx version of the intan recording software as an
-# optional software that can be turned
+# This section provides all possible headerless binary files in both the rhs and rhd
+# formats.
 
-# For One File Per Signal
-one_file_per_signal_filenames = [
+# RHD Binary Files for One File Per Signal
+one_file_per_signal_filenames_rhd = [
     "amplifier.dat",
     "auxiliary.dat",
     "supply.dat",
@@ -917,43 +917,73 @@ def read_rhd(filename, file_format: str):
 ]
 
 
-def create_one_file_per_signal_dict(dirname, rhs: bool = False):
+def create_one_file_per_signal_dict_rhd(dirname):
     """Function for One File Per Signal Type
 
     Parameters
     ----------
     dirname: pathlib.Path
         The folder to explore
-    rhs: bool, default: False
-        Whether this is an rhd or an rhs file
+
+    Returns
+    -------
+    raw_files_paths_dict: dict
+        A dict of all the file paths
     """
 
-    # if rhs we have an extra stream to add
+    raw_file_paths_dict = {}
+    for raw_index, raw_file in enumerate(one_file_per_signal_filenames_rhd):
+        if Path(dirname / raw_file).is_file():
+            raw_file_paths_dict[raw_index] = Path(dirname / raw_file)
+
+    raw_file_paths_dict[6] = Path(dirname / "time.dat")
+
+    return raw_file_paths_dict
+
+
+# RHS Binary Files for One File Per Signal
+one_file_per_signal_filenames_rhs = [
+    "amplifier.dat",
+    "auxiliary.dat",
+    "supply.dat",
+    "analogin.dat",
+    "analogout.dat" "digitalin.dat",
+    "digitalout.dat",
+]
+
+
+def create_one_file_per_signal_dict_rhs(dirname):
+    """Function for One File Per Signal Type
+
+    Parameters
+    ----------
+    dirname: pathlib.Path
+        The folder to explore
 
-    if rhs:
-        one_file_per_signal_filenames.insert(4, "analogout.dat")
+    Returns
+    -------
+    raw_files_paths_dict: dict
+        A dict of all the file paths
+    """
 
     raw_file_paths_dict = {}
-    for raw_index, raw_file in enumerate(one_file_per_signal_filenames):
+    for raw_index, raw_file in enumerate(one_file_per_signal_filenames_rhs):
         if Path(dirname / raw_file).is_file():
             raw_file_paths_dict[raw_index] = Path(dirname / raw_file)
-    if rhs:
-        raw_file_paths_dict[7] = Path(dirname / "time.dat")
-    else:
-        raw_file_paths_dict[6] = Path(dirname / "time.dat")
 
-    if rhs:
-        # 10 and 11 are hardcoded in the rhs_reader above so hardcoded here too
-        if Path(dirname / "dcamplifier.dat").is_file():
-            raw_file_paths_dict[10] = Path(dirname / "dcamplifier.dat")
-        if Path(dirname / "stim.dat").is_file():
-            raw_file_paths_dict[11] = Path(dirname / "stim.dat")
+    # we need time to be the last value
+    raw_file_paths_dict[15] = Path(dirname / "time.dat")
+    # 10 and 11 are hardcoded in the rhs_reader above so hardcoded here too
+    if Path(dirname / "dcamplifier.dat").is_file():
+        raw_file_paths_dict[10] = Path(dirname / "dcamplifier.dat")
+    if Path(dirname / "stim.dat").is_file():
+        raw_file_paths_dict[11] = Path(dirname / "stim.dat")
 
     return raw_file_paths_dict
 
 
-# For One File Per Channel
-possible_raw_file_prefixes = [
+# RHD Binary Files for One File Per Channel
+possible_raw_file_prefixes_rhd = [
     "amp",
     "aux",
     "vdd",
@@ -963,35 +993,71 @@ def create_one_file_per_signal_dict(dirname, rhs: bool = False):
 ]
 
 
-def create_one_file_per_channel_dict(dirname, rhs: bool = False):
+def create_one_file_per_channel_dict_rhd(dirname):
     """Utility function for One File Per Channel
 
     Parameters
     ----------
     dirname: pathlib.Path
         The folder to explore
-    rhs: bool, default: False
-        Whether this is an rhd or an rhs file
+
+    Returns
+    -------
+    raw_files_paths_dict: dict
+        A dict of all the file paths
     """
-    # if rhs we have an extra stream to add
-    if rhs:
-        possible_raw_file_prefixes.insert(4, "board-ANALOG-OUT")
 
     file_names = dirname.glob("**/*.dat")
     files = [file for file in file_names if file.is_file()]
     raw_file_paths_dict = {}
-    for raw_index, prefix in enumerate(possible_raw_file_prefixes):
+    for raw_index, prefix in enumerate(possible_raw_file_prefixes_rhd):
         raw_file_paths_dict[raw_index] = [file for file in files if prefix in file.name]
-    if rhs:
-        raw_file_paths_dict[7] = [Path(dirname / "time.dat")]
-    else:
-        raw_file_paths_dict[6] = [Path(dirname / "time.dat")]
-
-    if rhs:
-        # 10 and 11 are hardcoded in the rhs reader so hardcoded here
-        raw_file_paths_dict[10] = [file for file in files if "dc-" in file.name]
-        # we can find the files, but I can see how to read them out of header
-        # so for now we don't expose the stim files in one-file-per-channel
-        raw_file_paths_dict[11] = [file for file in files if "stim-" in file.name]
+
+    raw_file_paths_dict[6] = [Path(dirname / "time.dat")]
+
+    return raw_file_paths_dict
+
+
+# RHS Binary Files for One File Per Channel
+possible_raw_file_prefixes_rhs = [
+    "amp",
+    "aux",
+    "vdd",
+    "board-ANALOG-IN",
+    "board-ANALOG-OUT",
+    "board-DIGITAL-IN",
+    "board-DIGITAL-OUT",
+]
+
+
+def create_one_file_per_channel_dict_rhs(
+    dirname,
+):
+    """Utility function for One File Per Channel
+
+    Parameters
+    ----------
+    dirname: pathlib.Path
+        The folder to explore
+
+    Returns
+    -------
+    raw_files_paths_dict: dict
+        A dict of all the file paths
+    """
+
+    file_names = dirname.glob("**/*.dat")
+    files = [file for file in file_names if file.is_file()]
+    raw_file_paths_dict = {}
+    for raw_index, prefix in enumerate(possible_raw_file_prefixes_rhs):
+        raw_file_paths_dict[raw_index] = [file for file in files if prefix in file.name]
+    
+    # we need time to be the last value
+    raw_file_paths_dict[15] = [Path(dirname / "time.dat")]
+    # 10 and 11 are hardcoded in the rhs reader so hardcoded here
+    raw_file_paths_dict[10] = [file for file in files if "dc-" in file.name]
+    # we can find the files, but I can see how to read them out of header
+    # so for now we don't expose the stim files in one-file-per-channel
+    raw_file_paths_dict[11] = [file for file in files if "stim-" in file.name]
 
     return raw_file_paths_dict

From 10bf3c61b84bd7d98a029347ca2a6f2421d1c21c Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Fri, 3 May 2024 18:44:52 -0400
Subject: [PATCH 11/15] put streams in correct order

---
 neo/rawio/intanrawio.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/neo/rawio/intanrawio.py b/neo/rawio/intanrawio.py
index 6fe63c48e..9b875d9b0 100644
--- a/neo/rawio/intanrawio.py
+++ b/neo/rawio/intanrawio.py
@@ -212,7 +212,11 @@ def _parse_header(self):
 
         stream_ids = np.unique(signal_channels["stream_id"])
         signal_streams = np.zeros(stream_ids.size, dtype=_signal_stream_dtype)
-        signal_streams["id"] = stream_ids
+
+        # we need to sort the data because the string of 10 is mis-sorted.
+        stream_ids_sorted = sorted([int(stream_id) for stream_id in stream_ids])
+        signal_streams["id"] = [str(stream_id) for stream_id in stream_ids_sorted]
+
         for stream_index, stream_id in enumerate(stream_ids):
             if self.filename.endswith(".rhd"):
                 signal_streams["name"][stream_index] = stream_type_to_name_rhd.get(int(stream_id), "")

From cb869c3cf83c719aac6dbb9734b04d899de70de1 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Fri, 3 May 2024 18:52:12 -0400
Subject: [PATCH 12/15] fix test file naming.

---
 neo/test/iotest/test_intanio.py       | 2 +-
 neo/test/rawiotest/test_intanrawio.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/neo/test/iotest/test_intanio.py b/neo/test/iotest/test_intanio.py
index 7d15a5f99..bedd65bf8 100644
--- a/neo/test/iotest/test_intanio.py
+++ b/neo/test/iotest/test_intanio.py
@@ -20,7 +20,7 @@ class TestIntanIO(
         "intan/intan_fpc_test_231117_052630/info.rhd",
         "intan/intan_fps_test_231117_052500/info.rhd",
         "intan/intan_fpc_rhs_test_240329_091637/info.rhs",
-        "intan/intan_fps_rhs_test_240329_091636/info.rhs",
+        "intan/intan_fps_rhs_test_240329_091536/info.rhs",
     ]
 
 
diff --git a/neo/test/rawiotest/test_intanrawio.py b/neo/test/rawiotest/test_intanrawio.py
index 1666efc69..3f5ee3c7c 100644
--- a/neo/test/rawiotest/test_intanrawio.py
+++ b/neo/test/rawiotest/test_intanrawio.py
@@ -17,7 +17,7 @@ class TestIntanRawIO(
         "intan/intan_fpc_test_231117_052630/info.rhd",
         "intan/intan_fps_test_231117_052500/info.rhd",
         "intan/intan_fpc_rhs_test_240329_091637/info.rhs",
-        "intan/intan_fps_rhs_test_240329_091636/info.rhs",
+        "intan/intan_fps_rhs_test_240329_091536/info.rhs",
     ]
 
 

From ae41690477a3530c89fbfb18901f7bc983157990 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Sat, 4 May 2024 18:03:28 -0400
Subject: [PATCH 13/15] typo fix

---
 neo/rawio/intanrawio.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/neo/rawio/intanrawio.py b/neo/rawio/intanrawio.py
index 9b875d9b0..12621f9c4 100644
--- a/neo/rawio/intanrawio.py
+++ b/neo/rawio/intanrawio.py
@@ -176,7 +176,7 @@ def _parse_header(self):
         if self.file_format == "header-attached":
             timestamp = self._raw_data["timestamp"].flatten()
 
-        # timestamps are always 6 for rhd and 7 for rhs
+        # timestamps are always last stream for headerless binary files
         elif self.file_format == "one-file-per-signal":
             time_stream_index = max(self._raw_data.keys())
             timestamp = self._raw_data[time_stream_index]
@@ -951,7 +951,8 @@ def create_one_file_per_signal_dict_rhd(dirname):
     "auxiliary.dat",
     "supply.dat",
     "analogin.dat",
-    "analogout.dat" "digitalin.dat",
+    "analogout.dat",
+     "digitalin.dat",
     "digitalout.dat",
 ]
 

From 987e07b4bf2418d0999613176e552d2ec5c2f954 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Sat, 4 May 2024 18:31:05 -0400
Subject: [PATCH 14/15] make sure stream_ids are sorted

---
 neo/rawio/intanrawio.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/neo/rawio/intanrawio.py b/neo/rawio/intanrawio.py
index 12621f9c4..36f4dc1de 100644
--- a/neo/rawio/intanrawio.py
+++ b/neo/rawio/intanrawio.py
@@ -217,7 +217,7 @@ def _parse_header(self):
         stream_ids_sorted = sorted([int(stream_id) for stream_id in stream_ids])
         signal_streams["id"] = [str(stream_id) for stream_id in stream_ids_sorted]
 
-        for stream_index, stream_id in enumerate(stream_ids):
+        for stream_index, stream_id in enumerate(stream_ids_sorted):
             if self.filename.endswith(".rhd"):
                 signal_streams["name"][stream_index] = stream_type_to_name_rhd.get(int(stream_id), "")
             else:

From 6c5743f998470147d7bae9cd82c202ecfccd6843 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Sat, 4 May 2024 19:04:45 -0400
Subject: [PATCH 15/15] fix one-file-per-signal

---
 neo/rawio/intanrawio.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/neo/rawio/intanrawio.py b/neo/rawio/intanrawio.py
index 36f4dc1de..b4c7dc320 100644
--- a/neo/rawio/intanrawio.py
+++ b/neo/rawio/intanrawio.py
@@ -481,8 +481,8 @@ def read_rhs(filename, file_format: str):
         channels_by_type = {k: [] for k in [0, 3, 4, 5, 6]}
         if not file_format == "header-attached":
             # data_dtype for rhs is complicated. There is not 1, 2 (supply and aux),
-            # but there are dc-amp (10) and stim (11). we make timestamps (7)
-            data_dtype = {k: [] for k in [0, 3, 4, 5, 6, 7, 10, 11]}
+            # but there are dc-amp (10) and stim (11). we make timestamps (15)
+            data_dtype = {k: [] for k in [0, 3, 4, 5, 6, 10, 11, 15]}
         for g in range(global_info["nb_signal_group"]):
             group_info = read_variable_header(f, rhs_signal_group_header)
 
@@ -568,7 +568,7 @@ def read_rhs(filename, file_format: str):
             if file_format == "header-attached":
                 data_dtype += [(name + "_STIM", "uint16", BLOCK_SIZE)]
             else:
-                data_dtype[11] == "uint16"
+                data_dtype[11] = "uint16"
     else:
         warnings.warn("Stim not implemented for `one-file-per-channel` due to lack of test files")
 
@@ -952,7 +952,7 @@ def create_one_file_per_signal_dict_rhd(dirname):
     "supply.dat",
     "analogin.dat",
     "analogout.dat",
-     "digitalin.dat",
+    "digitalin.dat",
     "digitalout.dat",
 ]