Merge pull request #1476 from h-mayorquin/digital_channel_one_file_per_channel

Fix digital streams in Intan for the `one-file-per-channel` format in rhd.

Author: samuelgarcia

neo/rawio/intanrawio.py

@@ -53,18 +53,21 @@ class IntanRawIO(BaseRawIO):
     extension. Additionally it functions with RHS v 1.0 and RHD 1.0, 1.1, 1.2, 1.3, 2.0,
     3.0, and 3.1 files.
 
+    * The reader can handle three file formats 'header-attached', 'one-file-per-signal' and
+    'one-file-per-channel'.
+
     * Intan files contain amplifier channels labeled 'A', 'B' 'C' or 'D'
     depending on the port in which they were recorded along with the following
-    additional channels.
+    additional streams.
     0: 'RHD2000' amplifier channel
     1: 'RHD2000 auxiliary input channel',
     2: 'RHD2000 supply voltage channel',
     3: 'USB board ADC input channel',
     4: 'USB board digital input channel',
     5: 'USB board digital output channel'
 
-    * Due to the structure of the digital input and output channels these can be accessed
-    as one long vector, which must be post-processed.
+    * For the "header-attached" and "one-file-per-signal" formats, the structure of the digital input and output channels is
+    one long vector, which must be post-processed to extract individual digital channel information. See the intantech website for more information on performing this post-processing.
 
     Examples
     --------
@@ -511,7 +514,6 @@ def read_rhs(filename, file_format: str):
 
     # 0: RHS2000 amplifier channel.
     for chan_info in channels_by_type[0]:
-        name = chan_info["native_channel_name"]
         chan_info["sampling_rate"] = sr
         chan_info["units"] = "uV"
         chan_info["gain"] = 0.195
@@ -525,6 +527,7 @@ def read_rhs(filename, file_format: str):
             chan_info["dtype"] = "int16"
         ordered_channels.append(chan_info)
         if file_format == "header-attached":
+            name = chan_info["native_channel_name"]
             data_dtype += [(name, "uint16", BLOCK_SIZE)]
         else:
             data_dtype[0] = "int16"
@@ -533,8 +536,8 @@ def read_rhs(filename, file_format: str):
         # 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)
+            name = chan_info["native_channel_name"]
             chan_info_dc["native_channel_name"] = name + "_DC"
             chan_info_dc["sampling_rate"] = sr
             chan_info_dc["units"] = "mV"
@@ -553,8 +556,8 @@ def read_rhs(filename, file_format: str):
     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)
+            name = chan_info["native_channel_name"]
             chan_info_stim["native_channel_name"] = name + "_STIM"
             chan_info_stim["sampling_rate"] = sr
             # stim channel are complicated because they are coded
@@ -576,43 +579,51 @@ def read_rhs(filename, file_format: str):
 
     # 3: Analog input channel.
     # 4: Analog output channel.
-    for sig_type in [
-        3,
-        4,
-    ]:
+    for sig_type in [3, 4]:
         for chan_info in channels_by_type[sig_type]:
-            name = chan_info["native_channel_name"]
             chan_info["sampling_rate"] = sr
             chan_info["units"] = "V"
             chan_info["gain"] = 0.0003125
             chan_info["offset"] = -32768 * 0.0003125
             chan_info["dtype"] = "uint16"
             ordered_channels.append(chan_info)
             if file_format == "header-attached":
+                name = chan_info["native_channel_name"]
                 data_dtype += [(name, "uint16", BLOCK_SIZE)]
             else:
                 data_dtype[sig_type] = "uint16"
 
     # 5: Digital input channel.
     # 6: Digital output channel.
     for sig_type in [5, 6]:
-        if len(channels_by_type[sig_type]) > 0:
-            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
-            # 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:
+        if file_format in ["header-attached", "one-file-per-signal"]:
+            if len(channels_by_type[sig_type]) > 0:
+                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
+                # 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
+                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"
+        # This case behaves as a binary with 0 and 1 coded as uint16
+        elif file_format == "one-file-per-channel":
+            for chan_info in channels_by_type[sig_type]:
+                chan_info["sampling_rate"] = sr
+                chan_info["units"] = "TTL"
+                chan_info["gain"] = 1.0
+                chan_info["offset"] = 0.0
+                chan_info["dtype"] = "uint16"
+                ordered_channels.append(chan_info)
                 data_dtype[sig_type] = "uint16"
 
     if global_info["notch_filter_mode"] == 2 and global_info["major_version"] >= V("3.0"):
@@ -788,7 +799,6 @@ def read_rhd(filename, file_format: str):
 
     # 0: RHD2000 amplifier channel
     for chan_info in channels_by_type[0]:
-        name = chan_info["native_channel_name"]
         chan_info["sampling_rate"] = sr
         chan_info["units"] = "uV"
         chan_info["gain"] = 0.195
@@ -801,34 +811,35 @@ def read_rhd(filename, file_format: str):
         ordered_channels.append(chan_info)
 
         if file_format == "header-attached":
+            name = chan_info["native_channel_name"]
             data_dtype += [(name, "uint16", BLOCK_SIZE)]
         else:
             data_dtype[0] = "int16"
 
     # 1: RHD2000 auxiliary input channel
     for chan_info in channels_by_type[1]:
-        name = chan_info["native_channel_name"]
         chan_info["sampling_rate"] = sr / 4.0
         chan_info["units"] = "V"
         chan_info["gain"] = 0.0000374
         chan_info["offset"] = 0.0
         chan_info["dtype"] = "uint16"
         ordered_channels.append(chan_info)
         if file_format == "header-attached":
+            name = chan_info["native_channel_name"]
             data_dtype += [(name, "uint16", BLOCK_SIZE // 4)]
         else:
             data_dtype[1] = "uint16"
 
     # 2: RHD2000 supply voltage channel
     for chan_info in channels_by_type[2]:
-        name = chan_info["native_channel_name"]
         chan_info["sampling_rate"] = sr / BLOCK_SIZE
         chan_info["units"] = "V"
         chan_info["gain"] = 0.0000748
         chan_info["offset"] = 0.0
         chan_info["dtype"] = "uint16"
         ordered_channels.append(chan_info)
         if file_format == "header-attached":
+            name = chan_info["native_channel_name"]
             data_dtype += [(name, "uint16")]
         else:
             data_dtype[2] = "uint16"
@@ -847,7 +858,6 @@ def read_rhd(filename, file_format: str):
 
     # 3: USB board ADC input channel
     for chan_info in channels_by_type[3]:
-        name = chan_info["native_channel_name"]
         chan_info["sampling_rate"] = sr
         chan_info["units"] = "V"
         if global_info["eval_board_mode"] == 0:
@@ -862,32 +872,41 @@ def read_rhd(filename, file_format: str):
         chan_info["dtype"] = "uint16"
         ordered_channels.append(chan_info)
         if file_format == "header-attached":
+            name = chan_info["native_channel_name"]
             data_dtype += [(name, "uint16", BLOCK_SIZE)]
         else:
             data_dtype[3] = "uint16"
 
     # 4: USB board digital input channel
     # 5: USB board digital output channel
     for sig_type in [4, 5]:
-        # Now these are included so that user can obtain the
-        # dig signals and process them at the same time
-        if len(channels_by_type[sig_type]) > 0:
-            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:
+        if file_format in ["header-attached", "one-file-per-signal"]:
+            if len(channels_by_type[sig_type]) > 0:
+                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
+                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"
+        elif file_format == "one-file-per-channel":
+            for chan_info in channels_by_type[sig_type]:
+                chan_info["sampling_rate"] = sr
+                chan_info["units"] = "TTL"
+                chan_info["gain"] = 1.0
+                chan_info["offset"] = 0.0
+                chan_info["dtype"] = "uint16"
+                ordered_channels.append(chan_info)
                 data_dtype[sig_type] = "uint16"
 
     if global_info["notch_filter_mode"] == 2 and version >= V("3.0"):

neo/test/iotest/test_intanio.py

@@ -15,12 +15,14 @@ class TestIntanIO(
     ioclass = IntanIO
     entities_to_download = ["intan"]
     entities_to_test = [
-        "intan/intan_rhs_test_1.rhs",
-        "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_091637/info.rhs",
-        "intan/intan_fps_rhs_test_240329_091536/info.rhs",
+        "intan/intan_rhs_test_1.rhs",  # Format header-attached 
+        "intan/intan_rhd_test_1.rhd",  # Format header-attached
+        "intan/rhs_fpc_multistim_240514_082243/rhs_fpc_multistim_240514_082243.rhs",  # Format header-attached newer version
+        "intan/intan_fpc_test_231117_052630/info.rhd",  # Format one-file-per-channel
+        "intan/intan_fps_test_231117_052500/info.rhd",  # Format one file per signal
+        "intan/intan_fpc_rhs_test_240329_091637/info.rhs",  # Format one-file-per-channel
+        "intan/intan_fps_rhs_test_240329_091536/info.rhs",   # Format one-file-per-signal
+        "intan/rhd_fpc_multistim_240514_082044/info.rhd",  # Multiple digital channels one-file-per-channel rhd
     ]
 
 

neo/test/rawiotest/test_intanrawio.py

@@ -12,14 +12,17 @@ class TestIntanRawIO(
     rawioclass = IntanRawIO
     entities_to_download = ["intan"]
     entities_to_test = [
-        "intan/intan_rhs_test_1.rhs",
-        "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_091637/info.rhs",
-        "intan/intan_fps_rhs_test_240329_091536/info.rhs",
+        "intan/intan_rhs_test_1.rhs",  # Format header-attached 
+        "intan/intan_rhd_test_1.rhd",  # Format header-attached
+        "intan/rhs_fpc_multistim_240514_082243/rhs_fpc_multistim_240514_082243.rhs",  # Format header-attached newer version
+        "intan/intan_fpc_test_231117_052630/info.rhd",  # Format one-file-per-channel
+        "intan/intan_fps_test_231117_052500/info.rhd",  # Format one file per signal
+        "intan/intan_fpc_rhs_test_240329_091637/info.rhs",  # Format one-file-per-channel
+        "intan/intan_fps_rhs_test_240329_091536/info.rhs",   # Format one-file-per-signal
+        "intan/rhd_fpc_multistim_240514_082044/info.rhd",  # Multiple digital channels one-file-per-channel rhd
     ]
 
 
+
 if __name__ == "__main__":
     unittest.main()