wip

Author: zm711

neo/rawio/intanrawio.py

@@ -900,8 +900,17 @@ def read_rhs(filename, file_format: str):
         channel_number_dict = {name: len(stream_name_to_channel_info_list[name]) for name in names_to_count}
 
         # Both DC Amplifier and Stim streams have the same number of channels as the amplifier stream
+        # if using the `header-attached` or `one-file-per-signal` formats
+        # the amplifier data is stored in the same place in the header so no matter what the DC amp
+        # uses the same info as the RHS amp.
         channel_number_dict["DC Amplifier channel"] = channel_number_dict["RHS2000 amplifier channel"]
-        channel_number_dict["Stim channel"] = channel_number_dict["RHS2000 amplifier channel"]
+        if file_format != "one-file-per-channel":
+            channel_number_dict["Stim channel"] = channel_number_dict["RHS2000 amplifier channel"]
+        else:
+            raw_file_paths_dict = create_one_file_per_channel_dict_rhs(dirname=filename.parent)
+            channel_number_dict["Stim channel"] = len(raw_file_paths_dict["Stim channel"])
+            # but the user can shut off the normal amplifier and only save dc amplifier
+            channel_number_dict["RHS2000 amplifier channel"] = len(raw_file_paths_dict["RHS2000 amplifier channel"])
 
         header_size = f.tell()
 
@@ -915,24 +924,25 @@ def read_rhs(filename, file_format: str):
         memmap_data_dtype["timestamp"] = "int32"
         channel_number_dict["timestamp"] = 1
 
-    for chan_info in stream_name_to_channel_info_list["RHS2000 amplifier channel"]:
-        chan_info["sampling_rate"] = sr
-        chan_info["units"] = "uV"
-        chan_info["gain"] = 0.195
-        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_channel_info.append(chan_info)
-        if file_format == "header-attached":
-            name = chan_info["native_channel_name"]
-            memmap_data_dtype += [(name, "uint16", BLOCK_SIZE)]
-        else:
-            memmap_data_dtype["RHS2000 amplifier channel"] = "int16"
+    if file_format != "one-file-per-channel" or channel_number_dict["RHS2000 amplifier channel"] > 0:
+        for chan_info in stream_name_to_channel_info_list["RHS2000 amplifier channel"]:
+            chan_info["sampling_rate"] = sr
+            chan_info["units"] = "uV"
+            chan_info["gain"] = 0.195
+            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_channel_info.append(chan_info)
+            if file_format == "header-attached":
+                name = chan_info["native_channel_name"]
+                memmap_data_dtype += [(name, "uint16", BLOCK_SIZE)]
+            else:
+                memmap_data_dtype["RHS2000 amplifier channel"] = "int16"
 
     if bool(global_info["dc_amplifier_data_saved"]):
         # if we have dc amp we need to grab the correct number of channels
@@ -957,30 +967,26 @@ def read_rhs(filename, file_format: str):
     # so ideally at some point we need test data to confirm this is true
     # based on what Heberto and I read in the docs
     for chan_info in stream_name_to_channel_info_list["RHS2000 amplifier channel"]:
-        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
-        # with bits, they do not fit the gain/offset rawio strategy
-        chan_info_stim["units"] = "A"  # Amps
-        chan_info_stim["gain"] = global_info["stim_step_size"]
-        chan_info_stim["offset"] = 0.0
-        chan_info_stim["signal_type"] = 11  # put it in another group
-        chan_info_stim["dtype"] = "int16" # this change is due to bit decoding see note below
-        ordered_channel_info.append(chan_info_stim)
-        # Note that the data on disk is uint16 but the data is 
-        # then decoded as int16 so the chan_info is int16
-        if file_format == "header-attached":
-            memmap_data_dtype += [(name + "_STIM", "uint16", BLOCK_SIZE)]
-        else:
-            memmap_data_dtype["Stim channel"] = "uint16"
-        if file_format == "one-file-per-channel":
-            warning_msg = ("Stim decoding for `one-file-per-channel` is based on a reading of the documention "
-                           "and we would appreciate test data to ensure we've implemented this format "
-                           "appropriately. If you use the stim data please verify it is as you expected "
-                           "and if it is not then open an issue on the python-neo repo")
-            warnings.warn(warning_msg)
+        # we see which stim were activated
+        if any([chan_info["native_channel_name"] in stim_file.stem for stim_file in raw_file_paths_dict['Stim channel']]):
+            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
+            # with bits, they do not fit the gain/offset rawio strategy
+            chan_info_stim["units"] = "A"  # Amps
+            chan_info_stim["gain"] = global_info["stim_step_size"]
+            chan_info_stim["offset"] = 0.0
+            chan_info_stim["signal_type"] = 11  # put it in another group
+            chan_info_stim["dtype"] = "int16" # this change is due to bit decoding see note below
+            ordered_channel_info.append(chan_info_stim)
+            # Note that the data on disk is uint16 but the data is 
+            # then decoded as int16 so the chan_info is int16
+            if file_format == "header-attached":
+                memmap_data_dtype += [(name + "_STIM", "uint16", BLOCK_SIZE)]
+            else:
+                memmap_data_dtype["Stim channel"] = "uint16"
 
     # No supply or aux for rhs files (ie no stream_id 1 and 2)
     # We have an error above that requests test files to help if the spec is changed