From 15f4086f82b905036344819ef37dbf5f64dcaeeb Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Thu, 2 Feb 2023 13:55:24 -0500 Subject: [PATCH 01/30] working example --- element_interface/intan_loader.py | 268 ++++++++++++++++++++++++++++++ 1 file changed, 268 insertions(+) create mode 100644 element_interface/intan_loader.py diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py new file mode 100644 index 0000000..6846433 --- /dev/null +++ b/element_interface/intan_loader.py @@ -0,0 +1,268 @@ +import numpy as np +import os, sys, struct +from pathlib import Path +import matplotlib.pyplot as plt + + +def read_qstring(fid): + """Read Qt style QString. + + The first 32-bit unsigned number indicates the length of the string (in bytes). + If this number equals 0xFFFFFFFF, the string is null. + + Strings are stored as unicode. + """ + + (length,) = struct.unpack(" (os.fstat(fid.fileno()).st_size - fid.tell() + 1): + print(length) + raise Exception("Length too long.") + + # convert length from bytes to 16-bit Unicode words + length = int(length / 2) + + data = [] + for i in range(0, length): + (c,) = struct.unpack("= (3, 0): + a = "".join([chr(c) for c in data]) + else: + a = "".join([unichr(c) for c in data]) + + return a + + +def read_header(fid): + """Reads the Intan File Format header from the given file.""" + + # Check 'magic number' at beginning of file to make sure this is an Intan + # Technologies RHD2000 data file. + (magic_number,) = struct.unpack(" 0) and (signal_group_enabled > 0): + for signal_channel in range(0, signal_group_num_channels): + new_channel = { + "port_name": signal_group_name, + "port_prefix": signal_group_prefix, + "port_number": signal_group, + } + new_channel["native_channel_name"] = read_qstring(fid) + new_channel["custom_channel_name"] = read_qstring(fid) + ( + new_channel["native_order"], + new_channel["custom_order"], + signal_type, + channel_enabled, + new_channel["chip_channel"], + command_stream, + new_channel["board_stream"], + ) = struct.unpack( + " Date: Fri, 3 Feb 2023 06:55:09 -0500 Subject: [PATCH 02/30] code cleaning --- element_interface/intan_loader.py | 56 ++++++++++++++++--------------- 1 file changed, 29 insertions(+), 27 deletions(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index 6846433..603dfa2 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -224,20 +224,43 @@ def read_header(fid): return header -INBOX = Path("/Users/tolgadincer/ClientData/Utah_Alex/2020Data/RawData/Organoid21") -header_filename = INBOX / "032520_US_885kHz_sham/info.rhs" -with open(header_filename, "rb") as fid: - header = read_header(fid) +def load_rhs(folder: str, file_expr: str): + """Load rhs data + + Example: + # Read data + >>> signals, time = load_rhs("/home/inbox/organoids21/032520_US_885kHz_sham", file_expr="amp*dat") + + # Plot data + >>> for signal in signals: + >>> plt.plot(time, signal) + >>> plt.xlabel("Time (s)") + >>> plt.ylabel("Signal (microvolts)") + >>> plt.show() + + Args: + folder (str): Folder that contains info.rhs, time.dat, and *.dat files + file_expr (str): regex pattern of the file names to be read. + + Returns: + signals (np.array_like): Signal amplitudes in microvolts + time (np.array_like): Time stamps + """ + header_filepath = next(Path(folder).glob("info.rhs")) + with open(header_filepath, "rb") as fid: + header = read_header(fid) -def read_time(file_paths, time_filename="time.dat", header_filename="info.rhs"): + time_file = next(Path(folder).glob("time.dat")) time = ( - np.memmap(time_filename, dtype=np.int32, offset=2_000_000, shape=10000) + np.memmap(time_file, dtype=np.int32, offset=2_000_000, shape=10000) / header["frequency_parameters"]["amplifier_sample_rate"] ) + file_paths = list(Path(folder).glob(file_expr)) signals = np.empty([len(file_paths), len(time)]) + for i, file_path in enumerate(file_paths): signals[i, :] = np.memmap( file_path, dtype=np.int16, offset=2_000_000, shape=10000 @@ -245,24 +268,3 @@ def read_time(file_paths, time_filename="time.dat", header_filename="info.rhs"): signals = signals * 0.195 # Convert to microvolts return signals, time - - -INBOX = Path("/Users/tolgadincer/ClientData/Utah_Alex/2020Data/RawData/Organoid21") - -time_filename = INBOX / "032520_US_885kHz_sham/time.dat" -header_filename = INBOX / "032520_US_885kHz_sham/info.rhs" - -relative_paths = [ - "032520_US_885kHz_sham/amp-B-001.dat", - "032520_US_885kHz_sham/amp-B-005.dat", -] -file_paths = [INBOX / x for x in relative_paths] - -signals, time = read_time(file_paths, time_filename, header_filename) - -for signal in signals: - plt.plot(time, signal) -# plt.title("/".join(file_path.parts[-2:])) -plt.xlabel("Time (s)") -plt.ylabel("Signal (microvolts)") -plt.show() From 1c1b16909d8a8c0b8c7c54effbd64f6bcfe880be Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Fri, 3 Feb 2023 06:56:52 -0500 Subject: [PATCH 03/30] add time unit --- element_interface/intan_loader.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index 603dfa2..398d86d 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -244,7 +244,7 @@ def load_rhs(folder: str, file_expr: str): Returns: signals (np.array_like): Signal amplitudes in microvolts - time (np.array_like): Time stamps + time (np.array_like): Time stamps in seconds """ header_filepath = next(Path(folder).glob("info.rhs")) From 5b41b0afdf85cd68b0a759e5f7ecf7ef8f4e8958 Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Fri, 3 Feb 2023 10:30:37 -0500 Subject: [PATCH 04/30] read data based on the data type manual --- element_interface/intan_loader.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index 398d86d..e840581 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -254,7 +254,7 @@ def load_rhs(folder: str, file_expr: str): time_file = next(Path(folder).glob("time.dat")) time = ( - np.memmap(time_file, dtype=np.int32, offset=2_000_000, shape=10000) + np.memmap(time_file, dtype=np.int32) / header["frequency_parameters"]["amplifier_sample_rate"] ) @@ -262,9 +262,7 @@ def load_rhs(folder: str, file_expr: str): signals = np.empty([len(file_paths), len(time)]) for i, file_path in enumerate(file_paths): - signals[i, :] = np.memmap( - file_path, dtype=np.int16, offset=2_000_000, shape=10000 - ) + signals[i, :] = np.memmap(file_path, dtype=np.int16) signals = signals * 0.195 # Convert to microvolts return signals, time From c3f45402d6fcc4334f22aa86c94e834daca06f58 Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Fri, 3 Feb 2023 11:56:43 -0500 Subject: [PATCH 05/30] return header as well --- element_interface/intan_loader.py | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index e840581..68d50b4 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -229,11 +229,11 @@ def load_rhs(folder: str, file_expr: str): Example: # Read data - >>> signals, time = load_rhs("/home/inbox/organoids21/032520_US_885kHz_sham", file_expr="amp*dat") + >>> rhs_data = load_rhs("/home/inbox/organoids21/032520_US_885kHz_sham", file_expr="amp*dat") # Plot data - >>> for signal in signals: - >>> plt.plot(time, signal) + >>> for signal in rhs_data["signals"]: + >>> plt.plot(rhs_data["time"], signal) >>> plt.xlabel("Time (s)") >>> plt.ylabel("Signal (microvolts)") >>> plt.show() @@ -243,8 +243,10 @@ def load_rhs(folder: str, file_expr: str): file_expr (str): regex pattern of the file names to be read. Returns: - signals (np.array_like): Signal amplitudes in microvolts - time (np.array_like): Time stamps in seconds + rhs_data (dict): RHS data. + rhs_data["header"] (dict): Header. + rhs_data["signals"] (np.array_like): Signal amplitudes in microvolts. + rhs_data["timestamps"] (np.array_like): Relative timestamps in seconds. """ header_filepath = next(Path(folder).glob("info.rhs")) @@ -253,16 +255,17 @@ def load_rhs(folder: str, file_expr: str): time_file = next(Path(folder).glob("time.dat")) - time = ( + timestamps = ( np.memmap(time_file, dtype=np.int32) / header["frequency_parameters"]["amplifier_sample_rate"] ) file_paths = list(Path(folder).glob(file_expr)) - signals = np.empty([len(file_paths), len(time)]) + signals = np.empty([len(file_paths), len(timestamps)]) for i, file_path in enumerate(file_paths): signals[i, :] = np.memmap(file_path, dtype=np.int16) signals = signals * 0.195 # Convert to microvolts - return signals, time + rhs_data = dict(header=header, signals=signals, timestamps=timestamps) + return rhs_data From b7d1d70eba3da82c2d6cdfc5dd8407fe8ee04aed Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Fri, 3 Feb 2023 15:42:15 -0500 Subject: [PATCH 06/30] read other files as well --- element_interface/intan_loader.py | 38 ++++++++++++++++++++++--------- 1 file changed, 27 insertions(+), 11 deletions(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index 68d50b4..7ce304a 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -232,10 +232,9 @@ def load_rhs(folder: str, file_expr: str): >>> rhs_data = load_rhs("/home/inbox/organoids21/032520_US_885kHz_sham", file_expr="amp*dat") # Plot data - >>> for signal in rhs_data["signals"]: - >>> plt.plot(rhs_data["time"], signal) + >>> plt.plot(rhs_data["time"], rhs_data["recordings"]["amp-B-000.dat"]) >>> plt.xlabel("Time (s)") - >>> plt.ylabel("Signal (microvolts)") + >>> plt.ylabel("Reading") >>> plt.show() Args: @@ -245,7 +244,7 @@ def load_rhs(folder: str, file_expr: str): Returns: rhs_data (dict): RHS data. rhs_data["header"] (dict): Header. - rhs_data["signals"] (np.array_like): Signal amplitudes in microvolts. + rhs_data["recordings"] (dict): Readings from various files rhs_data["timestamps"] (np.array_like): Relative timestamps in seconds. """ @@ -260,12 +259,29 @@ def load_rhs(folder: str, file_expr: str): / header["frequency_parameters"]["amplifier_sample_rate"] ) - file_paths = list(Path(folder).glob(file_expr)) - signals = np.empty([len(file_paths), len(timestamps)]) + rhs_data = dict(header=header, timestamps=timestamps, recordings={}) + + file_paths = Path(folder).glob(file_expr) + file_paths = [x for x in file_paths if x.as_posix() != "time.dat"] + + for file_path in file_paths: + file_path = file_path.as_posix() + if "amp" in file_path: + signal = np.memmap(file_path, dtype=np.int16) + signal = signal * 0.195 # Convert to microvolts + elif "board-ANALOG-IN" in file_path or "board-ANALOG-OUT" in file_path: + signal = np.memmap(file_path, dtype=np.uint16) + signal = (signal - 32768) * 0.0003125 # Convert to volts + elif "dc-" in file_path: + signal = np.memmap(file_path, dtype=np.uint16) + signal = (signal - 512) * 19.23 # Convert to milivolts + elif "board-DIGITAL-IN" in file_path or "board-DIGITAL-OUT" in file_path: + signal = np.memmap(file_path, dtype=np.uint16) + elif "stim-" in file_path: + data = np.memmap(file_path, dtype=np.uint16) + i = np.bitwise_and(data, 255) * header["stim_step_size"] + sign = (128 - np.bitwise_and(data, 255)) / 128 + signal = i * sign + rhs_data["recordings"][Path(file_path).relative_to(folder).stem] = signal - for i, file_path in enumerate(file_paths): - signals[i, :] = np.memmap(file_path, dtype=np.int16) - signals = signals * 0.195 # Convert to microvolts - - rhs_data = dict(header=header, signals=signals, timestamps=timestamps) return rhs_data From f44416fa6047bf03b3e101adca06630a20a4d08a Mon Sep 17 00:00:00 2001 From: JaerongA Date: Mon, 6 Feb 2023 11:05:35 -0600 Subject: [PATCH 07/30] refactor: :art: streamline the code --- element_interface/intan_loader.py | 97 ++++++++++++++++++------------- 1 file changed, 55 insertions(+), 42 deletions(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index 7ce304a..d9def17 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -1,10 +1,9 @@ import numpy as np import os, sys, struct from pathlib import Path -import matplotlib.pyplot as plt -def read_qstring(fid): +def _read_qstring(fid): """Read Qt style QString. The first 32-bit unsigned number indicates the length of the string (in bytes). @@ -37,7 +36,7 @@ def read_qstring(fid): return a -def read_header(fid): +def _read_header(fid): """Reads the Intan File Format header from the given file.""" # Check 'magic number' at beginning of file to make sure this is an Intan @@ -53,13 +52,13 @@ def read_header(fid): (version["major"], version["minor"]) = struct.unpack(">> rhs_data = load_rhs("/home/inbox/organoids21/032520_US_885kHz_sham", file_expr="amp*dat") # Plot data + import matplotlib.pyplot as plt >>> plt.plot(rhs_data["time"], rhs_data["recordings"]["amp-B-000.dat"]) >>> plt.xlabel("Time (s)") >>> plt.ylabel("Reading") @@ -248,40 +248,53 @@ def load_rhs(folder: str, file_expr: str): rhs_data["timestamps"] (np.array_like): Relative timestamps in seconds. """ + rhs_data = {} + + # Get header header_filepath = next(Path(folder).glob("info.rhs")) with open(header_filepath, "rb") as fid: - header = read_header(fid) + rhs_data["header"] = _read_header(fid) - time_file = next(Path(folder).glob("time.dat")) - timestamps = ( + # Get timestamps + time_file = next(Path(folder).glob("time.dat")) + + rhs_data["timestamps"] = ( np.memmap(time_file, dtype=np.int32) - / header["frequency_parameters"]["amplifier_sample_rate"] + / rhs_data["header"]["frequency_parameters"]["amplifier_sample_rate"] ) - rhs_data = dict(header=header, timestamps=timestamps, recordings={}) - + # Get data files file_paths = Path(folder).glob(file_expr) - file_paths = [x for x in file_paths if x.as_posix() != "time.dat"] + + if file_expr == "*": + exclude_list = ["time", "info", "Zone.Identifier"] + + file_paths = [file for file in file_paths if not any([string in file.as_posix() for string in exclude_list])] + + # Get recording data + rhs_data["recordings"] = {} + + for file_path in sorted(file_paths): - for file_path in file_paths: - file_path = file_path.as_posix() - if "amp" in file_path: - signal = np.memmap(file_path, dtype=np.int16) + signal = np.memmap(file_path, dtype=np.int16) + signal_type = file_path.stem.split("-")[0] + + if signal_type == "amp": signal = signal * 0.195 # Convert to microvolts - elif "board-ANALOG-IN" in file_path or "board-ANALOG-OUT" in file_path: - signal = np.memmap(file_path, dtype=np.uint16) + + elif signal_type == "board": signal = (signal - 32768) * 0.0003125 # Convert to volts - elif "dc-" in file_path: - signal = np.memmap(file_path, dtype=np.uint16) + + elif signal_type == "dc": signal = (signal - 512) * 19.23 # Convert to milivolts - elif "board-DIGITAL-IN" in file_path or "board-DIGITAL-OUT" in file_path: - signal = np.memmap(file_path, dtype=np.uint16) - elif "stim-" in file_path: - data = np.memmap(file_path, dtype=np.uint16) - i = np.bitwise_and(data, 255) * header["stim_step_size"] - sign = (128 - np.bitwise_and(data, 255)) / 128 + + elif signal_type == "stim": + + i = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] + sign = (128 - np.bitwise_and(signal, 255)) / 128 signal = i * sign - rhs_data["recordings"][Path(file_path).relative_to(folder).stem] = signal + + rhs_data["recordings"][file_path.stem] = signal return rhs_data From 500ca38935b7afc86fc1789b235806604d0cfb6c Mon Sep 17 00:00:00 2001 From: JaerongA Date: Mon, 6 Feb 2023 11:12:30 -0600 Subject: [PATCH 08/30] Update docstring --- element_interface/intan_loader.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index d9def17..0dbf17b 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -239,7 +239,7 @@ def load_rhs(folder: str, file_expr: str = "*"): Args: folder (str): Folder that contains info.rhs, time.dat, and *.dat files - file_expr (str): regex pattern of the file names to be read. + file_expr (str): regex pattern of the file names to be read. Defaults to "*" (read all files). Returns: rhs_data (dict): RHS data. From fc5839fb45244d42e4dfdd7339093cd1cc765d13 Mon Sep 17 00:00:00 2001 From: JaerongA Date: Wed, 8 Feb 2023 15:59:59 -0600 Subject: [PATCH 09/30] remove unnecessary print statements --- element_interface/intan_loader.py | 8 -------- 1 file changed, 8 deletions(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index 0dbf17b..5a3d19d 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -52,14 +52,6 @@ def _read_header(fid): (version["major"], version["minor"]) = struct.unpack(" Date: Wed, 8 Feb 2023 17:03:41 -0600 Subject: [PATCH 10/30] apply regex to filter data files --- element_interface/intan_loader.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index 5a3d19d..2579e5b 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -260,10 +260,8 @@ def load_rhs(folder: str, file_expr: str = "*"): file_paths = Path(folder).glob(file_expr) if file_expr == "*": - exclude_list = ["time", "info", "Zone.Identifier"] - - file_paths = [file for file in file_paths if not any([string in file.as_posix() for string in exclude_list])] - + file_paths = list(folder.glob("[!info|!time|!Zone]*")) + # Get recording data rhs_data["recordings"] = {} From 30960f5aeeb3a8303d380e561a061fa47b57b094 Mon Sep 17 00:00:00 2001 From: JaerongA Date: Wed, 8 Feb 2023 17:06:36 -0600 Subject: [PATCH 11/30] Update element_interface/intan_loader.py Co-authored-by: Tolga Dincer --- element_interface/intan_loader.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index 2579e5b..dd8966d 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -223,7 +223,7 @@ def load_rhs(folder: str, file_expr: str = "*"): >>> rhs_data = load_rhs("/home/inbox/organoids21/032520_US_885kHz_sham", file_expr="amp*dat") # Plot data - import matplotlib.pyplot as plt + >>> import matplotlib.pyplot as plt >>> plt.plot(rhs_data["time"], rhs_data["recordings"]["amp-B-000.dat"]) >>> plt.xlabel("Time (s)") >>> plt.ylabel("Reading") From 0d251e9b9486929792d67541c4cf73a5ed90243c Mon Sep 17 00:00:00 2001 From: JaerongA Date: Wed, 8 Feb 2023 17:51:25 -0600 Subject: [PATCH 12/30] dtype=np.uint16 for some signal types --- element_interface/intan_loader.py | 43 ++++++++++++++----------------- 1 file changed, 20 insertions(+), 23 deletions(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index dd8966d..fd911ec 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -241,16 +241,15 @@ def load_rhs(folder: str, file_expr: str = "*"): """ rhs_data = {} - + # Get header header_filepath = next(Path(folder).glob("info.rhs")) with open(header_filepath, "rb") as fid: rhs_data["header"] = _read_header(fid) - # Get timestamps time_file = next(Path(folder).glob("time.dat")) - + rhs_data["timestamps"] = ( np.memmap(time_file, dtype=np.int32) / rhs_data["header"]["frequency_parameters"]["amplifier_sample_rate"] @@ -258,33 +257,31 @@ def load_rhs(folder: str, file_expr: str = "*"): # Get data files file_paths = Path(folder).glob(file_expr) - + if file_expr == "*": file_paths = list(folder.glob("[!info|!time|!Zone]*")) - + # Get recording data rhs_data["recordings"] = {} - - for file_path in sorted(file_paths): - signal = np.memmap(file_path, dtype=np.int16) + for file_path in sorted(file_paths): signal_type = file_path.stem.split("-")[0] - + if signal_type == "amp": + signal = np.memmap(file_path, dtype=np.int16) signal = signal * 0.195 # Convert to microvolts - - elif signal_type == "board": - signal = (signal - 32768) * 0.0003125 # Convert to volts - - elif signal_type == "dc": - signal = (signal - 512) * 19.23 # Convert to milivolts - - elif signal_type == "stim": - - i = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] - sign = (128 - np.bitwise_and(signal, 255)) / 128 - signal = i * sign - - rhs_data["recordings"][file_path.stem] = signal + else: + signal = np.memmap(file_path, dtype=np.uint16) + if signal_type == "board": + signal = (signal - 32768) * 0.0003125 # Convert to volts + elif signal_type == "dc": + signal = (signal - 512) * 19.23 # Convert to milivolts + + elif signal_type == "stim": + i = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] + sign = (128 - np.bitwise_and(signal, 255)) / 128 + signal = i * sign + + rhs_data["recordings"][file_path.stem] = signal return rhs_data From e8d31c43f395401ac7f7b6320d237a6e7611fbed Mon Sep 17 00:00:00 2001 From: JaerongA Date: Wed, 8 Feb 2023 18:03:10 -0600 Subject: [PATCH 13/30] revert regex filtering --- element_interface/intan_loader.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index fd911ec..220b408 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -259,7 +259,13 @@ def load_rhs(folder: str, file_expr: str = "*"): file_paths = Path(folder).glob(file_expr) if file_expr == "*": - file_paths = list(folder.glob("[!info|!time|!Zone]*")) + exclude_list = ["time", "info", "Zone.Identifier"] + + file_paths = [ + file + for file in file_paths + if not any([string in file.as_posix() for string in exclude_list]) + ] # Get recording data rhs_data["recordings"] = {} From 10f5e0e084c24f7a203edf9f96b5d3bcedfd0540 Mon Sep 17 00:00:00 2001 From: JaerongA Date: Thu, 9 Feb 2023 08:51:38 -0600 Subject: [PATCH 14/30] suggestions from code review --- element_interface/intan_loader.py | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index 220b408..bc1066d 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -276,18 +276,20 @@ def load_rhs(folder: str, file_expr: str = "*"): if signal_type == "amp": signal = np.memmap(file_path, dtype=np.int16) signal = signal * 0.195 # Convert to microvolts - else: + + elif signal_type == "board": signal = np.memmap(file_path, dtype=np.uint16) - if signal_type == "board": - signal = (signal - 32768) * 0.0003125 # Convert to volts + signal = (signal - 32768) * 0.0003125 # Convert to volts - elif signal_type == "dc": - signal = (signal - 512) * 19.23 # Convert to milivolts + elif signal_type == "dc": + signal = np.memmap(file_path, dtype=np.uint16) + signal = (signal - 512) * 19.23 # Convert to milivolts - elif signal_type == "stim": - i = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] - sign = (128 - np.bitwise_and(signal, 255)) / 128 - signal = i * sign + elif signal_type == "stim": + signal = np.memmap(file_path, dtype=np.uint16) + i = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] + sign = (128 - np.bitwise_and(signal, 255)) / 128 + signal = i * sign rhs_data["recordings"][file_path.stem] = signal return rhs_data From 661b705415c43ad95a053a228d7b1f6a694f9a64 Mon Sep 17 00:00:00 2001 From: JaerongA Date: Fri, 10 Feb 2023 10:19:43 -0600 Subject: [PATCH 15/30] Update element_interface/intan_loader.py fix constant from 255 to 256 Co-authored-by: Tolga Dincer --- element_interface/intan_loader.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index bc1066d..0ae0dbf 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -287,9 +287,9 @@ def load_rhs(folder: str, file_expr: str = "*"): elif signal_type == "stim": signal = np.memmap(file_path, dtype=np.uint16) - i = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] - sign = (128 - np.bitwise_and(signal, 255)) / 128 - signal = i * sign + current = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] + sign = (128 - np.bitwise_and(signal, 256)) / 128 + signal = current * sign rhs_data["recordings"][file_path.stem] = signal return rhs_data From c41260d18fda8b8ae3301f7029bc16aee3316a4e Mon Sep 17 00:00:00 2001 From: JaerongA Date: Fri, 10 Feb 2023 10:24:33 -0600 Subject: [PATCH 16/30] add a comment for the conversion fix --- element_interface/intan_loader.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index 0ae0dbf..dfa3b87 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -276,7 +276,7 @@ def load_rhs(folder: str, file_expr: str = "*"): if signal_type == "amp": signal = np.memmap(file_path, dtype=np.int16) signal = signal * 0.195 # Convert to microvolts - + elif signal_type == "board": signal = np.memmap(file_path, dtype=np.uint16) signal = (signal - 32768) * 0.0003125 # Convert to volts @@ -287,6 +287,7 @@ def load_rhs(folder: str, file_expr: str = "*"): elif signal_type == "stim": signal = np.memmap(file_path, dtype=np.uint16) + # convert the signal from 9-bit one's complement to standard encoding current = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] sign = (128 - np.bitwise_and(signal, 256)) / 128 signal = current * sign From 8b14781d7f852530fbf09d2950cc2151b7154ca1 Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Fri, 10 Feb 2023 13:04:05 -0500 Subject: [PATCH 17/30] Update element_interface/intan_loader.py Co-authored-by: Dimitri Yatsenko --- element_interface/intan_loader.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index dfa3b87..28fb780 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -289,7 +289,7 @@ def load_rhs(folder: str, file_expr: str = "*"): signal = np.memmap(file_path, dtype=np.uint16) # convert the signal from 9-bit one's complement to standard encoding current = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] - sign = (128 - np.bitwise_and(signal, 256)) / 128 + sign = 1 - np.bitwise_and(signal, 256) // 128 signal = current * sign rhs_data["recordings"][file_path.stem] = signal From 9f2221fc057b741eedbb31879b1767e8b4fe80c8 Mon Sep 17 00:00:00 2001 From: JaerongA Date: Fri, 10 Feb 2023 13:19:39 -0600 Subject: [PATCH 18/30] Update element_interface/intan_loader.py Co-authored-by: Dimitri Yatsenko --- element_interface/intan_loader.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index 28fb780..bcdb770 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -264,7 +264,7 @@ def load_rhs(folder: str, file_expr: str = "*"): file_paths = [ file for file in file_paths - if not any([string in file.as_posix() for string in exclude_list]) + if not any(string in file.as_posix() for string in exclude_list) ] # Get recording data From 283aac3d572e6471f2d7b0a2fa4d532012ab4e59 Mon Sep 17 00:00:00 2001 From: JaerongA Date: Mon, 13 Feb 2023 11:16:19 -0600 Subject: [PATCH 19/30] allow reading only info and timestamps --- element_interface/intan_loader.py | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index bcdb770..aa7134f 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -231,7 +231,7 @@ def load_rhs(folder: str, file_expr: str = "*"): Args: folder (str): Folder that contains info.rhs, time.dat, and *.dat files - file_expr (str): regex pattern of the file names to be read. Defaults to "*" (read all files). + file_expr (str): pattern matching of file names to be read. Defaults to "*" (read all files). Returns: rhs_data (dict): RHS data. @@ -258,14 +258,13 @@ def load_rhs(folder: str, file_expr: str = "*"): # Get data files file_paths = Path(folder).glob(file_expr) - if file_expr == "*": - exclude_list = ["time", "info", "Zone.Identifier"] + exclude_list = ["time", "info", "Zone.Identifier"] - file_paths = [ - file - for file in file_paths - if not any(string in file.as_posix() for string in exclude_list) - ] + file_paths = [ + file + for file in file_paths + if not any(string in file.as_posix() for string in exclude_list) + ] # Get recording data rhs_data["recordings"] = {} From 575b8e93890628fdbabfc64acbfa5ce98046ef6a Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Mon, 13 Feb 2023 12:36:35 -0500 Subject: [PATCH 20/30] fix empty file_path --- element_interface/intan_loader.py | 49 ++++++++++++++++--------------- 1 file changed, 26 insertions(+), 23 deletions(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index aa7134f..67ba570 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -269,27 +269,30 @@ def load_rhs(folder: str, file_expr: str = "*"): # Get recording data rhs_data["recordings"] = {} - for file_path in sorted(file_paths): - signal_type = file_path.stem.split("-")[0] - - if signal_type == "amp": - signal = np.memmap(file_path, dtype=np.int16) - signal = signal * 0.195 # Convert to microvolts - - elif signal_type == "board": - signal = np.memmap(file_path, dtype=np.uint16) - signal = (signal - 32768) * 0.0003125 # Convert to volts - - elif signal_type == "dc": - signal = np.memmap(file_path, dtype=np.uint16) - signal = (signal - 512) * 19.23 # Convert to milivolts - - elif signal_type == "stim": - signal = np.memmap(file_path, dtype=np.uint16) - # convert the signal from 9-bit one's complement to standard encoding - current = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] - sign = 1 - np.bitwise_and(signal, 256) // 128 - signal = current * sign - - rhs_data["recordings"][file_path.stem] = signal + if len(file_paths): + for file_path in sorted(file_paths): + signal_type = file_path.stem.split("-")[0] + + if signal_type == "amp": + signal = np.memmap(file_path, dtype=np.int16) + signal = signal * 0.195 # Convert to microvolts + + elif signal_type == "board": + signal = np.memmap(file_path, dtype=np.uint16) + signal = (signal - 32768) * 0.0003125 # Convert to volts + + elif signal_type == "dc": + signal = np.memmap(file_path, dtype=np.uint16) + signal = (signal - 512) * 19.23 # Convert to milivolts + + elif signal_type == "stim": + signal = np.memmap(file_path, dtype=np.uint16) + # convert the signal from 9-bit one's complement to standard encoding + current = ( + np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] + ) + sign = 1 - np.bitwise_and(signal, 256) // 128 + signal = current * sign + + rhs_data["recordings"][file_path.stem] = signal return rhs_data From d1c9c1ceb8417bb7d92957f79db9620887d4c437 Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Mon, 13 Feb 2023 12:37:55 -0500 Subject: [PATCH 21/30] version bump --- CHANGELOG.md | 5 +++++ element_interface/version.py | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 867c5f2..9ec279f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,10 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention. +## [0.6.0] - 2023-02-13 + ++ Add - Intan loader + ## [0.5.0] - 2023-01-09 + Remove - `recursive_search` function @@ -53,6 +57,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and + Add - Readers for: `ScanImage`, `Suite2p`, `CaImAn`. +[0.6.0]: https://github.com/datajoint/element-interface/releases/tag/0.6.0 [0.5.0]: https://github.com/datajoint/element-interface/releases/tag/0.5.0 [0.4.2]: https://github.com/datajoint/element-interface/releases/tag/0.4.2 [0.4.1]: https://github.com/datajoint/element-interface/releases/tag/0.4.1 diff --git a/element_interface/version.py b/element_interface/version.py index 20b1b3e..6d90ece 100644 --- a/element_interface/version.py +++ b/element_interface/version.py @@ -1,3 +1,3 @@ """Package metadata""" -__version__ = "0.5.0" +__version__ = "0.6.0" From 081ed02be20bf4465ebeff676023643301947d41 Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Mon, 13 Feb 2023 12:50:07 -0500 Subject: [PATCH 22/30] remove the condition before if --- element_interface/intan_loader.py | 49 +++++++++++++++---------------- 1 file changed, 23 insertions(+), 26 deletions(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index 67ba570..aa7134f 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -269,30 +269,27 @@ def load_rhs(folder: str, file_expr: str = "*"): # Get recording data rhs_data["recordings"] = {} - if len(file_paths): - for file_path in sorted(file_paths): - signal_type = file_path.stem.split("-")[0] - - if signal_type == "amp": - signal = np.memmap(file_path, dtype=np.int16) - signal = signal * 0.195 # Convert to microvolts - - elif signal_type == "board": - signal = np.memmap(file_path, dtype=np.uint16) - signal = (signal - 32768) * 0.0003125 # Convert to volts - - elif signal_type == "dc": - signal = np.memmap(file_path, dtype=np.uint16) - signal = (signal - 512) * 19.23 # Convert to milivolts - - elif signal_type == "stim": - signal = np.memmap(file_path, dtype=np.uint16) - # convert the signal from 9-bit one's complement to standard encoding - current = ( - np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] - ) - sign = 1 - np.bitwise_and(signal, 256) // 128 - signal = current * sign - - rhs_data["recordings"][file_path.stem] = signal + for file_path in sorted(file_paths): + signal_type = file_path.stem.split("-")[0] + + if signal_type == "amp": + signal = np.memmap(file_path, dtype=np.int16) + signal = signal * 0.195 # Convert to microvolts + + elif signal_type == "board": + signal = np.memmap(file_path, dtype=np.uint16) + signal = (signal - 32768) * 0.0003125 # Convert to volts + + elif signal_type == "dc": + signal = np.memmap(file_path, dtype=np.uint16) + signal = (signal - 512) * 19.23 # Convert to milivolts + + elif signal_type == "stim": + signal = np.memmap(file_path, dtype=np.uint16) + # convert the signal from 9-bit one's complement to standard encoding + current = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] + sign = 1 - np.bitwise_and(signal, 256) // 128 + signal = current * sign + + rhs_data["recordings"][file_path.stem] = signal return rhs_data From 449712acf1dabf5974ee5cb9922b50d25188c0f2 Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Mon, 13 Feb 2023 15:20:11 -0500 Subject: [PATCH 23/30] add source reference --- element_interface/intan_loader.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py index aa7134f..2ff8871 100644 --- a/element_interface/intan_loader.py +++ b/element_interface/intan_loader.py @@ -10,6 +10,8 @@ def _read_qstring(fid): If this number equals 0xFFFFFFFF, the string is null. Strings are stored as unicode. + + SOURCE: https://github.com/Intan-Technologies/load-rhs-notebook-python/blob/main/importrhsutilities.py """ (length,) = struct.unpack(">> rhs_data = load_rhs("/home/inbox/organoids21/032520_US_885kHz_sham", file_expr="amp*dat") From 3d056f2ac7dc04366a0e4c706306b1a6f83de80d Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Tue, 14 Feb 2023 17:37:59 -0500 Subject: [PATCH 24/30] single file loader --- element_interface/intan_loader.py | 302 ----- element_interface/intanloader/COPYING | 674 +++++++++++ element_interface/intanloader/__init__.py | 2 + .../intanloader/rhs_perchannel_loader.py | 85 ++ element_interface/intanloader/rhsutilities.py | 1037 +++++++++++++++++ 5 files changed, 1798 insertions(+), 302 deletions(-) delete mode 100644 element_interface/intan_loader.py create mode 100644 element_interface/intanloader/COPYING create mode 100644 element_interface/intanloader/__init__.py create mode 100644 element_interface/intanloader/rhs_perchannel_loader.py create mode 100644 element_interface/intanloader/rhsutilities.py diff --git a/element_interface/intan_loader.py b/element_interface/intan_loader.py deleted file mode 100644 index 2ff8871..0000000 --- a/element_interface/intan_loader.py +++ /dev/null @@ -1,302 +0,0 @@ -import numpy as np -import os, sys, struct -from pathlib import Path - - -def _read_qstring(fid): - """Read Qt style QString. - - The first 32-bit unsigned number indicates the length of the string (in bytes). - If this number equals 0xFFFFFFFF, the string is null. - - Strings are stored as unicode. - - SOURCE: https://github.com/Intan-Technologies/load-rhs-notebook-python/blob/main/importrhsutilities.py - """ - - (length,) = struct.unpack(" (os.fstat(fid.fileno()).st_size - fid.tell() + 1): - print(length) - raise Exception("Length too long.") - - # convert length from bytes to 16-bit Unicode words - length = int(length / 2) - - data = [] - for i in range(0, length): - (c,) = struct.unpack("= (3, 0): - a = "".join([chr(c) for c in data]) - else: - a = "".join([unichr(c) for c in data]) - - return a - - -def _read_header(fid): - """Reads the Intan File Format header from the given file. - - SOURCE: https://github.com/Intan-Technologies/load-rhs-notebook-python/blob/main/importrhsutilities.py - """ - - # Check 'magic number' at beginning of file to make sure this is an Intan - # Technologies RHD2000 data file. - (magic_number,) = struct.unpack(" 0) and (signal_group_enabled > 0): - for signal_channel in range(0, signal_group_num_channels): - new_channel = { - "port_name": signal_group_name, - "port_prefix": signal_group_prefix, - "port_number": signal_group, - } - new_channel["native_channel_name"] = _read_qstring(fid) - new_channel["custom_channel_name"] = _read_qstring(fid) - ( - new_channel["native_order"], - new_channel["custom_order"], - signal_type, - channel_enabled, - new_channel["chip_channel"], - command_stream, - new_channel["board_stream"], - ) = struct.unpack( - ">> rhs_data = load_rhs("/home/inbox/organoids21/032520_US_885kHz_sham", file_expr="amp*dat") - - # Plot data - >>> import matplotlib.pyplot as plt - >>> plt.plot(rhs_data["time"], rhs_data["recordings"]["amp-B-000.dat"]) - >>> plt.xlabel("Time (s)") - >>> plt.ylabel("Reading") - >>> plt.show() - - Args: - folder (str): Folder that contains info.rhs, time.dat, and *.dat files - file_expr (str): pattern matching of file names to be read. Defaults to "*" (read all files). - - Returns: - rhs_data (dict): RHS data. - rhs_data["header"] (dict): Header. - rhs_data["recordings"] (dict): Readings from various files - rhs_data["timestamps"] (np.array_like): Relative timestamps in seconds. - """ - - rhs_data = {} - - # Get header - header_filepath = next(Path(folder).glob("info.rhs")) - with open(header_filepath, "rb") as fid: - rhs_data["header"] = _read_header(fid) - - # Get timestamps - time_file = next(Path(folder).glob("time.dat")) - - rhs_data["timestamps"] = ( - np.memmap(time_file, dtype=np.int32) - / rhs_data["header"]["frequency_parameters"]["amplifier_sample_rate"] - ) - - # Get data files - file_paths = Path(folder).glob(file_expr) - - exclude_list = ["time", "info", "Zone.Identifier"] - - file_paths = [ - file - for file in file_paths - if not any(string in file.as_posix() for string in exclude_list) - ] - - # Get recording data - rhs_data["recordings"] = {} - - for file_path in sorted(file_paths): - signal_type = file_path.stem.split("-")[0] - - if signal_type == "amp": - signal = np.memmap(file_path, dtype=np.int16) - signal = signal * 0.195 # Convert to microvolts - - elif signal_type == "board": - signal = np.memmap(file_path, dtype=np.uint16) - signal = (signal - 32768) * 0.0003125 # Convert to volts - - elif signal_type == "dc": - signal = np.memmap(file_path, dtype=np.uint16) - signal = (signal - 512) * 19.23 # Convert to milivolts - - elif signal_type == "stim": - signal = np.memmap(file_path, dtype=np.uint16) - # convert the signal from 9-bit one's complement to standard encoding - current = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] - sign = 1 - np.bitwise_and(signal, 256) // 128 - signal = current * sign - - rhs_data["recordings"][file_path.stem] = signal - return rhs_data diff --git a/element_interface/intanloader/COPYING b/element_interface/intanloader/COPYING new file mode 100644 index 0000000..c65825e --- /dev/null +++ b/element_interface/intanloader/COPYING @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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But first, please read +. diff --git a/element_interface/intanloader/__init__.py b/element_interface/intanloader/__init__.py new file mode 100644 index 0000000..e3e8223 --- /dev/null +++ b/element_interface/intanloader/__init__.py @@ -0,0 +1,2 @@ +from .rhs_perchannel_loader import load_rhs +from .rhsutilities import load_file diff --git a/element_interface/intanloader/rhs_perchannel_loader.py b/element_interface/intanloader/rhs_perchannel_loader.py new file mode 100644 index 0000000..3b13683 --- /dev/null +++ b/element_interface/intanloader/rhs_perchannel_loader.py @@ -0,0 +1,85 @@ +import numpy as np +from pathlib import Path +from .rhsutilities import read_header + + +def load_rhs(folder: str, file_expr: str = "*"): + """Load rhs data + + Data type and coversions are based on https://intantech.com/files/Intan_RHS2000_data_file_formats.pdf. + + Example: + # Read data + >>> rhs_data = load_rhs("/home/inbox/organoids21/032520_US_885kHz_sham", file_expr="amp*dat") + + # Plot data + >>> import matplotlib.pyplot as plt + >>> plt.plot(rhs_data["time"], rhs_data["recordings"]["amp-B-000.dat"]) + >>> plt.xlabel("Time (s)") + >>> plt.ylabel("Reading") + >>> plt.show() + + Args: + folder (str): Folder that contains info.rhs, time.dat, and *.dat files + file_expr (str): pattern matching of file names to be read. Defaults to "*" (read all files). + + Returns: + rhs_data (dict): RHS data. + rhs_data["header"] (dict): Header. + rhs_data["recordings"] (dict): Readings from various files + rhs_data["timestamps"] (np.array_like): Relative timestamps in seconds. + """ + + rhs_data = {} + + # Get header + header_filepath = next(Path(folder).glob("info.rhs")) + with open(header_filepath, "rb") as fid: + rhs_data["header"] = read_header(fid) + + # Get timestamps + time_file = next(Path(folder).glob("time.dat")) + + rhs_data["timestamps"] = ( + np.memmap(time_file, dtype=np.int32) + / rhs_data["header"]["frequency_parameters"]["amplifier_sample_rate"] + ) + + # Get data files + file_paths = Path(folder).glob(file_expr) + + exclude_list = ["time", "info", "Zone.Identifier"] + + file_paths = [ + file + for file in file_paths + if not any(string in file.as_posix() for string in exclude_list) + ] + + # Get recording data + rhs_data["recordings"] = {} + + for file_path in sorted(file_paths): + signal_type = file_path.stem.split("-")[0] + + if signal_type == "amp": + signal = np.memmap(file_path, dtype=np.int16) + signal = signal * 0.195 # Convert to microvolts + + elif signal_type == "board": + signal = np.memmap(file_path, dtype=np.uint16) + signal = (signal - 32768) * 0.0003125 # Convert to volts + + elif signal_type == "dc": + signal = np.memmap(file_path, dtype=np.uint16) + signal = (signal - 512) * 19.23 # Convert to milivolts + + elif signal_type == "stim": + signal = np.memmap(file_path, dtype=np.uint16) + # convert the signal from 9-bit one's complement to standard encoding + current = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] + sign = 1 - np.bitwise_and(signal, 256) // 128 + signal = current * sign + + rhs_data["recordings"][file_path.stem] = signal + return rhs_data diff --git a/element_interface/intanloader/rhsutilities.py b/element_interface/intanloader/rhsutilities.py new file mode 100644 index 0000000..e90cf76 --- /dev/null +++ b/element_interface/intanloader/rhsutilities.py @@ -0,0 +1,1037 @@ +import sys, struct, math, os, time +import numpy as np +import matplotlib.pyplot as plt + +# Define plural function +def plural(n): + """Utility function to optionally pluralize words based on the value of n.""" + + if n == 1: + return "" + else: + return "s" + + +# Define read_qstring function +def read_qstring(fid): + """Read Qt style QString. + + The first 32-bit unsigned number indicates the length of the string (in bytes). + If this number equals 0xFFFFFFFF, the string is null. + + Strings are stored as unicode. + """ + + (length,) = struct.unpack(" (os.fstat(fid.fileno()).st_size - fid.tell() + 1): + print(length) + raise Exception("Length too long.") + + # convert length from bytes to 16-bit Unicode words + length = int(length / 2) + + data = [] + for i in range(0, length): + (c,) = struct.unpack("= (3, 0): + a = "".join([chr(c) for c in data]) + else: + a = "".join([unichr(c) for c in data]) + + return a + + +# Define read_header function +def read_header(fid): + """Reads the Intan File Format header from the given file.""" + + # Check 'magic number' at beginning of file to make sure this is an Intan + # Technologies RHD2000 data file. + (magic_number,) = struct.unpack(" 0) and (signal_group_enabled > 0): + for signal_channel in range(0, signal_group_num_channels): + new_channel = { + "port_name": signal_group_name, + "port_prefix": signal_group_prefix, + "port_number": signal_group, + } + new_channel["native_channel_name"] = read_qstring(fid) + new_channel["custom_channel_name"] = read_qstring(fid) + ( + new_channel["native_order"], + new_channel["custom_order"], + signal_type, + channel_enabled, + new_channel["chip_channel"], + command_stream, + new_channel["board_stream"], + ) = struct.unpack( + " 0: + bytes_per_block += N * 2 * header["num_amplifier_channels"] + + # Stimulation data, one per enabled amplifier channels + bytes_per_block += N * 2 * header["num_amplifier_channels"] + + # Board analog inputs are sampled at same rate as amplifiers + bytes_per_block += N * 2 * header["num_board_adc_channels"] + + # Board analog outputs are sampled at same rate as amplifiers + bytes_per_block += N * 2 * header["num_board_dac_channels"] + + # Board digital inputs are sampled at same rate as amplifiers + if header["num_board_dig_in_channels"] > 0: + bytes_per_block += N * 2 + + # Board digital outputs are sampled at same rate as amplifiers + if header["num_board_dig_out_channels"] > 0: + bytes_per_block += N * 2 + + return bytes_per_block + + +# Define read_one_data_block function +def read_one_data_block(data, header, indices, fid): + """Reads one 128-sample data block from fid into data, at the location indicated by indices.""" + + data["t"][indices["amplifier"] : (indices["amplifier"] + 128)] = np.array( + struct.unpack("<" + "i" * 128, fid.read(128 * 4)) + ) + + if header["num_amplifier_channels"] > 0: + tmp = np.fromfile( + fid, dtype="uint16", count=128 * header["num_amplifier_channels"] + ) + data["amplifier_data"][ + range(header["num_amplifier_channels"]), + indices["amplifier"] : (indices["amplifier"] + 128), + ] = tmp.reshape(header["num_amplifier_channels"], 128) + + # check if dc amplifier voltage was saved + if header["dc_amplifier_data_saved"]: + tmp = np.fromfile( + fid, dtype="uint16", count=128 * header["num_amplifier_channels"] + ) + data["dc_amplifier_data"][ + range(header["num_amplifier_channels"]), + indices["amplifier"] : (indices["amplifier"] + 128), + ] = tmp.reshape(header["num_amplifier_channels"], 128) + + # get the stimulation data + tmp = np.fromfile( + fid, dtype="uint16", count=128 * header["num_amplifier_channels"] + ) + data["stim_data_raw"][ + range(header["num_amplifier_channels"]), + indices["amplifier"] : (indices["amplifier"] + 128), + ] = tmp.reshape(header["num_amplifier_channels"], 128) + + if header["num_board_adc_channels"] > 0: + tmp = np.fromfile( + fid, dtype="uint16", count=128 * header["num_board_adc_channels"] + ) + data["board_adc_data"][ + range(header["num_board_adc_channels"]), + indices["board_adc"] : (indices["board_adc"] + 128), + ] = tmp.reshape(header["num_board_adc_channels"], 128) + + if header["num_board_dac_channels"] > 0: + tmp = np.fromfile( + fid, dtype="uint16", count=128 * header["num_board_dac_channels"] + ) + data["board_dac_data"][ + range(header["num_board_dac_channels"]), + indices["board_dac"] : (indices["board_dac"] + 128), + ] = tmp.reshape(header["num_board_dac_channels"], 128) + + if header["num_board_dig_in_channels"] > 0: + data["board_dig_in_raw"][ + indices["board_dig_in"] : (indices["board_dig_in"] + 128) + ] = np.array(struct.unpack("<" + "H" * 128, fid.read(256))) + + if header["num_board_dig_out_channels"] > 0: + data["board_dig_out_raw"][ + indices["board_dig_out"] : (indices["board_dig_out"] + 128) + ] = np.array(struct.unpack("<" + "H" * 128, fid.read(256))) + + +# Define data_to_result function +def data_to_result(header, data, data_present): + """Moves the header and data (if present) into a common object.""" + + result = {} + + stim_parameters = {} + stim_parameters["stim_step_size"] = header["stim_step_size"] + stim_parameters["charge_recovery_current_limit"] = header["recovery_current_limit"] + stim_parameters["charge_recovery_target_voltage"] = header[ + "recovery_target_voltage" + ] + stim_parameters["amp_settle_mode"] = header["amp_settle_mode"] + stim_parameters["charge_recovery_mode"] = header["charge_recovery_mode"] + result["stim_parameters"] = stim_parameters + + result["stim_channels"] = header["stim_channels"] + result["spike_triggers"] = header["spike_triggers"] + result["notes"] = header["notes"] + result["frequency_parameters"] = header["frequency_parameters"] + + result["reference_channel"] = header["reference_channel"] + result["amplifier_channels"] = header["amplifier_channels"] + result["board_adc_channels"] = header["board_adc_channels"] + result["board_dac_channels"] = header["board_dac_channels"] + + result["dc_amplifier_data_saved"] = header["dc_amplifier_data_saved"] + if header["dc_amplifier_data_saved"]: + result["dc_amplifier_channels"] = header["dc_amplifier_channels"] + + result["compliance_limit_channels"] = header["compliance_limit_channels"] + result["charge_recovery_channels"] = header["charge_recovery_channels"] + result["amp_settle_channels"] = header["amp_settle_channels"] + result["board_dig_in_channels"] = header["board_dig_in_channels"] + result["board_dig_out_channels"] = header["board_dig_out_channels"] + + if data_present > 0: + result["t"] = data["t"] + result["stim_data"] = data["stim_data"] + result["amplifier_data"] = data["amplifier_data"] + result["board_adc_data"] = data["board_adc_data"] + result["board_dac_data"] = data["board_dac_data"] + if header["dc_amplifier_data_saved"] > 0: + result["dc_amplifier_data"] = data["dc_amplifier_data"] + result["compliance_limit_data"] = data["compliance_limit_data"] + result["charge_recovery_data"] = data["charge_recovery_data"] + result["amp_settle_data"] = data["amp_settle_data"] + result["board_dig_in_data"] = data["board_dig_in_data"] + result["board_dig_out_data"] = data["board_dig_out_data"] + + return result + + +# Define plot_channel function +def plot_channel(channel_name, result): + # Find channel that corresponds to this name + channel_found, signal_type, signal_index = find_channel_in_header( + channel_name, result + ) + + # Plot this channel + if channel_found: + fig, ax = plt.subplots() + ax.set_title(channel_name) + ax.set_xlabel("Time (s)") + + if signal_type == "amplifier_channels": + ylabel = "Voltage (microVolts)" + signal_data_name = "amplifier_data" + + elif signal_type == "dc_amplifier_channels": + ylabel = "Voltage (Volts)" + signal_data_name = "dc_amplifier_data" + + elif signal_type == "stim_channels": + ylabel = "Current (microAmps)" + signal_data_name = "stim_data" + + elif signal_type == "amp_settle_channels": + ylabel = "Amp Settle Events (High or Low)" + signal_data_name = "amp_settle_data" + + elif signal_type == "charge_recovery_channels": + ylabel = "Charge Recovery Events (High or Low)" + signal_data_name = "charge_recovery_data" + + elif signal_type == "compliance_limit_channels": + ylabel = "Compliance Limit Events (High or Low)" + signal_data_name = "compliance_limit_data" + + elif signal_type == "board_adc_channels": + ylabel = "Voltage (Volts)" + signal_data_name = "board_adc_data" + + elif signal_type == "board_dac_channels": + ylabel = "Voltage (Volts)" + signal_data_name = "board_dac_data" + + elif signal_type == "board_dig_in_channels": + ylabel = "Digital In Events (High or Low)" + signal_data_name = "board_dig_in_data" + + elif signal_type == "board_dig_out_channels": + ylabel = "Digital Out Events (High or Low)" + signal_data_name = "board_dig_out_data" + + else: + raise Exception( + "Plotting not possible; signal type ", signal_type, " not found" + ) + + ax.set_ylabel(ylabel) + + ax.plot(result["t"], result[signal_data_name][signal_index, :]) + ax.margins(x=0, y=0) + + else: + raise Exception("Plotting not possible; channel ", channel_name, " not found") + + +# Define load_file function +def load_file(filename): + # Start timing + tic = time.time() + + # Open file + fid = open(filename, "rb") + filesize = os.path.getsize(filename) + + # Read file header + header = read_header(fid) + + # Output a summary of recorded data + print( + "Found {} amplifier channel{}.".format( + header["num_amplifier_channels"], plural(header["num_amplifier_channels"]) + ) + ) + print( + "Found {} board ADC channel{}.".format( + header["num_board_adc_channels"], plural(header["num_board_adc_channels"]) + ) + ) + print( + "Found {} board DAC channel{}.".format( + header["num_board_dac_channels"], plural(header["num_board_dac_channels"]) + ) + ) + print( + "Found {} board digital input channel{}.".format( + header["num_board_dig_in_channels"], + plural(header["num_board_dig_in_channels"]), + ) + ) + print( + "Found {} board digital output channel{}.".format( + header["num_board_dig_out_channels"], + plural(header["num_board_dig_out_channels"]), + ) + ) + print("") + + # Determine how many samples the data file contains + bytes_per_block = get_bytes_per_data_block(header) + print("{} bytes per data block".format(bytes_per_block)) + # How many data blocks remain in this file? + data_present = False + bytes_remaining = filesize - fid.tell() + if bytes_remaining > 0: + data_present = True + + if bytes_remaining % bytes_per_block != 0: + raise Exception( + "Something is wrong with file size : should have a whole number of data blocks" + ) + + num_data_blocks = int(bytes_remaining / bytes_per_block) + + # Calculate how many samples of each signal type are present + num_amplifier_samples = 128 * num_data_blocks + num_board_adc_samples = 128 * num_data_blocks + num_board_dac_samples = 128 * num_data_blocks + num_board_dig_in_samples = 128 * num_data_blocks + num_board_dig_out_samples = 128 * num_data_blocks + + record_time = num_amplifier_samples / header["sample_rate"] + + # Output a summary of contents of header file + if data_present: + print( + "File contains {:0.3f} seconds of data. Amplifiers were sampled at {:0.2f} kS/s.".format( + record_time, header["sample_rate"] / 1000 + ) + ) + else: + print( + "Header file contains no data. Amplifiers were sampled at {:0.2f} kS/s.".format( + header["sample_rate"] / 1000 + ) + ) + + if data_present: + # Pre-allocate memory for data + print("") + print("Allocating memory for data...") + + data = {} + data["t"] = np.zeros(num_amplifier_samples, dtype=np.int_) + + data["amplifier_data"] = np.zeros( + [header["num_amplifier_channels"], num_amplifier_samples], dtype=np.uint + ) + + if header["dc_amplifier_data_saved"]: + data["dc_amplifier_data"] = ( + np.zeros( + [header["num_amplifier_channels"], num_amplifier_samples], + dtype=np.uint, + ) + * header["dc_amplifier_data_saved"] + ) + + data["stim_data_raw"] = np.zeros( + [header["num_amplifier_channels"], num_amplifier_samples], dtype=np.int_ + ) + data["stim_data"] = np.zeros( + [header["num_amplifier_channels"], num_amplifier_samples], dtype=np.int_ + ) + + data["board_adc_data"] = np.zeros( + [header["num_board_adc_channels"], num_board_adc_samples], dtype=np.uint + ) + data["board_dac_data"] = np.zeros( + [header["num_board_dac_channels"], num_board_dac_samples], dtype=np.uint + ) + + # by default, this script interprets digital events (digital inputs and outputs) as booleans + # if unsigned int values are preferred(0 for False, 1 for True), replace the 'dtype=np.bool_' argument with 'dtype=np.uint' as shown + # the commented line below illustrates this for digital input data; the same can be done for digital out + + # data['board_dig_in_data'] = np.zeros([header['num_board_dig_in_channels'], num_board_dig_in_samples], dtype=np.uint) + data["board_dig_in_data"] = np.zeros( + [header["num_board_dig_in_channels"], num_board_dig_in_samples], + dtype=np.bool_, + ) + data["board_dig_in_raw"] = np.zeros(num_board_dig_in_samples, dtype=np.uint) + data["board_dig_out_data"] = np.zeros( + [header["num_board_dig_out_channels"], num_board_dig_out_samples], + dtype=np.bool_, + ) + data["board_dig_out_raw"] = np.zeros(num_board_dig_out_samples, dtype=np.uint) + + # Read sampled data from file. + print("Reading data from file...") + + # Initialize indices used in looping + indices = {} + indices["amplifier"] = 0 + indices["board_adc"] = 0 + indices["board_dac"] = 0 + indices["board_dig_in"] = 0 + indices["board_dig_out"] = 0 + + print_increment = 10 + percent_done = print_increment + for i in range(num_data_blocks): + read_one_data_block(data, header, indices, fid) + # Increment all indices in 128 + indices = {k: v + 128 for k, v in indices.items()} + + fraction_done = 100 * (1.0 * i / num_data_blocks) + if fraction_done >= percent_done: + print("{}% done...".format(percent_done)) + percent_done = percent_done + print_increment + + print("100% done...") + + # Make sure we have read exactly the right amount of data + bytes_remaining = filesize - fid.tell() + if bytes_remaining != 0: + raise Exception("Error: End of file not reached.") + + fid.close() + + if data_present: + print("Parsing data...") + + # Extract digital input channels to separate variables. + for i in range(header["num_board_dig_in_channels"]): + data["board_dig_in_data"][i, :] = np.not_equal( + np.bitwise_and( + data["board_dig_in_raw"], + (1 << header["board_dig_in_channels"][i]["native_order"]), + ), + 0, + ) + + # Extract digital output channels to separate variables. + for i in range(header["num_board_dig_out_channels"]): + data["board_dig_out_data"][i, :] = np.not_equal( + np.bitwise_and( + data["board_dig_out_raw"], + (1 << header["board_dig_out_channels"][i]["native_order"]), + ), + 0, + ) + + # Extract stimulation data + data["compliance_limit_data"] = ( + np.bitwise_and(data["stim_data_raw"], 32768) >= 1 + ) # get 2^15 bit, interpret as True or False + data["charge_recovery_data"] = ( + np.bitwise_and(data["stim_data_raw"], 16384) >= 1 + ) # get 2^14 bit, interpret as True or False + data["amp_settle_data"] = ( + np.bitwise_and(data["stim_data_raw"], 8192) >= 1 + ) # get 2^13 bit, interpret as True or False + data["stim_polarity"] = 1 - ( + 2 * (np.bitwise_and(data["stim_data_raw"], 256) >> 8) + ) # get 2^8 bit, interpret as +1 for 0_bit or -1 for 1_bit + + curr_amp = np.bitwise_and( + data["stim_data_raw"], 255 + ) # get least-significant 8 bits corresponding to the current amplitude + data["stim_data"] = ( + curr_amp * data["stim_polarity"] + ) # multiply current amplitude by the correct sign + + # # Scale voltage levels appropriately. + data["amplifier_data"] = np.multiply( + 0.195, (data["amplifier_data"].astype(np.int32) - 32768) + ) # units = microvolts + data["stim_data"] = np.multiply( + header["stim_step_size"], data["stim_data"] / 1.0e-6 + ) + + if header["dc_amplifier_data_saved"]: + data["dc_amplifier_data"] = np.multiply( + -0.01923, (data["dc_amplifier_data"].astype(np.int32) - 512) + ) # units = volts + + data["board_adc_data"] = np.multiply( + 0.0003125, (data["board_adc_data"].astype(np.int32) - 32768) + ) # units = volts + data["board_dac_data"] = np.multiply( + 0.0003125, (data["board_dac_data"].astype(np.int32) - 32768) + ) # units = volts + + # Check for gaps in timestamps. + num_gaps = np.sum(np.not_equal(data["t"][1:] - data["t"][:-1], 1)) + if num_gaps == 0: + print("No missing timestamps in data.") + else: + print( + "Warning: {0} gaps in timestamp data found. Time scale will not be uniform!".format( + num_gaps + ) + ) + + # Scale time steps (units = seconds). + data["t"] = data["t"] / header["sample_rate"] + + # If the software notch filter was selected during the recording, apply the + # same notch filter to amplifier data here. + if header["notch_filter_frequency"] > 0 and header["version"]["major"] < 3: + print_increment = 10 + percent_done = print_increment + for i in range(header["num_amplifier_channels"]): + data["amplifier_data"][i, :] = notch_filter( + data["amplifier_data"][i, :], + header["sample_rate"], + header["notch_filter_frequency"], + 10, + ) + if fraction_done >= percent_done: + print("{}% done...".format(percent_done)) + percent_done = percent_done + print_increment + else: + data = [] + + # Move variables to result struct. + result = data_to_result(header, data, data_present) + + print("Done! Elapsed time: {0:0.1f} seconds".format(time.time() - tic)) + + return result, data_present + + +# Define function print_all_channel_names +def print_all_channel_names(result): + + # Print all amplifier_channels + if "amplifier_channels" in result: + print_names_in_group(result["amplifier_channels"]) + + # Print all dc_amplifier_channels + if "dc_amplifier_channels" in result: + print_names_in_group(result["dc_amplifier_channels"]) + + # Print all stim_channels + if "stim_channels" in result: + print_names_in_group(result["stim_channels"]) + + # Print all amp_settle_channels + if "amp_settle_channels" in result: + print_names_in_group(result["amp_settle_channels"]) + + # Print all charge_recovery_channels + if "charge_recovery_channels" in result: + print_names_in_group(result["charge_recovery_channels"]) + + # Print all compliance_limit_channels + if "compliance_limit_channels" in result: + print_names_in_group(result["compliance_limit_channels"]) + + # Print all board_adc_channels + if "board_adc_channels" in result: + print_names_in_group(result["board_adc_channels"]) + + # Print all board_dac_channels + if "board_dac_channels" in result: + print_names_in_group(result["board_dac_channels"]) + + # Print all board_dig_in_channels + if "board_dig_in_channels" in result: + print_names_in_group(result["board_dig_in_channels"]) + + # Print all board_dig_out_channels + if "board_dig_out_channels" in result: + print_names_in_group(result["board_dig_out_channels"]) + + +# Define function print_names_in_group +def print_names_in_group(signal_group): + for this_channel in signal_group: + print(this_channel["custom_channel_name"]) From 1f9982768028df5e367b481025f75aded743f5b4 Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Wed, 15 Feb 2023 11:31:19 -0500 Subject: [PATCH 25/30] add code source --- element_interface/intanloader/rhsutilities.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/element_interface/intanloader/rhsutilities.py b/element_interface/intanloader/rhsutilities.py index e90cf76..5d0bae1 100644 --- a/element_interface/intanloader/rhsutilities.py +++ b/element_interface/intanloader/rhsutilities.py @@ -2,6 +2,9 @@ import numpy as np import matplotlib.pyplot as plt +# All the code in this file is taken from https://github.com/Intan-Technologies/load-rhs-notebook-python. +# The original license of the code is the COPYING file under the same directory. + # Define plural function def plural(n): """Utility function to optionally pluralize words based on the value of n.""" From 1fe2997b3c65e05afbf6ebf46ce3fa0037439556 Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Wed, 15 Feb 2023 11:50:38 -0500 Subject: [PATCH 26/30] Update element_interface/intanloader/rhsutilities.py Co-authored-by: JaerongA --- element_interface/intanloader/rhsutilities.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/element_interface/intanloader/rhsutilities.py b/element_interface/intanloader/rhsutilities.py index 5d0bae1..46bed7a 100644 --- a/element_interface/intanloader/rhsutilities.py +++ b/element_interface/intanloader/rhsutilities.py @@ -987,7 +987,7 @@ def load_file(filename): print("Done! Elapsed time: {0:0.1f} seconds".format(time.time() - tic)) - return result, data_present + return result # Define function print_all_channel_names From ec59cff9d1af57dc06af5027363149c191954007 Mon Sep 17 00:00:00 2001 From: JaerongA Date: Wed, 15 Feb 2023 13:02:40 -0600 Subject: [PATCH 27/30] output header --- element_interface/intanloader/rhsutilities.py | 1 + 1 file changed, 1 insertion(+) diff --git a/element_interface/intanloader/rhsutilities.py b/element_interface/intanloader/rhsutilities.py index 46bed7a..a04e442 100644 --- a/element_interface/intanloader/rhsutilities.py +++ b/element_interface/intanloader/rhsutilities.py @@ -651,6 +651,7 @@ def data_to_result(header, data, data_present): result["amp_settle_data"] = data["amp_settle_data"] result["board_dig_in_data"] = data["board_dig_in_data"] result["board_dig_out_data"] = data["board_dig_out_data"] + result["header"] = header return result From 947d27b36c78a8e2ba1ec7fdc92b4224f1032b3e Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Thu, 16 Feb 2023 15:15:51 -0500 Subject: [PATCH 28/30] change import --- element_interface/rhs_perchannel_loader.py | 80 ++++++++++++++++++++++ 1 file changed, 80 insertions(+) create mode 100644 element_interface/rhs_perchannel_loader.py diff --git a/element_interface/rhs_perchannel_loader.py b/element_interface/rhs_perchannel_loader.py new file mode 100644 index 0000000..6e77e98 --- /dev/null +++ b/element_interface/rhs_perchannel_loader.py @@ -0,0 +1,80 @@ +import numpy as np +from pathlib import Path +from intanrhsreader import read_header + + +def load_rhs(folder: str, file_expr: str = "*"): + """Load rhs data + + Data type and coversions are based on https://intantech.com/files/Intan_RHS2000_data_file_formats.pdf. + + Example: + # Read data + >>> rhs_data = load_rhs("/home/inbox/organoids21/032520_US_885kHz_sham", file_expr="amp*dat") + + # Plot data + >>> import matplotlib.pyplot as plt + >>> plt.plot(rhs_data["time"], rhs_data["recordings"]["amp-B-000.dat"]) + >>> plt.xlabel("Time (s)") + >>> plt.ylabel("Reading") + >>> plt.show() + + Args: + folder (str): Folder that contains info.rhs, time.dat, and *.dat files + file_expr (str): pattern matching of file names to be read. Defaults to "*" (read all files). + + Returns: + rhs_data (dict): RHS data. + rhs_data["header"] (dict): Header. + rhs_data["recordings"] (dict): Readings from various files + rhs_data["timestamps"] (np.array_like): Relative timestamps in seconds. + """ + + rhs_data = {} + + # Get header + header_filepath = next(Path(folder).glob("info.rhs")) + with open(header_filepath, "rb") as fid: + rhs_data["header"] = read_header(fid) + + # Get timestamps + time_file = next(Path(folder).glob("time.dat")) + + rhs_data["timestamps"] = ( + np.memmap(time_file, dtype=np.int32) / rhs_data["header"]["frequency_parameters"]["amplifier_sample_rate"] + ) + + # Get data files + file_paths = Path(folder).glob(file_expr) + + exclude_list = ["time", "info", "Zone.Identifier"] + + file_paths = [file for file in file_paths if not any(string in file.as_posix() for string in exclude_list)] + + # Get recording data + rhs_data["recordings"] = {} + + for file_path in sorted(file_paths): + signal_type = file_path.stem.split("-")[0] + + if signal_type == "amp": + signal = np.memmap(file_path, dtype=np.int16) + signal = signal * 0.195 # Convert to microvolts + + elif signal_type == "board": + signal = np.memmap(file_path, dtype=np.uint16) + signal = (signal - 32768) * 0.0003125 # Convert to volts + + elif signal_type == "dc": + signal = np.memmap(file_path, dtype=np.uint16) + signal = (signal - 512) * 19.23 # Convert to milivolts + + elif signal_type == "stim": + signal = np.memmap(file_path, dtype=np.uint16) + # convert the signal from 9-bit one's complement to standard encoding + current = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] + sign = 1 - np.bitwise_and(signal, 256) // 128 + signal = current * sign + + rhs_data["recordings"][file_path.stem] = signal + return rhs_data From 00c9ac7134b70794c94ce2066ff2cc04bdd37f6b Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Thu, 16 Feb 2023 15:17:07 -0500 Subject: [PATCH 29/30] remove module --- element_interface/intanloader/COPYING | 674 ----------- element_interface/intanloader/__init__.py | 2 - .../intanloader/rhs_perchannel_loader.py | 85 -- element_interface/intanloader/rhsutilities.py | 1041 ----------------- 4 files changed, 1802 deletions(-) delete mode 100644 element_interface/intanloader/COPYING delete mode 100644 element_interface/intanloader/__init__.py delete mode 100644 element_interface/intanloader/rhs_perchannel_loader.py delete mode 100644 element_interface/intanloader/rhsutilities.py diff --git a/element_interface/intanloader/COPYING b/element_interface/intanloader/COPYING deleted file mode 100644 index c65825e..0000000 --- a/element_interface/intanloader/COPYING +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. - - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. diff --git a/element_interface/intanloader/__init__.py b/element_interface/intanloader/__init__.py deleted file mode 100644 index e3e8223..0000000 --- a/element_interface/intanloader/__init__.py +++ /dev/null @@ -1,2 +0,0 @@ -from .rhs_perchannel_loader import load_rhs -from .rhsutilities import load_file diff --git a/element_interface/intanloader/rhs_perchannel_loader.py b/element_interface/intanloader/rhs_perchannel_loader.py deleted file mode 100644 index 3b13683..0000000 --- a/element_interface/intanloader/rhs_perchannel_loader.py +++ /dev/null @@ -1,85 +0,0 @@ -import numpy as np -from pathlib import Path -from .rhsutilities import read_header - - -def load_rhs(folder: str, file_expr: str = "*"): - """Load rhs data - - Data type and coversions are based on https://intantech.com/files/Intan_RHS2000_data_file_formats.pdf. - - Example: - # Read data - >>> rhs_data = load_rhs("/home/inbox/organoids21/032520_US_885kHz_sham", file_expr="amp*dat") - - # Plot data - >>> import matplotlib.pyplot as plt - >>> plt.plot(rhs_data["time"], rhs_data["recordings"]["amp-B-000.dat"]) - >>> plt.xlabel("Time (s)") - >>> plt.ylabel("Reading") - >>> plt.show() - - Args: - folder (str): Folder that contains info.rhs, time.dat, and *.dat files - file_expr (str): pattern matching of file names to be read. Defaults to "*" (read all files). - - Returns: - rhs_data (dict): RHS data. - rhs_data["header"] (dict): Header. - rhs_data["recordings"] (dict): Readings from various files - rhs_data["timestamps"] (np.array_like): Relative timestamps in seconds. - """ - - rhs_data = {} - - # Get header - header_filepath = next(Path(folder).glob("info.rhs")) - with open(header_filepath, "rb") as fid: - rhs_data["header"] = read_header(fid) - - # Get timestamps - time_file = next(Path(folder).glob("time.dat")) - - rhs_data["timestamps"] = ( - np.memmap(time_file, dtype=np.int32) - / rhs_data["header"]["frequency_parameters"]["amplifier_sample_rate"] - ) - - # Get data files - file_paths = Path(folder).glob(file_expr) - - exclude_list = ["time", "info", "Zone.Identifier"] - - file_paths = [ - file - for file in file_paths - if not any(string in file.as_posix() for string in exclude_list) - ] - - # Get recording data - rhs_data["recordings"] = {} - - for file_path in sorted(file_paths): - signal_type = file_path.stem.split("-")[0] - - if signal_type == "amp": - signal = np.memmap(file_path, dtype=np.int16) - signal = signal * 0.195 # Convert to microvolts - - elif signal_type == "board": - signal = np.memmap(file_path, dtype=np.uint16) - signal = (signal - 32768) * 0.0003125 # Convert to volts - - elif signal_type == "dc": - signal = np.memmap(file_path, dtype=np.uint16) - signal = (signal - 512) * 19.23 # Convert to milivolts - - elif signal_type == "stim": - signal = np.memmap(file_path, dtype=np.uint16) - # convert the signal from 9-bit one's complement to standard encoding - current = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"] - sign = 1 - np.bitwise_and(signal, 256) // 128 - signal = current * sign - - rhs_data["recordings"][file_path.stem] = signal - return rhs_data diff --git a/element_interface/intanloader/rhsutilities.py b/element_interface/intanloader/rhsutilities.py deleted file mode 100644 index a04e442..0000000 --- a/element_interface/intanloader/rhsutilities.py +++ /dev/null @@ -1,1041 +0,0 @@ -import sys, struct, math, os, time -import numpy as np -import matplotlib.pyplot as plt - -# All the code in this file is taken from https://github.com/Intan-Technologies/load-rhs-notebook-python. -# The original license of the code is the COPYING file under the same directory. - -# Define plural function -def plural(n): - """Utility function to optionally pluralize words based on the value of n.""" - - if n == 1: - return "" - else: - return "s" - - -# Define read_qstring function -def read_qstring(fid): - """Read Qt style QString. - - The first 32-bit unsigned number indicates the length of the string (in bytes). - If this number equals 0xFFFFFFFF, the string is null. - - Strings are stored as unicode. - """ - - (length,) = struct.unpack(" (os.fstat(fid.fileno()).st_size - fid.tell() + 1): - print(length) - raise Exception("Length too long.") - - # convert length from bytes to 16-bit Unicode words - length = int(length / 2) - - data = [] - for i in range(0, length): - (c,) = struct.unpack("= (3, 0): - a = "".join([chr(c) for c in data]) - else: - a = "".join([unichr(c) for c in data]) - - return a - - -# Define read_header function -def read_header(fid): - """Reads the Intan File Format header from the given file.""" - - # Check 'magic number' at beginning of file to make sure this is an Intan - # Technologies RHD2000 data file. - (magic_number,) = struct.unpack(" 0) and (signal_group_enabled > 0): - for signal_channel in range(0, signal_group_num_channels): - new_channel = { - "port_name": signal_group_name, - "port_prefix": signal_group_prefix, - "port_number": signal_group, - } - new_channel["native_channel_name"] = read_qstring(fid) - new_channel["custom_channel_name"] = read_qstring(fid) - ( - new_channel["native_order"], - new_channel["custom_order"], - signal_type, - channel_enabled, - new_channel["chip_channel"], - command_stream, - new_channel["board_stream"], - ) = struct.unpack( - " 0: - bytes_per_block += N * 2 * header["num_amplifier_channels"] - - # Stimulation data, one per enabled amplifier channels - bytes_per_block += N * 2 * header["num_amplifier_channels"] - - # Board analog inputs are sampled at same rate as amplifiers - bytes_per_block += N * 2 * header["num_board_adc_channels"] - - # Board analog outputs are sampled at same rate as amplifiers - bytes_per_block += N * 2 * header["num_board_dac_channels"] - - # Board digital inputs are sampled at same rate as amplifiers - if header["num_board_dig_in_channels"] > 0: - bytes_per_block += N * 2 - - # Board digital outputs are sampled at same rate as amplifiers - if header["num_board_dig_out_channels"] > 0: - bytes_per_block += N * 2 - - return bytes_per_block - - -# Define read_one_data_block function -def read_one_data_block(data, header, indices, fid): - """Reads one 128-sample data block from fid into data, at the location indicated by indices.""" - - data["t"][indices["amplifier"] : (indices["amplifier"] + 128)] = np.array( - struct.unpack("<" + "i" * 128, fid.read(128 * 4)) - ) - - if header["num_amplifier_channels"] > 0: - tmp = np.fromfile( - fid, dtype="uint16", count=128 * header["num_amplifier_channels"] - ) - data["amplifier_data"][ - range(header["num_amplifier_channels"]), - indices["amplifier"] : (indices["amplifier"] + 128), - ] = tmp.reshape(header["num_amplifier_channels"], 128) - - # check if dc amplifier voltage was saved - if header["dc_amplifier_data_saved"]: - tmp = np.fromfile( - fid, dtype="uint16", count=128 * header["num_amplifier_channels"] - ) - data["dc_amplifier_data"][ - range(header["num_amplifier_channels"]), - indices["amplifier"] : (indices["amplifier"] + 128), - ] = tmp.reshape(header["num_amplifier_channels"], 128) - - # get the stimulation data - tmp = np.fromfile( - fid, dtype="uint16", count=128 * header["num_amplifier_channels"] - ) - data["stim_data_raw"][ - range(header["num_amplifier_channels"]), - indices["amplifier"] : (indices["amplifier"] + 128), - ] = tmp.reshape(header["num_amplifier_channels"], 128) - - if header["num_board_adc_channels"] > 0: - tmp = np.fromfile( - fid, dtype="uint16", count=128 * header["num_board_adc_channels"] - ) - data["board_adc_data"][ - range(header["num_board_adc_channels"]), - indices["board_adc"] : (indices["board_adc"] + 128), - ] = tmp.reshape(header["num_board_adc_channels"], 128) - - if header["num_board_dac_channels"] > 0: - tmp = np.fromfile( - fid, dtype="uint16", count=128 * header["num_board_dac_channels"] - ) - data["board_dac_data"][ - range(header["num_board_dac_channels"]), - indices["board_dac"] : (indices["board_dac"] + 128), - ] = tmp.reshape(header["num_board_dac_channels"], 128) - - if header["num_board_dig_in_channels"] > 0: - data["board_dig_in_raw"][ - indices["board_dig_in"] : (indices["board_dig_in"] + 128) - ] = np.array(struct.unpack("<" + "H" * 128, fid.read(256))) - - if header["num_board_dig_out_channels"] > 0: - data["board_dig_out_raw"][ - indices["board_dig_out"] : (indices["board_dig_out"] + 128) - ] = np.array(struct.unpack("<" + "H" * 128, fid.read(256))) - - -# Define data_to_result function -def data_to_result(header, data, data_present): - """Moves the header and data (if present) into a common object.""" - - result = {} - - stim_parameters = {} - stim_parameters["stim_step_size"] = header["stim_step_size"] - stim_parameters["charge_recovery_current_limit"] = header["recovery_current_limit"] - stim_parameters["charge_recovery_target_voltage"] = header[ - "recovery_target_voltage" - ] - stim_parameters["amp_settle_mode"] = header["amp_settle_mode"] - stim_parameters["charge_recovery_mode"] = header["charge_recovery_mode"] - result["stim_parameters"] = stim_parameters - - result["stim_channels"] = header["stim_channels"] - result["spike_triggers"] = header["spike_triggers"] - result["notes"] = header["notes"] - result["frequency_parameters"] = header["frequency_parameters"] - - result["reference_channel"] = header["reference_channel"] - result["amplifier_channels"] = header["amplifier_channels"] - result["board_adc_channels"] = header["board_adc_channels"] - result["board_dac_channels"] = header["board_dac_channels"] - - result["dc_amplifier_data_saved"] = header["dc_amplifier_data_saved"] - if header["dc_amplifier_data_saved"]: - result["dc_amplifier_channels"] = header["dc_amplifier_channels"] - - result["compliance_limit_channels"] = header["compliance_limit_channels"] - result["charge_recovery_channels"] = header["charge_recovery_channels"] - result["amp_settle_channels"] = header["amp_settle_channels"] - result["board_dig_in_channels"] = header["board_dig_in_channels"] - result["board_dig_out_channels"] = header["board_dig_out_channels"] - - if data_present > 0: - result["t"] = data["t"] - result["stim_data"] = data["stim_data"] - result["amplifier_data"] = data["amplifier_data"] - result["board_adc_data"] = data["board_adc_data"] - result["board_dac_data"] = data["board_dac_data"] - if header["dc_amplifier_data_saved"] > 0: - result["dc_amplifier_data"] = data["dc_amplifier_data"] - result["compliance_limit_data"] = data["compliance_limit_data"] - result["charge_recovery_data"] = data["charge_recovery_data"] - result["amp_settle_data"] = data["amp_settle_data"] - result["board_dig_in_data"] = data["board_dig_in_data"] - result["board_dig_out_data"] = data["board_dig_out_data"] - result["header"] = header - - return result - - -# Define plot_channel function -def plot_channel(channel_name, result): - # Find channel that corresponds to this name - channel_found, signal_type, signal_index = find_channel_in_header( - channel_name, result - ) - - # Plot this channel - if channel_found: - fig, ax = plt.subplots() - ax.set_title(channel_name) - ax.set_xlabel("Time (s)") - - if signal_type == "amplifier_channels": - ylabel = "Voltage (microVolts)" - signal_data_name = "amplifier_data" - - elif signal_type == "dc_amplifier_channels": - ylabel = "Voltage (Volts)" - signal_data_name = "dc_amplifier_data" - - elif signal_type == "stim_channels": - ylabel = "Current (microAmps)" - signal_data_name = "stim_data" - - elif signal_type == "amp_settle_channels": - ylabel = "Amp Settle Events (High or Low)" - signal_data_name = "amp_settle_data" - - elif signal_type == "charge_recovery_channels": - ylabel = "Charge Recovery Events (High or Low)" - signal_data_name = "charge_recovery_data" - - elif signal_type == "compliance_limit_channels": - ylabel = "Compliance Limit Events (High or Low)" - signal_data_name = "compliance_limit_data" - - elif signal_type == "board_adc_channels": - ylabel = "Voltage (Volts)" - signal_data_name = "board_adc_data" - - elif signal_type == "board_dac_channels": - ylabel = "Voltage (Volts)" - signal_data_name = "board_dac_data" - - elif signal_type == "board_dig_in_channels": - ylabel = "Digital In Events (High or Low)" - signal_data_name = "board_dig_in_data" - - elif signal_type == "board_dig_out_channels": - ylabel = "Digital Out Events (High or Low)" - signal_data_name = "board_dig_out_data" - - else: - raise Exception( - "Plotting not possible; signal type ", signal_type, " not found" - ) - - ax.set_ylabel(ylabel) - - ax.plot(result["t"], result[signal_data_name][signal_index, :]) - ax.margins(x=0, y=0) - - else: - raise Exception("Plotting not possible; channel ", channel_name, " not found") - - -# Define load_file function -def load_file(filename): - # Start timing - tic = time.time() - - # Open file - fid = open(filename, "rb") - filesize = os.path.getsize(filename) - - # Read file header - header = read_header(fid) - - # Output a summary of recorded data - print( - "Found {} amplifier channel{}.".format( - header["num_amplifier_channels"], plural(header["num_amplifier_channels"]) - ) - ) - print( - "Found {} board ADC channel{}.".format( - header["num_board_adc_channels"], plural(header["num_board_adc_channels"]) - ) - ) - print( - "Found {} board DAC channel{}.".format( - header["num_board_dac_channels"], plural(header["num_board_dac_channels"]) - ) - ) - print( - "Found {} board digital input channel{}.".format( - header["num_board_dig_in_channels"], - plural(header["num_board_dig_in_channels"]), - ) - ) - print( - "Found {} board digital output channel{}.".format( - header["num_board_dig_out_channels"], - plural(header["num_board_dig_out_channels"]), - ) - ) - print("") - - # Determine how many samples the data file contains - bytes_per_block = get_bytes_per_data_block(header) - print("{} bytes per data block".format(bytes_per_block)) - # How many data blocks remain in this file? - data_present = False - bytes_remaining = filesize - fid.tell() - if bytes_remaining > 0: - data_present = True - - if bytes_remaining % bytes_per_block != 0: - raise Exception( - "Something is wrong with file size : should have a whole number of data blocks" - ) - - num_data_blocks = int(bytes_remaining / bytes_per_block) - - # Calculate how many samples of each signal type are present - num_amplifier_samples = 128 * num_data_blocks - num_board_adc_samples = 128 * num_data_blocks - num_board_dac_samples = 128 * num_data_blocks - num_board_dig_in_samples = 128 * num_data_blocks - num_board_dig_out_samples = 128 * num_data_blocks - - record_time = num_amplifier_samples / header["sample_rate"] - - # Output a summary of contents of header file - if data_present: - print( - "File contains {:0.3f} seconds of data. Amplifiers were sampled at {:0.2f} kS/s.".format( - record_time, header["sample_rate"] / 1000 - ) - ) - else: - print( - "Header file contains no data. Amplifiers were sampled at {:0.2f} kS/s.".format( - header["sample_rate"] / 1000 - ) - ) - - if data_present: - # Pre-allocate memory for data - print("") - print("Allocating memory for data...") - - data = {} - data["t"] = np.zeros(num_amplifier_samples, dtype=np.int_) - - data["amplifier_data"] = np.zeros( - [header["num_amplifier_channels"], num_amplifier_samples], dtype=np.uint - ) - - if header["dc_amplifier_data_saved"]: - data["dc_amplifier_data"] = ( - np.zeros( - [header["num_amplifier_channels"], num_amplifier_samples], - dtype=np.uint, - ) - * header["dc_amplifier_data_saved"] - ) - - data["stim_data_raw"] = np.zeros( - [header["num_amplifier_channels"], num_amplifier_samples], dtype=np.int_ - ) - data["stim_data"] = np.zeros( - [header["num_amplifier_channels"], num_amplifier_samples], dtype=np.int_ - ) - - data["board_adc_data"] = np.zeros( - [header["num_board_adc_channels"], num_board_adc_samples], dtype=np.uint - ) - data["board_dac_data"] = np.zeros( - [header["num_board_dac_channels"], num_board_dac_samples], dtype=np.uint - ) - - # by default, this script interprets digital events (digital inputs and outputs) as booleans - # if unsigned int values are preferred(0 for False, 1 for True), replace the 'dtype=np.bool_' argument with 'dtype=np.uint' as shown - # the commented line below illustrates this for digital input data; the same can be done for digital out - - # data['board_dig_in_data'] = np.zeros([header['num_board_dig_in_channels'], num_board_dig_in_samples], dtype=np.uint) - data["board_dig_in_data"] = np.zeros( - [header["num_board_dig_in_channels"], num_board_dig_in_samples], - dtype=np.bool_, - ) - data["board_dig_in_raw"] = np.zeros(num_board_dig_in_samples, dtype=np.uint) - data["board_dig_out_data"] = np.zeros( - [header["num_board_dig_out_channels"], num_board_dig_out_samples], - dtype=np.bool_, - ) - data["board_dig_out_raw"] = np.zeros(num_board_dig_out_samples, dtype=np.uint) - - # Read sampled data from file. - print("Reading data from file...") - - # Initialize indices used in looping - indices = {} - indices["amplifier"] = 0 - indices["board_adc"] = 0 - indices["board_dac"] = 0 - indices["board_dig_in"] = 0 - indices["board_dig_out"] = 0 - - print_increment = 10 - percent_done = print_increment - for i in range(num_data_blocks): - read_one_data_block(data, header, indices, fid) - # Increment all indices in 128 - indices = {k: v + 128 for k, v in indices.items()} - - fraction_done = 100 * (1.0 * i / num_data_blocks) - if fraction_done >= percent_done: - print("{}% done...".format(percent_done)) - percent_done = percent_done + print_increment - - print("100% done...") - - # Make sure we have read exactly the right amount of data - bytes_remaining = filesize - fid.tell() - if bytes_remaining != 0: - raise Exception("Error: End of file not reached.") - - fid.close() - - if data_present: - print("Parsing data...") - - # Extract digital input channels to separate variables. - for i in range(header["num_board_dig_in_channels"]): - data["board_dig_in_data"][i, :] = np.not_equal( - np.bitwise_and( - data["board_dig_in_raw"], - (1 << header["board_dig_in_channels"][i]["native_order"]), - ), - 0, - ) - - # Extract digital output channels to separate variables. - for i in range(header["num_board_dig_out_channels"]): - data["board_dig_out_data"][i, :] = np.not_equal( - np.bitwise_and( - data["board_dig_out_raw"], - (1 << header["board_dig_out_channels"][i]["native_order"]), - ), - 0, - ) - - # Extract stimulation data - data["compliance_limit_data"] = ( - np.bitwise_and(data["stim_data_raw"], 32768) >= 1 - ) # get 2^15 bit, interpret as True or False - data["charge_recovery_data"] = ( - np.bitwise_and(data["stim_data_raw"], 16384) >= 1 - ) # get 2^14 bit, interpret as True or False - data["amp_settle_data"] = ( - np.bitwise_and(data["stim_data_raw"], 8192) >= 1 - ) # get 2^13 bit, interpret as True or False - data["stim_polarity"] = 1 - ( - 2 * (np.bitwise_and(data["stim_data_raw"], 256) >> 8) - ) # get 2^8 bit, interpret as +1 for 0_bit or -1 for 1_bit - - curr_amp = np.bitwise_and( - data["stim_data_raw"], 255 - ) # get least-significant 8 bits corresponding to the current amplitude - data["stim_data"] = ( - curr_amp * data["stim_polarity"] - ) # multiply current amplitude by the correct sign - - # # Scale voltage levels appropriately. - data["amplifier_data"] = np.multiply( - 0.195, (data["amplifier_data"].astype(np.int32) - 32768) - ) # units = microvolts - data["stim_data"] = np.multiply( - header["stim_step_size"], data["stim_data"] / 1.0e-6 - ) - - if header["dc_amplifier_data_saved"]: - data["dc_amplifier_data"] = np.multiply( - -0.01923, (data["dc_amplifier_data"].astype(np.int32) - 512) - ) # units = volts - - data["board_adc_data"] = np.multiply( - 0.0003125, (data["board_adc_data"].astype(np.int32) - 32768) - ) # units = volts - data["board_dac_data"] = np.multiply( - 0.0003125, (data["board_dac_data"].astype(np.int32) - 32768) - ) # units = volts - - # Check for gaps in timestamps. - num_gaps = np.sum(np.not_equal(data["t"][1:] - data["t"][:-1], 1)) - if num_gaps == 0: - print("No missing timestamps in data.") - else: - print( - "Warning: {0} gaps in timestamp data found. Time scale will not be uniform!".format( - num_gaps - ) - ) - - # Scale time steps (units = seconds). - data["t"] = data["t"] / header["sample_rate"] - - # If the software notch filter was selected during the recording, apply the - # same notch filter to amplifier data here. - if header["notch_filter_frequency"] > 0 and header["version"]["major"] < 3: - print_increment = 10 - percent_done = print_increment - for i in range(header["num_amplifier_channels"]): - data["amplifier_data"][i, :] = notch_filter( - data["amplifier_data"][i, :], - header["sample_rate"], - header["notch_filter_frequency"], - 10, - ) - if fraction_done >= percent_done: - print("{}% done...".format(percent_done)) - percent_done = percent_done + print_increment - else: - data = [] - - # Move variables to result struct. - result = data_to_result(header, data, data_present) - - print("Done! Elapsed time: {0:0.1f} seconds".format(time.time() - tic)) - - return result - - -# Define function print_all_channel_names -def print_all_channel_names(result): - - # Print all amplifier_channels - if "amplifier_channels" in result: - print_names_in_group(result["amplifier_channels"]) - - # Print all dc_amplifier_channels - if "dc_amplifier_channels" in result: - print_names_in_group(result["dc_amplifier_channels"]) - - # Print all stim_channels - if "stim_channels" in result: - print_names_in_group(result["stim_channels"]) - - # Print all amp_settle_channels - if "amp_settle_channels" in result: - print_names_in_group(result["amp_settle_channels"]) - - # Print all charge_recovery_channels - if "charge_recovery_channels" in result: - print_names_in_group(result["charge_recovery_channels"]) - - # Print all compliance_limit_channels - if "compliance_limit_channels" in result: - print_names_in_group(result["compliance_limit_channels"]) - - # Print all board_adc_channels - if "board_adc_channels" in result: - print_names_in_group(result["board_adc_channels"]) - - # Print all board_dac_channels - if "board_dac_channels" in result: - print_names_in_group(result["board_dac_channels"]) - - # Print all board_dig_in_channels - if "board_dig_in_channels" in result: - print_names_in_group(result["board_dig_in_channels"]) - - # Print all board_dig_out_channels - if "board_dig_out_channels" in result: - print_names_in_group(result["board_dig_out_channels"]) - - -# Define function print_names_in_group -def print_names_in_group(signal_group): - for this_channel in signal_group: - print(this_channel["custom_channel_name"]) From e2819d6ea0392827d11952662cd7f1c9bee555e2 Mon Sep 17 00:00:00 2001 From: Tolga Dincer Date: Thu, 16 Feb 2023 15:21:14 -0500 Subject: [PATCH 30/30] blackify --- element_interface/rhs_perchannel_loader.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/element_interface/rhs_perchannel_loader.py b/element_interface/rhs_perchannel_loader.py index 6e77e98..62a6928 100644 --- a/element_interface/rhs_perchannel_loader.py +++ b/element_interface/rhs_perchannel_loader.py @@ -41,7 +41,8 @@ def load_rhs(folder: str, file_expr: str = "*"): time_file = next(Path(folder).glob("time.dat")) rhs_data["timestamps"] = ( - np.memmap(time_file, dtype=np.int32) / rhs_data["header"]["frequency_parameters"]["amplifier_sample_rate"] + np.memmap(time_file, dtype=np.int32) + / rhs_data["header"]["frequency_parameters"]["amplifier_sample_rate"] ) # Get data files @@ -49,7 +50,11 @@ def load_rhs(folder: str, file_expr: str = "*"): exclude_list = ["time", "info", "Zone.Identifier"] - file_paths = [file for file in file_paths if not any(string in file.as_posix() for string in exclude_list)] + file_paths = [ + file + for file in file_paths + if not any(string in file.as_posix() for string in exclude_list) + ] # Get recording data rhs_data["recordings"] = {}