Read Igor Binary Wave Files

bin/ibw_to_mat.py

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+#!/usr/bin/env python
+
+import argparse
+import os
+import sys
+
+import numpy as np
+import scipy.io as sio
+
+script_dir = os.path.dirname(os.path.abspath(__file__))
+vendor_dir = os.path.join(script_dir, "..", "vendor")
+sys.path.insert(0, vendor_dir)
+
+from ibwpy import ibwpy
+
+
+def create_parser():
+    parser = argparse.ArgumentParser(
+        description="Combine Igor Binary Wave files into a single matlab file that "
+        "can be read by ASCAM."
+    )
+    parser.add_argument("current", help="Current .ibw file.")
+    parser.add_argument("--command", help="Command Voltage .ibw file.")
+    parser.add_argument("--piezo", help="Piezo Voltage .ibw file.")
+    parser.add_argument(
+        "--sampling-rate",
+        dest="sampling_rate",
+        default=25000,
+        help="Piezo Voltage .ibw file.",
+    )
+    parser.add_argument("--output", help="Output filename.")
+
+    return parser
+
+
+def main():
+    parser = create_parser()
+    args = parser.parse_args()
+
+    # Load the three IBW files
+    current_data = ibwpy.load(args.current).array
+    if args.command:
+        command_data = ibwpy.load(args.command).array
+    if args.piezo:
+        piezo_data = ibwpy.load(args.piezo).array
+
+    # Sampling parameters
+    num_points = current_data.shape[0]  # Number of data points per sweep
+    num_sweeps = current_data.shape[1]  # Number of sweeps
+
+    # Create the time vector
+    time_vector = np.arange(num_points) / args.sampling_rate
+
+    # Create a dictionary to hold the data for ASCAM
+    ascam_data = {
+        "c001_Time": time_vector  # Time variable
+    }
+
+    # Populate the dictionary with data for each sweep
+    for i in range(num_sweeps):
+        # For each sweep, assign the corresponding data for Ipatch, Piezo, and Command
+        ascam_data[f"c002_Ipatch_{i + 1}"] = current_data[:, i]
+        if args.piezo:
+            ascam_data[f"c003_Piezo_{i + 1}"] = piezo_data[:, i]
+        if args.command:
+            ascam_data[f"c004_Command_{i + 1}"] = command_data[:, i]
+
+    # Save the data to a .mat file
+    sio.savemat(args.output, ascam_data)
+
+
+if __name__ == "__main__":
+    main()

vendor/ibwpy/LICENSE

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+MIT License
+
+Copyright (c) 2022 Hiroaki Takahashi
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

vendor/ibwpy/README.md

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+# ibwpy
+Read and write [Igor Pro](https://www.wavemetrics.com/) files (Igor binary wave) with Python
+
+## Installation
+### Install with pip (using Git, recommended)
+1. Install ibwpy with pip
+```bash
+$ python -m pip install git+https://github.com/MiLL4U/ibwpy.git
+```
+
+### Install with pip (without Git)
+1. download a wheel package (*.whl) from [Releases](https://github.com/MiLL4U/ibwpy/releases)
+
+2. Install ibwpy with pip
+```bash
+$ python -m pip install ibwpy-x.y.z-py3-none-any.whl
+```
+<span style="color: #FFAAAA">(replace x.y.z with the version of ibwpy which you downloaded)</span>
+
+### Install with git clone
+1. Clone this repository
+
+```bash
+$ git clone https://github.com/MiLL4U/ibwpy.git
+```
+
+2. Go into the repository
+
+```bash
+$ cd ibwpy
+```
+
+3. Install ibwpy with setup.py
+
+```bash
+$ python setup.py install
+```
+
+## Examples
+### Read
+Read wave from ibw file:
+```python
+import ibwpy as ip
+test_wave = ip.load("test_wave.ibw")
+print(test_wave)
+```
+
+### Make
+Make new wave from Numpy array
+```python
+import numpy as np
+
+arr_1 = np.array([[1., 2., 3.],
+                  [1.5, 2.5, 3.5]])
+wave_1 = ip.from_nparray(arr_1, 'wave1')
+# wave1 (IgorBinaryWave)
+# [[1.  2.  3. ]
+#  [1.5 2.5 3.5]]
+```
+
+### Calculation
+Treat wave as NumPy array:
+```python
+arr_2 = np.ones((2, 3))
+print(arr_2)
+# [[1. 1. 1.]
+#  [1. 1. 1.]]
+
+wave_1 = wave_1 + arr_2
+print(wave_1)
+# wave1 (IgorBinaryWave)
+# [[2.  3.  4. ]
+#  [2.5 3.5 4.5]]
+```
+
+### Save
+Save wave as ibw file
+```python
+wave_1.save("wave1.ibw")
+```

vendor/ibwpy/ibwpy/__init__.py

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+"""
+IBWPy
+=====
+
+Provides
+  1. Functions for reading/writing Igor binary wave (*.ibw) directly
+  2. Interfaces to edit ibw files as NumPy array
+"""
+
+from typing import List, Tuple, Union
+
+import numpy as np
+
+from .constants import DEFAULT_DTYPE, IBWDType
+from .igorbinarywave import BinaryWave5, BinaryWave5Loader
+from .waveheader import BinaryWaveHeader5
+
+
+def make(shape: Union[List[int], Tuple[int, ...]],
+         name: str, dtype: IBWDType = DEFAULT_DTYPE) -> BinaryWave5:
+    shape_tuple = tuple(shape)
+    header = BinaryWaveHeader5(shape=shape_tuple, name=name, dtype=dtype)
+    zeros = np.zeros(shape, dtype=dtype)
+    res = BinaryWave5(ibw_header=header, wave_values=zeros)
+    return res
+
+
+def from_nparray(array: np.ndarray, name: str) -> BinaryWave5:
+    header = BinaryWaveHeader5(shape=array.shape, name=name,
+                               dtype=str(array.dtype))
+    res = BinaryWave5(ibw_header=header, wave_values=array)
+    return res
+
+
+def load(path: str) -> BinaryWave5:
+    loader = BinaryWave5Loader(path)
+    res = loader.load()
+    return res

vendor/ibwpy/ibwpy/commonfunc.py

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+from .constants import TEXT_ENCODE, TEXT_ENCODE_2ND
+
+
+def decode_unicode(text_buf: bytes):
+    try:
+        res = text_buf.decode(TEXT_ENCODE)
+    except UnicodeDecodeError:
+        res = text_buf.decode(TEXT_ENCODE_2ND)
+    return res

vendor/ibwpy/ibwpy/constants.py

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+import datetime
+
+from typing_extensions import Literal
+
+IBWPY_VERSION = "1.0.4"
+
+IBWDType = Literal['float32', 'float64', 'int8', 'int16', 'int32']
+DEFAULT_DTYPE: IBWDType = 'float32'
+
+WAVE_HEADER_SIZE = 320
+
+DATETIME_OFFSET = datetime.datetime(1904, 1, 1, 0, 0, 0)
+MAX_WAVE_NAME_LENGTH = 31
+
+TEXT_ENCODE = 'utf-8'
+TEXT_ENCODE_2ND = 'shift_jis'
+DEFAULT_EOL = '\r'