h-mayorquin

"""
Script to create stubbed (reduced-size) Blackrock test files.

This creates small test files that preserve:
- All headers (basic + extended)
- A small amount of data (enough to test gap detection)
- The file structure and format

Usage:
    python stub_blackrock_files.py <input_dir> <output_dir> --samples <n>

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = [
#   "pyedflib>=0.1.36",
#   "numpy>=1.23"
# ]
# ///

"""
One-off script to create a short "stub" EDF/EDF+ from a full file by copying

h-mayorquin

"""
TIFF file stubber - Creates a stub of a TIFF file with only the first n pages.
Preserves all metadata, tags, and structure of the original pages.
"""

from pathlib import Path
import tifffile
import numpy as np

h-mayorquin

import h5py
import numpy as np
from typing import Optional
from scipy.sparse import csc_matrix
from pathlib import Path


def stub_caiman_hdf5(input_file: str, output_file: Optional[str] = None, n_timestamps: int = 10, n_units: Optional[int] = None, stub_one_photon_quantities: bool = True):
    """
    Create a stubbed version of a CaImAn HDF5 file with reduced units and timestamps.

h-mayorquin

%%{ init: {
      'theme':'base',
      'themeVariables': {
        'background': '#a7d2eb',          /* light backdrop */
        'lineColor' : '#09205A',          /* navy outlines / arrows */
        'primaryColor'  : '#005CA9',      /* dark blue */
        'secondaryColor': '#238FD6',      /* light blue */
        'tertiaryColor' : '#F57C00'       /* orange accent */
      }

h-mayorquin

import hdf5plugin
import h5py
import numpy as np
from hdmf.backends.hdf5.h5_utils import H5DataIO
from pynwb.testing.mock.file import mock_NWBFile
from pathlib import Path
from pynwb import NWBHDF5IO
from pynwb.file import TimeSeries
from neuroconv.tools.nwb_helpers import AVAILABLE_HDF5_COMPRESSION_METHODS

h-mayorquin

from pathlib import Path
import h5py
import numpy as np


# ────────────────────────────────────────────────────────────────────────────
def copy_group(
    src_group,
    dst_group,
    stub_frames: int,

h-mayorquin

#!/usr/bin/env python3
"""
stub_scan_image_file.py
──────────────────────────────────────────────────────────────────────────────
Functions for creating stub ScanImage TIFF files with modified metadata.
"""

import re
import shutil
import struct

h-mayorquin

from pathlib import Path
from pydub import AudioSegment
import numpy as np
import scipy.io.wavfile as wav

# Create output directory
output_dir = Path("audio_test_files")
output_dir.mkdir(exist_ok=True)

# Define output filenames with realistic names

h-mayorquin

def stub_ome_dataset(file_path, num_timepoints=3, output_dir=None):
    """
    Create a stubbed version of an OME-TIFF dataset based on a file path.
    
    Parameters:
    -----------
    file_path : str or Path
        Path to any TIFF file in the dataset
    num_timepoints : int, optional
        Number of timepoints to keep in the stub, default is 3