h-mayorquin

Tifffile library handling of axis names and array access

I am writing this gist to leave a script that show how tifffile interprets the tags of tiff of image width and image height and how that translates to the array access pattern.

TIFF Tag Mapping

According to the TIFF specification:

• Tag 256 (ImageWidth): Number of columns (horizontal extent, X axis) = width

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