h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = [
#     "numpy",
#     "tifffile",
#     "lxml",
# ]
# ///
import shutil, uuid
import xml.etree.ElementTree as ET

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = [
#     "numpy",
#     "tifffile",
#     "lxml",
# ]
# ///
"""Complete, faithful stub of TSeries-02022026-001 (multi-burst Brightness Over Time).

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = [
#     "numpy",
# ]
# ///
"""
Generate a stubbed version of the OneBox NP2014 dataset for testing.

Takes the full recording and produces a 1-second stub with anonymized

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = [
#     "tifffile",
#     "numpy",
# ]
# ///
"""
Create OME-TIFF files with different DimensionOrder values and verify that
tifffile respects the ordering for non-spatial dimensions (T, C, Z).

h-mayorquin

#!/usr/bin/env python3
import argparse
import os
import sys

HEADER_SIZE = 16_384  # bytes
RECORD_SIZE = 1_044   # bytes (UInt64 + 3x UInt32 + 512x Int16)


def stub_ncs(input_path: str, output_path: str, keep_records: int = 5) -> dict:

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = []
# ///
"""Stub Bruker PrairieView VoltageRecording (intracellular ephys) for a Bruker icephys fixture.

Surmeier Zhai 2025 'Somatic excitability' (current-clamp, mV) + 'Sr-oEPSC' (voltage-clamp, pA)
sessions. Each example = the VoltageRecording XML (verbatim, carries units/scaling/device) + the
CSV truncated to 100 samples (Time(ms), Primary). Picked to exercise mV vs pA, scaling Divisors,
Multiclamp700B device-name variants, old 2016 sessions (see INTRACELLULAR_EXAMPLES.md).

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = [
#     "imagecodecs",
#     "numpy",
#     "tifffile",
# ]
# ///
"""Stub the Surmeier BOT acetylcholine recording for ophys_testing_data on gin.

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = ["numpy", "tifffile"]
# ///
"""Stub the PV 5.5.64.600 Bruker ZSeries (plain Z-stack) for ophys_testing_data.

Source: bruker_binary.zip / bruker_binary/ZSeries-20231129-001/ (158-plane Z-stack,
single channel Ch2/"Green", 512x512 uint16, + References + RAWDATA binary + .nii export).
This is the first plain `ZSeries` (static Z-stack, no time) fixture; existing volumetric
fixtures are `TSeries ZSeries Element` (volume-over-time), a different Sequence type.

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = [
#     "numpy",
# ]
# ///
"""
Stub an Inscopix raw .imu file down to its first N samples.

Raw .imu layout (isxcore `IMUFile`, structs in `api/isxIMUFile.h`):

h-mayorquin

# /// script
# requires-python = ">=3.10"
# dependencies = [
#     "numpy",
# ]
# ///
"""
Stub an Inscopix raw .gpio file down to its first N event packets.

Raw .gpio layout (isxcore `NVista3GpioFile`, structs in