Python API

opentfraw.RawFile wraps a RawFileReader for ergonomic use from Python. Every attribute and method below also carries a docstring in the wheel itself (help(opentfraw.RawFile)); this page is a map of what's available.

import opentfraw

raw = opentfraw.RawFile("run.raw")

Attributes

Attribute	Type	Description
num_scans	int	Total number of scans
first_scan	int	Scan number of the first scan (usually 1)
last_scan	int	Scan number of the last scan
instrument_model	str | None	Detected instrument model (e.g. "Orbitrap Fusion Lumos")
created	float | None	Acquisition start time (Xcalibur audit tag FILETIME), Unix secs
sample_info	dict	Sample-sheet / sequence-row metadata for the acquisition
computer_name	str	Acquisition workstation's computer name
controller_count	int	Number of controllers in the file (MS plus auxiliary detectors)
acquisition_date	float | None	Acquisition timestamp decoded from raw_file_info, Unix secs

created and acquisition_date are two independently-decoded timestamps for the same acquisition event (one from the Xcalibur audit tag, the other from the raw-file-info preamble); they're expected to agree but aren't guaranteed to. Both are the instrument's local wall-clock time with no timezone attached.

Scan data

mz, intensity = raw.peaks(3)              # centroid peaks, float64/float32 numpy arrays
scan = raw.scan(3)                        # dict: ms_level, RT, charge, filter_string, ...
for scan in raw.iter_scans():             # equivalent to scan(n) for n in range(first_scan, last_scan+1)
    ...
raw.scan_filter(3)                        # canonical Thermo filter string, or None
raw.profile(3)                            # (mz, intensity) from the raw profile signal
raw.centroid_labels(3)                    # mz/intensity/resolution/noise/baseline/signal_to_noise

Per-scan and acquisition metadata

raw.scan_parameters(3)        # {label: value} trailer-extra dict, or None
raw.status_log(3)             # {label: value} instrument status log (temps, voltages, ...), or None
raw.error_log()               # [{"time": ..., "message": ...}, ...] in log order
raw.controllers()             # [{"index", "is_ms_controller", "controller_type", ...}, ...]
raw.instrument_method_text()  # best-effort UTF-16LE text/XML acquisition method blob, or None

status_log and scan_parameters are both per-scan generic-record streams decoded from the file, but distinct ones: scan_parameters mirrors the vendor reader's trailer-extra values, while status_log is the instrument-state-over-time log.

controllers() returns a one-element list for the common single-MS- controller case; multi-detector files (UV, PDA, Analog channels alongside MS) return one entry per controller.

Export

raw.to_mzml("run.mzML")

See mzML export for what the output covers.

Next

• Reader API (Rust)
• Scan data layouts