isoextract

A self-contained command-line tool for extracting data from Thermo Fisher isodat binary files. Each input file is parsed and the extracted data is written to a JSON output file in the same folder.

Supported file formats

Extension	Instrument type
.dxf	Continuous flow
.cf	Continuous flow (legacy)
.did	Dual inlet
.caf	Dual inlet (legacy)
.scn	Scan

Usage

isoextract [options] <file|dir> [...]

One or more files or directories can be provided. Directories are searched recursively for files with supported extensions. Files are processed in parallel.

Options

Option	Description
--version, -v	Print the version and exit
--prettyJSON	Pretty-print JSON output (number arrays are kept on one line)
--unabridged	Include verbose fields normally omitted: schema version numbers, app IDs, raw flags, etc.
--log [path]	Write a CSV summary of all processed files. Defaults to isoextract.log in the current directory; an explicit path can be provided: --log results/run.log
--file-list <path>	Read additional file/directory paths from a text file (one per line; lines starting with # are ignored)
--objects	Write a .objects.csv output file for each input file, listing every deserialized C++ object with its byte offset, class name, schema version, and parent–child relationships
--tree	Write a .tree.txt output file for each input file showing the object hierarchy as an indented tree
--dry-run	Parse files without writing the JSON output. All other output (--log, --objects, --tree, issues logs) is still written normally

Exit code

0 if all files were processed without errors, 1 if any file failed or was not found.

Output files

For each input file foo.dxf the following files are written:

File	Always?	Description
foo.dxf.json	yes	Extracted data
foo.dxf.issues.log	only on warnings/errors	Plain-text list of warnings and the error message (if any)
foo.dxf.objects.csv	with --objects	Per-object log (offset, class, version, hierarchy)
foo.dxf.tree.txt	with --tree	Indented object tree

JSON structure

Every output file has a meta block at the top:

{
  "meta": {
    "isoextract_version": "0.1.0.0",
    "file_type": "dxf",
    "file_size_bytes": 123456,
    "complete": true
  },
  ...
}

complete: false means parsing stopped early due to an error; the rest of the JSON contains whatever was extracted before the failure.

Log file format

The CSV written by --log has one row per file:

file,success,duration_ms,error
data/example.dxf,true,134,
data/broken.dxf,false,12,No reader registered for class 'CUnknown'

Examples

Process a single file:

isoextract sample.dxf

Process all files in a directory tree, pretty-printing the JSON:

isoextract /data/irms --prettyJSON

Process a directory and write a log:

isoextract /data/irms --log run.log

Process a hand-picked list:

isoextract --file-list batch.txt

Full diagnostic output (objects + tree + log):

isoextract /data/irms --objects --tree --prettyJSON --log

File format documentation

See docs/isodat_structure.md for an overview of how isodat files store data (MFC CArchive serialization, CRuntimeClass headers, sequential reading requirement, and per-extension entry points).

Building from source

Requires the .NET 8 SDK.

# Development build (produces bin/release/isoextract.dll, run with dotnet)
make build

# Release build for all three runtimes (linux-x64, osx-x64, win-x64) via Docker
make build-all

Live-reload during development (rebuilds and reruns on every save):

make dev