Project Structure

Project Structure

├── main.py                        # Guided terminal UI
├── fit_cli.py                     # FLIM fitting CLI
├── phasor_cli.py                  # Phasor analysis CLI
├── synth_cli.py                   # Synthetic known-truth PTU/SDT generator
├── build_and_sign.py              # PyInstaller build + codesign
├── validate_installation.py       # Installation sanity check (10 checks)
├── hardware_limits.py             # Hardware stress test - throughput & RAM headroom
├── requirements.txt
│
├── flimkit/
│   ├── configs.py                 # Default fitting parameters
│   ├── interactive.py             # Guided fitting launcher
│   ├── phasor_launcher.py         # Guided phasor launcher
│   ├── machine_irf/               # Machine IRF files - generated per system
│   │
│   ├── UI/
│   │   ├── gui.py                 # Tkinter desktop GUI
│   │   ├── roi_tools.py           # ROI drawing panel, RoiManager, per-ROI decay fitting
│   │   └── phasor_panel.py        # Embedded phasor view panel
│   │
│   ├── synth.py                   # Synthetic known-truth data generation
│   │
│   ├── formats/
│   │   ├── flim_file.py           # FLIMFile, detect_format - format dispatch
│   │   ├── PTU/
│   │   │   ├── reader.py          # PTUFile (wraps ptufile), read_pck
│   │   │   ├── decode.py          # Histogram extraction for tile stitching
│   │   │   ├── tools.py           # signal_from_PTUFile (xarray)
│   │   │   └── stitch.py          # Multi-tile stitching + registration
│   │   ├── BH/
│   │   │   ├── reader.py          # BHFile (wraps sdtfile)
│   │   │   └── writer.py          # .sdt writer, used by synth
│   │   ├── PS/
│   │   │   └── reader.py          # PSFile (wraps photonsfile)
│   │   └── ISS/
│   │       ├── reader.py          # ISSFile - TD triplet (experimental)
│   │       ├── fdflim.py          # .ifli FD-FLIM phasor (experimental)
│   │       └── image.py           # .ifi intensity image (experimental)
│   │
│   ├── FLIM/
│   │   ├── models.py              # Decay models + DE cost functions
│   │   ├── fitters.py             # fit_summed / fit_per_pixel (NNLS)
│   │   ├── fit_tools.py           # IRF alignment, bin utilities
│   │   ├── assemble.py            # Tile map assembly + global tau stats
│   │   └── irf_tools.py           # IRF estimation + machine IRF builder
│   │
│   ├── phasor/
│   │   ├── signal.py              # Phasor computation & calibration
│   │   ├── interactive.py         # Interactive cursor tool
│   │   ├── peaks.py               # Automatic peak detection
│   │   └── filters.py             # Spatial phasor filtering (gaussian/median/wavelet)
│   │
│   ├── image/
│   │   └── tools.py               # Intensity images, cell masking
│   │
│   └── utils/
│       ├── plotting.py            # Decay + pixel map plots
│       ├── enhanced_outputs.py    # TIFF exports, summary text
│       ├── lifetime_image.py      # Colourised lifetime images
│       ├── xlsx_tools.py          # FLIM microscope software Excel parsing
│       ├── xml_utils.py           # XLIF tile-position parsing
│       ├── misc.py                # Logging helpers
│       └── fancy.py               # Terminal banners
│
└── flimkit_tests/
    ├── run_tests.py
    ├── mock_data.py
    ├── conftest.py
    ├── test_complete_pipeline.py
│       ├── test_roi_decay_fit.py
        └── tests/
        ├── test_decode.py
        ├── test_integration.py
        └── test_xml_utils.py