lf_mri_platform/services/seq-interp/api.py

"""
seq_interp FastAPI service.

Endpoints:
  GET  /health              - liveness probe
  POST /interpret/          - upload .seq file, run full pipeline, return task_id
  GET  /status/             - status of all submitted tasks
  GET  /result/{task_id}    - full result: xml_text, post_json, metadata, waveforms
"""
from __future__ import annotations

import asyncio
import json
import os
import shutil
import uuid
from typing import Any

from fastapi import FastAPI, File, HTTPException, UploadFile

from src.config import config
from src.hardware.constraints import HardwareConstraints
from src.interfaces.pulseq_adapter import PulseqLoader
from src.core.synchronizer import Synchronizer
from src.interfaces.xml_generator import XMLGenerator
from src.interfaces.rf_exporter import RFExporter
from src.interfaces.gradient_exporter import GradientExporter
from src.interfaces.picoscope_exporter import PicoScopeExporter
from src.interfaces.post_request_generator import PostRequestGenerator

app = FastAPI(title="seq-interp", version="1.0.0")

UPLOAD_DIR = config.get("upload_dir", "data/input")
OUTPUT_DIR = config.get("output_dir", "data/output")
os.makedirs(UPLOAD_DIR, exist_ok=True)
os.makedirs(OUTPUT_DIR, exist_ok=True)

# in-memory cache: task_id -> {"status": str, "result": dict | None}
_tasks: dict[str, dict] = {}

_MAX_WAVEFORM_POINTS = 8000   # downsample for JSON transport

_STATUS_FILE = "_status.json"
_RESULT_FILE = "_result.json"


# -- disk persistence --------------------------------------------------------

def _task_dir(task_id: str) -> str:
    return os.path.join(OUTPUT_DIR, task_id)


def _persist_task(task_id: str, entry: dict) -> None:
    """Write task status (and result if present) to disk."""
    d = _task_dir(task_id)
    os.makedirs(d, exist_ok=True)
    with open(os.path.join(d, _STATUS_FILE), "w", encoding="utf-8") as f:
        json.dump({"status": entry["status"]}, f)
    if entry.get("result") is not None:
        with open(os.path.join(d, _RESULT_FILE), "w", encoding="utf-8") as f:
            json.dump(entry["result"], f, ensure_ascii=False)


def _load_task_from_disk(task_id: str) -> dict | None:
    """Restore task entry from disk (used after container restart)."""
    d = _task_dir(task_id)
    status_path = os.path.join(d, _STATUS_FILE)
    result_path = os.path.join(d, _RESULT_FILE)
    if not os.path.exists(status_path):
        return None
    with open(status_path, encoding="utf-8") as f:
        status = json.load(f).get("status", "unknown")
    result = None
    if os.path.exists(result_path):
        with open(result_path, encoding="utf-8") as f:
            result = json.load(f)
    return {"status": status, "result": result}


# -- helpers ----------------------------------------------------------------

def _downsample(arr, max_pts: int) -> list:
    """Convert numpy array to list, downsampling if too long."""
    try:
        import numpy as np
        a = np.asarray(arr, dtype=float).flatten()
        if len(a) > max_pts:
            idx = np.linspace(0, len(a) - 1, max_pts, dtype=int)
            a = a[idx]
        return [float(x) for x in a]
    except Exception:
        return []


def _extract_waveforms(seq_data: dict, sync_data: dict) -> dict:
    """Extract waveform arrays from seq_data for GUI display."""
    waveforms: dict[str, list] = {}
    for key in ("gx", "gy", "gz", "t_gx", "t_gy", "t_gz"):
        if key in seq_data:
            waveforms[key] = _downsample(seq_data[key], _MAX_WAVEFORM_POINTS)
    # RF
    for key in ("rf_amp", "rf_phase", "t_rf"):
        if key in seq_data:
            waveforms[key] = _downsample(seq_data[key], _MAX_WAVEFORM_POINTS)
    # Sync gate arrays
    for key in ("gate_adc", "gate_rf", "gate_tr_switch", "blocks_duration"):
        if key in sync_data:
            waveforms[key] = _downsample(sync_data[key], _MAX_WAVEFORM_POINTS)
    return waveforms


async def _run_pipeline(file_path: str, task_id: str) -> None:
    """Run the full interpretation pipeline and store result in _tasks."""
    out_dir = os.path.join(OUTPUT_DIR, task_id)
    os.makedirs(out_dir, exist_ok=True)
    try:
        hw = HardwareConstraints(json_path=config.get("hw_config_path"))
        hw_cfg = config.hw_config

        loader = PulseqLoader(hw)
        seq_data = await asyncio.to_thread(loader.load, file_path)
        params = seq_data.get("params", {})

        sync = Synchronizer(hw)
        sync_data = await asyncio.to_thread(sync.process, seq_data["sequence"])

        xml_gen = XMLGenerator()
        xml_path = os.path.join(out_dir, "sync_v2.xml")
        adc_values, adc_starts = await asyncio.to_thread(
            xml_gen.generate, sync_data, xml_path, hw
        )
        with open(xml_path, encoding="utf-8") as fh:
            xml_text = fh.read()

        export_tasks = [
            asyncio.to_thread(RFExporter().export, seq_data, params, out_dir)
        ]
        if all(k in seq_data for k in ("gx", "gy", "gz")):
            export_tasks.append(
                asyncio.to_thread(GradientExporter().export, seq_data, params, out_dir)
            )
        iadc = hw_cfg.get("iadc", {})
        export_tasks.append(asyncio.to_thread(
            PicoScopeExporter().generate,
            adc_values, adc_starts, out_dir, hw,
            sampling_freq=iadc.get("srate", 8e6),
            num_channels=iadc.get("n_channels", 3),
        ))
        await asyncio.gather(*export_tasks)

        post_gen = PostRequestGenerator()
        post_payload = post_gen.build(
            seq_data=seq_data,
            adc_values=adc_values,
            sequence_path=file_path,
            output_dir=out_dir,
            hw_cfg=hw_cfg,
            rf_raster_time=params.get("rf_raster_time", 1e-6),
        )
        post_gen.write(post_payload, out_dir)

        blocks = seq_data.get("blocks", [])
        total_s = sum(sync_data.get("blocks_duration", []))
        adc_blocks = [b for b in blocks if b.get("has_adc")]

        result: dict[str, Any] = {
            "task_id": task_id,
            "status": "completed",
            "output_dir": out_dir,
            "xml_text": xml_text,
            "post_json": post_payload,
            "metadata": {
                "block_count": len(blocks),
                "sync_block_count": sync_data.get("number_of_blocks", 0),
                "adc_count": len(adc_blocks),
                "adc_windows": len(adc_values),
                "total_duration_ms": round(total_s * 1e3, 4),
                "rf_raster_us": params.get("rf_raster_time", 1e-6) * 1e6,
                "grad_raster_us": params.get("grad_raster_time", 1e-5) * 1e6,
            },
            "waveforms": _extract_waveforms(seq_data, sync_data),
        }
        entry = {"status": "completed", "result": result}
        _tasks[task_id] = entry
        _persist_task(task_id, entry)

    except Exception as exc:
        entry = {"status": f"failed: {exc}", "result": None}
        _tasks[task_id] = entry
        _persist_task(task_id, entry)


# -- endpoints ----------------------------------------------------------------

@app.get("/health")
def health():
    return {"status": "ok"}


@app.post("/interpret/")
async def interpret_endpoint(file: UploadFile = File(...)):
    """Upload a .seq file and run the full interpretation pipeline."""
    task_id = str(uuid.uuid4())
    # Store the file under the task_id so parallel uploads never collide
    task_upload_dir = os.path.join(UPLOAD_DIR, task_id)
    os.makedirs(task_upload_dir, exist_ok=True)
    file_path = os.path.join(task_upload_dir, file.filename)
    with open(file_path, "wb") as buf:
        shutil.copyfileobj(file.file, buf)

    entry: dict = {"status": "processing", "result": None}
    _tasks[task_id] = entry
    _persist_task(task_id, entry)
    asyncio.create_task(_run_pipeline(file_path, task_id))
    return {"status": "accepted", "task_id": task_id,
            "message": f"Processing {file.filename}"}


@app.get("/status/")
def status_endpoint():
    """Return the status of all submitted tasks."""
    return {"tasks": {tid: v["status"] for tid, v in _tasks.items()}}


@app.get("/result/{task_id}")
def result_endpoint(task_id: str):
    """Return full interpretation result (xml_text, post_json, metadata, waveforms)."""
    entry = _tasks.get(task_id)
    if entry is None:
        # Container may have restarted — try restoring from disk
        entry = _load_task_from_disk(task_id)
        if entry is None:
            raise HTTPException(status_code=404, detail=f"Task '{task_id}' not found")
        _tasks[task_id] = entry   # restore to memory cache
    if entry["status"] == "processing":
        raise HTTPException(status_code=202, detail="Still processing")
    if entry["result"] is None:
        raise HTTPException(status_code=500, detail=entry["status"])
    return entry["result"]