run.py

"""
AutoBIDSify Executor
Runs a BIDS conversion using the package folder downloaded from AutoBIDSify
(contains _staging/BIDSPlan.yaml and trio files) against a local dataset folder.
"""
import sys
import threading
import io
from pathlib import Path
import tkinter as tk
from tkinter import filedialog, messagebox, scrolledtext

if getattr(sys, "frozen", False):
    _root = Path(sys._MEIPASS)
else:
    _root = Path(__file__).parent

sys.path.insert(0, str(_root))

from utils import read_yaml, info, warn
from converters.executor import execute_bids_plan


class StdoutRedirect(io.TextIOBase):
    def __init__(self, widget: scrolledtext.ScrolledText):
        self.widget = widget

    def write(self, text: str) -> int:
        self.widget.after(0, self._append, text)
        return len(text)

    def _append(self, text: str):
        self.widget.configure(state="normal")
        self.widget.insert("end", text)
        self.widget.see("end")
        self.widget.configure(state="disabled")


class App(tk.Tk):
    def __init__(self):
        super().__init__()
        self.title("AutoBIDSify Executor")
        self.resizable(True, True)
        self.minsize(640, 500)
        self._build_ui()

    def _build_ui(self):
        pad = {"padx": 12, "pady": 5}

        tk.Label(self, text="AutoBIDSify Executor", font=("Helvetica", 16, "bold")).pack(**pad, anchor="w")
        tk.Label(self, text="Convert your dataset to BIDS using the package downloaded from AutoBIDSify",
                 fg="gray").pack(padx=12, anchor="w")

        tk.Frame(self, height=8).pack()

        # ── Conversion package folder ──────────────────────────────────
        tk.Label(self, text="Step 1 — Select the conversion package folder downloaded from AutoBIDSify:",
                 font=("Helvetica", 11, "bold")).pack(padx=12, anchor="w")
        tk.Label(self, text="(The folder contains _staging/BIDSPlan.yaml, dataset_description.json, README.md, participants.tsv)",
                 fg="gray", font=("Helvetica", 9)).pack(padx=12, anchor="w")
        frm1 = tk.Frame(self)
        frm1.pack(fill="x", padx=12, pady=4)
        self.pkg_var = tk.StringVar()
        tk.Entry(frm1, textvariable=self.pkg_var, width=55).pack(side="left", expand=True, fill="x")
        tk.Button(frm1, text="Browse", command=self._browse_pkg).pack(side="left", padx=(6, 0))

        tk.Frame(self, height=6).pack()

        # ── Raw data folder ────────────────────────────────────────────
        tk.Label(self, text="Step 2 — Select your raw dataset folder:",
                 font=("Helvetica", 11, "bold")).pack(padx=12, anchor="w")
        tk.Label(self, text="(The original folder containing your DICOM, SNIRF, .mat, or NIfTI files)",
                 fg="gray", font=("Helvetica", 9)).pack(padx=12, anchor="w")
        frm2 = tk.Frame(self)
        frm2.pack(fill="x", padx=12, pady=4)
        self.input_var = tk.StringVar()
        tk.Entry(frm2, textvariable=self.input_var, width=55).pack(side="left", expand=True, fill="x")
        tk.Button(frm2, text="Browse", command=self._browse_input).pack(side="left", padx=(6, 0))

        tk.Frame(self, height=8).pack()

        # ── Run button ─────────────────────────────────────────────────
        self.run_btn = tk.Button(self, text="Run Conversion",
                                 font=("Helvetica", 12, "bold"),
                                 padx=16, pady=6,
                                 command=self._start_conversion)
        self.run_btn.pack(padx=12, anchor="w")

        # ── Log output ─────────────────────────────────────────────────
        tk.Label(self, text="Output:", anchor="w").pack(padx=12, anchor="w", pady=(8, 0))
        self.log = scrolledtext.ScrolledText(self, height=16, state="disabled",
                                             bg="black", fg="lightgreen",
                                             font=("Courier", 10))
        self.log.pack(fill="both", expand=True, padx=12, pady=(0, 12))

        redirect = StdoutRedirect(self.log)
        sys.stdout = redirect
        sys.stderr = redirect

    def _browse_pkg(self):
        path = filedialog.askdirectory(title="Select conversion package folder")
        if path:
            self.pkg_var.set(path)

    def _browse_input(self):
        path = filedialog.askdirectory(title="Select raw dataset folder")
        if path:
            self.input_var.set(path)

    def _start_conversion(self):
        pkg_path = self.pkg_var.get().strip()
        input_path = self.input_var.get().strip()

        if not pkg_path or not input_path:
            messagebox.showerror("Missing fields", "Please fill in both fields.")
            return

        pkg_dir = Path(pkg_path)
        input_root = Path(input_path)
        plan_file = pkg_dir / "_staging" / "BIDSPlan.yaml"

        if not plan_file.exists():
            messagebox.showerror("Not found",
                f"BIDSPlan.yaml not found inside the package folder.\n"
                f"Expected: {plan_file}\n\n"
                "Make sure you selected the folder downloaded from AutoBIDSify.")
            return

        if not input_root.is_dir():
            messagebox.showerror("Not found", f"Raw dataset folder not found:\n{input_root}")
            return

        self.run_btn.configure(state="disabled", text="Running...")
        threading.Thread(target=self._run, args=(plan_file, input_root, pkg_dir),
                         daemon=True).start()

    def _run(self, plan_file: Path, input_root: Path, output_dir: Path):
        try:
            plan_dict = read_yaml(plan_file)
            execute_bids_plan(input_root, output_dir, plan_dict, {})
            bids_out = output_dir / "bids_compatible"
            self.after(0, lambda: messagebox.showinfo(
                "Done", f"Conversion complete!\nBIDS dataset: {bids_out}"))
        except Exception as e:
            self.after(0, lambda: messagebox.showerror("Error", str(e)))
        finally:
            self.after(0, lambda: self.run_btn.configure(state="normal", text="Run Conversion"))


if __name__ == "__main__":
    app = App()
    app.mainloop()