Add cli for checking version and info of a nifty file

.github/workflows/main.yml

@@ -17,7 +17,7 @@ jobs:
     name: Test on ${{ matrix.os }} with Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
         python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
         os: [ubuntu-latest, windows-latest, macos-latest]

pyproject.toml

@@ -13,27 +13,39 @@ license = "MIT"
 license-files = ["LICENSE"]
 
 dependencies = [
-  "click",
   "tqdm",
   "numpy",
+  "rich-argparse",
   "nibabel",
   "pandas"]
 
 [project.optional-dependencies]
-extra = []
+show = [
+    "textual-image", # Used to show images in terminal
+    "pillow",    # Used to handle image data
+    "matplotlib" # Used for colormaps
+]
+napari = [
+    "napari[all]", # Used for interactive visualization
+]
 test = [
     "pytest",
     "pytest-cov",
+
 ]
 pypi = [
     "build" # Used for building wheels and uploading to pypi
 ]
-all = ["mri-toolkit[extra,test,pypi]"]
+all = ["mri-toolkit[extra,test,pypi,show,napari]"]
 
 
 [project.urls]
 Homepage = "https://github.com/scientificcomputing/mri-toolkit.git"
 
+
+[project.scripts]
+mritk = "mritk.cli:main"
+
 [tool.mypy]
 ignore_missing_imports = true # Does not show errors when importing untyped libraries
 files = [  # Folder to which files that should be checked by mypy

src/mritk/__init__.py

@@ -12,7 +12,7 @@
 meta = metadata("mri-toolkit")
 __version__ = meta["Version"]
 __author__ = meta["Author-email"]
-__license__ = meta["License"]
+__license__ = meta["license-expression"]
 __email__ = meta["Author-email"]
 __program_name__ = meta["Name"]
 

src/mritk/cli.py

@@ -1,32 +1,107 @@
 import logging
+from importlib.metadata import metadata
 from pathlib import Path
 import argparse
 from typing import Sequence, Optional
 
-from . import download_data
+from rich_argparse import RichHelpFormatter
+
+from . import download_data, info, statistics, show, napari
+
+
+def version_info():
+    from rich.console import Console
+    from rich.table import Table
+    from rich import box
+    import sys
+    import nibabel as nib
+    import numpy as np
+
+    console = Console()
+
+    meta = metadata("mri-toolkit")
+    toolkit_version = meta["Version"]
+    python_version = sys.version.split()[0]
+
+    table = Table(
+        title="MRI Toolkit Environment",
+        box=box.ROUNDED,  # Nice rounded corners
+        show_lines=True,  # Separator lines between rows
+        header_style="bold magenta",
+    )
+
+    table.add_column("Package", style="cyan", no_wrap=True)
+    table.add_column("Version", style="green", justify="right")
+
+    table.add_row("mri-toolkit", toolkit_version)
+    table.add_row("Python", python_version)
+    table.add_row("Nibabel", nib.__version__)
+    table.add_row("Numpy", np.__version__)
+
+    console.print(table)
 
 
 def setup_parser():
-    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser = argparse.ArgumentParser(formatter_class=RichHelpFormatter)
+    parser.add_argument("--version", action="store_true")
 
     subparsers = parser.add_subparsers(dest="command")
 
     # Download test data parser
-    download_parser = subparsers.add_parser("download-test-data", help="Download test data")
+    download_parser = subparsers.add_parser(
+        "download-test-data", help="Download test data", formatter_class=parser.formatter_class
+    )
     download_parser.add_argument("outdir", type=Path, help="Output directory to download test data")
 
+    info_parser = subparsers.add_parser(
+        "info", help="Display information about a file", formatter_class=parser.formatter_class
+    )
+    info_parser.add_argument("file", type=Path, help="File to display information about")
+
+    info_parser.add_argument(
+        "--json", action="store_true", help="Output information in JSON format"
+    )
+
+    stats_parser = subparsers.add_parser(
+        "stats", help="Compute MRI statistics", formatter_class=parser.formatter_class
+    )
+    statistics.cli.add_arguments(stats_parser)
+
+    show_parser = subparsers.add_parser(
+        "show", help="Show MRI data in a terminal", formatter_class=parser.formatter_class
+    )
+    show.add_arguments(show_parser)
+
+    napari_parser = subparsers.add_parser(
+        "napari", help="Show MRI data using napari", formatter_class=parser.formatter_class
+    )
+    napari.add_arguments(napari_parser)
+
     return parser
 
 
 def dispatch(parser: argparse.ArgumentParser, argv: Optional[Sequence[str]] = None) -> int:
     args = vars(parser.parse_args(argv))
+
+    if args.pop("version"):
+        version_info()
+        return 0
     logging.basicConfig(level=logging.INFO, format="%(asctime)s - %(levelname)s - %(message)s")
     command = args.pop("command")
     logger = logging.getLogger(__name__)
     try:
         if command == "download-test-data":
             outdir = args.pop("outdir")
             download_data.download_test_data(outdir)
+        elif command == "info":
+            file = args.pop("file")
+            info.nifty_info(file, json_output=args.pop("json"))
+        elif command == "stats":
+            statistics.cli.dispatch(args)
+        elif command == "show":
+            show.dispatch(args)
+        elif command == "napari":
+            napari.dispatch(args)
         else:
             logger.error(f"Unknown command {command}")
             parser.print_help()

src/mritk/data/io.py

@@ -18,7 +18,7 @@
 
 def load_mri_data(
     path: Path | str,
-    dtype: type,
+    dtype: type = np.float64,
     orient: bool = True,
 ) -> MRIData:
     suffix_regex = re.compile(r".+(?P<suffix>(\.nii(\.gz|)|\.mg(z|h)))")

src/mritk/info.py

@@ -0,0 +1,91 @@
+import json
+import typing
+from pathlib import Path
+import numpy as np
+import nibabel as nib
+from rich.console import Console
+from rich.table import Table
+from rich.panel import Panel
+from rich import box
+
+
+def custom_json(obj):
+    if isinstance(obj, np.ndarray):
+        return obj.tolist()
+    elif np.isscalar(obj):
+        return float(obj)
+    else:
+        return str(obj)
+
+
+def nifty_info(filename: Path, json_output: bool = False) -> dict[str, typing.Any]:
+    console = Console()
+
+    # 1. Load the NIfTI file
+
+    img = nib.load(str(filename))
+    header = img.header
+    affine = img.affine
+
+    # --- Part A: Extracting Dimensions & Resolution ---
+    img_shape = img.shape
+    zooms = header.get_zooms()
+    data_type = header.get_data_dtype()
+
+    data = {
+        "filename": str(filename),
+        "shape": img_shape,
+        "voxel_size_mm": zooms,
+        "data_type": data_type,
+        "affine": affine,
+    }
+
+    if json_output:
+        print(json.dumps(data, default=custom_json, indent=4))
+        return data
+
+    # Create a nice header panel
+    console.print(
+        Panel(
+            f"[bold blue]NIfTI File Analysis[/bold blue]\n[green]{filename}[/green]", expand=False
+        )
+    )
+
+    # Create a table for Basic Info
+    info_table = Table(
+        title="Basic Information",
+        box=box.SIMPLE_HEAVY,
+        show_header=True,
+        header_style="bold magenta",
+    )
+    info_table.add_column("Property", style="cyan")
+    info_table.add_column("Value", style="white")
+
+    # Format the tuples/lists as strings for the table
+    shape_str = ", ".join(map(str, img_shape))
+    zoom_str = ", ".join([f"{z:.2f}" for z in zooms])
+
+    info_table.add_row("Shape (x, y, z)", f"({shape_str})")
+    info_table.add_row("Voxel Size (mm)", f"({zoom_str})")
+    info_table.add_row("Data Type", str(data_type))
+
+    console.print(info_table)
+
+    # --- Part B: The Affine Matrix ---
+
+    console.print("\n[bold]Affine Transformation Matrix[/bold] (Voxel → World)", style="yellow")
+
+    # Create a specific table for the matrix to align numbers nicely
+    matrix_table = Table(show_header=False, box=box.ROUNDED, border_style="dim")
+
+    # Add 4 columns for the 4x4 matrix
+    for _ in range(4):
+        matrix_table.add_column(justify="right", style="green")
+
+    for row in affine:
+        # Format numbers to 4 decimal places for cleanliness
+        matrix_table.add_row(*[f"{val: .4f}" for val in row])
+
+    console.print(matrix_table)
+
+    return data