add support for directly give npz file as arg

Author: JosephBrunet

src/cardiotensor/scripts/visualize_streamlines.py

@@ -5,9 +5,14 @@
 CLI tool to visualize cardiac streamlines from a .npz file using FURY.
 Supports coloring by helix angle or elevation, custom colormaps,
 and optional screenshot export.
+
+Now accepts either:
+  1) a .conf file (as before, reads OUTPUT_PATH/streamlines.npz), or
+  2) a direct path to streamlines .npz
 """
 
 import argparse
+import sys
 from pathlib import Path
 
 import matplotlib.pyplot as plt
@@ -20,18 +25,22 @@
 def script():
     parser = argparse.ArgumentParser(
         description=(
-            "Visualize cardiac streamlines from a .npz file.\n"
-            "Streamlines are typically generated by Cardiotensor.\n"
-            "You can color them by helix angle (HA) or elevation angle,\n"
-            "adjust rendering style, crop regions, and save screenshots."
+            "Visualize cardiac streamlines.\n"
+            "Pass either a .conf file (will use OUTPUT_PATH/streamlines.npz) "
+            "or pass a streamlines .npz file directly.\n"
+            "You can color by helix angle (HA) or elevation angle, adjust rendering, crop, "
+            "and save screenshots."
         ),
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
     )
 
     parser.add_argument(
-        "conf_file",
+        "input_path",
         type=Path,
-        help="Path to configuration file (.conf) containing OUTPUT_PATH with streamlines.npz.",
+        help=(
+            "Path to either a configuration file (.conf) containing OUTPUT_PATH, "
+            "or directly to a streamlines .npz file."
+        ),
     )
     parser.add_argument(
         "--color-by",
@@ -142,10 +151,32 @@ def script():
             )
             chosen_cmap = helix_angle_cmap
 
-    # Read conf file only in CLI
-    params = read_conf_file(args.conf_file)
-    output_dir = Path(params.get("OUTPUT_PATH", "./output"))
-    streamlines_file = output_dir / "streamlines.npz"
+    # Resolve streamlines file depending on input type
+    if not args.input_path.exists():
+        print(f"❌ Input path not found: {args.input_path}")
+        sys.exit(1)
+
+    suffix = args.input_path.suffix.lower()
+
+    if suffix == ".conf":
+        # Read conf file and construct path to streamlines.npz
+        params = read_conf_file(args.input_path)
+        output_dir = Path(params.get("OUTPUT_PATH", "./output"))
+        streamlines_file = output_dir / "streamlines.npz"
+        if not streamlines_file.exists():
+            print(
+                f"❌ streamlines.npz not found at: {streamlines_file}\n"
+                f"(Derived from OUTPUT_PATH in {args.input_path})"
+            )
+            sys.exit(1)
+    elif suffix == ".npz":
+        # Direct .npz provided
+        streamlines_file = args.input_path
+    else:
+        print(
+            "❌ Unsupported input. Provide either a .conf file or a streamlines .npz file."
+        )
+        sys.exit(1)
 
     # Compute crop bounds if provided
     crop_bounds = None
@@ -156,7 +187,7 @@ def script():
             tuple(args.crop_z or [-float("inf"), float("inf")]),
         )
 
-    # Call Python function
+    # Call visualization
     visualize_streamlines(
         streamlines_file=streamlines_file,
         color_by=args.color_by,