Merge pull request #25 from SpikeInterface/clean-up-naming

Add naming convention and cleanup

Author: samuelgarcia

RELEASE_NOTES.md

@@ -0,0 +1,13 @@
+# RELEASES
+
+
+## 2025-10-02
+
+- Unified naming convention: `{manufacturer}/{model_name}/{model_name}.json`.
+- Added `generate_image.py` script to create probe images from JSON files.
+- Added test to ensure naming convention.
+- Added `RELEASE_NOTES.md` for tracking changes.
+
+### Changes in probes:
+- `sinaps`: folder renamed to `sinaps-research-platform`
+- `plexon`: manufacturer name in JSON files changed from `Plexon-SiNAPS` to `plexon`

generate_image.py

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+import argparse
+import numpy as np
+from pathlib import Path
+from probeinterface import Probe, read_probeinterface
+from probeinterface.plotting import plot_probe
+
+import matplotlib.pyplot as plt
+
+def load_probegroup_from_json(manufacturer, model_name):
+    """Load probegroup from JSON file based on manufacturer and model name."""
+    json_file = Path(__file__).parent / manufacturer / model_name / f"{model_name}.json"
+
+    # Create probe from JSON data
+    probegroup = read_probeinterface(json_file)
+    return probegroup
+
+def plot_and_save_probegroup(
+    probegroup, 
+    manufacturer, 
+    model_name,
+    with_contact_id=True,
+    title_fontsize=10, 
+    label_fontsize=5, 
+    contact_id_fontsize=5,
+    save_figure=False,
+    zoom_on_tip=False,
+    dpi=300,
+    figsize=(15, 15)
+):
+    """Plot probegroup and optionally save to file."""
+    probe = probegroup.probes[0]
+    if zoom_on_tip:
+        ncols = 2
+    else:
+        ncols = 1
+    fig, axs = plt.subplots(figsize=figsize, ncols=ncols)
+    if zoom_on_tip:
+        ax_full, ax_tip = axs
+    else:
+        ax_full = axs
+    plot_probe(probe, with_contact_id=with_contact_id, ax=ax_full)
+    for txt in ax_full.texts:
+        txt.set_fontsize(contact_id_fontsize)
+
+    title = f"{manufacturer} - {model_name}"
+    if probe.description:
+        title += f"\n{probe.description}"
+    title += f"\n{probe.get_contact_count()}ch {probe.get_shank_count()}shank(s)"
+    ax_full.set_ylabel("Y (µm)", fontsize=label_fontsize)
+    ax_full.tick_params(axis='both', which='major', labelsize=label_fontsize)
+
+    if zoom_on_tip:
+        ax_full.spines[['top', 'right']].set_visible(False)
+        ax_full.set_title("")
+        ax_full.set_xlabel("")
+        ax_tip.spines[['top', 'right']].set_visible(False)
+        plot_probe(probe, with_contact_id=with_contact_id, ax=ax_tip)
+        shank_tip_y = np.min(probe.probe_planar_contour[:, 1])
+        shank_left = np.min(probe.probe_planar_contour[:, 0])
+        shank_right = np.max(probe.probe_planar_contour[:, 0])
+        shank_width = shank_right - shank_left
+        ax_tip.set_xlim(shank_left - 0.5*shank_width, shank_right + 0.5*shank_width)
+        ax_tip.set_ylim(shank_tip_y - 20, 200)
+        ax_tip.set_title("")
+        fig.suptitle(title, fontsize=title_fontsize)
+    else:
+        ax_full.set_title(title, fontsize=title_fontsize)
+        ax_full.set_xlabel("X (µm)", fontsize=label_fontsize)
+
+    if save_figure:
+        save_dir = Path(__file__).parent / manufacturer / model_name
+        save_dir.mkdir(parents=True, exist_ok=True)
+        output_file = save_dir / f"{model_name}.png"
+        fig.savefig(output_file, dpi=dpi)
+        print(f"Image saved to: {output_file}")
+    else:
+        plt.show()
+    
+    plt.close(fig)
+
+def main():
+    parser = argparse.ArgumentParser(description="Generate probe images from JSON files")
+    parser.add_argument("manufacturer", help="Probe manufacturer name")
+    parser.add_argument("--model-name", help="Probe model name")
+    parser.add_argument("--with-ids", "-ids", action="store_true", help="Display contact IDs")
+    parser.add_argument("--save-figure", "-s", action="store_true", help="Save the figure to a file")
+    parser.add_argument("--zoom-on-tip", "-z", action="store_true", help="Zoom in on the probe tip")
+    parser.add_argument("--dpi", type=int, default=600, help="DPI for saved figure")
+    parser.add_argument("--title-fontsize", "-t", type=int, default=15, help="Font size for the title")
+    parser.add_argument("--label-fontsize", "-l", type=int, default=10, help="Font size for the labels")
+    parser.add_argument("--contact-id-fontsize", "-c", type=int, default=2, help="Font size for contact IDs")
+
+    args = parser.parse_args()
+    
+    try:
+        if args.model_name is None:
+            # find model names
+            manufacturer_dir = Path(__file__).parent / args.manufacturer
+            if not manufacturer_dir.exists() or not manufacturer_dir.is_dir():
+                raise FileNotFoundError(f"Manufacturer directory not found: {manufacturer_dir}")
+            model_names = [d.name for d in manufacturer_dir.iterdir() if d.is_dir()]
+        else:
+            model_names = [args.model_name]
+        for model_name in model_names:
+            # Load probegroup from JSON
+            probegroup = load_probegroup_from_json(args.manufacturer, model_name)
+
+            # Plot and save
+            plot_and_save_probegroup(
+                probegroup=probegroup,
+                manufacturer=args.manufacturer,
+                model_name=model_name,
+                save_figure=args.save_figure,
+                zoom_on_tip=args.zoom_on_tip,
+                with_contact_id=args.with_ids,
+                title_fontsize=args.title_fontsize,
+                label_fontsize=args.label_fontsize,
+                contact_id_fontsize=args.contact_id_fontsize,
+                dpi=args.dpi
+            )
+
+    except FileNotFoundError as e:
+        print(f"Error: {e}")
+    except Exception as e:
+        print(f"Unexpected error: {e}")
+
+if __name__ == "__main__":
+    main()