[Neuropixels] Add OpenEphys settings.xml channel fixing script

src/constantinople_lab_to_nwb/schierek_embargo_2024/schierek_embargo_2024_notes.md

@@ -157,3 +157,35 @@ We are using this computed time shift to shift the ephys timestamps.
 The following UML diagram shows the mapping of source data to NWB.
 
 ![nwb mapping](schierek_embargo_2024_uml.png)
+
+## OpenEphys XML Channel Fixer
+
+This utility helps fix OpenEphys `settings.xml` files when channels are accidentally dropped by the OpenEphys GUI.
+This issue can prevent proper data extraction using our extractors. The script identifies missing AP channels and adds
+them back to the XML configuration with the correct electrode positions.
+
+
+### Usage
+
+```python
+from constantinople_to_nwb.utils import fix_settings_xml_missing_channels
+import probeinterface
+from pathlib import Path
+
+# Path to the settings.xml file
+settings_path = Path("/path/to/your/Ephys Data/E003_2022-08-22_14-56-16/Record Node 103/settings.xml")
+
+# Fix the XML file
+modified_path = fix_settings_xml_missing_channels(
+    settings_xml_file_path=settings_path,
+    # Optional: specify AP stream name to verify the file can be read with probeinterface
+    stream_name="Record Node 103#Neuropix-PXI-100.0"
+)
+
+# Verify the channel configuration has been updated successfully
+ap_stream_name = "Record Node 103#Neuropix-PXI-100.0"  # The name of the AP recording stream
+probe = probeinterface.read_openephys(
+  settings_file=settings_path, stream_name=ap_stream_name
+)
+assert len(probe.contact_ids) == 384
+```

src/constantinople_lab_to_nwb/utils/__init__.py

@@ -1 +1,2 @@
+from .fix_xml_openephys import fix_settings_xml_missing_channels
 from .get_subject_metadata import get_subject_metadata_from_rat_info_folder

src/constantinople_lab_to_nwb/utils/fix_xml_openephys.py

@@ -0,0 +1,92 @@
+from pathlib import Path
+from typing import Union
+
+import numpy as np
+from lxml import etree
+
+
+def fix_settings_xml_missing_channels(
+    settings_xml_file_path: Union[str, Path],
+    ap_stream_name: str = None,
+):
+    """
+    Modify OpenEphys settings file (settings.xml) to include missing AP channels and their electrode positions.
+
+    This function:
+    1. Loads an XML settings file
+    2. Identifies missing AP channels
+    3. Adds missing channels with appropriate X/Y positions based on detected patterns
+    4. Overwrites the XML settings file with the updated configuration
+    5. Optionally, verifies the result using probeinterface
+
+    Args:
+        settings_xml_file_path (Union[str, Path]): Path to the input XML settings file
+        ap_stream_name (str): Name of the data stream for probeinterface verification (optional)
+
+    Raises:
+        FileNotFoundError: If the input file doesn't exist
+        ValueError: If the XML structure is invalid or required tags are missing
+        AssertionError: If the final probe configuration is invalid
+    """
+    settings_xml_file_path = Path(settings_xml_file_path)
+    if not settings_xml_file_path.exists():
+        raise FileNotFoundError(f"Settings file not found: {settings_xml_file_path}")
+
+    try:
+        tree = etree.parse(str(settings_xml_file_path))
+        root = tree.getroot()
+
+        # Locate the <CHANNELS>, <ELECTRODE_XPOS>, and <ELECTRODE_YPOS> tags
+        all_channels_from_channel_info = root.xpath(".//CHANNEL_INFO/CHANNEL")
+        # Extract AP channels
+        all_ap_channels = set(
+            sorted(
+                int(channel.attrib["number"])
+                for channel in all_channels_from_channel_info
+                if "AP" in channel.attrib["name"]
+            )
+        )
+
+        channels_tag = root.xpath(".//CHANNELS")[0]
+        electrode_xpos_tag = root.xpath(".//ELECTRODE_XPOS")[0]
+        electrode_ypos_tag = root.xpath(".//ELECTRODE_YPOS")[0]
+
+        # Extract channel numbers from the attributes
+        channel_numbers = sorted(int(attr[2:]) for attr in channels_tag.attrib.keys())
+
+        # Identify missing channels
+        missing_channels = sorted(all_ap_channels - set(channel_numbers))
+
+        # Detect repeating pattern in <ELECTRODE_XPOS> values
+        xpos_values = [int(value) for value in electrode_xpos_tag.attrib.values()]
+        pattern_length = next(
+            (i for i in range(1, len(xpos_values) // 2) if xpos_values[:i] == xpos_values[i : 2 * i]), len(xpos_values)
+        )
+        xpos_pattern = xpos_values[:pattern_length]
+
+        # Detect repeating pattern in <ELECTRODE_YPOS> values
+        ypos_values = [int(value) for value in electrode_ypos_tag.attrib.values()]
+        ypos_step = np.unique(np.diff(sorted(set(ypos_values))))[0]
+
+        # Insert missing channels
+        for missing_channel in missing_channels:
+            channels_tag.set(f"CH{missing_channel}", "0")
+            pattern_value = xpos_pattern[missing_channel % pattern_length]
+            electrode_xpos_tag.set(f"CH{missing_channel}", str(pattern_value))
+
+            pattern_value_ypos = (missing_channel // 2) * ypos_step  # 20
+            electrode_ypos_tag.set(f"CH{missing_channel}", str(pattern_value_ypos))
+
+        # Save the updated XML to a new file
+        tree.write(str(settings_xml_file_path), pretty_print=True)
+
+    except Exception as e:
+        print(f"Failed to modify settings XML: {str(e)}")
+        raise
+
+    if ap_stream_name is not None:
+        import probeinterface
+
+        probe = probeinterface.read_openephys(settings_file=settings_xml_file_path, stream_name=ap_stream_name)
+        assert len(probe.contact_ids) == 384
+        print("Probe configuration verified successfully.")