merge

Author: h-mayorquin

probeinterface/io.py

@@ -726,6 +726,7 @@ def write_csv(file, probe):
 # A map from probe type to geometry_parameters
 npx_probe = {
     # Neuropixels 1.0
+    # This probably should be None or something else because NOT ONLY the neuropixels 1.0 have that imDatPrb_type
     0: {
         "probe_name": "Neuropixels 1.0",
         "x_pitch": 32,
@@ -798,7 +799,7 @@ def write_csv(file, probe):
     },
     # Neuropixels 1.0-NHP Short (10mm)
     1015: {
-        "probe_name": "Neuropixels 1.0-NHP - medium",
+        "probe_name": "Neuropixels 1.0-NHP - short",
         "x_pitch": 32,
         "y_pitch": 20,
         "contact_width": 12,
@@ -918,7 +919,19 @@ def write_csv(file, probe):
     },
 }
 
-def read_imro(file):
+# Map imDatPrb_pn to imDatPrb_type when the latter is missing
+probe_number_to_probe_type = {
+    "PRB_1_4_0480_1": 0,
+    "PRB_1_4_0480_1_C": 0,
+    "NP1015": 1015,
+    "NP1022": 1022,
+    "NP1030": 1030,
+    "NP1031": 1031,
+    "NP1032": 1032,
+}
+
+    
+def read_imro(file: Union[str, Path]) -> Probe:
     """
     Read probe position from the imro file used in input of SpikeGlx and Open-Ephys for neuropixels probes.
 
@@ -940,7 +953,7 @@ def read_imro(file):
     return _read_imro_string(imro_str)
 
 
-def _read_imro_string(imro_str: str) -> Probe:
+def _read_imro_string(imro_str: str, imDatPrb_pn: str = None) -> Probe:
     """
     Low-level function to parse the imro table when presented as a string
     
@@ -959,6 +972,9 @@ def _read_imro_string(imro_str: str) -> Probe:
     else:
         raise RuntimeError(f'read_imro error, the header has a strange length: {len(header)}')
 
+    if imDatPrb_type in [0, None]:
+        imDatPrb_type = probe_number_to_probe_type[imDatPrb_pn] 
+    
     probe_information = npx_probe[imDatPrb_type]
     fields = probe_information["fields_in_imro_table"]
     contact_info = {k: [] for k in fields}
@@ -977,10 +993,9 @@ def _read_imro_string(imro_str: str) -> Probe:
 
 
     # compute position
-    x_idx = elec_ids % probe_information["ncol"]
-    y_idx = elec_ids // probe_information["ncol"]
-    x_pitch = probe_information["x_pitch"]
-    y_pitch = probe_information["y_pitch"]
+    y_idx, x_idx = np.divmod(elec_ids, npx_probe[imDatPrb_type]["ncol"])
+    x_pitch = npx_probe[imDatPrb_type ]["x_pitch"]
+    y_pitch = npx_probe[imDatPrb_type ]["y_pitch"]
 
     stagger =  np.mod(y_idx + 1, 2) * probe_information["stagger"]
     x_pos = x_idx * x_pitch + stagger
@@ -1106,8 +1121,9 @@ def read_spikeglx(file: Union[str, Path]) -> Probe:
 
     assert "imroTbl" in meta, "Could not find imroTbl field in meta file!"
     imro_table = meta['imroTbl']
+    imDatPrb_pn = meta.get("imDatPrb_pn", None)
 
-    probe = _read_imro_string(imro_table)
+    probe = _read_imro_string(imro_str=imro_table, imDatPrb_pn=imDatPrb_pn)
 
     # sometimes we need to slice the probe when not all channels are saved
     saved_chans = get_saved_channel_indices_from_spikeglx_meta(meta_file)