Remove channel index concept

doc/generate_format_example.py

@@ -33,7 +33,7 @@
 print(d.keys())
 
 fig, ax = plt.subplots(figsize=(8, 8))
-plot_probe(probe, with_channel_index=True, ax=ax)
+plot_probe(probe, ax=ax)
 ax.set_xlim(-50, 200)
 ax.set_ylim(-150, 120)
 

examples/ex_03_generate_probe_group.py

@@ -34,7 +34,7 @@
 
 print('probe0.get_contact_count()', probe0.get_contact_count())
 print('probe1.get_contact_count()', probe1.get_contact_count())
-print('probegroup.get_channel_count()', probegroup.get_channel_count())
+print('probegroup.get_contact_count()', probegroup.get_contact_count())
 
 ##############################################################################
 #  We can now plot all probes in the same axis:
@@ -44,6 +44,6 @@
 ##############################################################################
 #  or in separate axes:
 
-plot_probe_group(probegroup, same_axes=False, with_channel_index=True)
+plot_probe_group(probegroup, same_axes=False, with_contact_id=True)
 
 plt.show()

examples/ex_05_device_channel_indices.py

@@ -29,7 +29,7 @@
                                      xpitch=75, ypitch=75, y_shift_per_column=[0, -37.5, 0],
                                      contact_shapes='circle', contact_shape_params={'radius': 12})
 
-plot_probe(probe, with_channel_index=True)
+plot_probe(probe, with_contact_id=True)
 
 ##############################################################################
 # The Probe is not connected to any device yet:
@@ -51,7 +51,7 @@
 #  * the prbXX is the contact index ordered from 0 to N
 #  * the devXX is the channel index on the device (with the second half reversed)
 
-plot_probe(probe, with_channel_index=True, with_device_index=True)
+plot_probe(probe, with_contact_id=True, with_device_index=True)
 
 ##############################################################################
 # Very often we have several probes on the device and this can lead to even
@@ -85,6 +85,6 @@
 # The indices of the probe group can also be plotted:
 
 fig, ax = plt.subplots()
-plot_probe_group(probegroup, with_channel_index=True, same_axes=True, ax=ax)
+plot_probe_group(probegroup, with_contact_id=True, same_axes=True, ax=ax)
 
 plt.show()

examples/ex_06_import_export_to_file.py

@@ -98,6 +98,6 @@
     f.write(prb_two_tetrodes)
 
 two_tetrode = read_prb('two_tetrodes.prb')
-plot_probe_group(two_tetrode, same_axes=False, with_channel_index=True)
+plot_probe_group(two_tetrode, same_axes=False, with_contact_id=True)
 
 plt.show()

examples/ex_07_probe_generator.py

@@ -35,7 +35,7 @@
 df = probegroup.to_dataframe()
 df
 
-plot_probe_group(probegroup, with_channel_index=True, same_axes=True)
+plot_probe_group(probegroup, with_contact_id=True, same_axes=True)
 
 ##############################################################################
 # Generate a linear probe:
@@ -44,7 +44,7 @@
 from probeinterface import generate_linear_probe
 
 linear_probe = generate_linear_probe(num_elec=16, ypitch=20)
-plot_probe(linear_probe, with_channel_index=True)
+plot_probe(linear_probe, with_contact_id=True)
 
 ##############################################################################
 # Generate a multi-column probe:
@@ -57,7 +57,7 @@
                                              xpitch=22, ypitch=20,
                                              y_shift_per_column=[0, -10, 0],
                                              contact_shapes='square', contact_shape_params={'width': 12})
-plot_probe(multi_columns, with_channel_index=True, )
+plot_probe(multi_columns, with_contact_id=True, )
 
 ##############################################################################
 # Generate a square probe:

examples/ex_10_get_probe_from_library.py

@@ -39,7 +39,7 @@
 # When plotting, the channel indices are automatically displayed with
 # one-based notation (even if internally everything is still zero based):
 
-plot_probe(probe, with_channel_index=True)
+plot_probe(probe, with_contact_id=True)
 
 ##############################################################################
 

examples/ex_11_automatic_wiring.py

@@ -52,7 +52,7 @@
 #    * the lower "devXX" is the channel on the Intan device (zero-based)
 
 fig, ax = plt.subplots(figsize=(5, 15))
-plot_probe(probe, with_channel_index=True, with_device_index=True, ax=ax)
+plot_probe(probe, with_contact_id=True, with_device_index=True, ax=ax)
 
 
 plt.show()

resources/generate_cambridgeneurotech_libray.py

@@ -74,7 +74,7 @@ def convert_contact_shape(listCoord):
     listCoord = [float(s) for s in listCoord.split(' ')]
     return listCoord
 
-def get_channel_index(connector, probe_type):
+def get_contact_order(connector, probe_type):
     """
     Get the channel index given a connector and a probe_type.
     This will help to re-order the probe contact later on.
@@ -179,7 +179,7 @@ def create_CN_figure(probe_name, probe):
     plot_probe(probe, ax=ax,
             contacts_colors = ['#5bc5f2'] * n,  # made change to default color
             probe_shape_kwargs = dict(facecolor='#6f6f6e', edgecolor='k', lw=0.5, alpha=0.3), # made change to default color
-            with_channel_index=True)
+            with_contact_id=True)
 
     ax.set_xlabel(u'Width (\u03bcm)') #modif to legend
     ax.set_ylabel(u'Height (\u03bcm)') #modif to legend
@@ -244,18 +244,16 @@ def generate_all_probes():
                 #~ continue
             print('  ', probe_name)
 
-            channelIndex = get_channel_index(connector = connector, probe_type = probe_info['part'])
+            contact_order = get_contact_order(connector = connector, probe_type = probe_info['part'])
 
-            order = np.argsort(channelIndex)
-            probe = probe_unordered.get_slice(order)
+            sorted_indices = np.argsort(contact_order)
+            probe = probe_unordered.get_slice(sorted_indices)
 
-            probe.annotate(name=probe_name,
-                            manufacturer='cambridgeneurotech',
-                            first_index=1)
+            probe.annotate(name=probe_name, manufacturer='cambridgeneurotech')
 
             # one based in cambridge neurotech
-            contact_ids = np.arange(order.size) + 1
-            contact_ids =contact_ids.astype(str)
+            contact_ids = np.arange(sorted_indices.size) + 1
+            contact_ids = contact_ids.astype(str)
             probe.set_contact_ids(contact_ids)
 
             export_one_probe(probe_name, probe)

src/probeinterface/generator.py

@@ -148,6 +148,7 @@ def generate_multi_columns_probe(
     probe = Probe(ndim=2, si_units="um")
     probe.set_contacts(positions=positions, shapes=contact_shapes, shape_params=contact_shape_params)
     probe.create_auto_shape(probe_type="tip", margin=25)
+    probe.set_contact_ids(np.arange(positions.shape[0]).astype("str"))
 
     return probe
 

src/probeinterface/io.py

@@ -1067,7 +1067,7 @@ def _read_imro_string(imro_str: str, imDatPrb_pn: Optional[str] = None) -> Probe
     x_pos = x_idx * x_pitch + stagger
     y_pos = y_idx * y_pitch
 
-    if imDatPrb_type == 24:
+    if probe_description["shank_number"] > 1:
         shank_ids = np.array(contact_info["shank_id"])
         shank_pitch = probe_description["shank_pitch"]
         contact_ids = [f"s{shank_id}e{elec_id}" for shank_id, elec_id in zip(shank_ids, elec_ids)]
@@ -1468,13 +1468,13 @@ def read_openephys(
                 break
 
             stagger = np.mod(pos[1] / npx_probe[ptype]["y_pitch"] + 1, 2) * npx_probe[ptype]["stagger"]
-            shank_id = shank_ids[0] if ptype == 24 else 0
+            shank_id = shank_ids[i] if npx_probe[ptype]["shank_number"] > 1 else 0
 
             contact_id = int(
                 (pos[0] - stagger - npx_probe[ptype]["shank_pitch"] * shank_id) / npx_probe[ptype]["x_pitch"]
                 + npx_probe[ptype]["ncol"] * pos[1] / npx_probe[ptype]["y_pitch"]
             )
-            if ptype == 24:
+            if npx_probe[ptype]["shank_number"] > 1:
                 contact_ids.append(f"s{shank_id}e{contact_id}")
             else:
                 contact_ids.append(f"e{contact_id}")

src/probeinterface/plotting.py

@@ -13,11 +13,9 @@ def plot_probe(
     probe,
     ax=None,
     contacts_colors=None,
-    with_channel_index=False,
     with_contact_id=False,
     with_device_index=False,
     text_on_contact=None,
-    first_index="auto",
     contacts_values=None,
     cmap="viridis",
     title=True,
@@ -39,16 +37,12 @@ def plot_probe(
         The axis to plot the probe on. If None, an axis is created, by default None
     contacts_colors : matplotlib color, optional
         The color of the contacts, by default None
-    with_channel_index : bool, optional
-        If True, channel indices are displayed on top of the channels, by default False
     with_contact_id : bool, optional
         If True, channel ids are displayed on top of the channels, by default False
     with_device_index : bool, optional
         If True, device channel indices are displayed on top of the channels, by default False
     text_on_contact: None or list or numpy.array
         Addintional text to plot on each contact
-    first_index : str, optional
-        The first index of the contacts, by default 'auto' (taken from channel ids)
     contacts_values : np.array, optional
         Values to color the contacts with, by default None
     cmap : str, optional
@@ -92,16 +86,6 @@ def plot_probe(
     else:
         fig = ax.get_figure()
 
-    if first_index == "auto":
-        if "first_index" in probe.annotations:
-            first_index = probe.annotations["first_index"]
-        elif probe.annotations.get("manufacturer", None) == "neuronexus":
-            # neuronexus is one based indexing
-            first_index = 1
-        else:
-            first_index = 0
-    assert first_index in (0, 1)
-
     _probe_shape_kwargs = dict(facecolor="green", edgecolor="k", lw=0.5, alpha=0.3)
     _probe_shape_kwargs.update(probe_shape_kwargs)
 
@@ -154,13 +138,11 @@ def on_press(event):
         text_on_contact = np.asarray(text_on_contact)
         assert text_on_contact.size == probe.get_contact_count()
 
-    if with_channel_index or with_contact_id or with_device_index or text_on_contact is not None:
+    if with_contact_id or with_device_index or text_on_contact is not None:
         if probe.ndim == 3:
             raise NotImplementedError("Channel index is 2d only")
         for i in range(n):
             txt = []
-            if with_channel_index:
-                txt.append(f"{i + first_index}")
             if with_contact_id and probe.contact_ids is not None:
                 contact_id = probe.contact_ids[i]
                 txt.append(f"id{contact_id}")

src/probeinterface/probe.py

@@ -221,7 +221,9 @@ def get_shank_count(self) -> int:
         n = len(np.unique(self.shank_ids))
         return n
 
-    def set_contacts(self, positions, shapes="circle", shape_params={"radius": 10}, plane_axes=None, shank_ids=None):
+    def set_contacts(
+        self, positions, shapes="circle", shape_params={"radius": 10}, plane_axes=None, contact_ids=None, shank_ids=None
+    ):
         """Sets contacts to a Probe.
 
         This sets four attributes of the probe:
@@ -241,6 +243,8 @@ def set_contacts(self, positions, shapes="circle", shape_params={"radius": 10},
         plane_axes : np.array (num_contacts, 2, ndim)
             Defines the two axes of the contact plane for each electrode.
             The third dimension corresponds to the probe `ndim` (2d or 3d).
+        contact_ids: None or array of str
+            Defines the contact ids for the contacts. If None, contact ids are not assigned.
         shank_ids : None or array of str
             Defines the shank ids for the contacts. If None, then
             these are assigned to a unique Shank.
@@ -264,6 +268,9 @@ def set_contacts(self, positions, shapes="circle", shape_params={"radius": 10},
         plane_axes = np.array(plane_axes)
         self._contact_plane_axes = plane_axes
 
+        if contact_ids is not None:
+            self.set_contact_ids(contact_ids)
+
         if shank_ids is None:
             self._shank_ids = np.zeros(n, dtype=str)
         else:
@@ -402,9 +409,14 @@ def set_contact_ids(self, contact_ids: np.array | list):
 
         """
         contact_ids = np.asarray(contact_ids)
+        if np.all(contact_ids == ""):
+            self._contact_ids = None
+            return
+
+        assert np.unique(contact_ids).size == contact_ids.size, "Contact ids have to be unique within a Probe"
 
         if contact_ids.size != self.get_contact_count():
-            ValueError(f"channel_indices do not have the same size as number of contacts")
+            ValueError(f"contact_ids do not have the same size as number of contacts")
 
         if contact_ids.dtype.kind != "U":
             contact_ids = contact_ids.astype("U")

src/probeinterface/probegroup.py

@@ -24,7 +24,9 @@ def add_probe(self, probe):
 
     def _check_compatible(self, probe):
         if probe._probe_group is not None:
-            raise ValueError("This probe is already attached to another ProbeGroup")
+            raise ValueError(
+                "This probe is already attached to another ProbeGroup. Use probe.copy() to attach it to another ProbeGroup"
+            )
 
         if probe.ndim != self.probes[-1].ndim:
             raise ValueError("ndim are not compatible")
@@ -38,7 +40,7 @@ def _check_compatible(self, probe):
     def ndim(self):
         return self.probes[0].ndim
 
-    def get_channel_count(self):
+    def get_contact_count(self):
         """
         Total number of channels.
         """
@@ -144,7 +146,7 @@ def get_global_device_channel_indices(self):
         Note:
             channel -1 means not connected
         """
-        total_chan = self.get_channel_count()
+        total_chan = self.get_contact_count()
         channels = np.zeros(total_chan, dtype=[("probe_index", "int64"), ("device_channel_indices", "int64")])
         arr = self.to_numpy(complete=True)
         channels["probe_index"] = arr["probe_index"]
@@ -156,7 +158,7 @@ def set_global_device_channel_indices(self, channels):
         Set global indices for all probes
         """
         channels = np.asarray(channels)
-        if channels.size != self.get_channel_count():
+        if channels.size != self.get_contact_count():
             raise ValueError("Wrong channels size")
 
         # first reset previsous indices
@@ -187,14 +189,6 @@ def check_global_device_wiring_and_ids(self):
         if valid_chans.size != np.unique(valid_chans).size:
             raise ValueError("channel device index are not unique across probes")
 
-        # check unique ids for != ''
-        all_ids = self.get_global_contact_ids()
-        keep = [e != "" for e in all_ids]
-        valid_ids = all_ids[keep]
-
-        if valid_ids.size != np.unique(valid_ids).size:
-            raise ValueError("contact_ids are not unique across probes")
-
     def auto_generate_probe_ids(self, *args, **kwargs):
         """
         Annotate all probes with unique probe_id values.
@@ -230,13 +224,10 @@ def auto_generate_contact_ids(self, *args, **kwargs):
             `probeinterface.utils.generate_unique_ids`
         """
 
-        if any(p.contact_ids is not None for p in self.probes):
-            raise ValueError("Some contacts already have contact ids " "assigned.")
-
         if not args:
             args = 1e7, 1e8
         # 3rd argument has to be the number of probes
-        args = args[:2] + (self.get_channel_count(),)
+        args = args[:2] + (self.get_contact_count(),)
 
         contact_ids = generate_unique_ids(*args, **kwargs).astype(str)
 

tests/test_generator.py

@@ -27,7 +27,7 @@ def test_generate():
 
     #~ from probeinterface.plotting import plot_probe_group, plot_probe
     #~ import matplotlib.pyplot as plt
-    #~ plot_probe(multi_shank, with_channel_index=True,)
+    #~ plot_probe(multi_shank, with_contact_id=True,)
     #~ plt.show()
 
 if __name__ == '__main__':

tests/test_io/test_io.py

@@ -39,8 +39,8 @@ def test_probeinterface_format(tmp_path):
 
     # ~ from probeinterface.plotting import plot_probe_group
     # ~ import matplotlib.pyplot as plt
-    # ~ plot_probe_group(probegroup, with_channel_index=True, same_axes=False)
-    # ~ plot_probe_group(probegroup2, with_channel_index=True, same_axes=False)
+    # ~ plot_probe_group(probegroup, with_contact_id=True, same_axes=False)
+    # ~ plot_probe_group(probegroup2, with_contact_id=True, same_axes=False)
     # ~ plt.show()
 
 def test_writeprobeinterface(tmp_path):
@@ -210,7 +210,7 @@ def test_prb(tmp_path):
 
     # ~ from probeinterface.plotting import plot_probe_group
     # ~ import matplotlib.pyplot as plt
-    # ~ plot_probe_group(probegroup, with_channel_index=True, same_axes=False)
+    # ~ plot_probe_group(probegroup, with_contact_id=True, same_axes=False)
     # ~ plt.show()
 
     # from probeinterface.plotting import plot_probe

tests/test_io/test_openephys.py

@@ -117,5 +117,5 @@ def test_older_than_06_format():
 
 
 if __name__ == "__main__":
-    test_multiple_probes()
+    # test_multiple_probes()
     test_older_than_06_format()