Next release in pyproject

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 23.10.0
+    rev: 23.10.1
     hooks:
     -   id: black
         files: ^src/

README.md

@@ -52,7 +52,7 @@ Please [Star](https://github.com/SpikeInterface/probeinterface/stargazers) the p
 
 ProbeInterface aims to provide a common framework to handle probe information across neuroscience experiments.
 
-ProbeInterface is used by the [SpikeInterface](https://github.com/SpikeInterface/spikeinterface) package to attach a probe information to a recordng object.
+ProbeInterface is used by the [SpikeInterface](https://github.com/SpikeInterface/spikeinterface) package to attach probe information to a recording object.
 You can find detailed documentation in the [SpikeInterface documentation](https://spikeinterface.readthedocs.io/en/latest/modules/core.html#handling-probes).
 
 In practice, ProbeInterface is a lightweight package to handle:

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)
 

doc/release_notes.rst

@@ -6,6 +6,7 @@ Release notes
 .. toctree::
    :maxdepth: 1
 
+   releases/0.2.19.rst
    releases/0.2.18.rst
    releases/0.2.17.rst
    releases/0.2.16.rst

doc/releases/0.2.18.rst

@@ -9,6 +9,9 @@ Features
 
 * Extend probe constructor (name, serial_number, manufacturer, model_name) (#206)
 * Extend available NP2 probe types to commercial types (20** series) (#217)
+* Remove :code:`with_channel_index` argument from :code:`plot_probe` (#229)
+* Remove checker for unique contact ids in probe group (#229)
+* Unify usage of "contact" and remove "channel" notation (except for "device_channel_index") (#229)
 
 
 Bug fixes

doc/releases/0.2.19.rst

@@ -0,0 +1,10 @@
+probeinterface 0.2.19
+---------------------
+
+Nov, 2nd 2023
+
+
+Features
+^^^^^^^^
+
+* Unify NP reading with probe part number (#232)

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

@@ -18,6 +18,10 @@
 2023-06-14
 generate new library
 
+2023-10-30
+Generate new library with some fixes
+
+
 Derive probes to be used with SpikeInterface base on Cambridgeneurotech databases
 Probe library to match and add on
 https://gin.g-node.org/spikeinterface/probeinterface_library/src/master/cambridgeneurotech
@@ -36,16 +40,26 @@
 
 from pathlib import Path
 
+import json
+import shutil
+
 
 # work_dir = r"C:\Users\Windows\Dropbox (Scripps Research)\2021-01-SpikeInterface_CambridgeNeurotech"
 # work_dir = '.'
 # work_dir = '/home/samuel/Documents/SpikeInterface/2021-03-01-probeinterface_CambridgeNeurotech/'
 # work_dir = '/home/samuel/Documents/SpikeInterface/2022-05-20-probeinterface_CambridgeNeurotech/'
 # work_dir = '/home/samuel/Documents/SpikeInterface/2022-10-18-probeinterface_CambridgeNeurotech/'
-work_dir = '/home/samuel/OwnCloudCNRS/probeinterface/2023-06-14-probeinterface-CambridgeNeurotech/'
+# work_dir = '/home/samuel/OwnCloudCNRS/probeinterface/2023-06-14-probeinterface-CambridgeNeurotech/'
+work_dir = '/home/samuel/OwnCloudCNRS/probeinterface/2023-10-30-probeinterface-CambridgeNeurotech/'
+
+
+library_folder = '/home/samuel/Documents/SpikeInterface/probeinterface_library/cambridgeneurotech/'
+
+library_folder = Path(library_folder)
+
 work_dir = Path(work_dir).absolute()
 
-export_folder = work_dir / 'export_2023_06_14'
+export_folder = work_dir / 'export_2023_10_30'
 probe_map_file = work_dir /  'ProbeMaps_Final2023.xlsx'
 probe_info_table_file = work_dir  / 'ProbesDataBase_Final2023.csv'
 
@@ -74,7 +88,7 @@ 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 +193,7 @@ 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
@@ -244,22 +258,57 @@ 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)
 
 
+def synchronize_library():
+
+    for source_probe_file in export_folder.glob('**/*.json'):
+        # print()
+        print(source_probe_file.stem)
+        target_probe_file = library_folder / source_probe_file.parent.stem / source_probe_file.name
+        # print(target_probe_file)
+        with open(source_probe_file, mode='r')as source:
+            source_dict = json.load(source)
+
+        with open(target_probe_file, mode='r')as target:
+            target_dict = json.load(target)
+
+        source_dict.pop('version')
+
+        target_dict.pop('version')
+
+        # this was needed between version 0.2.17 > 0.2.18
+        # target_dict["probes"][0]["annotations"].pop("first_index")
+
+        same = source_dict == target_dict
+
+        # copy the json
+        shutil.copyfile(source_probe_file, target_probe_file)
+        if not same:
+            # copy the png
+            shutil.copyfile(source_probe_file.parent / (source_probe_file.stem + '.png'),
+                            target_probe_file.parent / (target_probe_file.stem + '.png')                      )
+
+
+
+
+
+
+    # library_folder
+
 if __name__ == '__main__':
-    generate_all_probes()
+    # generate_all_probes()
+    synchronize_library()

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