ndi.fun.probe.import.kilosort.getInfo
NDI.FUN.PROBE.IMPORT.KILOSORT.GETINFO - summarize the kilosort/phy output for a probe
[INFO, SUMMARY] = NDI.FUN.PROBE.IMPORT.KILOSORT.GETINFO(S, PROBE, ...)
Reads the curated Kilosort/Phy output directory for the probe PROBE in the
ndi.session S and returns a summary of what is there (without importing
anything or touching the database). This is useful for inspecting a sort
before calling NDI.FUN.PROBE.IMPORT.KILOSORT.PROBE.
The directory is located the same way as the importer:
[S.path]/[kilosort_dir]/[probe_directory]/[subdir]/
The [probe_directory] name comes from ndi.fun.file.elementDirectoryName;
for a probe named 'ctx' with reference 1 it is 'ctx_-_1'. Folders written
by older versions of NDI, which used a '|' separator ('ctx_|_1'), are still
found and used if they are present.
INFO is a structure with fields:
directory - the directory that was read
num_clusters - number of curated clusters
cluster_ids - vector of cluster ids
cluster_labels - string array of the label/tag for each cluster
unique_tags - string array of the distinct labels/tags present
tag_counts - number of clusters carrying each unique tag (parallel
to unique_tags)
num_spikes_total - total number of spikes across all clusters
num_spikes - vector of spike counts per cluster (parallel to cluster_ids)
would_import - logical vector, true for clusters whose tag is in
quality_labels (i.e. would be imported by default)
num_would_import - number of clusters that would be imported
num_templates - number of Kilosort templates (NaN if templates absent)
num_channels - number of channels in the templates (NaN if absent)
samples_per_template - samples per template waveform (NaN if absent)
binary_found - true if the raw binary recording could be located (used
by the importer to recalculate wide mean waveforms)
binary_file - resolved path to the raw binary ('' if not found)
binary_dat_path - the raw 'dat_path' string from params.py, if any ('')
binary_num_channels- channel count that would be used to read the binary (NaN)
SUMMARY is a multiline character array giving a human-readable version of INFO.
Name/value pairs (defaults match NDI.FUN.PROBE.IMPORT.KILOSORT.PROBE):
---------------------------------------------------------------------------------
| Parameter (default) | Description |
|--------------------------------|-----------------------------------------------|
| kilosort_dir ('kilosort') | Name of the directory holding kilosort output |
| subdir ('kilosort_output') | Subfolder within the probe's directory |
| noSubFolder (false) | If true, read directly from the probe's dir |
| quality_labels (["good" "mua"])| Labels that would be imported (for would_import)|
| binary_file ('') | Explicit path to the raw binary; when empty it|
| | is located from the .metadata sidecar (not |
| | params.py dat_path), for reporting. |
---------------------------------------------------------------------------------
Example:
S = ndi.session.dir('/path/to/session');
p = S.getprobes('type','n-trode');
[info, summary] = ndi.fun.probe.import.kilosort.getInfo(S, p{1});
disp(summary);
See also: NDI.FUN.PROBE.IMPORT.KILOSORT.PROBE