Open folders with user altered filenames in SpikeGLX #1608
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Co-authored-by: Alessio Buccino <[email protected]>
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OK, I added the tests and this should be ready for review. |
| @@ -82,14 +82,11 @@ class SpikeGLXRawIO(BaseRawWithBufferApiIO): | |||
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| Notes | |||
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| * Contrary to other implementations this IO reads the entire folder and subfolders and: | |||
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Changed this because it is not clear what other implementations this is referring to, probably the ones before but then I don't think it should be here.
| * For imec device both "ap" and "lf" are extracted so one device have several "streams" | ||
| * There are several versions depending the neuropixel probe generation (`1.x`/`2.x`/`3.x`) | ||
| * Here, we assume that the `meta` file has the same structure across all generations. | ||
| * This IO is developed based on neuropixel generation 2.0, single shank recordings. |
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I think this is a note of the first version but we have gradually added support. This supports the shanked version just fine and also NHP and other varieties.
| * Here, we assume that the `meta` file has the same structure across all generations. | ||
| * This IO is developed based on neuropixel generation 2.0, single shank recordings. | ||
| * This IO reads the entire folder and subfolders locating the `.bin` and `.meta` files | ||
| * Handles gates and triggers as segments (based on the `_gt0`, `_gt1`, `_t0` , `_t1` in filenames) |
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Added specific mention to gates and triggers as that is more in line with SpikeGLX documentation.
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| order_key = list({make_key(info) for info in info_list}) | ||
| order_key = sorted(order_key) | ||
| # This sets non-integers values before integers |
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So this section is the core of the PR. It uses the same mechanism that we have for gates and triggers before but also for probe index.:
- It creates a set of unique combinations of (gate, trigger) and (probe, port,dock).
- That combination is used to create the index (segment index and probe index)
- The parameters of info are used to assign the segment and probe index with a dict.
The normalize lambda unifies this behavior. Maybe there is a better naming but I could not come with anything, it just follows the convention that Sam had before.
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| # Define stream base on device [imec|nidq], device_index and stream_kind [ap|lf] for imec | ||
| for info in info_list: |
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This defines the stream here after all the information is available. Previously, it was done inside the extract_info_function.
| @@ -488,13 +513,15 @@ def extract_stream_info(meta_file, meta): | |||
| else: | |||
| # NIDQ case | |||
| has_sync_trace = False | |||
| fname = Path(meta_file).stem | |||
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| bin_file_path = meta["fileName"] | |||
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This is the part that uses the meta["fileName"] (the original one) instead of the file_path in the system (which the user might have changed).
| @@ -563,12 +593,15 @@ def extract_stream_info(meta_file, meta): | |||
| info["trigger_num"] = trigger_num | |||
| info["device"] = device | |||
| info["stream_kind"] = stream_kind | |||
| info["stream_name"] = stream_name | |||
| info["device_kind"] = meta.get("typeThis", device.split(".")[0]) | |||
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Get the device kind directly from the metadata. imec or nidq. All non-production probes should have this in their metadata. For production probes this would rely on file parsing as we were doing before:
Should fix #1606
To solve #1606 this does two things:
Both things should make the reader more robust.
I am preparing some data for gin where the filename was changed. I will change this from draft once I add that.