Closed adehad closed 5 years ago
- Need to
from glob import glob
for_load_metadata
What is your version of Python?
What is your version of Python?
Python 3.7.3
All except Assertion Error addressed by: ec4cf662b6fed28db206e7c7ba41285e010fdd57
for the assertion error could you send me your dataset?
Have attached it here, with the data binary: kilosort_dataset.zip
There are infinite values in amplitudes.npy
. I'll push a fix to skip these points but the real question is: why does kilosort find infinite values as amplitudes?
Same problem for template_features.npy
.
There are infinite values in
amplitudes.npy
. I'll push a fix to skip these points but the real question is: why does kilosort find infinite values as amplitudes?
Hmm, that does seem non-ideal. Those sort results had clusters that looked distinctly like noise, were these the problematic units?
Managed to get the new phy
gui running now (!).
Seem to have an error related to phycontrib
, is this because you are still in the transitioning phase to remove it as a dependency?:
[33m17:51:27.174 [W] model:49 29042/433611 values are inf in C:\Users\Adehad\preAutoMerge\amplitudes.npy, replacing by zero.[0m
[33m17:51:27.231 [W] model:49 25027/1300833 values are inf in C:\Users\Adehad\preAutoMerge\template_features.npy, replacing by zero.[0m
[31m17:51:27.331 [E] plugin:109 No module named 'phycontrib'
Traceback (most recent call last):
File "c:\conda\miniconda3\envs\phydev\lib\site-packages\phy\utils\plugin.py", line 107, in discover_plugins
mod = imp.load_module(modname, file, path, descr) # noqa
File "c:\conda\miniconda3\envs\phydev\lib\imp.py", line 234, in load_module
return load_source(name, filename, file)
File "c:\conda\miniconda3\envs\phydev\lib\imp.py", line 171, in load_source
module = _load(spec)
File "<frozen importlib._bootstrap>", line 696, in _load
File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 728, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "C:\SPB_Data\.phy\plugins\phycontrib_loader.py", line 3, in <module>
import phycontrib
ModuleNotFoundError: No module named 'phycontrib'[0m
[Am running on Windows, hence why I get those strange characters, I believe I opened a similar issue about them for the older phy
]
try to remove C:\SPB_Data\.phy\plugins\phycontrib_loader.py
?
try to remove
C:\SPB_Data\.phy\plugins\phycontrib_loader.py
?
Tactical. Can confirm that fixes the issue.
from glob import glob
for_load_metadata
https://github.com/cortex-lab/phylib/blob/f72d0a5f58ba1a741bfa88feba7ee0f64ef721c5/phylib/io/model.py#L321-L324self.dir_path
does not seem to be recognised as a Path object in_load_spike_samples
https://github.com/cortex-lab/phylib/blob/f72d0a5f58ba1a741bfa88feba7ee0f64ef721c5/phylib/io/model.py#L426-L429self.dir_path = Path(dir_path)
didn't work in the constructor for me, so I used this non-ideal work around.phy
GUI opens after this, but then produces an assertion error: