run rastermap on binarized data

[Pentabyteman]

Dear Team.

I was wondering whether it would be possible to run rastermap on already binarized data (meaning 0 = no spike; 1 = spike) and whether it would make more sense supplying just the peak, or setting the entire width at half maximum to 1 for the algorithms behind rastermap?

I tried to run the rastermap_singleneurons.ipnyb notebook with my own binarized matrix of 752 cells by 612 timepoints as this seemed the most applicable, however when I try to set n_clusters = None a ValueError gets raised in lines 363-364 of rastermap.py.

When I set n_clusters to some integer < 200, the following error occurs:

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
Cell In[7], line 1
----> 1 model = Rastermap(n_clusters=10, # None turns off clustering and sorts single neurons 
      2                   n_PCs=64, # use fewer PCs than neurons
      3                   locality=0.15, # some locality in sorting (this is a value from 0-1)
      4                   time_lag_window=15, # use future timepoints to compute correlation
      5                   normalize = None,
      6                   grid_upsample=0, # 0 turns off upsampling since we're using single neurons
      7                 ).fit(spks)
      8 y = model.embedding # neurons x 1
      9 isort = model.isort

File ~/miniconda3/envs/rastermap/lib/python3.8/site-packages/rastermap/rastermap.py:494, in Rastermap.fit(self, data, Usv, Vsv, U_nodes, itrain, compute_X_embedding, BBt)
    491     if (bin_size==0 or n_samples < bin_size or 
    492         (bin_size == 50 and n_samples < 1000)):
    493         bin_size = max(1, n_samples // 500)
--> 494     self.X_embedding = zscore(bin1d(X[igood][self.isort], bin_size, axis=0), axis=1)
    496 rmap_logger.info(f"rastermap complete, time {time.time() - t0:0.2f}sec")
    498 self.runtime = time.time() - t0

IndexError: index 751 is out of bounds for axis 0 with size 592

This happens both when explicitly setting bin_size = 0 or bin_size = 1

[Lucas97223]

I am running into the same issue. Any solution arose?

[carsen-stringer]

can you try the latest version of the code please and see if you still have this issue?

[alemessurier]

I'm getting the same error with the gui version (just installed today, and ran pip install rastermap[gui] --upgrade):

data matrix:
(152, 30863)
2024-10-17 16:13:37,981 [INFO] normalizing data across axis=1
2024-10-17 16:13:38,001 [INFO] binning in time with time_bin = 2
2024-10-17 16:13:38,062 [INFO] projecting out mean along axis=0
2024-10-17 16:13:38,081 [INFO] data normalized, 0.10sec
2024-10-17 16:13:38,082 [INFO] sorting activity: 150 valid samples by 30863 timepoints
2024-10-17 16:13:38,415 [INFO] n_PCs = 100 computed, 0.43sec
2024-10-17 16:13:38,482 [INFO] 30 clusters computed, time 0.50sec
2024-10-17 16:13:38,562 [INFO] clusters sorted, time 0.58sec
2024-10-17 16:13:38,585 [INFO] clusters upsampled, time 0.60sec

ERROR<<<
Traceback (most recent call last):
File "/Users/aml717/opt/anaconda3/envs/rastermap/lib/python3.9/runpy.py", line 197, in _run_module_as_main
ERROR<<<
return _run_code(code, main_globals, None,
File "/Users/aml717/opt/anaconda3/envs/rastermap/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/Users/aml717/opt/anaconda3/envs/rastermap/lib/python3.9/site-packages/rastermap/main.py", line 62, in
model.fit(data=X, Usv=Usv, Vsv=Vsv)
File "/Users/aml717/opt/anaconda3/envs/rastermap/lib/python3.9/site-packages/rastermap/rastermap.py", line 494, in fit
ERROR<<<
self.X_embedding = zscore(bin1d(X[igood][self.isort], bin_size, axis=0), axis=1)
IndexError: index 150 is out of bounds for axis 0 with size 150
Interrupted by error (not finished)

if it's useful here is my environment:

[carsen-stringer]

thanks everyone for catching this, this bug should be fixed now! please pip install git+https://github.com/mouseland/rastermap.git for the latest code, I will also push a new pypi release later today

[alemessurier]

works for me now! thanks!!

[carsen-stringer]

hurray! created the pypi will close the issue