Ethan Blackwood

Save memory by returning a sparse array from extract_binary_masks_from_structural_channel

3

# Description The docstring for `extract_binary_masks_from_structural_channel` says that it returns a sparse column format matrix, but it actually just returns an ndarray. I was running out of memory when trying...

I noticed that my CNMF runs were failing due to running out of memory when computing projections. Since I realized the main CNMF run function already has a mechanism for...

Include background component indices when removing empty/nan components in spatial.py

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# Description This fixes an indexing error in the "Eliminating empty and nan components" step that occurs when using seeded CNMF. The error I was getting is as follows: ```python...

Misleading warning emitted when saving movie without file_name to hdf5 (e.g. doing motion correction without saving first)

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Your setup: 1. Operating System (Linux, MacOS, Windows): Linux 2. Hardware type (x86, ARM..) and RAM: x86, 128 GB 3. Python Version (e.g. 3.9): 3.11 4. Caiman version (e.g. 1.9.12):...

I compiled on Windows and tried to launch, but it seems to expect a file called `EsotericIDE.Settings.xml` within the AppData folder. I tried just using a blank file, but this...

This adds a `--log-level` option for the 3 algorithms and allows setting it from the `run` series extension method (as either a string or `logging.X` int), which gets passed to...

Extends #311 (311 should be merged before this one). This combines a few changes I've made to functions that process the whole movie (other than motion correction and CNMF), to...

This is an enhancement to use seeded CNMF that I've been using regularly in my own code. Basically you just compute the seed however you want, save it as an...

I have a bunch of changes in my development fork/branch of this repository, and I'm trying to sort through them now, identify fixes that haven't been included in merged or...

Cache and decorator improvements

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Fixes #80, fixes #338. This started as a fix to #80 and the scope expanded a bit because I also wanted to get typing right. Here are the main changes:...