Improve performance of create_all_cell_csv

[stegiopast]

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Description

What is this PR

• Bug fix
• Addition of a new feature
• Other

Why is this PR needed?
In the function create_all_cell_csv() of cellfinder/analyse/analyse.py a df.append() call is used in a for loop, which slows down the runtime of the program to a significant extend.
(from hours to seconds)

What does this PR do?
Within the for loop over the points list a temporary matrix is constructed line by line by appending the following values separately (raw_coordinate[0],raw_coordinate[1],raw_coordinate[2],atlas_coordinate[0],atlas_coordinate[1],atlas_coordinate[2],structure,hemisphere). After the loop termination a dataframe is constructed via pd.DataFrame(temp_matrix, columns = list_of_colnames, index = None).

References

Please reference any existing issues/PRs that relate to this PR.

How has this PR been tested?

The code has been tested manually and during several cell detection runs.
So far i did not actively assure that any information is missing. I would be happy if you could assure that.

Is this a breaking change?

Strong improvement in run time

Does this PR require an update to the documentation?

No additional change in the handling of the tool.

Checklist:

• The code has been tested locally
• Tests have been added to cover all new functionality (unit & integration)
• The documentation has been updated to reflect any changes
• The code has been formatted with pre-commit

analyse.py.zip

[adamltyson]

Hey @stegiopast thanks for this. Just FYI I added your changes (from the zip file) to this branch. This looks to speed up this step in cellfinder by about 2x.

This also may address #356

[codecov]

Codecov Report

Base: 19.04% // Head: 18.92% // Decreases project coverage by -0.12% ⚠️

Coverage data is based on head (dbdba65) compared to base (e3b48c0).
Patch coverage: 0.00% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     brainglobe/cellfinder#220      +/-   ##
==========================================
- Coverage   19.04%   18.92%   -0.12%     
==========================================
  Files          25       25              
  Lines        1486     1495       +9     
==========================================
  Hits          283      283              
- Misses       1203     1212       +9     

Impacted Files	Coverage Δ
cellfinder/analyse/analyse.py	0.00% <0.00%> (ø)
cellfinder/extract/extract_cubes.py	0.00% <0.00%> (ø)
setup.py	0.00% <ø> (ø)

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