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Follow-ups from the coding session on 2025-03-11 #49

Merged
merged 68 commits into from
Mar 26, 2025
Merged

Follow-ups from the coding session on 2025-03-11 #49

merged 68 commits into from
Mar 26, 2025

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lguerard
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lguerard added 19 commits March 11, 2025 20:33
@lguerard @ehrenfeu
Add method for associating label images using 3DImageJSuite
86a3447
@lguerard @ehrenfeu
Fix the filtering of objects to use the calibrated method
97084b6
@lguerard @ehrenfeu
Use the morpholibj package to 2D dilate labels
408131c
@lguerard @ehrenfeu
Format imports
c542b19
@lguerard @ehrenfeu
Add method to write results to CSV
886613a
@lguerard @ehrenfeu
Add methods for 3D Maxima Finder and 3D Watershed
831d771
@lguerard @ehrenfeu
Add processing library to do basic methods
4dc4504 
Add one to apply a filter, to do rolling ball background subtraction and
thresholding
@lguerard
Add methods to get different metadata using bioformats
6fa4d69
@lguerard
Update method to support NaN (discarding them) and rounding results
0bdd98e
@lguerard
Add method to save in different file format
34d5880 
This method could be improved to be used in the stitching script
@lguerard
Add method to pad a string
15bc0c4
@lguerard
Add methods to find imaris and convert an image to IMS
6189088
@lguerard
Add missing imports and formatting
272df1f
@lguerard
Add methods to get different metadata from OMERO
c1a9332
@lguerard
Add method to delete annotation from OMERO
05e6a2e
@lguerard
Add methods to save an OMERO.table
fae0930
@lguerard
Add method to save IJ-ROIs to OMERO
de5c84a
@lguerard
Add missing imports and formatting
16dd961
@lguerard
Formatting
04a9f84
@ehrenfeu ehrenfeu added enhancement New feature or request unit testing A unit test should be created next-release Issues blocking the next release next-coding-session Look into during the next CS. labels Mar 18, 2025
@ehrenfeu ehrenfeu added this to the 1.5.0 milestone Mar 18, 2025
ehrenfeu
ehrenfeu requested changes Mar 18, 2025
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ehrenfeu added 7 commits March 25, 2025 15:42
@ehrenfeu
Indent to show as a fixed-width block
6b641bb
@ehrenfeu
One example should be enough
51f2cec 
As the 2nd example was not using the function in a different way, there
is no real need for it. If it's worth having the example with the
`range()`, `append` etc., we should make it the only one (and also make
it valid Python 2.7 syntax, i.e. no f-strings).
@ehrenfeu
Add empty line to fix docstring rendering
a65fe41
@ehrenfeu
Run black formatting (restore default line length of 88)
c35e312
@ehrenfeu
Notes section comes before Examples
caa1370 
https://numpydoc.readthedocs.io/en/latest/format.html#sections
@ehrenfeu
Minor updates on Notes section
99ab0f0
@ehrenfeu
Update function details
07f3064
@ehrenfeu ehrenfeu mentioned this pull request Mar 25, 2025
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The remaining linting error is only for BDV related files.

And with merging #39 into devel, and devel into this branch in f0a1c9c, the remaining linting errors have vanished!

💪🏼 🚀

ehrenfeu
ehrenfeu requested changes Mar 25, 2025
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Remaining open requests (plus the one attached below to this very comment):

@imcf imcf deleted a comment from codecov bot Mar 25, 2025
@ehrenfeu ehrenfeu force-pushed the coding-session/2025-03-11 branch from 69d9851 to f0a1c9c Compare March 25, 2025 22:20
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codecov bot commented Mar 25, 2025 •
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Codecov Report

Attention: Patch coverage is 7.05882% with 237 lines in your changes missing coverage. Please review.

Project coverage is 25.06%. Comparing base (b02198e) to head (8cef7bf).
Report is 73 commits behind head on devel.

Files with missing lines Patch % Lines
src/imcflibs/imagej/bioformats.py 2.17% 90 Missing ⚠️
src/imcflibs/imagej/misc.py 20.00% 56 Missing ⚠️
src/imcflibs/imagej/omerotools.py 0.00% 38 Missing ⚠️
src/imcflibs/imagej/processing.py 0.00% 31 Missing ⚠️
src/imcflibs/imagej/labelimage.py 0.00% 16 Missing ⚠️
src/imcflibs/imagej/objects3d.py 0.00% 3 Missing ⚠️
src/imcflibs/pathtools.py 50.00% 2 Missing ⚠️
src/imcflibs/imagej/shading.py 0.00% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##            devel      #49      +/-   ##
==========================================
- Coverage   28.19%   25.06%   -3.14%     
==========================================
  Files          24       25       +1     
  Lines        1426     1656     +230     
==========================================
+ Hits          402      415      +13     
- Misses       1024     1241     +217

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@ehrenfeu
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@lguerard how about we merge this PR now and address the remaining tasks in separate issues later on?

Remaining open requests (plus the one attached below to this very comment):

* docstring for `calculate_mean_and_stdv()`: [Add more methods following the coding session of 2025 03 11 #49 (comment)](https://github.com/imcf/python-imcflibs/pull/49#discussion_r2012334834)

* move `pad_number()` to `strtools`: [Add more methods following the coding session of 2025 03 11 #49 (comment)](https://github.com/imcf/python-imcflibs/pull/49#discussion_r2004100289)

* rename `apply_background_subtraction` to `rollingball_background_subtraction` or `apply_rollingball_bg_subtraction`: [Add more methods following the coding session of 2025 03 11 #49 (comment)](https://github.com/imcf/python-imcflibs/pull/49#discussion_r2010350151)

@ehrenfeu ehrenfeu merged commit bf97721 into imcf:devel Mar 26, 2025
3 of 5 checks passed
@ehrenfeu ehrenfeu changed the title Add more methods following the coding session of 2025 03 11 Follow-ups from the coding session 2025-03-11 Mar 26, 2025
@ehrenfeu ehrenfeu changed the title Follow-ups from the coding session 2025-03-11 Follow-ups from the coding session on 2025-03-11 Mar 26, 2025
This was referenced Mar 26, 2025
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@lguerard lguerard deleted the coding-session/2025-03-11 branch March 26, 2025 10:34
@ehrenfeu ehrenfeu mentioned this pull request Mar 26, 2025
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Labels
enhancement New feature or request next-coding-session Look into during the next CS. next-release Issues blocking the next release unit testing A unit test should be created
Projects
imcflibs
Status: Done
Milestone
1.5.0
Development

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@lguerard @ehrenfeu