Cellvoyager converter improvements #812

jluethi · 2024-08-12T14:00:50Z

Closes #782
Closes #628
Closes #137
Closes #287
Closes #586
Closes #627
Closes #457
Closes #636
Closes #348
Closes #589

Checklist before merging

I added an appropriate entry to CHANGELOG.md

github-actions · 2024-08-12T14:37:38Z

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)
fractal_tasks_core/cellvoyager
filenames.py	$This PR adds 10 to the number of statements in fractal_tasks_core/cellvoyager/filenames.py, taking it from 51 to 61.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/cellvoyager/filenames.py, which is 1.$	$This PR adds 0.32 percentage points to the coverage rate in fractal_tasks_core/cellvoyager/filenames.py, taking it from 98.03% (50/51) to 98.36% (60/61).$	$This PR does not seem to add statements to fractal_tasks_core/cellvoyager/filenames.py.$
metadata.py	$This PR adds 12 to the number of statements in fractal_tasks_core/cellvoyager/metadata.py, taking it from 113 to 125.$	$This PR adds 1 to the number of statements missing coverage in fractal_tasks_core/cellvoyager/metadata.py, taking it from 7 to 8.$	$This PR removes 0.21 percentage points from the coverage rate in fractal_tasks_core/cellvoyager/metadata.py, taking it from 93.8% (106/113) to 93.6% (117/125).$	$This PR does not seem to add statements to fractal_tasks_core/cellvoyager/metadata.py.$
fractal_tasks_core/tasks
cellvoyager_to_ome_zarr_compute.py	$This PR adds 6 to the number of statements in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_compute.py, taking it from 78 to 84.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_compute.py, which is 4.$	$This PR adds 0.37 percentage points to the coverage rate in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_compute.py, taking it from 94.87% (74/78) to 95.23% (80/84).$	$This PR does not seem to add statements to fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_compute.py.$
cellvoyager_to_ome_zarr_init.py	$This PR adds 3 to the number of statements in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init.py, taking it from 164 to 167.$	$This PR removes 8 from the number of statements missing coverage in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init.py, taking it from 25 to 17.$	$This PR adds 5.06 percentage points to the coverage rate in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init.py, taking it from 84.75% (139/164) to 89.82% (150/167).$	$This PR does not seem to add statements to fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init.py.$
cellvoyager_to_ome_zarr_init_multiplex.py	$This PR adds 8 to the number of statements in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init_multiplex.py, taking it from 198 to 206.$	$This PR adds 1 to the number of statements missing coverage in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init_multiplex.py, taking it from 20 to 21.$	$This PR removes 0.09 percentage points from the coverage rate in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init_multiplex.py, taking it from 89.89% (178/198) to 89.8% (185/206).$	$This PR does not seem to add statements to fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init_multiplex.py.$
io_models.py	$This PR adds 1 to the number of statements in fractal_tasks_core/tasks/io_models.py, taking it from 56 to 57.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/tasks/io_models.py, which is 0.$	$This PR doesn't change the coverage rate in fractal_tasks_core/tasks/io_models.py, which is 100% (57/57).$	$This PR does not seem to add statements to fractal_tasks_core/tasks/io_models.py.$
Project Total

_{This report was generated by python-coverage-comment-action}

jluethi added 2 commits August 12, 2024 15:21

Add failing test for arbitrary acquisition name (#782)

07ff81f

Add suport for arbitrary integers as acquisitions (closes #782)

c4ac1e2

jluethi mentioned this pull request Aug 12, 2024

Make multiplexing converter work with arbitrarily named acquisitions #782

Closed

jluethi added 2 commits August 12, 2024 16:17

Catch non-existant mlf & mrf files better (closes #628)

0df33fa

Fix omero channel naming for multiplexing

ffa6858

jluethi added 7 commits August 12, 2024 17:01

Switch to pandas-based mrf xml file reading

b2bf825

Update column naming in metadata parsing

d962184

Add type hints for read_mrf_file

eee8d6a

Drop defusexml dependency (closes #137)

7c4446a

Add channel exclusion feature (Closes #287, closes 627)

945e0c6

Update poetry lock file for defusexml removal

7170f67

Support multi-plate in cellvoyager converter

86b0de3

jluethi mentioned this pull request Aug 12, 2024

Test multi-plate support in cellvoyager converter #457

Closed

jluethi added 5 commits August 12, 2024 19:16

Add exclude_glob_patterns for converter

fc642cc

fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init.py

924d95e

Improve handling when no exclude patterns are specified

dc921b4

Fix bug in multiplexing task syntax

55fe5d3

Fix no include_patterns handling & add test for exclusion

efae2c2

jluethi mentioned this pull request Aug 13, 2024

Allow processing of subset of available channels in Create OME-Zarr #589

Closed

Update Changelog

265194f

jluethi marked this pull request as ready for review August 13, 2024 15:09

jluethi merged commit 4f38279 into main Aug 13, 2024
17 of 18 checks passed

jluethi deleted the cellvoyger_converter_improvements branch August 13, 2024 15:10

jluethi mentioned this pull request Oct 10, 2024

Test the multi-plate case of create_cellvoyager_ome_zarr_init #688

Closed

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Cellvoyager converter improvements #812

Cellvoyager converter improvements #812

jluethi commented Aug 12, 2024 •

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github-actions bot commented Aug 12, 2024 •

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Cellvoyager converter improvements #812

Cellvoyager converter improvements #812

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jluethi commented Aug 12, 2024 • edited Loading

Checklist before merging

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Coverage report

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