fix: autoload _cp_masks and escape glob metacharacters in paths#1421
Open
skpalan wants to merge 1 commit intoMouseLand:mainfrom
Open
fix: autoload _cp_masks and escape glob metacharacters in paths#1421skpalan wants to merge 1 commit intoMouseLand:mainfrom
skpalan wants to merge 1 commit intoMouseLand:mainfrom
Conversation
…racters in paths
Two fixes:
1. The GUI's mask auto-load (autoloadMasks checkbox) only searched for
`_masks.{ext}` and `_masks.tif`, but cellpose saves masks as
`_cp_masks.png`/`_cp_masks.tif`. Add `_cp_masks` patterns to the
search candidates so saved masks are found on reload.
2. `get_image_files()` passes folder paths directly to `glob.glob()`,
which interprets `[`, `]`, `?`, and `*` as pattern metacharacters.
Directories with these characters (e.g. `data[condition1]`) return
zero matches, raising ValueError. Use `glob.escape()` on the folder
portion before appending wildcards.
skpalan
force-pushed
the
fix/gui-autoload-cp-masks
branch
from
ad35da7 to
775a4b6
Compare
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
autoloadMaskscheckbox only searched for_masks.{ext}and_masks.tif, but cellpose itself saves masks as_cp_masks.png/_cp_masks.tif. Added_cp_maskspatterns to the search candidates so saved masks are found on reload.get_image_files()passes folder paths directly toglob.glob(), which interprets[,],?, and*as pattern metacharacters. Directories containing these characters (e.g.data[condition1]) silently return zero matches, raisingValueError: ERROR: no files in --dir folder. Now usesglob.escape()on the folder portion before appending wildcards.Test plan
.tifimage that has a corresponding_cp_masks.png→ mask auto-loads[brackets]in the path → A/D navigation works_masks.tifand_masks.pngpatterns still auto-load (backward compat)