[BUG] --save_rois does not appear to respect --savedir

[KaiAragaki]

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Describe the bug

I'm pretty sure this is due to my own incompetence (probably not a bug), but I can't seem to find what I'm doing wrong.

When I run cellpose from the command line, I expect to be able to set --savedir and have all the output go there. For my case, I'm interested in having ROIs go there in particular. However, ROIs are saved in the same directory as the original image. Curiously, including the --save_tif flag saves the tif masks to the path specified by --savedir even while the ROIs are being saved to the original image directory..

To Reproduce

The following command is used:

python -m cellpose --dir "./resources/my-images/" --savedir "./results/cellpose-masks/" --save_tif  --save_rois --verbose --use_gpu

Run log

Run logs

2025-10-22 11:36:50,896 [INFO] WRITING LOG OUTPUT TO /Users/kai/.cellpose/run.log
2025-10-22 11:36:50,896 [INFO] 
cellpose version:       4.0.7 
platform:               darwin 
python version:         3.13.5 
torch version:          2.8.0
2025-10-22 11:36:50,909 [INFO] ** TORCH MPS version installed and working. **
2025-10-22 11:36:50,909 [INFO] >>>> using GPU (MPS)
2025-10-22 11:36:50,909 [WARNING] the '--diam_mean' flag is deprecated in v4.0.1+ and no longer used
2025-10-22 11:36:50,910 [INFO] >>>> running cellpose on 7 images using all channels
2025-10-22 11:36:51,755 [INFO] >>>> loading model /Users/kai/.cellpose/models/cpsam
2025-10-22 11:36:52,179 [INFO] 0%|          | 0/7 [00:00<?, ?it/s]
2025-10-22 11:38:09,446 [INFO] 14%|#4        | 1/7 [01:17<07:43, 77.27s/it]
2025-10-22 11:39:27,365 [INFO] 29%|##8       | 2/7 [02:35<06:28, 77.65s/it]

[mrariden]

The --savedir flag requires an absolute path. I should add this to the documentation

[mrariden]

Instead of adjusting the docs, I'm allowing relative paths. This will be available in the next PR and with the next release version