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bug in saving precomputed meshes: unexpected keyword argument 'fuse' #600

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jefferis opened this issue Oct 6, 2023 · 3 comments
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bug The code is not performing according to the design or a design flaw is seriously impacting users. meshes Pertains to mesh objects or IO services.

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@jefferis
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jefferis commented Oct 6, 2023

Hi @william-silversmith. Hope all is good! I'm seeing a new (to me) error with cloudvolume 8.25.0 although 8.24.2 also gives this for @schlegelp.

This is from R but the python code should be obvious:

vol = cv$CloudVolume("precomputed://gs://manc-seg-2022-05/manc-seg-2022-05", use_https=TRUE)
vol$mesh$save(10118L, file_format='obj')

gives

── Python Exception Message ──────────────────────────────────────────────────────────────
Traceback (most recent call last):
  File "/Users/jefferis/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/cloudvolume/datasource/precomputed/mesh/unsharded.py", line 295, in save
    mesh = self.get(segids, fuse=True, remove_duplicate_vertices=True)
TypeError: get() got an unexpected keyword argument 'fuse'

── R Traceback ───────────────────────────────────────────────────────────────────────────
    ▆
 1. └─fafbseg::read_cloudvolume_meshes("10118", cloudvolume.url = "precomputed://gs://manc-seg-2022-05/manc-seg-2022-05")
 2.   └─fafbseg::save_cloudvolume_meshes(...) at fafbseg/R/cloudvolume-reticulate.R:207:2
 3.     └─vol$mesh$save(10118L, file_format = "obj") at fafbseg/R/cloudvolume-reticulate.R:93:4
 4.       └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
@william-silversmith
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Hi Greg, so sorry I missed this until now! I just pushed a fix that should be in the next release.

@william-silversmith william-silversmith added bug The code is not performing according to the design or a design flaw is seriously impacting users. meshes Pertains to mesh objects or IO services. labels Jul 1, 2024
william-silversmith added a commit that referenced this issue Jul 3, 2024
* wip: zarr download implementation

* feat: janky, but zarr image downloads work for non-timeseries

* feat: support label argument and faster fill_missing

* fix: support multiple fast fill bg colors

* feat: support basic commit_info

* feat: render zarr metadata and upload with commit_info

* fix: throw some default values in there

* feat: make axis mapping more general

* wip: zarr image upload

* fix: uploads not quite working, but are writing to disk

* fix: write out chunks metadata correctly

* fix: not working yet, but getting closer

* fix: don't compress metadata on disk

Zarr can't find those files with an extension.

* fix: zarr can't decode metadata without filters being present as a key

* fix: chunk size spatial dimensions were inverted

* fix: handle 5d chunk sizes

* feat: clear up cv vs zarr chunk size

* fix: handle missing .zarray files

* feat: add zarr, zarr2, and zarr3 to allowed formats

* fix: convert to list

* fix: convert to micrometers for zarr

* fix: incorrect use of add_scale

* feat: vol.mesh.save supports sharded meshes

Resolves #600

* fix: add cache_locking to n5

* fix+test: cross-format transfers are not supported (yet?)

* fix: n5 format can accept an info

* feat: add commit_info for n5

* feat: add exists and delete for zarr

* wip: zarr download implementation

* feat: janky, but zarr image downloads work for non-timeseries

* feat: support label argument and faster fill_missing

* fix: support multiple fast fill bg colors

* feat: support basic commit_info

* feat: render zarr metadata and upload with commit_info

* fix: throw some default values in there

* feat: make axis mapping more general

* wip: zarr image upload

* fix: uploads not quite working, but are writing to disk

* fix: write out chunks metadata correctly

* fix: not working yet, but getting closer

* fix: don't compress metadata on disk

Zarr can't find those files with an extension.

* fix: zarr can't decode metadata without filters being present as a key

* fix: chunk size spatial dimensions were inverted

* fix: handle 5d chunk sizes

* feat: clear up cv vs zarr chunk size

* fix: handle missing .zarray files

* feat: add zarr, zarr2, and zarr3 to allowed formats

* fix: convert to list

* fix: convert to micrometers for zarr

* fix: incorrect use of add_scale

* feat: add commit_info for n5

* feat: add exists and delete for zarr

* feat: add function for cross format transfers

* feat: add transfer_to across formats

* fix: enable cross format transfers

* feat: add transfer_by_rerendering to zarr

* fix: ensure encodings are reasonable

* fix: progress bar

* docs: remove erroneous comment

* fix: transfer_by_rerendering not respecting bbox

* feat: add method for getting the time resolution in seconds

* feat: more comprehensive units

* fix: more general logic for spatial resolution in nm

* feat: add error for multi-channel

* feat: support multiple channels

* feat: add some time related functions

* fix: better support for multiple channels

* fix: bounding box and negative indicies

* fix: more issue in downloading 3-channel images

* fix: ensure time is sliced with correct offset
@jefferis
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jefferis commented Jul 3, 2024

Thanks @william-silversmith !

@william-silversmith
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The next release is out! Should be fixed.

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