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Name option #147

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Name option #147

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e882a62
Add name_by option to allow name.ome.zarr
will-moore Jul 11, 2023
d80d276
Remove .pattern from image name
will-moore Jul 11, 2023
1d72626
Handle first plate Wells having no fields
will-moore Aug 7, 2023
6290b4b
Don't try to remove .pattern from image names
will-moore Aug 8, 2023
c73d400
Replace [] with () in zarr names
will-moore Aug 15, 2023
57da8bb
Add get_zarr_name(). Always use .ome.zarr
will-moore Aug 23, 2023
36e66c4
Update README with --name_by option
will-moore Aug 23, 2023
3ca2c58
Update README and masks.py to use ID.ome.zarr
will-moore Aug 23, 2023
ecf5a3e
Merge remote-tracking branch 'origin/master' into name_option
will-moore Oct 24, 2023
470ad2b
Use .ome.zarr in args help
will-moore Dec 14, 2023
a14f62a
Improve source-image example in README
will-moore Dec 14, 2023
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9 changes: 9 additions & 0 deletions src/omero_zarr/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -278,6 +278,15 @@ def _configure(self, parser: Parser) -> None:
default=None,
help="Maximum number of workers (only for use with bioformats2raw)",
)
export.add_argument(
"--name_by",
default="id",
choices=["id", "name"],
help=(
"How to name the Image or Plate zarr. Default 'id' is [ID].zarr. "
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That raises the question about the extension.
In both cases, the library is used to generate ome.zarr so in one case using .zarr and in the other case .ome.zarr is confusing

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In general I think we've stated elsewhere:

  • strongly SHOULD (bordering on MUST): .zarr
  • SHOULD: .ome.zarr

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@joshmoore You're suggesting we update the default behaviour to be [ID].ome.zarr instead of [ID].zarr?
Always using .ome.zarr (for name.ome.zarr or ID.ome.zarr) is more consistent, so I'm happy to do that, but that is more of a breaking change

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Breaking in the sense that you think current processes won't detect that something has already been exported and will re-export?

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No, just if you've got a workflow like:

$ omero zarr export Image:1
$ mv 1.zarr renamed_image.zarr

that workflow will need to change because 1.zarr will now be created as 1.ome.zarr

But that's not a major concern, so happy to make that change.

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👍 I'm personally a bit up in the air. A benefit of .zarr filesets are that other stuff can be stored in them which is why I don't think we should ever require .ome.zarr. On the flip side, what we do now will likely be the model that other submitters to BIA tend to follow, so it does make sense to do what we think is most strategic (and update any existing workflows as necessary). All that being said, 💯 for doing whatever consistently.

"'name' is [NAME].ome.zarr"
),
)
export.add_argument(
"object",
type=ProxyStringType("Image"),
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24 changes: 22 additions & 2 deletions src/omero_zarr/raw_pixels.py
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Expand Up @@ -41,12 +41,23 @@
from .util import marshal_axes, marshal_transformations, open_store, print_status


def sanitize_name(zarr_name: str) -> str:
# Avoids re.compile errors when writing Zarr data with the named root
# https://github.com/ome/omero-cli-zarr/pull/147#issuecomment-1669075660
return zarr_name.replace("[", "(").replace("]", ")")


def image_to_zarr(image: omero.gateway.ImageWrapper, args: argparse.Namespace) -> None:
target_dir = args.output
tile_width = args.tile_width
tile_height = args.tile_height
name_by = args.name_by

name = os.path.join(target_dir, "%s.zarr" % image.id)
if name_by == "name":
img_name = sanitize_name(image.name)
name = os.path.join(target_dir, "%s.ome.zarr" % img_name)
else:
name = os.path.join(target_dir, "%s.zarr" % image.id)
print(f"Exporting to {name} ({VERSION})")
store = open_store(name)
root = open_group(store)
Expand Down Expand Up @@ -245,7 +256,14 @@ def plate_to_zarr(plate: omero.gateway._PlateWrapper, args: argparse.Namespace)
total = n_rows * n_cols * (n_fields[1] - n_fields[0] + 1)

target_dir = args.output
name = os.path.join(target_dir, "%s.zarr" % plate.id)
name_by = args.name_by

if name_by == "name":
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Two quick notes:

  • this code is duplicated and could be made a method for possible sub-classing
  • I can live with this split in naming schemes, but it could be a surprise

plate_name = sanitize_name(plate.name)
name = os.path.join(target_dir, "%s.ome.zarr" % plate_name)
else:
name = os.path.join(target_dir, "%s.zarr" % plate.id)

store = open_store(name)
print(f"Exporting to {name} ({VERSION})")
root = open_group(store)
Expand Down Expand Up @@ -296,6 +314,8 @@ def plate_to_zarr(plate: omero.gateway._PlateWrapper, args: argparse.Namespace)
print_status(int(t0), int(time.time()), count, total)

# Update plate_metadata after each Well
if len(well_paths) == 0:
continue
write_plate_metadata(
root,
row_names,
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2 changes: 1 addition & 1 deletion src/omero_zarr/util.py
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Expand Up @@ -32,7 +32,7 @@ def print_status(t0: int, t: int, count: int, total: int) -> None:
"""
percent_done = float(count) * 100 / total
dt = t - t0
if dt > 0:
if dt > 0 and count > 0:
rate = float(count) / (t - t0)
eta_f = float(total - count) / rate
eta = time.strftime("%H:%M:%S", time.gmtime(eta_f))
Expand Down
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