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Task #12678 (closed)

Opened 7 years ago

Closed 23 months ago

Allow bfconvert file patterns to use configurable number of digits

Reported by: mlinkert Owned by:
Priority: minor Milestone: Unscheduled
Component: Bio-Formats Version: 5.0.5
Keywords: tools, export Cc: lifangfei@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.


See http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-December/004921.html.

Each of the replaceable number fields should allow a user-specified number of digits, so that e.g.

bfconvert input.ome.tiff output_%ssss.tiff

writes files name output_0000.tiff, output_0001.tiff, ...

Using "%s4" or similar instead would also be an option.

Change History (6)

comment:1 Changed 7 years ago by mlinkert

  • Milestone changed from 5.1.1 to 5.2.0-m1

comment:2 Changed 6 years ago by jamoore

  • Milestone changed from 5.2.0 to B-F-5.2.0

Splitting due to milestone decoupling.

comment:3 Changed 6 years ago by mlinkert

  • Keywords export added
  • Owner mlinkert deleted

No ongoing work here; this is primarily a string parsing and formatting issue, as bfconvert itself shouldn't need to be changed. The two methods to update would be https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-api/src/loci/formats/FormatTools.java#L1011 and https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-api/src/loci/formats/FormatTools.java#L1021. This may end up being breaking, so if not possible for 5.2.0 it's likely best to push to 5.3.0.

%[width][field type] similar to http://docs.oracle.com/javase/6/docs/api/java/util/Formatter.html is probably nicer to work with than "%ssss" or "%s4" or similar, but feel free to use whatever seems easiest to parse. The main thing is being able to specify the 0- (for numeric) or whitespace- (for string) padded width for any currently-supported field in the filename, and maintain backwards compatibility with existing behavior as much as possible. "docs/sphinx/users/comlinetools/conversion.txt" will also need to be updated with the new width syntax.

comment:4 Changed 5 years ago by sbesson

  • Milestone changed from B-F-5.2.0 to Unscheduled

comment:6 Changed 23 months ago by mlinkert

  • Resolution set to fixed
  • Status changed from new to closed

Added in https://github.com/ome/bioformats/pull/2550 and released in Bio-Formats 5.2.2.

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