Task #12678 (closed)
Opened 9 years ago
Closed 4 years 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. |
Description
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 9 years ago by mlinkert
- Milestone changed from 5.1.1 to 5.2.0-m1
comment:2 Changed 9 years ago by jamoore
- Milestone changed from 5.2.0 to B-F-5.2.0
comment:3 Changed 8 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 8 years ago by sbesson
- Milestone changed from B-F-5.2.0 to Unscheduled
comment:5 Changed 8 years ago by sbesson
comment:6 Changed 4 years 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.
Splitting due to milestone decoupling.