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Task #12189 (closed)

Opened 10 years ago

Closed 10 years ago

BUG : Used file list incorrect for multi-file CZI datasets

Reported by: bramalingam Owned by: mlinkert
Priority: minor Milestone: 5.0.2
Component: Bio-Formats Version: 5.0.1
Keywords: ZeissCZIReader Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by bramalingam)

Test Summary :

Data Folder : /ome/data_repo/from_Biozentrum_Basel/Charles/SPIM/large_timeseries_700GB/

System call :
candidates = ImportCandidates?(folder_depth_bioformats,reader, paths, handler;

--The CZI reader seems to have issues with grouping files / identifying number of datasets if the top-level folder is parsed via ImportCandidates?

-- When paths == /ome/data_repo/from_Biozentrum_Basel/Charles/SPIM/large_timeseries_700GB/

(Result : It does not group the files, imports every individual time point as an individual dataset).

--When paths == /ome/data_repo/from_Biozentrum_Basel/Charles/SPIM/large_timeseries_700GB/Image 17-24hpf-46hpf.czi
(Result : It groups files properly, imports the whole set as one dataset)- Expected result.

2) paths

paths =

/ome/data_repo/from_Biozentrum_Basel/Charles/SPIM/large_timeseries_700GB/Image 17-24hpf-46hpf.czi

candidates = handle(ImportCandidates?(folder_depth_bioformats,reader, paths, handler));

candidates reads the files correctly (does not read every individual files within the folder), But,
datasetno=candidates.getContainers().size;
datasetno

datasetno =

0

3) Grouping of T needs to be reviewed by the user(Might be a bug for T grouping)! Previous build (5.0 of bioformats) got the grouping of Z wrong as well. But that seems to be working properly now(5.0.1 bio-formats),
paths = /ome/data_repo/from_Biozentrum_Basel/Charles/SPIM/multiview_single_timepoint_61GB/Image 12c.czi

Change History (5)

comment:1 Changed 10 years ago by mlinkert

  • Milestone changed from Unscheduled to 5.0.2
  • Summary changed from BUG : Reading CZI files to BUG : Used file list incorrect for multi-file CZI datasets

comment:2 Changed 10 years ago by bramalingam

  • Description modified (diff)

comment:3 Changed 10 years ago by bramalingam

  • Description modified (diff)

comment:4 Changed 10 years ago by bramalingam

  • Description modified (diff)

comment:5 Changed 10 years ago by mlinkert

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

Fixed with https://github.com/openmicroscopy/bioformats/pull/1078; email forthcoming on ome-users/ome-devel with details of how to try this out prior to 5.0.2.

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