Task #12189 (new)
Opened 10 years ago
Last modified 10 years ago
BUG : Used file list incorrect for multi-file CZI datasets — at Version 2
| 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 seems to be wrong. Previous build (5.0 of bioformats) got the grouping of Z wrong as well. But that seems to be working properly now,
paths = /ome/data_repo/from_Biozentrum_Basel/Charles/SPIM/multiview_single_timepoint_61GB/Image 12c.czi
Change History (2)
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)
