New MM::StorageDevice and addition to the MMCore API#535

Draft

go2scope wants to merge 76 commits intomicro-manager:mainfrom

go2scope:mmstorage-draft

Commits on Feb 21, 2025

StorageDevice introduced - work in progress

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go2scope device introduced

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Storage instance added and MMCore plumbing

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storage instance: further work

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Storage API cleanup

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Minimal MMCore interface sketched out

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loadDataset added

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vector<int> arguments replaced with vector<long> to help with Swig

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implementation of data read functions

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storage instance methods populated

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nlohmann json library added

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StroageMnager copied from go2scope. Requres extensive refactoring

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cleaned up API signatures in MMCore

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storage manager refactored

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acquire zarr linked into the device adapter, other dependencies still missing

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static runtime selected

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temporarily commented out zar library

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Merge branch 'main' of https://github.com/go2scope/mmCoreAndDevicesSD

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zarr storage device created and separated from the upcoming tiff4 storage

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Merge branch 'main' of https://github.com/go2scope/mmCoreAndDevicesSD

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API modified to accomodate forwared declaration of pixel type

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further integration of zarr

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BigTIFF storage added (branch merged manually)

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G2STIFF parser added to BigTIFF storage driver

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BigTIFF storage - Add image, set dataset info

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G2STiff format: Fixes for read & write access on the same file stream

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image number initialized in constructor

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Set device interface version to 71. This will have to be updated on the system level to a different interface number

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bug fix: MMCore requires explicit declaration of any new device on multiple places

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Storage instance bug fix

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bug fixes in zarr storage

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MMCoreJ wrapper fix for storage API

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MMCore and MMDevice storage API refactored

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bug fixes and error messages

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comments and TODO items

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BigTIFF storage bug fixes, improved error reporting, file naming fixed

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bug fix in zarr driver, shape

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refactoring at various points in the storage pipeline

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redundant name removed from the MMCore::load API

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G2SBigTiff format reader fixes

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Random access support for G2SBigTiff format

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Go2Scope storage driver - DirectIO device property

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G2S storage driver: Write stream flush cycle property

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C++ G2S Storage tests

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C++ storage tests: Improved measurement and logging

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MMCore java wrapper: Native support for 16-bit (short[]) addImage

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Storage driver / BigTIFF: Axis order inverted (slowest chaning first)

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MMCore java wrapper fix (storage driver getImage)

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Merge branch 'main' into develop/zarr

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buf fixes for zarr writer

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zarr dimension order corrected

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update from lum development - support for chunking

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MMCore storage api extended to accomodate format discovery

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more updates from lum: chunking

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Merge branch 'develop/format' into develop/zarr

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reduntant files cleanup

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API for storage extended with new functions

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cleaned up unused files

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appendImage() added to device api

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bug fixes, missing API implemented

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isReadOnly added

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device adapter bug fixes and update to the latest API changes

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custom (mutable) metadata API added, non-restricted slowest dimension implemented for bigtiff, doc strings updated

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MMDevice API bug fixes, documentation update

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changes for the MMDevice API fix, added saveAndGet to MMCore to get image to display

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Set PlatformToolset to v142 for new projects
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Commits on Feb 25, 2025

changed API naming convention to include "dataset". Added freeze. Deleted AddImage and replaced with append.
nenada
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Commits on Apr 4, 2025

Commits on Apr 5, 2025

Commits on Apr 6, 2025

custom metadata disk layout format changed. Now in separate subdir.
nenada
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Commits on Apr 18, 2025

Commits on Oct 29, 2025

changed using to typedef to avoid swig compiler error

nenada
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device label bug fix in handle map in MMCore

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