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

Draft

go2scope wants to merge 76 commits into

micro-manager:mainfrom

go2scope:mmstorage-draft

Commits on Feb 21, 2025

StorageDevice introduced - work in progress

nenada
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marktsuchida
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2cf31dd
go2scope device introduced

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09cc8c9
Storage instance added and MMCore plumbing

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67d503b
storage instance: further work

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c7fb810
Storage API cleanup

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68b53f8
Minimal MMCore interface sketched out

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fdd7dc9
loadDataset added

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cc6a4c3
vector<int> arguments replaced with vector<long> to help with Swig

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8b0b3a3
implementation of data read functions

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9e744a0
storage instance methods populated

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58f105d
nlohmann json library added

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3d95a2f
StroageMnager copied from go2scope. Requres extensive refactoring

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8cbb354
cleaned up API signatures in MMCore

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ccbfbe1
storage manager refactored

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7b33e5b
acquire zarr linked into the device adapter, other dependencies still missing

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8cfa575
static runtime selected

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b2b3a6f
temporarily commented out zar library

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b3b8f89
Merge branch 'main' of https://github.com/go2scope/mmCoreAndDevicesSD

nenada
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d9f2c25
zarr storage device created and separated from the upcoming tiff4 storage

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de52c7f
Merge branch 'main' of https://github.com/go2scope/mmCoreAndDevicesSD

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7f0f9e8
API modified to accomodate forwared declaration of pixel type

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a38091c
further integration of zarr

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bc2a51f
BigTIFF storage added (branch merged manually)

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280e1f1
G2STIFF parser added to BigTIFF storage driver

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3273386
BigTIFF storage - Add image, set dataset info

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5abc468
G2STiff format: Fixes for read & write access on the same file stream

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4148ad0
image number initialized in constructor

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6595d47
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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cdc8ad0
bug fix: MMCore requires explicit declaration of any new device on multiple places

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0ce7061
Storage instance bug fix

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1a5ccab
bug fixes in zarr storage

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821ec13
MMCoreJ wrapper fix for storage API

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7be4a38
MMCore and MMDevice storage API refactored

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735abf7
bug fixes and error messages

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f921976
comments and TODO items

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e87917a
BigTIFF storage bug fixes, improved error reporting, file naming fixed

razrock
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68358c0
bug fix in zarr driver, shape

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27a181e
refactoring at various points in the storage pipeline

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1bb3fd3
redundant name removed from the MMCore::load API

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0e28e8c
G2SBigTiff format reader fixes

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c93f624
Random access support for G2SBigTiff format

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a39ada8
Go2Scope storage driver - DirectIO device property

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e7156c3
G2S storage driver: Write stream flush cycle property

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78f2da4
C++ G2S Storage tests

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6a20801
C++ storage tests: Improved measurement and logging

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10313f1
MMCore java wrapper: Native support for 16-bit (short[]) addImage

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fc805c7
Storage driver / BigTIFF: Axis order inverted (slowest chaning first)

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f3f177d
MMCore java wrapper fix (storage driver getImage)

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ba76bde
Merge branch 'main' into develop/zarr

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ff15d6f
buf fixes for zarr writer

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56c2b62
zarr dimension order corrected

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a6863a6
update from lum development - support for chunking

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5ab02c7
MMCore storage api extended to accomodate format discovery

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2831421
more updates from lum: chunking

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f38005a
Merge branch 'develop/format' into develop/zarr

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748aee4
reduntant files cleanup

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ca7da23
API for storage extended with new functions

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8a22919
cleaned up unused files

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1aa7a11
appendImage() added to device api

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1d5a9e5
bug fixes, missing API implemented

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0f360e1
isReadOnly added

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a814671
device adapter bug fixes and update to the latest API changes

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73071a7
custom (mutable) metadata API added, non-restricted slowest dimension implemented for bigtiff, doc strings updated

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5410231
MMDevice API bug fixes, documentation update

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af67cfa
changes for the MMDevice API fix, added saveAndGet to MMCore to get image to display

nenada
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6e8ef0d
Set PlatformToolset to v142 for new projects
marktsuchida
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d14d2c4

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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865b11e

Commits on Apr 4, 2025

metadata length parameter added to all functions accepting metadata strings
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3fa7f05
updated storage tests in C++
nenada
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d677379

Commits on Apr 5, 2025

dataset handle type changed from string to int
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3145826
updated storage tests to reflect the new API
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020d376

Commits on Apr 6, 2025

custom metadata disk layout format changed. Now in separate subdir.
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ec66d4f

Commits on Apr 18, 2025

Commits on Oct 29, 2025

changed using to typedef to avoid swig compiler error

nenada
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3cdf591
device label bug fix in handle map in MMCore

nenada
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adffae8