Feature/zarr#38

Draft

nsoblath wants to merge 73 commits intomainfrom

Commits on Sep 20, 2021

Merge tag 'v3.8.2' into develop
nsoblath-pnnl
committed

Commits on Apr 12, 2023

Updated Scarab to v3.9.3
nsoblath-pnnl
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Copied M3 over to M4 and tested building of the M4 library (still uses HDF5; to be replaced by Zarr)
nsoblath-pnnl
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Commits on Apr 13, 2023

Commits on Apr 14, 2023

Further work on M4Header, M4Monarch, and M4Stream
nsoblath-pnnl
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Commits on Apr 28, 2023

Commits on Jun 2, 2023

Progress on writing data
nsoblath-pnnl
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Commits on Jul 25, 2023

Incremental progress
nsoblath-pnnl
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Commits on Aug 16, 2023

create Doxyfile for graphical analysis

Raymond Dunn
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Raymond Dunn
committed

Commits on Aug 22, 2023

add function header Doxygen documentation to M4Header components

Raymond Dunn
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Raymond Dunn
committed
working on z5 testing with existing read and write programs that Noah had started

Raymond Dunn
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Raymond Dunn
committed
read and write operations working on file

Raymond Dunn
authored and
Raymond Dunn
committed

Commits on Aug 23, 2023

Working on reading streams from file

Raymond Dunn
authored and
Raymond Dunn
committed

Commits on Aug 28, 2023

working on reading streams

Raymond Dunn
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Raymond Dunn
committed
First clean operation of reading from streams

Raymond Dunn
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Raymond Dunn
committed

Commits on Aug 29, 2023

unique data per stream to validate identity of each stream/record

Raymond Dunn
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Raymond Dunn
committed

Commits on Sep 7, 2023

write/read unique data for two-scan datasets - base/inline version

Raymond Dunn
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Raymond Dunn
committed
misc updates/refinements to comments, etc. basic data

Raymond Dunn
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Raymond Dunn
committed

Commits on Sep 8, 2023

refinements for better documented code

Raymond Dunn
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Raymond Dunn
committed
create shorter typedefs for z5::xxxx datatypes to help with understanding code

Raymond Dunn
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Raymond Dunn
committed
forgot to save file

Raymond Dunn
authored and
Raymond Dunn
committed

Commits on Sep 15, 2023

writeMonarch program - work in progress

Raymond Dunn
authored and
Raymond Dunn
committed

Commits on Sep 18, 2023

work in progress

Raymond Dunn
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Raymond Dunn
committed
work in progress

Raymond Dunn
authored and
Raymond Dunn
committed

Commits on Sep 19, 2023

work in progress

Raymond Dunn
authored and
Raymond Dunn
committed
work in progress

Raymond Dunn
authored and
Raymond Dunn
committed

Commits on Sep 20, 2023

work in progress

Raymond Dunn
authored and
Raymond Dunn
committed
readMonarch: cleaner read of Monarch4 header, using ostream printing

Raymond Dunn
authored and
Raymond Dunn
committed

Commits on Sep 25, 2023

initial operation M4Header::WriteChannelStreams()

Raymond Dunn
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Raymond Dunn
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writing channel groups correctly, working on attributes

Raymond Dunn
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Raymond Dunn
committed
M4ChannelHeader::WriteToFile() writes channel attrs to correct position

Raymond Dunn
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Raymond Dunn
committed
M4Header::WriteChannelStreams() writes buffers to acquisitions group

Raymond Dunn
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Raymond Dunn
committed

Commits on Sep 26, 2023

M4Header::WriteChannelStreams() writes acquisitions in correct place

Raymond Dunn
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Raymond Dunn
committed
M4Header::WriteChannelCoherence() first operation

Raymond Dunn
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Raymond Dunn
committed
channel and stream groups written to hierarchy

Raymond Dunn
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Raymond Dunn
committed
M4Header::ReadChannelCoherence() first operation

Raymond Dunn
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Raymond Dunn
committed

Commits on Sep 28, 2023

preparing for integrating stream M4Stream objects

Raymond Dunn
authored and
Raymond Dunn
committed

Commits on Sep 29, 2023

state at end FY23

Raymond Dunn
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Raymond Dunn
committed

Commits on Oct 31, 2023

add missing test files

Raymond Dunn
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Raymond Dunn
committed

Commits on Nov 6, 2023

M4Header: read/write channel-streams - have to reverse col/row to row/col for Zarr/z5

Raymond Dunn
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Raymond Dunn
committed

Commits on Nov 7, 2023

Create attribute entry for number of streams in run

Raymond Dunn
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Raymond Dunn
committed
writeMonarch test print StreamHeader and ChannelHeader metadata for reference

Raymond Dunn
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Raymond Dunn
committed
M4StreamHeader::ReadFromFile() operational

Raymond Dunn
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Raymond Dunn
committed
M4ChannelHeader::ReadFromFile() operational

Raymond Dunn
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Raymond Dunn
committed

Commits on Nov 14, 2023

update nlohmann::json conversions with casts

Raymond Dunn
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Raymond Dunn
committed

Commits on Nov 21, 2023

remove some of the logging messages to improve readability

Raymond Dunn
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Raymond Dunn
committed
change z5/Zarr file reference to pointer to enable cleaner integration

Raymond Dunn
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Raymond Dunn
committed
Update group pointers

Raymond Dunn
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Raymond Dunn
committed

Commits on Nov 30, 2023

M4Monarch::WriteHeader()

Raymond Dunn
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Raymond Dunn
committed

Commits on Dec 1, 2023

create z5includes.hh to isolate z5/Zarr definitions for reuse

Raymond Dunn
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Raymond Dunn
committed

Commits on Dec 11, 2023

change z5 'typedefs' to 'using', clean compile

Raymond Dunn
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Raymond Dunn
committed
working on creating streams issues

Raymond Dunn
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Raymond Dunn
committed
partial answer to segfault creating streams, need to fix permanently

Raymond Dunn
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Raymond Dunn
committed

Commits on Dec 18, 2023

improved CTOR operation for M4Stream

Raymond Dunn
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Raymond Dunn
committed
improved CTOR operation for M4Stream

Raymond Dunn
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Raymond Dunn
committed
working M4Stream::FinalizeStream(), M4Stream::FinalizeCurrentAcq()

Raymond Dunn
authored and
Raymond Dunn
committed

Commits on Dec 29, 2023

final adaptation of M4Stream::Initialize() to z5/Zarr first clean build

Raymond Dunn
authored and
Raymond Dunn
committed
M4Stream finalizations working properly, attribute values look corrrect

Raymond Dunn
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Raymond Dunn
committed
release std::unique_ptr with reset() instead of release() which doesn't delete object.

Raymond Dunn
authored and
Raymond Dunn
committed

Commits on Dec 30, 2023

working on handling empty acquisitions properly

Raymond Dunn
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Raymond Dunn
committed
handling empty acquisitions properly during read

Raymond Dunn
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Raymond Dunn
committed

Commits on Jan 1, 2024

M4Stream CTOR()/initialize() harmonized write/read operation

Raymond Dunn
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Raymond Dunn
committed
adapt M4Stream::BuildIndex()

Raymond Dunn
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Raymond Dunn
committed

Commits on Jan 2, 2024

working on adapting M4Stream::ReadRecordAsIs() and M4Stream::WriteRecordAsIs()

Raymond Dunn
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Raymond Dunn
committed

Commits on Jan 17, 2024

Monarch4 pause: Jan2024

Raymond Dunn
authored and
Raymond Dunn
committed

Commits on Jan 14, 2025

Merge tag 'v3.8.3' into develop
nsoblath
committed

Commits on Jan 16, 2025

Merge tag 'v3.8.4' into develop
nsoblath
committed

Commits on Feb 18, 2025

Merge tag 'v3.8.5' into develop
nsoblath
committed

Commits on Jan 20, 2026

Merge tag 'v3.8.6' into develop
nsoblath
committed

Commits on Jan 23, 2026

Merge tag 'v3.8.7' into develop
nsoblath
committed

Commits on Mar 9, 2026

Merge branch 'develop' into feature/zarr
nsoblath-pnnl
committed