Re: HDF5dataset error & and suggestion for 2p image registration? #105
Description
Hi Lab,
After add BlockRegistartion and using BlockRegistration, I encounter HDF5Dataset error. Some packages are downgraded and this may evoke the old HDF5Dataset issue (HolyLab/RegisterDeformation.jl#13).
julia> using BlockRegistration
[ Info: Precompiling BlockRegistration [96be3cfc-dfc9-41f0-9424-fd41ed36fd5e]
WARNING: could not import CoordinateTransformations.transform into RegisterDeformation
ERROR: LoadError: UndefVarError: HDF5Dataset not defined
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/RegisterDeformation/IWvZQ/src/RegisterDeformation.jl:587
[2] include
@ ./Base.jl:419 [inlined]
[3] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base ./loading.jl:1554
[4] top-level scope
@ stdin:1
in expression starting at /home/donghoon/.julia/packages/RegisterDeformation/IWvZQ/src/RegisterDeformation.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile RegisterDeformation [c19381b7-cf49-59d7-881c-50dfbd227eaf] to /home/donghoon/.julia/compiled/v1.8/RegisterDeformation/jl_928gJP.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
@ Base ./loading.jl:1707
[3] compilecache
@ ./loading.jl:1651 [inlined]
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1337
[5] _require_prelocked(uuidkey::Base.PkgId)
@ Base ./loading.jl:1200
[6] macro expansion
@ ./loading.jl:1180 [inlined]
[7] macro expansion
@ ./lock.jl:223 [inlined]
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1144
[9] include
@ ./Base.jl:419 [inlined]
[10] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
@ Base ./loading.jl:1554
[11] top-level scope
@ stdin:1
in expression starting at /home/donghoon/.julia/packages/BlockRegistration/mLYy8/src/BlockRegistration.jl:1
in expression starting at stdin:1
ERROR: Failed to precompile BlockRegistration [96be3cfc-dfc9-41f0-9424-fd41ed36fd5e] to /home/donghoon/.julia/compiled/v1.8/BlockRegistration/jl_DUfkGP.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
@ Base ./loading.jl:1707
[3] compilecache
@ ./loading.jl:1651 [inlined]
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1337
[5] _require_prelocked(uuidkey::Base.PkgId)
@ Base ./loading.jl:1200
[6] macro expansion
@ ./loading.jl:1180 [inlined]
[7] macro expansion
@ ./lock.jl:223 [inlined]
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1144Two photon imaging with galvo-galvo scanning (conventional two photon microscopy i guess) suffers from some motion artifacts with a head-fixed animal. Specifically, there is a significant time gap between each line of a single image frame. Even though tissue warping is minimal, there is non-linear problems, one of which is motion artifact between different image lines (within a single frame). I thought RegisterQD may not be good for this problem. Thus, I wanted to try BlockRegistration. Or any suggestion?