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issue of reading visiumHD file #10

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Sophieliula opened this issue Jul 8, 2024 · 5 comments
Open

issue of reading visiumHD file #10

Sophieliula opened this issue Jul 8, 2024 · 5 comments

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@Sophieliula
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hd = cs.read_visiumHD(hd_dir)

  1. loading 2um binned data...
    Formatting cell polygons...
    Progress: 100%[==================================================] Time: 0:00:5039m
  2. 2um binned data loaded!
  3. loading 8um binned data...
    Formatting cell polygons...
    Progress: 100%[==================================================] Time: 0:00:02
  4. 8um binned data loaded!
  5. loading 16um binned data...
    Formatting cell polygons...
  6. 16um binned data loaded!
    MethodError: no method matching Union{Matrix{ColorTypes.Gray{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGBA{FixedPointNumbers.N0f8}}}(::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}})

Stacktrace:
[1] convert(#unused#::Type{Union{Matrix{ColorTypes.Gray{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGBA{FixedPointNumbers.N0f8}}}}, a::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}})
@ Base ./array.jl:554
[2] convert(#unused#::Type{Union{Nothing, Matrix{ColorTypes.Gray{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGBA{FixedPointNumbers.N0f8}}}}, x::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}})
@ Base ./some.jl:36
[3] CellScopes.VisiumImgObject(highresImage::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}}, lowresImage::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}}, fullresImage::Nothing, detectedTissue::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, alignedImage::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, jsonParameters::Dict{String, Any})
@ CellScopes ~/.julia/packages/CellScopes/pM38e/src/spatial/sp_objects.jl:249
[4] read_visiumHD(hd_dir::String; min_genes::Vector{Int64}, min_cells::Vector{Int64}, prefix::Nothing, postfix::Nothing, default_bin::String)
@ CellScopes ~/.julia/packages/CellScopes/pM38e/src/fileio.jl:660
[5] read_visiumHD(hd_dir::String)
@ CellScopes ~/.julia/packages/CellScopes/pM38e/src/fileio.jl:628
[6] top-level scope
@ In[6]:1
@HaojiaWu
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HaojiaWu commented Jul 9, 2024

I tried using hd = cs.read_visiumHD(hd_dir) to read the Spaceranger output from two samples again, and I couldn't reproduce the error you came across. Please make sure that hd_dir is the output directory from Spaceranger to use this function correctly. Other troubleshooting steps you can take include reinstalling CellScopes using Julia 1.8.4. I tested CellScopes on both Julia 1.7.3 and Julia 1.8.4, and it works fine. Other users have reported dependency issues with newer versions of Julia.

@liangxs7015
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Same issue on both Julia 1.8.4 and 1.7.3, any help for this?

  1. loading 2um binned data...
    Formatting cell polygons...
    Progress: 100%[==================================================] Time: 0:00:4239m
  2. 2um binned data loaded!
  3. loading 8um binned data...
    Formatting cell polygons...
    Progress: 100%[==================================================] Time: 0:00:05
  4. 8um binned data loaded!
  5. loading 16um binned data...
    Formatting cell polygons...
    Progress: 100%[==================================================] Time: 0:00:02
  6. 16um binned data loaded!
    MethodError: no method matching Union{Matrix{ColorTypes.Gray{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGBA{FixedPointNumbers.N0f8}}}(::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}})

Stacktrace:
[1] convert(#unused#::Type{Union{Matrix{ColorTypes.Gray{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGBA{FixedPointNumbers.N0f8}}}}, a::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}})
@ Base ./array.jl:554
[2] convert(#unused#::Type{Union{Nothing, Matrix{ColorTypes.Gray{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGBA{FixedPointNumbers.N0f8}}}}, x::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}})
@ Base ./some.jl:36
[3] CellScopes.VisiumImgObject(highresImage::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}}, lowresImage::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}}, fullresImage::Nothing, detectedTissue::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, alignedImage::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, jsonParameters::Dict{String, Any})
@ CellScopes ~/.julia/packages/CellScopes/XZUoC/src/spatial/sp_objects.jl:249
[4] read_visiumHD(hd_dir::String; min_genes::Vector{Int64}, min_cells::Vector{Int64}, prefix::Nothing, postfix::Nothing, default_bin::String)
@ CellScopes ~/.julia/packages/CellScopes/XZUoC/src/fileio.jl:660
[5] read_visiumHD(hd_dir::String)
@ CellScopes ~/.julia/packages/CellScopes/XZUoC/src/fileio.jl:628
[6] top-level scope
@ In[2]:1

@HaojiaWu
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I am transitioning everything to Julia 1.10.4, as older versions have too many dependency issues. Could you please try this and let me know if you come across any problems? Thanks.
https://github.com/HaojiaWu/CellScopes.jl/tree/dev

@liangxs7015
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Thanks for your reply, when running 'Pkg.add(url="https://github.com/TheHumphreysLab/CellScopes.jl")', I saw some issues:
┌ Interpolations
│ WARNING: method definition for checkbounds at /home/liangxs/.julia/packages/Interpolations/y4lLj/src/Interpolations.jl:454 declares type variable N but does not use it.
│ WARNING: method definition for checkbounds at /home/liangxs/.julia/packages/Interpolations/y4lLj/src/Interpolations.jl:457 declares type variable N but does not use it.
│ WARNING: method definition for GriddedInterpolation at /home/liangxs/.julia/packages/Interpolations/y4lLj/src/gridded/gridded.jl:37 declares type variable pad but does not use it.
│ WARNING: method definition for GriddedInterpolation at /home/liangxs/.julia/packages/Interpolations/y4lLj/src/gridded/gridded.jl:60 declares type variable pad but does not use it.
│ WARNING: method definition for interpolate! at /home/liangxs/.julia/packages/Interpolations/y4lLj/src/deprecations.jl:30 declares type variable TWeights but does not use it.
└
┌ VariantCallFormat
│ [ Info: Compiling VCF parser...
└
┌ PyCallUtils
│ WARNING: Method definition getindex(PyCall.PyObject, Union{AbstractString, Symbol}) in module PyCall at /home/liangxs/.julia/packages/PyCall/1gn3u/src/PyCall.jl:349 overwritten in module PyCallUtils at /home/liangxs/.julia/packages/PyCallUtils/GJ7TW/src/PyCallUtils.jl:45.
│ ERROR: Method overwriting is not permitted during Module precompilation. Use __precompile__(false) to opt-out of precompilation.
└
┌ CellScopes
│ WARNING: Method definition getindex(PyCall.PyObject, Union{AbstractString, Symbol}) in module PyCall at /home/liangxs/.julia/packages/PyCall/1gn3u/src/PyCall.jl:349 overwritten in module PyCallUtils at /home/liangxs/.julia/packages/PyCallUtils/GJ7TW/src/PyCallUtils.jl:45.
│ ERROR: Method overwriting is not permitted during Module precompilation. Use __precompile__(false) to opt-out of precompilation.
└

After cs.read_visiumHD(), the same error appeared again:

  1. loading 2um binned data...
    Formatting cell polygons...
    Progress: 100%[==================================================] Time: 0:00:52[39m
  2. 2um binned data loaded!
  3. loading 8um binned data...
    Formatting cell polygons...
    Progress: 100%[==================================================] Time: 0:00:041:39
  4. 8um binned data loaded!
  5. loading 16um binned data...
    Formatting cell polygons...
    Progress: 100%[==================================================] Time: 0:00:02
  6. 16um binned data loaded!
    MethodError: no method matching Union{Matrix{ColorTypes.Gray{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGBA{FixedPointNumbers.N0f8}}}(::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}})

Stacktrace:
[1] convert(::Type{Union{Matrix{ColorTypes.Gray{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGBA{FixedPointNumbers.N0f8}}}}, a::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}})
@ Base ./array.jl:665
[2] convert(::Type{Union{Nothing, Matrix{ColorTypes.Gray{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGBA{FixedPointNumbers.N0f8}}}}, x::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}})
@ Base ./some.jl:37
[3] CellScopes.VisiumImgObject(highresImage::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}}, lowresImage::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}}, fullresImage::Nothing, detectedTissue::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, alignedImage::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, jsonParameters::Dict{String, Any})
@ CellScopes ~/.julia/packages/CellScopes/XZUoC/src/spatial/sp_objects.jl:249
[4] read_visiumHD(hd_dir::String; min_genes::Vector{Int64}, min_cells::Vector{Int64}, prefix::Nothing, postfix::Nothing, default_bin::String)
@ CellScopes ~/.julia/packages/CellScopes/XZUoC/src/fileio.jl:660
[5] read_visiumHD(hd_dir::String)
@ CellScopes ~/.julia/packages/CellScopes/XZUoC/src/fileio.jl:621
[6] top-level scope
@ In[2]:1

Could you please help me figure out what the problem is? Any clues might be helpful is that the 'import CellScope as cs' produced Precompiling erros and I don't known whether it is associate with the failure of reading samples:
Precompiling CellScopes
✓ StructArrays → StructArraysGPUArraysCoreExt
? PyCallUtils
Info Given CellScopes was explicitly requested, output will be shown live
WARNING: Method definition getindex(PyCall.PyObject, Union{AbstractString, Symbol}) in module PyCall at /home/liangxs/.julia/packages/PyCall/1gn3u/src/PyCall.jl:349 overwritten in module PyCallUtils at /home/liangxs/.julia/packages/PyCallUtils/GJ7TW/src/PyCallUtils.jl:45.
ERROR: Method overwriting is not permitted during Module precompilation. Use __precompile__(false) to opt-out of precompilation.
? CellScopes
1 dependency successfully precompiled in 18 seconds. 575 already precompiled.
2 dependencies failed but may be precompilable after restarting julia
2 dependencies had output during precompilation:
┌ PyCallUtils
│ WARNING: Method definition getindex(PyCall.PyObject, Union{AbstractString, Symbol}) in module PyCall at /home/liangxs/.julia/packages/PyCall/1gn3u/src/PyCall.jl:349 overwritten in module PyCallUtils at /home/liangxs/.julia/packages/PyCallUtils/GJ7TW/src/PyCallUtils.jl:45.
│ ERROR: Method overwriting is not permitted during Module precompilation. Use __precompile__(false) to opt-out of precompilation.
└
┌ CellScopes
│ [Output was shown above]
└
[ Info: Precompiling CellScopes [708d50d9-0a30-4b01-8594-5d83c0e43023]
WARNING: Method definition getindex(PyCall.PyObject, Union{AbstractString, Symbol}) in module PyCall at /home/liangxs/.julia/packages/PyCall/1gn3u/src/PyCall.jl:349 overwritten in module PyCallUtils at /home/liangxs/.julia/packages/PyCallUtils/GJ7TW/src/PyCallUtils.jl:45.
ERROR: Method overwriting is not permitted during Module precompilation. Use __precompile__(false) to opt-out of precompilation.
[ Info: Skipping precompilation since precompile(false). Importing CellScopes [708d50d9-0a30-4b01-8594-5d83c0e43023].
The WebIO Jupyter extension was not detected. See the WebIO Jupyter integration documentation for more information.

Precompiling PyCallUtils
Info Given PyCallUtils was explicitly requested, output will be shown live
WARNING: Method definition getindex(PyCall.PyObject, Union{AbstractString, Symbol}) in module PyCall at /home/liangxs/.julia/packages/PyCall/1gn3u/src/PyCall.jl:349 overwritten in module PyCallUtils at /home/liangxs/.julia/packages/PyCallUtils/GJ7TW/src/PyCallUtils.jl:45.
ERROR: Method overwriting is not permitted during Module precompilation. Use __precompile__(false) to opt-out of precompilation.
? PyCallUtils
[ Info: Precompiling PyCallUtils [02651160-e6c3-11e9-0e2a-551f75d9519e]
WARNING: Method definition getindex(PyCall.PyObject, Union{AbstractString, Symbol}) in module PyCall at /home/liangxs/.julia/packages/PyCall/1gn3u/src/PyCall.jl:349 overwritten in module PyCallUtils at /home/liangxs/.julia/packages/PyCallUtils/GJ7TW/src/PyCallUtils.jl:45.
ERROR: Method overwriting is not permitted during Module precompilation. Use __precompile__(false) to opt-out of precompilation.
[ Info: Skipping precompilation since precompile(false). Importing PyCallUtils [02651160-e6c3-11e9-0e2a-551f75d9519e].
┌ Warning: Using an un-quoted Symbol on the LHS is deprecated. Write :SumValue = ... instead.
└ @ DataFramesMeta ~/.julia/packages/DataFramesMeta/Ga6VV/src/parsing.jl:387
Welcome to use CellScopes.jl!

@HaojiaWu
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As mentioned in the link provided (https://github.com/HaojiaWu/CellScopes.jl/tree/dev), if you are using Julia v1.10.4, please use the following command to install:

using Pkg
Pkg.add(PackageSpec(url="https://github.com/bicycle1885/Leiden.jl"))
Pkg.add(PackageSpec(url="https://github.com/HaojiaWu/CellScopes.jl", rev="dev"))

I reinstalled it on a fresh Linux machine, and the methods described above worked for me when reading VisiumHD data.

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@Sophieliula @HaojiaWu @liangxs7015