kharchenkolab / baysor Goto Github PK

bash-4.2$ ~/tool/Baysor/bin/baysor -i 500 -n 20 -p -c ~/tool/Baysor/iss.toml -o ./output_dapi -p ./data/pciSeq_3-3.csv ./data/DAPI_3-3_mask.tif
┌ Error: Can't parse argument -i
└ @ Baysor /home/vpetukhov/.julia/dev/Baysor/src/cli/common.jl:125
Usage: baysor <command> [options]

Commands:
        run             run segmentation of the dataset
        preview         generate preview diagnostics of the dataset

"/home/mike/Baysor/bin/julia-1.6.0//bin/julia -e 'ENV["JULIA_DEPOT_PATH"]="/home/mike/Baysor/bin/.julia/"; using PackageCompiler; import Baysor; create_sysimage(:Baysor; precompile_execution_file="$(dirname(pathof(Baysor)))/../bin/precompile.jl", replace_default=true)'
ERROR: UndefKeywordError: keyword argument sysimage_path not assigned
Stacktrace:
 [1] top-level scope
   @ none:1
make: *** [Makefile:20: /home/mike/Baysor/bin/julia-1.6.0//lib/julia/sys.so] Error 1"

   create_sysimage(packages::Vector{String}; kwargs...)

Create a system image that includes the package(s) in `packages` (given as a
string or vector). If the `packages` argument is not passed, all packages in the
project will be put into the sysimage.

An attempt to automatically find a compiler will be done but can also be given
explicitly by setting the environment variable `JULIA_CC` to a path to a
compiler (can also include extra arguments to the compiler, like `-g`).

### Keyword arguments:

- `sysimage_path::String`: The path to where the resulting sysimage should be saved.

- `project::String`: The project that should be active when the sysimage is created,
  defaults to the currently active project.

- `precompile_execution_file::Union{String, Vector{String}}`: A file or list of
  files that contain code from which precompilation statements should be recorded.

- `precompile_statements_file::Union{String, Vector{String}}`: A file or list of
  files that contain precompilation statements that should be included in the sysimage.

- `incremental::Bool`: If `true`, build the new sysimage on top of the sysimage
  of the current process otherwise build a new sysimage from scratch. Defaults to `true`.

- `filter_stdlibs::Bool`: If `true`, only include stdlibs that are in the project file.
  Defaults to `false`, only set to `true` if you know the potential pitfalls.

- `include_transitive_dependencies::Bool`: If `true`, explicitly put all
   transitive dependencies into the sysimage. This only makes a difference if some
   packages do not load all their dependencies when themselves are loaded. Defaults to `true`.

### Advanced keyword arguments

- `base_sysimage::Union{Nothing, String}`: If a `String`, names an existing sysimage upon which to build
   the new sysimage incrementally, instead of the sysimage of the current process. Defaults to `nothing`.
   Keyword argument `incremental` must be `true` if `base_sysimage` is not `nothing`.

- `cpu_target::String`: The value to use for `JULIA_CPU_TARGET` when building the system image. Defaults
  to `native`.

- `script::String`: Path to a file that gets executed in the `--output-o` process.

- `sysimage_build_args::Cmd`: A set of command line options that is used in the Julia process building the sysimage,
  for example `-O1 --check-bounds=yes`.
"""
function create_sysimage(packages::Union{Nothing, Symbol, Vector{String}, Vector{Symbol}}=nothing;
                         sysimage_path::String,
                         project::String=dirname(active_project()),
                         precompile_execution_file::Union{String, Vector{String}}=String[],
                         precompile_statements_file::Union{String, Vector{String}}=String[],
                         incremental::Bool=true,
                         filter_stdlibs::Bool=false,
                         cpu_target::String=NATIVE_CPU_TARGET,
                         script::Union{Nothing, String}=nothing,
                         sysimage_build_args::Cmd=``,
                         include_transitive_dependencies::Bool=true,
                         # Internal args
                         base_sysimage::Union{Nothing, String}=nothing,
                         julia_init_c_file=nothing,
                         version=nothing,
                         soname=nothing,
                         compat_level::String="major",
                         )

[ Info: PackageCompiler: Executing /home/mike/Baysor/bin/.julia/packages/Baysor/ujbBh/bin/precompile.jl => /tmp/jl_packagecompiler_JPdQYV/jl_Dd6oiU
ERROR: LoadError: LoadError: ArgumentError: Package DataFrames not found in current path:
- Run `import Pkg; Pkg.add("DataFrames")` to install the DataFrames package.

$ baysor preview -x x -y y --gene gene -c osm_fish.toml -o xxx mRNA_coords_raw_counting.csv
[21:44:21] Info: (2021-05-04) Run Baysor v0.4.3
[21:44:21] Info: Loading data...
[21:44:36] Error: UndefVarError(:DataFrame!)
|                 
|                 read_spatial_df(data_path::String; x_col::Symbol, y_col::Symbol, gene_col::Symbol, filter_cols::Bool) at spatial.jl:5
|                 read_spatial_df at spatial.jl:5 [inlined]
|                 load_df(data_path::String; x_col::Symbol, y_col::Symbol, gene_col::Symbol, min_molecules_per_gene::Int64, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) at initialization.jl:162
|                 (::Baysor.var"#load_df##kw")(::NamedTuple{(:x_col, :y_col, :gene_col, :min_molecules_per_gene), Tuple{Symbol, Symbol, Symbol, Int64}}, ::typeof(Baysor.load_df), data_path::String) at initialization.jl:162
|                 load_df(args::Dict{String, Any}; kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) at cli_wrappers.jl:75
|                 load_df(args::Dict{String, Any}) at cli_wrappers.jl:75
|                 run_cli_preview(args::Vector{String}) at cli_wrappers.jl:516
|                 run_cli(args::Vector{String}) at cli_wrappers.jl:623
|                 run_cli() at cli_wrappers.jl:604
|                 top-level scope at baysor:3
|                 eval at boot.jl:360 [inlined]
|                 include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) at loading.jl:1094
|                 _include(mapexpr::Function, mod::Module, _path::String) at loading.jl:1148
|                 include(mod::Module, _path::String) at Base.jl:386
|                 exec_options(opts::Base.JLOptions) at client.jl:285
|                 _start() at client.jl:485

$ head -n 6 spatial.jl 
import CSV
using DataFrames

function read_spatial_df(data_path; x_col::Symbol=:x, y_col::Symbol=:y, gene_col::Union{Symbol, Nothing}=:gene, filter_cols::Bool=false)
    df_spatial = DataFrame!(CSV.File(data_path));

baysor
ERROR: Unable to find compatible target in system image.

┌ Warning: No config file provided. Using default parameters.
└ @ Baysor ~/.julia/packages/Baysor/tda03/src/cli/main.jl:96
[14:22:30] Info: (2021-12-07) Run Baysor v0.5.1
[14:22:30] Info: Loading data...
[14:22:48] Info: Loaded 126550 transcripts
[14:22:49] Info: Loading segmentation mask...
[14:23:05] Info: Done
[14:23:05] Info: Estimating prior segmentation polygons...
[14:23:10] Error: MethodError(LightGraphs.kruskal_mst, ({165106, 163115} undirected simple Int64 graph with Float64 weights,), 0x0000000000007b62)
|
|                 border_mst(border_points::Vector{Vector{UInt32}}; min_edge_length::Float64, max_edge_length::Float64) at boundary_estimation.jl:65
|                 border_mst(border_points::Vector{Vector{UInt32}}) at boundary_estimation.jl:42
|                 _broadcast_getindex_evalf at broadcast.jl:670 [inlined]
|                 _broadcast_getindex at broadcast.jl:643 [inlined]
|                 getindex at broadcast.jl:597 [inlined]
|                 copy at broadcast.jl:943 [inlined]
|                 materialize at broadcast.jl:904 [inlined]
|                 extract_polygons_from_label_grid(grid_labels::Matrix{UInt32}; min_border_length::Int64, shape_method::Symbol, max_dev::Float64, exclude_labels::Vector{Int64}, offset::Vector{Float64}, grid_step::Float64) at boundary_estimation.jl:231
|                 (::Baysor.var"#extract_polygons_from_label_grid##kw")(::NamedTuple{(:grid_step,), Tuple{Float64}}, ::typeof(Baysor.extract_polygons_from_label_grid), grid_labels::Matrix{UInt32}) at boundary_estimation.jl:223
|                 load_prior_segmentation(df_spatial::DataFrames.DataFrame, args::Dict{String, Any}) at main.jl:297
|                 load_and_preprocess_data!(args::Dict{String, Any}) at main.jl:335
|                 run_cli_main(args::Vector{String}) at main.jl:442
|                 run_cli(args::Vector{String}) at common.jl:118
|                 run_cli() at common.jl:103
|                 top-level scope at baysor:3
|                 eval at boot.jl:373 [inlined]
|                 include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) at loading.jl:1196
|                 _include(mapexpr::Function, mod::Module, _path::String) at loading.jl:1253
|                 include(mod::Module, _path::String) at Base.jl:420
|                 exec_options(opts::Base.JLOptions) at client.jl:292
|                 _start() at client.jl:495
└ Baysor /Users/xvk205/.julia/packages/Baysor/tda03/src/cli/common.jl:132

┌ Warning: No config file provided. Using default parameters.
└ @ Baysor ~/.julia/packages/Baysor/tda03/src/cli/main.jl:96
[14:55:31] Info: (2021-12-07) Run Baysor v0.5.1
[14:55:31] Info: Loading data...
[14:55:50] Info: Loaded 126550 transcripts
[14:55:51] Info: Estimating noise level
[14:55:57] Info: Done
[14:55:59] Info: Clustering molecules...
Progress: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| Time: 0:00:14
  Iteration:                  306
  Max. difference:            0.0010753232764250476
  Fraction of probs changed:  0.6586013433425524
[14:56:17] Info: Algorithm stopped after 306 iterations. Error: 0.00108. Converged: true.
[14:56:17] Info: Done
[14:56:19] Info: Initializing algorithm. Scale: 40.0, scale std: 10.0, initial #components: 84366, #molecules: 126550.
[14:56:21] Info: Using 2D coordinates
Progress: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| Time: 0:01:28
  Iteration:        500
  Noise level, %:   22.36
  Num. components:  1455
[14:57:55] Info: Processing complete.
[14:58:02] Info: Estimating local colors
[14:58:32] Info: Saving results to ./results_C1-2/segmentation.csv
[14:58:33] Info: Plot diagnostics
[14:59:38] Info: Estimating boundary polygons
[15:00:07] Error: MethodError(LightGraphs.kruskal_mst, ({144, 157} undirected simple Int64 graph with Float64 weights,), 0x0000000000007b62)
|
|                 border_mst(border_points::Vector{Vector{UInt32}}; min_edge_length::Float64, max_edge_length::Float64) at boundary_estimation.jl:65
|                 border_mst(border_points::Vector{Vector{UInt32}}) at boundary_estimation.jl:42
|                 _broadcast_getindex_evalf at broadcast.jl:670 [inlined]
|                 _broadcast_getindex at broadcast.jl:643 [inlined]
|                 getindex at broadcast.jl:597 [inlined]
|                 copy at broadcast.jl:943 [inlined]
|                 materialize at broadcast.jl:904 [inlined]
|                 extract_polygons_from_label_grid(grid_labels::Matrix{UInt16}; min_border_length::Int64, shape_method::Symbol, max_dev::Float64, exclude_labels::Vector{Int64}, offset::Vector{Float64}, grid_step::Float64) at boundary_estimation.jl:231
|                 (::Baysor.var"#extract_polygons_from_label_grid##kw")(::NamedTuple{(:min_border_length, :shape_method, :max_dev, :exclude_labels, :offset, :grid_step), Tuple{Int64, Symbol, Float64, Vector{Int64}, Vector{Float64}, Float64}}, ::typeof(Baysor.extract_polygons_from_label_grid), grid_labels::Matrix{UInt16}) at boundary_estimation.jl:223
|                 boundary_polygons(pos_data::Matrix{Float64}, cell_labels::Vector{Int64}; min_x::Nothing, max_x::Nothing, grid_step::Float64, min_border_length::Int64, shape_method::Symbol, max_dev::Float64, bandwidth::Float64, exclude_labels::Vector{Int64}, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) at boundary_estimation.jl:270
|                 boundary_polygons at boundary_estimation.jl:254 [inlined]
|                 #boundary_polygons#214 at boundary_estimation.jl:248 [inlined]
|                 (::Baysor.var"#boundary_polygons##kw")(::NamedTuple{(:grid_step, :bandwidth), Tuple{Float64, Float64}}, ::typeof(Baysor.boundary_polygons), spatial_df::DataFrames.DataFrame, args::Vector{Int64}) at boundary_estimation.jl:248
|                 plot_transcript_assignment_panel(df_res::DataFrames.DataFrame, assignment::Vector{Int64}, args::Dict{String, Any}; clusters::Vector{Int64}, prior_polygons::Vector{Matrix{Float64}}, gene_colors::Vector{ColorTypes.Lab{Float64}}) at main.jl:212
|                 (::Baysor.var"#plot_transcript_assignment_panel##kw")(::NamedTuple{(:clusters, :prior_polygons, :gene_colors), Tuple{Vector{Int64}, Vector{Matrix{Float64}}, Vector{ColorTypes.Lab{Float64}}}}, ::typeof(Baysor.plot_transcript_assignment_panel), df_res::DataFrames.DataFrame, assignment::Vector{Int64}, args::Dict{String, Any}) at main.jl:205
|                 save_segmentation_results(bm_data::Baysor.BmmData{2}, gene_names::Vector{String}, args::Dict{String, Any}; mol_clusts::NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, comp_segs::Nothing, prior_polygons::Vector{Matrix{Float64}}) at main.jl:414
|                 (::Baysor.var"#save_segmentation_results##kw")(::NamedTuple{(:mol_clusts, :comp_segs, :prior_polygons), Tuple{NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, Nothing, Vector{Matrix{Float64}}}}, ::typeof(Baysor.save_segmentation_results), bm_data::Baysor.BmmData{2}, gene_names::Vector{String}, args::Dict{String, Any}) at main.jl:394
|                 run_cli_main(args::Vector{String}) at main.jl:479
|                 run_cli(args::Vector{String}) at common.jl:118
|                 run_cli() at common.jl:103
|                 top-level scope at baysor:3
|                 eval at boot.jl:373 [inlined]
|                 include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) at loading.jl:1196
|                 _include(mapexpr::Function, mod::Module, _path::String) at loading.jl:1253
|                 include(mod::Module, _path::String) at Base.jl:420
|                 exec_options(opts::Base.JLOptions) at client.jl:292
|                 _start() at client.jl:495
└ Baysor /Users/xvk205/.julia/packages/Baysor/tda03/src/cli/common.jl:132

baysor run \
  -i 500 \
  -c config.toml \
  -o out/ \
  -p \
  --save-polygons GeoJSON \
  coordinates.csv

[12:56:11] Info: (2021-06-03) Run Baysor v0.4.3                                                                                                                                                                    
[12:56:11] Info: Loading data...                                                                                                                                                                                   
[12:56:22] Info: Loaded 55099 transcripts                                                                                                                                                                          
[12:56:23] Info: Estimating noise level                                                                  
[12:56:27] Info: Done                                                                                    
[12:56:28] Info: Clustering molecules...                                                                 
Progress: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| Time: 0:00:01
  Iteration:                  60   
  Max. difference:            0.00232397696692227
  Fraction of probs changed:  0.558013757055482
[12:56:31] Info: Algorithm stopped after 60 iterations. Error: 0.00232. Converged: true.
[12:56:32] Info: Done
[12:56:33] Info: Initializing algorithm. Scale: 60, scale std: 15.0, initial #components: 36732, #molecules: 55099.
[12:56:38] Info: Using 2D coordinates                                                                    
Progress: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| Time: 0:01:05           Iteration:        500                                                                                  
  Noise level, %:   4.96                                                                                                                                                                                             Num. components:  3109                                                                                                                                                                                           
[12:57:48] Info: Processing complete.        
[12:58:00] Info: Estimating local colors                                                                                                                                                                           [12:58:28] Info: Saving results to out_plot/segmentation.csv                                                                                                                                                       
[12:58:29] Info: Plot diagnostics                                                                        
[12:59:18] Error: MethodError(Makie.backend_show, (CairoMakie.CairoBackend(CairoMakie.PNG, "/home/user/.julia/packages/CairoMakie/mjJN1/src/display.png", 1.0, 0.75), IOContext(IOStream(<file out_plot/segmentation_diagnostics.html>)), MIME type text/html, Scene (600px, 400px):
|                   36 Plots:                                                                                                                                                                                      |                     ├ Makie.Poly{Tuple{Vector{Vector{GeometryBasics.Point{2, Float32}}}}}                                                                                                                        |                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}              
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}              
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}              
|                     ├ Makie.Annotations{Tuple{Vector{Tuple{String, GeometryBasics.Point{2, Float32}}}}}                  
|                     ├ Makie.Text{Tuple{String}}                                                        
|                     ├ Makie.Lines{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}              
|                     ├ Makie.Annotations{Tuple{Vector{Tuple{String, GeometryBasics.Point{2, Float32}}}}}                                                                                                          
|                     ├ Makie.Text{Tuple{String}}
|                     ├ Makie.Lines{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.Lines{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.Lines{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.Text{Tuple{String}}
|                     ├ Makie.Poly{Tuple{Vector{Vector{GeometryBasics.Point{2, Float32}}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.Annotations{Tuple{Vector{Tuple{String, GeometryBasics.Point{2, Float32}}}}} 
|                     ├ Makie.Text{Tuple{String}}
|                     ├ Makie.Lines{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.Annotations{Tuple{Vector{Tuple{String, GeometryBasics.Point{2, Float32}}}}} 
|                     ├ Makie.Text{Tuple{String}}
|                     ├ Makie.Lines{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.Lines{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.Lines{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     └ Makie.Text{Tuple{String}}
|                   3 Child Scenes:
|                     ├ Scene (489px, 308px)
|                     ├ Scene (166px, 129px)
|                     └ Scene (180px, 150px)), 0x00000000000074ba)
|                 
|                 show(io::IOStream, m::MIME{Symbol("text/html")}, scene::Makie.Scene) at display.jl:117
|                 show(io::IOStream, m::MIME{Symbol("text/html")}, fig::Makie.Figure) at display.jl:106
|                 (::Baysor.var"#325#326"{NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, No
thing, DataFrames.DataFrame, Vector{Int64}, Dict{Symbol, Any}})(io::IOStream) at cli_wrappers.jl:245
|                 open(::Baysor.var"#325#326"{NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}
, Nothing, DataFrames.DataFrame, Vector{Int64}, Dict{Symbol, Any}}, ::String, ::Vararg{String, N} where N; kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) at io.jl:330
|                 open at io.jl:328 [inlined]
|                 plot_diagnostics_panel(df_res::DataFrames.DataFrame, assignment::Vector{Int64}, tracer::Dict{Symbol, Any}, args::Dict{String, Any}; clust_res::NamedTuple{(:exprs, :assignment, :diffs, :assignme
nt_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, comp_segs::Nothing) at cli_wrappers.jl:224
|                 plot_diagnostics_panel at cli_wrappers.jl:223 [inlined]
|                 save_segmentation_results(bm_data::Baysor.BmmData{2}, gene_names::Vector{String}, args::Dict{String, Any}; mol_clusts::NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs)
, Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, comp_segs::Nothing, prior_polygons::Vector{Matrix{Float64}}) at cli_wrappers.jl:492
|                 (::Baysor.var"#save_segmentation_results##kw")(::NamedTuple{(:mol_clusts, :comp_segs, :prior_polygons), Tuple{NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{M
atrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, Nothing, Vector{Matrix{Float64}}}}, ::typeof(Baysor.save_segmentation_results), bm_data::Baysor.BmmData{2}, gene_names::Vector{
String}, args::Dict{String, Any}) at cli_wrappers.jl:476
|                 run_cli_main(args::Vector{String}) at cli_wrappers.jl:557
|                 run_cli(args::Vector{String}) at cli_wrappers.jl:748
|                 run_cli() at cli_wrappers.jl:733
|                 top-level scope at baysor:3
|                 eval at boot.jl:360 [inlined]
|                 include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) at loading.jl:1094
|                 _include(mapexpr::Function, mod::Module, _path::String) at loading.jl:1148
|                 include(mod::Module, _path::String) at Base.jl:386
|                 exec_options(opts::Base.JLOptions) at client.jl:285
|                 _start() at client.jl:485
└ Baysor /home/user/.julia/packages/Baysor/4K0to/src/cli_wrappers.jl:762

baysor preview -x X -y Y -g gene coordinates.csv

[15:02:12] Info: (2021-06-03) Run Baysor v0.4.3
[15:02:12] Info: Loading data...
[15:02:22] Info: Loaded 55832 transcripts
[15:02:23] Info: Estimating noise level
[15:02:27] Info: Done
[15:02:27] Info: Estimating local neighborhoods
[15:02:27] Info: Estimating local colors
[15:03:03] Info: Building transcript plots
[15:03:40] Info: Building gene structure plot
[15:03:49] Info: Plotting
[15:03:51] Error: MethodError(Makie.backend_show, (CairoMakie.CairoBackend(CairoMakie.PNG, "/home/user/.julia/packages/CairoMakie/mjJN1/src/display.png", 1.0, 0.75), IOContext(IOStream(<file preview.html>)), MIME type text/html, Scene (2177px, 1809px):
|                   18 Plots:
|                     ├ Makie.Poly{Tuple{Vector{Vector{GeometryBasics.Point{2, Float32}}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.Annotations{Tuple{Vector{Tuple{String, GeometryBasics.Point{2, Float32}}}}}
|                     ├ Makie.Text{Tuple{String}}
|                     ├ Makie.Lines{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.Annotations{Tuple{Vector{Tuple{String, GeometryBasics.Point{2, Float32}}}}}
|                     ├ Makie.Text{Tuple{String}}
|                     ├ Makie.Lines{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.Lines{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     ├ Makie.Lines{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}
|                     └ Makie.Text{Tuple{String}}
|                   1 Child Scene:
|                     └ Scene (2106px, 1755px)), 0x00000000000074ba)
|                 
|                 show(io::IOStream, m::MIME{Symbol("text/html")}, scene::Makie.Scene) at display.jl:117
|                 show(io::IOStream, m::MIME{Symbol("text/html")}, fig::Makie.Figure) at display.jl:106
|                 (::Baysor.var"#347#348"{Dict{String, VegaLite.VLSpec}, Makie.Figure, Makie.Figure, Vector{Float64}})(io::IOStream) at cli_wrappers.jl:695
|                 open(::Baysor.var"#347#348"{Dict{String, VegaLite.VLSpec}, Makie.Figure, Makie.Figure, Vector{Float64}}, ::String, ::Vararg{String, N} where N; kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) at io.jl:330
|                 open(::Function, ::String, ::String) at io.jl:328
|                 run_cli_preview(args::Vector{String}) at cli_wrappers.jl:676
|                 run_cli(args::Vector{String}) at cli_wrappers.jl:752
|                 run_cli() at cli_wrappers.jl:733
|                 top-level scope at baysor:3
|                 eval at boot.jl:360 [inlined]
|                 include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) at loading.jl:1094
|                 _include(mapexpr::Function, mod::Module, _path::String) at loading.jl:1148
|                 include(mod::Module, _path::String) at Base.jl:386
|                 exec_options(opts::Base.JLOptions) at client.jl:285
|                 _start() at client.jl:485
└ Baysor /home/user/.julia/packages/Baysor/4K0to/src/cli_wrappers.jl:762

┌ Warning: No config file provided. Using default parameters.
└ @ Baysor /home/vpetukhov/.julia/dev/Baysor/src/cli/main.jl:91
[08:52:38] Info: (2021-11-03) Run Baysor v0.5.0
[08:52:38] Info: Loading data...
[08:52:52] Info: Loaded 1882562 transcripts
[08:52:52] Info: Loading segmentation mask...
[08:54:27] Info: Done
[08:54:27] Info: Estimating prior segmentation polygons...
[09:41:06] Info: Done
[09:41:07] Info: Estimating noise level
[09:42:50] Info: Done
[09:44:00] Info: Clustering molecules...
Progress: 100%|█████████████████████████████████████████| Time: 0:07:18
  Iteration:                  407
  Max. difference:            0.008663200982013564
  Fraction of probs changed:  0.4727828353063538
[09:52:44] Info: Algorithm stopped after 407 iterations. Error: 0.00866. Converged: true.
[09:52:45] Info: Done
[09:52:46] Info: Initializing algorithm. Scale: 145.626501218387, scale std: 12.348453881948412, initial #components: 50200, #molecules: 1882562.
[09:52:57] Info: Using 2D coordinates
Progress: 100%|█████████████████████████████████████████| Time: 0:57:39
  Iteration:        500
  Noise level, %:   2.36
  Num. components:  4974
[10:51:31] Info: Processing complete.
[10:52:16] Info: Estimating local colors
[10:52:51] Error: OutOfMemoryError()
|                 
|                 Array at boot.jl:450 [inlined]
|                 Array at boot.jl:458 [inlined]
|                 Array at boot.jl:465 [inlined]
|                 similar at abstractarray.jl:785 [inlined]
|                 similar at abstractarray.jl:784 [inlined]
|                 similar at broadcast.jl:197 [inlined]
|                 similar at broadcast.jl:196 [inlined]
|                 copy at broadcast.jl:908 [inlined]
|                 materialize at broadcast.jl:883 [inlined]
|                 covm(x::Matrix{Float64}, xmean::Vector{Float64}, vardim::Int64; corrected::Bool) at Statistics.jl:545
|                 covm at Statistics.jl:545 [inlined]
|                 fit(::Type{MultivariateStats.PCA}, X::Matrix{Float64}; method::Symbol, maxoutdim::Int64, pratio::Float64, mean::Nothing) at pca.jl:152
|                 fit at pca.jl:138 [inlined]
|                 gene_composition_transformation(count_matrix::Matrix{Float64}, confidence::Vector{Float64}; sample_size::Int64, seed::Int64, method::Symbol, return_all::Bool, n_pcs::Int64, out_dim::Int64, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) at neighborhood_composition.jl:68
|                 gene_composition_transformation at neighborhood_composition.jl:60 [inlined]
|                 gene_composition_colors(df_spatial::DataFrames.DataFrame, k::Int64; kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) at neighborhood_composition.jl:123
|                 gene_composition_colors at neighborhood_composition.jl:121 [inlined]
|                 save_segmentation_results(bm_data::Baysor.BmmData{2}, gene_names::Vector{String}, args::Dict{String, Any}; mol_clusts::NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, comp_segs::Nothing, prior_polygons::Vector{Matrix{Float64}}) at main.jl:393
|                 (::Baysor.var"#save_segmentation_results##kw")(::NamedTuple{(:mol_clusts, :comp_segs, :prior_polygons), Tuple{NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, Nothing, Vector{Matrix{Float64}}}}, ::typeof(Baysor.save_segmentation_results), bm_data::Baysor.BmmData{2}, gene_names::Vector{String}, args::Dict{String, Any}) at main.jl:389
|                 run_cli_main(args::Vector{String}) at main.jl:470
|                 run_cli(args::Vector{String}) at common.jl:118
|                 run_cli at common.jl:103 [inlined]
|                 julia_main at common.jl:139 [inlined]
|                 julia_main() at none:36
└ Baysor /home/vpetukhov/.julia/dev/Baysor/src/cli/common.jl:132

 ../../../Projects/Baysor/bin/Baysor preview detected_transcripts_topleft_crop.csv 
[10:44:34] Info: # CLI params: `detected_transcripts_topleft_crop.csv`
[10:44:34] Info: (2022-09-09) Run Baysor v0.5.2
[10:44:34] Info: Loading data...
[10:44:44] Error: ArgumentError("column name :gene not found in the data frame")
|                 
|                 lookupname at index.jl:392 [inlined]
|                 getindex at index.jl:401 [inlined]
|                 getindex(df::DataFrames.DataFrame, #unused#::typeof(!), col_ind::Symbol) at dataframe.jl:525
|                 getproperty at abstractdataframe.jl:378 [inlined]
|                 read_spatial_df(data_path::String; x_col::Symbol, y_col::Symbol, z_col::Symbol, gene_col::Symbol, filter_cols::Bool) at spatial.jl:35
|                 read_spatial_df at spatial.jl:5 [inlined]
|                 load_df(data_path::String; min_molecules_per_gene::Int64, exclude_genes::Vector{String}, kwargs::Base.Iterators.Pairs{Symbol, Symbol, NTuple{4, Symbol}, NamedTuple{(:x_col, :y_col, :z_col, :gene_col), NTuple{4, Symbol}}}) at initialization.jl:191
|                 (::Baysor.var"#load_df##kw")(::NamedTuple{(:x_col, :y_col, :z_col, :gene_col, :min_molecules_per_gene, :exclude_genes), Tuple{Symbol, Symbol, Symbol, Symbol, Int64, Vector{String}}}, ::typeof(Baysor.load_df), data_path::String) at initialization.jl:191
|                 load_df(args::Dict{String, Any}; kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) at common.jl:81
|                 load_df(args::Dict{String, Any}) at common.jl:79
|                 run_cli_preview(args::Vector{String}) at preview.jl:82
|                 run_cli(args::Vector{String}) at common.jl:156
|                 run_cli() at common.jl:137
|                 top-level scope at Baysor:4
|                 eval at boot.jl:360 [inlined]
|                 include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) at loading.jl:1116
|                 _include(mapexpr::Function, mod::Module, _path::String) at loading.jl:1170
|                 include(mod::Module, _path::String) at Base.jl:384
|                 exec_options(opts::Base.JLOptions) at client.jl:285
|                 _start() at client.jl:485
└ Baysor /data/gpfs/projects/punim0741/rlyu/Projects/Baysor/bin/.julia/packages/Baysor/K7Vqu/src/cli/common.jl:170

$julia ../convert_to_csv.jl goodPoints.mat cell_barcode_names.csv labels.npz
[ Info: Read allen_brain/visual_1020/20180505_BY3_1kgenes/goodPoints.mat
[ Info: Read allen_brain/visual_1020/20180505_BY3_1kgenes/cell_barcode_names.csv
ERROR: LoadError: ArgumentError: provide a valid sink argument, like `using DataFrames; CSV.read(source, DataFrame)`
Stacktrace:
 [1] read(source::String, sink::Nothing; copycols::Bool, kwargs::Base.Iterators.Pairs{Symbol, Int64, Tuple{Symbol}, NamedTuple{(:header,), Tuple{Int64}}})
   @ CSV ~/.julia/packages/CSV/9LsxT/src/CSV.jl:89
 [2] top-level scope
   @ ~/Workplace/DART-fish/Baysor/examples/STARmap/convert_to_csv.jl:19
in expression starting at /home/hsarkar/Workplace/DART-fish/Baysor/examples/STARmap/convert_to_csv.jl:19

[15:15:00] Info: (2021-10-28) Run Baysor v0.5.0
[15:15:00] Info: Loading data...
[15:15:10] Info: Loaded 5347668 transcripts
[15:15:12] Info: Estimating noise level
[15:15:19] Warning: Only k-nn random field is supported for 3D data
└ Baysor /home/vpetukhov/.julia/dev/Baysor/src/data_processing/triangulation.jl:30
[15:16:57] Info: Done
[15:16:57] Warning: Only k-nn random field is supported for 3D data
└ Baysor /home/vpetukhov/.julia/dev/Baysor/src/data_processing/triangulation.jl:30
[15:18:09] Info: Clustering molecules...
[15:18:09] Warning: Only k-nn random field is supported for 3D data
└ Baysor /home/vpetukhov/.julia/dev/Baysor/src/data_processing/triangulation.jl:30
[15:25:13] Info: Algorithm stopped after 263 iterations. Error: 0.00955. Converged: true.
[15:25:15] Info: Done
[15:25:16] Info: Initializing algorithm. Scale: 3.2142932583089294, scale std: 1.0218244756990273, initial #components: 3565112, #molecules: 5347668.
[15:27:19] Info: Using 3D coordinates
[20:40:46] Info: Processing complete.
[20:42:40] Info: Estimating local colors
[20:48:34] Info: Saving results to ./baysor_output/[project name]
[20:49:12] Info: Plot diagnostics
[20:49:50] Info: Estimating boundary polygons
[20:55:50] Error: InexactError(:trunc, UInt16, 65540)
|                 
|                 throw_inexacterror(f::Symbol, #unused#::Type{UInt16}, val::Int64) at boot.jl:602
|                 checked_trunc_uint at boot.jl:632 [inlined]
|                 toUInt16 at boot.jl:705 [inlined]
|                 UInt16 at boot.jl:755 [inlined]
|                 convert at number.jl:7 [inlined]
|                 setindex! at array.jl:841 [inlined]
|                 find_grid_point_labels_kde(pos_data::Matrix{Float64}, cell_labels::Vector{Int64}, min_x::Vector{Float64}, max_x::Vector{Float64}; grid_step::Float64, bandwidth::Float64, dens_threshold::Float64, min_molecules_per_cell::Int64, verbose::Bool) at boundary_estimation.jl:208
|                 (::Baysor.var"#find_grid_point_labels_kde##kw")(::NamedTuple{(:grid_step, :bandwidth), Tuple{Float64, Float64}}, ::typeof(Baysor.find_grid_point_labels_kde), pos_data::Matrix{Float64}, cell_labels::Vector{Int64}, min_x::Vector{Float64}, max_x::Vector{Float64}) at boundary_estimation.jl:159
|                 boundary_polygons(pos_data::Matrix{Float64}, cell_labels::Vector{Int64}; min_x::Nothing, max_x::Nothing, grid_step::Float64, min_border_length::Int64, shape_method::Symbol, max_dev::Float64, bandwidth::Float64, exclude_labels::Vector{Int64}, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) at boundary_estimation.jl:263
|                 boundary_polygons at boundary_estimation.jl:254 [inlined]
|                 #boundary_polygons#217 at boundary_estimation.jl:248 [inlined]
|                 (::Baysor.var"#boundary_polygons##kw")(::NamedTuple{(:grid_step, :bandwidth), Tuple{Float64, Float64}}, ::typeof(Baysor.boundary_polygons), spatial_df::DataFrames.DataFrame, args::Vector{Int64}) at boundary_estimation.jl:248
|                 (::Baysor.var"#333#337"{DataFrames.DataFrame, Vector{Int64}, Dict{String, Any}, Float64})(mask::BitVector) at main.jl:215
|                 #47 at ProgressMeter.jl:991 [inlined]
|                 iterate at generator.jl:47 [inlined]
|                 _collect(c::Vector{BitVector}, itr::Base.Generator{Vector{BitVector}, ProgressMeter.var"#47#50"{Distributed.RemoteChannel{Channel{Bool}}, Baysor.var"#333#337"{DataFrames.DataFrame, Vector{Int64}, Dict{String, Any}, Float64}}}, #unused#::Base.EltypeUnknown, isz::Base.HasShape{1}) at array.jl:691
|                 collect_similar(cont::Vector{BitVector}, itr::Base.Generator{Vector{BitVector}, ProgressMeter.var"#47#50"{Distributed.RemoteChannel{Channel{Bool}}, Baysor.var"#333#337"{DataFrames.DataFrame, Vector{Int64}, Dict{String, Any}, Float64}}}) at array.jl:606
|                 map(f::Function, A::Vector{BitVector}) at abstractarray.jl:2294
|                 macro expansion at ProgressMeter.jl:990 [inlined]
|                 macro expansion at task.jl:382 [inlined]
|                 macro expansion at ProgressMeter.jl:989 [inlined]
|                 macro expansion at task.jl:382 [inlined]
|                 progress_map(::Function, ::Vararg{Any, N} where N; mapfun::Function, progress::ProgressMeter.Progress, channel_bufflen::Int64, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) at ProgressMeter.jl:982
|                 progress_map(::Function, ::Vararg{Any, N} where N) at ProgressMeter.jl:978
|                 plot_transcript_assignment_panel(df_res::DataFrames.DataFrame, assignment::Vector{Int64}, args::Dict{String, Any}; clusters::Vector{Int64}, prior_polygons::Vector{Matrix{Float64}}, gene_colors::Vector{ColorTypes.Lab{Float64}}) at main.jl:215
|                 (::Baysor.var"#plot_transcript_assignment_panel##kw")(::NamedTuple{(:clusters, :prior_polygons, :gene_colors), Tuple{Vector{Int64}, Vector{Matrix{Float64}}, Vector{ColorTypes.Lab{Float64}}}}, ::typeof(Baysor.plot_transcript_assignment_panel), df_res::DataFrames.DataFrame, assignment::Vector{Int64}, args::Dict{String, Any}) at main.jl:200
|                 save_segmentation_results(bm_data::Baysor.BmmData{3}, gene_names::Vector{String}, args::Dict{String, Any}; mol_clusts::NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, comp_segs::Nothing, prior_polygons::Vector{Matrix{Float64}}) at main.jl:406
|                 (::Baysor.var"#save_segmentation_results##kw")(::NamedTuple{(:mol_clusts, :comp_segs, :prior_polygons), Tuple{NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, Nothing, Vector{Matrix{Float64}}}}, ::typeof(Baysor.save_segmentation_results), bm_data::Baysor.BmmData{3}, gene_names::Vector{String}, args::Dict{String, Any}) at main.jl:389
|                 run_cli_main(args::Vector{String}) at main.jl:470
|                 run_cli(args::Vector{String}) at common.jl:118
|                 run_cli at common.jl:103 [inlined]
|                 julia_main at common.jl:139 [inlined]
|                 julia_main() at none:36
└ Baysor /home/vpetukhov/.julia/dev/Baysor/src/cli/common.jl:132

# baysor run -x xc -y yc -z zc --gene target /var/data.csv :cell_id
┌ Warning: No config file provided. Using default parameters.
└ @ Baysor ~/.julia/packages/Baysor/RVP5y/src/cli/main.jl:91
[23:31:59] Info: (2022-01-03) Run Baysor v0.5.0
[23:31:59] Info: Loading data...
[23:32:22] Info: Loaded 6516 transcripts
[23:32:24] Error: ErrorException("The prior segmentation column 'cell_id' must be of integer type")
|
|                 error(s::String) at error.jl:33
|                 parse_prior_assignment(df_spatial::DataFrames.DataFrame, args::Dict{String, Any}) at main.jl:253
|                 load_prior_segmentation(df_spatial::DataFrames.DataFrame, args::Dict{String, Any}) at main.jl:273
|                 load_and_preprocess_data!(args::Dict{String, Any}) at main.jl:330
|                 run_cli_main(args::Vector{String}) at main.jl:433
|                 run_cli(args::Vector{String}) at common.jl:118
|                 run_cli() at common.jl:103
|                 top-level scope at baysor:4
|                 eval at boot.jl:360 [inlined]
|                 include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) at loading.jl:1094
|                 _include(mapexpr::Function, mod::Module, _path::String) at loading.jl:1148
|                 include(mod::Module, _path::String) at Base.jl:386
|                 exec_options(opts::Base.JLOptions) at client.jl:285
|                 _start() at client.jl:485
└ Baysor /root/.julia/packages/Baysor/RVP5y/src/cli/common.jl:132

grid_step = 1.0
@time polygons = B.boundary_polygons(df_spatial, df_spatial.cell, grid_step=grid_step);
length(polygons)

git clone https://github.com/kharchenkolab/Baysor.git
cd Baysor/bin
make

fatal: error thrown and no exception handler available.
InitError(mod=:XML2_jll, error=ErrorException("Artifact "XML2" was not installed correctly. Try `using Pkg; Pkg.instantiate()` to re-install all missing resources."))
error at ./error.jl:33

git clone https://github.com/kharchenkolab/Baysor.git
cd Baysor/bin
make

petar@/projects/petar/baysor_from_source/Baysor/bin$ make
make: Warning: File `Makefile' has modification time 26 s in the future
wget https://julialang-s3.julialang.org/bin/linux/x64/1.6/julia-1.6.4-linux-x86_64.tar.gz
--2022-08-02 14:27:24--  https://julialang-s3.julialang.org/bin/linux/x64/1.6/julia-1.6.4-linux-x86_64.tar.gz
Resolving julialang-s3.julialang.org (julialang-s3.julialang.org)... 151.101.2.49, 151.101.66.49, 151.101.130.49, ...
Connecting to julialang-s3.julialang.org (julialang-s3.julialang.org)|151.101.2.49|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 113341695 (108M) [application/x-tar]
Saving to: ‘julia-1.6.4-linux-x86_64.tar.gz’

100%[================================================================================================================================================================>] 113,341,695  215MB/s   in 0.5s

2022-08-02 14:27:25 (215 MB/s) - ‘julia-1.6.4-linux-x86_64.tar.gz’ saved [113341695/113341695]

rm -rf /nfsdata/projects/petar/baysor_from_source/Baysor/bin/julia-1.6.4/
tar xf julia-1.6.4-linux-x86_64.tar.gz && touch /nfsdata/projects/petar/baysor_from_source/Baysor/bin/julia-1.6.4//bin/julia_success
mkdir -p /nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/
echo 'empty!(DEPOT_PATH); push!(DEPOT_PATH, "/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/")' >> /nfsdata/projects/petar/baysor_from_source/Baysor/bin/julia-1.6.4//etc/julia/startup.jl
/nfsdata/projects/petar/baysor_from_source/Baysor/bin/julia-1.6.4//bin/julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/kharchenkolab/Baysor.git")); Pkg.add(Pkg.PackageSpec(name="PackageCompiler", version="2.0.2"));'
     Cloning git-repo `https://github.com/kharchenkolab/Baysor.git`
    Updating git-repo `https://github.com/kharchenkolab/Baysor.git`
   Resolving package versions...
julia version requirement for package `Baysor [cc9f9468]` not satisfied
  Installing known registries into `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/`


       Added registry `General` to `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/registries/General`
   Installed OpenEXR_jll ───────────────── v3.1.1+0
   Installed Glib_jll ──────────────────── v2.68.3+2
   Installed ImageQualityIndexes ───────── v0.3.3
   Installed PCRE_jll ──────────────────── v8.44.0+0
   Installed Formatting ────────────────── v0.4.2
   Installed LogExpFunctions ───────────── v0.3.17
   Installed PNGFiles ──────────────────── v0.3.16
   Installed FixedPointNumbers ─────────── v0.8.4
   Installed HDF5_jll ──────────────────── v1.12.2+1
   Installed x264_jll ──────────────────── v2021.5.5+0
   Installed DataValueInterfaces ───────── v1.0.0
   Installed NearestNeighborDescent ────── v0.3.5
   Installed Distributions ─────────────── v0.25.66
   Installed LaTeXStrings ──────────────── v1.3.0
   Installed IntegralArrays ────────────── v0.1.5
   Installed JSON ──────────────────────── v0.21.3
   Installed Vega ──────────────────────── v2.3.1
   Installed StructArrays ──────────────── v0.6.11
   Installed ConstructionBase ──────────── v1.4.0
   Installed MetaGraphs ────────────────── v0.7.1
   Installed libass_jll ────────────────── v0.15.1+0
   Installed OpenEXR ───────────────────── v0.3.2
   Installed ChangesOfVariables ────────── v0.1.4
   Installed TableTraitsUtils ──────────── v1.0.2
   Installed Xorg_libXext_jll ──────────── v1.3.4+4
   Installed OrderedCollections ────────── v1.4.1
   Installed MappedArrays ──────────────── v0.4.1
   Installed FFTViews ──────────────────── v0.3.2
   Installed Graphics ──────────────────── v1.1.2
   Installed HDF5 ──────────────────────── v0.16.10
   Installed ProgressMeter ─────────────── v1.7.2
   Installed StatsAPI ──────────────────── v1.2.2
   Installed Distances ─────────────────── v0.10.7
   Installed Inflate ───────────────────── v0.1.2
   Installed Gettext_jll ───────────────── v0.21.0+0
   Installed LoggingExtras ─────────────── v0.4.9
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    Updating `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/environments/v1.6/Project.toml`
  [cc9f9468] + Baysor v0.5.2 `https://github.com/kharchenkolab/Baysor.git#master`
    Updating `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/environments/v1.6/Manifest.toml`
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  [dee08c22] + RegionTrees v0.3.2
  [05181044] + RelocatableFolders v0.3.0
  [ae029012] + Requires v1.3.0
  [79098fc4] + Rmath v0.7.0
  [6038ab10] + Rotations v1.3.1
  [fdea26ae] + SIMD v3.4.1
  [7b38b023] + ScanByte v0.3.3
  [6c6a2e73] + Scratch v1.1.1
  [91c51154] + SentinelArrays v1.3.13
  [efcf1570] + Setfield v1.0.0
  [992d4aef] + Showoff v1.0.3
  [73760f76] + SignedDistanceFields v0.4.0
  [777ac1f9] + SimpleBufferStream v1.1.0
  [699a6c99] + SimpleTraits v0.9.4
  [47aef6b3] + SimpleWeightedGraphs v1.2.1
  [45858cf5] + Sixel v0.1.2
  [a2af1166] + SortingAlgorithms v1.0.1
  [276daf66] + SpecialFunctions v2.1.7
  [cae243ae] + StackViews v0.1.1
  [90137ffa] + StaticArrays v1.5.2
  [1e83bf80] + StaticArraysCore v1.0.1
  [82ae8749] + StatsAPI v1.2.2
  [2913bbd2] + StatsBase v0.33.20
  [4c63d2b9] + StatsFuns v1.0.1
  [09ab397b] + StructArrays v0.6.11
  [3783bdb8] + TableTraits v1.0.1
  [382cd787] + TableTraitsUtils v1.0.2
  [bd369af6] + Tables v1.7.0
  [62fd8b95] + TensorCore v0.1.1
  [b718987f] + TextWrap v1.0.1
  [731e570b] + TiffImages v0.6.0
  [06e1c1a7] + TiledIteration v0.3.1
  [3bb67fe8] + TranscodingStreams v0.9.6
  [c4f8c510] + UMAP v0.1.9
  [30578b45] + URIParser v0.4.1
  [5c2747f8] + URIs v1.4.0
  [3a884ed6] + UnPack v1.0.2
  [1cfade01] + UnicodeFun v0.4.1
  [239c3e63] + Vega v2.3.1
  [112f6efa] + VegaLite v2.6.0
  [72f80fcb] + VoronoiDelaunay v0.4.3
  [ea10d353] + WeakRefStrings v1.4.2
  [efce3f68] + WoodburyMatrices v0.5.5
  [68821587] + Arpack_jll v3.5.0+3
  [6e34b625] + Bzip2_jll v1.0.8+0
  [83423d85] + Cairo_jll v1.16.1+1
  [5ae413db] + EarCut_jll v2.2.3+0
  [2e619515] + Expat_jll v2.4.8+0
  [b22a6f82] + FFMPEG_jll v4.4.2+0
  [f5851436] + FFTW_jll v3.3.10+0
  [a3f928ae] + Fontconfig_jll v2.13.93+0
  [d7e528f0] + FreeType2_jll v2.10.4+0
  [559328eb] + FriBidi_jll v1.0.10+0
  [78b55507] + Gettext_jll v0.21.0+0
  [7746bdde] + Glib_jll v2.68.3+2
  [3b182d85] + Graphite2_jll v1.3.14+0
  [0234f1f7] + HDF5_jll v1.12.2+1
  [2e76f6c2] + HarfBuzz_jll v2.8.1+1
  [c73af94c] + ImageMagick_jll v6.9.10-12+3
  [905a6f67] + Imath_jll v3.1.2+0
  [1d5cc7b8] + IntelOpenMP_jll v2018.0.3+2
  [aacddb02] + JpegTurbo_jll v2.1.2+0
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  [dd4b983a] + LZO_jll v2.10.1+0
  [e9f186c6] + Libffi_jll v3.2.2+1
  [d4300ac3] + Libgcrypt_jll v1.8.7+0
  [7add5ba3] + Libgpg_error_jll v1.42.0+0
  [94ce4f54] + Libiconv_jll v1.16.1+1
  [4b2f31a3] + Libmount_jll v2.35.0+0
  [89763e89] + Libtiff_jll v4.4.0+0
  [38a345b3] + Libuuid_jll v2.36.0+0
  [856f044c] + MKL_jll v2022.0.0+0
  [e7412a2a] + Ogg_jll v1.3.5+1
  [18a262bb] + OpenEXR_jll v3.1.1+0
  [458c3c95] + OpenSSL_jll v1.1.17+0
  [efe28fd5] + OpenSpecFun_jll v0.5.5+0
  [91d4177d] + Opus_jll v1.3.2+0
  [2f80f16e] + PCRE_jll v8.44.0+0
  [36c8627f] + Pango_jll v1.50.3+0
  [30392449] + Pixman_jll v0.40.1+0
  [f50d1b31] + Rmath_jll v0.3.0+0
  [02c8fc9c] + XML2_jll v2.9.14+0
  [aed1982a] + XSLT_jll v1.1.34+0
  [4f6342f7] + Xorg_libX11_jll v1.6.9+4
  [0c0b7dd1] + Xorg_libXau_jll v1.0.9+4
  [a3789734] + Xorg_libXdmcp_jll v1.1.3+4
  [1082639a] + Xorg_libXext_jll v1.3.4+4
  [ea2f1a96] + Xorg_libXrender_jll v0.9.10+4
  [14d82f49] + Xorg_libpthread_stubs_jll v0.1.0+3
  [c7cfdc94] + Xorg_libxcb_jll v1.13.0+3
  [c5fb5394] + Xorg_xtrans_jll v1.4.0+3
  [3161d3a3] + Zstd_jll v1.5.2+0
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  [f638f0a6] + libfdk_aac_jll v2.0.2+0
  [b53b4c65] + libpng_jll v1.6.38+0
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  [f27f6e37] + libvorbis_jll v1.3.7+1
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  [0dad84c5] + ArgTools
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [8bb1440f] + DelimitedFiles
  [8ba89e20] + Distributed
  [f43a241f] + Downloads
  [9fa8497b] + Future
  [b77e0a4c] + InteractiveUtils
  [4af54fe1] + LazyArtifacts
  [b27032c2] + LibCURL
  [76f85450] + LibGit2
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [a63ad114] + Mmap
  [ca575930] + NetworkOptions
  [44cfe95a] + Pkg
  [de0858da] + Printf
  [3fa0cd96] + REPL
  [9a3f8284] + Random
  [ea8e919c] + SHA
  [9e88b42a] + Serialization
  [1a1011a3] + SharedArrays
  [6462fe0b] + Sockets
  [2f01184e] + SparseArrays
  [10745b16] + Statistics
  [4607b0f0] + SuiteSparse
  [fa267f1f] + TOML
  [a4e569a6] + Tar
  [8dfed614] + Test
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  [e66e0078] + CompilerSupportLibraries_jll
  [deac9b47] + LibCURL_jll
  [29816b5a] + LibSSH2_jll
  [c8ffd9c3] + MbedTLS_jll
  [14a3606d] + MozillaCACerts_jll
  [4536629a] + OpenBLAS_jll
  [05823500] + OpenLibm_jll
  [83775a58] + Zlib_jll
  [8e850ede] + nghttp2_jll
  [3f19e933] + p7zip_jll
    Building HDF5 → `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/9ffc57b9bb643bf3fce34f3daf9ff506ed2d8b7a/build.log`
Precompiling project...
  260 dependencies successfully precompiled in 325 seconds
   Resolving package versions...
julia version requirement for package `Baysor [cc9f9468]` not satisfied
julia version requirement for package `Baysor [cc9f9468]` not satisfied
   Installed RelocatableFolders ─ v0.1.3
   Installed PackageCompiler ──── v2.0.2
    Updating `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/environments/v1.6/Project.toml`
  [9b87118b] + PackageCompiler v2.0.2
    Updating `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/environments/v1.6/Manifest.toml`
  [9b87118b] + PackageCompiler v2.0.2
  [05181044] ↓ RelocatableFolders v0.3.0 ⇒ v0.1.3
Precompiling project...
  6 dependencies successfully precompiled in 283 seconds (255 already precompiled)
/nfsdata/projects/petar/baysor_from_source/Baysor/bin/julia-1.6.4//bin/julia -e 'using Pkg; Pkg.build(); using Baysor' && touch /nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia//deps_success
    Building HDF5 → `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/9ffc57b9bb643bf3fce34f3daf9ff506ed2d8b7a/build.log`
/nfsdata/projects/petar/baysor_from_source/Baysor/bin/julia-1.6.4//bin/julia -e 'ENV["JULIA_DEPOT_PATH"]="/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/"; using PackageCompiler; import Pkg; Pkg.activate(".."); Pkg.instantiate(); import Baysor; create_sysimage(:Baysor; precompile_execution_file="$(dirname(pathof(Baysor)))/../bin/precompile.jl", sysimage_path="BaysorSysimage.so")'
  Activating environment at `/nfsdata/projects/petar/baysor_from_source/Baysor/Project.toml`
     Cloning git-repo `https://github.com/VPetukhov/Vega.jl`
     Cloning git-repo `https://github.com/queryverse/VegaLite.jl.git`
ERROR: The manifest file you are using was most likely generated by a different version of Julia and is not compatible with this Julia version
Stacktrace:
 [1] load_urls(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec})
   @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:545
 [2] #download_source#57
   @ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:733 [inlined]
 [3] download_source
   @ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:732 [inlined]
 [4] instantiate(ctx::Pkg.Types.Context; manifest::Nothing, update_registry::Bool, verbose::Bool, platform::Base.BinaryPlatforms.Platform, allow_build::Bool, allow_autoprecomp::Bool, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:1408
 [5] instantiate
   @ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:1325 [inlined]
 [6] #instantiate#252
   @ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:1321 [inlined]
 [7] instantiate()
   @ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:1321
 [8] top-level scope
   @ none:1
make: *** [/nfsdata/projects/petar/baysor_from_source/Baysor/bin/julia-1.6.4//../BaysorSysimage.so] Error 1

(base) bash-4.2$ cd data/
(base) bash-4.2$ ~/tool/Baysor/bin/baysor run -i 500 -p -c ~/project/sparcle/data/iss.toml -o ./output_dapi -p spot.csv segmentation.tif
[17:08:12] Info: (2021-07-16) Run Baysor v0.5.0
[17:08:12] Info: Loading data...
[17:08:37] Info: Loaded 71907 transcripts
[17:08:38] Info: Loading segmentation mask...
[17:08:39] Warning: some versions of ImageMagick give spurious low-order bits for 32-bit TIFFs
└ ImageMagick /home/vpetukhov/.julia/packages/ImageMagick/b8swT/src/ImageMagick.jl:100
[17:08:44] Warning: Minimum transcript coordinates are < 1: (10, -1). Filling it with 0.
└ Baysor /home/vpetukhov/.julia/dev/Baysor/src/data_processing/initialization.jl:279
[17:08:45] Error: ArgumentError("reducing over an empty collection is not allowed")
|                 
|                 _empty_reduce_error() at reduce.jl:299
|                 reduce_empty(op::Function, #unused#::Type{UInt32}) at reduce.jl:309
|                 mapreduce_empty(#unused#::typeof(identity), op::Function, T::Type) at reduce.jl:343
|                 reduce_empty(op::Base.MappingRF{typeof(identity), typeof(max)}, #unused#::Type{UInt32}) at reduce.jl:329
|                 reduce_empty_iter at reduce.jl:355 [inlined]
|                 mapreduce_empty_iter(f::Function, op::Function, itr::Vector{UInt32}, ItrEltype::Base.HasEltype) at reduce.jl:351
|                 _mapreduce at reduce.jl:400 [inlined]
|                 _mapreduce_dim at reducedim.jl:318 [inlined]
|                 #mapreduce#672 at reducedim.jl:310 [inlined]
|                 mapreduce at reducedim.jl:310 [inlined]
|                 #_maximum#690 at reducedim.jl:878 [inlined]
|                 _maximum at reducedim.jl:878 [inlined]
|                 #_maximum#689 at reducedim.jl:877 [inlined]
|                 _maximum at reducedim.jl:877 [inlined]
|                 #maximum#687 at reducedim.jl:873 [inlined]
|                 maximum at reducedim.jl:873 [inlined]
|                 filter_segmentation_labels!(segmentation_labels::Vector{UInt32}, segment_per_transcript::Vector{Int64}; min_molecules_per_segment::Int64) at prior_segmentation.jl:74
|                 filter_segmentation_labels! at prior_segmentation.jl:74 [inlined]
|                 #filter_segmentation_labels!#91 at prior_segmentation.jl:68 [inlined]
|                 (::Baysor.var"#filter_segmentation_labels!##kw")(::NamedTuple{(:min_molecules_per_segment,), Tuple{Int64}}, ::typeof(Baysor.filter_segmentation_labels!), segmentation_labels::SparseArrays.SparseMatrixCSC{UInt32, Int64}, segment_per_transcript::Vector{Int64}) at prior_segmentation.jl:68
|                 load_prior_segmentation(df_spatial::DataFrames.DataFrame, args::Dict{String, Any}) at main.jl:280
|                 load_and_preprocess_data!(args::Dict{String, Any}) at main.jl:330
|                 run_cli_main(args::Vector{String}) at main.jl:433
|                 run_cli(args::Vector{String}) at common.jl:118
|                 run_cli at common.jl:103 [inlined]
|                 julia_main at common.jl:139 [inlined]
|                 julia_main() at none:36
└ Baysor /home/vpetukhov/.julia/dev/Baysor/src/cli/common.jl:132

sub_lims = [((11000, 13000), (12000, 13500)), ((11500, 13500), (8750, 10250))];

fig = B.plot_molecules(df_spatial, color=:ncv_color, markersize=0.5, xlims=(5000, 18000), ylims=(2500, 15500), size=(500, 500))
# for ((xs, xe), (ys, ye)) in sub_lims
#     Plots.plot!([xs, xs, xe, xe, xs], [ys, ye, ye, ys, ys], color="black", label="", lw=3.0, alpha=0.75)
# end

MK.save(plotsdir("/home/hsarkar/Workplace/DART-fish/BaysorAnalysis/data/raw_data/allen_brain/data_20180505/gene_coloring.png"), fig)
fig

Can't convert #004993 to a colorant

Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:33
  [2] rgbatuple(c::InlineStrings.String7)
    @ CairoMakie ~/.julia/packages/CairoMakie/0yMYf/src/utils.jl:93
  [3] (::CairoMakie.var"#26#27"{Makie.Scene, MakieCore.Scatter{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, FreeTypeAbstraction.FTFont, StaticArrays.SMatrix{4, 4, Float32, 16}, StaticArrays.SMatrix{4, 4, Float32, 16}, Cairo.CairoContext})(point::GeometryBasics.Point{2, Float32}, col::InlineStrings.String7, markersize::Float64, strokecolor::RGBA{Float32}, strokewidth::Float32, marker::Type, mo::GeometryBasics.Vec{2, Float32}, rotation::Makie.Quaternionf0)
    @ CairoMakie ~/.julia/packages/CairoMakie/0yMYf/src/primitives.jl:209
  [4] broadcast_foreach(::Function, ::Vector{GeometryBasics.Point{2, Float32}}, ::Vararg{Any, N} where N)
    @ Makie ~/.julia/packages/Makie/NL7Xw/src/utilities/utilities.jl:176
  [5] draw_atomic(scene::Makie.Scene, screen::CairoMakie.CairoScreen{Cairo.CairoSurfaceBase{UInt32}}, primitive::MakieCore.Scatter{Tuple{Vector{GeometryBasics.Point{2, Float32}}}})
    @ CairoMakie ~/.julia/packages/CairoMakie/0yMYf/src/primitives.jl:187
  [6] draw_plot(scene::Makie.Scene, screen::CairoMakie.CairoScreen{Cairo.CairoSurfaceBase{UInt32}}, primitive::MakieCore.Scatter{Tuple{Vector{GeometryBasics.Point{2, Float32}}}})
    @ CairoMakie ~/.julia/packages/CairoMakie/0yMYf/src/infrastructure.jl:240
  [7] cairo_draw(screen::CairoMakie.CairoScreen{Cairo.CairoSurfaceBase{UInt32}}, scene::Makie.Scene)
    @ CairoMakie ~/.julia/packages/CairoMakie/0yMYf/src/infrastructure.jl:173
  [8] backend_show(x::CairoMakie.CairoBackend, io::IOContext{IOStream}, #unused#::MIME{Symbol("image/png")}, scene::Makie.Scene)
    @ CairoMakie ~/.julia/packages/CairoMakie/0yMYf/src/infrastructure.jl:339
  [9] show(io::IOContext{IOStream}, m::MIME{Symbol("image/png")}, scene::Makie.Scene; update::Bool)
    @ Makie ~/.julia/packages/Makie/NL7Xw/src/display.jl:113
 [10] (::Makie.var"#914#915"{Float64, Float64, Bool, DataType, Makie.Scene})(s::IOStream)
    @ Makie ~/.julia/packages/Makie/NL7Xw/src/display.jl:252
 [11] open(::Makie.var"#914#915"{Float64, Float64, Bool, DataType, Makie.Scene}, ::String, ::Vararg{String, N} where N; kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Base ./io.jl:330
 [12] open
    @ ./io.jl:328 [inlined]
 [13] save(file::FileIO.File{FileIO.DataFormat{:PNG}, String}, fig::Makie.Figure; resolution::Tuple{Int64, Int64}, pt_per_unit::Float64, px_per_unit::Float64, update::Bool)
    @ Makie ~/.julia/packages/Makie/NL7Xw/src/display.jl:246
 [14] save(file::FileIO.File{FileIO.DataFormat{:PNG}, String}, fig::Makie.Figure)
    @ Makie ~/.julia/packages/Makie/NL7Xw/src/display.jl:228
 [15] save(filename::String, fig::Makie.Figure; args::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Makie ~/.julia/packages/Makie/NL7Xw/src/display.jl:218
 [16] save(filename::String, fig::Makie.Figure)
    @ Makie ~/.julia/packages/Makie/NL7Xw/src/display.jl:218
 [17] top-level scope
    @ In[44]:8
 [18] eval
    @ ./boot.jl:360 [inlined]
 [19] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:1116
 

sample_ids = Baysor.select_ids_uniformly(df_spatial.x, df_spatial.y, df_spatial.confidence,n= 2000)

MethodError: no method matching select_ids_uniformly(::Vector{Int64}, ::Vector{Int64}, ::Vector{Float64}; n=2000)
Closest candidates are:
  select_ids_uniformly(::Union{AbstractMatrix{var"#s84"} where var"#s84"<:Real, Vector{var"#s83"} where var"#s83"<:Real}) at /home/hsarkar/.julia/packages/Baysor/Mbd2S/src/data_processing/initialization.jl:302 got unsupported keyword argument "n"
  select_ids_uniformly(::Union{AbstractMatrix{var"#s81"} where var"#s81"<:Real, Vector{var"#s80"} where var"#s80"<:Real}, ::Union{Nothing, Vector{Float64}}; n, confidence_threshold) at /home/hsarkar/.julia/packages/Baysor/Mbd2S/src/data_processing/initialization.jl:302

Stacktrace:
 [1] top-level scope
   @ In[82]:1
 [2] eval
   @ ./boot.jl:360 [inlined]
 [3] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
   @ Base ./loading.jl:1116
  

print(first(df_spatial[!,[:x, :y, :confidence]],10))

 Row │ x      y      confidence 
     │ Int64  Int64  Float64    
─────┼──────────────────────────
   1 │   810   9292    0.0
   2 │  1943   9727    0.0
   3 │  2802  12527    0.999772
   4 │  3917  12000    0.999911
   5 │  2755  13641    0.999938
   6 │  2505  13139    0.999938
   7 │  2785  12526    0.999895

/home/segonzal/baysor run -i 500 -m 8 -s 14 -o ./output_no_dapi -p ./data/pciSeq_3-3.csv