add to_save flag to Vessel

Project.toml

@@ -6,6 +6,7 @@ version = "2.0.0"
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"

docs/src/man/config.md

@@ -19,7 +19,7 @@ Following the `write_results` list is defined.
 write_results: ["P"] # ["P", "Q", "u", "A"]
 ```
 
-Here you can specify which quantities to write in the output files (`P`ressure, `Q` flow, `u` velocity and `A`rea). These are all optional except for `P`.
+Here you can specify which quantities to write in the output files (`P`ressure, `Q` flow, `u` velocity and `A`rea). These are all optional but at least one is recommended.
 
 Then there are three main sections: `solver`, `blood`, and `network`.
 
@@ -69,6 +69,8 @@ This contains the list of vessels in the network. Each vessel has the following
 
 __Optional__ parameters are:
 
+- `to_save` a boolean flag (default `true`) to tell openBF to save results for the current vessel;
+
 - `M` is the number of division along the vessels used to compute the artery $\Delta x$. When not specified, openBF automatically meshes the arteries so that $\Delta x$ is at least $1 mm$;
 
 - `Pext` vessel external pressure in $Pa$, default $0.0 Pa$;

src/openBF.jl

@@ -22,6 +22,7 @@ using LinearAlgebra
 using DelimitedFiles
 
 using YAML
+using Glob
 using Graphs
 using ProgressMeter
 using Statistics

src/output.jl

@@ -14,11 +14,12 @@ See the License for the specific language governing permissions and
 limitations under the License.
 =#
 
-flush_to_temp(t::Float64, n::Network, tosave::Vector{String}) =
-    flush_to_temp.(t, values(n.vessels), Ref(tosave))
-function flush_to_temp(t::Float64, v::Vessel, tosave::Vector{String})
+flush_to_temp(t::Float64, n::Network, temp_save::Vector{String}) =
+    flush_to_temp.(t, values(n.vessels), Ref(temp_save))
+function flush_to_temp(t::Float64, v::Vessel, temp_save::Vector{String})
     for (l, a) in zip(("P", "Q", "A", "u"), (v.P, v.Q, v.A, v.u))
-        l ∉ tosave && continue
+        l ∉ temp_save && continue
+        l ∉ ("P", "A") && ~v.tosave && continue
         temp = open(v.label * "_$l.temp", "a")
         line = join((t, a[1], a[v.node2], a[v.node3], a[v.node4], a[end]), " ")
         println(temp, line)
@@ -27,21 +28,23 @@ function flush_to_temp(t::Float64, v::Vessel, tosave::Vector{String})
 end
 
 
-move_temp_to_last(n::Network, tosave::Vector{String}) =
-    move_temp_to_last.(values(n.vessels), Ref(tosave))
-function move_temp_to_last(v::Vessel, tosave::Vector{String})
+move_temp_to_last(n::Network, temp_save::Vector{String}) =
+    move_temp_to_last.(values(n.vessels), Ref(temp_save))
+function move_temp_to_last(v::Vessel, temp_save::Vector{String})
     for l in ("P", "Q", "A", "u")
-        l ∉ tosave && continue
-
+        l ∉ temp_save && continue
+        l ∉ ("P", "A") && ~v.tosave && continue
         mv(v.label * "_$l.temp", v.label * "_$l.last", force = true)
     end
 end
 
-append_last_to_out(n::Network, tosave::Vector{String}) =
-    append_last_to_out.(values(n.vessels), Ref(tosave))
-function append_last_to_out(v::Vessel, tosave::Vector{String})
+
+append_last_to_out(n::Network, temp_save::Vector{String}) =
+    append_last_to_out.(values(n.vessels), Ref(temp_save))
+function append_last_to_out(v::Vessel, temp_save::Vector{String})
     for l in ("P", "Q", "A", "u")
-        l ∉ tosave && continue
+        l ∉ temp_save && continue
+        l ∉ ("P", "A") && ~v.tosave && continue
         out_file = open(v.label * "_$l.out", "a")
         last_a = readdlm(v.label * "_$l.last")
         writedlm(out_file, last_a, " ")

src/simulation.jl

@@ -60,34 +60,40 @@ function get_inlet_file(config)
     end
     config["inlet_file"]
 end
-function run_simulation(
-    yaml_config::String;
-    verbose::Bool = true,
-    out_files::Bool = false,
-    conv_ceil::Bool = false,
-)
-    verbose && println("Loading config...")
-    config = load_yaml_config(yaml_config)
 
-    tosave = config["write_results"]
-    isempty(tosave) && (tosave = ["P", "A"])
-    "P" ∉ tosave && push!(tosave, "P")
-    "A" ∉ tosave && push!(tosave, "A")
+function preamble(yaml_config, verbose)
 
-    verbose && println("project name: $(config["project_name"])")
+    verbose && println("Loading config...")
+    config = load_yaml_config(yaml_config)
 
     project_name = config["project_name"]
-    blood = Blood(config["blood"])
-    heart = Heart(get_inlet_file(config))
+    verbose && println("project name: $project_name")
+
+    temp_save = deepcopy(get(config, "write_results", []))
+    "P" ∉ temp_save && push!(temp_save, "P")
+    "A" ∉ temp_save && push!(temp_save, "A")
 
-    # TODO: results dir from config
-    ########################################
-    results_dir = project_name * "_results"
+    results_dir = get(config, "output_directory", project_name * "_results")
     isdir(results_dir) && rm(results_dir, recursive = true)
     ~isdir(results_dir) && mkdir(results_dir)
     cp(yaml_config, joinpath(results_dir, yaml_config), force = true)
+    cp(config["inlet_file"], joinpath(results_dir, config["inlet_file"]), force = true)
     cd(results_dir)
-    #########################################
+
+    config, temp_save
+end
+
+function run_simulation(
+    yaml_config::String;
+    verbose::Bool = true,
+    out_files::Bool = false,
+    conv_ceil::Bool = false,
+)
+    initial_dir = pwd()
+    config, temp_save = preamble(yaml_config, verbose)
+
+    blood = Blood(config["blood"])
+    heart = Heart(get_inlet_file(config))
 
     network = Network(
         config["network"],
@@ -116,7 +122,7 @@ function run_simulation(
         verbose && next!(prog)
 
         if current_time >= checkpoints[counter]
-            flush_to_temp(current_time, network, tosave)
+            flush_to_temp(current_time, network, temp_save)
             counter += 1
         end
 
@@ -130,8 +136,8 @@ function run_simulation(
                 conv_error, error_loc = get_conv_error(network)
             end
 
-            move_temp_to_last(network, tosave)
-            out_files && append_last_to_out(network, tosave)
+            move_temp_to_last(network, temp_save)
+            out_files && append_last_to_out(network, temp_save)
 
             if verbose
                 if passed_cycles > 0
@@ -160,5 +166,15 @@ function run_simulation(
         end
         current_time += dt
     end
-    cd("..")
+    tokeep = get(config, "write_results", [])
+    cleanup.(values(network.vessels), Ref(tokeep))
+    cd(initial_dir)
+end
+
+function cleanup(v::Vessel, tokeep)
+    println("Cleaning outputs directory")
+    ~v.tosave && rm.(glob("$(v.label)_*"))
+    for l in ("P", "A", "Q", "u")
+        l ∉ tokeep && rm.(glob("$(v.label)_$l.*"), force=true)
+    end
 end

src/vessel.jl

@@ -29,6 +29,7 @@ end
 
 mutable struct Vessel
     label::SubString{String}
+    tosave::Bool
 
     #Topological notation
     sn::Int64
@@ -145,6 +146,7 @@ end
 
 function Vessel(config::Dict{Any,Any}, b::Blood, Ccfl::Float64)
     vessel_name = config["label"]
+    tosave = get(config, "to_save", true)
     sn = config["sn"]
     tn = config["tn"]
     Rp, Rd = radii(config)
@@ -270,6 +272,7 @@ function Vessel(config::Dict{Any,Any}, b::Blood, Ccfl::Float64)
 
     Vessel(
         vessel_name,
+        tosave,
         sn,
         tn,
         M,