Batch script

scripts/batch.jl

@@ -0,0 +1,102 @@
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+# Copyright 2021-2024, Ben Cardoen
+using Pkg; Pkg.activate(".")
+using SubPrecisionContactDetection
+using Images, Colors, DataFrames, CSV, Statistics, LinearAlgebra
+import Glob
+using ArgParse
+import ImageMagick
+import Logging
+import Random
+using ImageFiltering
+using Distributions
+using Base.Threads
+import JLD2
+
+using LoggingExtras, Dates
+
+# inpath="/home/bcardoen/cedar_data/test/MS_2024_09_19_TOM20_KDEL_PLIN_HUH7_OLEIC"
+# readdir(inpath)
+# regex="*[0,1].tif"
+# prefixes, regexes = buildregex(inpath, regex)
+
+# t = mktempdir()
+# subd = joinpath(t, "t2")
+# mkpath(subd)
+# Images.save(joinpath(subd, "a01.tif"), rand(200, 200))
+# Images.save(joinpath(subd, "b02.tif"), rand(200, 200))
+# Images.save(joinpath(subd, "c03.tif"), rand(200, 200))
+# rx = "*[1,2].tif"
+# paths, regexes = buildregex(subd, rx)
+# paths == ["1--2"]
+# regexes == ["*[1,2].tif"]
+
+# inpath="/home/bcardoen/cedar_data/test/MS_2024_09_19_TOM20_KDEL_PLIN_HUH7_OLEIC"
+# readdir(inpath)
+# regex="*[0,1,2].tif"
+# prefixes, regexes = buildregex(inpath, regex)
+
+
+
+function run_script()
+    date_format = "yyyy-mm-dd HH:MM:SS"
+    timestamp_logger(logger) = TransformerLogger(logger) do log
+      merge(log, (; message = "$(Dates.format(now(), date_format)) $(basename(log.file)):$(log.line): $(log.message)"))
+    end
+    ConsoleLogger(stdout, Logging.Info) |> timestamp_logger |> global_logger
+    parsed_args = parse_commandline_ercontacts()
+    @info "Parsed arguments:"
+    for (arg,val) in parsed_args
+        @info "  $arg  =>  $val"
+    end
+    inpath = parsed_args["inpath"]
+    op = parsed_args["outpath"]
+    rx = parsed_args["inregex"]
+    paths, regexes = buildregex(inpath, rx)
+    @info paths
+    @info regexes
+    for (p, r) in zip(paths, regexes)
+        pa = copy(parsed_args)
+        @info p, r
+        pa["inregex"] = r
+        pa["outpath"] = mkpath(joinpath(op, "p"))
+
+        for replicate in readdir(inpath; join=true)
+            r = basename(replicate)
+            for celltype in readdir(replicate; join=true)
+                ct = basename(celltype)
+                for cell in readdir(celltype; join=true)
+                    snr = basename(cell)
+                    # pa = copy(parsed_args)
+                    op = pa["outpath"]
+                    opx = joinpath(op, r, ct, snr)
+                    if isdir(opx)
+                        @warn "WARNING: Output directory exists --> PLEASE CHECK if this intended."
+                    end
+                    @info "Creating output path $(opx)"
+                    mkpath(opx)
+                    pa["inpath"]=cell
+                    pa["outpath"]=opx
+                    try
+        			    two_channel_contacts(pa)
+                    catch e
+                        @error("Failed executing due to $(e)")
+                    end
+                end
+            end
+        end
+    end
+end
+
+run_script()