Modernize executables in run subdirectory

run/Manifest.toml

@@ -0,0 +1,106 @@
+# This file is machine-generated - editing it directly is not advised
+
+[[ArgParse]]
+deps = ["Compat", "Test", "TextWrap"]
+git-tree-sha1 = "14d5789a99e6bea3e258d668ec09359a9feaf2d1"
+uuid = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
+version = "0.6.2"
+
+[[Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[Compat]]
+deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
+git-tree-sha1 = "ed2c4abadf84c53d9e58510b5fc48912c2336fbb"
+uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
+version = "2.2.0"
+
+[[Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[DelimitedFiles]]
+deps = ["Mmap"]
+uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+
+[[Distributed]]
+deps = ["Random", "Serialization", "Sockets"]
+uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+
+[[InteractiveUtils]]
+deps = ["Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[LibGit2]]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+
+[[Libdl]]
+uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+
+[[LinearAlgebra]]
+deps = ["Libdl"]
+uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
+[[Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[Mmap]]
+uuid = "a63ad114-7e13-5084-954f-fe012c677804"
+
+[[Pkg]]
+deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Test", "UUIDs"]
+uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+
+[[Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[[REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[Random]]
+deps = ["Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+
+[[Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
+[[SharedArrays]]
+deps = ["Distributed", "Mmap", "Random", "Serialization"]
+uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
+
+[[Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
+
+[[SparseArrays]]
+deps = ["LinearAlgebra", "Random"]
+uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[[Statistics]]
+deps = ["LinearAlgebra", "SparseArrays"]
+uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+
+[[Test]]
+deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[TextWrap]]
+deps = ["Compat", "Test"]
+git-tree-sha1 = "8355cc559e85469cd4dbe927c375f61d3750e002"
+uuid = "b718987f-49a8-5099-9789-dcd902bef87d"
+version = "0.3.0"
+
+[[UUIDs]]
+deps = ["Random", "SHA"]
+uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+
+[[Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

run/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"

run/megapress_rda_diff.jl

@@ -0,0 +1,36 @@
+
+
+using ArgParse
+using MagneticResonanceSignals
+
+function rda_diff(in1file, in2file, outfile; anonymize=true)
+    in1header,in1data = load_rda(in1file)
+    in2header,in2data = load_rda(in2file)
+    outheader = copy(in1header)
+    if anonymize
+        outheader["PatientName"] = "xxxxxxxxx"
+        outheader["PatientID"] = "xxx"
+        outheader["PatientBirthDate"] = "20000101"
+    end
+    save_rda(outfile, outheader, in1data .- in2data)
+end
+
+function megapress_argparse(arg_strings; extra_settings...)
+    settings = ArgParseSettings(;extra_settings...)
+    @add_arg_table settings begin
+        "--output", "-o"
+            help = "Output file name.  Default is autogenerated based on the input file names."
+        "input_files"
+            required=true
+            nargs=2
+            help = "Two input .rda files"
+    end
+    parse_args(arg_strings, settings)
+end
+
+# To test
+# megapress_argparse(["a", "b", "c"], exc_handler=ArgParse.debug_handler)
+
+parsed_args = megapress_argparse(ARGS)
+
+rda_diff(parsed_args["input_files"][1], parsed_args["input_files"][2], parsed_args["output"])

run/strip_twix_adjustment.jl

@@ -1,3 +1,9 @@
+#!/bin/bash
+#=
+exec julia --project=. -e 'include(popfirst!(ARGS))' \
+    "${BASH_SOURCE[0]}" "$@"
+=#
+
 using MagneticResonanceSignals
 using StaticArrays
 

run/twix_to_felix.jl

@@ -1,4 +1,8 @@
-#!/usr/bin/env julia
+#!/bin/bash
+#=
+exec julia --project=. -e 'include(popfirst!(ARGS))' \
+    "${BASH_SOURCE[0]}" "$@"
+=#
 
 using MagneticResonanceSignals
 using Statistics

run/twixheaders.jl

@@ -1,4 +1,8 @@
-#!/usr/bin/env julia
+#!/bin/bash
+#=
+exec julia --project=. -e 'include(popfirst!(ARGS))' \
+    "${BASH_SOURCE[0]}" "$@"
+=#
 
 # Script to extract twix headers into a new temporary directory