Merge pull request #33 from GeoscienceAustralia/VTEM

Vtem added. Many breaking changes

.github/workflows/main.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: ['1.5.3', '1.6', '1.7']
+        julia-version: ['1.7']
         julia-arch: [x64]
         # os: [ubuntu-latest, windows-latest, macOS-latest]
         # can't maintain on windows and mac all by my lonesome

.gitignore

@@ -14,3 +14,4 @@ Manifest.toml
 *err*
 docs/build/
 docs/src/generated/
+*summary*.txt

Project.toml

@@ -1,7 +1,7 @@
 name = "HiQGA"
 uuid = "01574e87-63b6-4466-925a-334cf7e21b6b"
 authors = ["richardt94 <[email protected]>"]
-version = "0.2.2"
+version = "0.3.0"
 
 [deps]
 DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
@@ -49,4 +49,4 @@ PyPlot = "2.10.0"
 Roots = "2.0.0"
 SpecialFunctions = "1.6 - 2.1.4"
 StatsBase = "0.33.16"
-julia = "1.5.3"
+julia = "1.7"

examples/workshop/worked_out/skytem_hiqga_transd/01_read_data.jl → examples/SkyTEM1D/Menindee/McMC/01_read_data.jl

@@ -32,7 +32,7 @@ soundings = transD_GP.SkyTEM1DInversion.read_survey_files(fname_dat = fname_dat,
 									 linenum          = linenum,
                                      startfrom        = 1,
 									 skipevery        = 1,
-									 dotillsounding   = nothing,
+									 dotillsounding   = 2,
 									 relerror         = relerror,
 									 units            = units,     
-									 makesounding     = true)
+									 makeqcplots      = true)

examples/SkyTEM1D/Menindee/02_set_options.jl → examples/SkyTEM1D/Menindee/McMC/02_set_options.jl

@@ -1,18 +1,19 @@
 ## same for all soundingss
-nsamples = 200001
+nsamples = 2001
 nchainspersounding = 5
 ppn = 48
 @assert mod(ppn, nchainspersounding+1) == 0
 zfixed   = [-1e5]
 ρfixed   = [1e12]
 zstart = 0.0
-showgeomplot = false
+showgeomplot = true
+plotfield = true
 extendfrac, dz = 1.06, 1.25
 nlayers = 52
 ρbg = 5.
 ntimesperdecade = 10
 nfreqsperdecade = 5
-useML = true
+useML = false
 ## make transD options
 nmin, nmax = 2, 40
 K = transD_GP.GP.OrstUhn()
@@ -26,13 +27,10 @@ sddc = 0.01
 save_freq = 100
 Tmax = 2.50
 nchainsatone = 1
-## plot n random soundings and a background response
-using Random
-nplot = 2
-nplot = min(nplot, length(soundings))
-opt = transD_GP.SkyTEM1DInversion.makeoperatorandoptions(
-                            rseed = 2,
-                            soundings,
+restart = false
+## plot 1 random sounding and a background response
+aem, opt, zall = transD_GP.makeAEMoperatorandoptions(
+                            soundings[rand(1:length(soundings))];
                             zfixed = zfixed,
                             ρfixed = ρfixed,
                             zstart = zstart,
@@ -54,6 +52,7 @@ opt = transD_GP.SkyTEM1DInversion.makeoperatorandoptions(
                             fbounds = fbounds,
                             save_freq = save_freq,
                             showgeomplot = showgeomplot,
+                            plotfield,
                             λ = λ,
-                            δ = δ
+                            δ = δ, restart
 )

examples/SkyTEM1D/Menindee/McMC/03_parallel_run.jl

@@ -0,0 +1,24 @@
+## MPI Init
+using MPIClusterManagers, Distributed
+import MPI
+MPI.Init()
+rank = MPI.Comm_rank(MPI.COMM_WORLD)
+sz = MPI.Comm_size(MPI.COMM_WORLD)
+if rank == 0
+    @info "size is $sz"
+end
+manager = MPIClusterManagers.start_main_loop(MPI_TRANSPORT_ALL)
+@info "there are $(nworkers()) workers"
+include("01_read_data.jl")
+include("02_set_options.jl")
+## set up McMC
+@everywhere using Distributed
+@everywhere using HiQGA.transD_GP
+## do the parallel soundings
+@info "starting"
+transD_GP.loopacrossAEMsoundings(soundings, aem, opt;
+                    Tmax, nsamples, nchainsatone, nchainspersounding, ppn)
+
+MPIClusterManagers.stop_main_loop(manager)
+rmprocs(workers())
+exit()

examples/SkyTEM1D/Menindee/McMC/04_plot.jl

@@ -0,0 +1,16 @@
+dr = 20
+idx = 1:100:length(soundings)
+burninfrac = 0.5
+vmin, vmax = -2.5, 0.5
+transD_GP.summaryAEMimages(soundings, opt;
+    zall, dr, dz, cmap="turbo", burninfrac, 
+    vmin=vmin, vmax=vmax, idx, useML,
+    preferEright=true, saveplot=true)
+##
+computeforwards = true
+nforwards = 5
+nbins = 50
+transD_GP.plotindividualAEMsoundings(soundings, aem, opt, idx;
+    burninfrac, nbins, computeforwards, zall,
+    nforwards)
+

examples/SkyTEM1D/Menindee/em_with_noise_calibration_lines.hdr → examples/SkyTEM1D/Menindee/McMC/em_with_noise_calibration_lines.hdr

@@ -1,31 +1,31 @@
-1	fiducial
-2	line
-3	flight
-4	datetime
-5	date
-6	utc_time
-7	angleX
-8	angleY
-9	frame_height
-10	longitude
-11	latitude
-12	easting
-13	northing
-14	ground_elevation_aem
-15	ground_elevation_lidar_aem_merged
-16	gps_height
-17	groundspeed
-18	frame_roll
-19	frame_pitch
-20	frame_yaw
-21	frame_dx
-22	frame_dy
-23	frame_dz
-24	HM_current
-25	LM_current
-26-42	LM_Z
-43-67	HM_Z
-68-84	LM_Z_rerr
-85-109	HM_Z_rerr
-110-126	LM_Z_noise
-127-151	HM_Z_noise
+1	fiducial
+2	line
+3	flight
+4	datetime
+5	date
+6	utc_time
+7	angleX
+8	angleY
+9	frame_height
+10	longitude
+11	latitude
+12	easting
+13	northing
+14	ground_elevation_aem
+15	ground_elevation_lidar_aem_merged
+16	gps_height
+17	groundspeed
+18	frame_roll
+19	frame_pitch
+20	frame_yaw
+21	frame_dx
+22	frame_dy
+23	frame_dz
+24	HM_current
+25	LM_current
+26-42	LM_Z
+43-67	HM_Z
+68-84	LM_Z_rerr
+85-109	HM_Z_rerr
+110-126	LM_Z_noise
+127-151	HM_Z_noise