Merge pull request #276 from slimgroup/ex-fix

Update example for new SlimPlotting
slimgroup · Oct 29, 2024 · b299fc3 · b299fc3
2 parents 591f117 + e11d276
commit b299fc3
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diff --git a/.github/workflows/ci-examples.yml b/.github/workflows/ci-examples.yml
@@ -77,7 +77,7 @@ jobs:
 
       - name: Install packages
         run: |
-          julia -e 'using Pkg;Pkg.add(["SlimPlotting", "PyPlot", "NLopt", "Flux", "JOLI", "Zygote", "IterativeSolvers", "SlimOptim", "HDF5", "SegyIO", "SetIntersectionProjection"])'
+          julia -e 'using Pkg;Pkg.add(["SlimPlotting", "PythonPlot", "NLopt", "Flux", "JOLI", "Zygote", "IterativeSolvers", "SlimOptim", "HDF5", "SegyIO", "SetIntersectionProjection"])'
           julia -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd()))'
 
       - name: Run examples

diff --git a/README.md b/README.md
@@ -128,7 +128,7 @@ run(`wget ftp://slim.gatech.edu/data/SoftwareRelease/WaveformInversion.jl/2DFWI/
 The first step is to load the velocity model and the observed data into Julia, as well as setting up bound constraints for the inversion, which prevent too high or low velocities in the final result. Furthermore, we define an 8 Hertz Ricker wavelet as the source function:
 
 ```Julia
-using PyPlot, HDF5, SegyIO, JUDI, SlimOptim, Statistics, Random
+using PythonPlot, HDF5, SegyIO, JUDI, SlimOptim, Statistics, Random
 
 # Load starting model
 n, d, o, m0 = read(h5open("overthrust_2D_initial_model.h5", "r"), "n", "d", "o", "m0")
@@ -204,7 +204,7 @@ run(`wget ftp://slim.gatech.edu/data/SoftwareRelease/Imaging.jl/2DLSRTM/marmousi
 Once again, load the starting model and the data and set up the source wavelet. For this example, we use a Ricker wavelet with 30 Hertz peak frequency. For setting up matrix-free linear operators, an `info` structure with the dimensions of the problem is required:
 
 ```Julia
-using PyPlot, HDF5, JUDI, SegyIO, Random
+using PythonPlot, HDF5, JUDI, SegyIO, Random
 
 # Load smooth migration velocity model
 n,d,o,m0 = read(h5open("marmousi_migration_velocity.h5","r"), "n", "d", "o", "m0")

diff --git a/docker/Dockerfile.base b/docker/Dockerfile.base
@@ -51,7 +51,7 @@ RUN for pkg in "SegyIO" "JOLI" "JUDI" "SlimOptim" "InvertibleNetworks"; do \
 		julia -e "using Pkg;Pkg.develop(\"$pkg\");using $pkg"; \
 	done
 RUN for pkg in "LineSearches" "Optim" "DSP" "Dierckx" "NLopt" "FFTW" "SetIntersectionProjection" "IterativeSolvers" "JLD" \
-               "Flux" "Zygote" "JLD2" "HDF5" "PyPlot" "PyCall" "Distributed" "Images" "SlimPlotting"; do \
+               "Flux" "Zygote" "JLD2" "HDF5" "PythonPlot" "PyCall" "Distributed" "Images" "SlimPlotting"; do \
 		julia -e "using Pkg;Pkg.add(\"$pkg\"); using $pkg"; \
 	done
 

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,6 +1,6 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
+PythonPlot = "274fc56d-3b97-40fa-a1cd-1b4a50311bf9"
 Weave = "44d3d7a6-8a23-5bf8-98c5-b353f8df5ec9"
 
 [compat]

diff --git a/docs/src/basics.md b/docs/src/basics.md
@@ -113,7 +113,7 @@ d_obs = F*q
 We can plot a 2D shot record by accessing the `.data` field of the `judiVector`, which contains the data in the original (non-vectorized) dimensions:
 
 ```julia
-using PyPlot
+using PythonPlot
 imshow(d_obs.data[1], vmin=-5, vmax=5, cmap="seismic", aspect="auto")
 ```
 
@@ -230,7 +230,7 @@ d_obs = Pr*A_inv*Ps'*q
 The 3D shot records are still saved as 2D arrays of dimensions `time x (nxrec*nyrec)`:
 
 ```julia
-using PyPlot
+using PythonPlot
 imshow(d_obs.data[1], vmin=-.4, vmax=.4, cmap="seismic", aspect="auto")
 ```
 
@@ -495,7 +495,7 @@ u = A_inv*Ps'*q
 This return an abstract data vector called `judiWavefield`. Similar to `judiVectors`, we can access the data for each source number `i` via `u.data[i]`. The data is a 3D array of size `(nt, nx, nz)` for 2D and a 4D array of size `(nt, nx, ny, nz)` for 3D. We can plot the wavefield of the 600th time step with:
 
 ```julia
-using PyPlot
+using PythonPlot
 imshow(u.data[1][600, :, :]', vmin=-5, vmax=5, cmap="seismic", aspect="auto")
 ```
 

diff --git a/docs/src/inversion.md b/docs/src/inversion.md
@@ -36,7 +36,7 @@ run(`wget ftp://slim.gatech.edu/data/SoftwareRelease/WaveformInversion.jl/2DFWI/
 The first step is to load the velocity model and the observed data into Julia, as well as setting up bound constraints for the inversion, which prevent too high or low velocities in the final result. Furthermore, we define an 8 Hertz Ricker wavelet as the source function:
 
 ```julia
-using PyPlot, HDF5, SegyIO, JUDI, SlimOptim, Statistics, Random
+using PythonPlot, HDF5, SegyIO, JUDI, SlimOptim, Statistics, Random
 
 # Load starting model
 n, d, o, m0 = read(h5open("overthrust_2D_initial_model.h5", "r"), "n", "d", "o", "m0")
@@ -118,7 +118,7 @@ run(`wget ftp://slim.gatech.edu/data/SoftwareRelease/Imaging.jl/2DLSRTM/marmousi
 Once again, load the starting model and the data and set up the source wavelet. For this example, we use a Ricker wavelet with 30 Hertz peak frequency.
 
 ```julia
-using PyPlot, HDF5, JUDI, SegyIO, Random
+using PythonPlot, HDF5, JUDI, SegyIO, Random
 
 # Load smooth migration velocity model
 n,d,o,m0 = read(h5open("marmousi_migration_velocity.h5","r"), "n", "d", "o", "m0")

diff --git a/examples/README.md b/examples/README.md
@@ -15,7 +15,7 @@ Pkg.add("JLD")
 Pkg.add("JLD2")
 
 # Plotting
-Pkg.add("PyPlot")
+Pkg.add("PythonPlot")
 Pkg.add("SlimPlotting")
 
 # Optimization

diff --git a/examples/compressive_splsrtm/BP_synthetic_2004/generate_data_bp2004.jl b/examples/compressive_splsrtm/BP_synthetic_2004/generate_data_bp2004.jl
@@ -9,7 +9,7 @@
 # Set up path where data will be saved
 data_path = "/path/to/data/"
 
-using JUDI, SegyIO, JLD, PyPlot
+using JUDI, SegyIO, JLD, PythonPlot
 
 # Load velocity
 if !isfile("bp_synthetic_2004_true_velocity.jld")

diff --git a/examples/compressive_splsrtm/BP_synthetic_2004/rtm_bp_2004_freq.jl b/examples/compressive_splsrtm/BP_synthetic_2004/rtm_bp_2004_freq.jl
@@ -7,7 +7,7 @@
 # Set up path where data will be saved
 data_path = "/path/to/data/"
 
-using JUDI, SegyIO, JLD, PyPlot, LinearAlgebra
+using JUDI, SegyIO, JLD, PythonPlot, LinearAlgebra
 
 # Load velocity model
 if !isfile("bp_synthetic_2004_migration_velocity.jld")

diff --git a/examples/compressive_splsrtm/BP_synthetic_2004/splsrtm_bp_2004_freq.jl b/examples/compressive_splsrtm/BP_synthetic_2004/splsrtm_bp_2004_freq.jl
@@ -7,7 +7,7 @@
 # Set up path where data will be saved
 data_path = "/path/to/data/"
 
-using JUDI, SegyIO, JLD, PyPlot, JOLI, Random, LinearAlgebra
+using JUDI, SegyIO, JLD, PythonPlot, JOLI, Random, LinearAlgebra
 
 # Load velocity model(replace with correct paths)
 if !isfile("bp_synthetic_2004_migration_velocity.jld")

diff --git a/examples/compressive_splsrtm/Figure1/compare_imaging_conditions.jl b/examples/compressive_splsrtm/Figure1/compare_imaging_conditions.jl
@@ -4,7 +4,7 @@
 # Date: January 2017
 #
 
-using JUDI, PyPlot, JLD, SegyIO, LinearAlgebra
+using JUDI, PythonPlot, JLD, SegyIO, LinearAlgebra
 
 # Load Sigsbee model
 if !isfile("sigsbee2A_model.jld")

diff --git a/examples/compressive_splsrtm/Figure2/compare_imaging_time_frequency.jl b/examples/compressive_splsrtm/Figure2/compare_imaging_time_frequency.jl
@@ -4,7 +4,7 @@
 # Date: January 2017
 #
 
-using JUDI, PyPlot, JLD, SegyIO, LinearAlgebra
+using JUDI, PythonPlot, JLD, SegyIO, LinearAlgebra
 
 # Load Marmousi (4 km x 2 km)
 if !isfile("marmousi_small.jld")

diff --git a/examples/compressive_splsrtm/Sigsbee2A/generate_data_sigsbee.jl b/examples/compressive_splsrtm/Sigsbee2A/generate_data_sigsbee.jl
@@ -8,7 +8,7 @@
 file_path="/path/to/data/"
 file_name="sigsbee2A_marine"
 
-using JUDI, PyPlot, JLD, SegyIO
+using JUDI, PythonPlot, JLD, SegyIO
 
 # Load Sigsbee model
 if !isfile("sigsbee2A_model.jld")

diff --git a/examples/compressive_splsrtm/Sigsbee2A/rtm_sigsbee.jl b/examples/compressive_splsrtm/Sigsbee2A/rtm_sigsbee.jl
@@ -8,7 +8,7 @@
 path_to_data = "/path/to/directory/"
 data_name = "sigsbee2A_marine"  # common base name of all shots
 
-using JUDI, PyPlot, JLD, SegyIO
+using JUDI, PythonPlot, JLD, SegyIO
 
 # Load Sigsbee model
 M = load("sigsbee2A_model.jld")

diff --git a/examples/compressive_splsrtm/Sigsbee2A/splsrtm_sigsbee_frequency_domain.jl b/examples/compressive_splsrtm/Sigsbee2A/splsrtm_sigsbee_frequency_domain.jl
@@ -9,7 +9,7 @@
 path_to_data="/home/pwitte3/.julia/dev/JUDI/examples/compressive_splsrtm/Sigsbee2A/"
 data_name = "sigsbee2A_marine"  # common base name of all shots
 
-using JUDI, PyPlot, JLD, SegyIO, JOLI, Random, LinearAlgebra
+using JUDI, PythonPlot, JLD, SegyIO, JOLI, Random, LinearAlgebra
 
 # Load Sigsbee model
 M = load("sigsbee2A_model.jld")

diff --git a/examples/compressive_splsrtm/Sigsbee2A/splsrtm_sigsbee_time_domain.jl b/examples/compressive_splsrtm/Sigsbee2A/splsrtm_sigsbee_time_domain.jl
@@ -9,7 +9,7 @@
 path_to_data="/home/pwitte3/.julia/dev/JUDI/examples/compressive_splsrtm/Sigsbee2A/"
 data_name = "sigsbee2A_marine"  # common base name of all shots
 
-using JUDI, PyPlot, JLD, SegyIO, JOLI, Random
+using JUDI, PythonPlot, JLD, SegyIO, JOLI, Random
 
 # Load Sigsbee model
 M = load("sigsbee2A_model.jld")

diff --git a/examples/field_examples/viking_graben_line12/fwi/fwi_pqn.jl b/examples/field_examples/viking_graben_line12/fwi/fwi_pqn.jl
@@ -209,7 +209,7 @@ for k in 1:nworkers()
     @spawnat workers()[k] ENV["GOMP_CPU_AFFINITY"] = "$(place1)-$(place2)";
 end
 
-@everywhere using Distributed, JUDI.TimeModeling, SlimOptim, LinearAlgebra, PyPlot, SetIntersectionProjection, SegyIO
+@everywhere using Distributed, JUDI.TimeModeling, SlimOptim, LinearAlgebra, PythonPlot, SetIntersectionProjection, SegyIO
 
 function objective(m, d_obs, wb_mask)
 

diff --git a/examples/field_examples/viking_graben_line12/proc/p0_geom_check.ipynb b/examples/field_examples/viking_graben_line12/proc/p0_geom_check.ipynb
@@ -34,7 +34,7 @@
     "import numpy as np\n",
     "import pandas as pd\n",
     "import matplotlib\n",
-    "import matplotlib.pyplot as plt\n",
+    "import matplotlib.PythonPlot as plt\n",
     "import seaborn as sns\n",
     "from rsf.proj import *\n",
     "import rsf.api as sf"

diff --git a/examples/field_examples/viking_graben_line12/proc/p1_deghost.ipynb b/examples/field_examples/viking_graben_line12/proc/p1_deghost.ipynb
@@ -47,7 +47,7 @@
     "from scipy.signal import periodogram, welch\n",
     "from wiggle.wiggle import wiggle\n",
     "import matplotlib\n",
-    "import matplotlib.pyplot as plt\n",
+    "import matplotlib.PythonPlot as plt\n",
     "from scipy.interpolate import griddata\n",
     "from scipy.interpolate import Rbf"
    ]

diff --git a/examples/field_examples/viking_graben_line12/proc/p2_gain.ipynb b/examples/field_examples/viking_graben_line12/proc/p2_gain.ipynb
@@ -52,7 +52,7 @@
     "from scipy.signal import periodogram, welch\n",
     "from wiggle.wiggle import wiggle\n",
     "import matplotlib\n",
-    "import matplotlib.pyplot as plt\n",
+    "import matplotlib.PythonPlot as plt\n",
     "from scipy.interpolate import griddata\n",
     "from scipy.interpolate import Rbf"
    ]

diff --git a/examples/field_examples/viking_graben_line12/proc/p3_mute.ipynb b/examples/field_examples/viking_graben_line12/proc/p3_mute.ipynb
@@ -55,7 +55,7 @@
     "from scipy.signal import periodogram, welch\n",
     "from wiggle.wiggle import wiggle\n",
     "import matplotlib\n",
-    "import matplotlib.pyplot as plt\n",
+    "import matplotlib.PythonPlot as plt\n",
     "from scipy.interpolate import griddata\n",
     "from scipy.interpolate import Rbf"
    ]

diff --git a/examples/field_examples/viking_graben_line12/proc/p4_dip.ipynb b/examples/field_examples/viking_graben_line12/proc/p4_dip.ipynb
@@ -58,7 +58,7 @@
     "from scipy.signal import periodogram, welch\n",
     "from wiggle.wiggle import wiggle\n",
     "import matplotlib\n",
-    "import matplotlib.pyplot as plt\n",
+    "import matplotlib.PythonPlot as plt\n",
     "from scipy.interpolate import griddata\n",
     "from scipy.interpolate import Rbf"
    ]

diff --git a/examples/field_examples/viking_graben_line12/proc/p5_radon.ipynb b/examples/field_examples/viking_graben_line12/proc/p5_radon.ipynb
@@ -64,7 +64,7 @@
     "from scipy.signal import periodogram, welch\n",
     "from wiggle.wiggle import wiggle\n",
     "import matplotlib\n",
-    "import matplotlib.pyplot as plt\n",
+    "import matplotlib.PythonPlot as plt\n",
     "from scipy.interpolate import griddata\n",
     "from scipy.interpolate import Rbf"
    ]

diff --git a/examples/field_examples/viking_graben_line12/proc/p6_velpick.ipynb b/examples/field_examples/viking_graben_line12/proc/p6_velpick.ipynb
@@ -63,7 +63,7 @@
     "from scipy.signal import periodogram, welch\n",
     "from wiggle.wiggle import wiggle\n",
     "import matplotlib\n",
-    "import matplotlib.pyplot as plt\n",
+    "import matplotlib.PythonPlot as plt\n",
     "from scipy.interpolate import griddata\n",
     "from scipy.interpolate import Rbf"
    ]

diff --git a/examples/field_examples/viking_graben_line12/qc/qc_logs.ipynb b/examples/field_examples/viking_graben_line12/qc/qc_logs.ipynb
@@ -12,7 +12,7 @@
     "using SegyIO\n",
     "using Interpolations\n",
     "using PyCall\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using HDF5\n",
     "using DelimitedFiles\n",
     "using ImageFiltering"

diff --git a/examples/notebooks/01_intro.ipynb b/examples/notebooks/01_intro.ipynb
@@ -17,7 +17,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "using JUDI, PyPlot, LinearAlgebra"
+    "using JUDI, PythonPlot, LinearAlgebra"
    ]
   },
   {

diff --git a/examples/notebooks/02_fwi_example_NLopt.ipynb b/examples/notebooks/02_fwi_example_NLopt.ipynb
@@ -20,7 +20,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "using SegyIO, HDF5, PyPlot, JUDI, NLopt, Random, LinearAlgebra, Printf"
+    "using SegyIO, HDF5, PythonPlot, JUDI, NLopt, Random, LinearAlgebra, Printf"
    ]
   },
   {

diff --git a/examples/notebooks/03_constrained_fwi.ipynb b/examples/notebooks/03_constrained_fwi.ipynb
@@ -35,7 +35,7 @@
    "outputs": [],
    "source": [
     "# Add packages needed\n",
-    "# PyPlot is already installed in the environment\n",
+    "# PythonPlot is already installed in the environment\n",
     "# using Pkg\n",
     "# Pkg.add([\"Distributed\", \"SlimOptim\", \"JUDI\", \"SetIntersectionProjection\"])"
    ]
@@ -46,7 +46,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "using Distributed, JUDI, SlimOptim, LinearAlgebra, PyPlot, SetIntersectionProjection, Printf"
+    "using Distributed, JUDI, SlimOptim, LinearAlgebra, PythonPlot, SetIntersectionProjection, Printf"
    ]
   },
   {

diff --git a/examples/notebooks/04_judi_leading_edge_tutorial.ipynb b/examples/notebooks/04_judi_leading_edge_tutorial.ipynb
@@ -144,7 +144,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "\n",
     "i = 8\n",
     "figure(figsize=(15,6))\n",

diff --git a/examples/notebooks/05_custom_misfit.ipynb b/examples/notebooks/05_custom_misfit.ipynb
@@ -57,7 +57,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "using SegyIO, HDF5, PyPlot, JUDI, Random, LinearAlgebra, Printf, SlimPlotting, SlimOptim, Statistics"
+    "using SegyIO, HDF5, PythonPlot, JUDI, Random, LinearAlgebra, Printf, SlimPlotting, SlimOptim, Statistics"
    ]
   },
   {

diff --git a/examples/notebooks/06_automatic_differentiation.ipynb b/examples/notebooks/06_automatic_differentiation.ipynb
@@ -418,7 +418,7 @@
     }
    ],
    "source": [
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "plot(x, label=\"true\")\n",
     "plot(summary.minimizer, label=\"Recovered\")\n",
     "legend()"

diff --git a/examples/scripts/extended_source_lsqr.jl b/examples/scripts/extended_source_lsqr.jl
@@ -4,7 +4,7 @@
 # Date: January 2017
 #
 
-using JUDI, SegyIO, LinearAlgebra, PyPlot, IterativeSolvers, JOLI
+using JUDI, SegyIO, LinearAlgebra, PythonPlot, IterativeSolvers, JOLI
 
 # Set up model structure
 n = (120, 100)   # (x,y,z) or (x,z)

diff --git a/examples/scripts/fwi_example_2D.jl b/examples/scripts/fwi_example_2D.jl
@@ -4,7 +4,7 @@
 #
 
 using Statistics, Random, LinearAlgebra
-using JUDI, HDF5, SegyIO, SlimOptim, SlimPlotting
+using JUDI, HDF5, SegyIO, SlimOptim, PythonPlot, SlimPlotting
 
 # Load starting model
 n,d,o,m0 = read(h5open("$(JUDI.JUDI_DATA)/overthrust_model.h5","r"), "n", "d", "o", "m0")

diff --git a/examples/scripts/fwi_example_ADloss.jl b/examples/scripts/fwi_example_ADloss.jl
@@ -3,7 +3,7 @@
 # Date: September 2022
 #
 
-using Statistics, Random, LinearAlgebra, PyPlot, Distributed
+using Statistics, Random, LinearAlgebra, PythonPlot, Distributed
 using JUDI, SlimOptim, HDF5, SegyIO
 @everywhere using JUDI.FFTW, Zygote
 

diff --git a/examples/scripts/fwi_example_constraints.jl b/examples/scripts/fwi_example_constraints.jl
@@ -6,7 +6,7 @@
 # Date: January 2022
 
 using Statistics, Random, LinearAlgebra
-using JUDI, SlimOptim, HDF5, SegyIO, PyPlot
+using JUDI, SlimOptim, HDF5, SegyIO, PythonPlot
 using SetIntersectionProjection
 
 # Load starting model

diff --git a/examples/scripts/fwi_example_minConf.jl b/examples/scripts/fwi_example_minConf.jl
@@ -3,7 +3,7 @@
 # Date: December 2017
 #
 
-using Statistics, Random, LinearAlgebra, PyPlot
+using Statistics, Random, LinearAlgebra, PythonPlot
 using JUDI, SlimOptim, HDF5, SegyIO
 
 # Load starting model

diff --git a/examples/scripts/fwi_example_studentst.jl b/examples/scripts/fwi_example_studentst.jl
@@ -3,7 +3,7 @@
 # Date: September 2022
 #
 
-using Statistics, Random, LinearAlgebra, PyPlot, SlimPlotting
+using Statistics, Random, LinearAlgebra, PythonPlot, SlimPlotting
 using JUDI, SlimOptim, HDF5, SegyIO
 
 # Load starting model

diff --git a/examples/scripts/fwi_gauss_newton.jl b/examples/scripts/fwi_gauss_newton.jl
@@ -4,7 +4,7 @@
 #
 
 using Statistics, Random, LinearAlgebra
-using JUDI, HDF5, SegyIO, PyPlot, IterativeSolvers
+using JUDI, HDF5, SegyIO, PythonPlot, IterativeSolvers
 
 # Load starting model
 n,d,o,m0 = read(h5open("$(JUDI.JUDI_DATA)/overthrust_model.h5","r"), "n", "d", "o", "m0")

diff --git a/examples/scripts/illum.jl b/examples/scripts/illum.jl
@@ -3,7 +3,7 @@
 # Author: Mathias Louboutin, [email protected]
 # February 2022
 
-using JUDI, HDF5, SlimPlotting, PyPlot, LinearAlgebra, Downloads, SlimPlotting, Distributed
+using JUDI, HDF5, SlimPlotting, PythonPlot, LinearAlgebra, Downloads, SlimPlotting, Distributed
 
 # Load model
 data_path = dirname(pathof(JUDI))*"/../data/"