Use Numpy's RNG instead of global seeds

simpeg · Nov 18, 2024 · 6abde83 · 6abde83
1 parent 0ef5021
commit 6abde83
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Showing 15 changed files with 99 additions and 66 deletions.
diff --git a/notebooks/03-gravity/fwd_gravity_anomaly_3d.ipynb b/notebooks/03-gravity/fwd_gravity_anomaly_3d.ipynb
@@ -123,10 +123,12 @@
    "outputs": [],
    "source": [
     "[x_topo, y_topo] = np.meshgrid(np.linspace(-200, 200, 41), np.linspace(-200, 200, 41))\n",
+    "\n",
+    "rng = np.random.default_rng(seed=737)\n",
     "z_topo = (\n",
     "    -15 * np.exp(-(x_topo**2 + y_topo**2) / 80**2)\n",
     "    + 100.0\n",
-    "    + 0.5 * np.random.rand(*x_topo.shape)\n",
+    "    + rng.uniform(low=0.0, high=0.5, size=x_topo.shape)\n",
     ")"
    ]
   },
@@ -139,8 +141,7 @@
      "iopub.status.busy": "2024-07-24T17:50:17.868023Z",
      "iopub.status.idle": "2024-07-24T17:50:18.225050Z",
      "shell.execute_reply": "2024-07-24T17:50:18.224263Z"
-    },
-    "scrolled": false
+    }
    },
    "outputs": [
     {
@@ -723,9 +724,9 @@
     "    fname = dir_path + \"gravity_topo.txt\"\n",
     "    np.savetxt(fname, np.c_[topo_xyz], fmt=\"%.4e\")\n",
     "\n",
-    "    np.random.seed(737)\n",
+    "    rng = np.random.default_rng(seed=737)\n",
     "    maximum_anomaly = np.max(np.abs(dpred))\n",
-    "    noise = 0.02 * maximum_anomaly * np.random.normal(size=len(dpred))\n",
+    "    noise = rng.normal(scale=0.02 * maximum_anomaly, size=len(dpred))\n",
     "    fname = dir_path + \"gravity_data.obs\"\n",
     "    np.savetxt(fname, np.c_[receiver_locations, dpred + noise], fmt=\"%.4e\")"
    ]
@@ -751,5 +752,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/03-gravity/fwd_gravity_gradiometry_3d.ipynb b/notebooks/03-gravity/fwd_gravity_gradiometry_3d.ipynb
@@ -125,10 +125,11 @@
    "outputs": [],
    "source": [
     "[x_topo, y_topo] = np.meshgrid(np.linspace(-200, 200, 41), np.linspace(-200, 200, 41))\n",
+    "rng = np.random.default_rng(seed=737)\n",
     "z_topo = (\n",
     "    -15 * np.exp(-(x_topo**2 + y_topo**2) / 80**2)\n",
     "    + 100.0\n",
-    "    + 0.5 * np.random.rand(*x_topo.shape)\n",
+    "    + rng.uniform(low=0.0, high=0.5, size=x_topo.shape)\n",
     ")"
    ]
   },
@@ -778,5 +779,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/04-magnetics/fwd_magnetics_induced_3d.ipynb b/notebooks/04-magnetics/fwd_magnetics_induced_3d.ipynb
@@ -123,10 +123,11 @@
    "outputs": [],
    "source": [
     "[x_topo, y_topo] = np.meshgrid(np.linspace(-200, 200, 41), np.linspace(-200, 200, 41))\n",
+    "rng = np.random.default_rng(seed=737)\n",
     "z_topo = (\n",
     "    -15 * np.exp(-(x_topo**2 + y_topo**2) / 80**2)\n",
     "    + 100.0\n",
-    "    + 0.5 * np.random.rand(*x_topo.shape)\n",
+    "    + rng.uniform(low=0.0, high=0.5, size=x_topo.shape)\n",
     ")"
    ]
   },
@@ -706,9 +707,9 @@
     "    fname = dir_path + \"magnetics_topo.txt\"\n",
     "    np.savetxt(fname, np.c_[topo_xyz], fmt=\"%.4e\")\n",
     "\n",
-    "    np.random.seed(211)\n",
+    "    rng = np.random.default_rng(seed=211)\n",
     "    maximum_anomaly = np.max(np.abs(dpred))\n",
-    "    noise = 0.02 * maximum_anomaly * np.random.normal(size=len(dpred))\n",
+    "    noise = rng.normal(scale=0.02 * maximum_anomaly, size=len(dpred))\n",
     "    fname = dir_path + \"magnetics_data.obs\"\n",
     "    np.savetxt(fname, np.c_[receiver_locations, dpred + noise], fmt=\"%.4e\")"
    ]
@@ -741,5 +742,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/04-magnetics/fwd_magnetics_mvi_3d.ipynb b/notebooks/04-magnetics/fwd_magnetics_mvi_3d.ipynb
@@ -134,10 +134,11 @@
    "outputs": [],
    "source": [
     "[x_topo, y_topo] = np.meshgrid(np.linspace(-200, 200, 41), np.linspace(-200, 200, 41))\n",
+    "rng = np.random.default_rng(seed=42)\n",
     "z_topo = (\n",
     "    -15 * np.exp(-(x_topo**2 + y_topo**2) / 80**2)\n",
     "    + 100.0\n",
-    "    + 0.5 * np.random.rand(*x_topo.shape)\n",
+    "    + rng.uniform(scale=0.5, size=x_topo.shape)\n",
     ")"
    ]
   },
@@ -583,8 +584,7 @@
      "iopub.status.busy": "2024-07-17T17:48:42.969668Z",
      "iopub.status.idle": "2024-07-17T17:48:42.974834Z",
      "shell.execute_reply": "2024-07-17T17:48:42.974163Z"
-    },
-    "scrolled": false
+    }
    },
    "outputs": [],
    "source": [
@@ -627,8 +627,7 @@
      "iopub.status.busy": "2024-07-17T17:48:42.991011Z",
      "iopub.status.idle": "2024-07-17T17:48:43.433606Z",
      "shell.execute_reply": "2024-07-17T17:48:43.432840Z"
-    },
-    "scrolled": false
+    }
    },
    "outputs": [
     {
@@ -863,5 +862,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/05-dcr/fwd_dcr_1d.ipynb b/notebooks/05-dcr/fwd_dcr_1d.ipynb
@@ -435,8 +435,8 @@
     "    if not os.path.exists(dir_path):\n",
     "        os.mkdir(dir_path)\n",
     "\n",
-    "    np.random.seed(145)\n",
-    "    noise = 0.025 * dpred_resistivity * np.random.normal(size=len(dpred_resistivity))\n",
+    "    rng = np.random.default_rng(seed=145)\n",
+    "    noise = rng.normal(scale=0.025 * dpred_resistivity, size=len(dpred_resistivity))\n",
     "\n",
     "    data_array = np.c_[\n",
     "        survey.locations_a,\n",
@@ -471,5 +471,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/05-dcr/fwd_dcr_2d.ipynb b/notebooks/05-dcr/fwd_dcr_2d.ipynb
@@ -1046,9 +1046,9 @@
     "        os.mkdir(dir_path)\n",
     "\n",
     "    # Add 5% Gaussian noise to each datum\n",
-    "    np.random.seed(225)\n",
+    "    rng = np.random.default_rng(seed=225)\n",
     "    std = 0.05 * np.abs(dpred_con)\n",
-    "    dc_noise = std * np.random.normal(size=len(dpred_con))\n",
+    "    dc_noise = rng.normal(scale=std, size=len(dpred_con))\n",
     "    dobs = dpred_con + dc_noise\n",
     "\n",
     "    # Create a survey with the original electrode locations\n",
@@ -1102,5 +1102,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/05-dcr/fwd_dcr_3d.ipynb b/notebooks/05-dcr/fwd_dcr_3d.ipynb
@@ -177,8 +177,7 @@
      "iopub.status.busy": "2024-07-17T17:49:48.097426Z",
      "iopub.status.idle": "2024-07-17T17:49:48.981316Z",
      "shell.execute_reply": "2024-07-17T17:49:48.980667Z"
-    },
-    "scrolled": false
+    }
    },
    "outputs": [
     {
@@ -820,8 +819,7 @@
      "iopub.status.busy": "2024-07-17T17:50:25.388911Z",
      "iopub.status.idle": "2024-07-17T17:50:25.394480Z",
      "shell.execute_reply": "2024-07-17T17:50:25.393823Z"
-    },
-    "scrolled": false
+    }
    },
    "outputs": [
     {
@@ -1018,9 +1016,9 @@
     "        os.mkdir(dir_path)\n",
     "\n",
     "    # Add 10% Gaussian noise to each datum\n",
-    "    np.random.seed(433)\n",
+    "    rng = np.random.default_rng(seed=433)\n",
     "    std = 0.1 * np.abs(dpred_con)\n",
-    "    noise = std * np.random.normal(size=len(dpred_con))\n",
+    "    noise = rng.normal(scale=std, size=len(dpred_con))\n",
     "    dobs = dpred_con + noise\n",
     "\n",
     "    # Create dictionary that stores line IDs\n",
@@ -1085,5 +1083,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/06-ip/fwd_ip_2d.ipynb b/notebooks/06-ip/fwd_ip_2d.ipynb
@@ -792,9 +792,9 @@
     "        os.mkdir(dir_path)\n",
     "\n",
     "    # Add 5% Gaussian noise to each datum\n",
-    "    np.random.seed(225)\n",
+    "    rng = np.random.default_rng(seed=225)\n",
     "    std = 5e-3 * np.ones_like(dpred_ip)\n",
-    "    ip_noise = std * np.random.normal(size=len(dpred_ip))\n",
+    "    ip_noise = rng.normal(scale=std, size=len(dpred_ip))\n",
     "    dobs = dpred_ip + ip_noise\n",
     "\n",
     "    # Create a survey with the original electrode locations\n",
@@ -848,5 +848,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/06-ip/fwd_ip_3d.ipynb b/notebooks/06-ip/fwd_ip_3d.ipynb
@@ -1007,9 +1007,9 @@
     "        os.mkdir(dir_path)\n",
     "\n",
     "    # Add 10% Gaussian noise to each datum\n",
-    "    np.random.seed(433)\n",
+    "    rng = np.random.default_rng(seed=433)\n",
     "    std = 5e-3 * np.ones_like(dpred_ip)\n",
-    "    noise = std * np.random.normal(size=len(dpred_ip))\n",
+    "    noise = rng.normal(scale=std, size=len(dpred_ip))\n",
     "    dobs = dpred_ip + noise\n",
     "\n",
     "    # Create dictionary that stores line IDs\n",
@@ -1074,5 +1074,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/07-fdem/fwd_fdem_1d.ipynb b/notebooks/07-fdem/fwd_fdem_1d.ipynb
@@ -570,11 +570,10 @@
     "    if not os.path.exists(dir_path):\n",
     "        os.mkdir(dir_path)\n",
     "\n",
-    "    np.random.seed(222)\n",
-    "    noise = (\n",
-    "        0.05\n",
-    "        * np.abs(dpred_conductivity)\n",
-    "        * np.random.normal(size=len(dpred_conductivity))\n",
+    "    rng = np.random.default_rng(seed=222)\n",
+    "    noise = rng.normal(\n",
+    "        scale=0.05 * np.abs(dpred_conductivity),\n",
+    "        size=len(dpred_conductivity),\n",
     "    )\n",
     "    dpred_out = dpred_conductivity + noise\n",
     "\n",
@@ -615,5 +614,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/08-tdem/fwd_tdem_1d.ipynb b/notebooks/08-tdem/fwd_tdem_1d.ipynb
@@ -1057,11 +1057,10 @@
     "    if not os.path.exists(dir_path):\n",
     "        os.mkdir(dir_path)\n",
     "\n",
-    "    np.random.seed(347)\n",
-    "    noise = (\n",
-    "        0.05\n",
-    "        * np.abs(dpred_conductivity)\n",
-    "        * np.random.normal(size=len(dpred_conductivity))\n",
+    "    rng = np.random.default_rng(seed=347)\n",
+    "    noise = rng.normal(\n",
+    "        scale=0.05 * np.abs(dpred_conductivity),\n",
+    "        size=len(dpred_conductivity),\n",
     "    )\n",
     "    dpred_conductivity += noise\n",
     "    fname = dir_path + \"em1dtm_data.txt\"\n",
@@ -1096,5 +1095,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/08-tdem/fwd_tdem_3d.ipynb b/notebooks/08-tdem/fwd_tdem_3d.ipynb
@@ -932,7 +932,9 @@
     "\n",
     "    # Write data with 2% noise added\n",
     "    fname = dir_path + \"tdem_data.obs\"\n",
-    "    dpred = dpred + 0.02 * np.abs(dpred) * np.random.rand(len(dpred))\n",
+    "    rng = np.random.default_rng(seed=42)\n",
+    "    noise = rng.uniform(low=0.0, high=0.02 * np.abs(dpred), size=len(dpred))\n",
+    "    dpred += noise\n",
     "    t_vec = np.kron(np.ones(ntx), time_channels)\n",
     "    receiver_locations = np.kron(receiver_locations, np.ones((len(time_channels), 1)))\n",
     "\n",
@@ -967,5 +969,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/11-joint-inversion/plot_inv_3_cross_gradient_pf.ipynb b/notebooks/11-joint-inversion/plot_inv_3_cross_gradient_pf.ipynb
@@ -90,9 +90,7 @@
     "    directives,\n",
     "    inversion,\n",
     "    utils,\n",
-    ")\n",
-    "\n",
-    "np.random.seed(0)"
+    ")"
    ]
   },
   {