diff --git a/docs/_downloads/021b6cf14de4fd76c7a3e2f90a173578/hdf5.ipynb b/docs/_downloads/021b6cf14de4fd76c7a3e2f90a173578/hdf5.ipynb index e74d9ad0..442ab11a 100644 --- a/docs/_downloads/021b6cf14de4fd76c7a3e2f90a173578/hdf5.ipynb +++ b/docs/_downloads/021b6cf14de4fd76c7a3e2f90a173578/hdf5.ipynb @@ -136,7 +136,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/docs/_downloads/16ec1efc89ed8eeea10bd844b92557de/plot_rectilinear_mesh_1d.ipynb b/docs/_downloads/16ec1efc89ed8eeea10bd844b92557de/plot_rectilinear_mesh_1d.ipynb index a0e38877..113acf7c 100644 --- a/docs/_downloads/16ec1efc89ed8eeea10bd844b92557de/plot_rectilinear_mesh_1d.ipynb +++ b/docs/_downloads/16ec1efc89ed8eeea10bd844b92557de/plot_rectilinear_mesh_1d.ipynb @@ -277,7 +277,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/docs/_downloads/36c869e825ae3b16a184379512e44203/plot_model_2d.ipynb b/docs/_downloads/36c869e825ae3b16a184379512e44203/plot_model_2d.ipynb index 5f0b2097..282aea23 100644 --- a/docs/_downloads/36c869e825ae3b16a184379512e44203/plot_model_2d.ipynb +++ b/docs/_downloads/36c869e825ae3b16a184379512e44203/plot_model_2d.ipynb @@ -64,7 +64,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/docs/_downloads/36d592b131669bd825431209f21f3531/plot_histogram_2d.ipynb b/docs/_downloads/36d592b131669bd825431209f21f3531/plot_histogram_2d.ipynb index 0729e6c0..10183a99 100644 --- a/docs/_downloads/36d592b131669bd825431209f21f3531/plot_histogram_2d.ipynb +++ b/docs/_downloads/36d592b131669bd825431209f21f3531/plot_histogram_2d.ipynb @@ -450,7 +450,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/docs/_downloads/48f0be9987c0cd931b23ce187c305d56/plot_inference_2d_resolve.py b/docs/_downloads/48f0be9987c0cd931b23ce187c305d56/plot_inference_2d_resolve.py index b0f4d8a7..bdb4c9e3 100644 --- a/docs/_downloads/48f0be9987c0cd931b23ce187c305d56/plot_inference_2d_resolve.py +++ b/docs/_downloads/48f0be9987c0cd931b23ce187c305d56/plot_inference_2d_resolve.py @@ -38,6 +38,9 @@ def plot_2d_summary(folder, data_type, model_type): "cmap" : 'jet' } + import warnings + warnings.filterwarnings('error') + fig = plt.figure(figsize=(16, 8)) plt.suptitle("{} {}".format(data_type, model_type)) gs0 = fig.add_gridspec(6, 2, hspace=1.0) @@ -134,17 +137,16 @@ def plot_2d_summary(folder, data_type, model_type): results_2d.plot_data_elevation(linewidth=0.3, ax=ax1); results_2d.plot_elevation(linewidth=0.3, ax=ax1); - - plt.show() - # plt.savefig('{}_{}.png'.format(data_type, model_type), dpi=300) + # plt.show() + plt.savefig('{}_{}.png'.format(data_type, model_type), dpi=300) if __name__ == '__main__': models = ['glacial', 'saline_clay', 'resistive_dolomites', 'resistive_basement', 'coastal_salt_water', 'ice_over_salt_water'] for model in models: - try: + # try: plot_2d_summary("../../../Parallel_Inference/", "resolve", model) - except Exception as e: - print(model) - print(e) - pass + # except Exception as e: + # print(model) + # print(e) + # pass diff --git a/docs/_downloads/525bc65bfe238dea5610d6856bece19c/plot_model_3d.ipynb b/docs/_downloads/525bc65bfe238dea5610d6856bece19c/plot_model_3d.ipynb index 5852e922..bb27e1d4 100644 --- a/docs/_downloads/525bc65bfe238dea5610d6856bece19c/plot_model_3d.ipynb +++ b/docs/_downloads/525bc65bfe238dea5610d6856bece19c/plot_model_3d.ipynb @@ -205,7 +205,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/docs/_downloads/6651de36bdd3440bb761887dd2b00831/plot_histogram_1d.ipynb b/docs/_downloads/6651de36bdd3440bb761887dd2b00831/plot_histogram_1d.ipynb index c11a36ee..cd1ad796 100644 --- a/docs/_downloads/6651de36bdd3440bb761887dd2b00831/plot_histogram_1d.ipynb +++ b/docs/_downloads/6651de36bdd3440bb761887dd2b00831/plot_histogram_1d.ipynb @@ -320,7 +320,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/docs/_downloads/6dec5e41149e94d435270c1dffe803e1/plot_rectilinear_mesh_2d.ipynb b/docs/_downloads/6dec5e41149e94d435270c1dffe803e1/plot_rectilinear_mesh_2d.ipynb index b44ac50a..2b586765 100644 --- a/docs/_downloads/6dec5e41149e94d435270c1dffe803e1/plot_rectilinear_mesh_2d.ipynb +++ b/docs/_downloads/6dec5e41149e94d435270c1dffe803e1/plot_rectilinear_mesh_2d.ipynb @@ -320,7 +320,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/docs/_downloads/7d8af6f7b40a771fd3b189fc4fd80360/plot_model_1d.ipynb b/docs/_downloads/7d8af6f7b40a771fd3b189fc4fd80360/plot_model_1d.ipynb index ef36201d..fdc0d8cb 100644 --- a/docs/_downloads/7d8af6f7b40a771fd3b189fc4fd80360/plot_model_1d.ipynb +++ b/docs/_downloads/7d8af6f7b40a771fd3b189fc4fd80360/plot_model_1d.ipynb @@ -219,7 +219,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/docs/_downloads/83471875085bd5964f72b6b955c92f62/test.py b/docs/_downloads/83471875085bd5964f72b6b955c92f62/test.py new file mode 100644 index 00000000..47b3655f --- /dev/null +++ b/docs/_downloads/83471875085bd5964f72b6b955c92f62/test.py @@ -0,0 +1,75 @@ +""" +2D Posterior analysis of Resolve inference +------------------------------------------ + +All plotting in GeoBIPy can be carried out using the 3D inference class + +""" + +import matplotlib.pyplot as plt +import numpy as np +from geobipy import Model +from geobipy import Inference2D + +def plot_2d_summary(folder, data_type, model_type): + #%% + # Inference for a line of inferences + # ++++++++++++++++++++++++++++++++++ + # + # We can instantiate the inference handler by providing a path to the directory containing + # HDF5 files generated by GeoBIPy. + # + # The InfereceXD classes are low memory. They only read information from the HDF5 files + # as and when it is needed. + # + # The first time you use these classes to create plots, expect longer initial processing times. + # I precompute expensive properties and store them in the HDF5 files for later use. + + from numpy.random import Generator + from numpy.random import PCG64DXSM + generator = PCG64DXSM(seed=0) + prng = Generator(generator) + + #%% + results_2d = Inference2D.fromHdf('{}/{}/{}/0.0.h5'.format(folder, data_type, model_type), prng=prng) + + kwargs = { + "log" : 10, + "cmap" : 'jet' + } + + true_model = Model.create_synthetic_model(model_type) + true_model.mesh.y_edges = true_model.mesh.y_edges / 10.0 + + kwargs['vmin'] = np.log10(np.min(true_model.values)) + kwargs['vmax'] = np.log10(np.max(true_model.values)) + + t = results_2d.inference_1d(index=7) + + plt.figure() + t.model.plot_posteriors(edges_kwargs={ + 'transpose': True, + 'trim': False}, + values_kwargs={ + 'colorbar': False, + 'flipY': True, + 'xscale': 'log', + 'credible_interval_kwargs': { + }}) + + tmp = t.model.values.posterior + + + plt.show(block=True) + # plt.savefig('{}_{}.png'.format(data_type, model_type), dpi=300) + +if __name__ == '__main__': + models = ['glacial']#, 'saline_clay', 'resistive_dolomites', 'resistive_basement', 'coastal_salt_water', 'ice_over_salt_water'] + + for model in models: + # try: + plot_2d_summary("../../../Parallel_Inference/", "resolve", model) + # except Exception as e: + # print(model) + # print(e) + # pass diff --git a/docs/_downloads/93b8636d5d11f2858e28438141a2ee46/plot_tempest_datapoint.ipynb b/docs/_downloads/93b8636d5d11f2858e28438141a2ee46/plot_tempest_datapoint.ipynb index 444c73cb..6a148661 100644 --- a/docs/_downloads/93b8636d5d11f2858e28438141a2ee46/plot_tempest_datapoint.ipynb +++ b/docs/_downloads/93b8636d5d11f2858e28438141a2ee46/plot_tempest_datapoint.ipynb @@ -222,7 +222,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/docs/_downloads/93e086b68a2d08aac2f637ab24f17e8a/plot_histogram_3d.ipynb b/docs/_downloads/93e086b68a2d08aac2f637ab24f17e8a/plot_histogram_3d.ipynb index 101bfe05..5c74b00c 100644 --- a/docs/_downloads/93e086b68a2d08aac2f637ab24f17e8a/plot_histogram_3d.ipynb +++ b/docs/_downloads/93e086b68a2d08aac2f637ab24f17e8a/plot_histogram_3d.ipynb @@ -302,7 +302,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/docs/_downloads/b7483b08f4f927c644b97f4bf2cf523c/plot_rectilinear_mesh_3d.ipynb b/docs/_downloads/b7483b08f4f927c644b97f4bf2cf523c/plot_rectilinear_mesh_3d.ipynb index 3190281b..b9a6f373 100644 --- a/docs/_downloads/b7483b08f4f927c644b97f4bf2cf523c/plot_rectilinear_mesh_3d.ipynb +++ b/docs/_downloads/b7483b08f4f927c644b97f4bf2cf523c/plot_rectilinear_mesh_3d.ipynb @@ -194,7 +194,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/docs/_downloads/bc82bea3a5dd7bdba60b65220891d9e5/examples_python.zip b/docs/_downloads/bc82bea3a5dd7bdba60b65220891d9e5/examples_python.zip index b846978f..a046fda6 100644 Binary files a/docs/_downloads/bc82bea3a5dd7bdba60b65220891d9e5/examples_python.zip and b/docs/_downloads/bc82bea3a5dd7bdba60b65220891d9e5/examples_python.zip differ diff --git a/docs/_downloads/e43324a965564fecaa251424c676fc0e/plot_StatArray.ipynb b/docs/_downloads/e43324a965564fecaa251424c676fc0e/plot_StatArray.ipynb index ffc0a4e4..364e8e4a 100644 --- a/docs/_downloads/e43324a965564fecaa251424c676fc0e/plot_StatArray.ipynb +++ b/docs/_downloads/e43324a965564fecaa251424c676fc0e/plot_StatArray.ipynb @@ -1074,7 +1074,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/docs/_downloads/fb625db3c50d423b1b7881136ffdeec8/examples_jupyter.zip b/docs/_downloads/fb625db3c50d423b1b7881136ffdeec8/examples_jupyter.zip index a7dfdc0b..1d3b6206 100644 Binary files a/docs/_downloads/fb625db3c50d423b1b7881136ffdeec8/examples_jupyter.zip and b/docs/_downloads/fb625db3c50d423b1b7881136ffdeec8/examples_jupyter.zip differ diff --git a/docs/_downloads/fbbc3367a4d5c657e951c760d8b85bb4/plot_distributions.ipynb b/docs/_downloads/fbbc3367a4d5c657e951c760d8b85bb4/plot_distributions.ipynb index 27c764c5..364db040 100644 --- a/docs/_downloads/fbbc3367a4d5c657e951c760d8b85bb4/plot_distributions.ipynb +++ b/docs/_downloads/fbbc3367a4d5c657e951c760d8b85bb4/plot_distributions.ipynb @@ -100,7 +100,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/docs/_images/sphx_glr_plot_StatArray_001.png b/docs/_images/sphx_glr_plot_StatArray_001.png index 1cb794ec..fca4589b 100644 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b/docs/_sources/content/getting_started/installation.rst.txt @@ -40,21 +40,21 @@ To run this code in parallel you will need both an MPI library and the python wr MPI ^^^ -If you are installing GeoBIPy on a parallel machine, I would think that you have access to prebuilt MPI libraries. -If you are on a local laptop, you will need to install one. +If you are installing GeoBIPy on a parallel machine, I would think that you have access to prebuilt MPI libraries. +If you are on a local laptop, you will need to install one. mpi4py ^^^^^^ -At this point, if you have an mpi4py module already installed, please remove it (you can check with "pip list"). -If you started with a clean installation you should not have to worry about this. -To test whether a new install of mpi4py will see the mpi library you have, just type "which mpicc". -The path that you see should point to the implementation that you want mpi4py to link to. -Make sure you are about to install mpi4py to the correct python installation. -If you type 'which python' it should return the path to the correct python distribution. +At this point, if you have an mpi4py module already installed, please remove it (you can check with "pip list"). +If you started with a clean installation you should not have to worry about this. +To test whether a new install of mpi4py will see the mpi library you have, just type "which mpicc". +The path that you see should point to the implementation that you want mpi4py to link to. +Make sure you are about to install mpi4py to the correct python installation. +If you type 'which python' it should return the path to the correct python distribution. If you are using environments, make sure you have activated the correct one. -Next, use "pip install mpi4py --no-cache-dir". This last option is very important, without it, pip might install its own MPI library called MPICH2. +Next, use "env MPICC= python -m pip install mpi4py". This last option is very important, without it, pip might install its own MPI library called MPICH2. I would try to avoid this because if you need to install the HDF5 library you will need know which directories to link to (see `Installing parallel HDF5 and h5py`_). At the end of the day, h5py needs to communicate with both the correct HDF5 library and mpi4py, and both of those need to communicate with the same MPI library. @@ -92,14 +92,14 @@ This will install h5py and compile the source. Installing the time domain forward modeller =========================================== -Ross Brodie at Geoscience Australia has written a great forward modeller, gatdaem1D, in C++ with a python interface. +Ross Brodie at Geoscience Australia has written a great forward modeller, gatdaem1D, in C++ with a python interface. You can obtain that code here at the `GA repository`_ .. _`GA repository`: https://github.com/GeoscienceAustralia/ga-aem Go ahead and "git clone" that repository. -These instructions only describe how to install Ross' forward modeller, but it is part of a larger code base for inversion. +These instructions only describe how to install Ross' forward modeller, but it is part of a larger code base for inversion. If you wish to install his entire package, please follow his instructions. Prerequisites @@ -192,4 +192,3 @@ Type, pip install . You should now have access to the time domain forward modeller within geobipy. - diff --git a/docs/_sources/examples/Data/plot_frequency_dataset.rst.txt b/docs/_sources/examples/Data/plot_frequency_dataset.rst.txt index 5fb05b04..dcd9562f 100644 --- a/docs/_sources/examples/Data/plot_frequency_dataset.rst.txt +++ b/docs/_sources/examples/Data/plot_frequency_dataset.rst.txt @@ -457,7 +457,7 @@ A summary will now show the properties of the line. FdemData x: - | Name: Easting (m) 0x174e7e4d0 + | Name: Easting (m) 0x171f2ff50 | Shape: (6710,) | Values: [586852.29 586852.23 586852.17 ... 586123.57 586123.2 586122.82] | Min: 586122.82 @@ -465,7 +465,7 @@ A summary will now show the properties of the line. | has_posterior: False y: - | Name: Northing (m) 0x174e7ecd0 + | Name: Northing (m) 0x171f2fe50 | Shape: (6710,) | Values: [4639119.38 4639122.68 4639125.98 ... 4661765.26 4661768.84 4661772.42] | Min: 4639119.38 @@ -473,7 +473,7 @@ A summary will now show the properties of the line. | has_posterior: False z: - | Name: Height (m) 0x174e7e150 + | Name: Height (m) 0x171f2f950 | Shape: (6710,) | Values: [36.115 36.498 36.835 ... 27.799 27.704 27.601] | Min: 23.830000000000002 @@ -481,7 +481,7 @@ A summary will now show the properties of the line. | has_posterior: False elevation: - | Name: Elevation (m) 0x174e7e050 + | Name: Elevation (m) 0x171f2f9d0 | Shape: (6710,) | Values: [1246.84 1246.71 1246.61 ... 1337.94 1337.96 1338.02] | Min: 1213.18 @@ -493,7 +493,7 @@ A summary will now show the properties of the line. | In_Phase 129550.0, Quadrature 380.0, Quadrature 1776.0, Quadrature 3345.0, Quadrature 8171.0, | Quadrature 41020.0, Quadrature 129550.0 data: - | Name: Data (ppm) 0x174f4d350 + | Name: Data (ppm) 0x171dd6c50 | Shape: (80520,) | Values: [145.3 435.8 260.6 ... 749.2 976.5 928.3] | Min: 37.7 @@ -501,7 +501,7 @@ A summary will now show the properties of the line. | has_posterior: False predicted data: - | Name: Predicted Data (ppm) 0x174f4d350 + | Name: Predicted Data (ppm) 0x1744559d0 | Shape: (80520,) | Values: [0. 0. 0. ... 0. 0. 0.] | Min: 0.0 @@ -509,7 +509,7 @@ A summary will now show the properties of the line. | has_posterior: False std: - | Name: std (ppm) 0x174f4d350 + | Name: std (ppm) 0x1744559d0 | Shape: (80520,) | Values: [1.453 4.358 2.606 ... 7.492 9.765 9.283] | Min: 0.37700000000000006 @@ -517,7 +517,7 @@ A summary will now show the properties of the line. | has_posterior: False line number: - | Name: Line number 0x174e7d250 + | Name: Line number 0x171f2fb50 | Shape: (6710,) | Values: [30010. 30010. 30010. ... 30010. 30010. 30010.] | Min: 30010.0 @@ -525,7 +525,7 @@ A summary will now show the properties of the line. | has_posterior: False fiducial: - | Name: Fiducial 0x174e7da50 + | Name: Fiducial 0x171f2fbd0 | Shape: (6710,) | Values: [30000 30000 30000 ... 30670 30670 30670] | Min: 30000 @@ -533,7 +533,7 @@ A summary will now show the properties of the line. | has_posterior: False relative error: - | Name: Relative error (%) 0x174e7e7d0 + | Name: Relative error (%) 0x171f2eb50 | Shape: (6710, 1) | Values: [[0.01] | [0.01] @@ -547,7 +547,7 @@ A summary will now show the properties of the line. | has_posterior: False additive error: - | Name: Additive error (ppm) 0x174e7e750 + | Name: Additive error (ppm) 0x171f2ebd0 | Shape: (6710, 1) | Values: [[0.] | [0.] @@ -714,7 +714,7 @@ See the Resolve.stm files. .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 2.948 seconds) + **Total running time of the script:** (0 minutes 3.419 seconds) .. _sphx_glr_download_examples_Data_plot_frequency_dataset.py: diff --git a/docs/_sources/examples/Data/plot_pointcloud3d.rst.txt b/docs/_sources/examples/Data/plot_pointcloud3d.rst.txt index 6cfb0147..a2368982 100644 --- a/docs/_sources/examples/Data/plot_pointcloud3d.rst.txt +++ b/docs/_sources/examples/Data/plot_pointcloud3d.rst.txt @@ -87,7 +87,7 @@ Append pointclouds together .. code-block:: none - + @@ -112,34 +112,34 @@ Write a summary of the contents of the point cloud Point x: - | Name: Easting (m) 0x174553ed0 + | Name: Easting (m) 0x17202bdd0 | Shape: (400,) - | Values: [-0.36850848 -0.22497904 -0.42452287 ... 0.24392363 0.74209804 - | 0.35181645] - | Min: -0.9991390932309943 - | Max: 0.9972526847985668 + | Values: [-0.77740663 -0.95465929 -0.8004366 ... 0.70222895 0.89988598 + | 0.73299721] + | Min: -0.9954311373841322 + | Max: 0.993880974076909 | has_posterior: False y: - | Name: Northing (m) 0x174552950 + | Name: Northing (m) 0x17202be50 | Shape: (400,) - | Values: [-0.77647668 -0.74756667 -0.4778044 ... 0.6441633 0.31716597 - | 0.62345157] - | Min: -0.9992693648479871 - | Max: 0.997306127444181 + | Values: [-0.09996723 -0.19608163 -0.81129254 ... 0.32732432 0.28247145 + | 0.18550653] + | Min: -0.9990801618390335 + | Max: 0.9898571038906161 | has_posterior: False z: - | Name: Height (m) 0x174550f50 + | Name: Height (m) 0x17202bed0 | Shape: (400,) - | Values: [ 0.13076579 0.14932083 0.1417104 ... 0.1194774 -0.11075939 - | 0.09476474] - | Min: -1.8793846688041962 - | Max: 0.2236799646282707 + | Values: [-0.32666931 -1.06724139 -0.65206219 ... -0.1062743 -0.0664333 + | -0.07198795] + | Min: -1.873647454522015 + | Max: 0.22854378054627222 | has_posterior: False elevation: - | Name: Elevation (m) 0x174552c50 + | Name: Elevation (m) 0x17202bf50 | Shape: (400,) | Values: [0. 0. 0. ... 0. 0. 0.] | Min: 0.0 @@ -196,7 +196,7 @@ Plot the locations with Height as colour .. code-block:: none - (, , ) + (, , ) @@ -282,16 +282,16 @@ Grid the points using a triangulated CloughTocher, or minimum curvature interpol .. code-block:: none - surface [WARNING]: 2 unusable points were supplied; these will be ignored. + surface [WARNING]: 4 unusable points were supplied; these will be ignored. surface [WARNING]: You should have pre-processed the data with block-mean, -median, or -mode. surface [WARNING]: Check that previous processing steps write results with enough decimals. surface [WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding. - surface [WARNING]: 2 unusable points were supplied; these will be ignored. + surface [WARNING]: 4 unusable points were supplied; these will be ignored. surface [WARNING]: You should have pre-processed the data with block-mean, -median, or -mode. surface [WARNING]: Check that previous processing steps write results with enough decimals. surface [WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding. - (, , ) + (, , ) @@ -325,12 +325,12 @@ For lots of points, these surfaces can look noisy. Using a block filter will hel .. code-block:: none - surface [WARNING]: 2 unusable points were supplied; these will be ignored. + surface [WARNING]: 3 unusable points were supplied; these will be ignored. surface [WARNING]: You should have pre-processed the data with block-mean, -median, or -mode. surface [WARNING]: Check that previous processing steps write results with enough decimals. surface [WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding. - (, , ) + (, , ) @@ -404,7 +404,7 @@ Read in the xyz co-ordinates in columns 2,3,4 from a file. Skip 1 header line. .. code-block:: none - + @@ -443,7 +443,7 @@ Read in the xyz co-ordinates in columns 2,3,4 from a file. Skip 1 header line. .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 3.231 seconds) + **Total running time of the script:** (0 minutes 3.710 seconds) .. _sphx_glr_download_examples_Data_plot_pointcloud3d.py: diff --git a/docs/_sources/examples/Data/plot_skytem_dataset.rst.txt b/docs/_sources/examples/Data/plot_skytem_dataset.rst.txt index c0ba0c8a..cde0ae27 100644 --- a/docs/_sources/examples/Data/plot_skytem_dataset.rst.txt +++ b/docs/_sources/examples/Data/plot_skytem_dataset.rst.txt @@ -389,7 +389,7 @@ Example system files are contained in .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 2.262 seconds) + **Total running time of the script:** (0 minutes 2.633 seconds) .. _sphx_glr_download_examples_Data_plot_skytem_dataset.py: diff --git a/docs/_sources/examples/Data/plot_tempest_dataset.rst.txt b/docs/_sources/examples/Data/plot_tempest_dataset.rst.txt index 60d59278..79510de7 100644 --- a/docs/_sources/examples/Data/plot_tempest_dataset.rst.txt +++ b/docs/_sources/examples/Data/plot_tempest_dataset.rst.txt @@ -237,7 +237,7 @@ Or, plot specific channels in the data .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 3.684 seconds) + **Total running time of the script:** (0 minutes 3.941 seconds) .. _sphx_glr_download_examples_Data_plot_tempest_dataset.py: diff --git a/docs/_sources/examples/Data/sg_execution_times.rst.txt b/docs/_sources/examples/Data/sg_execution_times.rst.txt index 81e6890a..3f30fe1a 100644 --- a/docs/_sources/examples/Data/sg_execution_times.rst.txt +++ b/docs/_sources/examples/Data/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**00:12.125** total execution time for 4 files **from examples/Data**: +**00:13.703** total execution time for 4 files **from examples/Data**: .. container:: @@ -33,14 +33,14 @@ Computation times - Time - Mem (MB) * - :ref:`sphx_glr_examples_Data_plot_tempest_dataset.py` (``plot_tempest_dataset.py``) - - 00:03.684 + - 00:03.941 - 0.0 * - :ref:`sphx_glr_examples_Data_plot_pointcloud3d.py` (``plot_pointcloud3d.py``) - - 00:03.231 + - 00:03.710 - 0.0 * - :ref:`sphx_glr_examples_Data_plot_frequency_dataset.py` (``plot_frequency_dataset.py``) - - 00:02.948 + - 00:03.419 - 0.0 * - :ref:`sphx_glr_examples_Data_plot_skytem_dataset.py` (``plot_skytem_dataset.py``) - - 00:02.262 + - 00:02.633 - 0.0 diff --git a/docs/_sources/examples/Datapoints/plot_resolve_datapoint.rst.txt b/docs/_sources/examples/Datapoints/plot_resolve_datapoint.rst.txt index 4ba90e85..c90cac5e 100644 --- a/docs/_sources/examples/Datapoints/plot_resolve_datapoint.rst.txt +++ b/docs/_sources/examples/Datapoints/plot_resolve_datapoint.rst.txt @@ -320,7 +320,7 @@ Prepare the dataset so that we can read a point at a time. .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 7.847 seconds) + **Total running time of the script:** (0 minutes 7.442 seconds) .. _sphx_glr_download_examples_Datapoints_plot_resolve_datapoint.py: diff --git a/docs/_sources/examples/Datapoints/plot_skytem_datapoint.rst.txt b/docs/_sources/examples/Datapoints/plot_skytem_datapoint.rst.txt index 43e8f3b6..59eb854c 100644 --- a/docs/_sources/examples/Datapoints/plot_skytem_datapoint.rst.txt +++ b/docs/_sources/examples/Datapoints/plot_skytem_datapoint.rst.txt @@ -262,8 +262,8 @@ This allows us to evaluate the likelihood of the predicted data .. code-block:: none - -320327.7331520332 - 643134.8665683006 + -320327.7331520334 + 643134.8665683013 @@ -349,7 +349,7 @@ Compute the misfit between observed and predicted data .. code-block:: none - 19656.31514467779 + 19656.31514467768 @@ -550,7 +550,7 @@ Example data files are contained in .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 1.918 seconds) + **Total running time of the script:** (0 minutes 1.960 seconds) .. _sphx_glr_download_examples_Datapoints_plot_skytem_datapoint.py: diff --git a/docs/_sources/examples/Datapoints/plot_tempest_datapoint.rst.txt b/docs/_sources/examples/Datapoints/plot_tempest_datapoint.rst.txt index 841f30a7..bfc5edd0 100644 --- a/docs/_sources/examples/Datapoints/plot_tempest_datapoint.rst.txt +++ b/docs/_sources/examples/Datapoints/plot_tempest_datapoint.rst.txt @@ -418,7 +418,7 @@ Note we are not using the priors to accept or reject perturbations. .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 1.044 seconds) + **Total running time of the script:** (0 minutes 1.134 seconds) .. _sphx_glr_download_examples_Datapoints_plot_tempest_datapoint.py: diff --git a/docs/_sources/examples/Datapoints/sg_execution_times.rst.txt b/docs/_sources/examples/Datapoints/sg_execution_times.rst.txt index 56401233..7b1e301d 100644 --- a/docs/_sources/examples/Datapoints/sg_execution_times.rst.txt +++ b/docs/_sources/examples/Datapoints/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**00:10.809** total execution time for 3 files **from examples/Datapoints**: +**00:10.536** total execution time for 3 files **from examples/Datapoints**: .. container:: @@ -33,11 +33,11 @@ Computation times - Time - Mem (MB) * - :ref:`sphx_glr_examples_Datapoints_plot_resolve_datapoint.py` (``plot_resolve_datapoint.py``) - - 00:07.847 + - 00:07.442 - 0.0 * - :ref:`sphx_glr_examples_Datapoints_plot_skytem_datapoint.py` (``plot_skytem_datapoint.py``) - - 00:01.918 + - 00:01.960 - 0.0 * - :ref:`sphx_glr_examples_Datapoints_plot_tempest_datapoint.py` (``plot_tempest_datapoint.py``) - - 00:01.044 + - 00:01.134 - 0.0 diff --git a/docs/_sources/examples/Distributions/plot_distributions.rst.txt b/docs/_sources/examples/Distributions/plot_distributions.rst.txt index 5ec421b6..dfd43b2b 100644 --- a/docs/_sources/examples/Distributions/plot_distributions.rst.txt +++ b/docs/_sources/examples/Distributions/plot_distributions.rst.txt @@ -41,6 +41,15 @@ Handles the initialization of different statistical distribution +.. rst-class:: sphx-glr-script-out + + .. code-block:: none + + /Users/nfoks/codes/repositories/geobipy/geobipy/src/classes/mesh/RectilinearMesh1D.py:693: SyntaxWarning: invalid escape sequence '\s' + """Compute the gradient + /Users/nfoks/codes/repositories/geobipy/geobipy/src/classes/mesh/RectilinearMesh1D.py:1448: SyntaxWarning: invalid escape sequence '\l' + """Setup the priors of the mesh. + @@ -82,7 +91,7 @@ Univariate Normal Distribution .. code-block:: none - [] + [] @@ -157,7 +166,7 @@ Uniform Distribution .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 3.207 seconds) + **Total running time of the script:** (0 minutes 35.141 seconds) .. _sphx_glr_download_examples_Distributions_plot_distributions.py: diff --git a/docs/_sources/examples/Distributions/sg_execution_times.rst.txt b/docs/_sources/examples/Distributions/sg_execution_times.rst.txt index f7b8845c..4fccafa8 100644 --- a/docs/_sources/examples/Distributions/sg_execution_times.rst.txt +++ b/docs/_sources/examples/Distributions/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**00:03.207** total execution time for 1 file **from examples/Distributions**: +**00:35.141** total execution time for 1 file **from examples/Distributions**: .. container:: @@ -33,5 +33,5 @@ Computation times - Time - Mem (MB) * - :ref:`sphx_glr_examples_Distributions_plot_distributions.py` (``plot_distributions.py``) - - 00:03.207 + - 00:35.141 - 0.0 diff --git a/docs/_sources/examples/Inference_1D/plot_inference_1d_resolve.rst.txt b/docs/_sources/examples/Inference_1D/plot_inference_1d_resolve.rst.txt index 85d18a74..b97bd8ee 100644 --- a/docs/_sources/examples/Inference_1D/plot_inference_1d_resolve.rst.txt +++ b/docs/_sources/examples/Inference_1D/plot_inference_1d_resolve.rst.txt @@ -163,28 +163,28 @@ The directory where HDF files will be stored Files are being created for data files ..//..//supplementary////data//Resolve_glacial.csv and system files ..//..//supplementary////data//..//data/FdemSystem2.stm Created hdf5 file for line 0.0 with 79 data points Created hdf5 files 79 total data points - Created hdf5 files in 0:00:00.099114 h:m:s - i=500, k=2, acc=*46.800, 0.005 s/Model, 2.727 s Elapsed, eta=--:--:-- h:m:s + Created hdf5 files in 0:00:00.099843 h:m:s + i=500, k=1, acc=*57.000, 0.005 s/Model, 2.320 s Elapsed, eta=--:--:-- h:m:s - i=1000, k=3, acc=*57.400, 0.006 s/Model, 5.934 s Elapsed, eta=--:--:-- h:m:s + i=1000, k=3, acc=*46.400, 0.006 s/Model, 5.429 s Elapsed, eta=--:--:-- h:m:s - i=1500, k=3, acc=*18.600, 0.008 s/Model, 9.752 s Elapsed, eta=--:--:-- h:m:s + i=1500, k=2, acc=*57.200, 0.006 s/Model, 8.442 s Elapsed, eta=--:--:-- h:m:s - i=2000, k=2, acc=*9.200, 0.007 s/Model, 13.477 s Elapsed, eta=--:--:-- h:m:s + i=2000, k=3, acc=*21.400, 0.007 s/Model, 11.734 s Elapsed, eta=--:--:-- h:m:s - i=2500, k=3, acc=*10.200, 0.008 s/Model, 17.422 s Elapsed, eta=--:--:-- h:m:s + i=2500, k=2, acc=*13.200, 0.008 s/Model, 15.529 s Elapsed, eta=--:--:-- h:m:s - i=3000, k=4, acc=*12.200, 0.007 s/Model, 21.055 s Elapsed, eta=--:--:-- h:m:s + i=3000, k=3, acc=*13.600, 0.008 s/Model, 19.454 s Elapsed, eta=--:--:-- h:m:s - i=3500, k=3, acc=*12.800, 0.008 s/Model, 24.952 s Elapsed, eta=--:--:-- h:m:s + i=3500, k=2, acc=*12.800, 0.008 s/Model, 23.455 s Elapsed, eta=--:--:-- h:m:s - i=4000, k=3, acc=*17.600, 0.008 s/Model, 28.722 s Elapsed, eta=--:--:-- h:m:s + i=4000, k=4, acc=*13.600, 0.007 s/Model, 26.993 s Elapsed, eta=--:--:-- h:m:s - i=4500, k=3, acc=*13.400, 0.007 s/Model, 32.463 s Elapsed, eta=--:--:-- h:m:s + i=4500, k=3, acc=*11.800, 0.008 s/Model, 30.783 s Elapsed, eta=--:--:-- h:m:s - i=5000, k=3, acc=*15.600, 0.008 s/Model, 36.314 s Elapsed, eta=--:--:-- h:m:s + i=5000, k=3, acc=*10.600, 0.008 s/Model, 34.653 s Elapsed, eta=--:--:-- h:m:s - Remaining Points -30/1 || Elapsed Time: 0:00:37.097808 h:m:s || ETA 0:00:01.196703 h:m:s + Remaining Points -30/1 || Elapsed Time: 0:00:35.770894 h:m:s || ETA 0:00:01.153900 h:m:s @@ -192,7 +192,7 @@ The directory where HDF files will be stored .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 37.529 seconds) + **Total running time of the script:** (0 minutes 36.274 seconds) .. _sphx_glr_download_examples_Inference_1D_plot_inference_1d_resolve.py: diff --git a/docs/_sources/examples/Inference_1D/plot_inference_1d_skytem.rst.txt b/docs/_sources/examples/Inference_1D/plot_inference_1d_skytem.rst.txt index 00a06810..b6a55307 100644 --- a/docs/_sources/examples/Inference_1D/plot_inference_1d_skytem.rst.txt +++ b/docs/_sources/examples/Inference_1D/plot_inference_1d_skytem.rst.txt @@ -163,10 +163,10 @@ The directory where HDF files will be stored Files are being created for data files ..//..//supplementary////data//Skytem_glacial.csv and system files ['..//..//supplementary////data//..//data//SkytemHM.stm', '..//..//supplementary////data//..//data//SkytemLM.stm'] Created hdf5 file for line 0.0 with 79 data points Created hdf5 files 79 total data points - Created hdf5 files in 0:00:00.182385 h:m:s - i=5000, k=4, acc=*29.700, 0.010 s/Model, 49.131 s Elapsed, eta=--:--:-- h:m:s + Created hdf5 files in 0:00:00.201672 h:m:s + i=5000, k=6, acc=*23.360, 0.011 s/Model, 56.638 s Elapsed, eta=--:--:-- h:m:s - Remaining Points -2/1 || Elapsed Time: 0:00:50.176460 h:m:s || ETA 0:00:16.725487 h:m:s + Remaining Points -2/1 || Elapsed Time: 0:00:57.771511 h:m:s || ETA 0:00:19.257170 h:m:s @@ -174,7 +174,7 @@ The directory where HDF files will be stored .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 50.833 seconds) + **Total running time of the script:** (0 minutes 58.417 seconds) .. _sphx_glr_download_examples_Inference_1D_plot_inference_1d_skytem.py: diff --git a/docs/_sources/examples/Inference_1D/plot_inference_1d_tempest.rst.txt b/docs/_sources/examples/Inference_1D/plot_inference_1d_tempest.rst.txt index be0c7427..573eb0f7 100644 --- a/docs/_sources/examples/Inference_1D/plot_inference_1d_tempest.rst.txt +++ b/docs/_sources/examples/Inference_1D/plot_inference_1d_tempest.rst.txt @@ -165,10 +165,10 @@ The directory where HDF files will be stored Files are being created for data files ..//..//supplementary////data//Tempest_glacial.csv and system files ..//..//supplementary////data//..//data/tempest.stm Created hdf5 file for line 0.0 with 79 data points Created hdf5 files 79 total data points - Created hdf5 files in 0:00:00.270921 h:m:s - i=5000, k=5, acc=*21.720, 0.013 s/Model, 66.800 s Elapsed, eta=--:--:-- h:m:s + Created hdf5 files in 0:00:00.408380 h:m:s + i=5000, k=5, acc=*15.680, 0.016 s/Model, 79.402 s Elapsed, eta=--:--:-- h:m:s - Remaining Points -2/1 || Elapsed Time: 0:01:07.758676 h:m:s || ETA 0:00:22.586225 h:m:s + Remaining Points -2/1 || Elapsed Time: 0:01:20.780798 h:m:s || ETA 0:00:26.926933 h:m:s @@ -176,7 +176,7 @@ The directory where HDF files will be stored .. rst-class:: sphx-glr-timing - **Total running time of the script:** (1 minutes 8.394 seconds) + **Total running time of the script:** (1 minutes 21.625 seconds) .. _sphx_glr_download_examples_Inference_1D_plot_inference_1d_tempest.py: diff --git a/docs/_sources/examples/Inference_1D/sg_execution_times.rst.txt b/docs/_sources/examples/Inference_1D/sg_execution_times.rst.txt index a90f09d4..cfde444b 100644 --- a/docs/_sources/examples/Inference_1D/sg_execution_times.rst.txt +++ b/docs/_sources/examples/Inference_1D/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**02:36.756** total execution time for 3 files **from examples/Inference_1D**: +**02:56.316** total execution time for 3 files **from examples/Inference_1D**: .. container:: @@ -33,11 +33,11 @@ Computation times - Time - Mem (MB) * - :ref:`sphx_glr_examples_Inference_1D_plot_inference_1d_tempest.py` (``plot_inference_1d_tempest.py``) - - 01:08.394 + - 01:21.625 - 0.0 * - :ref:`sphx_glr_examples_Inference_1D_plot_inference_1d_skytem.py` (``plot_inference_1d_skytem.py``) - - 00:50.833 + - 00:58.417 - 0.0 * - :ref:`sphx_glr_examples_Inference_1D_plot_inference_1d_resolve.py` (``plot_inference_1d_resolve.py``) - - 00:37.529 + - 00:36.274 - 0.0 diff --git a/docs/_sources/examples/Inference_2D/plot_inference_2d_resolve.rst.txt b/docs/_sources/examples/Inference_2D/plot_inference_2d_resolve.rst.txt index 0b717e40..eabeb538 100644 --- a/docs/_sources/examples/Inference_2D/plot_inference_2d_resolve.rst.txt +++ b/docs/_sources/examples/Inference_2D/plot_inference_2d_resolve.rst.txt @@ -23,7 +23,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class -.. GENERATED FROM PYTHON SOURCE LINES 8-151 +.. GENERATED FROM PYTHON SOURCE LINES 8-153 @@ -73,41 +73,8 @@ All plotting in GeoBIPy can be carried out using the 3D inference class :class: sphx-glr-multi-img -.. rst-class:: sphx-glr-script-out - .. code-block:: none - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) - - - - - - -| .. code-block:: Python @@ -144,6 +111,9 @@ All plotting in GeoBIPy can be carried out using the 3D inference class "cmap" : 'jet' } + import warnings + warnings.filterwarnings('error') + fig = plt.figure(figsize=(16, 8)) plt.suptitle("{} {}".format(data_type, model_type)) gs0 = fig.add_gridspec(6, 2, hspace=1.0) @@ -240,25 +210,24 @@ All plotting in GeoBIPy can be carried out using the 3D inference class results_2d.plot_data_elevation(linewidth=0.3, ax=ax1); results_2d.plot_elevation(linewidth=0.3, ax=ax1); - - plt.show() - # plt.savefig('{}_{}.png'.format(data_type, model_type), dpi=300) + # plt.show() + plt.savefig('{}_{}.png'.format(data_type, model_type), dpi=300) if __name__ == '__main__': models = ['glacial', 'saline_clay', 'resistive_dolomites', 'resistive_basement', 'coastal_salt_water', 'ice_over_salt_water'] for model in models: - try: + # try: plot_2d_summary("../../../Parallel_Inference/", "resolve", model) - except Exception as e: - print(model) - print(e) - pass + # except Exception as e: + # print(model) + # print(e) + # pass .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 26.429 seconds) + **Total running time of the script:** (0 minutes 49.364 seconds) .. _sphx_glr_download_examples_Inference_2D_plot_inference_2d_resolve.py: diff --git a/docs/_sources/examples/Inference_2D/plot_inference_2d_skytem.rst.txt b/docs/_sources/examples/Inference_2D/plot_inference_2d_skytem.rst.txt index bbd6d0e6..58b16df9 100644 --- a/docs/_sources/examples/Inference_2D/plot_inference_2d_skytem.rst.txt +++ b/docs/_sources/examples/Inference_2D/plot_inference_2d_skytem.rst.txt @@ -86,7 +86,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | Number of Cells: | | 79 | Cell Centres: - | | Name: Easting (m) 0x174c38ad0 + | | Name: Easting (m) 0x16d1776d0 | | Shape: (79,) | | Values: [ 0. 1. 2. ... 76. 77. 78.] | | Min: 0.0 @@ -94,7 +94,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | | has_posterior: False | | Cell Edges: - | | Name: Easting (m) 0x174c3a150 + | | Name: Easting (m) 0x16d174650 | | Shape: (80,) | | Values: [-0.5 0.5 1.5 ... 76.5 77.5 78.5] | | Min: -0.5 @@ -104,7 +104,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | log: | | None | relativeTo: - | | Name: 0x174763e50 + | | Name: 0x16d336350 | | Shape: (1,) | | Values: [0.] | | Min: 0.0 @@ -116,25 +116,25 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | Number of Cells: | | 132 | Cell Centres: - | | Name: elevation (m) 0x17c642950 + | | Name: elevation (m) 0x16d1774d0 | | Shape: (132,) - | | Values: [ -3.1875 -7.7625 -12.3375 ... -593.3625 -597.9375 -602.5125] - | | Min: -602.5125 - | | Max: -3.1875 + | | Values: [ -2.2875 -6.8625 -11.4375 ... -592.4625 -597.0375 -601.6125] + | | Min: -601.6125 + | | Max: -2.2875 | | has_posterior: False | | Cell Edges: - | | Name: elevation (m) 0x174db9bd0 + | | Name: elevation (m) 0x16d176850 | | Shape: (133,) - | | Values: [ -0.9 -5.475 -10.05 ... -595.65 -600.225 -604.8 ] - | | Min: -604.8 - | | Max: -0.9 + | | Values: [ 0. -4.575 -9.15 ... -594.75 -599.325 -603.9 ] + | | Min: -603.9 + | | Max: 0.0 | | has_posterior: False | | log: | | None | relativeTo: - | | Name: Elevation (m) 0x174760fd0 + | | Name: Elevation (m) 0x16d176bd0 | | Shape: (79,) | | Values: [0. 0. 0. ... 0. 0. 0.] | | Min: 0.0 @@ -142,28 +142,20 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | | has_posterior: False | values: - | Name: Mean Conductivity ($\frac{S}{m}$) 0x174c3a7d0 + | Name: Mean Conductivity ($\frac{S}{m}$) 0x16d176ad0 | Shape: (79, 132) - | Values: [[0.01052122 0.01052122 0.01016692 ... 0.01850636 0.01850636 0.01850636] - | [0.01021697 0.01021697 0.01015663 ... 0.01602748 0.01602748 0.01602748] - | [0.01011127 0.01011127 0.00988057 ... 0.01737969 0.01737969 0.01737969] + | Values: [[0.01033856 0.01033856 0.01032608 ... 0.01558398 0.01558398 0.01558398] + | [0.01000897 0.01000897 0.00993591 ... 0.01545486 0.01545486 0.01545486] + | [0.00955219 0.00955219 0.0095664 ... 0.01290829 0.01290829 0.01290829] | ... - | [0.06832709 0.06832709 0.09870112 ... 0.09669862 0.09669862 0.09669862] - | [0.08105957 0.08105957 0.09663905 ... 0.0909106 0.0909106 0.0909106 ] - | [0.09148174 0.09148174 0.10054793 ... 0.11236812 0.11236812 0.11236812]] - | Min: 0.006980451543462376 - | Max: 0.2038321789145052 + | [0.06767155 0.06767155 0.08087337 ... 0.09781396 0.09781396 0.09781396] + | [0.08127294 0.08127294 0.09146854 ... 0.09884747 0.09884747 0.09884747] + | [0.09182078 0.09182078 0.09720053 ... 0.09911276 0.09911276 0.09911276]] + | Min: 0.008142645729506102 + | Max: 0.18736281207027317 | has_posterior: False - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) Model: mesh: | RectilinearMesh2D: @@ -173,7 +165,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | Number of Cells: | | 79 | Cell Centres: - | | Name: Easting (m) 0x174c809d0 + | | Name: Easting (m) 0x16ba249d0 | | Shape: (79,) | | Values: [ 0. 1. 2. ... 76. 77. 78.] | | Min: 0.0 @@ -181,7 +173,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | | has_posterior: False | | Cell Edges: - | | Name: Easting (m) 0x174c82ed0 + | | Name: Easting (m) 0x16ba24ed0 | | Shape: (80,) | | Values: [-0.5 0.5 1.5 ... 76.5 77.5 78.5] | | Min: -0.5 @@ -191,7 +183,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | log: | | None | relativeTo: - | | Name: 0x174216550 + | | Name: 0x16a2943d0 | | Shape: (1,) | | Values: [0.] | | Min: 0.0 @@ -203,25 +195,25 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | Number of Cells: | | 132 | Cell Centres: - | | Name: elevation (m) 0x174c803d0 + | | Name: elevation (m) 0x16ba272d0 | | Shape: (132,) - | | Values: [ -3.1875 -7.7625 -12.3375 ... -593.3625 -597.9375 -602.5125] - | | Min: -602.5125 - | | Max: -3.1875 + | | Values: [ -2.2875 -6.8625 -11.4375 ... -592.4625 -597.0375 -601.6125] + | | Min: -601.6125 + | | Max: -2.2875 | | has_posterior: False | | Cell Edges: - | | Name: elevation (m) 0x174c82550 + | | Name: elevation (m) 0x16ba274d0 | | Shape: (133,) - | | Values: [ -0.9 -5.475 -10.05 ... -595.65 -600.225 -604.8 ] - | | Min: -604.8 - | | Max: -0.9 + | | Values: [ 0. -4.575 -9.15 ... -594.75 -599.325 -603.9 ] + | | Min: -603.9 + | | Max: 0.0 | | has_posterior: False | | log: | | None | relativeTo: - | | Name: Elevation (m) 0x174c829d0 + | | Name: Elevation (m) 0x16ba27350 | | Shape: (79,) | | Values: [0. 0. 0. ... 0. 0. 0.] | | Min: 0.0 @@ -229,24 +221,20 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | | has_posterior: False | values: - | Name: Mean Conductivity ($\frac{S}{m}$) 0x174d53e50 + | Name: Mean Conductivity ($\frac{S}{m}$) 0x16ba27650 | Shape: (79, 132) - | Values: [[0.01033463 0.01033463 0.01022367 ... 0.01134772 0.01134772 0.01134772] - | [0.01093141 0.01093141 0.01079545 ... 0.01121704 0.01121704 0.01121704] - | [0.0102224 0.0102224 0.00899369 ... 0.01413742 0.01413742 0.01413742] + | Values: [[0.01004342 0.01004342 0.01004776 ... 0.01059402 0.01059402 0.01059402] + | [0.01216306 0.01216306 0.01200007 ... 0.01053094 0.01053094 0.01053094] + | [0.0096322 0.0096322 0.00961509 ... 0.01266093 0.01266093 0.01266093] | ... - | [0.06788858 0.06788858 0.10332184 ... 0.07437715 0.07437715 0.07437715] - | [0.08031206 0.08031206 0.09714714 ... 0.07756677 0.07756677 0.07756677] - | [0.09189958 0.09189958 0.09936831 ... 0.10561892 0.10561892 0.10561892]] - | Min: 0.007064692235206785 - | Max: 0.7521657625958085 + | [0.06790468 0.06790468 0.08216413 ... 0.09468115 0.09468115 0.09468115] + | [0.08066093 0.08066093 0.09027033 ... 0.09565939 0.09565939 0.09565939] + | [0.0918785 0.0918785 0.09698753 ... 0.10118202 0.10118202 0.10118202]] + | Min: 0.005722230815170164 + | Max: 0.7350287210217844 | has_posterior: False - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) Model: mesh: | RectilinearMesh2D: @@ -256,7 +244,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | Number of Cells: | | 79 | Cell Centres: - | | Name: Easting (m) 0x174a72cd0 + | | Name: Easting (m) 0x16b9002d0 | | Shape: (79,) | | Values: [ 0. 1. 2. ... 76. 77. 78.] | | Min: 0.0 @@ -264,7 +252,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | | has_posterior: False | | Cell Edges: - | | Name: Easting (m) 0x17be64150 + | | Name: Easting (m) 0x16b9ab550 | | Shape: (80,) | | Values: [-0.5 0.5 1.5 ... 76.5 77.5 78.5] | | Min: -0.5 @@ -274,7 +262,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | log: | | None | relativeTo: - | | Name: 0x174685f50 + | | Name: 0x169562550 | | Shape: (1,) | | Values: [0.] | | Min: 0.0 @@ -286,25 +274,25 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | Number of Cells: | | 132 | Cell Centres: - | | Name: elevation (m) 0x17be64450 + | | Name: elevation (m) 0x16b9a9250 | | Shape: (132,) - | | Values: [ -3.1875 -7.7625 -12.3375 ... -593.3625 -597.9375 -602.5125] - | | Min: -602.5125 - | | Max: -3.1875 + | | Values: [ -2.2875 -6.8625 -11.4375 ... -592.4625 -597.0375 -601.6125] + | | Min: -601.6125 + | | Max: -2.2875 | | has_posterior: False | | Cell Edges: - | | Name: elevation (m) 0x17be645d0 + | | Name: elevation (m) 0x16b9ab350 | | Shape: (133,) - | | Values: [ -0.9 -5.475 -10.05 ... -595.65 -600.225 -604.8 ] - | | Min: -604.8 - | | Max: -0.9 + | | Values: [ 0. -4.575 -9.15 ... -594.75 -599.325 -603.9 ] + | | Min: -603.9 + | | Max: 0.0 | | has_posterior: False | | log: | | None | relativeTo: - | | Name: Elevation (m) 0x17be64550 + | | Name: Elevation (m) 0x16b9ab250 | | Shape: (79,) | | Values: [0. 0. 0. ... 0. 0. 0.] | | Min: 0.0 @@ -312,24 +300,20 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | | has_posterior: False | values: - | Name: Mean Conductivity ($\frac{S}{m}$) 0x174a73c50 + | Name: Mean Conductivity ($\frac{S}{m}$) 0x16b900dd0 | Shape: (79, 132) - | Values: [[0.02112514 0.02112514 0.02118673 ... 0.01963369 0.01963369 0.01963369] - | [0.02012794 0.02012794 0.02015706 ... 0.02045956 0.02045956 0.02045956] - | [0.01982581 0.01982581 0.01989992 ... 0.01430375 0.01430375 0.01430375] + | Values: [[0.02108286 0.02108286 0.02105478 ... 0.01970014 0.01970014 0.01970014] + | [0.02020133 0.02020133 0.02021404 ... 0.01697529 0.01697529 0.01697529] + | [0.01980096 0.01980096 0.01984157 ... 0.01531969 0.01531969 0.01531969] | ... - | [0.00482815 0.00482815 0.00482815 ... 0.01235529 0.01235529 0.01235529] - | [0.00347338 0.00347338 0.00347337 ... 0.00904771 0.00904771 0.00904771] - | [0.00280732 0.00280732 0.00278377 ... 0.01122587 0.01122587 0.01122587]] - | Min: 0.000917330743874903 - | Max: 6.893577245253312 + | [0.00553428 0.00553428 0.00546494 ... 0.0027545 0.0027545 0.0027545 ] + | [0.00378312 0.00378312 0.00377909 ... 0.00262642 0.00262642 0.00262642] + | [0.00296382 0.00296382 0.0029272 ... 0.00213216 0.00213216 0.00213216]] + | Min: 0.0008988345212684541 + | Max: 0.0391244257801508 | has_posterior: False - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) Model: mesh: | RectilinearMesh2D: @@ -339,7 +323,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | Number of Cells: | | 79 | Cell Centres: - | | Name: Easting (m) 0x1752740d0 + | | Name: Easting (m) 0x16d979bd0 | | Shape: (79,) | | Values: [ 0. 1. 2. ... 76. 77. 78.] | | Min: 0.0 @@ -347,7 +331,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | | has_posterior: False | | Cell Edges: - | | Name: Easting (m) 0x174cbc6d0 + | | Name: Easting (m) 0x16d979850 | | Shape: (80,) | | Values: [-0.5 0.5 1.5 ... 76.5 77.5 78.5] | | Min: -0.5 @@ -357,7 +341,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | log: | | None | relativeTo: - | | Name: 0x1752135d0 + | | Name: 0x16b7868d0 | | Shape: (1,) | | Values: [0.] | | Min: 0.0 @@ -369,25 +353,25 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | Number of Cells: | | 132 | Cell Centres: - | | Name: elevation (m) 0x174cbead0 + | | Name: elevation (m) 0x16d979a50 | | Shape: (132,) - | | Values: [ -3.1875 -7.7625 -12.3375 ... -593.3625 -597.9375 -602.5125] - | | Min: -602.5125 - | | Max: -3.1875 + | | Values: [ -2.2875 -6.8625 -11.4375 ... -592.4625 -597.0375 -601.6125] + | | Min: -601.6125 + | | Max: -2.2875 | | has_posterior: False | | Cell Edges: - | | Name: elevation (m) 0x174cbd6d0 + | | Name: elevation (m) 0x16d97a0d0 | | Shape: (133,) - | | Values: [ -0.9 -5.475 -10.05 ... -595.65 -600.225 -604.8 ] - | | Min: -604.8 - | | Max: -0.9 + | | Values: [ 0. -4.575 -9.15 ... -594.75 -599.325 -603.9 ] + | | Min: -603.9 + | | Max: 0.0 | | has_posterior: False | | log: | | None | relativeTo: - | | Name: Elevation (m) 0x174cbe5d0 + | | Name: Elevation (m) 0x16d979f50 | | Shape: (79,) | | Values: [0. 0. 0. ... 0. 0. 0.] | | Min: 0.0 @@ -395,24 +379,20 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | | has_posterior: False | values: - | Name: Mean Conductivity ($\frac{S}{m}$) 0x175277ad0 + | Name: Mean Conductivity ($\frac{S}{m}$) 0x16d953cd0 | Shape: (79, 132) - | Values: [[0.01171106 0.01171106 0.01150474 ... 0.0209344 0.0209344 0.0209344 ] - | [0.00998759 0.00998759 0.01002506 ... 0.00200545 0.00200545 0.00200545] - | [0.00967387 0.00967387 0.00963086 ... 0.002998 0.002998 0.002998 ] + | Values: [[0.01104549 0.01104549 0.01088691 ... 0.01524806 0.01524806 0.01524806] + | [0.01093171 0.01093171 0.01060605 ... 0.01539332 0.01539332 0.01539332] + | [0.01055781 0.01055781 0.01051885 ... 0.01532385 0.01532385 0.01532385] | ... - | [0.06916639 0.06916639 0.07805965 ... 0.09969281 0.09969281 0.09969281] - | [0.08151576 0.08151576 0.09357014 ... 0.09817375 0.09817375 0.09817375] - | [0.09210769 0.09210769 0.09923809 ... 0.11325164 0.11325164 0.11325164]] - | Min: 0.001399862547383794 - | Max: 0.23489486426293366 + | [0.06858216 0.06858216 0.07381497 ... 0.09939759 0.09939759 0.09939759] + | [0.0811231 0.0811231 0.09235 ... 0.09950496 0.09950496 0.09950496] + | [0.09142048 0.09142048 0.09655967 ... 0.09905984 0.09905984 0.09905984]] + | Min: 0.00249077338478267 + | Max: 0.21372916933340144 | has_posterior: False - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) Model: mesh: | RectilinearMesh2D: @@ -422,7 +402,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | Number of Cells: | | 79 | Cell Centres: - | | Name: Easting (m) 0x17a89efd0 + | | Name: Easting (m) 0x16d5f7650 | | Shape: (79,) | | Values: [ 0. 1. 2. ... 76. 77. 78.] | | Min: 0.0 @@ -430,7 +410,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | | has_posterior: False | | Cell Edges: - | | Name: Easting (m) 0x1750123d0 + | | Name: Easting (m) 0x16d950150 | | Shape: (80,) | | Values: [-0.5 0.5 1.5 ... 76.5 77.5 78.5] | | Min: -0.5 @@ -440,7 +420,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | log: | | None | relativeTo: - | | Name: 0x17b8cf5d0 + | | Name: 0x1695aa3d0 | | Shape: (1,) | | Values: [0.] | | Min: 0.0 @@ -452,25 +432,25 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | Number of Cells: | | 132 | Cell Centres: - | | Name: elevation (m) 0x175013bd0 + | | Name: elevation (m) 0x16d951550 | | Shape: (132,) - | | Values: [ -3.1875 -7.7625 -12.3375 ... -593.3625 -597.9375 -602.5125] - | | Min: -602.5125 - | | Max: -3.1875 + | | Values: [ -2.2875 -6.8625 -11.4375 ... -592.4625 -597.0375 -601.6125] + | | Min: -601.6125 + | | Max: -2.2875 | | has_posterior: False | | Cell Edges: - | | Name: elevation (m) 0x1750127d0 + | | Name: elevation (m) 0x16d951f50 | | Shape: (133,) - | | Values: [ -0.9 -5.475 -10.05 ... -595.65 -600.225 -604.8 ] - | | Min: -604.8 - | | Max: -0.9 + | | Values: [ 0. -4.575 -9.15 ... -594.75 -599.325 -603.9 ] + | | Min: -603.9 + | | Max: 0.0 | | has_posterior: False | | log: | | None | relativeTo: - | | Name: Elevation (m) 0x175010050 + | | Name: Elevation (m) 0x16d9506d0 | | Shape: (79,) | | Values: [0. 0. 0. ... 0. 0. 0.] | | Min: 0.0 @@ -478,24 +458,20 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | | has_posterior: False | values: - | Name: Mean Conductivity ($\frac{S}{m}$) 0x174cbc350 + | Name: Mean Conductivity ($\frac{S}{m}$) 0x16d5f70d0 | Shape: (79, 132) - | Values: [[1.02274906 1.02274906 1.0245564 ... 1.09249798 1.09249798 1.09249798] - | [1.02246109 1.02246109 1.02490237 ... 0.79417678 0.79417678 0.79417678] - | [1.02655439 1.02655439 1.02684903 ... 1.16477248 1.16477248 1.16477248] + | Values: [[1.02245403 1.02245403 1.02307401 ... 0.92933622 0.92933622 0.92933622] + | [1.02230576 1.02230576 1.02472151 ... 0.7725808 0.7725808 0.7725808 ] + | [1.02240853 1.02240853 1.02261644 ... 0.92778441 0.92778441 0.92778441] | ... - | [0.18075689 0.18075689 0.18075689 ... 0.04261216 0.04261216 0.04261216] - | [0.14798426 0.14798426 0.14798426 ... 0.03894156 0.03894156 0.03894156] - | [0.08446099 0.08446099 0.08446099 ... 0.03091314 0.03091314 0.03091314]] - | Min: 0.004061097299450205 - | Max: 37.321525320580754 + | [0.17953964 0.17953964 0.17953964 ... 0.04600592 0.04600592 0.04600592] + | [0.14131043 0.14131043 0.14131043 ... 0.03121664 0.03121664 0.03121664] + | [0.0826337 0.0826337 0.0826337 ... 0.02682797 0.02682797 0.02682797]] + | Min: 0.005438953651048253 + | Max: 4.1999468303264145 | has_posterior: False - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) Model: mesh: | RectilinearMesh2D: @@ -505,7 +481,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | Number of Cells: | | 79 | Cell Centres: - | | Name: Easting (m) 0x179ed4ad0 + | | Name: Easting (m) 0x16cd233d0 | | Shape: (79,) | | Values: [ 0. 1. 2. ... 76. 77. 78.] | | Min: 0.0 @@ -513,7 +489,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | | has_posterior: False | | Cell Edges: - | | Name: Easting (m) 0x179ed4450 + | | Name: Easting (m) 0x16d470350 | | Shape: (80,) | | Values: [-0.5 0.5 1.5 ... 76.5 77.5 78.5] | | Min: -0.5 @@ -523,7 +499,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | log: | | None | relativeTo: - | | Name: 0x17abcd5d0 + | | Name: 0x16b9015d0 | | Shape: (1,) | | Values: [0.] | | Min: 0.0 @@ -535,25 +511,25 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | Number of Cells: | | 132 | Cell Centres: - | | Name: elevation (m) 0x179ed4050 + | | Name: elevation (m) 0x16d470050 | | Shape: (132,) - | | Values: [ -3.1875 -7.7625 -12.3375 ... -593.3625 -597.9375 -602.5125] - | | Min: -602.5125 - | | Max: -3.1875 + | | Values: [ -2.2875 -6.8625 -11.4375 ... -592.4625 -597.0375 -601.6125] + | | Min: -601.6125 + | | Max: -2.2875 | | has_posterior: False | | Cell Edges: - | | Name: elevation (m) 0x179ed4d50 + | | Name: elevation (m) 0x16d470c50 | | Shape: (133,) - | | Values: [ -0.9 -5.475 -10.05 ... -595.65 -600.225 -604.8 ] - | | Min: -604.8 - | | Max: -0.9 + | | Values: [ 0. -4.575 -9.15 ... -594.75 -599.325 -603.9 ] + | | Min: -603.9 + | | Max: 0.0 | | has_posterior: False | | log: | | None | relativeTo: - | | Name: Elevation (m) 0x179ed4bd0 + | | Name: Elevation (m) 0x16d4708d0 | | Shape: (79,) | | Values: [0. 0. 0. ... 0. 0. 0.] | | Min: 0.0 @@ -561,24 +537,20 @@ All plotting in GeoBIPy can be carried out using the 3D inference class | | has_posterior: False | values: - | Name: Mean Conductivity ($\frac{S}{m}$) 0x179bd7ed0 + | Name: Mean Conductivity ($\frac{S}{m}$) 0x16cd22e50 | Shape: (79, 132) - | Values: [[0.00050436 0.00050436 0.00050445 ... 0.00059394 0.00059394 0.00059394] - | [0.00020876 0.00020876 0.00020876 ... 0.00077604 0.00077604 0.00077604] - | [0.00075824 0.00075824 0.00075833 ... 0.00102201 0.00102201 0.00102201] + | Values: [[0.00045657 0.00045657 0.0004565 ... 0.00054201 0.00054201 0.00054201] + | [0.0004992 0.0004992 0.00049929 ... 0.0006536 0.0006536 0.0006536 ] + | [0.00061429 0.00061429 0.00061429 ... 0.00094599 0.00094599 0.00094599] | ... - | [0.00853636 0.00853636 0.00853721 ... 0.00245846 0.00245846 0.00245846] - | [0.00904365 0.00904365 0.0090973 ... 0.00309043 0.00309043 0.00309043] - | [0.00937106 0.00937106 0.00953559 ... 0.0040001 0.0040001 0.0040001 ]] - | Min: 0.0002087568574496072 - | Max: 4.3269122357161915 + | [0.00828275 0.00828275 0.00829302 ... 0.00850303 0.00850303 0.00850303] + | [0.00901768 0.00901768 0.00902754 ... 0.00835599 0.00835599 0.00835599] + | [0.00925272 0.00925272 0.00930022 ... 0.00957266 0.00957266 0.00957266]] + | Min: 0.00039894971238615474 + | Max: 1.1039260435132408 | has_posterior: False - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) @@ -737,7 +709,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 23.702 seconds) + **Total running time of the script:** (0 minutes 32.201 seconds) .. _sphx_glr_download_examples_Inference_2D_plot_inference_2d_skytem.py: diff --git a/docs/_sources/examples/Inference_2D/plot_inference_2d_tempest.rst.txt b/docs/_sources/examples/Inference_2D/plot_inference_2d_tempest.rst.txt index 108b6074..58f0897c 100644 --- a/docs/_sources/examples/Inference_2D/plot_inference_2d_tempest.rst.txt +++ b/docs/_sources/examples/Inference_2D/plot_inference_2d_tempest.rst.txt @@ -73,45 +73,8 @@ All plotting in GeoBIPy can be carried out using the 3D inference class :class: sphx-glr-multi-img -.. rst-class:: sphx-glr-script-out - - .. code-block:: none - - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:2039: RuntimeWarning: invalid value encountered in scalar add - self._mtx[1, 2] += ty - /usr/local/Caskroom/mambaforge/base/envs/geobipy/lib/python3.12/site-packages/matplotlib/transforms.py:372: RuntimeWarning: invalid value encountered in scalar subtract - return (x0, y0, x1 - x0, y1 - y0) - - - - - - -| + + .. code-block:: Python @@ -264,7 +227,7 @@ All plotting in GeoBIPy can be carried out using the 3D inference class .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 23.279 seconds) + **Total running time of the script:** (0 minutes 33.754 seconds) .. _sphx_glr_download_examples_Inference_2D_plot_inference_2d_tempest.py: diff --git a/docs/_sources/examples/Inference_2D/sg_execution_times.rst.txt b/docs/_sources/examples/Inference_2D/sg_execution_times.rst.txt index 8873bd50..cf1fd683 100644 --- a/docs/_sources/examples/Inference_2D/sg_execution_times.rst.txt +++ b/docs/_sources/examples/Inference_2D/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**01:13.411** total execution time for 3 files **from examples/Inference_2D**: +**01:55.319** total execution time for 4 files **from examples/Inference_2D**: .. container:: @@ -33,11 +33,14 @@ Computation times - Time - Mem (MB) * - :ref:`sphx_glr_examples_Inference_2D_plot_inference_2d_resolve.py` (``plot_inference_2d_resolve.py``) - - 00:26.429 + - 00:49.364 + - 0.0 + * - :ref:`sphx_glr_examples_Inference_2D_plot_inference_2d_tempest.py` (``plot_inference_2d_tempest.py``) + - 00:33.754 - 0.0 * - :ref:`sphx_glr_examples_Inference_2D_plot_inference_2d_skytem.py` (``plot_inference_2d_skytem.py``) - - 00:23.702 + - 00:32.201 - 0.0 - * - :ref:`sphx_glr_examples_Inference_2D_plot_inference_2d_tempest.py` (``plot_inference_2d_tempest.py``) - - 00:23.279 + * - :ref:`sphx_glr_examples_Inference_2D_test.py` (``test.py``) + - 00:00.000 - 0.0 diff --git a/docs/_sources/examples/Inference_2D/test.rst.txt b/docs/_sources/examples/Inference_2D/test.rst.txt new file mode 100644 index 00000000..48663021 --- /dev/null +++ b/docs/_sources/examples/Inference_2D/test.rst.txt @@ -0,0 +1,119 @@ + +.. DO NOT EDIT. +.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. +.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: +.. "examples/Inference_2D/test.py" +.. LINE NUMBERS ARE GIVEN BELOW. + +.. only:: html + + .. note:: + :class: sphx-glr-download-link-note + + :ref:`Go to the end ` + to download the full example code. + +.. rst-class:: sphx-glr-example-title + +.. _sphx_glr_examples_Inference_2D_test.py: + + +2D Posterior analysis of Resolve inference +------------------------------------------ + +All plotting in GeoBIPy can be carried out using the 3D inference class + +.. GENERATED FROM PYTHON SOURCE LINES 8-76 + +.. code-block:: Python + + + import matplotlib.pyplot as plt + import numpy as np + from geobipy import Model + from geobipy import Inference2D + + def plot_2d_summary(folder, data_type, model_type): + #%% + # Inference for a line of inferences + # ++++++++++++++++++++++++++++++++++ + # + # We can instantiate the inference handler by providing a path to the directory containing + # HDF5 files generated by GeoBIPy. + # + # The InfereceXD classes are low memory. They only read information from the HDF5 files + # as and when it is needed. + # + # The first time you use these classes to create plots, expect longer initial processing times. + # I precompute expensive properties and store them in the HDF5 files for later use. + + from numpy.random import Generator + from numpy.random import PCG64DXSM + generator = PCG64DXSM(seed=0) + prng = Generator(generator) + + #%% + results_2d = Inference2D.fromHdf('{}/{}/{}/0.0.h5'.format(folder, data_type, model_type), prng=prng) + + kwargs = { + "log" : 10, + "cmap" : 'jet' + } + + true_model = Model.create_synthetic_model(model_type) + true_model.mesh.y_edges = true_model.mesh.y_edges / 10.0 + + kwargs['vmin'] = np.log10(np.min(true_model.values)) + kwargs['vmax'] = np.log10(np.max(true_model.values)) + + t = results_2d.inference_1d(index=7) + + plt.figure() + t.model.plot_posteriors(edges_kwargs={ + 'transpose': True, + 'trim': False}, + values_kwargs={ + 'colorbar': False, + 'flipY': True, + 'xscale': 'log', + 'credible_interval_kwargs': { + }}) + + tmp = t.model.values.posterior + + + plt.show(block=True) + # plt.savefig('{}_{}.png'.format(data_type, model_type), dpi=300) + + if __name__ == '__main__': + models = ['glacial']#, 'saline_clay', 'resistive_dolomites', 'resistive_basement', 'coastal_salt_water', 'ice_over_salt_water'] + + for model in models: + # try: + plot_2d_summary("../../../Parallel_Inference/", "resolve", model) + # except Exception as e: + # print(model) + # print(e) + # pass + + +.. _sphx_glr_download_examples_Inference_2D_test.py: + +.. only:: html + + .. container:: sphx-glr-footer sphx-glr-footer-example + + .. container:: sphx-glr-download sphx-glr-download-jupyter + + :download:`Download Jupyter notebook: test.ipynb ` + + .. container:: sphx-glr-download sphx-glr-download-python + + :download:`Download Python source code: test.py ` + + +.. only:: html + + .. rst-class:: sphx-glr-signature + + `Gallery generated by Sphinx-Gallery `_ diff --git a/docs/_sources/examples/Meshes/plot_rectilinear_mesh_1d.rst.txt b/docs/_sources/examples/Meshes/plot_rectilinear_mesh_1d.rst.txt index 5b262cbb..4dcc8684 100644 --- a/docs/_sources/examples/Meshes/plot_rectilinear_mesh_1d.rst.txt +++ b/docs/_sources/examples/Meshes/plot_rectilinear_mesh_1d.rst.txt @@ -620,7 +620,7 @@ Expanded .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 4.482 seconds) + **Total running time of the script:** (0 minutes 8.030 seconds) .. _sphx_glr_download_examples_Meshes_plot_rectilinear_mesh_1d.py: diff --git a/docs/_sources/examples/Meshes/plot_rectilinear_mesh_2d.rst.txt b/docs/_sources/examples/Meshes/plot_rectilinear_mesh_2d.rst.txt index 7bb991e0..2a772bf5 100644 --- a/docs/_sources/examples/Meshes/plot_rectilinear_mesh_2d.rst.txt +++ b/docs/_sources/examples/Meshes/plot_rectilinear_mesh_2d.rst.txt @@ -114,7 +114,7 @@ We can plot the grid lines of the mesh. .. code-block:: none - (, , ) + (, , ) @@ -271,7 +271,7 @@ Compute the mean over an interval for the mesh. .. code-block:: none - (array([[9., 9., 9., ..., 9., 9., 9.]]), [6.8, 12.4]) + (array([[9., 9., 9., 9., 9., 9., 9., 9., 9., 9., 9., 9., 9., 9., 9.]]), [6.8, 12.4]) @@ -294,9 +294,12 @@ Compute the mean over multiple intervals for the mesh. .. code-block:: none - (array([[ 9., 9., 9., ..., 9., 9., 9.], - [nan, nan, nan, ..., nan, nan, nan], - [nan, nan, nan, ..., nan, nan, nan]]), [6.8, 12.4, 20.0, 40.0]) + (array([[ 9., 9., 9., 9., 9., 9., 9., 9., 9., 9., 9., 9., 9., + 9., 9.], + [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, + nan, nan], + [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, + nan, nan]]), [6.8, 12.4, 20.0, 40.0]) @@ -322,7 +325,10 @@ We can specify either axis (array([[ 1.], [ 2.], [ 3.], - ..., + [ 4.], + [ 5.], + [ 6.], + [ 7.], [ 8.], [ 9.], [10.]]), [2.8, 4.2]) @@ -347,7 +353,10 @@ We can specify either axis (array([[ 1., nan, 1.], [ 2., nan, 2.], [ 3., nan, 3.], - ..., + [ 4., nan, 4.], + [ 5., nan, 5.], + [ 6., nan, 6.], + [ 7., nan, 7.], [ 8., nan, 8.], [ 9., nan, 9.], [10., nan, 10.]]), [2.8, 4.2, 5.1, 8.4]) @@ -417,7 +426,7 @@ Resample a grid .. code-block:: none - (, , ) + (, , ) @@ -481,7 +490,7 @@ Axes in log space .. code-block:: none - (, , ) + (, , ) @@ -593,7 +602,7 @@ RelativeTo .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 1.873 seconds) + **Total running time of the script:** (0 minutes 3.314 seconds) .. _sphx_glr_download_examples_Meshes_plot_rectilinear_mesh_2d.py: diff --git a/docs/_sources/examples/Meshes/plot_rectilinear_mesh_3d.rst.txt b/docs/_sources/examples/Meshes/plot_rectilinear_mesh_3d.rst.txt index f665959e..2b33bf4f 100644 --- a/docs/_sources/examples/Meshes/plot_rectilinear_mesh_3d.rst.txt +++ b/docs/_sources/examples/Meshes/plot_rectilinear_mesh_3d.rst.txt @@ -317,7 +317,7 @@ We can plot the mesh in 3D! .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 1.848 seconds) + **Total running time of the script:** (0 minutes 11.321 seconds) .. _sphx_glr_download_examples_Meshes_plot_rectilinear_mesh_3d.py: diff --git a/docs/_sources/examples/Meshes/sg_execution_times.rst.txt b/docs/_sources/examples/Meshes/sg_execution_times.rst.txt index fbd890f2..a660162d 100644 --- a/docs/_sources/examples/Meshes/sg_execution_times.rst.txt +++ b/docs/_sources/examples/Meshes/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**00:08.203** total execution time for 3 files **from examples/Meshes**: +**00:22.664** total execution time for 3 files **from examples/Meshes**: .. container:: @@ -32,12 +32,12 @@ Computation times * - Example - Time - Mem (MB) + * - :ref:`sphx_glr_examples_Meshes_plot_rectilinear_mesh_3d.py` (``plot_rectilinear_mesh_3d.py``) + - 00:11.321 + - 0.0 * - :ref:`sphx_glr_examples_Meshes_plot_rectilinear_mesh_1d.py` (``plot_rectilinear_mesh_1d.py``) - - 00:04.482 + - 00:08.030 - 0.0 * - :ref:`sphx_glr_examples_Meshes_plot_rectilinear_mesh_2d.py` (``plot_rectilinear_mesh_2d.py``) - - 00:01.873 - - 0.0 - * - :ref:`sphx_glr_examples_Meshes_plot_rectilinear_mesh_3d.py` (``plot_rectilinear_mesh_3d.py``) - - 00:01.848 + - 00:03.314 - 0.0 diff --git a/docs/_sources/examples/Models/plot_model_1d.rst.txt b/docs/_sources/examples/Models/plot_model_1d.rst.txt index 6e0213a0..2221222e 100644 --- a/docs/_sources/examples/Models/plot_model_1d.rst.txt +++ b/docs/_sources/examples/Models/plot_model_1d.rst.txt @@ -351,7 +351,7 @@ fig = plt.figure(figsize=(8, 6)) .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 3.052 seconds) + **Total running time of the script:** (0 minutes 3.360 seconds) .. _sphx_glr_download_examples_Models_plot_model_1d.py: diff --git a/docs/_sources/examples/Models/plot_model_2d.rst.txt b/docs/_sources/examples/Models/plot_model_2d.rst.txt index 8f354cfc..e7b7f190 100644 --- a/docs/_sources/examples/Models/plot_model_2d.rst.txt +++ b/docs/_sources/examples/Models/plot_model_2d.rst.txt @@ -113,7 +113,7 @@ Specify some cell centres in x and y .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 0.247 seconds) + **Total running time of the script:** (0 minutes 0.237 seconds) .. _sphx_glr_download_examples_Models_plot_model_2d.py: diff --git a/docs/_sources/examples/Models/plot_model_3d.rst.txt b/docs/_sources/examples/Models/plot_model_3d.rst.txt index 1262f372..89b5d115 100644 --- a/docs/_sources/examples/Models/plot_model_3d.rst.txt +++ b/docs/_sources/examples/Models/plot_model_3d.rst.txt @@ -120,7 +120,7 @@ Specify some cell centres in x and y .. code-block:: none - (, , ) + (, , ) @@ -203,7 +203,7 @@ Specify some cell centres in x and y .. code-block:: none - (, , ) + (, , ) @@ -266,7 +266,7 @@ We can plot the mesh in 3D! .. code-block:: none - (, , ) + (, , ) @@ -331,7 +331,7 @@ We can plot the mesh in 3D! .. code-block:: none - (, , ) + (, , ) @@ -381,7 +381,7 @@ We can plot the mesh in 3D! .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 0.810 seconds) + **Total running time of the script:** (0 minutes 1.140 seconds) .. _sphx_glr_download_examples_Models_plot_model_3d.py: diff --git a/docs/_sources/examples/Models/sg_execution_times.rst.txt b/docs/_sources/examples/Models/sg_execution_times.rst.txt index cfd1dbe0..1a97bb5f 100644 --- a/docs/_sources/examples/Models/sg_execution_times.rst.txt +++ b/docs/_sources/examples/Models/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**00:04.109** total execution time for 3 files **from examples/Models**: +**00:04.736** total execution time for 3 files **from examples/Models**: .. container:: @@ -33,11 +33,11 @@ Computation times - Time - Mem (MB) * - :ref:`sphx_glr_examples_Models_plot_model_1d.py` (``plot_model_1d.py``) - - 00:03.052 + - 00:03.360 - 0.0 * - :ref:`sphx_glr_examples_Models_plot_model_3d.py` (``plot_model_3d.py``) - - 00:00.810 + - 00:01.140 - 0.0 * - :ref:`sphx_glr_examples_Models_plot_model_2d.py` (``plot_model_2d.py``) - - 00:00.247 + - 00:00.237 - 0.0 diff --git a/docs/_sources/examples/Statistics/plot_StatArray.rst.txt b/docs/_sources/examples/Statistics/plot_StatArray.rst.txt index d52c67d8..5981831c 100644 --- a/docs/_sources/examples/Statistics/plot_StatArray.rst.txt +++ b/docs/_sources/examples/Statistics/plot_StatArray.rst.txt @@ -90,21 +90,21 @@ Instantiating a new StatArray class .. code-block:: none - Name: 1 0x169c7d550 + Name: 1 0x170707ad0 Shape: (1,) Values: [0.] Min: 0.0 Max: 0.0 has_posterior: False - Name: 10 0x169c7e450 + Name: 10 0x1707041d0 Shape: (10,) Values: [0. 0. 0. ... 0. 0. 0.] Min: 0.0 Max: 0.0 has_posterior: False - Name: (2, 10) 0x169384e50 + Name: (2, 10) 0x170705c50 Shape: (2, 10) Values: [[0. 0. 0. ... 0. 0. 0.] [0. 0. 0. ... 0. 0. 0.]] @@ -112,25 +112,25 @@ Instantiating a new StatArray class Max: 0.0 has_posterior: False - Name: 45.454 0x169385f50 + Name: 45.454 0x170706fd0 Shape: (1,) Values: [45.454] Min: 45.454 Max: 45.454 has_posterior: False - Name: 45.454 0x1683fe950 + Name: 45.454 0x1707058d0 Shape: (1,) Values: [45.454] Min: 45.454 Max: 45.454 has_posterior: False - Name: Density ($\frac{g}{cc}$) 0x1695c9e50 + Name: Density ($\frac{g}{cc}$) 0x170706ed0 Shape: (1,) - Values: [0.9749187] - Min: 0.9749187044718027 - Max: 0.9749187044718027 + Values: [-0.81925455] + Min: -0.8192545455077754 + Max: -0.8192545455077754 has_posterior: False @@ -202,11 +202,11 @@ We can also attach a proposal distribution .. code-block:: none - Name: Density ($\frac{g}{cc}$) 0x1695c9e50 + Name: Density ($\frac{g}{cc}$) 0x170706ed0 Shape: (1,) - Values: [0.9749187] - Min: 0.9749187044718027 - Max: 0.9749187044718027 + Values: [-0.81925455] + Min: -0.8192545455077754 + Max: -0.8192545455077754 Prior: | Uniform Distribution: | Min: -2.0 @@ -290,7 +290,7 @@ Or we can only generate samples that simultaneously satisfy the prior. .. code-block:: none - [1.51308498] + [-0.28108827] @@ -315,7 +315,7 @@ We can perturb the variable by drawing from the attached proposal distribution. .. code-block:: none - Name: Density ($\frac{g}{cc}$) 0x1695c9e50 + Name: Density ($\frac{g}{cc}$) 0x170706ed0 Shape: (1,) Values: [0.38188467] Min: 0.38188466718060166 @@ -457,7 +457,7 @@ This produces a single probability. .. code-block:: none - 0.20188095665063005 + 0.33888096006650337 @@ -1590,7 +1590,7 @@ We can also define a 2D array .. code-block:: none - 'Name: Density ($\\frac{g}{cc}$) 0x1742c39d0\nShape: (50, 100)\nValues: [[ 2.06611328 -0.96894773 0.47361096 ... 0.16917278 -0.04668624\n -1.67011115]\n [-2.65469689 0.85834291 0.34430906 ... 1.28800911 1.1144927\n -0.24695526]\n [-0.75278061 -1.2438372 -1.07790459 ... -0.084758 -0.25569134\n -0.2208334 ]\n ...\n [ 1.62844768 -1.09228456 0.26267186 ... -0.09846557 -0.38299931\n -0.80442456]\n [ 0.66077354 -1.37006434 -0.89252653 ... 1.21600984 -1.48399493\n 0.22944182]\n [-0.97250913 0.70182171 0.11826363 ... -1.39823221 0.26741883\n -0.11541463]]\nMin: -3.46634472149419\nMax: 3.4539286867724015\nhas_posterior: False\n' + 'Name: Density ($\\frac{g}{cc}$) 0x16fbf1550\nShape: (50, 100)\nValues: [[-4.01780133e-01 3.16635145e-01 -5.27750195e-01 ... -2.44618399e+00\n -4.96050117e-01 6.25365537e-01]\n [-4.81076204e-01 -9.74014990e-01 -2.11325212e+00 ... 1.81726048e-01\n 2.03762749e-01 -8.72069096e-01]\n [-7.25459267e-01 5.59232504e-01 -1.38786869e+00 ... 6.21068169e-01\n -2.59833364e+00 -1.14244762e+00]\n ...\n [-1.12094718e+00 1.09285179e+00 -8.49788982e-01 ... -1.72570923e+00\n 4.99544999e-01 5.42242587e-01]\n [ 2.82865259e-01 -1.18059731e-04 -1.52188899e-01 ... 1.13864002e-01\n 7.13026322e-01 -1.02252865e+00]\n [-4.71123302e-01 -4.93942524e-01 6.77625263e-01 ... -1.27237018e+00\n -2.27635302e+00 1.60185139e+00]]\nMin: -3.2916747712189056\nMax: 3.5748933990954637\nhas_posterior: False\n' @@ -1866,7 +1866,7 @@ Create a stacked area plot of a 2D StatArray .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 2.954 seconds) + **Total running time of the script:** (0 minutes 3.542 seconds) .. _sphx_glr_download_examples_Statistics_plot_StatArray.py: diff --git a/docs/_sources/examples/Statistics/plot_histogram_1d.rst.txt b/docs/_sources/examples/Statistics/plot_histogram_1d.rst.txt index 5ca9ae2a..435e3c27 100644 --- a/docs/_sources/examples/Statistics/plot_histogram_1d.rst.txt +++ b/docs/_sources/examples/Statistics/plot_histogram_1d.rst.txt @@ -147,7 +147,7 @@ Get the median, and 95% confidence values .. code-block:: none - (0.030000000000000027, -1.83, 1.8899999999999997) + (-0.030000000000000027, -2.01, 1.8299999999999996) @@ -439,7 +439,7 @@ We can update the histogram with some new values | Number of Cells: | | 100 | Cell Centres: - | | Name: bins (m) 0x16925c3d0 + | | Name: bins (m) 0x166a0bed0 | | Shape: (100,) | | Values: [-2.97 -2.91 -2.85 ... 2.85 2.91 2.97] | | Min: -2.9699999999999998 @@ -447,7 +447,7 @@ We can update the histogram with some new values | | has_posterior: False | | Cell Edges: - | | Name: bins (m) 0x16925cbd0 + | | Name: bins (m) 0x166a0a950 | | Shape: (101,) | | Values: [-3. -2.94 -2.88 ... 2.88 2.94 3. ] | | Min: -3.0 @@ -457,7 +457,7 @@ We can update the histogram with some new values | log: | | None | relativeTo: - | | Name: 0x16940a5d0 + | | Name: 0x167d420d0 | | Shape: (1,) | | Values: [0.] | | Min: 0.0 @@ -465,11 +465,11 @@ We can update the histogram with some new values | | has_posterior: False | values: - | Name: Frequency 0x1694bd050 + | Name: Frequency 0x167d41ad0 | Shape: (100,) - | Values: [0 3 1 ... 0 3 1] + | Values: [0 0 2 ... 2 2 0] | Min: 0 - | Max: 78 + | Max: 86 | has_posterior: False @@ -480,7 +480,7 @@ We can update the histogram with some new values .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 1.206 seconds) + **Total running time of the script:** (0 minutes 1.342 seconds) .. _sphx_glr_download_examples_Statistics_plot_histogram_1d.py: diff --git a/docs/_sources/examples/Statistics/plot_histogram_2d.rst.txt b/docs/_sources/examples/Statistics/plot_histogram_2d.rst.txt index b802767d..146e84a6 100644 --- a/docs/_sources/examples/Statistics/plot_histogram_2d.rst.txt +++ b/docs/_sources/examples/Statistics/plot_histogram_2d.rst.txt @@ -164,7 +164,7 @@ Update the histogram counts .. code-block:: none - (, , ) + (, , ) @@ -330,7 +330,7 @@ Take the mean or median estimates from the histogram .. code-block:: none - + @@ -353,8 +353,27 @@ Get the range between credible intervals .. code-block:: none - StatArray([2.74747475, 3.23232323, 4.2020202 , ..., 2.66666667, - 4.36363636, 3.63636364]) + StatArray([4.92929293, 3.55555556, 2.50505051, 4.44444444, 4.92929293, + 3.15151515, 3.7979798 , 4.12121212, 4.36363636, 3.31313131, + 4.36363636, 3.95959596, 3.7979798 , 3.63636364, 4.12121212, + 4.04040404, 3.87878788, 4.12121212, 3.95959596, 3.7979798 , + 3.95959596, 4.28282828, 3.87878788, 3.95959596, 3.7979798 , + 3.95959596, 3.95959596, 3.95959596, 3.95959596, 3.95959596, + 3.95959596, 4.04040404, 3.95959596, 3.95959596, 3.87878788, + 3.87878788, 4.04040404, 3.95959596, 3.87878788, 3.87878788, + 3.87878788, 3.87878788, 3.87878788, 3.87878788, 3.87878788, + 3.87878788, 3.87878788, 3.87878788, 3.87878788, 3.87878788, + 3.95959596, 3.87878788, 3.87878788, 3.87878788, 3.87878788, + 3.87878788, 3.87878788, 3.87878788, 3.87878788, 3.87878788, + 3.95959596, 3.87878788, 3.87878788, 3.87878788, 3.87878788, + 3.95959596, 3.87878788, 3.95959596, 3.87878788, 3.95959596, + 3.95959596, 3.95959596, 3.87878788, 3.87878788, 3.87878788, + 3.95959596, 3.95959596, 3.87878788, 3.95959596, 3.87878788, + 3.95959596, 3.7979798 , 3.95959596, 3.95959596, 3.87878788, + 3.95959596, 3.87878788, 3.7979798 , 3.87878788, 3.87878788, + 3.87878788, 4.36363636, 4.28282828, 4.2020202 , 4.28282828, + 4.52525253, 4.44444444, 4.12121212, 3.63636364, 4.04040404, + 2.98989899, 3.7979798 , 2.90909091, 3.63636364]) @@ -490,7 +509,7 @@ Update the histogram counts .. code-block:: none - (, , ) + (, , ) @@ -642,7 +661,7 @@ Take the mean or median estimates from the histogram .. code-block:: none - + @@ -665,8 +684,27 @@ Get the range between credible intervals .. code-block:: none - StatArray([2.58585859, 2.02020202, 2.18181818, ..., 4.76767677, - 3.7979798 , 4.84848485]) + StatArray([4.12121212, 3.47474747, 3.15151515, 4.12121212, 4.36363636, + 3.63636364, 3.87878788, 4.84848485, 3.63636364, 3.71717172, + 4.2020202 , 4.04040404, 3.7979798 , 3.39393939, 4.12121212, + 3.7979798 , 4.28282828, 3.7979798 , 3.95959596, 3.87878788, + 4.04040404, 3.95959596, 3.87878788, 3.95959596, 3.87878788, + 4.04040404, 3.95959596, 3.95959596, 3.95959596, 3.87878788, + 3.95959596, 3.87878788, 3.87878788, 3.87878788, 3.87878788, + 3.95959596, 3.87878788, 3.87878788, 3.87878788, 3.87878788, + 3.87878788, 3.87878788, 3.87878788, 3.87878788, 3.87878788, + 3.87878788, 3.87878788, 3.87878788, 3.95959596, 3.87878788, + 3.87878788, 3.87878788, 3.87878788, 3.95959596, 3.87878788, + 3.87878788, 4.04040404, 3.87878788, 3.95959596, 3.95959596, + 3.87878788, 3.87878788, 3.87878788, 3.87878788, 3.87878788, + 3.87878788, 3.87878788, 3.87878788, 3.87878788, 3.87878788, + 3.95959596, 3.87878788, 3.87878788, 3.95959596, 3.87878788, + 3.95959596, 3.87878788, 3.87878788, 3.87878788, 3.95959596, + 3.95959596, 3.95959596, 3.87878788, 3.7979798 , 3.87878788, + 3.71717172, 3.87878788, 4.04040404, 4.2020202 , 3.7979798 , + 3.95959596, 4.12121212, 3.7979798 , 3.71717172, 4.2020202 , + 3.55555556, 3.95959596, 3.71717172, 3.87878788, 4.76767677, + 3.95959596, 4.52525253, 4.36363636, 3.31313131]) @@ -762,7 +800,7 @@ We can map the credible range to an opacity or transparency .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 9.433 seconds) + **Total running time of the script:** (0 minutes 32.906 seconds) .. _sphx_glr_download_examples_Statistics_plot_histogram_2d.py: diff --git a/docs/_sources/examples/Statistics/plot_histogram_3d.rst.txt b/docs/_sources/examples/Statistics/plot_histogram_3d.rst.txt index c4617233..eaeab416 100644 --- a/docs/_sources/examples/Statistics/plot_histogram_3d.rst.txt +++ b/docs/_sources/examples/Statistics/plot_histogram_3d.rst.txt @@ -438,7 +438,7 @@ Take the median estimate from the histogram .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 9.857 seconds) + **Total running time of the script:** (0 minutes 11.648 seconds) .. _sphx_glr_download_examples_Statistics_plot_histogram_3d.py: diff --git a/docs/_sources/examples/Statistics/sg_execution_times.rst.txt b/docs/_sources/examples/Statistics/sg_execution_times.rst.txt index 76e06bb2..43c72895 100644 --- a/docs/_sources/examples/Statistics/sg_execution_times.rst.txt +++ b/docs/_sources/examples/Statistics/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**00:23.450** total execution time for 4 files **from examples/Statistics**: +**00:48.096** total execution time for 4 files **from examples/Statistics**: .. container:: @@ -32,15 +32,15 @@ Computation times * - Example - Time - Mem (MB) - * - :ref:`sphx_glr_examples_Statistics_plot_histogram_3d.py` (``plot_histogram_3d.py``) - - 00:09.857 - - 0.0 * - :ref:`sphx_glr_examples_Statistics_plot_histogram_2d.py` (``plot_histogram_2d.py``) - - 00:09.433 + - 00:32.906 + - 0.0 + * - :ref:`sphx_glr_examples_Statistics_plot_histogram_3d.py` (``plot_histogram_3d.py``) + - 00:11.648 - 0.0 * - :ref:`sphx_glr_examples_Statistics_plot_StatArray.py` (``plot_StatArray.py``) - - 00:02.954 + - 00:03.542 - 0.0 * - :ref:`sphx_glr_examples_Statistics_plot_histogram_1d.py` (``plot_histogram_1d.py``) - - 00:01.206 + - 00:00.000 - 0.0 diff --git a/docs/_sources/examples/index.rst.txt b/docs/_sources/examples/index.rst.txt index 92dfedad..28f1a741 100644 --- a/docs/_sources/examples/index.rst.txt +++ b/docs/_sources/examples/index.rst.txt @@ -579,6 +579,23 @@ In both cases, you will need to write an options file (also shown in these examp +.. raw:: html + +
+ +.. only:: html + + .. image:: /examples/Inference_2D/images/thumb/sphx_glr_test_thumb.png + :alt: + + :ref:`sphx_glr_examples_Inference_2D_test.py` + +.. raw:: html + +
2D Posterior analysis of Resolve inference
+
+ + .. raw:: html
@@ -624,6 +641,7 @@ In both cases, you will need to write an options file (also shown in these examp :hidden: /examples/Inference_2D/plot_inference_2d_resolve + /examples/Inference_2D/test /examples/Inference_2D/plot_inference_2d_skytem /examples/Inference_2D/plot_inference_2d_tempest diff --git a/docs/_sources/sg_execution_times.rst.txt b/docs/_sources/sg_execution_times.rst.txt index 98c04a8e..de38efe1 100644 --- a/docs/_sources/sg_execution_times.rst.txt +++ b/docs/_sources/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**04:52.070** total execution time for 25 files **from all galleries**: +**01:55.319** total execution time for 26 files **from all galleries**: .. container:: @@ -32,78 +32,81 @@ Computation times * - Example - Time - Mem (MB) - * - :ref:`sphx_glr_examples_Inference_1D_plot_inference_1d_tempest.py` (``examples/Inference_1D/plot_inference_1d_tempest.py``) - - 01:08.394 - - 0.0 - * - :ref:`sphx_glr_examples_Inference_1D_plot_inference_1d_skytem.py` (``examples/Inference_1D/plot_inference_1d_skytem.py``) - - 00:50.833 - - 0.0 - * - :ref:`sphx_glr_examples_Inference_1D_plot_inference_1d_resolve.py` (``examples/Inference_1D/plot_inference_1d_resolve.py``) - - 00:37.529 - - 0.0 * - :ref:`sphx_glr_examples_Inference_2D_plot_inference_2d_resolve.py` (``examples/Inference_2D/plot_inference_2d_resolve.py``) - - 00:26.429 - - 0.0 - * - :ref:`sphx_glr_examples_Inference_2D_plot_inference_2d_skytem.py` (``examples/Inference_2D/plot_inference_2d_skytem.py``) - - 00:23.702 + - 00:49.364 - 0.0 * - :ref:`sphx_glr_examples_Inference_2D_plot_inference_2d_tempest.py` (``examples/Inference_2D/plot_inference_2d_tempest.py``) - - 00:23.279 + - 00:33.754 - 0.0 - * - :ref:`sphx_glr_examples_Statistics_plot_histogram_3d.py` (``examples/Statistics/plot_histogram_3d.py``) - - 00:09.857 + * - :ref:`sphx_glr_examples_Inference_2D_plot_inference_2d_skytem.py` (``examples/Inference_2D/plot_inference_2d_skytem.py``) + - 00:32.201 - 0.0 - * - :ref:`sphx_glr_examples_Statistics_plot_histogram_2d.py` (``examples/Statistics/plot_histogram_2d.py``) - - 00:09.433 + * - :ref:`sphx_glr_examples_Data_plot_frequency_dataset.py` (``examples/Data/plot_frequency_dataset.py``) + - 00:00.000 - 0.0 - * - :ref:`sphx_glr_examples_Datapoints_plot_resolve_datapoint.py` (``examples/Datapoints/plot_resolve_datapoint.py``) - - 00:07.847 + * - :ref:`sphx_glr_examples_Data_plot_pointcloud3d.py` (``examples/Data/plot_pointcloud3d.py``) + - 00:00.000 - 0.0 - * - :ref:`sphx_glr_examples_Meshes_plot_rectilinear_mesh_1d.py` (``examples/Meshes/plot_rectilinear_mesh_1d.py``) - - 00:04.482 + * - :ref:`sphx_glr_examples_Data_plot_skytem_dataset.py` (``examples/Data/plot_skytem_dataset.py``) + - 00:00.000 - 0.0 * - :ref:`sphx_glr_examples_Data_plot_tempest_dataset.py` (``examples/Data/plot_tempest_dataset.py``) - - 00:03.684 + - 00:00.000 - 0.0 - * - :ref:`sphx_glr_examples_Data_plot_pointcloud3d.py` (``examples/Data/plot_pointcloud3d.py``) - - 00:03.231 + * - :ref:`sphx_glr_examples_Datapoints_plot_resolve_datapoint.py` (``examples/Datapoints/plot_resolve_datapoint.py``) + - 00:00.000 + - 0.0 + * - :ref:`sphx_glr_examples_Datapoints_plot_skytem_datapoint.py` (``examples/Datapoints/plot_skytem_datapoint.py``) + - 00:00.000 + - 0.0 + * - :ref:`sphx_glr_examples_Datapoints_plot_tempest_datapoint.py` (``examples/Datapoints/plot_tempest_datapoint.py``) + - 00:00.000 - 0.0 * - :ref:`sphx_glr_examples_Distributions_plot_distributions.py` (``examples/Distributions/plot_distributions.py``) - - 00:03.207 + - 00:00.000 - 0.0 - * - :ref:`sphx_glr_examples_Models_plot_model_1d.py` (``examples/Models/plot_model_1d.py``) - - 00:03.052 + * - :ref:`sphx_glr_examples_HDF5_hdf5.py` (``examples/HDF5/hdf5.py``) + - 00:00.000 - 0.0 - * - :ref:`sphx_glr_examples_Statistics_plot_StatArray.py` (``examples/Statistics/plot_StatArray.py``) - - 00:02.954 + * - :ref:`sphx_glr_examples_Inference_1D_plot_inference_1d_resolve.py` (``examples/Inference_1D/plot_inference_1d_resolve.py``) + - 00:00.000 - 0.0 - * - :ref:`sphx_glr_examples_Data_plot_frequency_dataset.py` (``examples/Data/plot_frequency_dataset.py``) - - 00:02.948 + * - :ref:`sphx_glr_examples_Inference_1D_plot_inference_1d_skytem.py` (``examples/Inference_1D/plot_inference_1d_skytem.py``) + - 00:00.000 - 0.0 - * - :ref:`sphx_glr_examples_Data_plot_skytem_dataset.py` (``examples/Data/plot_skytem_dataset.py``) - - 00:02.262 + * - :ref:`sphx_glr_examples_Inference_1D_plot_inference_1d_tempest.py` (``examples/Inference_1D/plot_inference_1d_tempest.py``) + - 00:00.000 - 0.0 - * - :ref:`sphx_glr_examples_Datapoints_plot_skytem_datapoint.py` (``examples/Datapoints/plot_skytem_datapoint.py``) - - 00:01.918 + * - :ref:`sphx_glr_examples_Inference_2D_test.py` (``examples/Inference_2D/test.py``) + - 00:00.000 + - 0.0 + * - :ref:`sphx_glr_examples_Meshes_plot_rectilinear_mesh_1d.py` (``examples/Meshes/plot_rectilinear_mesh_1d.py``) + - 00:00.000 - 0.0 * - :ref:`sphx_glr_examples_Meshes_plot_rectilinear_mesh_2d.py` (``examples/Meshes/plot_rectilinear_mesh_2d.py``) - - 00:01.873 + - 00:00.000 - 0.0 * - :ref:`sphx_glr_examples_Meshes_plot_rectilinear_mesh_3d.py` (``examples/Meshes/plot_rectilinear_mesh_3d.py``) - - 00:01.848 + - 00:00.000 - 0.0 - * - :ref:`sphx_glr_examples_Statistics_plot_histogram_1d.py` (``examples/Statistics/plot_histogram_1d.py``) - - 00:01.206 + * - :ref:`sphx_glr_examples_Models_plot_model_1d.py` (``examples/Models/plot_model_1d.py``) + - 00:00.000 - 0.0 - * - :ref:`sphx_glr_examples_Datapoints_plot_tempest_datapoint.py` (``examples/Datapoints/plot_tempest_datapoint.py``) - - 00:01.044 + * - :ref:`sphx_glr_examples_Models_plot_model_2d.py` (``examples/Models/plot_model_2d.py``) + - 00:00.000 - 0.0 * - :ref:`sphx_glr_examples_Models_plot_model_3d.py` (``examples/Models/plot_model_3d.py``) - - 00:00.810 + - 00:00.000 - 0.0 - * - :ref:`sphx_glr_examples_Models_plot_model_2d.py` (``examples/Models/plot_model_2d.py``) - - 00:00.247 + * - :ref:`sphx_glr_examples_Statistics_plot_StatArray.py` (``examples/Statistics/plot_StatArray.py``) + - 00:00.000 - 0.0 - * - :ref:`sphx_glr_examples_HDF5_hdf5.py` (``examples/HDF5/hdf5.py``) + * - :ref:`sphx_glr_examples_Statistics_plot_histogram_1d.py` (``examples/Statistics/plot_histogram_1d.py``) + - 00:00.000 + - 0.0 + * - :ref:`sphx_glr_examples_Statistics_plot_histogram_2d.py` (``examples/Statistics/plot_histogram_2d.py``) + - 00:00.000 + - 0.0 + * - :ref:`sphx_glr_examples_Statistics_plot_histogram_3d.py` (``examples/Statistics/plot_histogram_3d.py``) - 00:00.000 - 0.0 diff --git a/docs/_static/basic.css b/docs/_static/basic.css index 30fee9d0..f316efcb 100644 --- a/docs/_static/basic.css +++ b/docs/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/docs/_static/doctools.js b/docs/_static/doctools.js index d06a71d7..4d67807d 100644 --- a/docs/_static/doctools.js +++ b/docs/_static/doctools.js @@ -4,7 +4,7 @@ * * Base JavaScript utilities for all Sphinx HTML documentation. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/docs/_static/graphviz.css b/docs/_static/graphviz.css index 8d81c02e..027576e3 100644 --- a/docs/_static/graphviz.css +++ b/docs/_static/graphviz.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- graphviz extension. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/docs/_static/language_data.js b/docs/_static/language_data.js index 250f5665..367b8ed8 100644 --- a/docs/_static/language_data.js +++ b/docs/_static/language_data.js @@ -5,7 +5,7 @@ * This script contains the language-specific data used by searchtools.js, * namely the list of stopwords, stemmer, scorer and splitter. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -13,7 +13,7 @@ var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; -/* Non-minified version is copied as a separate JS file, is available */ +/* Non-minified version is copied as a separate JS file, if available */ /** * Porter Stemmer diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js index 7918c3fa..92da3f8b 100644 --- a/docs/_static/searchtools.js +++ b/docs/_static/searchtools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for the full-text search. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -99,7 +99,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => { .then((data) => { if (data) listItem.appendChild( - Search.makeSearchSummary(data, searchTerms) + Search.makeSearchSummary(data, searchTerms, anchor) ); // highlight search terms in the summary if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js @@ -116,8 +116,8 @@ const _finishSearch = (resultCount) => { ); else Search.status.innerText = _( - `Search finished, found ${resultCount} page(s) matching the search query.` - ); + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); }; const _displayNextItem = ( results, @@ -137,6 +137,22 @@ const _displayNextItem = ( // search finished, update title and status message else _finishSearch(resultCount); }; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; /** * Default splitQuery function. Can be overridden in ``sphinx.search`` with a @@ -160,13 +176,26 @@ const Search = { _queued_query: null, _pulse_status: -1, - htmlToText: (htmlString) => { + htmlToText: (htmlString, anchor) => { const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + for (const removalQuery of [".headerlinks", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent !== undefined) return docContent.textContent; + if (docContent) return docContent.textContent; + console.warn( - "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." ); return ""; }, @@ -239,16 +268,7 @@ const Search = { else Search.deferQuery(query); }, - /** - * execute search (requires search index to be loaded) - */ - query: (query) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - + _parseQuery: (query) => { // stem the search terms and add them to the correct list const stemmer = new Stemmer(); const searchTerms = new Set(); @@ -284,16 +304,32 @@ const Search = { // console.info("required: ", [...searchTerms]); // console.info("excluded: ", [...excludedTerms]); - // array of [docname, title, anchor, descr, score, filename] - let results = []; + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + _removeChildren(document.getElementById("search-progress")); - const queryLower = query.toLowerCase(); + const queryLower = query.toLowerCase().trim(); for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { for (const [file, id] of foundTitles) { let score = Math.round(100 * queryLower.length / title.length) - results.push([ + normalResults.push([ docNames[file], titles[file] !== title ? `${titles[file]} > ${title}` : title, id !== null ? "#" + id : "", @@ -308,46 +344,47 @@ const Search = { // search for explicit entries in index directives for (const [entry, foundEntries] of Object.entries(indexEntries)) { if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id] of foundEntries) { - let score = Math.round(100 * queryLower.length / entry.length) - results.push([ + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ docNames[file], titles[file], id ? "#" + id : "", null, score, filenames[file], - ]); + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } } } } // lookup as object objectTerms.forEach((term) => - results.push(...Search.performObjectSearch(term, objectTerms)) + normalResults.push(...Search.performObjectSearch(term, objectTerms)) ); // lookup as search terms in fulltext - results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); // let the scorer override scores with a custom scoring function - if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); - - // now sort the results by score (in opposite order of appearance, since the - // display function below uses pop() to retrieve items) and then - // alphabetically - results.sort((a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; - }); + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; // remove duplicate search results // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept @@ -361,7 +398,12 @@ const Search = { return acc; }, []); - results = results.reverse(); + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); // for debugging //Search.lastresults = results.slice(); // a copy @@ -466,14 +508,18 @@ const Search = { // add support for partial matches if (word.length > 2) { const escapedWord = _escapeRegExp(word); - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord) && !terms[word]) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord) && !titleTerms[word]) - arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); - }); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } } // no match but word was a required one @@ -496,9 +542,8 @@ const Search = { // create the mapping files.forEach((file) => { - if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) - fileMap.get(file).push(word); - else fileMap.set(file, [word]); + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); }); }); @@ -549,8 +594,8 @@ const Search = { * search summary for a given text. keywords is a list * of stemmed words. */ - makeSearchSummary: (htmlText, keywords) => { - const text = Search.htmlToText(htmlText); + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); if (text === "") return null; const textLower = text.toLowerCase(); diff --git a/docs/content/api/api.html b/docs/content/api/api.html index 99ba726e..5227253c 100644 --- a/docs/content/api/api.html +++ b/docs/content/api/api.html @@ -7,7 +7,7 @@ API — GeoBIPy 1.0.0 documentation - + @@ -21,8 +21,9 @@ - + + diff --git a/docs/content/api/base/HDF.html b/docs/content/api/base/HDF.html index a18f576a..1524669b 100644 --- a/docs/content/api/base/HDF.html +++ b/docs/content/api/base/HDF.html @@ -7,7 +7,7 @@ Heirarchical Data Format (HDF) — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + @@ -140,7 +140,7 @@

  • groupName (str or list of str) – The group(s) path within the hdf5 file to read from. i.e. ‘/group1/group1a’

  • key (str or list of str) – The key(s) in the group to read

  • index (slice, optional) – Specifies the index’th entry of the data to return. If the group was created using a createHDF procedure in parallel with the nRepeats option, index specifies the index’th entry from which to read the data.

    • -

  • necessary. (Any other parameters in **kwargs are optional but may be necessary if an object's .fromHDF() procedure requires extra arguments. Refer to the object you wish to read in to determine whether extra arguments are) –

    • +

  • necessary. (Any other parameters in **kwargs are optional but may be necessary if an object's .fromHDF() procedure requires extra arguments. Refer to the object you wish to read in to determine whether extra arguments are)

    • Returns:
    @@ -164,7 +164,7 @@

  • groupName (str or list of str) – The group(s) path within the hdf5 file(s) to read from. i.e. ‘/group1/group1a’

  • key (str or list of str) – The key(s) in the group to read

  • index (slice, optional) – Specifies the index’th entry of the data to return. If the group was created using a createHDF procedure in parallel with the nRepeats option, index specifies the index’th entry from which to read the data.

    • -

  • necessary. (Any other parameters in **kwargs are optional but may be necessary if an object's .fromHDF() procedure requires extra arguments. Refer to the object you wish to read in to determine whether extra arguments are) –

    • +

  • necessary. (Any other parameters in **kwargs are optional but may be necessary if an object's .fromHDF() procedure requires extra arguments. Refer to the object you wish to read in to determine whether extra arguments are)

    • Returns:
    @@ -224,7 +224,7 @@

    • hObj (h5py._hl.dataset.Dataset or h5py._hl.group.Group) – A h5py object from which to read entries.

    • index (slice, optional) – Specifies the index’th entry of the data to return. If the group was created using a createHDF procedure in parallel with the nRepeats option, index specifies the index’th entry from which to read the data.

      • -

    • necessary. (Any other parameters in **kwargs are optional but may be necessary if an object's .fromHDF() procedure requires extra arguments. Refer to the object you wish to read in to determine whether extra arguments are) –

      • +

    • necessary. (Any other parameters in **kwargs are optional but may be necessary if an object's .fromHDF() procedure requires extra arguments. Refer to the object you wish to read in to determine whether extra arguments are)

    Returns:
    diff --git a/docs/content/api/base/MPI.html b/docs/content/api/base/MPI.html index 167e69dd..ecf6fd32 100644 --- a/docs/content/api/base/MPI.html +++ b/docs/content/api/base/MPI.html @@ -7,7 +7,7 @@ MPI wrapper functions — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/base/base.html b/docs/content/api/base/base.html index c5b39bbb..b324706e 100644 --- a/docs/content/api/base/base.html +++ b/docs/content/api/base/base.html @@ -7,7 +7,7 @@ Core routines needed for GeoBIPy — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/base/fileIO.html b/docs/content/api/base/fileIO.html index c30c899e..f0e50b95 100644 --- a/docs/content/api/base/fileIO.html +++ b/docs/content/api/base/fileIO.html @@ -7,7 +7,7 @@ fileIO — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + @@ -185,7 +185,7 @@

    Check if all files in fNames exist on disk

    Parameters:
    -

    fNames (list of str) –

    +

    fNames (list of str)

    Returns:

    out – Whether all files exist or not

    diff --git a/docs/content/api/base/interpolation.html b/docs/content/api/base/interpolation.html index 42f17327..f74cb63e 100644 --- a/docs/content/api/base/interpolation.html +++ b/docs/content/api/base/interpolation.html @@ -7,7 +7,7 @@ Interpolation — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/base/plotting.html b/docs/content/api/base/plotting.html index ee07b36b..5985d802 100644 --- a/docs/content/api/base/plotting.html +++ b/docs/content/api/base/plotting.html @@ -7,7 +7,7 @@ plotting — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + @@ -559,8 +559,8 @@
    Parameters:
      -

    • x (array_like) –

      • -

    • y (array_like) –

      • +

    • x (array_like)

      • +

    • y (array_like)

    • flipY (bool, optional) – Flip the y axis

    • xscale (str, optional) – Scale the x axis? e.g. xscale = ‘linear’ or ‘log’

    • yscale (str, optional) – Scale the y axis? e.g. yscale = ‘linear’ or ‘log’

      • diff --git a/docs/content/api/base/utilities.html b/docs/content/api/base/utilities.html index f5540d7e..9f08897e 100644 --- a/docs/content/api/base/utilities.html +++ b/docs/content/api/base/utilities.html @@ -7,7 +7,7 @@ utilities — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/classes.html b/docs/content/api/classes/classes.html index eaf784ac..9eefd31f 100644 --- a/docs/content/api/classes/classes.html +++ b/docs/content/api/classes/classes.html @@ -7,7 +7,7 @@ Classes used in GeoBIPy — GeoBIPy 1.0.0 documentation - + @@ -21,8 +21,9 @@ - + + diff --git a/docs/content/api/classes/core/StatArray.html b/docs/content/api/classes/core/StatArray.html index 004c65b2..e9b49066 100644 --- a/docs/content/api/classes/core/StatArray.html +++ b/docs/content/api/classes/core/StatArray.html @@ -7,7 +7,7 @@ StatArray — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + @@ -585,12 +585,12 @@

      StatArray
      Parameters:
        -

      • nSamples –

        • -

      • log –

        • -

      • mean_bounds –

        • -

      • variance_bounds –

        • +

      • nSamples

        • +

      • log

        • +

      • mean_bounds

        • +

      • variance_bounds

      • k (ints) – Two ints with starting and ending # of clusters

        • -

      • tolerance –

        • +

      • tolerance

    diff --git a/docs/content/api/classes/core/core.html b/docs/content/api/classes/core/core.html index fb2aeeb0..2311863e 100644 --- a/docs/content/api/classes/core/core.html +++ b/docs/content/api/classes/core/core.html @@ -7,7 +7,7 @@ Core classes — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/core/myObject.html b/docs/content/api/classes/core/myObject.html index 9dcae3ea..f072b464 100644 --- a/docs/content/api/classes/core/myObject.html +++ b/docs/content/api/classes/core/myObject.html @@ -7,7 +7,7 @@ Core object class — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/data/data.html b/docs/content/api/classes/data/data.html index 7ab626ac..e3ab3738 100644 --- a/docs/content/api/classes/data/data.html +++ b/docs/content/api/classes/data/data.html @@ -7,7 +7,7 @@ Data classes — GeoBIPy 1.0.0 documentation - + @@ -21,8 +21,9 @@ - + + diff --git a/docs/content/api/classes/data/datapoint/EmDataPoint.html b/docs/content/api/classes/data/datapoint/EmDataPoint.html index 1dcaf76a..0b45988c 100644 --- a/docs/content/api/classes/data/datapoint/EmDataPoint.html +++ b/docs/content/api/classes/data/datapoint/EmDataPoint.html @@ -7,7 +7,7 @@ EmDataPoint — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/data/datapoint/FdemDataPoint.html b/docs/content/api/classes/data/datapoint/FdemDataPoint.html index 6d4f122e..6b843e0e 100644 --- a/docs/content/api/classes/data/datapoint/FdemDataPoint.html +++ b/docs/content/api/classes/data/datapoint/FdemDataPoint.html @@ -7,7 +7,7 @@ FdemDataPoint — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/data/datapoint/TdemDataPoint.html b/docs/content/api/classes/data/datapoint/TdemDataPoint.html index c00e2e0c..f3152b07 100644 --- a/docs/content/api/classes/data/datapoint/TdemDataPoint.html +++ b/docs/content/api/classes/data/datapoint/TdemDataPoint.html @@ -7,7 +7,7 @@ TdemDataPoint — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + @@ -291,7 +291,7 @@

    TdemDataPoint
    Parameters:
    -

    log –

    +

    log

    diff --git a/docs/content/api/classes/data/datapoint/Tempest_dataPoint.html b/docs/content/api/classes/data/datapoint/Tempest_dataPoint.html index f078c378..149f4dfe 100644 --- a/docs/content/api/classes/data/datapoint/Tempest_dataPoint.html +++ b/docs/content/api/classes/data/datapoint/Tempest_dataPoint.html @@ -7,7 +7,7 @@ Tempest_datapoint — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + @@ -221,7 +221,7 @@

    Tempest_datapoint
    Parameters:
    -

    log –

    +

    log

    diff --git a/docs/content/api/classes/data/datapoint/datapoint.html b/docs/content/api/classes/data/datapoint/datapoint.html index 362fa6af..090721c6 100644 --- a/docs/content/api/classes/data/datapoint/datapoint.html +++ b/docs/content/api/classes/data/datapoint/datapoint.html @@ -7,7 +7,7 @@ DataPoint — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + @@ -299,7 +299,7 @@

    DataPoint
    Parameters:
    -

    log –

    +

    log

    diff --git a/docs/content/api/classes/data/datapoint/datapointrst.html b/docs/content/api/classes/data/datapoint/datapointrst.html index 1f40e80f..daa21aba 100644 --- a/docs/content/api/classes/data/datapoint/datapointrst.html +++ b/docs/content/api/classes/data/datapoint/datapointrst.html @@ -7,7 +7,7 @@ Datapoint classes — GeoBIPy 1.0.0 documentation - + @@ -21,8 +21,9 @@ - + + diff --git a/docs/content/api/classes/data/dataset/Data.html b/docs/content/api/classes/data/dataset/Data.html index 259c7540..fa656563 100644 --- a/docs/content/api/classes/data/dataset/Data.html +++ b/docs/content/api/classes/data/dataset/Data.html @@ -7,7 +7,7 @@ Data — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/data/dataset/FdemData.html b/docs/content/api/classes/data/dataset/FdemData.html index a8e0d9ca..fbbb6f32 100644 --- a/docs/content/api/classes/data/dataset/FdemData.html +++ b/docs/content/api/classes/data/dataset/FdemData.html @@ -7,7 +7,7 @@ FdemData — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/data/dataset/TdemData.html b/docs/content/api/classes/data/dataset/TdemData.html index e074d4b2..e0df2262 100644 --- a/docs/content/api/classes/data/dataset/TdemData.html +++ b/docs/content/api/classes/data/dataset/TdemData.html @@ -7,7 +7,7 @@ TdemData — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/data/dataset/TempestData.html b/docs/content/api/classes/data/dataset/TempestData.html index a3586bc8..359c3ae1 100644 --- a/docs/content/api/classes/data/dataset/TempestData.html +++ b/docs/content/api/classes/data/dataset/TempestData.html @@ -7,7 +7,7 @@ TempestData — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/data/dataset/dataset.html b/docs/content/api/classes/data/dataset/dataset.html index bf8cec19..273277dc 100644 --- a/docs/content/api/classes/data/dataset/dataset.html +++ b/docs/content/api/classes/data/dataset/dataset.html @@ -7,7 +7,7 @@ Dataset classes — GeoBIPy 1.0.0 documentation - + @@ -21,8 +21,9 @@ - + + diff --git a/docs/content/api/classes/mesh/RectilinearMesh1D.html b/docs/content/api/classes/mesh/RectilinearMesh1D.html index 6f6812e2..0c34e3e9 100644 --- a/docs/content/api/classes/mesh/RectilinearMesh1D.html +++ b/docs/content/api/classes/mesh/RectilinearMesh1D.html @@ -7,7 +7,7 @@ RectilinearMesh1D — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/mesh/RectilinearMesh2D.html b/docs/content/api/classes/mesh/RectilinearMesh2D.html index bdb2426b..a8e23f10 100644 --- a/docs/content/api/classes/mesh/RectilinearMesh2D.html +++ b/docs/content/api/classes/mesh/RectilinearMesh2D.html @@ -7,7 +7,7 @@ RectilinearMesh2D — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/mesh/RectilinearMesh2D_stitched.html b/docs/content/api/classes/mesh/RectilinearMesh2D_stitched.html index 7a51c0d0..95f6aac9 100644 --- a/docs/content/api/classes/mesh/RectilinearMesh2D_stitched.html +++ b/docs/content/api/classes/mesh/RectilinearMesh2D_stitched.html @@ -7,7 +7,7 @@ RectilinearMesh2D_stitched — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/mesh/RectilinearMesh3D.html b/docs/content/api/classes/mesh/RectilinearMesh3D.html index 59fa66b4..6bc1e26a 100644 --- a/docs/content/api/classes/mesh/RectilinearMesh3D.html +++ b/docs/content/api/classes/mesh/RectilinearMesh3D.html @@ -7,7 +7,7 @@ RectilinearMesh3D — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/mesh/mesh.html b/docs/content/api/classes/mesh/mesh.html index d0acf86b..4cfd7569 100644 --- a/docs/content/api/classes/mesh/mesh.html +++ b/docs/content/api/classes/mesh/mesh.html @@ -7,7 +7,7 @@ Mesh classes — GeoBIPy 1.0.0 documentation - + @@ -21,8 +21,9 @@ - + + diff --git a/docs/content/api/classes/model/Model_.html b/docs/content/api/classes/model/Model_.html index 81e2c741..393e2acc 100644 --- a/docs/content/api/classes/model/Model_.html +++ b/docs/content/api/classes/model/Model_.html @@ -7,7 +7,7 @@ Model — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/model/model.html b/docs/content/api/classes/model/model.html index 899777e6..3ab863e0 100644 --- a/docs/content/api/classes/model/model.html +++ b/docs/content/api/classes/model/model.html @@ -7,7 +7,7 @@ Model classes — GeoBIPy 1.0.0 documentation - + @@ -21,8 +21,9 @@ - + + diff --git a/docs/content/api/classes/pointcloud/Point.html b/docs/content/api/classes/pointcloud/Point.html index 05e3c6ec..3f10f397 100644 --- a/docs/content/api/classes/pointcloud/Point.html +++ b/docs/content/api/classes/pointcloud/Point.html @@ -7,7 +7,7 @@ Point — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/pointcloud/pointcloud.html b/docs/content/api/classes/pointcloud/pointcloud.html index dfd03031..99e20107 100644 --- a/docs/content/api/classes/pointcloud/pointcloud.html +++ b/docs/content/api/classes/pointcloud/pointcloud.html @@ -7,7 +7,7 @@ Pointcloud classes — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/statistics/Distribution.html b/docs/content/api/classes/statistics/Distribution.html index 3a62c626..b4eb6760 100644 --- a/docs/content/api/classes/statistics/Distribution.html +++ b/docs/content/api/classes/statistics/Distribution.html @@ -7,7 +7,7 @@ Distribution Wrapper — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/statistics/GammaDistribution.html b/docs/content/api/classes/statistics/GammaDistribution.html index ad070371..f4c50afb 100644 --- a/docs/content/api/classes/statistics/GammaDistribution.html +++ b/docs/content/api/classes/statistics/GammaDistribution.html @@ -7,7 +7,7 @@ Gamma Distribution — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/statistics/Histogram.html b/docs/content/api/classes/statistics/Histogram.html index 380dfef5..78e87bd2 100644 --- a/docs/content/api/classes/statistics/Histogram.html +++ b/docs/content/api/classes/statistics/Histogram.html @@ -7,7 +7,7 @@ Histogram — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + @@ -364,7 +364,7 @@

    Histogram
    -transparency(percent=95.0, log=None, axis=0)
    +transparency(percent=95.0, log=None, axis=0, **kwargs)

    Return a transparency value between 0 and 1 based on the difference between credible invervals of the hitmap.

    Higher ranges in credibility are mapped to more transparency.

    diff --git a/docs/content/api/classes/statistics/MvNormalDistribution.html b/docs/content/api/classes/statistics/MvNormalDistribution.html index f65cf21f..e1fec68f 100644 --- a/docs/content/api/classes/statistics/MvNormalDistribution.html +++ b/docs/content/api/classes/statistics/MvNormalDistribution.html @@ -7,7 +7,7 @@ MvNormal — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/statistics/NormalDistribution.html b/docs/content/api/classes/statistics/NormalDistribution.html index 57acea14..a5a0a568 100644 --- a/docs/content/api/classes/statistics/NormalDistribution.html +++ b/docs/content/api/classes/statistics/NormalDistribution.html @@ -7,7 +7,7 @@ Normal distribution — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/statistics/OrderStatistics.html b/docs/content/api/classes/statistics/OrderStatistics.html index bc70dcb0..086eb317 100644 --- a/docs/content/api/classes/statistics/OrderStatistics.html +++ b/docs/content/api/classes/statistics/OrderStatistics.html @@ -7,7 +7,7 @@ Order Statistics — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/statistics/UniformDistribution.html b/docs/content/api/classes/statistics/UniformDistribution.html index fb4c87f2..d0d61c29 100644 --- a/docs/content/api/classes/statistics/UniformDistribution.html +++ b/docs/content/api/classes/statistics/UniformDistribution.html @@ -7,7 +7,7 @@ Uniform distribution — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/statistics/baseDistribution.html b/docs/content/api/classes/statistics/baseDistribution.html index 70e25a8a..4f8b0b03 100644 --- a/docs/content/api/classes/statistics/baseDistribution.html +++ b/docs/content/api/classes/statistics/baseDistribution.html @@ -7,7 +7,7 @@ baseDistribution — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/statistics/statistics.html b/docs/content/api/classes/statistics/statistics.html index 5b1bf68b..5f76c692 100644 --- a/docs/content/api/classes/statistics/statistics.html +++ b/docs/content/api/classes/statistics/statistics.html @@ -7,7 +7,7 @@ Statistics classes — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/system/CircularLoop.html b/docs/content/api/classes/system/CircularLoop.html index 6cf18f37..5ff947b0 100644 --- a/docs/content/api/classes/system/CircularLoop.html +++ b/docs/content/api/classes/system/CircularLoop.html @@ -7,7 +7,7 @@ Circular Loop — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/system/EmLoop.html b/docs/content/api/classes/system/EmLoop.html index e483aef0..3861b62c 100644 --- a/docs/content/api/classes/system/EmLoop.html +++ b/docs/content/api/classes/system/EmLoop.html @@ -7,7 +7,7 @@ EmLoop — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/system/FdemSystem.html b/docs/content/api/classes/system/FdemSystem.html index 86cc1377..e00d2e43 100644 --- a/docs/content/api/classes/system/FdemSystem.html +++ b/docs/content/api/classes/system/FdemSystem.html @@ -7,7 +7,7 @@ Frequency domain system — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/system/TdemSystem.html b/docs/content/api/classes/system/TdemSystem.html index a8862b3e..9f4a0812 100644 --- a/docs/content/api/classes/system/TdemSystem.html +++ b/docs/content/api/classes/system/TdemSystem.html @@ -7,7 +7,7 @@ Time domain system — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/api/classes/system/system.html b/docs/content/api/classes/system/system.html index 544b8bdb..e9882903 100644 --- a/docs/content/api/classes/system/system.html +++ b/docs/content/api/classes/system/system.html @@ -7,7 +7,7 @@ System classes — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/getting_started/getting_started.html b/docs/content/getting_started/getting_started.html index deaac767..99e43ed6 100644 --- a/docs/content/getting_started/getting_started.html +++ b/docs/content/getting_started/getting_started.html @@ -7,7 +7,7 @@ Getting Started — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/content/getting_started/installation.html b/docs/content/getting_started/installation.html index fef00801..bb054cdd 100644 --- a/docs/content/getting_started/installation.html +++ b/docs/content/getting_started/installation.html @@ -7,7 +7,7 @@ Installing GeoBIPy — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + @@ -137,7 +137,7 @@

    mpi4py< Make sure you are about to install mpi4py to the correct python installation. If you type ‘which python’ it should return the path to the correct python distribution. If you are using environments, make sure you have activated the correct one.

    -

    Next, use “pip install mpi4py –no-cache-dir”. This last option is very important, without it, pip might install its own MPI library called MPICH2. +

    Next, use “env MPICC=<Your mpicc compiler> python -m pip install mpi4py”. This last option is very important, without it, pip might install its own MPI library called MPICH2. I would try to avoid this because if you need to install the HDF5 library you will need know which directories to link to (see Installing parallel HDF5 and h5py).

    At the end of the day, h5py needs to communicate with both the correct HDF5 library and mpi4py, and both of those need to communicate with the same MPI library.

    diff --git a/docs/examples/Data/README.html b/docs/examples/Data/README.html index c5289717..24e568b6 100644 --- a/docs/examples/Data/README.html +++ b/docs/examples/Data/README.html @@ -7,7 +7,7 @@ Data — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + diff --git a/docs/examples/Data/plot_frequency_dataset.html b/docs/examples/Data/plot_frequency_dataset.html index 831f6b30..ed5662cc 100644 --- a/docs/examples/Data/plot_frequency_dataset.html +++ b/docs/examples/Data/plot_frequency_dataset.html @@ -7,7 +7,7 @@ Frequency domain dataset — GeoBIPy 1.0.0 documentation - + @@ -21,7 +21,7 @@ - + @@ -305,7 +305,7 @@

    Obtain a line from the data set
    FdemData
 x:
-|   Name: Easting (m) 0x174e7e4d0
+|   Name: Easting (m) 0x171f2ff50
 |   Shape: (6710,)
 |   Values: [586852.29 586852.23 586852.17 ... 586123.57 586123.2  586122.82]
 |   Min: 586122.82
@@ -313,7 +313,7 @@ 
    Obtain a line from the data setthe supplementary folder in this repository
    
 
    See the Resolve.stm files.
    
-
    Total running time of the script: (0 minutes 2.948 seconds)
    
+
    Total running time of the script: (0 minutes 3.419 seconds)

    -
    <geobipy.src.classes.pointcloud.Point.Point object at 0x174793240>
+
    <geobipy.src.classes.pointcloud.Point.Point object at 0x17211e2a0>
 
    
 
    
 
    Write a summary of the contents of the point cloud
    
@@ -143,34 +143,34 @@
 
    Point
 x:
-|   Name: Easting (m) 0x174553ed0
+|   Name: Easting (m) 0x17202bdd0
 |   Shape: (400,)
-|   Values: [-0.36850848 -0.22497904 -0.42452287 ...  0.24392363  0.74209804
-|     0.35181645]
-|   Min: -0.9991390932309943
-|   Max: 0.9972526847985668
+|   Values: [-0.77740663 -0.95465929 -0.8004366  ...  0.70222895  0.89988598
+|     0.73299721]
+|   Min: -0.9954311373841322
+|   Max: 0.993880974076909
 |   has_posterior: False
 
 y:
-|   Name: Northing (m) 0x174552950
+|   Name: Northing (m) 0x17202be50
 |   Shape: (400,)
-|   Values: [-0.77647668 -0.74756667 -0.4778044  ...  0.6441633   0.31716597
-|     0.62345157]
-|   Min: -0.9992693648479871
-|   Max: 0.997306127444181
+|   Values: [-0.09996723 -0.19608163 -0.81129254 ...  0.32732432  0.28247145
+|     0.18550653]
+|   Min: -0.9990801618390335
+|   Max: 0.9898571038906161
 |   has_posterior: False
 
 z:
-|   Name: Height (m) 0x174550f50
+|   Name: Height (m) 0x17202bed0
 |   Shape: (400,)
-|   Values: [ 0.13076579  0.14932083  0.1417104  ...  0.1194774  -0.11075939
-|     0.09476474]
-|   Min: -1.8793846688041962
-|   Max: 0.2236799646282707
+|   Values: [-0.32666931 -1.06724139 -0.65206219 ... -0.1062743  -0.0664333
+|    -0.07198795]
+|   Min: -1.873647454522015
+|   Max: 0.22854378054627222
 |   has_posterior: False
 
 elevation:
-|   Name: Elevation (m) 0x174552c50
+|   Name: Elevation (m) 0x17202bf50
 |   Shape: (400,)
 |   Values: [0. 0. 0. ... 0. 0. 0.]
 |   Min: 0.0
@@ -188,7 +188,7 @@
 PC3D.scatter2D(edgecolor='k')
    -plot pointcloud3d
    (<Axes: xlabel='Easting (m)', ylabel='Northing (m)'>, <matplotlib.collections.PathCollection object at 0x174ff2cc0>, <matplotlib.colorbar.Colorbar object at 0x174ff30e0>)
+plot pointcloud3d
    (<Axes: xlabel='Easting (m)', ylabel='Northing (m)'>, <matplotlib.collections.PathCollection object at 0x172120f20>, <matplotlib.colorbar.Colorbar object at 0x17200d670>)
 
    
 
    
 
    Plotting routines take matplotlib arguments for customization
    
@@ -222,16 +222,16 @@
 PC3D.map(dx=0.01, dy=0.01, method='sibson', mask=0.03)
    -plot pointcloud3d
    surface [WARNING]: 2 unusable points were supplied; these will be ignored.
+plot pointcloud3d
    surface [WARNING]: 4 unusable points were supplied; these will be ignored.
 surface [WARNING]: You should have pre-processed the data with block-mean, -median, or -mode.
 surface [WARNING]: Check that previous processing steps write results with enough decimals.
 surface [WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding.
-surface [WARNING]: 2 unusable points were supplied; these will be ignored.
+surface [WARNING]: 4 unusable points were supplied; these will be ignored.
 surface [WARNING]: You should have pre-processed the data with block-mean, -median, or -mode.
 surface [WARNING]: Check that previous processing steps write results with enough decimals.
 surface [WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding.
 
-(<Axes: >, <matplotlib.collections.QuadMesh object at 0x174a561e0>, <matplotlib.colorbar.Colorbar object at 0x169e47200>)
+(<Axes: >, <matplotlib.collections.QuadMesh object at 0x17433d4c0>, <matplotlib.colorbar.Colorbar object at 0x17436a390>)
 
    
 
    
 
    For lots of points, these surfaces can look noisy. Using a block filter will help
    
@@ -244,12 +244,12 @@
 PCsub.map(dx=0.01, dy=0.01, method='sibson', mask=0.03)
    -plot pointcloud3d
    surface [WARNING]: 2 unusable points were supplied; these will be ignored.
+plot pointcloud3d
    surface [WARNING]: 3 unusable points were supplied; these will be ignored.
 surface [WARNING]: You should have pre-processed the data with block-mean, -median, or -mode.
 surface [WARNING]: Check that previous processing steps write results with enough decimals.
 surface [WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding.
 
-(<Axes: >, <matplotlib.collections.QuadMesh object at 0x17515ac60>, <matplotlib.colorbar.Colorbar object at 0x1688298e0>)
+(<Axes: >, <matplotlib.collections.QuadMesh object at 0x171ca6f60>, <matplotlib.colorbar.Colorbar object at 0x17450f8c0>)
 
    
 
    
 
    We can perform spatial searches on the 3D point cloud
    
@@ -277,7 +277,7 @@
 PC3D.read_csv(filename=dataFolder + 'Resolve1.txt')
    -
    <geobipy.src.classes.pointcloud.Point.Point object at 0x174d678d0>
+
    <geobipy.src.classes.pointcloud.Point.Point object at 0x1745c1c10>
 
    
 
    
 
    plt.figure()
@@ -296,7 +296,7 @@
 plt.show()
 
    
 
    
-plot pointcloud3d
    Total running time of the script: (0 minutes 3.231 seconds)
    
+plot pointcloud3d
    Total running time of the script: (0 minutes 3.710 seconds)
    -scatter plot of channel 10

    Total running time of the script: (0 minutes 3.684 seconds)

    +scatter plot of channel 10

    Total running time of the script: (0 minutes 3.941 seconds)