Merge branch 'develop' into main

agilescientific · Apr 6, 2022 · 24e2e79 · 24e2e79
2 parents 68997c0 + 71a5397
commit 24e2e79
Show file tree

Hide file tree

Showing 15 changed files with 1,573 additions and 43 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,9 +1,17 @@
 # Changelog
 
+## 0.5.4 — 6 April 2022
+
+- Fixed small issue with the Klauder wavelet not working when `autocorrelation` was `False`.
+- Changed the names of the `convolve` arguments to `arr` and `v` to better match NumPy.
+- The version number is now correctly stored in the `__version__` attribute.
+- Added a User Guide notebook on [making wavelets](https://code.agilescientific.com/bruges/userguide/Making_wavelets.html).
+- Added a User Guide notebook on [seismic attributes](https://code.agilescientific.com/bruges/userguide/Seismic_attributes.html).
+
 ## 0.5.3 — 21 February 2022
 
-- Fixed [issue #92](https://github.com/agile-geoscience/bruges/issues/92): the Ormsby, Ormsby FFT and Klauder wavelets now behave as expected when 2D arrays (lists of frequency parameters, essentially) are passed. A filter bank (array of wavelets) is returned.
-- Fixed [issue #93](https://github.com/agile-geoscience/bruges/issues/93): the Sinc, Cosine and Gabor wavelets now behave as expected when `sym` is passed.
+- Fixed [issue #92](https://github.com/agilescientific/bruges/issues/92): the Ormsby, Ormsby FFT and Klauder wavelets now behave as expected when 2D arrays (lists of frequency parameters, essentially) are passed. A filter bank (array of wavelets) is returned.
+- Fixed [issue #93](https://github.com/agilescientific/bruges/issues/93): the Sinc, Cosine and Gabor wavelets now behave as expected when `sym` is passed.
 - `reflection.convolve()` now works properly when the axis is specified, and a verbose option was added to show the input and output array shapes (helps with troubleshooting).
 
 ## 0.5.2 — 18 February 2022
@@ -58,7 +66,7 @@
 - Moved `rotate_phase()` to `bruges.filters` and it now should handle 2D and 3D seismic correctly. You can also pass an array-like of phases to get a 'phase bank' of rotations, similar to how this works with frequencies and wavelet banks.
 
 ## v0.4 — 27 November 2020
-- **Breaking change:** fixed numerous minor issues with `attribute.energy()`, see [issue 78](https://github.com/agile-geoscience/bruges/issues/78). Note that it now expects time to be in the last dimension of the array. The function now runs on n-D data and is also about 15 times faster.
+- **Breaking change:** fixed numerous minor issues with `attribute.energy()`, see [issue 78](https://github.com/agilescientific/bruges/issues/78). Note that it now expects time to be in the last dimension of the array. The function now runs on n-D data and is also about 15 times faster.
 - Multiple fixes to the documentation, thanks especially to Jesper Dramsch and Adriana Gordon.
 - Added the `filters.berlage()` wavelet, a causal, minimum phase wavelet good for marine airgun sources.
 - Added the `filters.generalized()` wavelet, of which the Ricker is a special case, as defined by Wang 2015, Geophys J Int 203, p1172ff.

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -4,17 +4,17 @@
 
 There are several important ways you can help; here are some examples:
 
-- Submitting bug reports and feature requests: see [Issues](https://github.com/agile-geoscience/bruges/issues).
+- Submitting bug reports and feature requests: see [Issues](https://github.com/agilescientific/bruges/issues).
 - Proposing code for bug fixes and new features, then [making a pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests).
 - Fixing typos and generally improving the documentation.
 - Writing tutorials, examples, and how-to documents.
 
 
 ## Code of conduct
 
-We're fortunate to be part of a large professional community that conducts itself with mutual respect and consideration for others. Agile's [Code of Conduct](https://github.com/agile-geoscience/community/blob/main/CODE_OF_CONDUCT.md) is part of protecting these features for everyone, everywhere. Please read it.
+We're fortunate to be part of a large professional community that conducts itself with mutual respect and consideration for others. Agile's [Code of Conduct](https://github.com/agilescientific/community/blob/main/CODE_OF_CONDUCT.md) is part of protecting these features for everyone, everywhere. Please read it.
 
 
 ## Authorship
 
-If you contribute a pull request to the project, please add yourself to `AUTHORS.md`.
+If you contribute a pull request to the project, please add yourself to `AUTHORS.md`.
diff --git a/README.md b/README.md
@@ -4,8 +4,8 @@
 
 In other words, it's just a load of functions that implement important equations in (mostly seismic) geophysics, from Aki-Richards to Zoeppritz.
 
-[![Run tests](https://github.com/agile-geoscience/bruges/actions/workflows/run-tests.yml/badge.svg)](https://github.com/agile-geoscience/bruges/actions/workflows/run-tests.yml)
-[![Build docs](https://github.com/agile-geoscience/bruges/actions/workflows/build-docs.yml/badge.svg)](https://github.com/agile-geoscience/bruges/actions/workflows/build-docs.yml)
+[![Run tests](https://github.com/agilescientific/bruges/actions/workflows/run-tests.yml/badge.svg)](https://github.com/agilescientific/bruges/actions/workflows/run-tests.yml)
+[![Build docs](https://github.com/agilescientific/bruges/actions/workflows/build-docs.yml/badge.svg)](https://github.com/agilescientific/bruges/actions/workflows/build-docs.yml)
 [![PyPI version](https://img.shields.io/pypi/v/bruges.svg)](https://pypi.python.org/pypi/bruges/)
 [![PyPI versions](https://img.shields.io/pypi/pyversions/bruges.svg)](https://pypi.org/project/bruges//)
 [![PyPI license](https://img.shields.io/pypi/l/bruges.svg)](https://pypi.org/project/bruges/)
@@ -32,7 +32,7 @@ This produces two arrays: amplitude `w` and time `t`.
 ## Links
 
 - [Documentation](https://code.agilescientific.com/bruges)
-- [Issue Tracker](https://github.com/agile-geoscience/bruges/issues/)
+- [Issue Tracker](https://github.com/agilescientific/bruges/issues/)
 - [PyPi](http://pypi.python.org/pypi/bruges/)
 - [Agile's website](http://www.agilescientific.com)
 

diff --git a/bruges/__init__.py b/bruges/__init__.py
@@ -17,8 +17,17 @@
 from .get_bruges import get_bruges
 from .bruges import BrugesError
 
-__version__ = "unknown"
+from pkg_resources import get_distribution, DistributionNotFound
+
 try:
-    from ._version import __version__
-except ImportError:
-    pass
+    VERSION = get_distribution(__name__).version
+except DistributionNotFound:
+    try:
+        from ._version import version as VERSION
+    except ImportError:
+        raise ImportError(
+            "Failed to find (autogenerated) _version.py. "
+            "This might be because you are installing from GitHub's tarballs, "
+            "use the PyPI ones."
+            )
+__version__ = VERSION
diff --git a/bruges/filters/convolve.py b/bruges/filters/convolve.py
@@ -8,43 +8,43 @@
 from bruges.util import apply_along_axis
 
 
-def convolve(arr, wavelet, axis=-1, verbose=False):
+def convolve(arr, v, axis=-1, verbose=False):
     """
     Convolve n-dimensional arr with a 1D wavelet or 2D wavelet bank.
     
     Args:
         arr (ndarray): The trace, or 2D section, or volume.
-        wavelet (ndarray): The wavelet, must be 1D function or a 2D wavelet 'bank'.
+        v (ndarray): The wavelet, must be 1D function or a 2D wavelet 'bank'.
             If a wavelet bank, time should be on the last axis.
         axis (int): The time axis of the arr data. In other words, the axis
             corresponding to a single 'trace'. If you index into this axis,
             you will get a single 'trace'.
         verbose (bool): If True, print out the shapes of the inputs and output.
 
     Returns:
-        ndarray: Discrete, linear convolution of `arr` and `wavelet`.
+        ndarray: Discrete, linear convolution of `arr` and `v`.
     """
-    if wavelet.shape[-1] > arr.shape[axis]:
-        raise TypeError("Wavelet must shorter in time than the arr.")
+    if v.shape[-1] > arr.shape[axis]:
+        raise TypeError("v (e.g. wavelet) must be shorter in time than arr (e.g. reflectivity).")
 
     arr_ = np.moveaxis(np.asanyarray(arr), axis, -1)
 
     # Compute the target shape of the final synthetic.
-    outshape = wavelet.shape[:-1] + arr_.shape
+    outshape = v.shape[:-1] + arr_.shape
 
-    # Force wavelet and arr to both be 2D.
-    bank = np.atleast_2d(wavelet)   
+    # Force v and arr to both be 2D.
+    bank = np.atleast_2d(v)   
     arr_2d = arr_.reshape((-1, arr_.shape[-1]))
 
     # Compute synthetic.
     syn = np.array([apply_along_axis(np.convolve, arr_2d, w, mode='same') for w in bank])
 
-    pos = axis + wavelet.ndim - 1
+    pos = axis + v.ndim - 1
 
     out = np.moveaxis(syn.reshape(outshape), -1, pos)
 
     # Show the shapes of the data we're handling.
     if verbose:
-        print(arr.shape, ' * ', wavelet.shape, ' -> ', out.shape)
+        print(arr.shape, ' * ', v.shape, ' -> ', out.shape)
 
     return out
diff --git a/bruges/filters/wavelets.py b/bruges/filters/wavelets.py
@@ -368,6 +368,8 @@ def klauder(duration, dt, f,
 
     if autocorrelate:
         w = [np.correlate(c_, c_, mode='same') for c_ in c]
+    else:
+        w = c
 
     w = np.squeeze(w) / np.amax(w)
 

diff --git a/docs/_static/ormsby-vs-ormsby_fft.png b/docs/_static/ormsby-vs-ormsby_fft.png
diff --git a/docs/_userguide/Making_wavelets.ipynb b/docs/_userguide/Making_wavelets.ipynb
diff --git a/docs/_userguide/Quick_start_wedge.ipynb b/docs/_userguide/Quick_start_wedge.ipynb
diff --git a/docs/_userguide/Seismic_attributes.ipynb b/docs/_userguide/Seismic_attributes.ipynb
diff --git a/docs/_userguide/Wedge_models.ipynb b/docs/_userguide/Wedge_models.ipynb
diff --git a/docs/conf.py b/docs/conf.py
@@ -58,6 +58,10 @@ def setup(app):
 
 myst_enable_extensions = ["dollarmath", "amsmath"]
 
+# MyST notebook execution
+jupyter_execute_notebooks = 'force'
+execution_timeout = 120
+
 # Apidoc automation
 # https://pypi.org/project/sphinxcontrib-apidoc/
 # The apidoc extension and this code automatically update apidoc.

diff --git a/docs/data/F3_seismic.npy b/docs/data/F3_seismic.npy
diff --git a/docs/index.rst b/docs/index.rst
@@ -3,7 +3,7 @@
 .. container:: noclass
    :name: forkongithub
 
-   `Fork on GitHub <https://github.com/agile-geoscience/bruges>`_
+   `Fork on GitHub <https://github.com/agilescientific/bruges>`_
 
 bruges is a
 ===========
@@ -54,7 +54,9 @@ User guide
 
     installation
     userguide/Quick_start_wedge.ipynb
+    userguide/Making_wavelets.ipynb
     userguide/Wedge_models.ipynb
+    userguide/Seismic_attributes.ipynb
 
 
 API reference
@@ -94,8 +96,8 @@ Indices and tables
     :hidden:
 
     PyPI releases <https://pypi.org/project/bruges/>
-    Code in GitHub <https://github.com/agile-geoscience/bruges>
-    Issue tracker <https://github.com/agile-geoscience/bruges/issues>
+    Code in GitHub <https://github.com/agilescientific/bruges>
+    Issue tracker <https://github.com/agilescientific/bruges/issues>
     Community guidelines <https://code.agilescientific.com/community>
     Agile's software <https://code.agilescientific.com>
     Agile's website <https://www.agilescientific.com>
diff --git a/setup.cfg b/setup.cfg
@@ -6,7 +6,7 @@ author_email = [email protected]
 description = A library of geophysical equations.
 long_description = file: README.md
 long_description_content_type = text/markdown
-url = https://github.com/agile-geoscience/bruges
+url = https://github.com/agilescientific/bruges
 classifiers =
     Intended Audience :: Science/Research
     Development Status :: 4 - Beta