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v1.4.0 (#270)
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Allow vector's to be smaller than domain
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@prisae
prisae authored Feb 9, 2022
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79 changes: 44 additions & 35 deletions CHANGELOG.rst
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Expand Up @@ -6,37 +6,46 @@ Changelog
""""""""""


*latest* will become v1.4.0
---------------------------
v1.4.0 : Meshing: improve vector
--------------------------------

**2022-02-09**

- Meshes: Non-backwards compatible changes in ``construct_mesh``
(``origin_and_widths``; ``estimate_gridding_options``) when providing
``vector``'s (implemented non-backwards compatible as the old rules were not
intuitive nor logic; previous meshes can still be obtained, mostly, by
setting the parameters carefully).

- Meshes: Non-backwards compatible change in ``construct_mesh``
(``origin_and_widths``; ``estimate_gridding_options``). It is implemented
non-backwards compatible as the old rules were not intuitive nor logic. The
previous meshes can still be obtained by setting the parameters carefully.
- Priority-order changed to ``domain > distance > vector`` (before it was
``domain > vector > distance``).
- A ``vector`` is new cut to the corresponding domain, if ``domain`` or
``distance`` was defined as well (cut at the first point where
``vector <= domain[0]``, ``vector >= domain[1]``).
- A provided ``vector`` is new trimmed to the corresponding domain if it is
larger than a also provided domain (from ``domain`` or ``distance``);
trimmed at the first point where
``vector <= domain[0]``, ``vector >= domain[1]``.
- A ``vector`` can new also be smaller than the defined domain, and the
domain is then filled according to the normal rules; the last cell of
``vector`` in each direction is taken as starting width for the expansion.

- Removed functions and modules that were deprecated in v1.2.1.
- Bugfixes and maintenance:

- Bugfix when adding ``add_noise`` explicitly to ``Simulation.compute()``.
- Removed functions and modules that were deprecated in v1.2.1.
- Fixed kwargs-error when adding ``add_noise`` explicitly to
``Simulation.compute()``.
- Python 3.10 added to tests; Python 3.7 tests reduced to minimum.

- Maintenance: Python 3.10 added to tests; Python 3.7 reduced to minimum.


v1.3.2: Bugfix CLI-select
-------------------------
v1.3.2 : Bugfix CLI-select
--------------------------

**2021-12-01**

CLI: Add ``remove_empty`` to parameter file; set to ``False`` by default
(pre-v1.3.1 behaviour, and therefore backwards compatible).


v1.3.1: Select: remove empty pairs
----------------------------------
v1.3.1 : Select: remove empty pairs
-----------------------------------

**2021-11-20**

Expand All @@ -46,8 +55,8 @@ v1.3.1: Select: remove empty pairs
- Maintenance: Added a cron to GHA; 20th of every month at 14:14.


v1.3.0: File-based computations
-------------------------------
v1.3.0 : File-based computations
--------------------------------

**2021-10-27**

Expand Down Expand Up @@ -81,8 +90,8 @@ v1.3.0: File-based computations



v1.2.1: Remove optimize & bug fix
---------------------------------
v1.2.1 : Remove optimize & bug fix
----------------------------------

**2021-08-22**

Expand All @@ -104,8 +113,8 @@ v1.2.1: Remove optimize & bug fix
``Simulation.{misfit;gradient}``.


v1.2.0: White noise
-------------------
v1.2.0 : White noise
--------------------

**2021-07-27**

Expand Down Expand Up @@ -151,8 +160,8 @@ v1.2.0: White noise
- Simplified (unified) ``_edge_curl_factor`` (private fct).


v1.1.0: Adjoint-fix for electric receivers
------------------------------------------
v1.1.0 : Adjoint-fix for electric receivers
-------------------------------------------

**2021-06-30**

Expand Down Expand Up @@ -210,8 +219,8 @@ The changes in more detail:
set in the parameter file, which overwrites the described default behaviour.


v1.0.0: Stable API
------------------
v1.0.0 : Stable API
-------------------

**2021-05-28**

Expand Down Expand Up @@ -511,8 +520,8 @@ Detailed changes by module
""""""""""


v0.17.0: Magnetics in Simulation
--------------------------------
v0.17.0 : Magnetics in Simulation
---------------------------------

**2021-03-03**

Expand Down Expand Up @@ -544,8 +553,8 @@ v0.17.0: Magnetics in Simulation
stuff. Currently only stores the data selection to output data.


v0.16.1: Verbosity & Logging
----------------------------
v0.16.1 : Verbosity & Logging
-----------------------------

**2021-02-09**

Expand Down Expand Up @@ -577,8 +586,8 @@ v0.16.1: Verbosity & Logging
above).


v0.16.0: Arbitrarily shaped sources
-----------------------------------
v0.16.0 : Arbitrarily shaped sources
------------------------------------

**2021-01-13**

Expand Down Expand Up @@ -628,8 +637,8 @@ v0.16.0: Arbitrarily shaped sources
``map_coordinates``.


v0.15.3: Move to EMSiG
----------------------
v0.15.3 : Move to EMSiG
-----------------------

**2020-12-09**

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71 changes: 40 additions & 31 deletions emg3d/meshes.py
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Expand Up @@ -371,11 +371,19 @@ def construct_mesh(frequency, properties, center, domain=None, vector=None,
where ``center=(cx, cy, cz)``.
vector : {tuple, ndarray, dict, None}, optional
Contains vectors of mesh-edges that should be used. If provided, the
vector *must* at least include all of the survey domain, to which
extent it will be cut. Format: ``(xvector, yvector, zvector)`` or
Contains vectors of mesh-edges that should be used. Format:
``(xvector, yvector, zvector)`` or
``{'x': xvector, 'y': yvector, 'z': zvector}``.
If also ``domain`` or ``distance`` is defined, the following happens:
- There must be at least two cells within the domain, otherwise
``vector`` is set to None.
- Where the ``vector`` is outside the domain, it will be trimmed to it.
- Where the ``vector`` is smaller than the domain, it will be extended
following the normal rules. The last cell-width in each direction
will be taken as starting cell width, together with the domain
stretching factor.
It can be None, or individual ndarrays can be None (e.g., ``(xvector,
yvector, None)``), in which case you have to provide a ``domain`` or
``distance``. If only one ndarray is provided it is applied to all
Expand Down Expand Up @@ -627,8 +635,7 @@ def origin_and_widths(frequency, properties, center, domain=None, vector=None,

else:
raise ValueError(
"At least one of `domain`, `distance`, "
"and `vector` must be provided."
"At least one of `domain`/`distance`/`vector` must be provided."
)

# Check vector if provided
Expand All @@ -643,12 +650,9 @@ def origin_and_widths(frequency, properties, center, domain=None, vector=None,
if vmax.size > 1:
vector = vector[:vmax[1]]

# Ensure vector spans whole domain.
if vmin.size == 0 or vmax.size == 0:
raise ValueError(
"Provided vector MUST at least include "
"all of the survey domain."
)
# If vector is outside domain, set to None.
if len(vector) < 3:
vector = None

# Seasurface related checks.
if seasurface is not None:
Expand Down Expand Up @@ -700,32 +704,37 @@ def origin_and_widths(frequency, properties, center, domain=None, vector=None,
for sa in np.linspace(1.0, stretching[0], nsa):

if vector is None:
cpart = [center, center]
dlr = [dmin, dmin]
nx0 = 0
else:
cpart = [vector[0], vector[-1]]
dlr = [vector[1]-vector[0], vector[-1]-vector[-2]]
nx0 = 1

# Get current stretched grid cell sizes.
thxl = dmin*sa**np.arange(nx) # Left of origin.
thxr = dmin*sa**np.arange(nx) # Right of origin.
# Get current stretched grid cell sizes.
thxl = dlr[0]*sa**np.arange(nx0, nx) # Left of origin.
thxr = dlr[1]*sa**np.arange(nx0, nx) # Right of origin.

# Adjust stretching for seasurface if required.
if seasurface is not None and seasurface > center:
t_nx = np.r_[center, center+np.cumsum(thxr)]
ii = np.argmin(abs(t_nx-seasurface))
thxr[:ii] *= abs(seasurface-center)/np.sum(thxr[:ii])
# Adjust stretching for seasurface if required.
if seasurface is not None and seasurface > cpart[1]:
t_nx = np.r_[cpart[1], cpart[1]+np.cumsum(thxr)]
ii = np.argmin(abs(t_nx-seasurface))
thxr[:ii] *= abs(seasurface-cpart[1])/np.sum(thxr[:ii])

# Fill from center to left and right domain.
nl = np.sum((center-np.cumsum(thxl)) > domain[0]) + 1
nr = np.sum((center+np.cumsum(thxr)) < domain[1]) + 1
# Fill from center to left and right domain.
nl = np.sum((cpart[0]-np.cumsum(thxl)) >= domain[0]) + (1-nx0)
nr = np.sum((cpart[1]+np.cumsum(thxr)) <= domain[1]) + (1-nx0)

# Create the current hx-array.
# Create the current hx-array.
if vector is None:
hx = np.r_[thxl[:nl][::-1], thxr[:nr]]

# Get actual domain:
asurv_domain = [center - np.sum(thxl[:nl]),
center + np.sum(thxr[:nr])]

else:
# Store actual domain, current hx-array, and number of cells.
asurv_domain = [vector[0], vector[-1]]
hx = np.diff(vector)
hx = np.r_[thxl[:nl][::-1], np.diff(vector), thxr[:nr]]

# Get actual domain:
asurv_domain = [cpart[0] - np.sum(thxl[:nl]),
cpart[1] + np.sum(thxr[:nr])]

# Expand for seasurface if necessary.
if seasurface is not None and seasurface > asurv_domain[-1]:
Expand Down
46 changes: 27 additions & 19 deletions tests/test_meshes.py
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Expand Up @@ -251,12 +251,9 @@ def test_errors(self, capsys):
with pytest.raises(TypeError, match='Unexpected '):
meshes.origin_and_widths(1, 1, 0, [-1, 1], unknown=True)

with pytest.raises(ValueError, match="At least one of `domain`, `d"):
with pytest.raises(ValueError, match="At least one of `domain`/`d"):
meshes.origin_and_widths(1, 1, 0)

with pytest.raises(ValueError, match="Provided vector MUST at least"):
meshes.origin_and_widths(1, 1, 0, [-1, 1], np.array([0, 1, 2]))

with pytest.raises(ValueError, match="The `seasurface` must be bigge"):
meshes.origin_and_widths(1, 1, 0, [-1, 1], seasurface=-2)

Expand Down Expand Up @@ -312,24 +309,35 @@ def test_basics(self, capsys):

def test_domain_vector(self):
inp = {'frequency': 1/np.pi, 'properties': 9*mu_0, 'center': 0.0,
'stretching': [1, 1]}
'stretching': [1, 1.5]}

x01, hx1 = meshes.origin_and_widths(domain=[-1, 1], **inp)
x02, hx2 = meshes.origin_and_widths(vector=np.array([-1, 0, 1]), **inp)

x01b, hx1b = meshes.origin_and_widths( # vector will be set to None
domain=[-1, 1], vector=[-2, -1, 0], **inp)
assert_allclose(x01, x01b)
assert_allclose(hx1, hx1b)

vector2 = np.array([-1, 0, 1])
x02, hx2 = meshes.origin_and_widths(vector=vector2, **inp)
assert np.in1d(vector2, x02 + np.cumsum(hx2)).all()

vector3 = np.array([-2, -1, 0, 1, 2])
x03, hx3 = meshes.origin_and_widths( # vector will be cut
domain=[-1, 1], vector=np.array([-2, -1, 0, 1, 2]), **inp)
x04, hx4 = meshes.origin_and_widths( # vector will be cut
distance=[1, 1], vector=np.array([-2, -1, 0, 1, 2]), **inp)
assert_allclose(x01, x02)
assert_allclose(x01, x03)
assert_allclose(x01, x04)
assert_allclose(hx1, hx2)
assert_allclose(hx1, hx3)
assert_allclose(hx1, hx4)
domain=[-1, 1], vector=vector3, **inp)
assert np.in1d(vector3[1:-1], x03 + np.cumsum(hx3)).all()
assert not np.in1d(vector3[0], x03 + np.cumsum(hx3))
assert not np.in1d(vector3[-1], x03 + np.cumsum(hx3))

x03, hx3 = meshes.origin_and_widths(
1/np.pi, 9*mu_0, 0.0, distance=[1, 1], stretching=[1, 1])
assert_allclose(x01, x03)
assert_allclose(hx1, hx3)
x04, hx4 = meshes.origin_and_widths( # vector will be cut
distance=[1, 1], vector=vector3, **inp)
assert_allclose(x03, x04)
assert_allclose(hx3, hx4)

x05, hx5 = meshes.origin_and_widths( # vector will be expanded
distance=[2.0, 2.0], vector=vector2, **inp)
print(x05 + np.cumsum(hx5))
assert np.in1d(np.array([-2, -1, 0, 1, 2]), x05 + np.cumsum(hx5)).all()

def test_seasurface(self):
x01, hx1 = meshes.origin_and_widths(
Expand Down

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