.gitlab-ci.yml

+workflow:
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event"
+    - if: $CI_COMMIT_BRANCH && $CI_OPEN_MERGE_REQUESTS
+      when: never
+    - if: $CI_COMMIT_BRANCH
+    - if: $CI_COMMIT_TAG
+
 before_script:
     # Install requirements for empyre:
-    - conda env create -q # -q: quiet/ no progressbar, because it spams the log!
-    - conda init bash  # needed from conda 4.4 onwards, see https://stackoverflow.com/a/55507956/2286972
-    - source ~/.bashrc  # Reldad bashrc to apply changes made by conda init
+    - source ${CONDA_DIR}/etc/profile.d/conda.sh
+    - conda create -q --name empyre # -q: quiet/ no progressbar, because it spams the log!
     - conda activate empyre
+    - conda install -y python numpy sphinx pip setuptools jupyter pandoc uv
+    - uv pip install .[tests,docs]
     - conda info --envs
     # Install jutil via deploy token access:  # TODO: still needed?
     #- pip install git+https://empyre:"$JUTIL_DEPLOY_TOKEN"@jugit.fz-juelich.de/j.ungermann/jutil.git
@@ -14,18 +23,19 @@ stages:
 
 test_style:
     stage: test
-    image: continuumio/miniconda3:latest
+    image: condaforge/miniforge3:latest
     script:
-        # -m: only run tests marked with "flake8"
-        - pyroma . --min=10  # Checks setup.py for cheese! Maximum cheese 10!
-        - python setup.py test --addopts "--flake8 -m flake8"
+        - pip install pre-commit
+        - pre-commit install
+        - pre-commit run --all-files
 
 test_function:
     stage: test
-    image: continuumio/miniconda3:latest
+    image: condaforge/miniforge3:latest
     script:
         # Execute all tests and also check coverage with --cov:
-        - python setup.py test --addopts "--cov"
+        - pip install "numpy>=2"
+        - pytest --cov
     artifacts:
         paths:
             - .coverage
@@ -33,13 +43,13 @@ test_function:
 
 test_docs:
     stage: test
-    image: continuumio/miniconda3:latest
+    image: condaforge/miniforge3:latest
     script:
         # -f: Force overwriting of any existing generated files.
         # -e: Put documentation for each module on its own page.
         # -o: Directory to place the output files. If it does not exist, it is created.
         # last parameter: module path
-        - python setup.py  clean  # TODO: Simplest way to generate version.py without doing anything else?
+        # - python setup.py  clean  # TODO: Simplest way to generate version.py without doing anything else?
         #- sphinx-apidoc -f -e -o docs/api src/empyre
         # Build the documentation from 'docs' and put into 'build/sphinx':
         - sphinx-build docs build/sphinx -W  # -w fails the build if warnings appear!
@@ -50,9 +60,10 @@ test_docs:
 
 test_install:
     stage: test
-    image: continuumio/miniconda3:latest
+    image: condaforge/miniforge3:latest
     before_script: []  # before_script not needed here!
     script:
+        - conda install -y "python<3.12"
         - pip install .[all]
 
 pages:
@@ -71,11 +82,11 @@ pages:
 
 pypi:
     stage: deploy
-    image: continuumio/miniconda3:latest
+    image: condaforge/miniforge3:latest
     before_script: []  # before_script not needed here!
     script:
-        - pip install twine
-        - python setup.py sdist bdist_wheel
+        - pip install hatch twine
+        - hatch build
         - twine upload -u __token__ -p $PYPI_ACCESS_TOKEN dist/*  # -u user -p password upload_source
     rules:  # similar to only/except, but newer!
         # Job is executed if branch is master AND if a tag is building which matches the regular expression!

.pre-commit-config.yaml

+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+  - id: trailing-whitespace
+    files: ^src/
+  - id: end-of-file-fixer
+    files: ^src/
+  - id: check-yaml
+  - id: check-added-large-files
+- repo: https://github.com/pycqa/flake8
+  rev: 7.0.0
+  hooks:
+  - id: flake8
+    exclude: ^prototypes/
+- repo: https://github.com/regebro/pyroma
+  rev: "4.2"
+  hooks:
+  - id: pyroma
\ No newline at end of file

MANIFEST.in

 include src/empyre/vis/mplstyles/*.mplstyle
+graft tests

authors.json

@@ -38,5 +38,13 @@
         "gitlab": "wessels",
         "contribution": "Discussions, testing",
         "orcid": "0000-0001-5526-639X"
+    },
+    {
+        "displayname": "Matthew Bryan",
+        "authorname": "Bryan, Matthew",
+        "affiliation": "CEA-Leti",
+        "gitlab": "bryan",
+        "orcid": "0000-0001-9134-384X",
+        "contribution": "Small bugfixes, CI and conda packaging"
     }
-]
+]
\ No newline at end of file

docs/conf.py

@@ -33,13 +33,11 @@ author = 'Jan Caron'
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.viewcode',
-    'numpydoc',
-    'nbsphinx',
-    'nbsphinx_link'
-    ]
+extensions = ['sphinx.ext.autodoc',
+              'sphinx.ext.viewcode',
+              'numpydoc',
+              'nbsphinx',
+              'nbsphinx_link']
 
 numpydoc_show_class_members = False
 add_module_names = False
@@ -78,3 +76,7 @@ html_logo = 'EMPyRe Logo.png'
 # the doc.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
 html_favicon = 'icon.ico'
+
+# cannot cache unpickable configuration value: 'nbsphinx_custom_formats
+# See https://github.com/sphinx-doc/sphinx/issues/12300
+suppress_warnings = ["config.cache"]

environment.yml

-# Create environment with "conda env create", update with "conda env update"!
-# This file contains the top level dependencies of the empyre project!
-# requirements.txt also contains sub-dependencies, generated by "pip freeze > requirements.txt"!
-# Add new dependencies here, then "conda env update", then "pip freeze > requirements.txt"!
-# To see if compatible upgrades are available for the current packages, use "conda upgrade --all"!
-# When packages are deprecated/deleted, it may be best to recreate the environment from scratch!
-
-name: empyre
-
-channels:
-  - defaults  # Default conda channels, on top to keep highest priority!
-  - conda-forge  # Used for hyperspy, pyFFTW!
-
-dependencies:
-  # Basic:
-  - python=3.7
-  - setuptools
-  - numpy=1.17
-  - scipy=1.3
-  - tqdm=4.36
-  - scikit-image=0.15
-  # File IO:
-  - hyperspy=1.5
-  - hyperspy-gui-ipywidgets=1.2
-  #- h5py=2.9  # TODO: dependency of hyperspy? Not needed here?
-  # Plotting and colors:
-  - matplotlib=3.1
-  - Pillow=6.1
-  - cmocean=2.0
-  # 3D plotting:
-  - mayavi=4.7
-  - ipyevents=0.7
-  - ipywidgets=7.5
-  # Testing:
-  - pytest=5.0
-  - pytest-cov=2.7
-  - pytest-flake8=1.0
-  - pytest-runner=5.1
-  - pyroma  # Checks setup.py for cheese!
-  #- pytest-mpl=0.10  # Needed for testing hyperspy! # TODO: Use for pyramid/plotting library, too!
-  - coverage=4.5
-  # Documentation:
-  - sphinx=2.4
-  - numpydoc=0.9
-  - sphinx_rtd_theme=0.4
-  - nbsphinx=0.7
-  - nbsphinx-link=1.3
-  - pandoc=2.11
-  # IPython and notebooks:
-  - ipython=7.7
-  - jupyter=1.0
-  - nb_conda=2.2
-  #- ptvsd=4.3  # Cell debugging in VS Code
-  - rope=0.16  # for refactoring in VS Code
-  # TODO: - ipywidgets
-  # TODO: Add back GUI dependencies!
-  # TODO: Get Jutil from gitlab (currently doesn't work, git and cygwin don't play nice,...
-  # TODO: ...because one is Unix, ond is Windows).
-  # Fast computation:
-  - pyFFTW=0.11
-  # TODO: ? - pathos  # pathos.multiprocessing uses dill instead of pickle
-  # PIP installations:
-  #- pip=19.0
-#  - pip:
-#    # ALSO NEEDS JUTIL!
-#    - "git+ssh://gitlab@iffgit.fz-juelich.de/unger/jutil.git"
-  # Misc.:
-  - nodejs=12.8  # TODO: Needs to be fixed to prevent errors! Check again if needed in future!

pyproject.toml

+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "empyre"
+dynamic = ["version"]
+description = "Electron Microscopy Python Reconstruction"
+readme = "README.rst"
+license = "GPL-3.0-or-later"
+requires-python = ">=3.6"
+authors = [
+    { name = "Jan Caron", email = "j.caron@fz-juelich.de" },
+]
+keywords = [
+    "Electron Microscopy",
+    "Inverse Problem Solving",
+    "Model-based Reconstrution",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Topic :: Scientific/Engineering",
+]
+dependencies = [
+    "matplotlib >= 3.2",
+    "numpy >= 1.17",
+    "Pillow",
+    "scikit-image",
+    "scipy",
+    "tqdm",
+]
+
+[project.optional-dependencies]
+3d = [
+    "mayavi >= 4.7",
+]
+all = [
+    "cmocean",
+    "pyfftw",
+]
+colors = [
+    "cmocean",
+]
+docs = [
+    "nbsphinx",
+    "nbsphinx_link",
+    "numpydoc",
+    "pandoc",
+    "sphinx",
+    "sphinx_rtd_theme",
+]
+fftw = [
+    "pyfftw",
+]
+io = [
+    "hyperspy",
+    "tvtk",
+]
+tests = [
+    "coverage",
+    "pyroma",
+    "pytest",
+    "pytest-cov",
+    "pytest-flake8",
+    "pytest-runner",
+]
+
+[project.urls]
+Homepage = "https://iffgit.fz-juelich.de/empyre/empyre"
+
+[tool.hatch.version]
+path = "src/empyre/__init__.py"
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "/src",
+    "/tests",
+]

setup.cfg

@@ -2,71 +2,6 @@
 # setup.cfg
 # :copyright: Copyright 2020 Jan Caron
 
-
-# CONFIGURATION FOR SETUP.PY:
-
-[metadata]
-name = empyre
-version = 0.2.1
-author = Jan Caron
-author-email = j.caron@fz-juelich.de
-description = Electron Microscopy Python Reconstruction
-long-description = file: README.rst
-url = https://iffgit.fz-juelich.de/empyre/empyre
-license = GPLv3
-classifiers =
-    Development Status :: 3 - Alpha
-    Intended Audience :: Developers
-    Intended Audience :: Science/Research
-    License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-    Programming Language :: Python :: 3.7
-    Topic :: Scientific/Engineering
-    Operating System :: OS Independent
-keywords =
-    Electron Microscopy
-    Inverse Problem Solving
-    Model-based Reconstrution
-
-[options]
-zip_safe = False
-include_package_data = True
-package_dir =
-    =src
-packages = find:
-python_requires = >=3.6
-setup_requires =
-    setuptools
-install_requires =
-    numpy >= 1.17
-    matplotlib >= 3
-    scikit-image
-    tqdm
-    scipy
-    Pillow
-
-[options.packages.find]
-where = src
-
-[options.extras_require]
-io =
-    hyperspy
-    tvtk
-fftw =
-    pyfftw
-colors =
-    cmocean
-3d =
-    mayavi >= 4.7
-all =
-    pyfftw
-    cmocean
-tests =
-    pyroma
-    coverage
-    pytest
-    pytest-cov
-    pytest-flake8
-    pytest-runner
 # TODO: pip install .[io] is not working because hyperspy depends on trait which has no wheels on PyPI at the moment...
 # TODO: See https://github.com/hyperspy/hyperspy/issues/2315 and https://github.com/enthought/traits/issues/357
 # TODO: Add hyperspy back as soon (if?) this is resolved... Until then: install hyperspy with conda!
@@ -86,13 +21,20 @@ omit =
 [flake8]
 max-line-length = 120
 ignore =
-    E402  # module import not at top of file
-    E124  # closing bracket does not match visual indentation
-    E125  # continuation line with same indent as next logical line
-    E226  # missing whitespace around arithmetic operator
-    W503  # line break before binary operator
-    W504  # line break after binary operator
-    E741  # do not use variables named ‘l’, ‘O’, or ‘I’
+    # module import not at top of file
+    E402
+    # closing bracket does not match visual indentation
+    E124
+    # continuation line with same indent as next logical line
+    E125
+    # missing whitespace around arithmetic operator
+    E226
+    # line break before binary operator
+    W503
+    # line break after binary operator
+    W504
+    # do not use variables named ‘l’, ‘O’, or ‘I’
+    E741
 per-file-ignores =
     */__init__.py: F401, F403, F405, F821
     # F401: module imported but unused

setup.py

-#!python
-# coding=utf-8
-"""Setup for testing, building, distributing and installing the 'EMPyRe'-package"""
-
-
-import os
-import subprocess
-from setuptools import setup, config
-
-
-# Read version from setup.py:
-version = config.read_configuration('setup.cfg')['metadata']['version']
-# Get current git revision:
-try:
-    git_rev = subprocess.check_output(['git', 'rev-parse', 'HEAD']).strip().decode()
-except Exception:
-    git_rev = "???"
-# Write both to version.py:
-print(R'writing src\empyre\version.py')
-with open(os.path.join(os.path.dirname(__file__), 'src', 'empyre', 'version.py'), 'w') as vfile:
-    vfile.write('# -*- coding: utf-8 -*-\n' +
-                '""""This file was automatically generated by `setup.py`"""\n' +
-                f'version = "{version}"\n' +
-                f'git_revision = "{git_rev}"\n')
-
-# Run setup (reads metadata & options from setup.cfg):
-print(R'running setup.py')
-setup()

src/empyre/__init__.py

@@ -11,16 +11,13 @@ from . import models
 from . import reconstruct
 from . import vis
 from . import utils
-from .version import version as __version__
-from .version import git_revision as __git_revision__
+
+__version__ = "0.3.4"
+__git_revision__ = "undefined"
 
 import logging
 _log = logging.getLogger(__name__)
-_log.info(f'Imported EMPyRe V-{__version__} GIT-{__git_revision__}')
+_log.info(f'Imported EMPyRe V-{__version__}')
 del logging
 
-
 __all__ = ['fields', 'io', 'models', 'reconstruct', 'vis', 'utils']
-
-
-del version

src/empyre/fields/field.py

@@ -10,8 +10,13 @@ from numbers import Number
 from numpy.lib.mixins import NDArrayOperatorsMixin
 
 import numpy as np
-from numpy.core import numeric
-from scipy.ndimage import interpolation
+try:
+    #  numpy >= 2
+    from numpy.lib.array_utils import normalize_axis_tuple
+except ModuleNotFoundError:
+    #  numpy < 2
+    from numpy.core.numeric import normalize_axis_tuple
+from scipy import ndimage
 
 from ..utils import Quaternion
 
@@ -163,6 +168,8 @@ class Field(NDArrayOperatorsMixin):
         # outputs = kwargs.pop('out', ())  # TODO: Necessary?
         outputs = kwargs.pop('out', (None,)*ufunc.nout)  # Defaults to tuple of None (currently: nout=1 all the time)
         outputs_arr = tuple([np.asarray(out) if isinstance(out, Field) else out for out in outputs])
+        if all(a is None for a in outputs_arr):
+            outputs_arr = None
         # Cannot handle items that have __array_ufunc__ (other than our own).
         for item in inputs + outputs:
             if hasattr(item, '__array_ufunc__') and not isinstance(item, Field):  # Something else with __array_ufunc__:
@@ -197,7 +204,7 @@ class Field(NDArrayOperatorsMixin):
                 axis = ax_full if axis is None else axis  # This keeps possible components untouched if axis was None!
                 # axis=-1 reduces over the vector components, if they exist
                 # Takes care of pot. neg. indices, ensures tuple!
-                axis = numeric.normalize_axis_tuple(axis, len(field.shape))
+                axis = normalize_axis_tuple(axis, len(field.shape))
                 kwargs['axis'] = axis  # Put normalized axis back into kwargs!
                 if tuple(sorted(axis)) in (ax_full, ax_full_wc):
                     full_reduction = True  # Full reduction (or reduction to just components) takes place:
@@ -386,7 +393,7 @@ class Field(NDArrayOperatorsMixin):
         return Field(self.data.copy(), self.scale, self.vector)
 
     def rotate(self, angle, axis='z', **kwargs):
-        """Rotate the :class:`~.Field`, based on :meth:`~scipy.ndimage.interpolation.rotate`.
+        """Rotate the :class:`~.Field`, based on :meth:`~scipy.ndimage.rotate`.
 
         Rotation direction is from the first towards the second axis. Works for 2D and 3D Fields.
 
@@ -404,9 +411,9 @@ class Field(NDArrayOperatorsMixin):
 
         Notes
         -----
-        All additional kwargs are passed through to :meth:`~scipy.ndimage.interpolation.rotate`.
+        All additional kwargs are passed through to :meth:`~scipy.ndimage.rotate`.
         The `reshape` parameter, controlling if the output shape is adapted so that the input array is contained
-        completely in the output is False per default, contrary to :meth:`~scipy.ndimage.interpolation.rotate`,
+        completely in the output is False per default, contrary to :meth:`~scipy.ndimage.rotate`,
         where it is True.
 
         """
@@ -425,12 +432,12 @@ class Field(NDArrayOperatorsMixin):
         if axis in ('x', 'z'):
             np_angle *= -1
         if not self.vector:  # Scalar field:
-            data_new = interpolation.rotate(self.data, np_angle, axes=axes, **kwargs)
+            data_new = ndimage.rotate(self.data, np_angle, axes=axes, **kwargs)
         else:  # Vector field:
             # Rotate coordinate system:
             comps = [np.asarray(comp) for comp in self.comp]
             if self.ncomp == 3:
-                data_new = np.stack([interpolation.rotate(c, np_angle, axes=axes, **kwargs) for c in comps], axis=-1)
+                data_new = np.stack([ndimage.rotate(c, np_angle, axes=axes, **kwargs) for c in comps], axis=-1)
                 # Up till now, only the coordinates are rotated, now we need to rotate the vectors inside the voxels:
                 rot_axis = {'x': 2, 'y': 1, 'z': 0}[axis]
                 i, j, k = axes[0], axes[1], rot_axis  # next line only works if i != j != k
@@ -442,8 +449,8 @@ class Field(NDArrayOperatorsMixin):
                 data_new = quat.matrix.dot(data_new.reshape((-1, 3)).T).T.reshape(data_new.shape)
             elif self.ncomp == 2:
                 u_comp, v_comp = comps
-                u_rot = interpolation.rotate(u_comp, np_angle, axes=axes, **kwargs)
-                v_rot = interpolation.rotate(v_comp, np_angle, axes=axes, **kwargs)
+                u_rot = ndimage.rotate(u_comp, np_angle, axes=axes, **kwargs)
+                v_rot = ndimage.rotate(v_comp, np_angle, axes=axes, **kwargs)
                 # Up till now, only the coordinates are rotated, now we need to rotate the vectors inside the voxels:
                 ang_rad = np.deg2rad(angle)
                 u_mix = np.cos(ang_rad)*u_rot - np.sin(ang_rad)*v_rot
@@ -667,10 +674,10 @@ class Field(NDArrayOperatorsMixin):
         """
         self._log.debug('Calling zoom')
         if not self.vector:  # Scalar field:
-            data_new = interpolation.zoom(self.data, zoom, **kwargs)
+            data_new = ndimage.zoom(self.data, zoom, **kwargs)
         else:  # Vector field:
             comps = [np.asarray(comp) for comp in self.comp]
-            data_new = np.stack([interpolation.zoom(comp, zoom, **kwargs) for comp in comps], axis=-1)
+            data_new = np.stack([ndimage.zoom(comp, zoom, **kwargs) for comp in comps], axis=-1)
         if isinstance(zoom, Number):  # Zoom is the same for each dimension!
             zoom = (zoom,) * len(self.dim)
         scale_new = tuple([self.scale[i]/z for i, z in enumerate(zoom)])
@@ -687,7 +694,7 @@ class Field(NDArrayOperatorsMixin):
         self._log.debug('Calling flip')
         if self.vector and axis is None:
             axis = tuple(range(len(self.dim)))
-        axis = numeric.normalize_axis_tuple(axis, len(self.shape))  # Make sure, axis is a tuple!
+        axis = normalize_axis_tuple(axis, len(self.shape))  # Make sure, axis is a tuple!
         data_new = np.flip(self.data, axis, **kwargs).copy()  # Only flips space, not component direction!
         if self.vector:
             flip_vec = [

src/empyre/io/field_plugins/vtk.py

@@ -11,7 +11,7 @@ from numbers import Number
 import numpy as np
 
 from ...fields.field import Field
-from ...utils.misc import interp_to_regular_grid
+from ...utils.misc import interp_to_regular_grid, restrict_points
 from ...vis import colors
 
 
@@ -20,7 +20,7 @@ _log = logging.getLogger(__name__)
 file_extensions = ('.vtk',)  # Recognised file extensions
 
 
-def reader(filename, scale=None, vector=None, **kwargs):
+def reader(filename, scale=None, vector=None, bounds=None, **kwargs):
     """More infos at:
 
     overview: https://docs.enthought.com/mayavi/mayavi/data.html
@@ -88,6 +88,10 @@ def reader(filename, scale=None, vector=None, **kwargs):
             scale = (scale,) * 3
         elif isinstance(scale, tuple):
             assert len(scale) == 3, f'Each dimension (z, y, x) needs a scale, but {scale} was given!'
+        # Crop data to required range, if necessary
+        if bounds is not None:
+            _log.info('Restrict data')
+            point_array, data_array = restrict_points(point_array, data_array, bounds)
         data = interp_to_regular_grid(point_array, data_array, scale, **kwargs)
     else:
         raise TypeError('Data type of {} not understood!'.format(output))

src/empyre/utils/misc.py

@@ -15,7 +15,7 @@ from scipy.spatial import cKDTree, qhull
 from scipy.interpolate import LinearNDInterpolator
 
 
-__all__ = ['levi_civita', 'interp_to_regular_grid']
+__all__ = ['levi_civita', 'interp_to_regular_grid', 'restrict_points']
 _log = logging.getLogger(__name__)
 
 
@@ -121,3 +121,39 @@ def interp_to_regular_grid(points, values, scale, scale_factor=1, step=1, convex
         # Set these points to zero (NOTE: This can take a looooong time):
         interpolation[mask, :] = 0
     return np.squeeze(interpolation)
+
+
+def restrict_points(point_array, data_array, bounds):
+    """Restrict range of point_array and data_array
+
+    Parameters
+    ----------
+    points_array : np.ndarray, (N, 3)
+        Array of points, describing the location of the values that should be interpolated. Three columns x, y, z!
+    data_array : np.ndarray, (N, c)
+        Array of values that should be interpolated to the new grid. `c` is the number of components (`1` for scalar
+        fields, `3` for normal 3D vector fields).
+    bounds : tuple of 6 values
+        Restrict data range to given bounds, x0, x1, y0, y1, z0, z1.
+
+    Returns
+    -------
+    point_restricted: np.ndarray
+        Cut out of the array of points inside the bounds, describing the location of the values that should be
+        interpolated. Three columns x, y, z!
+    value_restricted: np.ndarray
+        Cut out of the array of values inside the bounds, describing the location of the values that should be
+        interpolated. Three columns x, y, z!
+
+    """
+    point_restricted = []
+    data_restricted = []
+    for i, pos in enumerate(point_array):
+        if bounds[0] <= pos[0] <= bounds[1]:
+            if bounds[2] <= pos[1] <= bounds[3]:
+                if bounds[4] <= pos[2] <= bounds[5]:
+                    point_restricted.append(pos)
+                    data_restricted.append(data_array[i])
+    point_restricted = np.array(point_restricted)
+    data_restricted = np.array(data_restricted)
+    return point_restricted, data_restricted

src/empyre/vis/colors.py

@@ -64,7 +64,7 @@ class Colormap3D(colors.Colormap, metaclass=abc.ABCMeta):
 
         """
         self._log.debug('Calling rgb_from_vector')
-        x, y, z = np.asarray(vector)
+        x, y, z = vector
         R = np.sqrt(x ** 2 + y ** 2 + z ** 2)
         R_max = vmax if vmax is not None else R.max() + 1E-30
         # FIRST color dimension: HUE (1D ring/angular direction)

src/empyre/vis/mplstyles/empyre-image.mplstyle

 ### MATPLOTLIB STYLESHEET FOR EMPYRE IMAGES
 
-text.usetex                   : True      ## use TeX to render text
-
 font.family                   : serif     ## default font family (use serifs)
 font.serif                    : cm        ## Computer Modern (LaTeX font)
 

src/empyre/vis/mplstyles/empyre-plot.mplstyle

 ### MATPLOTLIB STYLESHEET FOR EMPYRE PLOTS
 
-text.usetex                   : True      ## use TeX to render text
-
 font.family                   : serif     ## default font family (use serifs)
 font.serif                    : cm        ## Computer Modern (LaTeX font)
 

src/empyre/vis/mplstyles/empyre-save.mplstyle

 ### MATPLOTLIB STYLESHEET FOR SAVING EMPYRE IMAGES AND PLOTS
 
-text.usetex          : True      ## use TeX to render text
-
 font.family          : serif     ## default font family (use serifs)
 font.serif           : cm        ## Computer Modern (LaTeX font)