Bcdi

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* Feature: implement ``publication/bcdi_diffpattern_from_reconstruction.py``, to
compare with the experimental measurement in the crystal frame.

* Refactor: simplify PRTF calculations.

* Feature: implement the inplane rocking curve at CRISTAL.

* Feature: implement ``graph_utils.savefig`` to save figures for publication with and
without labels.

* Feature: implement ``angular_profile.py`` to calculate the width of linecuts through
the center of mass of a 2D object at different angles.

* Feature: implement ``line_profile.py`` to calculate line profiles along particular
directions in 2D or 3D objects.

----------------

* Feature: implement ``interpolate_cdi.py``, to interpolate the intensity of masked
voxels using the centrosymmetry property

* Feature: implement the interpolation of the reciprocal space data in the laboratory
frame using the linearized transformation matrix

* Refactor: update the calculation of the transformation matrices when chi is non-zero

* Feature: allow different voxel sizes in each dimension in ``strain.py``
(NOT BACK COMPATIBLE)

* Feature: implement validation functions in ``utils.validation.py`` for commonly used
parameters, implement related unit tests

* Refactor: merge the class SetupPostprocessing and SetupPreprocessing in a single
class Setup due to code redundances

* Feature: implement ``linecut_diffpattern.py``, a GUI to get a linecut of a 3D
diffraction pattern along a desired direction

* Feature: add a GUI to ``prtf_bcdi.py``, to get a linecut of the 3D PRTF along a
desired direction

* Feature: implement ``center_of_rotation.py``, to calculate the distance of the
crystal to the center of rotation

* Bug: in ``facet_strain.py``, solve bugs in plane fitting when the facet is parallel
to an axis

* Feature: implement ``rotate_scan.py``, to rotate a 3D reciprocal space map around a
vector

* Refactor: in ``modes_decomposition.py``, implement skipping alignment between datasets
or aligning based on a support

-------------

* Feature: implement support for MAXIV NANOMAX beamline

* Feature: implement ``rocking_curves.py`` to follow the evolution of the Bragg peak
between several rocking curves

* Feature: implement ``flatten_modulus.py`` to remove low frequency artefacts in the
modulus reconstructed by phase retrieval

* Feature: implement ``xcca_3D_map.py`` to calculate the angular cross-correlation
CCF(q,q) over a range in q

* Feature: implement ``view_ccf.py`` and ``view_ccf_map.py`` to plot the
cross-correlation function output

* Feature: implement the 3D angular X-ray cross-correlation analysis

* Refactor: allow the reloading of binned data and its orthogonalization in
``preprocess_cdi.py`` and ``preprocess_bcdi.py``

* Feature: implement ``crop_npz.py`` to crop combined stacked data to the desired size

* Feature: implement ``scan_analysis.py`` to plot interactively the integrated
intensity in a region of interest for a 1D scan

* Feature: implement ``view_mesh.py`` to plot interactively the integrated intensity
in a region of interest for a 2D mesh

* Refactor: when gridding forward CDI data, reverse the rotation direction to
compensate the rotation of Ewald sphere

* Refactor: updated ``extract_bulk_surface.py`` to use module functions

* Bug: treat correctly the case angle=pi/2 during the interpolation of CDI data onto
the laboratory frame

* Refactor: solve instabilities resulting from duplicate vertices after smoothing in
``facet_strain.py``

* Refactor: modify ``polarplot.py`` to use module functions instead of inline script

* Feature: implement ``coefficient_variation.py`` to compare several reconstructed
modulus of a BCDI dataset

* Feature: implement diffraction_angles.py`` to find Bragg reflections for a particular
goniometer setup, based on xrayutilities

* Feature: add the option of restarting masking the aliens during preprocessing,
not back compatible with previous versions

* Feature: implement simultaneous masking over the 3 axes in two new preprocessing
scripts ``preprocess_bcdi.py`` and ``preprocess_cdi.py``

* Feature: implement ``domain_orientation.py`` to find the orientation of domains in a
3D forward CDI dataset of mesocrystal

* Feature: implement ``simu_diffpattern_CDI.py`` to find in 3D the Bragg peaks positions
of a mesocrystal (supported unit cells: FCC, simple cubic, BCC and BCT)

* Feature: implement ``fit_1D curve.py`` to fit simultaneously ranges of a 1D curve with
gaussian lineshapes

* Feature: implement ``fit_background.py`` to interactively determine the background in
1D reciprocal space curves

* Refactor: in ``multislices_plot()`` and ``contour_slices()``, allow to plot the data
at user-defined slices positions.

* Feature: implement ``prtf_bcdi_2D.py`` to calculate the PRTF also for 2D cases.

-------------

* Feature: implement ``3Dobject_movie.py``, creating movies of a real-space 3D object.

* Feature: implement ``modes_decomposition.py``, decomposition of a set of reconstructed
object in orthogonal modes (adapted from PyNX)

* Bug: correct the calculation of q when data is binned

* implement scripts to visualize isosurfaces of reciprocal/real space including
publication options (in /publication/)

* implement ``algorithms_utils.py``, featuring psf and image deconvolution using
Richardson-Lucy algorithm

* implement separate PRTF resolution estimation for CDI (``prtf_cdi.py``) and BCDI
(``bcdi_prtf.py``) datasets

* Feature: implement ``angular_average.py`` to average 3D CDI reciprocal space data in
1D curve

* Feature: implement view_psf to plot the psf output of a phase retrieval with partial
coherence

* Refactor: change name of ``make_support.py`` to ``rescale_support.py``

-------------
* Feature: implement ``supportMaker()`` class to define a support from a set of planes

* Feature: implement ``maskMaker()`` class for easier implementation of new masking
features

* Debug ``prepare_bcdi_mask.py`` for energy scans at ID01

* Feature: implement ``utils/scripts/make_support.py``, to rescale a support for phasing
with a larger FFT window

* Feature/refactor: implement ``prepare_cdi_mask.py`` for forward CDI, rename existing
as ``prepare_bcdi_mask.py`` for Bragg CDI

* Feature: add the possibility to change the detector distance in ``simu_noise.py``

* Feature: add the possibility to pre-process data acquired without scans, e.g. in a
macro (no spec file)

* Feature: in ``strain.py``, implement phase unwrapping so that the phase range can be
larger than 2*pi

* Feature: in ``facet_strain.py``, implement edge removal for more precise statistics
on facet strain

* Feature: in ``facet_strain.py``, allow anisotropic voxel size and user-defined
reference axis in the stereographic projection

-------------

* Feature: implement facet detection using a stereographic projection in
``facet_recognition/scripts/facet_strain.py``

* Feature: Converted ``bcdi/facet_recognition/scripts/facet_strain.py``

* Feature: implement ``bcdi/facet_recognition/facets_utils.py``

* Refactor: exclude voxels left over by coordination number selection in
``postprocessing/postprocessing_utils.find_bulk()``

* Refactor: use the mean amplitude of the surface layer to define the bulk in
``postprocessing/postprocessing_utils.find_bulk()``

* Feature: enable PRTF resolution calculation for simulated data

* Feature: create ``preprocessing/scripts/apodize.py`` to apodize reciprocal space data

* Feature: implement 3d Tukey and 3d Blackman windows for apodization in
``postprocessing_utils()``

* Feature: in ``postprocessing/scripts/resolution_prtf.py``, allow for binning the
detector plane

* Bug: in ``postprocessing/scripts/strain.py``, correct the original array size taking
into account the binning factor

* Feature: implement ``postprocessing_utils.bin_data()``