Update docstrings for release 0.0.9

HISTORY.rst

@@ -1,7 +1,7 @@
 Version 0.0.9
 -------------
 
-* Feature: implement support for MAX IV NANOMAX beamline
+* Feature: implement support for MAXIV NANOMAX beamline
 
 * Feature: implement rocking_curves.py to follow the evolution of the Bragg peak between several rocking curves
 
@@ -11,11 +11,9 @@ Version 0.0.9
 
 * Feature: implement view_ccf.py and view_ccf_map.py to plot the cross-correlation function output
 
-* Remove preprocess_bcdi_sequential.py, which was not maintained anymore. Use preprocess_bcdi_combined.py instead
-
 * Feature: implement the 3D angular X-ray cross-correlation analysis
 
-* Refactor: allow the reloading of binned data and its orthogonalization in preprocess_cdi_combined.py and preprocess_bcdi_combined.py
+* 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
 
@@ -25,7 +23,7 @@ Version 0.0.9
 
 * Refactor: when gridding forward CDI data, reverse the rotation direction to compensate the rotation of Ewald sphere
 
-* Refactor: converted /postprocessing/scripts/extract_bulk_surface.py
+* 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
 
@@ -39,9 +37,7 @@ Version 0.0.9
 
 * Feature: add the option of restarting masking the aliens during preprocessing, not back compatible with previous versions
 
-* Refactor: rename prepare_(b)cdi_mask.py preprocess_(b)cdi_sequential.py
-
-* Feature: implement simultaneous masking over the 3 axes in two new preprocessing scripts preprocess_(b)cdi_combinedl.py
+* 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
 

README.rst

@@ -7,15 +7,15 @@ Introduction
 
 BCDI stands for *Bragg coherent X-ray diffraction imaging*. It can be used for:
 
-* pre-processing BCDI and forward CDI data (masking aliens, detector gaps...) before phase retrieval
+* pre-processing BCDI and forward CDI data (masking aliens, detector gaps ...) before phase retrieval
 
 * post-processing phased data (phase offset and phase ramp removal, averaging, apodization, ...)
 
-* data analysis on diffraction data (stereographic projection, angular cross-correlation analysis)
+* data analysis on diffraction data (stereographic projection, angular cross-correlation analysis, domain orientation fitting ...)
 
-* data analysis on phased data (resolution calculation, statistics on the retrieved strain...)
+* data analysis on phased data (resolution calculation, statistics on the retrieved strain ...)
 
-* simulation of diffraction intensity (including noise, detector gaps, displacement fields...)
+* simulation of diffraction intensity (including noise, detector gaps, displacement field ...)
 
 * creating figures for publication using templates
 
@@ -43,7 +43,7 @@ BCDI can be used as a python library with the following main modules:
 
 8) :mod:`bcdi.utils`: data loading, fitting functions ...
 
-8) :mod:`bcdi.xcca`: X-ray cross-correlation analysis related methods
+9) :mod:`bcdi.xcca`: X-ray cross-correlation analysis related methods
 
 Acknowledgment and third party packages
 =======================================
@@ -102,7 +102,7 @@ Changelog
 =========
 
 .. include:: ../HISTORY.rst
-  :end-before: Version 0.0.6
+  :end-before: Version 0.0.8
 
 See the full :doc:`Changelog<changelog>`
 

bcdi/graph/graph_utils.py

@@ -1045,8 +1045,8 @@ def mlab_contour3d(x, y, z, scalars, contours, extent, nb_labels, fig_size=(400,
     :param scalars: scalar field at each voxel.
     :param contours: integer/list specifying number/list of contours. Specifying a list of values will only give the
      requested contours asked for.
-    :param extent:[xmin, xmax, ymin, ymax, zmin, zmax] Default is the x, y, z arrays extent.
-     Use this to change the extent of the object created.
+    :param extent: [xmin, xmax, ymin, ymax, zmin, zmax] Default is the x, y, z arrays extent. Use this to change
+     the extent of the object created.
     :param nb_labels: the number of labels along each direction.
     :param fig_size: the size of the scene created, in pixels.
     :param azimuth: the azimuthal angle (in degrees, 0-360), i.e. the angle subtended by the position vector on a sphere
@@ -1055,7 +1055,7 @@ def mlab_contour3d(x, y, z, scalars, contours, extent, nb_labels, fig_size=(400,
      and the z-axis. It can be a list of angles for several plots.
     :param distance: a positive floating point number representing the distance from the focal point to place the
      camera. It can be a list of the same length as aimut. If ‘auto’ is passed, the distance is computed to have a best
-      fit of objects in the frame.
+     fit of objects in the frame.
     :param roll: absolute roll angle of the camera. It can be a list of angles for several plots.
     :param vmin: vmin is used to scale the colormap. If None, the min of the data will be used.
     :param vmax: vmax is used to scale the colormap. If None, the max of the data will be used.
@@ -1144,8 +1144,8 @@ def mlab_points3d(x, y, z, scalars, extent, nb_labels, fig_size=(400, 350), azim
     :param y: y position of voxels (numpy.mgrid)
     :param z: z position of voxels (numpy.mgrid)
     :param scalars: scalar field at each voxel.
-    :param extent:[xmin, xmax, ymin, ymax, zmin, zmax] Default is the x, y, z arrays extent.
-     Use this to change the extent of the object created.
+    :param extent: [xmin, xmax, ymin, ymax, zmin, zmax] Default is the x, y, z arrays extent. Use this to change the
+     extent of the object created.
     :param nb_labels: the number of labels along each direction.
     :param fig_size: the size of the scene created, in pixels.
     :param azimuth: the azimuthal angle (in degrees, 0-360), i.e. the angle subtended by the position vector on a sphere
@@ -1154,11 +1154,11 @@ def mlab_points3d(x, y, z, scalars, extent, nb_labels, fig_size=(400, 350), azim
      and the z-axis. It can be a list of angles for several plots.
     :param distance: a positive floating point number representing the distance from the focal point to place the
      camera. It can be a list of the same length as aimut. If ‘auto’ is passed, the distance is computed to have a best
-      fit of objects in the frame.
+     fit of objects in the frame.
     :param roll: absolute roll angle of the camera. It can be a list of angles for several plots.
     :param mode: the mode of the glyphs. Available modes are: ‘2darrow’, ‘2dcircle’, ‘2dcross’, ‘2ddash’, ‘2ddiamond’,
      ‘2dhooked_arrow’, ‘2dsquare’, ‘2dthick_arrow’, ‘2dthick_cross’, ‘2dtriangle’, ‘2dvertex’, ‘arrow’, ‘axes’, ‘cone’,
-      ‘cube’, ‘cylinder’, ‘point’, ‘sphere’
+     ‘cube’, ‘cylinder’, ‘point’, ‘sphere’
     :param vmin: vmin is used to scale the colormap. If None, the min of the data will be used.
     :param vmax: vmax is used to scale the colormap. If None, the max of the data will be used.
     :param opacity:	the overall opacity of the vtk object. Must be a float. Default: 1.0

bcdi/preprocessing/preprocessing_utils.py

@@ -760,8 +760,7 @@ def center_fft(data, mask, detector, frames_logical, centering='max', fft_option
 def check_cdi_angle(data, mask, cdi_angle, frames_logical, debugging=False):
     """
     In forward CDI experiment, check if there is no overlap in the measurement angles, crop it otherwise. Flip the
-    rotation direction to convert sample angles into detector angles.
-     Update data, mask and frames_logical accordingly.
+    rotation direction to convert sample angles into detector angles. Update data, mask and frames_logical accordingly.
 
     :param data: 3D forward CDI dataset before gridding.
     :param mask: 3D mask
@@ -2291,6 +2290,7 @@ def load_nanomax_data(logfile, detector, flatfield, hotpixels, background, norma
                       debugging=False):
     """
     Load Nanomax data, apply filters and concatenate it for phasing.
+
     :param logfile: path of the . fio file containing the information about the scan
     :param detector: the detector object: Class experiment_utils.Detector()
     :param flatfield: the 2D flatfield array
@@ -2303,7 +2303,7 @@ def load_nanomax_data(logfile, detector, flatfield, hotpixels, background, norma
      - the 3D data array in the detector frame and the 3D mask array
      - the monitor values for normalization
      - frames_logical: array of initial length the number of measured frames. In case of padding the length changes.
-       A frame whose index is set to 1 means that it is used, 0 means not used, -1 means padded (added) frame.
+        A frame whose index is set to 1 means that it is used, 0 means not used, -1 means padded (added) frame.
     """
     import hdf5plugin  # should be imported before h5py
     import h5py

setup.py

@@ -99,7 +99,7 @@
                         BCDI stands for *Bragg coherent X-ray diffraction imaging*. It can be used for:\n\n\
                         1. Pre-processing BCDI and forward CDI data (masking aliens, detector gaps...) before phase retrieval.\n\
                         2. Post-processing phased data (phase offset and phase ramp removal, averaging, apodization...).\n\
-                        3. Data analysis on diffraction data (stereographic projection, X-ray cross correlation analysis, domain orientation fitting ...).\n\
+                        3. Data analysis on diffraction data (stereographic projection, angular cross correlation analysis, domain orientation fitting ...).\n\
                         4. Data analysis on phased data (resolution calculation, statistics on the retrieved strain...).\n\
                         5. Simulation of diffraction intensity (including noise, detector gaps, displacement...).\n\
                         6. Making figures for publication using templates.\n\n",