Merge pull request #225 from carnisj/release

Prepare for release v0.2.2

MANIFEST.in

@@ -8,15 +8,16 @@ recursive-include doc *.rst
 include doc/conf.py
 include doc/make.bat
 include doc/Makefile
-include doc/example/modes_S11.h5
-include doc/example/S11_config_preprocessing.yml
-include doc/example/S11_config_postprocessing.yml
-include doc/example/alien_removal.PNG
-include doc/example/hotpixel_removal.PNG
+include bcdi/examples/S11_modes.h5
+include bcdi/examples/config_preprocessing.yml
+include bcdi/examples/config_postprocessing.yml
+include bcdi/examples/S11_config_preprocessing.yml
+include bcdi/examples/S11_config_postprocessing.yml
 include bcdi/preprocessing/alias_dict_2018.txt
 include bcdi/preprocessing/alias_dict_2019.txt
 include bcdi/preprocessing/alias_dict_2020.txt
 include bcdi/preprocessing/alias_dict_2021.txt
 include tests/postprocessing/3572_fa.vtk
-include conf/config_preprocessing.yml
-include conf/config_postprocessing.yml
+include doc/example/alien_removal.PNG
+include doc/example/hotpixel_removal.PNG
+include doc/example/files_preprocessing.PNG

bcdi/__init__.py

@@ -6,4 +6,4 @@
 #       authors:
 #         Jerome Carnis, carnis_jerome@yahoo.fr
 """The main bcdi package, which contains the whole framework."""
-__version__ = "0.2.1"
+__version__ = "0.2.2"

doc/example/S11_config_postprocessing.yml → bcdi/examples/S11_config_postprocessing.yml

@@ -5,16 +5,16 @@ save_dir: "C:/Users/Jerome/Documents/data/CXIDB-I182/CH4760/test/"
 # images will be saved here,
 # leave it to None otherwise (default to data directory's parent)
 data_dir: "C:/Users/Jerome/Documents/data/CXIDB-I182/CH4760/S11/"
-# leave None to use the beamline default, or provide the full path to the output of the
-# phase retrieval.
+# leave None to use the beamline default, or provide the full path to the data.
 sample_name: "S"
 # string in front of the scan number in the folder name.
 comment: ""  # comment in filenames, should start with _
-#########################################################
-# parameters used when averaging several reconstruction #
-#########################################################
+##########################################################
+# parameters used when averaging several reconstructions #
+##########################################################
 sort_method: "variance/mean"
 # 'mean_amplitude' or 'variance' or 'variance/mean' or 'volume', metric for averaging
+averaging_space: "reciprocal_space"  # 'direct_space' or 'reciprocal_space'
 correlation_threshold: 0.90
 ###################################
 # parameters related to centering #
@@ -72,6 +72,7 @@ strain_method: "default"  # 'default' or 'defect'.
 beamline: "ID01"  # name of the beamline, used for data loading and normalization
 # by monitor and orthogonalisation
 # supported beamlines: 'ID01', 'SIXS_2018', 'SIXS_2019', 'CRISTAL', 'P10', '34ID'
+is_series: True  # specific to series measurement at P10
 actuators: None
 # Optional dictionary that can be used to define the entries
 # corresponding to actuators in data files
@@ -129,8 +130,20 @@ custom_motors: {
 # detector related parameters #
 ###############################
 detector: "Maxipix"  # "Eiger2M", "Maxipix", "Eiger4M", "Merlin", "Timepix" or "Dummy"
-pixel_size: None
+custom_pixelsize: None
 # use this to declare the pixel size of the "Dummy" detector if different from 55e-6
+center_roi_x: None  # horizontal pixel number of the center of the ROI for data
+# loading, leave None to use the full detector
+center_roi_y: None  # vertical pixel number of the center of the ROI for data
+# loading, leave None to use the full detector
+roi_detector: None
+# [Vstart, Vstop, Hstart, Hstop]. If "center_roi_x" or "center_roi_y" are not None,
+# it will consider that the current values in roi_detector define a window around the
+# pixel [center_roi_y, center_roi_x] and the final output will be
+# [center_roi_y - roi_detector[0], center_roi_y + roi_detector[1],
+# center_roi_x - roi_detector[2], center_roi_x + roi_detector[3]].
+# leave None to use the full detector.
+# Use with center_fft='skip' if you want this exact size.
 template_imagefile: "data_mpx4_%05d.edf.gz"
 # template for ID01: 'data_mpx4_%05d.edf.gz' or 'align_eiger2M_%05d.edf.gz'
 # template for SIXS_2018: 'align.spec_ascan_mu_%05d.nxs'
@@ -202,11 +215,6 @@ reference_spacing: None  # for calibrating the thermal expansion,
 # if None it is fixed to 3.9236/norm(reflection) Pt
 reference_temperature: None
 # used to calibrate the thermal expansion, if None it is fixed to 293.15K (RT)
-##########################################################
-# parameters for averaging several reconstructed objects #
-##########################################################
-averaging_space: "reciprocal_space"  # 'direct_space' or 'reciprocal_space'
-threshold_avg: 0.90  # minimum correlation within reconstructed object for averaging
 #################################################
 # parameters for phase averaging or apodization #
 #################################################

bcdi/examples/__init__.py

@@ -0,0 +1,13 @@
+# -*- coding: utf-8 -*-
+
+# BCDI: tools for pre(post)-processing Bragg coherent X-ray diffraction imaging data
+#   (c) 07/2017-06/2019 : CNRS UMR 7344 IM2NP
+#   (c) 07/2019-05/2021 : DESY PHOTON SCIENCE
+#       authors:
+#         Jerome Carnis, carnis_jerome@yahoo.fr
+
+"""
+BCDI examples.
+
+This package contains examples about preprocessing and postprocessing scripts.
+"""

conf/config_postprocessing.yml → bcdi/examples/config_postprocessing.yml

@@ -5,14 +5,13 @@ save_dir: "C:/Users/Jerome/Documents/data/dataset_P10/test/"
 # images will be saved here,
 # leave it to None otherwise (default to data directory's parent)
 data_dir: None
-# leave None to use the beamline default, or provide the full path to the output of the
-# phase retrieval.
+# leave None to use the beamline default, or provide the full path to the data.
 sample_name: "B15_syn_S1_2"
 # string in front of the scan number in the folder name.
 comment: ""  # comment in filenames, should start with _
-#########################################################
-# parameters used when averaging several reconstruction #
-#########################################################
+##########################################################
+# parameters used when averaging several reconstructions #
+##########################################################
 sort_method: "variance/mean"
 # 'mean_amplitude' or 'variance' or 'variance/mean' or 'volume', metric for averaging
 averaging_space: "reciprocal_space"  # 'direct_space' or 'reciprocal_space'
@@ -131,7 +130,7 @@ custom_motors: {
 # detector related parameters #
 ###############################
 detector: "Eiger4M"  # "Eiger2M", "Maxipix", "Eiger4M", "Merlin", "Timepix" or "Dummy"
-pixel_size: None
+custom_pixelsize: None
 # use this to declare the pixel size of the "Dummy" detector if different from 55e-6
 center_roi_x: 1577  # horizontal pixel number of the center of the ROI for data
 # loading, leave None to use the full detector

conf/config_preprocessing.yml → bcdi/examples/config_preprocessing.yml

@@ -3,11 +3,8 @@ root_folder: "C:/Users/Jerome/Documents/data/dataset_P10/"
 # folder of the experiment, where all scans are stored
 save_dir: "C:/Users/Jerome/Documents/data/dataset_P10/test/"
 # images will be saved here, leave it to None otherwise
-data_dir: None  # leave None to use the beamline default,
-# '' empty string when there is no subfolder
-# (data directly in the scan folder), or a non-empty string for the subfolder name
-# (default to scan_folder/pynx/ or scan_folder/pynxraw/
-# depending on the setting of use_rawdata)
+data_dir: None
+# leave None to use the beamline default, or provide the full path to the data.
 sample_name: "B15_syn_S1_2"  # str or list of str of sample names
 # (string in front of the scan number in the folder name).
 # If only one name is indicated, it will be repeated to match the number of scans.

bcdi/postprocessing/postprocessing_runner.py

@@ -147,7 +147,7 @@ def run(prm):
         roi=roi_detector,
         binning=phasing_binning,
         preprocessing_binning=preprocessing_binning,
-        pixel_size=prm.get("pixel_size"),
+        custom_pixelsize=prm.get("custom_pixelsize"),
     )
 
     ####################################