Merge branch 'develop'

avigan · Jun 14, 2022 · 4b3b096 · 4b3b096
2 parents 3b70dcb + 62a2291
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diff --git a/README.md b/README.md
@@ -45,6 +45,25 @@ Please cite the following reference if you use this pipeline in a scientific pub
 
 * [Vigan, 2020, ASCL, ascl:2009.002](https://ui.adsabs.harvard.edu/abs/2020ascl.soft09002V/abstract)
 
+Or simply use the following Bibtex entry:
+
+```
+@MISC{2020ascl.soft09002V,
+       author = {{Vigan}, Arthur},
+        title = "{vlt-sphere: Automatic VLT/SPHERE data reduction and analysis}",
+     keywords = {Software},
+         year = 2020,
+        month = sep,
+          doi = {10.5281/zenodo.6563998},
+          eid = {ascl:2009.002},
+        pages = {ascl:2009.002},
+archivePrefix = {ascl},
+       eprint = {2009.002},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2020ascl.soft09002V},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+```
+
 Moreover, the development of the SPHERE instrument has demanded a tremendous effort from many scientists, who have devoted several years of their life to design, build, test and commission the instrument. To recognize this work, we kindly ask you to cite the relevant instrumental papers in your scientific work. The reference papers for the instrument and its observing mode are:
 
 SPHERE:
@@ -73,7 +92,8 @@ With important contributions from:
  * Dino Mesa (INAF/OAPD): IFS pre-processing
  * ESO personnel in general: SPHERE pipeline and calibration procedures
 
-And bug reports with suggested fix from:
+And small improvements, or bug reports with suggested fix from:
  * Wolfgang Brandner (@Rumpelstil)
  * Tomas Stolker (@tomasstolker)
  * Karthikeyan Singaravelan (@tirkarthi)
+ * Chen Xie (@ChenXie-astro)
diff --git a/examples/ifs_reduction.py b/examples/ifs_reduction.py
@@ -1,32 +1,49 @@
 import sphere.IFS as IFS
 
-#####################################################################
-# Starting in the present version of the pipeline, the default      #
-# -1.75° true North offset is automatically added to the derotation #
-# angles. The offset value can be modified in the configuration of  #
-# the reduction:                                                    #
-#                                                                   #
-#   >>> reduction.config[\'cal_true_north\'] = xxx                  #
-#                                                                   #
-# To avoid any issues, make sure to:                                #
-#   * either reprocess data previously processed with version <1.4  #
-#   * or take into account the offset in your astrometric analysis  #
-#####################################################################
+###############################################################################
+# Since version 1.4 of the pipeline, the default -1.75° true North offset is  #
+# automatically added to the derotation angles. The offset value can be       #
+# modified in the configuration of the reduction:                             #
+#                                                                             #
+#   >>> reduction.config[\'cal_true_north\'] = xxx                            #
+#                                                                             #
+# To avoid any issues, make sure to:                                          #
+#   * either reprocess data previously processed with version <1.4            #
+#   * or take into account the offset in your astrometric analysis            #
+###############################################################################
 
 ####################################################@
 # full reduction
 #
 
 #%% init reduction
-reduction = IFS.Reduction('/Users/avigan/data/sphere-test-target/IFS/', log_level='info')
+reduction = IFS.Reduction('/Users/avigan/data/sphere-test-target/IFS/',
+                          clean_start=True,
+                          log_level='info',
+                          user_config=None)
+
+###############################################################################
+# It is possible to provide a default INI configuration file to set some (or  #
+# all) of the reduction parameters to a default value different from the ones #
+# hard-coded in the sphere package. This is done with the keyword:            #
+#   user_config='~/path/to/the/file/config.ini'                               #
+# The increasing priority for setting reduction parameters is the following:  #
+#   0- default values hard-coded in the sphere package                        #
+#   1- values contained in the file pointed by the user_config keyword, if a  #
+#      file path is provided and exists                                       #
+#   2- values contained in a reduction_config.json file left in the reduction #
+#      directory by a previous reduction                                      #
+#   3- values manually set by the user (see examples below)                   #
+###############################################################################
 
 #%% configuration
 reduction.config['preproc_collapse_science'] = True
 reduction.config['preproc_collapse_type']    = 'coadd'
 reduction.config['preproc_coadd_value']      = 2
+reduction.config['combine_center_selection'] = 'first'
 reduction.config['center_high_pass_waffle']  = True
 reduction.config['clean']                    = False
-reduction.show_config()
+print(reduction.config)
 
 #%% reduction
 reduction.full_reduction()
@@ -36,7 +53,10 @@
 #
 
 #%% init reduction
-reduction = IFS.Reduction('/Users/avigan/data/sphere-test-target/IFS/', log_level='info')
+reduction = IFS.Reduction('/Users/avigan/data/sphere-test-target/IFS/',
+                          clean_start=True,
+                          log_level='info',
+                          user_config=None)
 
 #%% sorting
 reduction.sort_files()
@@ -61,8 +81,8 @@
 reduction.sph_ifs_wavelength_recalibration(high_pass=True, offset=(-3, 0), plot=True)
 reduction.sph_ifs_star_center(high_pass_psf=False, high_pass_waffle=True, offset=(-3, 0), plot=True)
 reduction.sph_ifs_combine_data(cpix=True, psf_dim=80, science_dim=200, correct_anamorphism=True,
-                               shift_method='interp', manual_center=None, coarse_centering=False,
-                               save_scaled=False)
+                               shift_method='interp', manual_center=None, center_selection='time',
+                               coarse_centering=False, save_scaled=False)
 
 #%% cleaning
-reduction.sph_ifs_clean(delete_raw=False, delete_products=False)
+reduction.sph_ifs_clean(delete_raw=False, delete_products=False, delete_config=False)
diff --git a/examples/irdis_imaging_reduction.py b/examples/irdis_imaging_reduction.py
@@ -1,34 +1,51 @@
 import sphere.IRDIS as IRDIS
 
-#####################################################################
-# Starting in the present version of the pipeline, the default      #
-# -1.75° true North offset is automatically added to the derotation #
-# angles. The offset value can be modified in the configuration of  #
-# the reduction:                                                    #
-#                                                                   #
-#   >>> reduction.config[\'cal_true_north\'] = xxx                  #
-#                                                                   #
-# To avoid any issues, make sure to:                                #
-#   * either reprocess data previously processed with version <1.4  #
-#   * or take into account the offset in your astrometric analysis  #
-#####################################################################
+###############################################################################
+# Since version 1.4 of the pipeline, the default -1.75° true North offset is  #
+# automatically added to the derotation angles. The offset value can be       #
+# modified in the configuration of the reduction:                             #
+#                                                                             #
+#   >>> reduction.config[\'cal_true_north\'] = xxx                            #
+#                                                                             #
+# To avoid any issues, make sure to:                                          #
+#   * either reprocess data previously processed with version <1.4            #
+#   * or take into account the offset in your astrometric analysis            #
+###############################################################################
 
 ####################################################@
 # full reduction
 #
 
 #%% init reduction
-reduction = IRDIS.ImagingReduction('/Users/avigan/data/sphere-test-target/IRD/DBI/', log_level='info')
+reduction = IRDIS.ImagingReduction('/Users/avigan/data/sphere-test-target/IRD/DBI/',
+                                   clean_start=True,
+                                   log_level='info',
+                                   user_config=None)
+
+###############################################################################
+# It is possible to provide a default INI configuration file to set some (or  #
+# all) of the reduction parameters to a default value different from the ones #
+# hard-coded in the sphere package. This is done with the keyword:            #
+#   user_config='~/path/to/the/file/config.ini'                               #
+# The increasing priority for setting reduction parameters is the following:  #
+#   0- default values hard-coded in the sphere package                        #
+#   1- values contained in the file pointed by the user_config keyword, if a  #
+#      file path is provided and exists                                       #
+#   2- values contained in a reduction_config.json file left in the reduction #
+#      directory by a previous reduction                                      #
+#   3- values manually set by the user (see examples below)                   #
+###############################################################################
 
 #%% configuration
 reduction.config['combine_psf_dim']          = 80
 reduction.config['combine_science_dim']      = 400
 reduction.config['combine_shift_method']     = 'fft'
+reduction.config['combine_center_selection'] = 'first'
 reduction.config['preproc_collapse_science'] = True
 reduction.config['preproc_collapse_type']    = 'mean'
 reduction.config['center_high_pass_waffle']  = True
 reduction.config['clean']                    = False
-reduction.show_config()
+print(reduction.config)
 
 #%% reduction
 reduction.full_reduction()
@@ -38,7 +55,10 @@
 #
 
 #%% init reduction
-reduction = IRDIS.ImagingReduction('/Users/avigan/data/sphere-test-target/IRD/DBI/', log_level='info')
+reduction = IRDIS.ImagingReduction('/Users/avigan/data/sphere-test-target/IRD/DBI/',
+                                   clean_start=True,
+                                   log_level='info',
+                                   user_config=None)
 
 #%% sorting
 reduction.sort_files()
@@ -57,8 +77,8 @@
 #%% high-level science processing
 reduction.sph_ird_star_center(high_pass_psf=True, high_pass_waffle=False, offset=(0, 0), plot=True)
 reduction.sph_ird_combine_data(cpix=True, psf_dim=80, science_dim=200, correct_anamorphism=True,
-                               shift_method='interp', manual_center=None, coarse_centering=False,
-                               save_scaled=False)
+                               shift_method='interp', manual_center=None, center_selection='time',
+                               coarse_centering=False, save_scaled=False)
 
 #%% cleaning
-reduction.sph_ird_clean(delete_raw=False, delete_products=False)
+reduction.sph_ird_clean(delete_raw=False, delete_products=False, delete_config=False)
diff --git a/examples/irdis_spectro_reduction.py b/examples/irdis_spectro_reduction.py
@@ -5,12 +5,30 @@
 #
 
 #%% init reduction
-reduction = IRDIS.SpectroReduction('/Users/avigan/data/sphere-test-target/IRD/LSS/', log_level='info')
+reduction = IRDIS.SpectroReduction('/Users/avigan/data/sphere-test-target/IRD/LSS/',
+                                   clean_start=True,
+                                   log_level='info',
+                                   user_config=None)
+
+###############################################################################
+# It is possible to provide a default INI configuration file to set some (or  #
+# all) of the reduction parameters to a default value different from the ones #
+# hard-coded in the sphere package. This is done with the keyword:            #
+#   user_config='~/path/to/the/file/config.ini'                               #
+# The increasing priority for setting reduction parameters is the following:  #
+#   0- default values hard-coded in the sphere package                        #
+#   1- values contained in the file pointed by the user_config keyword, if a  #
+#      file path is provided and exists                                       #
+#   2- values contained in a reduction_config.json file left in the reduction #
+#      directory by a previous reduction                                      #
+#   3- values manually set by the user (see examples below)                   #
+###############################################################################
 
 #%% configuration
 reduction.config['combine_science_dim'] = 300
+reduction.config['combine_center_selection'] = 'first'
 reduction.config['clean'] = False
-reduction.show_config()
+print(reduction.config)
 
 #%% reduction
 reduction.full_reduction()
@@ -20,7 +38,10 @@
 #
 
 #%% init reduction
-reduction = IRDIS.SpectroReduction('/Users/avigan/data/sphere-test-target/IRD/LSS/', log_level='info')
+reduction = IRDIS.SpectroReduction('/Users/avigan/data/sphere-test-target/IRD/LSS/',
+                                   clean_start=True,
+                                   log_level='info',
+                                   user_config=None)
 
 #%% sorting
 reduction.sort_files()
@@ -42,7 +63,8 @@
 reduction.sph_ird_wavelength_recalibration(fit_scaling=True, plot=True)
 reduction.sph_ird_combine_data(cpix=True, psf_dim=80, science_dim=300,
                                correct_mrs_chromatism=True, split_posang=True,
-                               shift_method='fft', manual_center=None, coarse_centering=False)
+                               shift_method='fft', manual_center=None, center_selection='time',
+                               coarse_centering=False)
 
 #%% cleaning
-reduction.sph_ird_clean(delete_raw=False, delete_products=False)
+reduction.sph_ird_clean(delete_raw=False, delete_products=False, delete_config=False)
diff --git a/examples/sparta_reduction.py b/examples/sparta_reduction.py
@@ -5,7 +5,24 @@
 #
 
 #%% init reduction
-reduction = SPARTA.Reduction('/Users/avigan/data/sphere-test-target/SPARTA/', log_level='info')
+reduction = SPARTA.Reduction('/Users/avigan/data/sphere-test-target/SPARTA/',
+                             clean_start=True,
+                             log_level='info',
+                             user_config=None)
+
+###############################################################################
+# It is possible to provide a default INI configuration file to set some (or  #
+# all) of the reduction parameters to a default value different from the ones #
+# hard-coded in the sphere package. This is done with the keyword:            #
+#   user_config='~/path/to/the/file/config.ini'                               #
+# The increasing priority for setting reduction parameters is the following:  #
+#   0- default values hard-coded in the sphere package                        #
+#   1- values contained in the file pointed by the user_config keyword, if a  #
+#      file path is provided and exists                                       #
+#   2- values contained in a reduction_config.json file left in the reduction #
+#      directory by a previous reduction                                      #
+#   3- values manually set by the user (see examples below)                   #
+###############################################################################
 
 #%% configuration
 reduction.config['misc_plot'] = True
@@ -19,7 +36,10 @@
 #
 
 #%% init reduction
-reduction = SPARTA.Reduction('/Users/avigan/data/sphere-test-target/SPARTA/', log_level='info')
+reduction = SPARTA.Reduction('/Users/avigan/data/sphere-test-target/SPARTA/',
+                             clean_start=True,
+                             log_level='info',
+                             user_config=None)
 
 #%% sorting
 reduction.sort_files()

diff --git a/examples/sphere_dataset.py b/examples/sphere_dataset.py
@@ -1,7 +1,8 @@
 import sphere.SPHERE as SPHERE
 
 #%% init data set
-ds = SPHERE.Dataset('/Users/avigan/data/sphere-test-target/', log_level='info')
+ds = SPHERE.Dataset('/Users/avigan/data/sphere-test-target/',
+                    log_level='info')
 
 print('IRDIS reductions:')
 for red in ds.IRDIS_reductions:

diff --git a/setup.py b/setup.py
@@ -9,7 +9,7 @@
 # setup
 setup(
     name='vlt-sphere',
-    version='1.5.1',
+    version='1.6,
     description='Reduction and analysis code for the VLT/SPHERE instrument',
     long_description=long_description,
     long_description_content_type='text/markdown',