Merge branch 'develop' into master

README.md

@@ -1,6 +1,8 @@
 VLT/SPHERE
 ==========
 
+<img src="https://img.shields.io/badge/Python->3.5-yellow.svg?style=flat"> [<img src="https://img.shields.io/pypi/v/vlt-sphere.svg?colorB=<brightgreen>">](https://pypi.org/project/vlt-sphere/) [<img src="https://img.shields.io/github/v/release/avigan/SPHERE?color=red">](https://github.com/avigan/SPHERE/releases/tag/v1.3) [<img src="https://img.shields.io/github/release-date/avigan/SPHERE">](https://github.com/avigan/SPHERE/releases/tag/v1.3) [<img src="https://img.shields.io/github/license/avigan/SPHERE?color=blue">](https://github.com/avigan/SPHERE/blob/master/LICENSE) [<img src="https://img.shields.io/badge/ascl-2009.002-blue.svg?colorB=262255" alt="ascl:2009.002" />](https://ascl.net/2009.002) [<img src="https://img.shields.io/badge/ADS%20reference-Vigan%20(2020)-blueviolet">](https://ui.adsabs.harvard.edu/abs/2020ascl.soft09002V/abstract)
+
 Information
 -----------
 
@@ -39,7 +41,11 @@ The package is not fully documented, but [examples are provided](https://github.
 Credits
 -------
 
-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:
+Please cite the following reference if you use this pipeline in a scientific publication:
+
+* [Vigan, 2020, ASCL, ascl:2009.002](https://ui.adsabs.harvard.edu/abs/2020ascl.soft09002V/abstract)
+
+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:
  * General description: [Beuzit et al., 2019, A&A, 631, A155](https://ui.adsabs.harvard.edu/abs/2019A%26A...631A.155B/abstract)
@@ -65,4 +71,4 @@ With important contributions from:
  * Julien Milli (IPAG/UGA): Support of SPARTA files
  * Jean-Françoise Sauvage (ONERA): Support of SPARTA files
  * Dino Mesa (INAF/OAPD): IFS pre-processing
- * ESO personnel in general: SPHERE pipeline and calibration procedures
+ * ESO personnel in general: SPHERE pipeline and calibration procedures

examples/ifs_reduction.py

@@ -1,5 +1,18 @@
 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  #
+#####################################################################
+
 ####################################################@
 # full reduction
 #
@@ -11,6 +24,8 @@
 reduction.config['preproc_collapse_science'] = True
 reduction.config['preproc_collapse_type']    = 'coadd'
 reduction.config['preproc_coadd_value']      = 2
+reduction.config['center_high_pass_waffle']  = True
+reduction.config['clean']                    = False
 reduction.show_config()
 
 #%% reduction
@@ -44,7 +59,7 @@
 
 #%% high-level science processing
 reduction.sph_ifs_wavelength_recalibration(high_pass=True, offset=(-3, 0), plot=True)
-reduction.sph_ifs_star_center(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)

examples/irdis_imaging_reduction.py

@@ -1,5 +1,18 @@
 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  #
+#####################################################################
+
 ####################################################@
 # full reduction
 #
@@ -13,6 +26,8 @@
 reduction.config['combine_shift_method']     = 'fft'
 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()
 
 #%% reduction
@@ -40,7 +55,7 @@
                                      collapse_psf=True, collapse_center=True)
 
 #%% high-level science processing
-reduction.sph_ird_star_center(high_pass=True, offset=(0, 0), plot=True)
+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)

examples/irdis_spectro_reduction.py

@@ -9,7 +9,7 @@
 
 #%% configuration
 reduction.config['combine_science_dim'] = 300
-reduction.config['clean'] = True
+reduction.config['clean'] = False
 reduction.show_config()
 
 #%% reduction
@@ -38,7 +38,7 @@
                                      collapse_center=True)
 
 #%% high-level science processing
-reduction.sph_ird_star_center(high_pass=False, plot=True)
+reduction.sph_ird_star_center(high_pass_psf=False, high_pass_waffle=True, plot=True)
 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,

setup.py

@@ -9,7 +9,7 @@
 # setup
 setup(
     name='vlt-sphere',
-    version='1.3',
+    version='1.4',
     description='Reduction and analysis code for the VLT/SPHERE instrument',
     long_description=long_description,
     long_description_content_type='text/markdown',