From fd5eb032c9bc2bf528ff1337f52ae0ace08c4f0d Mon Sep 17 00:00:00 2001
From: Arthur Vigan <arthur.vigan@lam.fr>
Date: Wed, 30 Aug 2017 14:55:12 +0200
Subject: [PATCH] Added combine_correct_anamorphism parameter in configuration
 files

---
 examples/standard_irdis_reduction.py | 4 ++--
 pysphere/IRDIS.py                    | 9 +++++----
 pysphere/instruments/IFS.ini         | 3 ++-
 pysphere/instruments/IRDIS.ini       | 3 ++-
 4 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/examples/standard_irdis_reduction.py b/examples/standard_irdis_reduction.py
index 7a289c8..66605a7 100644
--- a/examples/standard_irdis_reduction.py
+++ b/examples/standard_irdis_reduction.py
@@ -2,7 +2,7 @@
 import pysphere.IRDIS as IRDIS
 
 
-root_path = '/Users/avigan/data/pySPHERE-test/IRD/'
+root_path = '/Users/avigan/data/pySPHERE-test/IRD2/'
 
 red = IRDIS.ImagingReduction(root_path)
 
@@ -26,5 +26,5 @@
 #                                collapse_science=False, collapse_type='mean', coadd_value=2,
 #                                collapse_psf=True, collapse_center=True)
 # red.sph_ird_star_center(high_pass=False, display=False, save=True)
-red.sph_ird_combine_data(cpix=True, psf_dim=100, science_dim=400, correct_anamorphism=True, save_scaled=False)
+# red.sph_ird_combine_data(cpix=True, psf_dim=100, science_dim=400, correct_anamorphism=True, save_scaled=False)
 # red.sph_ird_clean(delete_raw=False, delete_products=False)
diff --git a/pysphere/IRDIS.py b/pysphere/IRDIS.py
index 549c4ac..1e723c7 100644
--- a/pysphere/IRDIS.py
+++ b/pysphere/IRDIS.py
@@ -151,7 +151,7 @@ def create_static_calibrations(self):
     
     def preprocess_science(self):
         '''
-        Extract images in data cubes
+        Extract images in data cubes, clean and collapse
         '''
         
         self.sph_ird_preprocess_science()
@@ -159,8 +159,8 @@ def preprocess_science(self):
 
     def process_science(self):
         '''
-        Perform star center and combine cubes into final (x,y,time,lambda)
-        cubes
+        Perform star center, combine cubes into final (x,y,time,lambda)
+        cubes, correct anamorphism and scale the images
         '''
         
         self.sph_ird_star_center()
@@ -169,7 +169,8 @@ def process_science(self):
     
     def clean(self):
         '''
-        Clean the reduction directory
+        Clean the reduction directory, leaving only the raw and products
+        sub-directory
         '''
         
         self.sph_ird_clean()
diff --git a/pysphere/instruments/IFS.ini b/pysphere/instruments/IFS.ini
index 74133dc..fcfac24 100644
--- a/pysphere/instruments/IFS.ini
+++ b/pysphere/instruments/IFS.ini
@@ -39,7 +39,8 @@ center_save = True
 combine_cpix = True
 combine_psf_dim = 80
 combine_science_dim = 290
-combine_wave_scaled = False
+combine_correct_anamorphism = True
+combine_save_scaled = False
 
 # clean
 clean_delete_raw = False
diff --git a/pysphere/instruments/IRDIS.ini b/pysphere/instruments/IRDIS.ini
index 2502dda..7c186d1 100644
--- a/pysphere/instruments/IRDIS.ini
+++ b/pysphere/instruments/IRDIS.ini
@@ -38,7 +38,8 @@ center_save = True
 combine_cpix = True
 combine_psf_dim = 100
 combine_science_dim = 800
-combine_wave_scaled = False
+combine_correct_anamorphism = True
+combine_save_scaled = False
 
 # clean
 clean_delete_raw = False