From c8e1cb1a29ba822c97f3788dad6888886cafffa0 Mon Sep 17 00:00:00 2001
From: Marco Cammarata <marcocamma@gmail.com>
Date: Tue, 22 Nov 2016 05:30:48 -0800
Subject: [PATCH] changes (now default parameters are defined in alignment)

---
 alignment.py        | 4 ++--
 xanes_analyzeRun.py | 7 +++++--
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/alignment.py b/alignment.py
index 8f713da..df53c77 100644
--- a/alignment.py
+++ b/alignment.py
@@ -29,7 +29,7 @@ g_fit_default_kw = dict(
     transy           = 0,
     error_transy     = 3,
     limit_transy     = ( -50,50 ),
-    rotation         = 0.01,
+    rotation         = 0.00,
     error_rotation   = 0.005,
     limit_rotation   = (-0.06,0.06),
     scalex           = 1,
@@ -38,7 +38,7 @@ g_fit_default_kw = dict(
     scaley           = 1,
     error_scaley     = 0.05,
     limit_scaley     = (0.8,1.2),
-    shear            = 0.01,
+    shear            = 0.00,
     error_shear      = 0.001,
     limit_shear      = (-0.2,0.2),
     igauss1cen       = 512,
diff --git a/xanes_analyzeRun.py b/xanes_analyzeRun.py
index 77f8e4a..a70a521 100644
--- a/xanes_analyzeRun.py
+++ b/xanes_analyzeRun.py
@@ -100,6 +100,7 @@ class AnalyzeRun(object):
   def __init__(self,run,initAlign="auto",swapx=g_swapx,swapy=g_swapy):
     """ swapx → swap x axis of first spectrometer
         swapy → swap y axis of first spectrometer
+        initAlign: use None if you want default transformation parameters
     """
     self.d = readDataset(run)
     if isinstance(run,str):
@@ -119,7 +120,8 @@ class AnalyzeRun(object):
       if initAlign is None:
         print("Set to default transform")
         self.initAlign = self.setDefaultTransform()
-    #self.initAlign  = initAlign
+      else:
+        self.initAlign  = initAlign
 
   def getShot(self,shot=0,calib=None,bkgSub="line",roi=g_roi_height):
     # read data
@@ -261,7 +263,8 @@ class AnalyzeRun(object):
     alignment.clearCache(); # nedded for multiprocessing can leave bad parameters in the cache
 
   def setDefaultTransform( self ):
-    t = dict( scalex=0.65,rotation=0.0,transx=90, iblur1=4.3,fix_iblur1=False )
+    #dict( scalex=0.65,rotation=0.0,transx=90, iblur1=4.3,fix_iblur1=False )
+    t = alignment.g_fit_default_kw
     self.initAlign = t
     return t