change to reconstruct cold frames and swapped cameras corrections

IR_image_tools.py

@@ -2,7 +2,7 @@
 """
 Created on Wed May  9 14:56:32 2018
 
-@author: holn
+@author: Holger Niemann, Peter Drewelow, Yu Gao
 
 mainly to clean up the downloadversionIRdata code
 Tools for:
@@ -14,6 +14,12 @@ Tools for:
 """
 import numpy as np
 import matplotlib.pyplot as plt
+from IR_config_constants import portcamdict,IRCamRefImagespath
+import h5py
+from os.path import join, basename
+import glob
+
+
 
 def bestimmtheitsmaß_general(data,fit):
     R=0
@@ -79,7 +85,7 @@ def check_coldframe(coldframe,references=None,threshold=0.5,plot_it=False):
 def check_coldframe_by_refframe(coldframe,reference_frame,threshold=0.8,plot_it=False):
     references=[]
     shapi=np.shape(reference_frame)
-    for i in [int(shapi[1]//4),int(shapi[1]//2),int(shapi[1]//4*3)]:
+    for i in [int(shapi[1]//5),int(shapi[1]//2),int(shapi[1]//4*3)]:
         dataline=reference_frame[0:shapi[0],i]    
         references.append(dataline-np.mean(dataline))
     return check_coldframe(coldframe,references,threshold,plot_it)
@@ -145,7 +151,7 @@ def correct_images(images,badpixels):
         print("done")
     return images
 
-def restore_pixels(frame, bad_pixel):
+def restore_pixels(frame, bad_pixel):# code from Peter from JET
     # make sure bad pixel are provided as mask and list  
     if type(bad_pixel) is list:
         blist = bad_pixel
@@ -247,9 +253,11 @@ def generate_new_hot_image(cold,reference_cold,reference_hot):
     else:
         return reference_hot+(cold-reference_cold)
     
-def calculate_gain_offset_image(cold_image,hot_image=None,reference_cold=None,reference_hot=None):
+def calculate_gain_offset_image_pix(cold_image,hot_image=None,reference_cold=None,reference_hot=None,bose=1):    
     if hot_image==None:
         hot_image=generate_new_hot_image(cold_image,reference_cold,reference_hot)
+    if bose>0:
+        print("calculate gain and offset")        
     Sh_ref =  hot_image[ ( np.int( np.shape(hot_image)[0]   /2  )  ) ][np.int( (np.shape(hot_image)[1]   /2  ) ) ]          
     Sc_ref =  cold_image[ ( np.int(  (np.shape(cold_image)[0])  /2 )  ) ][( np.int(  (np.shape(cold_image)[1])  /2 ) ) ]  
     Gain_rel =  ( Sh_ref  - Sc_ref ) / ( hot_image  - cold_image)    
@@ -257,3 +265,50 @@ def calculate_gain_offset_image(cold_image,hot_image=None,reference_cold=None,re
     Off_c_rel = Sc_ref -   cold_image*Gain_rel    
     Offset_rel  = ( Off_h_rel + Off_c_rel ) /2
     return Gain_rel,Offset_rel
+
+def calculate_gain_offset_image(cold_image,hot_image=None,reference_cold=None,reference_hot=None,bose=1):    
+    if hot_image==None:
+        hot_image=generate_new_hot_image(cold_image,reference_cold,reference_hot)
+    if bose>0:
+        print("calculate gain and offset")  
+    
+#    Sh_ref =  hot_image[ ( np.int( np.shape(hot_image)[0]   /2  )  ) ][np.int( (np.shape(hot_image)[1]   /2  ) ) ]          
+#    Sc_ref =  cold_image[ ( np.int(  (np.shape(cold_image)[0])  /2 )  ) ][( np.int(  (np.shape(cold_image)[1])  /2 ) ) ]  
+    print(hot_image[( np.int( np.shape(hot_image)[0]/2) )-2: (np.int( np.shape(hot_image)[0]/2))+3,np.int((np.shape(hot_image)[1]/2))-2:np.int((np.shape(hot_image)[1]/2))+3 ])
+    print(cold_image[( np.int( np.shape(hot_image)[0]/2) )-2: (np.int( np.shape(hot_image)[0]/2))+3,np.int((np.shape(hot_image)[1]/2))-2:np.int((np.shape(hot_image)[1]/2))+3 ])
+    Sh_ref =  np.mean( hot_image[( np.int( np.shape(hot_image)[0]/2) )-2: (np.int( np.shape(hot_image)[0]/2))+3,np.int((np.shape(hot_image)[1]/2))-2:np.int((np.shape(hot_image)[1]/2))+3 ])    
+    Sc_ref =  np.mean(cold_image[( np.int( np.shape(cold_image)[0]/2) )-2: (np.int( np.shape(cold_image)[0]/2))+3,np.int((np.shape(cold_image)[1]/2))-2:np.int((np.shape(cold_image)[1]/2))+3 ])    
+    Gain_rel =  ( Sh_ref  - Sc_ref ) / ( hot_image  - cold_image)    
+    Off_h_rel = Sh_ref -   hot_image*Gain_rel
+    Off_c_rel = Sc_ref -   cold_image*Gain_rel    
+    Offset_rel  = ( Off_h_rel + Off_c_rel ) /2
+    return Gain_rel,Offset_rel    
+
+    
+#%% functions from Yu Gao
+""" functions by Yu Gao"""
+    
+def load_ref_images(port, exposuretime):
+  '''
+  load the reference cold and hot frame during calibration from local files.
+  @port: e.g. 'AEF10'
+  @exposuretime: int number.
+  '''
+  cameraname = portcamdict['OP1.2a'][port]
+  foldername = cameraname.split('_')[0] + '_' + cameraname.split('_')[2]
+  scanpath = join(IRCamRefImagespath, foldername)
+  coldref, hotref = [], []
+  for filename in glob.iglob(scanpath + '\*' + str(int(exposuretime)) + 'us.h5', recursive=True):
+    if 'hot' in filename:
+      print (filename)
+      with h5py.File(filename, 'r') as h5in:
+        hotref = h5in[basename(filename)].value
+    elif 'cold' in filename:
+      print (filename)
+      with h5py.File(filename, 'r') as h5in:
+        coldref = h5in[basename(filename)].value
+  return coldref, hotref
+
+def reconstruct_coldframe (exposuretime, sT, a, bnew, coldref):
+  cirebuild = a * sT + bnew * exposuretime + coldref
+  return cirebuild
\ No newline at end of file

__init__.py

+from . import IR_image_tools
+from . import downloadversionIRdata
+from . import IR_config_constants
\ No newline at end of file