New Developed Codes for SAXS-GiSAXS_XPCS

chxtools/Mask_Maker.py

@@ -0,0 +1,131 @@
+from chx_libs import *
+from chx_generic_functions import show_img
+
+
+#####
+#load data by databroker    
+
+
+def get_sid_filenames(header):
+    """get a bluesky scan_id, unique_id, filename by giveing uid and detector
+
+    Parameters
+    ----------
+    header: a header of a bluesky scan, e.g. db[-1]
+
+    Returns
+    -------
+    scan_id: integer
+    unique_id: string, a full string of a uid
+    filename: sring
+
+    Usuage:
+    sid,uid, filenames   = get_sid_filenames(db[uid])
+
+    """   
+
+    keys = [k for k, v in header.descriptors[0]['data_keys'].items()     if 'external' in v]
+    events = get_events( header, keys, handler_overrides={key: RawHandler for key in keys})
+    key, = keys   
+    filenames =  [  str( ev['data'][key][0]) + '_'+ str(ev['data'][key][2]['seq_id']) for ev in events]     
+    sid = header['start']['scan_id']
+    uid= header['start']['uid']
+
+    return sid,uid, filenames   
+
+
+def load_data( uid , detector = 'eiger4m_single_image'  ):
+    """load bluesky scan data by giveing uid and detector
+
+    Parameters
+    ----------
+    uid: unique ID of a bluesky scan
+    detector: the used area detector
+
+    Returns
+    -------
+    image data: a pims frames series
+    if not success read the uid, will return image data as 0
+
+    Usuage:
+    imgs = load_data( uid, detector  )
+    md = imgs.md
+    """   
+    hdr = db[uid]
+    flag =1
+    while flag<4 and flag !=0:    
+        try:
+            ev, = get_events(hdr, [detector]) 
+            flag =0 
+        except:
+            flag += 1        
+            print ('Trying again ...!')
+
+    if flag:
+        print ("Can't Load Data!")
+        uid = '00000'  #in case of failling load data
+        imgs = 0
+    else:
+        imgs = ev['data'][detector]
+    #print (imgs)
+    return imgs
+
+def get_frames_from_dscan(  hdr, detector = 'eiger4m_single_image' ):
+    ev = get_events(hdr, [detector]) 
+    length = int( hdr['start']['plan_args']['num'] )
+    shape = hdr['descriptors'][0]['data_keys'][detector]['shape'][:2]
+    imgs = np.zeros( [  length, shape[1],shape[0]]  )
+    for i in range(   int( hdr['start']['plan_args']['num'] ) ):
+        imgs[i] =  next(ev)['data']['eiger4m_single_image'][0]   
+
+    return np.array( imgs )
+
+def load_metadata(hdr, name):
+    seq_of_img_stacks = get_images(hdr, name)
+    return seq_of_img_stacks[0].md
+def load_images(hdr, name):
+    seq_of_img_stacks = get_images(hdr, name)  # 1 x 21 x 2167 x 2070
+    return np.squeeze(np.asarray(seq_of_img_stacks))
+
+
+def RemoveHot( img,threshold= 1E7, plot_=True ):
+    mask = np.ones_like( np.array( img )    )
+    badp = np.where(  np.array(img) >= threshold )
+    if len(badp[0])!=0:                
+        mask[badp] = 0  
+    if plot_:
+        show_img( mask )
+    return mask
+
+
+############
+###plot data
+
+
+
+
+
+
+
+
+
+def get_avg_img( data_series, sampling = 100, plot_ = False ,  *argv,**kwargs):   
+    '''Get average imagef from a data_series by every sampling number to save time'''
+    avg_img = np.average(data_series[:: sampling], axis=0)
+    if plot_:
+        fig, ax = plt.subplots()
+        uid = 'uid'
+        if 'uid' in kwargs.keys():
+            uid = kwargs['uid'] 
+
+        im = ax.imshow(avg_img , cmap='viridis',origin='lower',
+                   norm= LogNorm(vmin=0.001, vmax=1e2))
+        #ax.set_title("Masked Averaged Image")
+        ax.set_title('Uid= %s--Masked Averaged Image'%uid)
+        fig.colorbar(im)
+        plt.show()
+    return avg_img
+
+
+
+