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NSLS-II · Oct 24, 2020 · 5cf2ec0 · 5cf2ec0
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diff --git a/pyCHX/v2/_commonspeckle/DataGonio.py b/pyCHX/v2/_commonspeckle/DataGonio.py
@@ -16,7 +16,9 @@
 import skbeam.core.roi as roi
 import skbeam.core.correlation as corr
 import skbeam.core.utils as utils
-from pyCHX.v2._commonspeckle.chx_generic_functions import average_array_withNan #common
+from pyCHX.v2._commonspeckle.chx_generic_functions import (
+    average_array_withNan,
+)  # common
 
 
 def convert_Qmap(
@@ -837,21 +839,19 @@ def _generate_qxyz_maps(self):
             x = np.arange(self.width) - self.x0
             y = np.arange(self.height) - self.y0
             X, Y = np.meshgrid(x, y)
-            R = np.sqrt(X**2 + Y**2)
+            R = np.sqrt(X ** 2 + Y ** 2)
 
-            #twotheta = np.arctan(self.r_map()*c) # radians
-            theta_f = np.arctan2( X*c, 1 ) # radians
-            #alpha_f_prime = np.arctan2( Y*c, 1 ) # radians
-            alpha_f = np.arctan2( Y*c*np.cos(theta_f), 1 ) # radians
+            # twotheta = np.arctan(self.r_map()*c) # radians
+            theta_f = np.arctan2(X * c, 1)  # radians
+            # alpha_f_prime = np.arctan2( Y*c, 1 ) # radians
+            alpha_f = np.arctan2(Y * c * np.cos(theta_f), 1)  # radians
 
+            self.qx_map_data1 = self.get_k() * np.sin(theta_f) * np.cos(alpha_f)
+            self.qy_map_data1 = self.get_k() * (
+                np.cos(theta_f) * np.cos(alpha_f) - 1
+            )  # TODO: Check sign
+            self.qz_map_data1 = -1.0 * self.get_k() * np.sin(alpha_f)
 
-            self.qx_map_data1 = self.get_k()*np.sin(theta_f)*np.cos(alpha_f)
-            self.qy_map_data1 = self.get_k()*( np.cos(theta_f)*np.cos(alpha_f) - 1 ) # TODO: Check sign
-            self.qz_map_data1 = -1.0*self.get_k()*np.sin(alpha_f)
-
-            self.qr_map_data1 = np.sign(self.qx_map_data1)*np.sqrt(np.square(self.qx_map_data1) + np.square(self.qy_map_data1))
-
-
-
-
-
+            self.qr_map_data1 = np.sign(self.qx_map_data1) * np.sqrt(
+                np.square(self.qx_map_data1) + np.square(self.qy_map_data1)
+            )
diff --git a/pyCHX/v2/_commonspeckle/SAXS.py b/pyCHX/v2/_commonspeckle/SAXS.py
@@ -7,11 +7,16 @@
 # import numpy as np
 from lmfit import Model
 from lmfit import minimize, Parameters, Parameter, report_fit, fit_report
-#import matplotlib as mpl
-#import matplotlib.pyplot as plt
-#from matplotlib.colors import LogNorm
-from pyCHX.v2._commonspeckle.chx_libs import * #common
-from pyCHX.v2._commonspeckle.chx_generic_functions import show_img, plot1D, find_index #common
+
+# import matplotlib as mpl
+# import matplotlib.pyplot as plt
+# from matplotlib.colors import LogNorm
+from pyCHX.v2._commonspeckle.chx_libs import *  # common
+from pyCHX.v2._commonspeckle.chx_generic_functions import (
+    show_img,
+    plot1D,
+    find_index,
+)  # common
 from scipy.special import gamma, gammaln
 from scipy.optimize import leastsq, curve_fit, least_squares
 

diff --git a/pyCHX/v2/_commonspeckle/Stitching.py b/pyCHX/v2/_commonspeckle/Stitching.py
@@ -2,8 +2,10 @@
 import numpy as np
 from scipy.signal import savgol_filter as sf
 import matplotlib.pyplot as plt
-from pyCHX.v2._commonspeckle.chx_generic_functions import show_img, plot1D #common
-from pyCHX.v2._commonspeckle.DataGonio import convert_Qmap #common #TODO how much overlap with skbeam.core.recip
+from pyCHX.v2._commonspeckle.chx_generic_functions import show_img, plot1D  # common
+from pyCHX.v2._commonspeckle.DataGonio import (
+    convert_Qmap,
+)  # common #TODO how much overlap with skbeam.core.recip
 
 
 def get_base_all_filenames(inDir, base_filename_cut_length=-7):
@@ -253,12 +255,17 @@ def stitch_WAXS_in_Qspace(
     return Intensity_map, qxs, qzs
 
 
-def plot_qmap_in_folder( inDir ): #TODO is this made for SMI as per docstring?
-    '''YG. Sep 27@SMI
+def plot_qmap_in_folder(inDir):  # TODO is this made for SMI as per docstring?
+    """YG. Sep 27@SMI
     Plot Qmap data from inDir, which contains qmap data and extent data
-    '''
-    from pyCHX.v2._commonspeckle.chx_generic_functions import show_img #common #TODO why importing in a function?
-    from pyCHX.v2._commonspeckle.chx_libs import cmap_vge_hdr, plt #common #TODO why importing in a function?
+    """
+    from pyCHX.v2._commonspeckle.chx_generic_functions import (
+        show_img,
+    )  # common #TODO why importing in a function?
+    from pyCHX.v2._commonspeckle.chx_libs import (
+        cmap_vge_hdr,
+        plt,
+    )  # common #TODO why importing in a function?
     import pickle as cpl
 
     fp = get_base_all_filenames(inDir, base_filename_cut_length=-10)

diff --git a/pyCHX/v2/_commonspeckle/Two_Time_Correlation_Function.py b/pyCHX/v2/_commonspeckle/Two_Time_Correlation_Function.py
@@ -16,27 +16,45 @@
 import itertools
 import matplotlib.pyplot as plt
 from matplotlib.colors import LogNorm
-from pyCHX.v2._commonspeckle.chx_libs import  ( colors as colors_array,  markers as markers_array, markers_copy, lstyles, Figure, RUN_GUI) #common
-#from pyCHX.chx_libs import  colors_ as mcolors,  markers_ as markers
-from pyCHX.v2._commonspeckle.chx_libs import    mcolors,    markers, multi_tau_lags, colors #common
-#from modest_image import ModestImage, imshow #common
-
-def delays( num_lev=3, num_buf=4, time=1 ): 
-    ''' DOCUMENT delays(time=)
-        return array of delays.
-        KEYWORD:  time: scale delays by time ( should be time between frames)
-     '''
-    if num_buf%2!=0:print ("nobuf must be even!!!"    )
-    dly=np.zeros( (num_lev+1)*int(num_buf/2) +1  )        
-    dict_dly ={}
-    for i in range( 1,num_lev+1):
-        if i==1:imin= 1
-        else:imin= int(num_buf/2)+1
-        ptr=(i-1)*int(num_buf/2)+ np.arange(imin,num_buf+1)
-        dly[ptr]= np.arange( imin, num_buf+1) *2**(i-1)            
-        dict_dly[i] = dly[ptr-1]            
-        dly*=time
-        #print (i, ptr, imin)
+from pyCHX.v2._commonspeckle.chx_libs import (
+    colors as colors_array,
+    markers as markers_array,
+    markers_copy,
+    lstyles,
+    Figure,
+    RUN_GUI,
+)  # common
+
+# from pyCHX.chx_libs import  colors_ as mcolors,  markers_ as markers
+from pyCHX.v2._commonspeckle.chx_libs import (
+    mcolors,
+    markers,
+    multi_tau_lags,
+    colors,
+)  # common
+
+# from modest_image import ModestImage, imshow #common
+
+
+def delays(num_lev=3, num_buf=4, time=1):
+    """DOCUMENT delays(time=)
+    return array of delays.
+    KEYWORD:  time: scale delays by time ( should be time between frames)
+    """
+    if num_buf % 2 != 0:
+        print("nobuf must be even!!!")
+    dly = np.zeros((num_lev + 1) * int(num_buf / 2) + 1)
+    dict_dly = {}
+    for i in range(1, num_lev + 1):
+        if i == 1:
+            imin = 1
+        else:
+            imin = int(num_buf / 2) + 1
+        ptr = (i - 1) * int(num_buf / 2) + np.arange(imin, num_buf + 1)
+        dly[ptr] = np.arange(imin, num_buf + 1) * 2 ** (i - 1)
+        dict_dly[i] = dly[ptr - 1]
+        dly *= time
+        # print (i, ptr, imin)
     return dly, dict_dly