Merge pull request #46 from ambarb/v2_common_essential_modules

V2 common essential modules for _commonspeckle

pyCHX/XPCS_XSVS_SAXS_Multi_2017_V4.py

@@ -1,7 +1,7 @@
 #python XPCS_XSVS_SAXS_Multi_2017_V4.py 
 
 
-from pyCHX.chx_packages import *
+from pyCHX.chx_packages import * 
 from pyCHX.chx_xpcs_xsvs_jupyter import run_xpcs_xsvs_single
 
 def XPCS_XSVS_SAXS_Multi(  start_time, stop_time, run_pargs,  suf_ids = None, 

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.chx_generic_functions import average_array_withNan
+from pyCHX.v2._commonspeckle.chx_generic_functions import (
+    average_array_withNan,
+)  # common
 
 
 def convert_Qmap(

pyCHX/v2/_commonspeckle/SAXS.py

@@ -11,8 +11,12 @@
 # import matplotlib as mpl
 # import matplotlib.pyplot as plt
 # from matplotlib.colors import LogNorm
-from pyCHX.chx_libs import *
-from pyCHX.chx_generic_functions import show_img, plot1D, find_index
+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
 

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.chx_generic_functions import show_img, plot1D
-from pyCHX.DataGonio import convert_Qmap
+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):
+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.chx_generic_functions import show_img
-    from pyCHX.chx_libs import cmap_vge_hdr, plt
+    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)

pyCHX/v2/_commonspeckle/Two_Time_Correlation_Function.py

@@ -16,7 +16,7 @@
 import itertools
 import matplotlib.pyplot as plt
 from matplotlib.colors import LogNorm
-from pyCHX.chx_libs import (
+from pyCHX.v2._commonspeckle.chx_libs import (
     colors as colors_array,
     markers as markers_array,
     markers_copy,
@@ -26,7 +26,12 @@
 )  # common
 
 # from pyCHX.chx_libs import  colors_ as mcolors,  markers_ as markers
-from pyCHX.chx_libs import mcolors, markers, multi_tau_lags, colors  # common
+from pyCHX.v2._commonspeckle.chx_libs import (
+    mcolors,
+    markers,
+    multi_tau_lags,
+    colors,
+)  # common
 
 # from modest_image import ModestImage, imshow #common
 

pyCHX/v2/_commonspeckle/XPCS_GiSAXS.py

@@ -4,10 +4,10 @@
 This module is for the GiSAXS XPCS analysis 
 """
 
-from pyCHX.chx_generic_functions import *
-from pyCHX.chx_compress import ( compress_eigerdata, read_compressed_eigerdata,init_compress_eigerdata, get_avg_imgc,Multifile) 
-from pyCHX.chx_correlationc import ( cal_g2c )
-from pyCHX.chx_libs import  ( colors, markers, colors_,  markers_)
+from pyCHX.v2._commonspeckle.chx_generic_functions import * #common
+from pyCHX.v2._commonspeckle.chx_compress import ( compress_eigerdata, read_compressed_eigerdata,init_compress_eigerdata, get_avg_imgc,Multifile) #common 
+from pyCHX.v2._commonspeckle.chx_correlationc import ( cal_g2c ) #common
+from pyCHX.v2._commonspeckle.chx_libs import  ( colors, markers, colors_,  markers_) #common
 from skbeam.core.accumulators.binned_statistic import BinnedStatistic2D,BinnedStatistic1D
 
 

pyCHX/v2/_commonspeckle/XPCS_SAXS.py

@@ -4,20 +4,20 @@
 This module is for the SAXS XPCS analysis 
 """
 
-from pyCHX.chx_libs import  ( colors, colors_copy, markers, markers_copy,
-                                 colors_,  markers_, )
+from pyCHX.v2._commonspeckle.chx_libs import  ( colors, colors_copy, markers, markers_copy,
+                                                colors_,  markers_, ) #common
 
-from pyCHX.chx_libs import  ( Figure, RUN_GUI )
+from pyCHX.v2._commonspeckle.chx_libs import  ( Figure, RUN_GUI ) #common
 
-from pyCHX.chx_generic_functions import *
+from pyCHX.v2._commonspeckle.chx_generic_functions import * #common
 from scipy.special import erf
 
-from pyCHX.chx_compress_analysis import ( compress_eigerdata, read_compressed_eigerdata,
+from pyCHX.v2._commonspeckle.chx_compress_analysis import ( compress_eigerdata, read_compressed_eigerdata,
                                              init_compress_eigerdata,
-                                             Multifile,get_each_ring_mean_intensityc,get_avg_imgc, mean_intensityc )
+                                             Multifile,get_each_ring_mean_intensityc,get_avg_imgc, mean_intensityc ) #common
 
-from pyCHX.chx_correlationc import ( cal_g2c,Get_Pixel_Arrayc,auto_two_Arrayc,get_pixelist_interp_iq,)
-from pyCHX.chx_correlationp import ( cal_g2p)
+from pyCHX.v2._commonspeckle.chx_correlationc import ( cal_g2c,Get_Pixel_Arrayc,auto_two_Arrayc,get_pixelist_interp_iq,) #common
+from pyCHX.v2._commonspeckle.chx_correlationp import ( cal_g2p) #common
 
 
 from pandas import DataFrame