Merge pull request #51 from neutrons/pd245_add_bank_by_bank_nexus_file_read

Pd245 add bank by bank nexus file read

Author: Kvieta1990

pystog/cli.py

@@ -29,7 +29,7 @@ def pystog_cli(kwargs=None):
         args = parser.parse_args()
         if args.json:
             print("loading config from '%s'" % args.json)
-            with open(args.json, 'r') as f:
+            with open(args.json, "r") as f:
                 kwargs = json.load(f)
 
         else:
@@ -41,34 +41,37 @@ def pystog_cli(kwargs=None):
 
     # Merge S(Q) files
     stog = StoG(**kwargs)
-    stog.read_all_data(skiprows=3)
-    stog.merge_data()
-    stog.write_out_merged_sq()
-
-    # Initial S(Q) -> g(r) transform
-    stog.transform_merged()
-    stog.write_out_merged_gr()
-
-    # TODO: Add the lowR minimizer here
-    # print stog.get_lowR_mean_square()
-
-    # Set the S(Q) and g(r) if no Fourier Filter
-    r = stog.r_master[stog.gr_title]
-    q = stog.q_master[stog.sq_title]
-    sq = stog.sq_master[stog.sq_title]
-    gr_out = stog.gr_master[stog.gr_title]
-
-    # Apply Fourier Filter
-    if "FourierFilter" in kwargs:
-        q, sq, r, gr_out = stog.fourier_filter()
-
-    # Apply Lorch Modification
-    if kwargs["LorchFlag"]:
-        r, gr_out = stog.apply_lorch(q, sq, r)
-
-    # Apply final scale number
-    stog._add_keen_fq(q, sq)
-    stog._add_keen_gr(r, gr_out)
+    if "NexusFile" in kwargs:
+        stog.read_all_nexus_file_banks()
+    else:
+        stog.read_all_data(skiprows=3)
+        stog.merge_data()
+        stog.write_out_merged_sq()
+
+        # Initial S(Q) -> g(r) transform
+        stog.transform_merged()
+        stog.write_out_merged_gr()
+
+        # TODO: Add the lowR minimizer here
+        # print stog.get_lowR_mean_square()
+
+        # Set the S(Q) and g(r) if no Fourier Filter
+        r = stog.r_master[stog.gr_title]
+        q = stog.q_master[stog.sq_title]
+        sq = stog.sq_master[stog.sq_title]
+        gr_out = stog.gr_master[stog.gr_title]
+
+        # Apply Fourier Filter
+        if "FourierFilter" in kwargs:
+            q, sq, r, gr_out = stog.fourier_filter()
+
+        # Apply Lorch Modification
+        if kwargs["LorchFlag"]:
+            r, gr_out = stog.apply_lorch(q, sq, r)
+
+        # Apply final scale number
+        stog._add_keen_fq(q, sq)
+        stog._add_keen_gr(r, gr_out)
 
 
 if __name__ == "__main__":