From 3e5dfe47e9677a80844b981804591d6cba69804e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Chlo=C3=AB=20Bullard?=
 <68021211+chloeann95@users.noreply.github.com>
Date: Mon, 13 Mar 2023 04:46:15 -0400
Subject: [PATCH 1/3] Added input morph parameters to the output [WIP]

---
 diffpy/pdfmorph/pdfmorphapp.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/diffpy/pdfmorph/pdfmorphapp.py b/diffpy/pdfmorph/pdfmorphapp.py
index ac211ea7..88837ce7 100755
--- a/diffpy/pdfmorph/pdfmorphapp.py
+++ b/diffpy/pdfmorph/pdfmorphapp.py
@@ -199,6 +199,9 @@ def main():
     xref, yref = getPDFFromFile(pargs[1])
 
     # Get configuration values
+    scale_in = 'None'
+    stretch_in = 'None'
+    smear_in = 'None'
     config = {}
     config["rmin"] = opts.rmin
     config["rmax"] = opts.rmax
@@ -215,16 +218,19 @@ def main():
 
     ## Scale
     if opts.scale is not None:
+        scale_in = opts.scale
         chain.append(morphs.MorphScale())
         config["scale"] = opts.scale
         refpars.append("scale")
     ## Stretch
     if opts.stretch is not None:
+        stretch_in = opts.stretch
         chain.append(morphs.MorphStretch())
         config["stretch"] = opts.stretch
         refpars.append("stretch")
     ## Smear
     if opts.smear is not None:
+        smear_in = opts.smear
         chain.append(morphs.MorphXtalPDFtoRDF())
         chain.append(morphs.MorphSmear())
         chain.append(morphs.MorphXtalRDFtoPDF())
@@ -305,9 +311,16 @@ def main():
     chain[0] = morphs.Morph()
     chain(xobj, yobj, xref, yref)
 
+    morphs_in = "\nInput morphing parameters:"
+    morphs_in += f"\n scale = {scale_in}"
+    morphs_in += f"\n stretch = {stretch_in}"
+    morphs_in += f"\n smear = {smear_in}"
+    print(morphs_in)
+
     items = list(config.items())
     items.sort()
-    output = "\n".join("# %s = %f" % i for i in items)
+    output = "\n Optimized morphing parameters:"
+    output += "\n".join("# %s = %f" % i for i in items)
     output += "\n# Rw = %f" % rw
     output += "\n# Pearson = %f" % pcc
     print(output)
@@ -315,6 +328,7 @@ def main():
         header = "# PDF created by pdfmorph\n"
         header += "# from %s\n" % os.path.abspath(pargs[0])
 
+        header += morphs_in
         header += output
         if opts.savefile == "-":
             outfile = sys.stdout

From 49ec4b7e7d3de5efd2aa97abf68e09d966a66e14 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Chlo=C3=AB=20Bullard?=
 <68021211+chloeann95@users.noreply.github.com>
Date: Mon, 13 Mar 2023 04:55:14 -0400
Subject: [PATCH 2/3] added some fixed

---
 diffpy/pdfmorph/pdfmorphapp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/diffpy/pdfmorph/pdfmorphapp.py b/diffpy/pdfmorph/pdfmorphapp.py
index 88837ce7..1944d9cd 100755
--- a/diffpy/pdfmorph/pdfmorphapp.py
+++ b/diffpy/pdfmorph/pdfmorphapp.py
@@ -319,7 +319,7 @@ def main():
 
     items = list(config.items())
     items.sort()
-    output = "\n Optimized morphing parameters:"
+    output = "\nOptimized morphing parameters:\n"
     output += "\n".join("# %s = %f" % i for i in items)
     output += "\n# Rw = %f" % rw
     output += "\n# Pearson = %f" % pcc

From f4268d97abee00811cd6191e86f2f78ec974b50f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Chlo=C3=AB=20Bullard?=
 <68021211+chloeann95@users.noreply.github.com>
Date: Mon, 13 Mar 2023 04:57:42 -0400
Subject: [PATCH 3/3] added # to printed data for formatting

---
 diffpy/pdfmorph/pdfmorphapp.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/diffpy/pdfmorph/pdfmorphapp.py b/diffpy/pdfmorph/pdfmorphapp.py
index 1944d9cd..371a22b4 100755
--- a/diffpy/pdfmorph/pdfmorphapp.py
+++ b/diffpy/pdfmorph/pdfmorphapp.py
@@ -311,15 +311,15 @@ def main():
     chain[0] = morphs.Morph()
     chain(xobj, yobj, xref, yref)
 
-    morphs_in = "\nInput morphing parameters:"
-    morphs_in += f"\n scale = {scale_in}"
-    morphs_in += f"\n stretch = {stretch_in}"
-    morphs_in += f"\n smear = {smear_in}"
+    morphs_in = "\n# Input morphing parameters:"
+    morphs_in += f"\n# scale = {scale_in}"
+    morphs_in += f"\n# stretch = {stretch_in}"
+    morphs_in += f"\n# smear = {smear_in}"
     print(morphs_in)
 
     items = list(config.items())
     items.sort()
-    output = "\nOptimized morphing parameters:\n"
+    output = "\n# Optimized morphing parameters:\n"
     output += "\n".join("# %s = %f" % i for i in items)
     output += "\n# Rw = %f" % rw
     output += "\n# Pearson = %f" % pcc