From 43f51fe9e419d56111627881b8712e1d32ead428 Mon Sep 17 00:00:00 2001 From: Sara Frank Date: Tue, 15 Nov 2022 13:03:50 -0500 Subject: [PATCH 1/4] added DS_store to ignore and test edit --- .gitignore | 2 ++ diffpy/pdfmorph/pdfmorphapp.py | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 2a087b7d..36ed155a 100644 --- a/.gitignore +++ b/.gitignore @@ -90,5 +90,7 @@ ENV/ # pycharm .idea/ +# Mac +.DS_Store # Rever rever/ diff --git a/diffpy/pdfmorph/pdfmorphapp.py b/diffpy/pdfmorph/pdfmorphapp.py index c86aa1a5..c77000d1 100755 --- a/diffpy/pdfmorph/pdfmorphapp.py +++ b/diffpy/pdfmorph/pdfmorphapp.py @@ -95,7 +95,7 @@ def createOptionParser(): group.add_option('-n', '--noplot', action="store_false", dest="plot", help="Do not show the plot.") group.add_option('--pmin', type="float", - help="Minimum r-value to plot. Defaults to RMIN.") + help="Minimum r-value to . Defaults to RMIN.") #deleted plot group.add_option('--pmax', type="float", help="Maximum r-value to plot. Defaults to RMAX.") group.add_option('--maglim', type="float", From b4c6596ed4c2aee4bcc11fe6d41a52adf52a061d Mon Sep 17 00:00:00 2001 From: Sara Frank Date: Thu, 17 Nov 2022 13:29:58 -0500 Subject: [PATCH 2/4] Undid deletion from test --- 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 c77000d1..c86aa1a5 100755 --- a/diffpy/pdfmorph/pdfmorphapp.py +++ b/diffpy/pdfmorph/pdfmorphapp.py @@ -95,7 +95,7 @@ def createOptionParser(): group.add_option('-n', '--noplot', action="store_false", dest="plot", help="Do not show the plot.") group.add_option('--pmin', type="float", - help="Minimum r-value to . Defaults to RMIN.") #deleted plot + help="Minimum r-value to plot. Defaults to RMIN.") group.add_option('--pmax', type="float", help="Maximum r-value to plot. Defaults to RMAX.") group.add_option('--maglim', type="float", From 722ac0ddaef59e77fef5387c1ce475832403da27 Mon Sep 17 00:00:00 2001 From: Sara Frank Date: Thu, 17 Nov 2022 13:51:21 -0500 Subject: [PATCH 3/4] Added comment under manipulations --- diffpy/pdfmorph/pdfmorphapp.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/diffpy/pdfmorph/pdfmorphapp.py b/diffpy/pdfmorph/pdfmorphapp.py index c86aa1a5..15b64545 100755 --- a/diffpy/pdfmorph/pdfmorphapp.py +++ b/diffpy/pdfmorph/pdfmorphapp.py @@ -58,7 +58,8 @@ def createOptionParser(): group = optparse.OptionGroup(parser, "Manipulations", """These options select the manipulations that are to be applied to the PDF from FILE1. The passed values will be refined unless specifically -excluded with the -a or -x options.""") +excluded with the -a or -x options. If no option is specified, the PDFs from FILE1 and FILE2 will +be plotted without any manipulations.""") parser.add_option_group(group) group.add_option('-a', '--apply', action="store_false", dest="refine", help="Apply manipulations but do not refine.") From 543e51478bb922cb4dc9ab28047c71f57c8ff4e9 Mon Sep 17 00:00:00 2001 From: Sara Frank Date: Thu, 17 Nov 2022 15:02:14 -0500 Subject: [PATCH 4/4] Added no morphing will just plot comment to documentation in index --- doc/source/index.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/doc/source/index.rst b/doc/source/index.rst index 713ca397..51f252e1 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -20,7 +20,7 @@ scale due to differences in incident flux, for example. ``PDFmorph`` will do its best to correct for these benign effects before computing and plotting the difference curve. One measured PDF (typically that collected under higher temperature) is identified as the target PDF and -the second PDF is then morphed by "stretching" (chaning the r-axis to +the second PDF is then morphed by "stretching" (changing the r-axis to simulate a uniform lattice expansion), "smearing" (broadening peaks through a uniform convolution to simulate increased thermal motion), and "scaling" (self-explanatory). PDFmorph will vary the amplitude of the @@ -29,6 +29,8 @@ the target PDFs, then plot them on top of each other with the difference plotted below. There are also a few other morphing transformations in the program. +If no morphing transformation is specified, ``PDFmorph`` will return just +the plotted PDFs. Finally, we note that though ``PDFmorph`` should work on other spectra that are not PDFs, it has not been extensively tested beyond the PDF.