From cf037f0724e88e9ffee9c89f78be67199ebeb247 Mon Sep 17 00:00:00 2001
From: dennisbrookner <debrookner@gmail.com>
Date: Thu, 21 Dec 2023 12:28:12 -0500
Subject: [PATCH] implementation of weighting in matchmaps, .mr

---
 src/matchmaps/_compute_mr_diff.py        | 13 +++++++++++++
 src/matchmaps/_compute_realspace_diff.py |  1 +
 src/matchmaps/_utils.py                  |  2 +-
 3 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/matchmaps/_compute_mr_diff.py b/src/matchmaps/_compute_mr_diff.py
index 7e13d1b..7043d28 100644
--- a/src/matchmaps/_compute_mr_diff.py
+++ b/src/matchmaps/_compute_mr_diff.py
@@ -378,6 +378,18 @@ def parse_arguments():
         ),
     )
 
+    parser.add_argument(
+        "--alpha",
+        required=False,
+        type=float,
+        default=0,
+        help=(
+            "Alpha to use for error weighting of F-obs prior to Fourier Transform. "
+            "Weights are computed as: 1 / ((1+(alpha*(SigF^2)) / <SigF>^2). "
+            "Default value is alpha=0, e.g., no weighting is performed. "
+        )
+    )
+
     parser.add_argument(
         "--verbose",
         "-v",
@@ -467,6 +479,7 @@ def main():
         dmin=args.dmin,
         spacing=args.spacing,
         radius=args.unmasked_radius,
+        alpha=args.alpha,
         on_as_stationary=args.on_as_stationary,
         keep_temp_files=args.keep_temp_files,
         no_bss = args.no_bss
diff --git a/src/matchmaps/_compute_realspace_diff.py b/src/matchmaps/_compute_realspace_diff.py
index 501a65e..0e068e0 100755
--- a/src/matchmaps/_compute_realspace_diff.py
+++ b/src/matchmaps/_compute_realspace_diff.py
@@ -480,6 +480,7 @@ def main():
         dmin=args.dmin,
         spacing=args.spacing,
         radius=args.unmasked_radius,
+        alpha=args.alpha,
         on_as_stationary=args.on_as_stationary,
         keep_temp_files=args.keep_temp_files,
         no_bss = args.no_bss,
diff --git a/src/matchmaps/_utils.py b/src/matchmaps/_utils.py
index 7c9a7a4..d24d614 100644
--- a/src/matchmaps/_utils.py
+++ b/src/matchmaps/_utils.py
@@ -108,7 +108,7 @@ def _subparser(selection):
 
 
 def make_floatgrid_from_mtz(
-    mtz, spacing, F, SigF, Phi, spacegroup="P1", dmin=None, alpha=0.2
+    mtz, spacing, F, SigF, Phi, spacegroup="P1", dmin=None, alpha=0
 ):
     """
     Make a gemmi.FloatGrid from an rs.DataSet.