From 7555b5ec1aaab974fa6ff08072a6aa33abb584df Mon Sep 17 00:00:00 2001
From: tjlane <thomas.joseph.lane@gmail.com>
Date: Sun, 3 Nov 2024 18:20:18 +0000
Subject: [PATCH] remove index matching code

---
 meteor/diffmaps.py                       |  2 +-
 meteor/scripts/compute_difference_map.py |  1 -
 meteor/tv.py                             |  9 ---------
 meteor/validate.py                       | 11 ++++++-----
 test/unit/test_tv.py                     |  6 +++---
 5 files changed, 10 insertions(+), 19 deletions(-)

diff --git a/meteor/diffmaps.py b/meteor/diffmaps.py
index b555f88..37d8143 100644
--- a/meteor/diffmaps.py
+++ b/meteor/diffmaps.py
@@ -8,7 +8,7 @@
 import reciprocalspaceship as rs
 
 from .rsmap import Map, _assert_is_map
-from .settings import DEFAULT_KPARAMS_TO_SCAN, MAP_SAMPLING
+from .settings import DEFAULT_KPARAMS_TO_SCAN
 from .utils import filter_common_indices
 from .validate import ScalarMaximizer, map_negentropy
 
diff --git a/meteor/scripts/compute_difference_map.py b/meteor/scripts/compute_difference_map.py
index de554b6..d631289 100644
--- a/meteor/scripts/compute_difference_map.py
+++ b/meteor/scripts/compute_difference_map.py
@@ -4,7 +4,6 @@
 
 from typing import Any
 
-import numpy as np
 import structlog
 
 from meteor.rsmap import Map
diff --git a/meteor/tv.py b/meteor/tv.py
index 0cec605..364bf96 100644
--- a/meteor/tv.py
+++ b/meteor/tv.py
@@ -191,15 +191,6 @@ def negentropy_objective(tv_weight: float) -> float:
     if difference_map.has_uncertainties:
         final_map.set_uncertainties(difference_map.uncertainties)
 
-    # sometimes `from_ccp4_map` adds reflections -- systematic absences or
-    # reflections just beyond the resolution limt; remove those
-    extra_indices = final_map.index.difference(difference_map.index)
-    final_map.drop(extra_indices, inplace=True)
-    sym_diff = difference_map.index.symmetric_difference(final_map.index)
-    if len(sym_diff) > 0:
-        msg = "something went wrong, input and output coefficients do not have identical indices"
-        raise IndexError(msg)
-
     if full_output:
         initial_negentropy = negentropy(realspace_map_array)
         tv_result = TvDenoiseResult(
diff --git a/meteor/validate.py b/meteor/validate.py
index 93a2cc1..eaa247f 100644
--- a/meteor/validate.py
+++ b/meteor/validate.py
@@ -7,8 +7,9 @@
 import numpy as np
 from scipy.optimize import minimize_scalar
 from scipy.stats import differential_entropy
-from .settings import MAP_SAMPLING
+
 from .rsmap import Map
+from .settings import MAP_SAMPLING
 
 
 def negentropy(samples: np.ndarray, *, tolerance: float = 0.1) -> float:
@@ -63,7 +64,7 @@ def negentropy(samples: np.ndarray, *, tolerance: float = 0.1) -> float:
     return float(neg_e)
 
 
-def map_negentropy(map: Map, *, tolerance: float = 0.1) -> float:
+def map_negentropy(map_to_assess: Map, *, tolerance: float = 0.1) -> float:
     """
     Computes the negentropy of a crystallographic map.
 
@@ -74,8 +75,8 @@ def map_negentropy(map: Map, *, tolerance: float = 0.1) -> float:
 
     Parameters
     ----------
-    samples: np.ndarray
-        A numpy array of sample data for which to calculate the negentropy.
+    map_to_assess: Map
+        The map (coefficients) we will compute the negentropy for.
 
     tolerance: float
         Tolerance level determining if the negentropy is suspiciously negative. Defaults to 0.1.
@@ -90,7 +91,7 @@ def map_negentropy(map: Map, *, tolerance: float = 0.1) -> float:
     ValueError: If the computed negentropy is less than the negative tolerance,
                 indicating potential issues with the computation.
     """
-    realspace_map = map.to_ccp4_map(map_sampling=MAP_SAMPLING)
+    realspace_map = map_to_assess.to_ccp4_map(map_sampling=MAP_SAMPLING)
     realspace_map_array = np.array(realspace_map.grid)
     return negentropy(realspace_map_array, tolerance=tolerance)
 
diff --git a/test/unit/test_tv.py b/test/unit/test_tv.py
index f8a945f..baf597c 100644
--- a/test/unit/test_tv.py
+++ b/test/unit/test_tv.py
@@ -134,14 +134,14 @@ def rms_to_noise_free(test_map: Map) -> float:
     )
 
 
-def test_final_map_has_reported_negentropy(random_difference_map: Map) -> None:
+def test_final_map_has_reported_negentropy(noisy_map: Map) -> None:
     # regression test -- previously the written map had different indices --> discrepency
     weight = 0.01
     output_map, metadata = tv.tv_denoise_difference_map(
-        random_difference_map,
+        noisy_map,
         weights_to_scan=[weight],
         full_output=True,
     )
     actual_negentropy = map_negentropy(output_map)
     assert np.isclose(actual_negentropy, metadata.optimal_negentropy), "final/metadata mismatch"
-    assert np.isclose(actual_negentropy, metadata.negentropy_at_weights[-1]), "final/optimizer"
\ No newline at end of file
+    assert np.isclose(actual_negentropy, metadata.negentropy_at_weights[-1]), "final/optimizer"