From 4785a42f081533e629f3e9d9a7ace81a853cb5ad Mon Sep 17 00:00:00 2001
From: csaundersshultz <csaundersshultz@gmail.com>
Date: Mon, 15 Sep 2025 09:31:26 -0800
Subject: [PATCH] Update mdccm with dropped stations

Fix mdccm calculation for LTS so it reflects which pairs were kept and dropped. Save max cross-corr values through time, then use element_weights to drop the correct station pairs and update mdccm.
also correct ltsva function description to say 90% confidence intervals.
---
 lts_array/classes/lts_classes.py | 12 +++++++++---
 lts_array/ltsva.py               |  4 ++--
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/lts_array/classes/lts_classes.py b/lts_array/classes/lts_classes.py
index 45142c7..f98827f 100644
--- a/lts_array/classes/lts_classes.py
+++ b/lts_array/classes/lts_classes.py
@@ -829,6 +829,8 @@ def __init__(self, data):
         self.stdict = {}
         # Confidence value for uncertainty calculation
         self.p = 0.90
+        # Pre-allocate max cross-corr values for all pairs and timesteps (median of this is mdccm)
+        self.cij_maxs = np.full((self.co_array_num, data.nits), np.nan)
         # Check co-array rank for least squares problem
         if (np.linalg.matrix_rank(self.xij) < self.dimension_number):
             raise RuntimeError('Co-array is ill posed for the least squares problem. Check array coordinates. xij rank < ' + str(self.dimension_number))
@@ -851,6 +853,7 @@ def calculate_co_array(self, data):
 
     def correlate(self, data):
         """ Cross correlate the time series data.
+            Save maximum correlations for each timestep to update mccm with dropped station pairs
         """
         for jj in range(0, data.nits):
             # Get time from middle of window, except for the end.
@@ -869,14 +872,14 @@ def correlate(self, data):
                 # MATLAB's xcorr w/ 'coeff' normalization:
                 # unit auto-correlations.
                 self.cij[:, k] = (np.correlate(data.data[t0_ind:tf_ind, self.idx_pair[k][0]], data.data[t0_ind:tf_ind, self.idx_pair[k][1]], mode='full') / np.sqrt(np.sum(data.data[t0_ind:tf_ind, self.idx_pair[k][0]] * data.data[t0_ind:tf_ind, self.idx_pair[k][0]]) * np.sum(data.data[t0_ind:tf_ind, self.idx_pair[k][1]] * data.data[t0_ind:tf_ind, self.idx_pair[k][1]]))) # noqa
-            # Find the median of the cross-correlation maxima
-            self.mdccm[jj] = np.nanmedian(self.cij.max(axis=0))
+            self.cij_maxs[:, jj] = self.cij.max(axis=0) #save cij_maxs for this time step
             # Form the time delay vector and save it
             delay = np.argmax(self.cij, axis=0) + 1
             self.tau[:, jj] = (data.winlensamp - delay) / data.sampling_rate
             self.time_delay_mad[jj] = 1.4826 * np.median(
                 np.abs(self.tau[:, jj]))
-
+        
+        self.mdccm = np.nanmedian(self.cij_maxs, axis=0) #calculate mdccm for all time steps
         self.tau = np.reshape(self.tau, (self.co_array_num, data.nits, 1))
 
 
@@ -1023,6 +1026,9 @@ def solve(self, data):
         # Use the best slowness coefficients to determine dropped stations
         # Calculate uncertainties at 90% confidence
         self.lts_vel, self.lts_baz, self.element_weights, self.sigma_tau, self.conf_int_vel, self.conf_int_baz = post_process(self.dimension_number, self.co_array_num, data.alpha, self.h, data.nits, self.tau, self.xij, self.slowness_coeffs, self.lts_vel, self.lts_baz, self.element_weights, self.sigma_tau, self.p, self.conf_int_vel, self.conf_int_baz) # noqa
+        # Correct the mdccm value according to the dropped station pairs
+        masked_cij = np.where(self.element_weights == 1, self.cij_maxs, np.nan)
+        self.mdccm = np.nanmedian(masked_cij, axis=0)
         # Find dropped stations from weights
         # Map dropped data points back to elements.
         for jj in range(0, data.nits):
diff --git a/lts_array/ltsva.py b/lts_array/ltsva.py
index f2f069f..f88d826 100644
--- a/lts_array/ltsva.py
+++ b/lts_array/ltsva.py
@@ -33,8 +33,8 @@ def ltsva(st, lat_list, lon_list, window_length, window_overlap, alpha=1.0, plot
             ``mdccm`` (array): An array of median cross-correlation maxima.
             ``stdict`` (dict): A dictionary of flagged element pairs.
             ``sigma_tau`` (array): An array of sigma_tau values.
-            ``conf_int_vel`` (array): An array of 95% confidence intervals for the trace velocity.
-            ``conf_int_baz`` (array): An array of 95% confidence intervals for the back-azimuth.
+            ``conf_int_vel`` (array): An array of 90% confidence intervals for the trace velocity.
+            ``conf_int_baz`` (array): An array of 90% confidence intervals for the back-azimuth.
 
     """