From 5a25a552e32288b5199414674996822c270fd914 Mon Sep 17 00:00:00 2001
From: Scott Staniewicz <scott.stanie@gmail.com>
Date: Mon, 3 Feb 2025 11:31:01 -0500
Subject: [PATCH 1/4] Refactor `select_reference_point` to pick centroid of
 candidates

---
 src/dolphin/timeseries.py | 56 ++++++++++++++++++++++-----
 tests/test_timeseries.py  | 80 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 126 insertions(+), 10 deletions(-)

diff --git a/src/dolphin/timeseries.py b/src/dolphin/timeseries.py
index d9bf08cb..7ffcf9c6 100644
--- a/src/dolphin/timeseries.py
+++ b/src/dolphin/timeseries.py
@@ -136,7 +136,6 @@ def run(
     unwrapped_paths = sorted(unwrapped_paths, key=str)
     Path(output_dir).mkdir(exist_ok=True, parents=True)
 
-    condition_func = argmax_index if condition == CallFunc.MAX else argmin_index
     if reference_point == (-1, -1):
         logger.info("Selecting a reference point for unwrapped interferograms")
         ref_point = select_reference_point(
@@ -1171,7 +1170,8 @@ def select_reference_point(
     *,
     condition_file: PathOrStr,
     output_dir: Path,
-    condition_func: Callable[[ArrayLike], tuple[int, ...]] = argmin_index,
+    condition: CallFunc = CallFunc.MAX,
+    candidate_threshold: float = 0.95,
     ccl_file_list: Sequence[PathOrStr] | None = None,
     block_shape: tuple[int, int] = (256, 256),
     num_threads: int = 4,
@@ -1192,9 +1192,17 @@ def select_reference_point(
         temporal coherence in `ccl_file_list`
     output_dir: Path
         Path to store the computed "conncomp_intersection.tif" raster
-    condition_func: Callable[[ArrayLike, ]]
-        The function to apply to the condition file,
-        for example numpy.argmin which finds the pixel with lowest value
+    condition_func: CallFunc
+        The function to apply to the condition file, for example CallFunc.MIN
+        which finds the pixel with lowest value.
+        Default = CallFunc.MAX
+    candidate_threshold: float
+        The threshold for the condition function to be considered a candidate
+        reference point pixel.
+        If the condition function is CallFunc.MAX, then only pixels with values
+        in `condition_file` greater than `candidate_threshold` will be considered
+        a candidate.
+        Default = 0.95
     ccl_file_list : Sequence[PathOrStr]
         List of connected component label phase files.
     block_shape : tuple[int, int]
@@ -1239,11 +1247,39 @@ def select_reference_point(
             msg += f"Proceeding using only {condition_file = }"
             logger.warning(msg, exc_info=True)
 
-    # Mask out where the conncomps aren't equal to the largest
-    condition_file_values.mask = condition_file_values.mask | (~isin_largest_conncomp)
-
-    # Pick the (unmasked) point with the condition applied to condition file
-    ref_row, ref_col = condition_func(condition_file_values)
+    # Create a candidate mask: above threshold:
+    if condition == CallFunc.MAX:
+        is_candidate = condition_file_values > candidate_threshold
+    else:  # CallFunc.MIN
+        is_candidate = condition_file_values < candidate_threshold
+    # Add the candidate mask to the conncomp mask, masking where the conncomps aren't
+    # equal to the largest component label
+    is_candidate &= isin_largest_conncomp
+
+    # 2) Label the connected components of candidate pixels.
+    labeled, n_objects = ndimage.label(is_candidate, structure=np.ones((3, 3)))
+
+    if n_objects > 0:
+        logger.warning(
+            f"No pixels above threshold={candidate_threshold}. Choosing best among available."
+        )
+        condition_func = argmax_index if condition == CallFunc.MAX else argmin_index
+        ref_row, ref_col = condition_func(condition_file_values)
+    else:
+        # 3) Find the largest connected component.
+        label_counts = np.bincount(labeled.ravel())
+        label_counts[0] = 0  # ignore background label "0"
+        largest_label = label_counts.argmax()
+        largest_component = labeled == largest_label
+
+        # 4) Compute the float centroid of this largest component.
+        row_c, col_c = ndimage.center_of_mass(largest_component)
+
+        # 5) Among valid pixels in that region, find the one closest to the centroid.
+        rows, cols = np.nonzero(largest_component)
+        dist_sq = (rows - row_c) ** 2 + (cols - col_c) ** 2
+        i_min = dist_sq.argmin()
+        ref_row, ref_col = rows[i_min], cols[i_min]
 
     # Cast to `int` to avoid having `np.int64` types
     ref_point = ReferencePoint(int(ref_row), int(ref_col))
diff --git a/tests/test_timeseries.py b/tests/test_timeseries.py
index 515d1850..5766db07 100644
--- a/tests/test_timeseries.py
+++ b/tests/test_timeseries.py
@@ -7,6 +7,7 @@
 from numpy.linalg import lstsq as lstsq_numpy
 
 from dolphin import io, timeseries
+from dolphin.timeseries import CallFunc
 from dolphin.utils import format_dates
 
 NUM_DATES = 10
@@ -272,6 +273,85 @@ def test_stack_unweighted(self, data, x_arr, expected_velo):
         npt.assert_allclose(velocities, expected_velo, atol=1e-5)
 
 
+class TestReferencePoint:
+    def test_all_ones_center(self, tmp_path):
+        # All coherence=1 => pick the true center pixel.
+        shape = (31, 31)
+        arr = np.ones(shape, dtype="float32")
+
+        coh_file = tmp_path / "coh_ones.tif"
+        io.write_arr(arr=arr, output_name=coh_file)
+
+        ref_point = timeseries.select_reference_point(
+            condition_file=coh_file,
+            output_dir=tmp_path,
+            condition=CallFunc.MAX,
+            candidate_threshold=0.95,  # everything is above 0.95
+            ccl_file_list=None,
+        )
+        npt.assert_equal((ref_point.row, ref_point.col), (15, 15))
+
+    def test_half_03_half_099(self, tmp_path):
+        # Left half=0.3, right half=0.99 => reference point should be
+        # near the center of the right side.
+        shape = (31, 31)
+        arr = np.full(shape, 0.3, dtype="float32")
+        # Make right half, 16 to 30, high coherence
+        arr[:, 16:] = 0.99
+
+        coh_file = tmp_path / "coh_half_03_099.tif"
+        io.write_arr(arr=arr, output_name=coh_file)
+
+        ref_point = timeseries.select_reference_point(
+            condition_file=coh_file,
+            output_dir=tmp_path,
+            condition=CallFunc.MAX,
+            candidate_threshold=0.95,
+            ccl_file_list=None,
+        )
+        # Expect the center row=15, and roughly col=23 for columns 16..30.
+        npt.assert_equal((ref_point.row, ref_point.col), (15, 23))
+
+    def test_with_conncomp(self, tmp_path):
+        """Make a temporal coherence with left half=0.3, right half=1.0.
+
+        Make the connected-component labels have top half=0, bottom half=1.
+
+        Reference point is in the bottom-right quadrant where
+        coherence > threshold AND conncomp == 1
+        """
+        shape = (31, 31)
+
+        # Coherence array: left half=0.3, right half=1.0
+        coh = np.full(shape, 0.3, dtype="float32")
+        coh[:, 16:] = 1.0
+
+        coh_file = tmp_path / "coh_left03_right1.tif"
+        io.write_arr(arr=coh, output_name=coh_file)
+
+        # ConnComp label: top half=0, bottom half=1
+        # So only rows >= 15 are labeled '1'.
+        ccl = np.zeros(shape, dtype="uint16")
+        ccl[16:, :] = 1
+
+        ccl_file1 = tmp_path / "conncomp_bottom_half.tif"
+        io.write_arr(arr=ccl, output_name=ccl_file1)
+        # Add another conncomp file with all good pixels
+        ccl_file2 = tmp_path / "conncomp_full.tif"
+        io.write_arr(arr=np.ones_like(ccl), output_name=ccl_file2)
+
+        ref_point = timeseries.select_reference_point(
+            ccl_file_list=[ccl_file1, ccl_file2],
+            condition_file=coh_file,
+            output_dir=tmp_path,
+            condition=CallFunc.MAX,
+            candidate_threshold=0.95,
+        )
+
+        # Bottom half => rows [16..30], right half => cols [16..30].
+        npt.assert_equal((ref_point.row, ref_point.col), (23, 23))
+
+
 if __name__ == "__main__":
     sar_dates = make_sar_dates()
     sar_phases = make_sar_phases(sar_dates)

From 2c25c08e78e083c62a7fc7d8d5e6808133b8b7ce Mon Sep 17 00:00:00 2001
From: Scott Staniewicz <scott.stanie@gmail.com>
Date: Mon, 3 Feb 2025 11:38:16 -0500
Subject: [PATCH 2/4] Fix unclear commends and logic

---
 src/dolphin/timeseries.py | 41 ++++++++++++++++++++++++---------------
 1 file changed, 25 insertions(+), 16 deletions(-)

diff --git a/src/dolphin/timeseries.py b/src/dolphin/timeseries.py
index 7ffcf9c6..4ad07c46 100644
--- a/src/dolphin/timeseries.py
+++ b/src/dolphin/timeseries.py
@@ -46,6 +46,7 @@ def run(
     condition: CallFunc,
     output_dir: PathOrStr,
     method: InversionMethod = InversionMethod.L1,
+    reference_candidate_threshold: float = 0.95,
     run_velocity: bool = False,
     corr_paths: Sequence[PathOrStr] | None = None,
     weight_velocity_by_corr: bool = False,
@@ -79,6 +80,13 @@ def run(
         Inversion method to use when solving Ax = b.
         Default is L2, which uses least squares to solve Ax = b (faster).
         "L1" minimizes |Ax - b|_1 at each pixel.
+    reference_candidate_threshold: float
+        The threshold for the condition function to be considered a candidate
+        reference point pixel.
+        If the condition function is CallFunc.MAX, then only pixels with values
+        in `condition_file` greater than `reference_candidate_threshold` will be
+        considered a candidate.
+        Default = 0.95
     run_velocity : bool
         Whether to run velocity estimation on the inverted phase series
     corr_paths : Sequence[Path], optional
@@ -141,7 +149,8 @@ def run(
         ref_point = select_reference_point(
             condition_file=condition_file,
             output_dir=Path(output_dir),
-            condition_func=condition_func,
+            condition=condition,
+            candidate_threshold=reference_candidate_threshold,
             ccl_file_list=conncomp_paths,
         )
     else:
@@ -968,11 +977,10 @@ def invert_unw_network(
     suffix = ".tif"
     # Create the `n_sar_dates - 1` output files (skipping the 0 reference raster)
     out_paths = [
-        Path(output_dir) / (f"{format_dates(ref_date, d)}{suffix}")
-        for d in sar_dates[1:]
+        Path(output_dir) / f"{format_dates(ref_date, d)}{suffix}" for d in sar_dates[1:]
     ]
     out_residuals_paths = [
-        Path(output_dir) / (f"residuals_{format_dates(ref_date, d)}{suffix}")
+        Path(output_dir) / f"residuals_{format_dates(ref_date, d)}{suffix}"
         for d in sar_dates[1:]
     ]
     if all(p.exists() for p in out_paths):
@@ -1192,7 +1200,7 @@ def select_reference_point(
         temporal coherence in `ccl_file_list`
     output_dir: Path
         Path to store the computed "conncomp_intersection.tif" raster
-    condition_func: CallFunc
+    condition: CallFunc
         The function to apply to the condition file, for example CallFunc.MIN
         which finds the pixel with lowest value.
         Default = CallFunc.MAX
@@ -1233,6 +1241,7 @@ def select_reference_point(
     logger.info("Selecting reference point")
     condition_file_values = io.load_gdal(condition_file, masked=True)
 
+    # Start with all points as valid candidates
     isin_largest_conncomp = np.ones(condition_file_values.shape, dtype=bool)
     if ccl_file_list:
         try:
@@ -1247,35 +1256,35 @@ def select_reference_point(
             msg += f"Proceeding using only {condition_file = }"
             logger.warning(msg, exc_info=True)
 
-    # Create a candidate mask: above threshold:
+    # Find pixels meeting the threshold criteria
     if condition == CallFunc.MAX:
         is_candidate = condition_file_values > candidate_threshold
     else:  # CallFunc.MIN
         is_candidate = condition_file_values < candidate_threshold
-    # Add the candidate mask to the conncomp mask, masking where the conncomps aren't
-    # equal to the largest component label
+
+    # Restrict candidates to the largest connected component region
     is_candidate &= isin_largest_conncomp
 
-    # 2) Label the connected components of candidate pixels.
+    # Find connected regions within candidate pixels
     labeled, n_objects = ndimage.label(is_candidate, structure=np.ones((3, 3)))
 
-    if n_objects > 0:
+    if n_objects == 0:
+        # If no candidates meet threshold, pick best available point
         logger.warning(
-            f"No pixels above threshold={candidate_threshold}. Choosing best among available."
+            f"No pixels above threshold={candidate_threshold}. Choosing best among"
+            " available."
         )
         condition_func = argmax_index if condition == CallFunc.MAX else argmin_index
         ref_row, ref_col = condition_func(condition_file_values)
     else:
-        # 3) Find the largest connected component.
+        # Find the largest region of connected candidate pixels
         label_counts = np.bincount(labeled.ravel())
-        label_counts[0] = 0  # ignore background label "0"
+        label_counts[0] = 0  # ignore background
         largest_label = label_counts.argmax()
         largest_component = labeled == largest_label
 
-        # 4) Compute the float centroid of this largest component.
+        # Select point closest to center of largest region
         row_c, col_c = ndimage.center_of_mass(largest_component)
-
-        # 5) Among valid pixels in that region, find the one closest to the centroid.
         rows, cols = np.nonzero(largest_component)
         dist_sq = (rows - row_c) ** 2 + (cols - col_c) ** 2
         i_min = dist_sq.argmin()

From f09e5be677e3952a3f7975039201587e30694c35 Mon Sep 17 00:00:00 2001
From: Scott Staniewicz <scott.stanie@gmail.com>
Date: Mon, 3 Feb 2025 13:59:04 -0500
Subject: [PATCH 3/4] Rename `condition_file` to `quality_file`, remove option
 for min/max

---
 CHANGELOG.md                           | 22 ++++++++-
 src/dolphin/_cli_timeseries.py         | 12 +----
 src/dolphin/timeseries.py              | 66 ++++++++++----------------
 src/dolphin/workflows/config/_enums.py |  8 ----
 src/dolphin/workflows/displacement.py  |  7 +--
 tests/test_timeseries.py               | 10 ++--
 6 files changed, 53 insertions(+), 72 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1bb5d0c8..c44dc97d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,8 +1,26 @@
 # Changelog
 
-## [Unreleased](https://github.com/isce-framework/dolphin/compare/v0.30.0...main)
+## [Unreleased](https://github.com/isce-framework/dolphin/compare/v0.35.1...main)
 
-## [0.35.0](https://github.com/isce-framework/dolphin/compare/v0.34.0...v0.35.0) - 2025-12-09
+### Changed
+
+- `timeseries.py`: Auto reference point selection
+  - Picks the center of mass instead of arbitrary `argmax` result
+  - Rename `condition_file` to `quality_file`
+
+### Changed
+- Removed `condition` parameter in `timeeries` reference point functions
+- Removed `CallFunc` enum
+
+## [0.35.1](https://github.com/isce-framework/dolphin/compare/v0.35.0...v0.35.1) - 2025-01-15
+
+### Fixed
+
+- `filtering.py` Fix in_bounds_pixels masking, set default to 25 km
+- Set `output_reference_idx` separately from `compressed_reference_idx` during phase linking setup
+
+
+## [0.35.0](https://github.com/isce-framework/dolphin/compare/v0.34.0...v0.35.0) - 2025-01-09
 
 ### Added
 
diff --git a/src/dolphin/_cli_timeseries.py b/src/dolphin/_cli_timeseries.py
index 567904e2..f220de72 100644
--- a/src/dolphin/_cli_timeseries.py
+++ b/src/dolphin/_cli_timeseries.py
@@ -5,7 +5,6 @@
 
 from dolphin._log import setup_logging
 from dolphin.timeseries import InversionMethod
-from dolphin.workflows import CallFunc
 
 if TYPE_CHECKING:
     _SubparserType = argparse._SubParsersAction[argparse.ArgumentParser]
@@ -57,21 +56,12 @@ def get_parser(subparser=None, subcommand_name="timeseries") -> argparse.Argumen
         ),
     )
     parser.add_argument(
-        "--condition-file",
+        "--quality-file",
         help=(
             "A file with the same size as each raster, like amplitude dispersion or "
             "temporal coherence to find reference point"
         ),
     )
-    parser.add_argument(
-        "--condition",
-        type=CallFunc,
-        default=CallFunc.MIN,
-        help=(
-            "A condition to apply to condition file to find the reference point. "
-            "Options are [min, max]. default=min"
-        ),
-    )
     parser.add_argument(
         "--method",
         type=InversionMethod,
diff --git a/src/dolphin/timeseries.py b/src/dolphin/timeseries.py
index 2a6820f3..e561d856 100644
--- a/src/dolphin/timeseries.py
+++ b/src/dolphin/timeseries.py
@@ -19,7 +19,6 @@
 from dolphin._overviews import ImageType, create_overviews
 from dolphin._types import PathOrStr, ReferencePoint
 from dolphin.utils import flatten, format_dates, full_suffix, get_nearest_date_idx
-from dolphin.workflows import CallFunc
 
 T = TypeVar("T")
 DateOrDatetime = datetime | date
@@ -42,8 +41,7 @@ class ReferencePointError(ValueError):
 def run(
     unwrapped_paths: Sequence[PathOrStr],
     conncomp_paths: Sequence[PathOrStr] | None,
-    condition_file: PathOrStr,
-    condition: CallFunc,
+    quality_file: PathOrStr,
     output_dir: PathOrStr,
     method: InversionMethod = InversionMethod.L1,
     reference_candidate_threshold: float = 0.95,
@@ -67,13 +65,9 @@ def run(
         Sequence unwrapped interferograms to invert.
     conncomp_paths : Sequence[Path]
         Sequence connected component files, one per file in `unwrapped_paths`
-    condition_file: PathOrStr
+    quality_file: PathOrStr
         A file with the same size as each raster, like amplitude dispersion or
         temporal coherence
-    condition: CallFunc
-        The function to apply to the condition file,
-        for example numpy.argmin which finds the pixel with lowest value
-        the options are [min, max]
     output_dir : Path
         Path to the output directory.
     method : str, choices = "L1", "L2"
@@ -81,12 +75,11 @@ def run(
         Default is L2, which uses least squares to solve Ax = b (faster).
         "L1" minimizes |Ax - b|_1 at each pixel.
     reference_candidate_threshold: float
-        The threshold for the condition function to be considered a candidate
+        The threshold for the quality metric to be considered a candidate
         reference point pixel.
-        If the condition function is CallFunc.MAX, then only pixels with values
-        in `condition_file` greater than `reference_candidate_threshold` will be
-        considered a candidate.
-        Default = 0.95
+        Only pixels with values in `quality_file` greater than
+        `reference_candidate_threshold` will be considered a candidate.
+        Default is 0.95.
     run_velocity : bool
         Whether to run velocity estimation on the inverted phase series
     corr_paths : Sequence[Path], optional
@@ -147,9 +140,8 @@ def run(
     if reference_point == (-1, -1):
         logger.info("Selecting a reference point for unwrapped interferograms")
         ref_point = select_reference_point(
-            condition_file=condition_file,
+            quality_file=quality_file,
             output_dir=Path(output_dir),
-            condition=condition,
             candidate_threshold=reference_candidate_threshold,
             ccl_file_list=conncomp_paths,
         )
@@ -1176,9 +1168,8 @@ def correlation_to_variance(correlation: ArrayLike, nlooks: int) -> Array:
 
 def select_reference_point(
     *,
-    condition_file: PathOrStr,
+    quality_file: PathOrStr,
     output_dir: Path,
-    condition: CallFunc = CallFunc.MAX,
     candidate_threshold: float = 0.95,
     ccl_file_list: Sequence[PathOrStr] | None = None,
     block_shape: tuple[int, int] = (256, 256),
@@ -1186,30 +1177,27 @@ def select_reference_point(
 ) -> ReferencePoint:
     """Automatically select a reference point for a stack of unwrapped interferograms.
 
-    Uses the condition file and (optionally) connected component labels.
+    Uses the quality file and (optionally) connected component labels.
     The point is selected which
 
-    1. has the condition applied to condition file. for example: has the lowest
-       amplitude dispersion
-    2. (optionally) is within intersection of all nonzero connected component labels
+    1. (optionally) is within intersection of all nonzero connected component labels
+    2. Has value in `quality_file` above the threshold `candidate_threshold`
+
+    Among all points which meet this, the centroid selected using the function
+    `scipy.ndimage.center_of_mass`.
 
     Parameters
     ----------
-    condition_file: PathOrStr
-        A file with the same size as each raster, like amplitude dispersion or
-        temporal coherence in `ccl_file_list`
+    quality_file: PathOrStr
+        A file with the same size as each raster in `ccl_file_list` containing a quality
+        metric, such as temporal coherence.
     output_dir: Path
         Path to store the computed "conncomp_intersection.tif" raster
-    condition: CallFunc
-        The function to apply to the condition file, for example CallFunc.MIN
-        which finds the pixel with lowest value.
-        Default = CallFunc.MAX
     candidate_threshold: float
-        The threshold for the condition function to be considered a candidate
+        The threshold for the quality metric function to be considered a candidate
         reference point pixel.
-        If the condition function is CallFunc.MAX, then only pixels with values
-        in `condition_file` greater than `candidate_threshold` will be considered
-        a candidate.
+        Only pixels with values in `quality_file` greater than `candidate_threshold` are
+        considered a candidate.
         Default = 0.95
     ccl_file_list : Sequence[PathOrStr]
         List of connected component label phase files.
@@ -1239,10 +1227,10 @@ def select_reference_point(
         return ref_point
 
     logger.info("Selecting reference point")
-    condition_file_values = io.load_gdal(condition_file, masked=True)
+    quality_file_values = io.load_gdal(quality_file, masked=True)
 
     # Start with all points as valid candidates
-    isin_largest_conncomp = np.ones(condition_file_values.shape, dtype=bool)
+    isin_largest_conncomp = np.ones(quality_file_values.shape, dtype=bool)
     if ccl_file_list:
         try:
             isin_largest_conncomp = _get_largest_conncomp_mask(
@@ -1253,14 +1241,11 @@ def select_reference_point(
             )
         except ReferencePointError:
             msg = "Unable to find find a connected component intersection."
-            msg += f"Proceeding using only {condition_file = }"
+            msg += f"Proceeding using only {quality_file = }"
             logger.warning(msg, exc_info=True)
 
     # Find pixels meeting the threshold criteria
-    if condition == CallFunc.MAX:
-        is_candidate = condition_file_values > candidate_threshold
-    else:  # CallFunc.MIN
-        is_candidate = condition_file_values < candidate_threshold
+    is_candidate = quality_file_values > candidate_threshold
 
     # Restrict candidates to the largest connected component region
     is_candidate &= isin_largest_conncomp
@@ -1274,8 +1259,7 @@ def select_reference_point(
             f"No pixels above threshold={candidate_threshold}. Choosing best among"
             " available."
         )
-        condition_func = argmax_index if condition == CallFunc.MAX else argmin_index
-        ref_row, ref_col = condition_func(condition_file_values)
+        ref_row, ref_col = argmax_index(quality_file_values)
     else:
         # Find the largest region of connected candidate pixels
         label_counts = np.bincount(labeled.ravel())
diff --git a/src/dolphin/workflows/config/_enums.py b/src/dolphin/workflows/config/_enums.py
index 40500287..efb2514d 100644
--- a/src/dolphin/workflows/config/_enums.py
+++ b/src/dolphin/workflows/config/_enums.py
@@ -1,7 +1,6 @@
 from enum import Enum
 
 __all__ = [
-    "CallFunc",
     "ShpMethod",
     "UnwrapMethod",
 ]
@@ -25,10 +24,3 @@ class UnwrapMethod(str, Enum):
     PHASS = "phass"
     SPURT = "spurt"
     WHIRLWIND = "whirlwind"
-
-
-class CallFunc(str, Enum):
-    """Call function for the timeseries method to find reference point."""
-
-    MIN = "min"
-    MAX = "max"
diff --git a/src/dolphin/workflows/displacement.py b/src/dolphin/workflows/displacement.py
index 14fd5648..097ff753 100755
--- a/src/dolphin/workflows/displacement.py
+++ b/src/dolphin/workflows/displacement.py
@@ -16,7 +16,6 @@
 from dolphin import __version__, io, timeseries, utils
 from dolphin._log import log_runtime, setup_logging
 from dolphin.timeseries import ReferencePoint
-from dolphin.workflows import CallFunc
 
 from . import stitching_bursts, unwrapping, wrapped_phase
 from ._utils import _create_burst_cfg, _remove_dir_if_empty, parse_ionosphere_files
@@ -260,8 +259,10 @@ def run(
             unwrapped_paths=unwrapped_paths,
             conncomp_paths=conncomp_paths,
             corr_paths=stitched_paths.interferometric_corr_paths,
-            condition_file=stitched_paths.temp_coh_file,
-            condition=CallFunc.MAX,
+            quality_file=stitched_paths.temp_coh_file,
+            # TODO: Right now aew don't have the option to pick a different candidate
+            # or quality file.
+            reference_candidate_threshold=0.95,
             output_dir=ts_opts._directory,
             method=timeseries.InversionMethod(ts_opts.method),
             run_velocity=ts_opts.run_velocity,
diff --git a/tests/test_timeseries.py b/tests/test_timeseries.py
index 5766db07..4c503ab6 100644
--- a/tests/test_timeseries.py
+++ b/tests/test_timeseries.py
@@ -7,7 +7,6 @@
 from numpy.linalg import lstsq as lstsq_numpy
 
 from dolphin import io, timeseries
-from dolphin.timeseries import CallFunc
 from dolphin.utils import format_dates
 
 NUM_DATES = 10
@@ -283,9 +282,8 @@ def test_all_ones_center(self, tmp_path):
         io.write_arr(arr=arr, output_name=coh_file)
 
         ref_point = timeseries.select_reference_point(
-            condition_file=coh_file,
+            quality_file=coh_file,
             output_dir=tmp_path,
-            condition=CallFunc.MAX,
             candidate_threshold=0.95,  # everything is above 0.95
             ccl_file_list=None,
         )
@@ -303,9 +301,8 @@ def test_half_03_half_099(self, tmp_path):
         io.write_arr(arr=arr, output_name=coh_file)
 
         ref_point = timeseries.select_reference_point(
-            condition_file=coh_file,
+            quality_file=coh_file,
             output_dir=tmp_path,
-            condition=CallFunc.MAX,
             candidate_threshold=0.95,
             ccl_file_list=None,
         )
@@ -342,9 +339,8 @@ def test_with_conncomp(self, tmp_path):
 
         ref_point = timeseries.select_reference_point(
             ccl_file_list=[ccl_file1, ccl_file2],
-            condition_file=coh_file,
+            quality_file=coh_file,
             output_dir=tmp_path,
-            condition=CallFunc.MAX,
             candidate_threshold=0.95,
         )
 

From b1c8327fee1052a2bf1dc536b71d9bf3d858a8f7 Mon Sep 17 00:00:00 2001
From: Scott Staniewicz <scott.stanie@gmail.com>
Date: Mon, 3 Feb 2025 14:57:34 -0500
Subject: [PATCH 4/4] Fix typos [skip ci]

---
 CHANGELOG.md                          | 5 +++--
 src/dolphin/timeseries.py             | 2 +-
 src/dolphin/workflows/displacement.py | 4 ++--
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c44dc97d..3912118d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,8 +8,9 @@
   - Picks the center of mass instead of arbitrary `argmax` result
   - Rename `condition_file` to `quality_file`
 
-### Changed
-- Removed `condition` parameter in `timeeries` reference point functions
+### Removed
+
+- Removed `condition` parameter in `timeseries` reference point functions
 - Removed `CallFunc` enum
 
 ## [0.35.1](https://github.com/isce-framework/dolphin/compare/v0.35.0...v0.35.1) - 2025-01-15
diff --git a/src/dolphin/timeseries.py b/src/dolphin/timeseries.py
index e561d856..9d39f7cc 100644
--- a/src/dolphin/timeseries.py
+++ b/src/dolphin/timeseries.py
@@ -1240,7 +1240,7 @@ def select_reference_point(
                 num_threads=num_threads,
             )
         except ReferencePointError:
-            msg = "Unable to find find a connected component intersection."
+            msg = "Unable to find a connected component intersection."
             msg += f"Proceeding using only {quality_file = }"
             logger.warning(msg, exc_info=True)
 
diff --git a/src/dolphin/workflows/displacement.py b/src/dolphin/workflows/displacement.py
index 097ff753..2914550b 100755
--- a/src/dolphin/workflows/displacement.py
+++ b/src/dolphin/workflows/displacement.py
@@ -259,9 +259,9 @@ def run(
             unwrapped_paths=unwrapped_paths,
             conncomp_paths=conncomp_paths,
             corr_paths=stitched_paths.interferometric_corr_paths,
+            # TODO: Right now we don't have the option to pick a different candidate
+            # or quality file. Figure out if this is worth exposing
             quality_file=stitched_paths.temp_coh_file,
-            # TODO: Right now aew don't have the option to pick a different candidate
-            # or quality file.
             reference_candidate_threshold=0.95,
             output_dir=ts_opts._directory,
             method=timeseries.InversionMethod(ts_opts.method),