From 793237fda62ed683f8ba305703ed0958cb1a1c37 Mon Sep 17 00:00:00 2001
From: Christoph Sommer <christoph.sommer@ist.ac.at>
Date: Mon, 16 Oct 2023 16:16:20 +0200
Subject: [PATCH] Update setup.cfg fiexes @2 / Expose normalization parameter
 of phase_cross_correlation() to user

---
 setup.cfg                            |  6 ++++--
 src/napari_correct_drift/__init__.py |  2 +-
 src/napari_correct_drift/_core.py    | 20 ++++++++++++++++++--
 src/napari_correct_drift/_widget.py  | 14 ++++++++++++++
 4 files changed, 37 insertions(+), 5 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index e352200..a9065ec 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = napari-correct-drift
-version = 0.0.2
+version = 0.2.0
 description = Drift correction 2D/3D for Napari similar to Fijis Correct 3D drift
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -32,8 +32,10 @@ project_urls =
 packages = find:
 install_requires =
     numpy
-    magicgui
     qtpy
+    pandas
+    scikit-image
+    scipy
 
 python_requires = >=3.8
 include_package_data = True
diff --git a/src/napari_correct_drift/__init__.py b/src/napari_correct_drift/__init__.py
index d006a79..08ae347 100644
--- a/src/napari_correct_drift/__init__.py
+++ b/src/napari_correct_drift/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.0.2"
+__version__ = "0.2.0"
 
 from ._core import ArrayAxesStandardizer, CorrectDrift, ROIRect
 from ._sample_data import sample_2d, sample_3d, sample_3d_ch
diff --git a/src/napari_correct_drift/_core.py b/src/napari_correct_drift/_core.py
index 32d86b4..5972b7c 100644
--- a/src/napari_correct_drift/_core.py
+++ b/src/napari_correct_drift/_core.py
@@ -380,16 +380,27 @@ def estimate_drift(
         increment: int = 1,
         upsample_factor: int = 1,
         roi: ROIRect = None,
+        normalization: str = "phase",
         mode: str = "relative",
     ):
         if mode == "relative":
             return self._estimate_drift_relative(
-                t0, channel, increment, upsample_factor, roi
+                t0,
+                channel,
+                increment,
+                upsample_factor,
+                normalization,
+                roi,
             )
 
         elif mode == "absolute":
             return self._estimate_drift_absolute(
-                t0, channel, increment, upsample_factor, roi
+                t0,
+                channel,
+                increment,
+                upsample_factor,
+                normalization,
+                roi,
             )
 
         else:
@@ -401,6 +412,7 @@ def _estimate_drift_relative(
         channel: int = 0,
         increment: int = 1,
         upsample_factor: int = 1,
+        normalization: str = "phase",
         roi: ROIRect = None,
     ):
         offsets_rel = np.zeros((self.T, 3))
@@ -451,12 +463,14 @@ def _estimate_drift_relative(
                     action="ignore",
                     category=RuntimeWarning,
                 )
+
                 offset, _, _ = phase_cross_correlation(
                     ref_img,
                     mov_img,
                     upsample_factor=upsample_factor,
                     return_error="always",
                     disambiguate=True,
+                    normalization=normalization,
                 )
 
             offset = np.asarray(offset, dtype="float32")
@@ -491,6 +505,7 @@ def _estimate_drift_absolute(
         channel: int = 0,
         increment: int = 1,
         upsample_factor: int = 1,
+        normalization: str = "phase",
         roi: ROIRect = None,
     ):
         if not self.is_multi_channel:
@@ -533,6 +548,7 @@ def _estimate_drift_absolute(
                     upsample_factor=upsample_factor,
                     return_error="always",
                     disambiguate=True,
+                    normalization=normalization,
                 )
 
             offset = -np.asarray(offset, dtype="float32")
diff --git a/src/napari_correct_drift/_widget.py b/src/napari_correct_drift/_widget.py
index 22a1337..e1e334a 100644
--- a/src/napari_correct_drift/_widget.py
+++ b/src/napari_correct_drift/_widget.py
@@ -347,6 +347,14 @@ def _init_other_params(self):
         parameter_layout.addWidget(self.extend_output, i, 1)
         i += 1
 
+        # phase normalization
+        self.normalization_box = QCheckBox()
+        self.normalization_box.setChecked(True)
+
+        parameter_layout.addWidget(QLabel("Use phase normalization"), i, 0)
+        parameter_layout.addWidget(self.normalization_box, i, 1)
+        i += 1
+
         parameter_panel.setLayout(parameter_layout)
         self.main_layout.addWidget(parameter_panel)
 
@@ -395,6 +403,11 @@ def estimate_drift(self):
         # get increment
         upsample_factor = self.upsample_box.value()
 
+        # get increment
+        normalization = None
+        if self.normalization_box.isChecked():
+            normalization = "phase"
+
         use_roi = self.roi_checkbox.isChecked()
 
         roi = None
@@ -426,6 +439,7 @@ def estimate_drift(self):
             upsample_factor=upsample_factor,
             roi=roi,
             mode=estimate_mode,
+            normalization=normalization,
         )
 
         if increment > 1: