From 66d083545bd25151f82910cebedcaca9f5994f97 Mon Sep 17 00:00:00 2001
From: EuanPyle <euanpyle@gmail.com>
Date: Fri, 10 Jun 2022 16:12:42 +0100
Subject: [PATCH] Convert rln input in A to unbinned pixels for Align_Z

---
 lil_aretomo/aretomo.py | 12 +++++++++---
 lil_aretomo/utils.py   |  9 ++++++++-
 2 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/lil_aretomo/aretomo.py b/lil_aretomo/aretomo.py
index d3c0d7b..275fafd 100644
--- a/lil_aretomo/aretomo.py
+++ b/lil_aretomo/aretomo.py
@@ -7,6 +7,7 @@
     align_tilt_series_aretomo,
     find_binning_factor,
     check_aretomo_availability,
+    thickness_ang2pix,
 )
 
 console = Console(record=True)
@@ -21,7 +22,7 @@ def run_aretomo_alignment(
         target_pixel_size: Optional[float] = 10,
         nominal_rotation_angle: Optional[float] = None,
         n_patches_xy: Optional[Tuple[int, int]] = (5, 4),
-        thickness_for_alignment: Optional[float] = 800,
+        thickness_for_alignment: Optional[float] = 1500,
         correct_tilt_angle_offset: Optional[bool] = False	
 ):
     """Run aretomo alignment on a single tilt-series
@@ -40,9 +41,9 @@ def run_aretomo_alignment(
     axis. AreTomo does not need this information but it might help.
     (optional) n_patches_xy: if local_align is True, AreTomo will carry out patch tracking. 
     Specify the number of patches in X and Y here as tuple. Default is 5 in X,4 in Y.
-    (optional) thickness_for_alignment: thickness in Z in unbinned pixels for which AreTomo will use in the alignment.
+    (optional) thickness_for_alignment: thickness in Z in Ang for which AreTomo will use in the alignment.
     This is useful is there is a lot of empty space at the top and bottom of your tomogram.
-    See AreTomo manual for full explanation: this sets -AlignZ. Default is 800.
+    See AreTomo manual for full explanation: this sets -AlignZ. Default is 1500.
     (optional) correct_tilt_angle_offset: Apply tilt angle offset correction, yes or no.
     Default is no. See AreTomo manual for full explanation: yes; adds the -TiltCor 1 argument
     """
@@ -62,6 +63,11 @@ def run_aretomo_alignment(
         target_pixel_size=target_pixel_size
     )
     
+    thickness_for_alignment = thickness_ang2pix(
+        pixel_size=pixel_size,
+        thickness_for_alignment=thickness_for_alignment
+    )
+        	
     align_tilt_series_aretomo(
         tilt_series_file=tilt_series_file,
         output_directory=output_directory,
diff --git a/lil_aretomo/utils.py b/lil_aretomo/utils.py
index fc49cc7..6ab023a 100644
--- a/lil_aretomo/utils.py
+++ b/lil_aretomo/utils.py
@@ -33,7 +33,7 @@ def align_tilt_series_aretomo(
         nominal_rotation_angle: bool or float,
         local_alignments: bool,
         n_patches_xy: Tuple[int, int],
-        thickness_for_alignment: float,
+        thickness_for_alignment: int,
         correct_tilt_angle_offset: bool
 ):
     output_file_name = Path(
@@ -96,3 +96,10 @@ def force_symlink(src: Path, link_name: Path):
 def check_aretomo_availability():
     """Check for an installation of AreTomo on the PATH."""
     return shutil.which('AreTomo') is not None
+    
+def thickness_ang2pix(
+        pixel_size: float,
+        thickness_for_alignment: float
+    ) -> int:
+    thickness_for_alignment = round(thickness_for_alignment / pixel_size)
+    return thickness_for_alignment