From f0ec985e5e855f53162940665d316c9507482a2b Mon Sep 17 00:00:00 2001
From: Jordan DeKraker <jordan.dekraker@mail.mcgill.ca>
Date: Sun, 22 Dec 2024 11:07:14 -0500
Subject: [PATCH] removed epsilon from warps

---
 hippunfold/workflow/rules/native_surf.smk   |  8 ++++++++
 hippunfold/workflow/scripts/create_warps.py | 17 -----------------
 2 files changed, 8 insertions(+), 17 deletions(-)

diff --git a/hippunfold/workflow/rules/native_surf.smk b/hippunfold/workflow/rules/native_surf.smk
index 63288089..1052c6ab 100644
--- a/hippunfold/workflow/rules/native_surf.smk
+++ b/hippunfold/workflow/rules/native_surf.smk
@@ -411,6 +411,8 @@ rule compute_halfthick_mask:
         ),
     group:
         "subj"
+    container:
+        config["singularity"]["autotop"]
     shell:
         "c3d {input.coords} -threshold {params.threshold_tofrom} 1 0 {input.mask} -multiply -o {output}"
 
@@ -454,6 +456,8 @@ rule register_midthickness:
         ),
     group:
         "subj"
+    container:
+        config["singularity"]["autotop"]
     shell:
         "greedy -d 3 -i {input.fixed} {input.moving} -n 30 -o {output.warp}"
 
@@ -508,6 +512,8 @@ rule apply_halfsurf_warp_to_img:
         ),
     group:
         "subj"
+    container:
+        config["singularity"]["autotop"]
     shell:
         "greedy -d 3  -rf {input.fixed} -rm {input.moving} {output.warped}  -r {input.warp} "
 
@@ -541,6 +547,8 @@ rule convert_warp_from_itk_to_world:
         ),
     group:
         "subj"
+    container:
+        config["singularity"]["autotop"]
     shell:
         "wb_command -convert-warpfield -from-itk {input} -to-world {output}"
 
diff --git a/hippunfold/workflow/scripts/create_warps.py b/hippunfold/workflow/scripts/create_warps.py
index 84664d89..cc6f566e 100644
--- a/hippunfold/workflow/scripts/create_warps.py
+++ b/hippunfold/workflow/scripts/create_warps.py
@@ -159,23 +159,6 @@ def summary(name, array):
     + (np.random.rand(coord_flat_ap.shape[0]) - 0.5) * 1e-6,
 )
 
-# get unfolded grid (from 0 to 1, not world coords), using meshgrid:
-#  note: indexing='ij' to swap the ordering of x and y
-epsilon = snakemake.params.epsilon
-(unfold_gx, unfold_gy, unfold_gz) = np.meshgrid(
-    np.linspace(
-        0 + float(epsilon[0]), unfold_dims[0] - float(epsilon[0]), unfold_dims[0]
-    ),
-    np.linspace(
-        0 + float(epsilon[1]), unfold_dims[1] - float(epsilon[1]), unfold_dims[1]
-    ),
-    np.linspace(
-        0 + float(epsilon[2]), unfold_dims[2] - float(epsilon[2]), unfold_dims[2]
-    ),
-    indexing="ij",
-)
-summary("points", points)
-
 
 # perform the interpolation