From 35806ce2c57bc071d705d1284b94a7027eeba33d Mon Sep 17 00:00:00 2001
From: Jordan DeKraker <jordan.dekraker@mail.mcgill.ca>
Date: Wed, 26 Jun 2024 12:24:55 -0400
Subject: [PATCH] removed epsilon and unused variables

---
 hippunfold/config/snakebids.yml             |  4 ----
 hippunfold/workflow/rules/warps.smk         |  2 --
 hippunfold/workflow/scripts/create_warps.py | 25 +++++----------------
 3 files changed, 5 insertions(+), 26 deletions(-)

diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
index d3a3f1bc..c374ab19 100644
--- a/hippunfold/config/snakebids.yml
+++ b/hippunfold/config/snakebids.yml
@@ -608,10 +608,6 @@ unfold_vol_ref:
       - '2.5'
     orient: RPI
 
-unfold_crop_epsilon_fractions:
-    - 0
-    - 0
-    - 0.0625 #1/16
 
 # space for uniform unfolded grid:
 #  currently only used for interpolating hipp subfields on surface
diff --git a/hippunfold/workflow/rules/warps.smk b/hippunfold/workflow/rules/warps.smk
index 47501f12..1dd4a1d4 100644
--- a/hippunfold/workflow/rules/warps.smk
+++ b/hippunfold/workflow/rules/warps.smk
@@ -168,7 +168,6 @@ rule create_warps_hipp:
         labelmap=get_labels_for_laplace,
     params:
         gm_labels=lambda wildcards: config["laplace_labels"]["AP"]["gm"],
-        epsilon=lambda wildcards: config["unfold_crop_epsilon_fractions"],
     resources:
         mem_mb=16000,
     output:
@@ -294,7 +293,6 @@ rule create_warps_dentate:
         labelmap=get_labels_for_laplace,
     params:
         gm_labels=lambda wildcards: config["laplace_labels"]["PD"]["sink"],
-        epsilon=lambda wildcards: config["unfold_crop_epsilon_fractions"],
     resources:
         mem_mb=16000,
     output:
diff --git a/hippunfold/workflow/scripts/create_warps.py b/hippunfold/workflow/scripts/create_warps.py
index 57e47246..7c6df89e 100644
--- a/hippunfold/workflow/scripts/create_warps.py
+++ b/hippunfold/workflow/scripts/create_warps.py
@@ -105,26 +105,7 @@ def summary(name, array):
 coord_flat_pd_unnorm = coord_flat_pd * unfold_dims[1]
 coord_flat_io_unnorm = coord_flat_io * unfold_dims[2]
 
-# 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("unfold_gx", unfold_gx)
-summary("unfold_gy", unfold_gy)
-summary("unfold_gz", unfold_gz)
-
-# perform the interpolation
+# get unfolded grid 
 
 points = np.stack(
     [
@@ -137,6 +118,10 @@ def summary(name, array):
     ],
     axis=1,
 )
+summary("points", points)
+
+
+# perform the interpolation
 
 interp_ap = naturalneighbor.griddata(
     points,