fresh branch for clean changes

hippunfold/config/snakebids.yml

@@ -159,6 +159,7 @@ parse_args:
   --inject_template:
     choices:
       - 'upenn'
+      - 'dHCP'
       - 'MBMv2'
       - 'MBMv3'
       - 'CIVM'
@@ -327,11 +328,15 @@ parse_args:
       - synthseg_v0.2
       - neonateT1w_v2
 
+
+
+
+# --- surface specific configuration -- 
+
 autotop_labels:
   - 'hipp'
   - 'dentate'
 
-
 surf_types:
   hipp:
     - midthickness

hippunfold/workflow/rules/common.smk

@@ -24,41 +24,69 @@ def get_modality_suffix(modality):
 
 
 def get_final_spec():
-    if len(config["hemi"]) == 2:
-        specs = expand(
+    specs = expand(
+        bids(
+            root=root,
+            datatype="surf",
+            den="{density}",
+            space="{space}",
+            hemi="{hemi}",
+            label="{autotop}",
+            suffix="surfaces.spec",
+            **config["subj_wildcards"],
+        ),
+        density=config["output_density"],
+        space=ref_spaces,
+        hemi=config["hemi"],
+        autotop=config["autotop_labels"],
+        allow_missing=True,
+    )
+    return specs
+
+
+def get_final_surf():
+    gii = []
+    gii.extend(
+        expand(
             bids(
                 root=root,
                 datatype="surf",
                 den="{density}",
+                suffix="{surfname}.surf.gii",
                 space="{space}",
+                hemi="{hemi}",
                 label="{autotop}",
-                suffix="surfaces.spec",
                 **config["subj_wildcards"],
             ),
             density=config["output_density"],
             space=ref_spaces,
+            hemi=config["hemi"],
             autotop=config["autotop_labels"],
+            surfname=config["surf_types"]["hipp"],
             allow_missing=True,
         )
-    else:
-        specs = expand(
+    )
+    gii.extend(
+        expand(
             bids(
                 root=root,
                 datatype="surf",
                 den="{density}",
+                suffix="{surfname}.surf.gii",
                 space="{space}",
                 hemi="{hemi}",
                 label="{autotop}",
-                suffix="surfaces.spec",
                 **config["subj_wildcards"],
             ),
             density=config["output_density"],
             space=ref_spaces,
             hemi=config["hemi"],
             autotop=config["autotop_labels"],
+            surfname=config["surf_types"]["dentate"],
             allow_missing=True,
         )
-    return specs
+    )
+    return gii
 
 
 def get_final_subfields():
@@ -313,6 +341,7 @@ def get_final_qc():
 def get_final_subj_output():
     subj_output = []
     subj_output.extend(get_final_spec())
+    subj_output.extend(get_final_surf())
     subj_output.extend(get_final_subfields())
     subj_output.extend(get_final_coords())
     subj_output.extend(get_final_transforms())

hippunfold/workflow/rules/warps.smk

@@ -167,7 +167,6 @@ rule create_warps_hipp:
         ),
         labelmap=get_labels_for_laplace,
     params:
-        interp_method="linear",
         gm_labels=lambda wildcards: config["laplace_labels"]["AP"]["gm"],
         epsilon=lambda wildcards: config["unfold_crop_epsilon_fractions"],
     resources:
@@ -226,8 +225,6 @@ rule create_warps_hipp:
             hemi="{hemi}",
             suffix="create_warps-hipp.txt"
         ),
-    container:
-        config["singularity"]["autotop"]
     script:
         "../scripts/create_warps.py"
 
@@ -294,7 +291,6 @@ rule create_warps_dentate:
         ),
         labelmap=get_labels_for_laplace,
     params:
-        interp_method="linear",
         gm_labels=lambda wildcards: config["laplace_labels"]["PD"]["sink"],
         epsilon=lambda wildcards: config["unfold_crop_epsilon_fractions"],
     resources:
@@ -353,8 +349,6 @@ rule create_warps_dentate:
             hemi="{hemi}",
             suffix="create_warps-dentate.txt"
         ),
-    container:
-        config["singularity"]["autotop"]
     script:
         "../scripts/create_warps.py"
 

hippunfold/workflow/scripts/create_warps.py

@@ -1,7 +1,7 @@
 import nibabel as nib
 import numpy as np
-from scipy.interpolate import griddata
-from scipy.interpolate import NearestNDInterpolator
+import naturalneighbor
+from scipy.stats import zscore
 
 logfile = open(snakemake.log[0], "w")
 print(f"Start", file=logfile, flush=True)
@@ -25,9 +25,6 @@ def summary(name, array):
     return
 
 
-# params:
-interp_method = snakemake.params.interp_method
-
 # load unfolded coordinate map
 # unfold_ref_nib = nib.load(snakemake.input.unfold_ref_nii)
 unfold_phys_coords_nib = nib.load(snakemake.input.unfold_phys_coords_nii)
@@ -66,7 +63,7 @@ def summary(name, array):
 # the unfolded space, using scipy's griddata (equivalent to matlab scatteredInterpolant).
 
 
-coord_flat_ap = coord_ap[mask == True]  # matlab: Laplace_AP = coord_ap(mask==1);
+coord_flat_ap = coord_ap[mask == True]
 coord_flat_pd = coord_pd[mask == True]
 coord_flat_io = coord_io[mask == True]
 
@@ -75,15 +72,11 @@ def summary(name, array):
 summary("coord_flat_io", coord_flat_io)
 
 # unravel indices of mask voxels into subscripts...
-(i_L, j_L, k_L) = np.unravel_index(
-    idxgm, sz
-)  # matlab: [i_L,j_L,k_L]=ind2sub(sz,idxgm);
+(i_L, j_L, k_L) = np.unravel_index(idxgm, sz)
 summary("i_L", i_L)
 
 # ... and stack into vectors ...
-native_coords_mat = np.vstack(
-    (i_L, j_L, k_L, np.ones(i_L.shape))
-)  # matlab: native_coords_mat = [i_L-1, j_L-1, k_L-1,ones(size(i_L))]';
+native_coords_mat = np.vstack((i_L, j_L, k_L, np.ones(i_L.shape)))
 summary("native_coords_mat", native_coords_mat)
 
 
@@ -104,74 +97,63 @@ def summary(name, array):
 
 # scattered interpolation / griddata:
 
-# matlab:  interp_X = scatteredInterpolant(Laplace_AP,Laplace_PD,Laplace_IO,native_coords_phys(:,1),interp,extrap);
-
 # we have points defined by coord_flat_{ap,pd,io}, and corresponding value as native_coords_phys[:,i]
 # and we want to interpolate on a grid in the unfolded space
 
-# add some noise to avoid perfectly overlapping datapoints!
-points = (
-    coord_flat_ap + (np.random.rand(coord_flat_ap.shape[0]) - 0.5) * 1e-6,
-    coord_flat_pd + (np.random.rand(coord_flat_ap.shape[0]) - 0.5) * 1e-6,
-    coord_flat_io + (np.random.rand(coord_flat_ap.shape[0]) - 0.5) * 1e-6,
-)
+# unnormalize and add a bit of noise so points don't ever perfectly overlap
+coord_flat_ap_unnorm = coord_flat_ap * unfold_dims[0]
+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]), 1 - float(epsilon[0]), unfold_dims[0]),
-    np.linspace(0 + float(epsilon[1]), 1 - float(epsilon[1]), unfold_dims[1]),
-    np.linspace(0 + float(epsilon[2]), 1 - float(epsilon[2]), unfold_dims[2]),
+    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",
 )
-
-# tuple for use in griddata:
-unfold_xi = (unfold_gx, unfold_gy, unfold_gz)
 summary("unfold_gx", unfold_gx)
 summary("unfold_gy", unfold_gy)
 summary("unfold_gz", unfold_gz)
 
-# perform the interpolation, filling in outside values as 0
-#  TODO: linear vs cubic?  we were using "natural" interpolation in matlab
-#         so far, linear seems close enough..
-interp_ap = griddata(
-    points, values=native_coords_phys[:, 0], xi=unfold_xi, method=interp_method
-)
-summary("interp_ap", interp_ap)
-interp_pd = griddata(
-    points, values=native_coords_phys[:, 1], xi=unfold_xi, method=interp_method
-)
-summary("interp_pd", interp_pd)
-interp_io = griddata(
-    points, values=native_coords_phys[:, 2], xi=unfold_xi, method=interp_method
+# perform the interpolation
+
+points = np.stack(
+    [
+        coord_flat_ap * unfold_dims[0]
+        + (np.random.rand(coord_flat_ap.shape[0]) - 0.5) * 1e-6,
+        coord_flat_pd * unfold_dims[1]
+        + (np.random.rand(coord_flat_ap.shape[0]) - 0.5) * 1e-6,
+        coord_flat_io * unfold_dims[2]
+        + (np.random.rand(coord_flat_ap.shape[0]) - 0.5) * 1e-6,
+    ],
+    axis=1,
 )
-summary("interp_io", interp_ap)
 
-# fill NaNs (NN interpolater allows for extrapolation!)
-[x, y, z] = np.where(np.invert(np.isnan(interp_ap)))
-interp = NearestNDInterpolator(
-    np.c_[x, y, z], interp_ap[np.invert(np.isnan(interp_ap))]
+interp_ap = naturalneighbor.griddata(
+    points,
+    native_coords_phys[:, 0],
+    [[0, unfold_dims[0], 1], [0, unfold_dims[1], 1], [0, unfold_dims[2], 1]],
 )
-[qx, qy, qz] = np.where(np.isnan(interp_ap))
-fill = interp(qx, qy, qz)
-interp_ap[np.isnan(interp_ap)] = fill
-
-[x, y, z] = np.where(np.invert(np.isnan(interp_pd)))
-interp = NearestNDInterpolator(
-    np.c_[x, y, z], interp_pd[np.invert(np.isnan(interp_pd))]
+interp_pd = naturalneighbor.griddata(
+    points,
+    native_coords_phys[:, 1],
+    [[0, unfold_dims[0], 1], [0, unfold_dims[1], 1], [0, unfold_dims[2], 1]],
 )
-[qx, qy, qz] = np.where(np.isnan(interp_pd))
-fill = interp(qx, qy, qz)
-interp_pd[np.isnan(interp_pd)] = fill
-
-[x, y, z] = np.where(np.invert(np.isnan(interp_io)))
-interp = NearestNDInterpolator(
-    np.c_[x, y, z], interp_io[np.invert(np.isnan(interp_io))]
+interp_io = naturalneighbor.griddata(
+    points,
+    native_coords_phys[:, 2],
+    [[0, unfold_dims[0], 1], [0, unfold_dims[1], 1], [0, unfold_dims[2], 1]],
 )
-[qx, qy, qz] = np.where(np.isnan(interp_io))
-fill = interp(qx, qy, qz)
-interp_io[np.isnan(interp_io)] = fill
+
 
 # prepare maps for writing as warp file:
 
@@ -180,10 +162,11 @@ def summary(name, array):
 mapToNative[:, :, :, 0, 0] = interp_ap
 mapToNative[:, :, :, 0, 1] = interp_pd
 mapToNative[:, :, :, 0, 2] = interp_io
-# TODO: interpolate nans more better
-mapToNative[np.isnan(mapToNative)] = 0
 summary("mapToNative", mapToNative)
 
+mapToNative[np.isnan(mapToNative)] = 0
+
+
 # mapToNative has the absolute coordinates, but we want them relative to the
 # unfolded grid, so we subtract it out:
 displacementToNative = mapToNative - unfold_grid_phys
@@ -219,13 +202,6 @@ def summary(name, array):
 # The image affine from the unfolded grid takes points from 0 to N to world coords, so
 # just need to un-normalize, then multiply by affine
 
-# unnormalize
-coord_flat_ap_unnorm = coord_flat_ap * unfold_dims[0]
-coord_flat_pd_unnorm = coord_flat_pd * unfold_dims[1]
-coord_flat_io_unnorm = coord_flat_io * unfold_dims[2]
-
-summary("coord_flat_ap_unnorm", coord_flat_ap_unnorm)
-
 
 # reshape for multiplication (affine * vec)
 coord_flat_unnorm_vec = np.stack(
@@ -250,7 +226,7 @@ def summary(name, array):
 summary("uvw_phys", uvw_phys)
 
 # now we have the absolute unfold world coords for each native grid point
-#  but we need the displacement from the native grid point world coord
+# but we need the displacement from the native grid point world coord
 
 # the native world coords are in native_coords_phys
 # so we subtract it

pyproject.toml

@@ -12,6 +12,7 @@ appdirs = "^1.4.4"
 Jinja2 = "^3.0.3"
 pygraphviz = "1.7"
 Pygments = "^2.10.0"
+naturalneighbor = "0.2.1"
 
 
 [tool.poetry.dev-dependencies]