Merge branch 'master' of github.com:scilus/scilpy

docs/source/fake_files/uncompress.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
 
 
-def uncompress():
+def streamlines_to_voxel_coordinates():
     pass

scilpy/denoise/asym_filtering.py

@@ -523,7 +523,7 @@ def cosine_filtering(in_sh, sh_order=8, sh_basis='descoteaux07',
         Filtered signal as SH coefficients in full SH basis.
     """
     # Load the sphere used for projection of SH
-    sphere = get_sphere(sphere_str)
+    sphere = get_sphere(name=sphere_str)
 
     # Normalized filter for each sf direction
     weights = _get_cosine_weights(sphere, dot_sharpness, sigma)

scilpy/image/volume_operations.py

@@ -284,14 +284,16 @@ def register_image(static, static_grid2world, moving, moving_grid2world,
     # Then, rigid transformation (translation + rotation)
     transform = RigidTransform3D()
     rigid = reg_obj.optimize(static, moving, transform, params0,
-                             static_grid2world, moving_grid2world,
+                             static_grid2world=static_grid2world,
+                             moving_grid2world=moving_grid2world,
                              starting_affine=c_of_mass.affine)
 
     if transformation_type == 'affine':
         # Finally, affine transformation (translation + rotation + scaling)
         transform = AffineTransform3D()
         affine = reg_obj.optimize(static, moving, transform, params0,
-                                  static_grid2world, moving_grid2world,
+                                  static_grid2world=static_grid2world,
+                                  moving_grid2world=moving_grid2world,
                                   starting_affine=rigid.affine)
 
         mapper = affine

scilpy/io/btensor.py

@@ -192,7 +192,7 @@ def generate_btensor_input(in_dwis, in_bvals, in_bvecs, in_bdeltas,
     ub_deltas_full = np.take_along_axis(np.asarray(ub_deltas_full),
                                         sorted_indices, axis=0)
     # Creating the corresponding gtab
-    gtab_full = gradient_table(bvals_full, bvecs_full,
+    gtab_full = gradient_table(bvals_full, bvecs=bvecs_full,
                                b0_threshold=bvals_full.min(),
                                btens=b_shapes)
 

scilpy/io/deprecator.py

@@ -66,7 +66,8 @@ def deprecate_script(script, message, from_version):
     def _deprecation_decorator(func):
         @wraps(func)
         def _wrapper(*args, **kwargs):
-            if cmp_pkg_version(current_version, expiration_version) >= 0:
+            if cmp_pkg_version(current_version,
+                               pkg_version_str=expiration_version) >= 0:
                 footer = f"""\
                           {message}
                           {EXPIRATION_FOOTER.format(

scilpy/tracking/propagator.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 
-import dipy
+from dipy.data import get_sphere
 from dipy.io.stateful_tractogram import Space, Origin
 from dipy.reconst.shm import sh_to_sf_matrix
 
@@ -278,7 +278,7 @@ def __init__(self, datavolume, step_size, rk_order, dipy_sphere,
         """
         super().__init__(datavolume, step_size, rk_order, space, origin)
 
-        self.sphere = dipy.data.get_sphere(dipy_sphere).subdivide(n=sub_sphere)
+        self.sphere = get_sphere(name=dipy_sphere).subdivide(n=sub_sphere)
         self.dirs = np.zeros(len(self.sphere.vertices), dtype=np.ndarray)
         for i in range(len(self.sphere.vertices)):
             self.dirs[i] = TrackingDirection(self.sphere.vertices[i], i)

scilpy/tracking/tracker.py

@@ -3,18 +3,15 @@
 import itertools
 import logging
 import multiprocessing
-from operator import mod
 import os
 import sys
 from tempfile import TemporaryDirectory
-from time import perf_counter
 import traceback
 from typing import Union
 from tqdm import tqdm
 
 import numpy as np
 from dipy.data import get_sphere
-from dipy.core.sphere import HemiSphere
 from dipy.io.stateful_tractogram import Space
 from dipy.reconst.shm import sh_to_sf_matrix
 from dipy.tracking.streamlinespeed import compress_streamlines
@@ -535,7 +532,7 @@ def __init__(self, sh, mask, seeds, step_size, max_nbr_pts,
             np.array_split(seeds + 0.5, np.ceil(len(seeds)/batch_size))
 
         if sphere is None:
-            self.sphere = get_sphere("repulsion724")
+            self.sphere = get_sphere(name="repulsion724")
         else:
             self.sphere = sphere
 

scilpy/tracking/utils.py

@@ -322,7 +322,7 @@ def get_direction_getter(in_img, algo, sphere, sub_sphere, theta, sh_basis,
     img_data = nib.load(in_img).get_fdata(dtype=np.float32)
 
     sphere = HemiSphere.from_sphere(
-        get_sphere(sphere)).subdivide(n=sub_sphere)
+        get_sphere(name=sphere)).subdivide(n=sub_sphere)
 
     # Theta depends on user choice and algorithm
     theta = get_theta(theta, algo)

scilpy/tractanalysis/connectivity_segmentation.py

@@ -96,7 +96,8 @@ def compute_connectivity(indices, atlas_data, real_labels, segmenting_func):
     ----------
     indices: ArraySequence
         The list of 3D indices [i, j, k] of all voxels traversed by all
-        streamlines. This is the output of our uncompress function.
+        streamlines. This is the output of the
+        streamlines_to_voxel_coordinates function.
     atlas_data: np.ndarray
         The loaded image containing the labels.
     real_labels: np.ndarray
@@ -155,9 +156,9 @@ def construct_hdf5_from_connectivity(
     sft: StatefulTractogram
         The tractogram.
     indices: ArraySequence
-        Results from uncompress.
+        Results from streamlines_to_voxel_coordinates.
     points_to_idx: ArraySequence
-        Results from uncompress.
+        Results from streamlines_to_voxel_coordinates.
     real_labels: np.ndarray
         The labels.
     con_info: dict

scilpy/tractanalysis/fibertube_scoring.py

@@ -12,7 +12,7 @@
                                              dist_segment_segment,
                                              dist_point_segment)
 from scilpy.tracking.utils import tqdm_if_verbose
-from scilpy.tractograms.uncompress import uncompress
+from scilpy.tractograms.uncompress import streamlines_to_voxel_coordinates
 
 
 def fibertube_density(sft, samples_per_voxel_axis, verbose=False):
@@ -61,10 +61,10 @@ def fibertube_density(sft, samples_per_voxel_axis, verbose=False):
                            len(sft.streamlines))
     max_diameter = np.max(diameters)
 
-    # Everything will be in vox and corner for uncompress.
+    # Everything will be in vox and corner for streamlines_to_voxel_coordinates.
     sft.to_vox()
     sft.to_corner()
-    vox_idx_for_streamline = uncompress(sft.streamlines)
+    vox_idx_for_streamline = streamlines_to_voxel_coordinates(sft.streamlines)
     mask_idx = np.concatenate(vox_idx_for_streamline)
     mask = np.zeros((sft.dimensions), dtype=np.uint8)
     # Numpy array indexing in 3D works like this
@@ -222,7 +222,7 @@ def min_external_distance(sft, verbose):
                 min_external_distance = external_distance
                 min_external_distance_vec = (
                     get_external_vector_from_centerline_vector(vector, rp, rq)
-                    )
+                )
 
     return min_external_distance, min_external_distance_vec
 

scilpy/tractanalysis/todi.py

@@ -37,7 +37,7 @@ def __init__(self, img_shape, sphere_type='repulsion724'):
         """
         assert len(img_shape) == 3
 
-        self.sphere = get_sphere(sphere_type)
+        self.sphere = get_sphere(name=sphere_type)
         self.nb_sphere_vts = len(self.sphere.vertices)
 
         self.img_shape = img_shape

scilpy/tractograms/streamline_and_mask_operations.py

@@ -9,7 +9,7 @@
 
 from scipy.ndimage import map_coordinates
 
-from scilpy.tractograms.uncompress import uncompress
+from scilpy.tractograms.uncompress import streamlines_to_voxel_coordinates
 from scilpy.tractograms.streamline_operations import \
     resample_streamlines_step_size
 
@@ -87,8 +87,8 @@ def get_head_tail_density_maps(sft, point_to_select=1, to_millimeters=False):
         streamlines = sft.streamlines
 
     dimensions = sft.dimensions
-    # Uncompress the streamlines to get the indices of the voxels intersected
-    list_indices, points_to_indices = uncompress(
+    # Get the indices of the voxels intersected
+    list_indices, points_to_indices = streamlines_to_voxel_coordinates(
         streamlines, return_mapping=True)
 
     # Initialize the endpoints maps
@@ -292,13 +292,16 @@ def cut_streamlines_with_mask(
     sft.to_vox()
     sft.to_corner()
 
-    # Uncompress the streamlines to get the indices of the voxels
+    # Get the indices of the voxels
     # intersected by the streamlines and the mapping from points to indices
-    indices, points_to_idx = uncompress(sft.streamlines,
-                                        return_mapping=True)
+    indices, points_to_idx = streamlines_to_voxel_coordinates(
+        sft.streamlines,
+        return_mapping=True
+    )
 
     if len(sft.streamlines[0]) != len(points_to_idx[0]):
-        raise ValueError("Error in the uncompress function. Try running the "
+        raise ValueError("Error in the streamlines_to_voxel_coordinates "
+                         "function. Try running the "
                          "scil_tractogram_remove_invalid.py script with the \n"
                          "--remove_single_point and "
                          "--remove_overlapping_points options.")
@@ -383,10 +386,14 @@ def cut_streamlines_between_labels(
     mask = label_data_2 != unique_vals[1]
     label_data_2[mask] = 0
 
-    (indices, points_to_idx) = uncompress(sft.streamlines, return_mapping=True)
+    (indices, points_to_idx) = streamlines_to_voxel_coordinates(
+        sft.streamlines,
+        return_mapping=True
+    )
 
     if len(sft.streamlines[0]) != len(points_to_idx[0]):
-        raise ValueError("Error in the uncompress function. Try running the "
+        raise ValueError("Error in the streamlines_to_voxel_coordinates "
+                         "function. Try running the "
                          "scil_tractogram_remove_invalid.py script with the \n"
                          "--remove_single_point and "
                          "--remove_overlapping_points options.")
@@ -624,15 +631,8 @@ def compute_streamline_segment(orig_strl, inter_vox, in_vox_idx, out_vox_idx,
     nb_points = nb_points_orig_strl + nb_add_points
     orig_segment_len = len(orig_strl[in_strl_point:out_strl_point + 1])
 
-    # TODO: Fix the bug in `uncompress` and remove this
-    # There is a bug with `uncompress` where the number of `points_to_indices`
-    # is not the same as the number of points in the streamline. This is
-    # a temporary fix.
-    segment_len = min(
-        nb_points,
-        orig_segment_len + nb_add_points)
     # Initialize the new streamline segment
-    segment = np.zeros((segment_len, 3))
+    segment = np.zeros((nb_points, 3))
     # offset for indexing in case there are new points
     offset = 0
 

scilpy/tractograms/tests/test_streamline_and_mask_operations.py

@@ -21,7 +21,7 @@
     get_head_tail_density_maps,
     CuttingStyle)
 from scilpy.image.labels import get_labels_from_mask
-from scilpy.tractograms.uncompress import uncompress
+from scilpy.tractograms.uncompress import streamlines_to_voxel_coordinates
 
 
 fetch_data(get_testing_files_dict(), keys=['tractograms.zip'])
@@ -147,12 +147,15 @@ def test_trim_streamline_in_mask():
     sft.to_vox()
     sft.to_corner()
 
-    idices, points_to_idx = uncompress(sft.streamlines, return_mapping=True)
-    strl_indices = idices[0]
-    points_to_idices = points_to_idx[0]
+    indices, points_to_idx = streamlines_to_voxel_coordinates(
+        sft.streamlines,
+        return_mapping=True
+    )
+    strl_indices = indices[0]
+    points_to_indices = points_to_idx[0]
 
     cut = _trim_streamline_in_mask(
-        strl_indices, sft.streamlines[0], points_to_idices, center_roi)
+        strl_indices, sft.streamlines[0], points_to_indices, center_roi)
 
     in_result = os.path.join(SCILPY_HOME, 'tractograms',
                              'streamline_and_mask_operations',
@@ -200,12 +203,15 @@ def test_trim_streamline_in_mask_keep_longest():
     sft.to_vox()
     sft.to_corner()
 
-    idices, points_to_idx = uncompress(sft.streamlines, return_mapping=True)
-    strl_indices = idices[0]
-    points_to_idices = points_to_idx[0]
+    indices, points_to_idx = streamlines_to_voxel_coordinates(
+        sft.streamlines,
+        return_mapping=True
+    )
+    strl_indices = indices[0]
+    points_to_indices = points_to_idx[0]
 
     cut = _trim_streamline_in_mask_keep_longest(
-        strl_indices, sft.streamlines[0], points_to_idices, center_roi)
+        strl_indices, sft.streamlines[0], points_to_indices, center_roi)
 
     in_result = os.path.join(SCILPY_HOME, 'tractograms',
                              'streamline_and_mask_operations',
@@ -250,12 +256,15 @@ def test_trim_streamline_endpoints_in_mask():
     sft.to_vox()
     sft.to_corner()
 
-    idices, points_to_idx = uncompress(sft.streamlines, return_mapping=True)
-    strl_indices = idices[0]
-    points_to_idices = points_to_idx[0]
+    indices, points_to_idx = streamlines_to_voxel_coordinates(
+        sft.streamlines,
+        return_mapping=True
+    )
+    strl_indices = indices[0]
+    points_to_indices = points_to_idx[0]
 
     cut = _trim_streamline_endpoints_in_mask(
-        strl_indices, sft.streamlines[0], points_to_idices,
+        strl_indices, sft.streamlines[0], points_to_indices,
         head_tail_offset_rois)
 
     in_result = os.path.join(SCILPY_HOME, 'tractograms',
@@ -334,10 +343,14 @@ def test_compute_streamline_segment():
 
     # Split head and tail from mask
     roi_data_1, roi_data_2 = split_mask_blobs_kmeans(
-        head_tail_offset_rois, nb_clusters=2)
-
-    (indices, points_to_idx) = uncompress(one_sft.streamlines,
-                                          return_mapping=True)
+        head_tail_offset_rois,
+        nb_clusters=2
+    )
+
+    (indices, points_to_idx) = streamlines_to_voxel_coordinates(
+        one_sft.streamlines,
+        return_mapping=True
+    )
 
     strl_indices = indices[0]
     # Find the first and last "voxels" of the streamline that are in the

scilpy/tractograms/uncompress.pyx

@@ -32,7 +32,7 @@ cdef struct Pointers:
 
 @cython.boundscheck(False)
 @cython.cdivision(True)
-def uncompress(streamlines, return_mapping=False):
+def streamlines_to_voxel_coordinates(streamlines, return_mapping=False):
     """
     Get the indices of the voxels traversed by each streamline; then returns
     an ArraySequence of indices, i.e. [i, j, k] coordinates.
@@ -102,7 +102,9 @@ def uncompress(streamlines, return_mapping=False):
     pointers.points_to_index_out = &points_to_index_view_out[0]
 
     while 1:
-        at_point = _uncompress(&pointers, at_point, max_points - 1)
+        at_point = _streamlines_to_voxel_coordinates(&pointers, 
+                                                     at_point, 
+                                                     max_points - 1)
         if pointers.lengths_in == pointers.lengths_in_end:
             # Job finished, we can return the streamlines
             break
@@ -147,7 +149,7 @@ cdef inline void c_get_closest_edge(double *p,
 
 @cython.boundscheck(False)
 @cython.cdivision(True)
-cdef cnp.npy_intp _uncompress(
+cdef cnp.npy_intp _streamlines_to_voxel_coordinates(
         Pointers* pointers,
         cnp.npy_intp at_point,
         cnp.npy_intp max_points) nogil:

scripts/scil_aodf_metrics.py

@@ -142,7 +142,7 @@ def main():
     sh_img = nib.load(args.in_sh)
     sh = sh_img.get_fdata()
 
-    sphere = get_sphere(args.sphere)
+    sphere = get_sphere(name=args.sphere)
 
     sh_basis, is_legacy = parse_sh_basis_arg(args)
     sh_order, full_basis = get_sh_order_and_fullness(sh.shape[-1])

scripts/scil_bids_validate.py

@@ -154,7 +154,7 @@ def get_data(layout, nSub, dwis, t1s, fs, default_readout, clean):
         Default readout time
 
     clean: Boolean
-        If set, if some critical files are missing it will
+        If True, if some critical files are missing it will
         remove this specific subject/session/run
 
     Returns

scripts/scil_fodf_metrics.py

@@ -146,7 +146,7 @@ def main():
     mask = get_data_as_mask(nib.load(args.mask),
                             dtype=bool) if args.mask else None
 
-    sphere = get_sphere(args.sphere)
+    sphere = get_sphere(name=args.sphere)
     sh_basis, is_legacy = parse_sh_basis_arg(args)
 
     # Computing peaks

scripts/scil_mti_maps_MT.py

@@ -182,8 +182,7 @@ def main():
     contrast_names_og = contrast_names
 
     # check data
-    input_maps_flat_list = [m for _list in input_maps_lists for m in _list]
-    assert_inputs_exist(parser, args.in_mtoff_pd + input_maps_flat_list,
+    assert_inputs_exist(parser, args.in_mtoff_pd + input_maps_lists,
                         optional=args.in_mtoff_t1 or [] + [args.mask])
 
     # Define reference image for saving maps