DOC - rename uncompress fct to streamlines_to_voxel_coordinates

docs/source/fake_files/uncompress.py

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

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/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
 
@@ -89,8 +89,8 @@ 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
@@ -294,13 +294,16 @@ 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.")
@@ -385,10 +388,14 @@ 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.")
@@ -627,15 +634,8 @@ 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

@@ -12,7 +12,7 @@ cimport numpy as cnp
 
 cdef struct Pointers:
     # Incremented when we complete a streamline. Saved at the start of each
-    # streamline because we need to start anew if we resize data_out
+    # streamline because we need to start a new if we resize data_out
     cnp.npy_intp *lengths_in
     cnp.npy_intp *lengths_out
     cnp.npy_intp *offsets_in
@@ -34,7 +34,7 @@ cdef struct Pointers:
 @cython.boundscheck(False)
 @cython.wraparound(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.
@@ -104,7 +104,9 @@ 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
@@ -150,7 +152,7 @@ cdef inline void c_get_closest_edge(double *p,
 @cython.boundscheck(False)
 @cython.wraparound(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_tractogram_segment_connections_from_labels.py

@@ -84,7 +84,7 @@
     compute_connectivity,
     construct_hdf5_from_connectivity,
     extract_longest_segments_from_profile)
-from scilpy.tractograms.uncompress import uncompress
+from scilpy.tractograms.uncompress import streamlines_to_voxel_coordinates
 
 
 def _get_output_paths(args):
@@ -277,7 +277,10 @@ def main():
     # Get the indices of the voxels traversed by each streamline
     logging.info('*** Computing voxels traversed by each streamline ***')
     time1 = time.time()
-    indices, points_to_idx = uncompress(sft.streamlines, return_mapping=True)
+    indices, points_to_idx = streamlines_to_voxel_coordinates(
+        sft.streamlines,
+        return_mapping=True
+    )
     time2 = time.time()
     logging.info('    Streamlines intersection took {} sec.'.format(
         round(time2 - time1, 2)))