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Volumes modules #747

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merged 9 commits into from
Oct 16, 2023
Merged

Volumes modules #747

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9c1071f
count non-zero: move nibabel loading to main
EmmaRenauld Sep 21, 2023
63ecbb8
Move image.operations -> image.volume_math and utils.image -> utils.v…
EmmaRenauld Sep 21, 2023
8c6a2db
Move resample_volume into volume_operations
EmmaRenauld Sep 21, 2023
179c44d
Encapsultate main of scil_flip_volume
EmmaRenauld Sep 21, 2023
3348a8c
Move image.datasets -> image.volume_space_management
EmmaRenauld Sep 21, 2023
56af868
Encapsulate main of scil_crop_volume.py
EmmaRenauld Sep 21, 2023
0c0140e
Move back bounding box to scil_crop_volume. ToDo elsewhere
EmmaRenauld Oct 4, 2023
f0702a6
Answer comment: change dataset to datavolume
EmmaRenauld Oct 4, 2023
8d18f33
Fix left-over wrong import
EmmaRenauld Oct 5, 2023
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Move image.datasets -> image.volume_space_management
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@EmmaRenauld
EmmaRenauld committed Oct 5, 2023
commit 3348a8c6ab0c73824f3cc5ad19f609ad1c7df04e
35 changes: 35 additions & 0 deletions scilpy/image/datasets.py → scilpy/image/volume_space_management.py
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Expand Up @@ -4,6 4,41 @@
from dipy.core.interpolation import trilinear_interpolate4d, \
nearestneighbor_interpolate
from dipy.io.stateful_tractogram import Origin, Space
from dipy.segment.mask import bounding_box


from scilpy.utils.util import voxel_to_world


class WorldBoundingBox(object):
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@AlexVCaron AlexVCaron Sep 21, 2023 •
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We need to discuss this more. This class is used as a pickle in the scil_crop_volume.py script. Moving it here won't work, it must be a top of module to be picklable (https://docs.python.org/3/library/pickle.html).

And even, it will bug all pickled WorldBoundingBox kept by scilpy user (a pickle is bound to the module in which it was created, which is main up till now). As such, the script parameters --input_bbox won't work with old boxes.

If we intend to deprecate those boxes, we should deprecate this pickle usage instead and rely on another saving method for the bounding box. It is legacy and really the worst way of doing this job.

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@arnaudbore @frheault @EmmaRenauld I would move this code back to the script, if we all agree. With a todo to change the way it works, remove pickling from the solution.

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@EmmaRenauld EmmaRenauld Sep 21, 2023 •
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Ok.

@frheault , I will remove scil_crop_volume from files to give to people at the retreat. Seems more complicated than expected.

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@AlexVCaron Tests were passing, though. Do you have an example of pickle file that we could add to the tests?

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We do not test the input and output pickle, so we don't check this behavior. I'll prepare a little package for here and the retreat.

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Here is some data. You have the pickled bbox, created from the current master.

Loading the box does not work. However, contrary to what I thought, it is still possible to create and load boxes with the bbox class in the module. I still think we should change to another way than pickle, but we'll talk about it at the retreat.

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Thanks. I will try to play with this eventually.

"""
Used in scil_crop_volume.
toDo. See if can be merged with class Dataset below
"""
def __init__(self, minimums, maximums, voxel_size):
self.minimums = minimums
self.maximums = maximums
self.voxel_size = voxel_size


def compute_nifti_bounding_box(img):
"""Finds bounding box from data and transforms it in world space for use
on data with different attributes like voxel size.

Used in scil_crop_volume.
toDo. See if can be merged with class Dataset below
"""
data = img.get_fdata(dtype=np.float32, caching='unchanged')
affine = img.affine
voxel_size = img.header.get_zooms()[0:3]

voxel_bb_mins, voxel_bb_maxs = bounding_box(data)

world_bb_mins = voxel_to_world(voxel_bb_mins, affine)
world_bb_maxs = voxel_to_world(voxel_bb_maxs, affine)
wbbox = WorldBoundingBox(world_bb_mins, world_bb_maxs, voxel_size)

return wbbox


class DataVolume(object):
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6 changes: 3 additions & 3 deletions scilpy/tracking/propagator.py
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Expand Up @@ -33,7 33,7 @@ def __init__(self, dataset, step_size, rk_order, space, origin):
"""
Parameters
----------
dataset: scilpy.image.datasets.DataVolume
dataset: scilpy.image.volume_space_management.DataVolume
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Trackable Dataset object.
step_size: float
The step size for tracking. Important: step size should be in the
Expand Down Expand Up @@ -255,7 255,7 @@ def __init__(self, dataset, step_size, rk_order, dipy_sphere,
"""
Parameters
----------
dataset: scilpy.image.datasets.DataVolume
dataset: scilpy.image.volume_space_management.DataVolume
Trackable Dataset object.
step_size: float
The step size for tracking.
Expand Down Expand Up @@ -321,7 321,7 @@ def __init__(self, dataset, step_size,

Parameters
----------
dataset: scilpy.image.datasets.DataVolume
dataset: scilpy.image.volume_space_management.DataVolume
Trackable Dataset object.
step_size: float
The step size for tracking.
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2 changes: 1 addition & 1 deletion scilpy/tracking/tracker.py
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Expand Up @@ -17,7 17,7 @@
from dipy.reconst.shm import sh_to_sf_matrix
from dipy.tracking.streamlinespeed import compress_streamlines

from scilpy.image.datasets import DataVolume
from scilpy.image.volume_space_management import DataVolume
from scilpy.tracking.propagator import AbstractPropagator, PropagationStatus
from scilpy.reconst.utils import find_order_from_nb_coeff
from scilpy.tracking.seed import SeedGenerator
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2 changes: 1 addition & 1 deletion scripts/scil_compute_local_tracking_dev.py
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Expand Up @@ -59,7 59,7 @@
add_verbose_arg,
assert_inputs_exist, assert_outputs_exist,
verify_compression_th)
from scilpy.image.datasets import DataVolume
from scilpy.image.volume_space_management import DataVolume
from scilpy.tracking.propagator import ODFPropagator
from scilpy.tracking.seed import SeedGenerator
from scilpy.tracking.tools import get_theta
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27 changes: 1 addition & 26 deletions scripts/scil_crop_volume.py
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Expand Up @@ -14,7 14,7 @@
import argparse
import pickle

from dipy.segment.mask import crop, bounding_box
from dipy.segment.mask import crop
import nibabel as nib
import numpy as np

Expand All @@ -23,31 23,6 @@
assert_outputs_exist)
from scilpy.utils.util import voxel_to_world, world_to_voxel

# TODO move that elsewhere


class WorldBoundingBox(object):
def __init__(self, minimums, maximums, voxel_size):
self.minimums = minimums
self.maximums = maximums
self.voxel_size = voxel_size


def compute_nifti_bounding_box(img):
"""Finds bounding box from data and transforms it in world space for use
on data with different attributes like voxel size."""
data = img.get_fdata(dtype=np.float32, caching='unchanged')
affine = img.affine
voxel_size = img.header.get_zooms()[0:3]

voxel_bb_mins, voxel_bb_maxs = bounding_box(data)

world_bb_mins = voxel_to_world(voxel_bb_mins, affine)
world_bb_maxs = voxel_to_world(voxel_bb_maxs, affine)
wbbox = WorldBoundingBox(world_bb_mins, world_bb_maxs, voxel_size)

return wbbox


def crop_nifti(img, wbbox):
"""Applies cropping from a world space defined bounding box and fixes the
Expand Down