From d399f6459c57dc54932832b649c372b37cde9f2a Mon Sep 17 00:00:00 2001 From: Desk3505 Date: Mon, 14 Jul 2025 09:46:55 -0400 Subject: [PATCH 1/9] RAPGraph 0.1 untested --- scilpy/tracking/rap.py | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/scilpy/tracking/rap.py b/scilpy/tracking/rap.py index 552c15e58..6d08b7930 100644 --- a/scilpy/tracking/rap.py +++ b/scilpy/tracking/rap.py @@ -1,6 +1,7 @@ # -*- coding: utf-8 -*- import numpy as np +from Quactography.quactography.quac_matrix_adj_build import build_mat class RAP: @@ -61,10 +62,21 @@ def rap_multistep_propagate(self, line, prev_direction): class RAPGraph(RAP): - def __init__(self, mask_rap, propagator, max_nbr_pts, neighboorhood_size): + def __init__(self, mask_rap, propagator, max_nbr_pts, neighboorhood_size, fodf): super().__init__(mask_rap, propagator, max_nbr_pts) self.neighboorhood_size = neighboorhood_size + self.fodf = fodf def rap_multistep_propagate(self, line, prev_direction): - raise NotImplementedError \ No newline at end of file + is_line_valid = True + list_of_end_points = [] + try: + if self.max_nbr_pts + len(list_of_end_points)> 17: + raise ValueError("RAPGraph: max number of points exceeded") + except ValueError as e: + print(e) + is_line_valid = False + return line, prev_direction, is_line_valid + line.append(build_mat(self.mask_rap, self.fodf, "output_graph", line[-1], list_of_end_points)) + return line, prev_direction, is_line_valid From ca379595716751c26674cd9e1606f08d97b27c04 Mon Sep 17 00:00:00 2001 From: desk3505 Date: Thu, 24 Jul 2025 11:14:31 -0400 Subject: [PATCH 2/9] WIP, in wait for end point mask --- scilpy/tracking/rap.py | 15 +++++++-------- scripts/scil_tracking_local_dev.py | 5 +++-- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/scilpy/tracking/rap.py b/scilpy/tracking/rap.py index 6d08b7930..2086ac497 100644 --- a/scilpy/tracking/rap.py +++ b/scilpy/tracking/rap.py @@ -1,7 +1,6 @@ # -*- coding: utf-8 -*- import numpy as np -from Quactography.quactography.quac_matrix_adj_build import build_mat class RAP: @@ -64,19 +63,19 @@ def rap_multistep_propagate(self, line, prev_direction): class RAPGraph(RAP): def __init__(self, mask_rap, propagator, max_nbr_pts, neighboorhood_size, fodf): super().__init__(mask_rap, propagator, max_nbr_pts) + from quactography.scripts.quac_matrix_adj_build import build_mat + self.neighboorhood_size = neighboorhood_size self.fodf = fodf def rap_multistep_propagate(self, line, prev_direction): is_line_valid = True - list_of_end_points = [] - try: - if self.max_nbr_pts + len(list_of_end_points)> 17: - raise ValueError("RAPGraph: max number of points exceeded") - except ValueError as e: - print(e) + list_of_end_points = [] #from end point mask, end of the ROI to create the graph with anatomically possible line + + if self.max_nbr_pts + len(list_of_end_points)> 17: + print("RAPGraph: max number of points exceeded") is_line_valid = False return line, prev_direction, is_line_valid - line.append(build_mat(self.mask_rap, self.fodf, "output_graph", line[-1], list_of_end_points)) + line.extend(quack_rap(self.mask_rap, self.fodf, line[-1], list_of_end_points)) return line, prev_direction, is_line_valid diff --git a/scripts/scil_tracking_local_dev.py b/scripts/scil_tracking_local_dev.py index e0742c67f..a1da6846c 100755 --- a/scripts/scil_tracking_local_dev.py +++ b/scripts/scil_tracking_local_dev.py @@ -156,8 +156,9 @@ def _build_arg_parser(): 'Region-Adaptive Propagation tractography will start within ' 'this mask.') track_g.add_argument('--rap_method', default='None', - choices=['None', 'continue'], - help="Region-Adaptive Propagation tractography method " + choices=['None', 'continue', ['quack']], + help="Region-Adaptive Propagation tractography method." \ + "To use option quack, you must install Quacktography " " [%(default)s]") m_g = p.add_argument_group('Memory options') From a4bce6e4bc99c876df2d13311ddbdea251a52cb3 Mon Sep 17 00:00:00 2001 From: desk3505 Date: Fri, 1 Aug 2025 14:26:08 -0400 Subject: [PATCH 3/9] Added arguements for Quack RAP method --- scilpy/tracking/rap.py | 32 +++++++++++++++++++----------- scripts/scil_tracking_local_dev.py | 14 ++++++++++++- 2 files changed, 33 insertions(+), 13 deletions(-) diff --git a/scilpy/tracking/rap.py b/scilpy/tracking/rap.py index 2086ac497..f3ebb39a8 100644 --- a/scilpy/tracking/rap.py +++ b/scilpy/tracking/rap.py @@ -61,21 +61,29 @@ def rap_multistep_propagate(self, line, prev_direction): class RAPGraph(RAP): - def __init__(self, mask_rap, propagator, max_nbr_pts, neighboorhood_size, fodf): + def __init__(self, mask_rap, propagator, max_nbr_pts, fodf, reps, alpha): + """ + fodf: DataVolume + The FODF volume used to compute the RAP. + reps: int + Number of repetitions used in the quantum circuit. + alpha: float + Initial paramater to search the cost landscape. + """ super().__init__(mask_rap, propagator, max_nbr_pts) - from quactography.scripts.quac_matrix_adj_build import build_mat + from quactography.scripts.quac_matrix_adj_build import quack_rap - self.neighboorhood_size = neighboorhood_size self.fodf = fodf + self.reps = reps + self.alpha = alpha def rap_multistep_propagate(self, line, prev_direction): - is_line_valid = True - list_of_end_points = [] #from end point mask, end of the ROI to create the graph with anatomically possible line - - if self.max_nbr_pts + len(list_of_end_points)> 17: - print("RAPGraph: max number of points exceeded") - is_line_valid = False - return line, prev_direction, is_line_valid - line.extend(quack_rap(self.mask_rap, self.fodf, line[-1], list_of_end_points)) - return line, prev_direction, is_line_valid + seg, prev_dir, is_line_valid = (quack_rap(self.mask_rap, self.fodf, line[-1], + reps = self.reps, + alpha = self.alpha, + prev_direction = prev_direction, + theta = self.propagator.theta, + threshold = self.propagator.sf_threshold,)) + line.extend(seg) + return line, prev_dir, is_line_valid diff --git a/scripts/scil_tracking_local_dev.py b/scripts/scil_tracking_local_dev.py index a1da6846c..7fe69e116 100755 --- a/scripts/scil_tracking_local_dev.py +++ b/scripts/scil_tracking_local_dev.py @@ -67,7 +67,7 @@ load_matrix_in_any_format) from scilpy.image.volume_space_management import DataVolume from scilpy.tracking.propagator import ODFPropagator -from scilpy.tracking.rap import RAPContinue +from scilpy.tracking.rap import RAPContinue, RAPGraph from scilpy.tracking.seed import SeedGenerator, CustomSeedsDispenser from scilpy.tracking.tracker import Tracker from scilpy.tracking.utils import (add_mandatory_options_tracking, @@ -160,6 +160,14 @@ def _build_arg_parser(): help="Region-Adaptive Propagation tractography method." \ "To use option quack, you must install Quacktography " " [%(default)s]") + track_g.add_argument('--reps', type=int, default=2, + help='Number of repetitions for the RAP method. ' + 'Default: 2. This is only used for the quack ' + 'method, not for continue.') + track_g.add_argument('--alpha', type=float, default=1.5, + help='Alpha parameter for the RAP method. ' + 'Default: 1.5. This is only used for the quack ' + 'method, not for continue.') m_g = p.add_argument_group('Memory options') add_processes_arg(m_g) @@ -293,6 +301,10 @@ def main(): if args.rap_method == "continue": rap = RAPContinue(rap_mask, propagator, max_nbr_pts, step_size=vox_step_size) + elif args.rap_method == "quack": + rap = RAPGraph(rap_mask, propagator, max_nbr_pts, fodf=dataset, reps=args.reps, + alpha=args.alpha) + else: rap = None From 79298f8d56e0fc665e8fa0b06a46a09e988dce95 Mon Sep 17 00:00:00 2001 From: desk3505 Date: Fri, 1 Aug 2025 14:38:06 -0400 Subject: [PATCH 4/9] Doc string RAPGraph --- scilpy/tracking/rap.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/scilpy/tracking/rap.py b/scilpy/tracking/rap.py index f3ebb39a8..f37b485a6 100644 --- a/scilpy/tracking/rap.py +++ b/scilpy/tracking/rap.py @@ -63,6 +63,10 @@ def rap_multistep_propagate(self, line, prev_direction): class RAPGraph(RAP): def __init__(self, mask_rap, propagator, max_nbr_pts, fodf, reps, alpha): """ + RAPGraph class for the quantum Graph solution for a region. + + Parameters + ---------- fodf: DataVolume The FODF volume used to compute the RAP. reps: int From a05b1021460740030921e150c82672582b959dfe Mon Sep 17 00:00:00 2001 From: Desk3505 Date: Mon, 4 Aug 2025 16:20:28 -0400 Subject: [PATCH 5/9] update on comments, try/except on library import and definition of rap_methods --- scilpy/tracking/rap.py | 10 +++++++--- scripts/scil_tracking_local_dev.py | 6 ++++-- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/scilpy/tracking/rap.py b/scilpy/tracking/rap.py index f37b485a6..ff56ebfd3 100644 --- a/scilpy/tracking/rap.py +++ b/scilpy/tracking/rap.py @@ -75,7 +75,11 @@ def __init__(self, mask_rap, propagator, max_nbr_pts, fodf, reps, alpha): Initial paramater to search the cost landscape. """ super().__init__(mask_rap, propagator, max_nbr_pts) - from quactography.scripts.quac_matrix_adj_build import quack_rap + try: + from quactography.scripts.quac_matrix_adj_build import quack_rap + except ImportError: + raise ImportError("quactography is not installed. " + "Please install it to use RAPGraph.") self.fodf = fodf self.reps = reps @@ -83,11 +87,11 @@ def __init__(self, mask_rap, propagator, max_nbr_pts, fodf, reps, alpha): def rap_multistep_propagate(self, line, prev_direction): - seg, prev_dir, is_line_valid = (quack_rap(self.mask_rap, self.fodf, line[-1], + seg, prev_dir, is_line_valid = quack_rap(self.mask_rap, self.fodf, line[-1], reps = self.reps, alpha = self.alpha, prev_direction = prev_direction, theta = self.propagator.theta, - threshold = self.propagator.sf_threshold,)) + threshold = self.propagator.sf_threshold) line.extend(seg) return line, prev_dir, is_line_valid diff --git a/scripts/scil_tracking_local_dev.py b/scripts/scil_tracking_local_dev.py index 7fe69e116..bc623c83e 100755 --- a/scripts/scil_tracking_local_dev.py +++ b/scripts/scil_tracking_local_dev.py @@ -156,9 +156,11 @@ def _build_arg_parser(): 'Region-Adaptive Propagation tractography will start within ' 'this mask.') track_g.add_argument('--rap_method', default='None', - choices=['None', 'continue', ['quack']], + choices=['None', 'continue', 'quack'], help="Region-Adaptive Propagation tractography method." \ - "To use option quack, you must install Quacktography " + "To use option quack, you must install Quacktography " \ + "continue : goes straight in the RAP mask, " \ + "quack : uses a graph solution by quantum approach. " \ " [%(default)s]") track_g.add_argument('--reps', type=int, default=2, help='Number of repetitions for the RAP method. 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b/scripts/scil_volume_stats_in_labels.py old mode 100755 new mode 100644 From f1761d5cb9c10c06eaaf30fa69034eec5037a118 Mon Sep 17 00:00:00 2001 From: Desk3505 Date: Thu, 7 Aug 2025 09:24:55 -0400 Subject: [PATCH 7/9] permission change --- src/scilpy/cli/scil_NODDI_maps.py | 0 src/scilpy/cli/scil_NODDI_priors.py | 0 src/scilpy/cli/scil_aodf_metrics.py | 0 src/scilpy/cli/scil_bids_validate.py | 0 src/scilpy/cli/scil_bingham_metrics.py | 0 src/scilpy/cli/scil_btensor_metrics.py | 0 src/scilpy/cli/scil_bundle_alter_to_target_dice.py | 0 src/scilpy/cli/scil_bundle_clean_qbx_clusters.py | 0 src/scilpy/cli/scil_bundle_compute_centroid.py | 0 src/scilpy/cli/scil_bundle_compute_endpoints_map.py | 0 src/scilpy/cli/scil_bundle_diameter.py | 0 src/scilpy/cli/scil_bundle_explore_bundleseg.py | 0 src/scilpy/cli/scil_bundle_filter_by_occurence.py | 0 src/scilpy/cli/scil_bundle_fixel_analysis.py | 0 src/scilpy/cli/scil_bundle_generate_priors.py | 0 src/scilpy/cli/scil_bundle_label_map.py | 0 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a/src/scilpy/cli/scil_viz_volume_screenshot_mosaic.py b/src/scilpy/cli/scil_viz_volume_screenshot_mosaic.py old mode 100644 new mode 100755 diff --git a/src/scilpy/cli/scil_volume_apply_transform.py b/src/scilpy/cli/scil_volume_apply_transform.py old mode 100644 new mode 100755 diff --git a/src/scilpy/cli/scil_volume_b0_synthesis.py b/src/scilpy/cli/scil_volume_b0_synthesis.py old mode 100644 new mode 100755 diff --git a/src/scilpy/cli/scil_volume_count_non_zero_voxels.py b/src/scilpy/cli/scil_volume_count_non_zero_voxels.py old mode 100644 new mode 100755 diff --git a/src/scilpy/cli/scil_volume_crop.py b/src/scilpy/cli/scil_volume_crop.py old mode 100644 new mode 100755 diff --git a/src/scilpy/cli/scil_volume_distance_map.py b/src/scilpy/cli/scil_volume_distance_map.py old mode 100644 new mode 100755 diff --git a/src/scilpy/cli/scil_volume_flip.py b/src/scilpy/cli/scil_volume_flip.py old mode 100644 new mode 100755 diff --git a/src/scilpy/cli/scil_volume_math.py b/src/scilpy/cli/scil_volume_math.py old mode 100644 new mode 100755 diff --git a/src/scilpy/cli/scil_volume_pairwise_comparison.py b/src/scilpy/cli/scil_volume_pairwise_comparison.py old mode 100644 new mode 100755 diff --git a/src/scilpy/cli/scil_volume_remove_outliers_ransac.py b/src/scilpy/cli/scil_volume_remove_outliers_ransac.py old mode 100644 new mode 100755 diff --git a/src/scilpy/cli/scil_volume_resample.py b/src/scilpy/cli/scil_volume_resample.py old mode 100644 new mode 100755 diff --git a/src/scilpy/cli/scil_volume_reshape.py b/src/scilpy/cli/scil_volume_reshape.py old mode 100644 new mode 100755 diff --git a/src/scilpy/cli/scil_volume_reslice_to_reference.py b/src/scilpy/cli/scil_volume_reslice_to_reference.py old mode 100644 new mode 100755 diff --git a/src/scilpy/cli/scil_volume_stats_in_ROI.py b/src/scilpy/cli/scil_volume_stats_in_ROI.py old mode 100644 new mode 100755 diff --git a/src/scilpy/cli/scil_volume_stats_in_labels.py b/src/scilpy/cli/scil_volume_stats_in_labels.py old mode 100644 new mode 100755 diff --git a/src/scilpy/data/mni_icbm152_t1_tal_nlin_asym_09c_masked_2_5.nii.gz b/src/scilpy/data/mni_icbm152_t1_tal_nlin_asym_09c_masked_2_5.nii.gz old mode 100644 new mode 100755 From f1d0b58fe070942193fc342b89effaa1dc87edfd Mon Sep 17 00:00:00 2001 From: Desk3505 Date: Tue, 12 Aug 2025 14:21:19 -0400 Subject: [PATCH 8/9] RAPGraph fonctionnal with classical Dijkstra solution --- src/scilpy/cli/scil_tracking_local_dev.py | 2 +- src/scilpy/tracking/rap.py | 20 ++++++++++++-------- 2 files changed, 13 insertions(+), 9 deletions(-) diff --git a/src/scilpy/cli/scil_tracking_local_dev.py b/src/scilpy/cli/scil_tracking_local_dev.py index bc623c83e..b52ae5a62 100755 --- a/src/scilpy/cli/scil_tracking_local_dev.py +++ b/src/scilpy/cli/scil_tracking_local_dev.py @@ -304,7 +304,7 @@ def main(): rap = RAPContinue(rap_mask, propagator, max_nbr_pts, step_size=vox_step_size) elif args.rap_method == "quack": - rap = RAPGraph(rap_mask, propagator, max_nbr_pts, fodf=dataset, reps=args.reps, + rap = RAPGraph(rap_mask, rap_img, propagator, max_nbr_pts, fodf=odf_sh_img, reps=args.reps, alpha=args.alpha) else: diff --git a/src/scilpy/tracking/rap.py b/src/scilpy/tracking/rap.py index ff56ebfd3..1da4c337c 100644 --- a/src/scilpy/tracking/rap.py +++ b/src/scilpy/tracking/rap.py @@ -61,7 +61,7 @@ def rap_multistep_propagate(self, line, prev_direction): class RAPGraph(RAP): - def __init__(self, mask_rap, propagator, max_nbr_pts, fodf, reps, alpha): + def __init__(self, mask_rap, rap_img, propagator, max_nbr_pts, fodf, reps, alpha): """ RAPGraph class for the quantum Graph solution for a region. @@ -75,22 +75,26 @@ def __init__(self, mask_rap, propagator, max_nbr_pts, fodf, reps, alpha): Initial paramater to search the cost landscape. """ super().__init__(mask_rap, propagator, max_nbr_pts) - try: - from quactography.scripts.quac_matrix_adj_build import quack_rap - except ImportError: - raise ImportError("quactography is not installed. " - "Please install it to use RAPGraph.") + self.fodf = fodf + self.rap_img = rap_img self.reps = reps self.alpha = alpha def rap_multistep_propagate(self, line, prev_direction): - seg, prev_dir, is_line_valid = quack_rap(self.mask_rap, self.fodf, line[-1], + try: + from quactography.solver.rap_tracking import quack_rap + except ImportError: + raise ImportError("quactography is not installed. " + "Please install it to use RAPGraph.") + + prev_dir = np.array(prev_direction).round().astype(int) + seg, prev_dir, is_line_valid = quack_rap(self.rap_img, self.fodf, line[-1].round().astype(int), reps = self.reps, alpha = self.alpha, - prev_direction = prev_direction, + prev_direction = prev_dir, theta = self.propagator.theta, threshold = self.propagator.sf_threshold) line.extend(seg) From 5d7bc152ffb7891c52e6985b32b6ad8a1afc0a6f Mon Sep 17 00:00:00 2001 From: desk3505 Date: Thu, 28 Aug 2025 11:32:58 -0400 Subject: [PATCH 9/9] cleaned, added suggestion from Emmanuel and completed prof of concept --- src/scilpy/cli/scil_tracking_local_dev.py | 22 ++++++++++++---------- src/scilpy/tracking/propagator.py | 2 +- src/scilpy/tracking/rap.py | 11 ++++++++--- 3 files changed, 21 insertions(+), 14 deletions(-) diff --git a/src/scilpy/cli/scil_tracking_local_dev.py b/src/scilpy/cli/scil_tracking_local_dev.py index b52ae5a62..d5c10e79d 100755 --- a/src/scilpy/cli/scil_tracking_local_dev.py +++ b/src/scilpy/cli/scil_tracking_local_dev.py @@ -151,25 +151,27 @@ def _build_arg_parser(): "with -nt 1,000,000, \nyou can create tractogram_2 " "with \n--skip 1,000,000.") - track_g.add_argument('--rap_mask', default=None, + rap_g = p.add_argument_group('RAP options') + rap_g.add_argument('--rap_mask', default=None, help='Region-Adaptive Propagation mask (.nii.gz).\n' 'Region-Adaptive Propagation tractography will start within ' 'this mask.') - track_g.add_argument('--rap_method', default='None', + rap_g.add_argument('--rap_method', default='None', choices=['None', 'continue', 'quack'], - help="Region-Adaptive Propagation tractography method." \ - "To use option quack, you must install Quacktography " \ - "continue : goes straight in the RAP mask, " \ - "quack : uses a graph solution by quantum approach. " \ + help="Region-Adaptive Propagation tractography method.\n" + "To use option quack, you must install Quacktography \n" + "continue : goes straight in the RAP mask, \n" + "quack : uses a graph solution by quantum approach. " " [%(default)s]") - track_g.add_argument('--reps', type=int, default=2, - help='Number of repetitions for the RAP method. ' + rap_g.add_argument('--reps', type=int, default=2, + help='Number of repetitions for the RAP method. \n' 'Default: 2. This is only used for the quack ' 'method, not for continue.') - track_g.add_argument('--alpha', type=float, default=1.5, - help='Alpha parameter for the RAP method. ' + rap_g.add_argument('--alpha', type=float, default=1.5, + help='Alpha parameter for the RAP method. \n' 'Default: 1.5. This is only used for the quack ' 'method, not for continue.') + m_g = p.add_argument_group('Memory options') add_processes_arg(m_g) diff --git a/src/scilpy/tracking/propagator.py b/src/scilpy/tracking/propagator.py index 777f46c53..a5aa32ecc 100644 --- a/src/scilpy/tracking/propagator.py +++ b/src/scilpy/tracking/propagator.py @@ -402,7 +402,7 @@ def __init__(self, datavolume, step_size, get_sh_order_and_fullness(self.datavolume.nb_coeffs) self.basis = basis self.is_legacy = is_legacy - self.B = sh_to_sf_matrix(self.sphere, sh_order, self.basis, + self.B = sh_to_sf_matrix(self.sphere, sh_order=sh_order, basis_type=self.basis, smooth=0.006, return_inv=False, full_basis=full_basis, legacy=self.is_legacy) diff --git a/src/scilpy/tracking/rap.py b/src/scilpy/tracking/rap.py index 1da4c337c..2a51a60b0 100644 --- a/src/scilpy/tracking/rap.py +++ b/src/scilpy/tracking/rap.py @@ -1,6 +1,8 @@ # -*- coding: utf-8 -*- import numpy as np +from scilpy.tracking.utils import TrackingDirection + class RAP: @@ -88,9 +90,10 @@ def rap_multistep_propagate(self, line, prev_direction): from quactography.solver.rap_tracking import quack_rap except ImportError: raise ImportError("quactography is not installed. " - "Please install it to use RAPGraph.") + "Please install it to use RAPGraph.\n" + "Add: Follow instructions here: https://github.com/scilus/quactography") - prev_dir = np.array(prev_direction).round().astype(int) + prev_dir = np.array(prev_direction) seg, prev_dir, is_line_valid = quack_rap(self.rap_img, self.fodf, line[-1].round().astype(int), reps = self.reps, alpha = self.alpha, @@ -98,4 +101,6 @@ def rap_multistep_propagate(self, line, prev_direction): theta = self.propagator.theta, threshold = self.propagator.sf_threshold) line.extend(seg) - return line, prev_dir, is_line_valid + last_dir = TrackingDirection(prev_direction) + + return line, last_dir, is_line_valid