boostrsa 0.0.1.dev0__tar.gz → 0.0.1.dev4__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (28) hide show
  1. boostrsa-0.0.1.dev4/PKG-INFO +84 -0
  2. boostrsa-0.0.1.dev4/README.md +67 -0
  3. {boostrsa-0.0.1.dev0 → boostrsa-0.0.1.dev4}/setup.py +3 -2
  4. boostrsa-0.0.1.dev4/src/boostrsa/boostrsa_types.py +6 -0
  5. {boostrsa-0.0.1.dev0/src → boostrsa-0.0.1.dev4/src/boostrsa}/cores/cpgpu/stats.py +4 -4
  6. boostrsa-0.0.1.dev4/src/boostrsa/cores/gpu/__init__.py +0 -0
  7. {boostrsa-0.0.1.dev0/src → boostrsa-0.0.1.dev4/src/boostrsa}/cores/gpu/matrix.py +1 -1
  8. boostrsa-0.0.1.dev4/src/boostrsa/searchlight.py +233 -0
  9. boostrsa-0.0.1.dev4/src/boostrsa.egg-info/PKG-INFO +84 -0
  10. boostrsa-0.0.1.dev4/src/boostrsa.egg-info/SOURCES.txt +21 -0
  11. boostrsa-0.0.1.dev4/src/boostrsa.egg-info/top_level.txt +1 -0
  12. boostrsa-0.0.1.dev4/tests/test_module1.py +3 -0
  13. boostrsa-0.0.1.dev0/PKG-INFO +0 -27
  14. boostrsa-0.0.1.dev0/README.md +0 -14
  15. boostrsa-0.0.1.dev0/src/boostrsa.egg-info/PKG-INFO +0 -27
  16. boostrsa-0.0.1.dev0/src/boostrsa.egg-info/SOURCES.txt +0 -17
  17. boostrsa-0.0.1.dev0/src/boostrsa.egg-info/top_level.txt +0 -1
  18. {boostrsa-0.0.1.dev0 → boostrsa-0.0.1.dev4}/LICENSE.txt +0 -0
  19. {boostrsa-0.0.1.dev0 → boostrsa-0.0.1.dev4}/setup.cfg +0 -0
  20. {boostrsa-0.0.1.dev0/src/cores → boostrsa-0.0.1.dev4/src/boostrsa}/__init__.py +0 -0
  21. {boostrsa-0.0.1.dev0/src/cores/cpgpu → boostrsa-0.0.1.dev4/src/boostrsa/cores}/__init__.py +0 -0
  22. {boostrsa-0.0.1.dev0/src/cores/cpu → boostrsa-0.0.1.dev4/src/boostrsa/cores/cpgpu}/__init__.py +0 -0
  23. {boostrsa-0.0.1.dev0/src/cores/gpu → boostrsa-0.0.1.dev4/src/boostrsa/cores/cpu}/__init__.py +0 -0
  24. {boostrsa-0.0.1.dev0/src → boostrsa-0.0.1.dev4/src/boostrsa}/cores/cpu/matrix.py +0 -0
  25. {boostrsa-0.0.1.dev0/src → boostrsa-0.0.1.dev4/src/boostrsa}/cores/gpu/basic_operations.py +0 -0
  26. {boostrsa-0.0.1.dev0/src → boostrsa-0.0.1.dev4/src/boostrsa}/cores/gpu/mask.py +0 -0
  27. {boostrsa-0.0.1.dev0 → boostrsa-0.0.1.dev4}/src/boostrsa.egg-info/dependency_links.txt +0 -0
  28. {boostrsa-0.0.1.dev0 → boostrsa-0.0.1.dev4}/src/boostrsa.egg-info/requires.txt +0 -0
@@ -0,0 +1,84 @@
1
+ Metadata-Version: 2.1
2
+ Name: boostrsa
3
+ Version: 0.0.1.dev4
4
+ Summary: This is toolbox for boosting calculation speed using GPU
5
+ Home-page: https://github.com/SeojinYoon/boostrsa.git
6
+ Author: seojin
7
+ Author-email: pures1@hanyang.ac.kr
8
+ Classifier: Programming Language :: Python :: 3
9
+ Classifier: License :: OSI Approved :: MIT License
10
+ Classifier: Operating System :: OS Independent
11
+ Requires-Python: >=3.8
12
+ Description-Content-Type: text/markdown
13
+ License-File: LICENSE.txt
14
+ Requires-Dist: numpy
15
+ Requires-Dist: pandas
16
+ Requires-Dist: tqdm
17
+
18
+
19
+ # Boostrsa
20
+
21
+ This library is based on rsatoolbox(https://github.com/rsagroup/rsatoolbox).
22
+
23
+ The purpose of library is made to boost calcuation speed for searchlight RSA(Representational Similarity Analysis). However, It is still in development, so this library only includes tools for boosting crossnobis distance calculation for constructing RDM(Representational Dissimilartiy Matrix) on the whole brain.
24
+
25
+ ## How it works?
26
+
27
+ Basically, this library uses a Nvidia's GPU instead of CPU for parallel processing. In the searchlight analysis, the data targeted for constructing the RDM in volvxes a voxel and its neighboring voxels. That is well-suited for parallel processing since the calculations for each target are independent of one another. This library utilizes GPU-compatible libraries such as Numba and Cupy to facilitate this process.
28
+
29
+ ## Dependencies
30
+
31
+ To use this library, you need to have a Nvidia's GPU and CUDA. Additionally, this library heavily relies on Cupy and Numba. It is essential to install the appropriate versions of these libraries.
32
+
33
+ ### cupy
34
+
35
+ Cupy is designed to work with specific versions of CUDA. See cupy's guide and install appropriate version in correspond to your system (https://github.com/cupy/cupy).
36
+
37
+ Please check your cuda version to install cupy.
38
+ - versions
39
+ - cupy-cuda10x (for cuda 10)
40
+ - cupy-cuda11x (for cuda 11)
41
+ - cupy-cuda12x (for cuda 12)
42
+
43
+
44
+ If you installed the cuda10 in your computer, then install cupy-cuda10x. install cupy-cuda10x. ex) pip install cupy-cuda10x
45
+
46
+ ### numba
47
+
48
+ The numba library is a powerful tool that enbales python functions to be compiled to machine code at runtime using the LLVM. One of its key features is the ability to generate native code for different architectures, including CPUs and GPUs, which greatly accelerates the execution of data-heavy and computationally intense python code.
49
+
50
+ Please see installation guideline of numba (https://numba.pydata.org/numba-doc/latest/user/installing.html).
51
+
52
+ Pip installation).
53
+
54
+ - pip install numba
55
+
56
+ ### rsatoolbox
57
+
58
+ The rsatoolbox is a Python library specifically designed for Representational Similarity Analysis (RSA).
59
+
60
+ Please see installation guideline of rsatoolbox (https://github.com/rsagroup/rsatoolbox)
61
+
62
+ - pip install rsatoolbox
63
+
64
+ # Installation
65
+
66
+ pip install boostrsa
67
+
68
+ # Checked version
69
+
70
+ These are the latest checked environment.
71
+
72
+ - OS
73
+ - Linux, ubuntu - 21.10
74
+ - numba
75
+ - 0.57.0 ~ 0.59.1 is fine to use
76
+ - cupy
77
+ - cupy-cuda11x
78
+ - cupy-cuda12x
79
+
80
+ # Future works
81
+
82
+ - Add calculation sources to get neighbors and centers (boost)
83
+ - Add RSA sources (boost)
84
+ - Support other calculation methods except crossnobis distance
@@ -0,0 +1,67 @@
1
+
2
+ # Boostrsa
3
+
4
+ This library is based on rsatoolbox(https://github.com/rsagroup/rsatoolbox).
5
+
6
+ The purpose of library is made to boost calcuation speed for searchlight RSA(Representational Similarity Analysis). However, It is still in development, so this library only includes tools for boosting crossnobis distance calculation for constructing RDM(Representational Dissimilartiy Matrix) on the whole brain.
7
+
8
+ ## How it works?
9
+
10
+ Basically, this library uses a Nvidia's GPU instead of CPU for parallel processing. In the searchlight analysis, the data targeted for constructing the RDM in volvxes a voxel and its neighboring voxels. That is well-suited for parallel processing since the calculations for each target are independent of one another. This library utilizes GPU-compatible libraries such as Numba and Cupy to facilitate this process.
11
+
12
+ ## Dependencies
13
+
14
+ To use this library, you need to have a Nvidia's GPU and CUDA. Additionally, this library heavily relies on Cupy and Numba. It is essential to install the appropriate versions of these libraries.
15
+
16
+ ### cupy
17
+
18
+ Cupy is designed to work with specific versions of CUDA. See cupy's guide and install appropriate version in correspond to your system (https://github.com/cupy/cupy).
19
+
20
+ Please check your cuda version to install cupy.
21
+ - versions
22
+ - cupy-cuda10x (for cuda 10)
23
+ - cupy-cuda11x (for cuda 11)
24
+ - cupy-cuda12x (for cuda 12)
25
+
26
+
27
+ If you installed the cuda10 in your computer, then install cupy-cuda10x. install cupy-cuda10x. ex) pip install cupy-cuda10x
28
+
29
+ ### numba
30
+
31
+ The numba library is a powerful tool that enbales python functions to be compiled to machine code at runtime using the LLVM. One of its key features is the ability to generate native code for different architectures, including CPUs and GPUs, which greatly accelerates the execution of data-heavy and computationally intense python code.
32
+
33
+ Please see installation guideline of numba (https://numba.pydata.org/numba-doc/latest/user/installing.html).
34
+
35
+ Pip installation).
36
+
37
+ - pip install numba
38
+
39
+ ### rsatoolbox
40
+
41
+ The rsatoolbox is a Python library specifically designed for Representational Similarity Analysis (RSA).
42
+
43
+ Please see installation guideline of rsatoolbox (https://github.com/rsagroup/rsatoolbox)
44
+
45
+ - pip install rsatoolbox
46
+
47
+ # Installation
48
+
49
+ pip install boostrsa
50
+
51
+ # Checked version
52
+
53
+ These are the latest checked environment.
54
+
55
+ - OS
56
+ - Linux, ubuntu - 21.10
57
+ - numba
58
+ - 0.57.0 ~ 0.59.1 is fine to use
59
+ - cupy
60
+ - cupy-cuda11x
61
+ - cupy-cuda12x
62
+
63
+ # Future works
64
+
65
+ - Add calculation sources to get neighbors and centers (boost)
66
+ - Add RSA sources (boost)
67
+ - Support other calculation methods except crossnobis distance
@@ -8,12 +8,13 @@ with open("README.md", "r") as fh:
8
8
 
9
9
  setup(
10
10
  name = "boostrsa",
11
- version = "0.0.1dev",
11
+ version = "0.0.1dev4",
12
12
  author = "seojin",
13
13
  author_email = "pures1@hanyang.ac.kr",
14
14
  description = "This is toolbox for boosting calculation speed using GPU",
15
15
  long_description = long_description,
16
16
  long_description_content_type="text/markdown",
17
+ url = "https://github.com/SeojinYoon/boostrsa.git",
17
18
  packages = find_packages(where = "src"),
18
19
  package_dir = {"": "src"},
19
20
  classifiers = [
@@ -21,7 +22,7 @@ setup(
21
22
  "License :: OSI Approved :: MIT License",
22
23
  "Operating System :: OS Independent",
23
24
  ],
24
- python_requires='>=3.9',
25
+ python_requires='>=3.8',
25
26
  install_requires = [
26
27
  "numpy",
27
28
  "pandas",
@@ -0,0 +1,6 @@
1
+
2
+ class ShrinkageMethod:
3
+ shrinkage_eye = "shrinkage_eye"
4
+ shrinkage_diag = "shrinkage_diag"
5
+
6
+
@@ -2,10 +2,10 @@
2
2
  import numpy as np
3
3
  import cupy as cp
4
4
  from numba import cuda, jit
5
- from boostrsa.src.types import ShrinkageMethod
6
- from boostrsa.src.gpu.basic_operations import outer_sum_square, outer_sum
7
- from boostrsa.src.gpu.matrix import diag, eyes
8
- from boostrsa.src.gpu.basic_operations import scaling
5
+ from boostrsa.boostrsa_types import ShrinkageMethod
6
+ from boostrsa.cores.gpu.basic_operations import outer_sum_square, outer_sum
7
+ from boostrsa.cores.gpu.matrix import diag, eyes
8
+ from boostrsa.cores.gpu.basic_operations import scaling
9
9
 
10
10
  def _covariance_eye(residuals, threads_per_block = 1024):
11
11
  """
File without changes
@@ -1,6 +1,6 @@
1
1
 
2
2
  from numba import cuda, jit
3
- from basic_operations import matmul
3
+ from boostrsa.cores.gpu.basic_operations import matmul
4
4
 
5
5
  @jit(nopython=True)
6
6
  def upper_tri_1d_index(i, j, n_col, k):
@@ -0,0 +1,233 @@
1
+
2
+ # Common Libraries
3
+ import numpy as np
4
+ from numba import cuda, jit
5
+ import cupy as cp
6
+ import itertools
7
+ from tqdm import trange
8
+
9
+ # Custom Libraries
10
+ from boostrsa.boostrsa_types import ShrinkageMethod
11
+ from boostrsa.cores.cpu.matrix import convert_1d_to_symmertic, mean_fold_variance
12
+ from boostrsa.cores.cpgpu.stats import _covariance_diag, _covariance_eye
13
+ from boostrsa.cores.gpu.mask import set_mask
14
+ from boostrsa.cores.gpu.matrix import calc_kernel, rdm_from_kernel
15
+
16
+ # Functions
17
+ def calc_sl_precision(residuals,
18
+ neighbors,
19
+ n_split_data,
20
+ masking_indexes,
21
+ n_thread_per_block = 1024,
22
+ shrinkage_method = "shrinkage_diag"):
23
+ """
24
+ Calculate precision
25
+
26
+ :param residuals(np.ndarray): , shape: (#run, #point, #channel)
27
+ :param neighbors(np.ndarray): , shape: (#center, #neighbor)
28
+ :param n_split_data(int): how many datas to process at once
29
+ :param masking_indexes(np.array): , shape: (#channel) / index of masking brain
30
+ :param n_thread_per_block(int): block per thread
31
+
32
+ return (np.ndarray), shape: (#channel, #run, #neighbor, #neighbor)
33
+ """
34
+
35
+ n_run = residuals.shape[0]
36
+ n_p = residuals.shape[1]
37
+ n_channel = residuals.shape[-1]
38
+
39
+ n_center = len(neighbors)
40
+ n_block = int(np.ceil(n_split_data / n_thread_per_block))
41
+ n_neighbor = neighbors.shape[-1]
42
+ r, c = np.triu_indices(n_neighbor, k = 0)
43
+
44
+ mempool = cp.get_default_memory_pool()
45
+
46
+ chunk_precisions = []
47
+ for i in trange(0, n_center, n_split_data):
48
+ # select neighbors
49
+ target_neighbors = neighbors[i:i + n_split_data, :]
50
+ len_target = len(target_neighbors)
51
+
52
+ # output_1d
53
+ mask_out = cuda.to_device(np.zeros((len_target, n_channel)))
54
+
55
+ # Make mask - neighbor
56
+ set_mask[n_block, n_thread_per_block](target_neighbors, masking_indexes, mask_out)
57
+
58
+ # sync
59
+ cuda.synchronize()
60
+
61
+ # Apply mask
62
+ cpu_mask = mask_out.copy_to_host()
63
+ masked_residuals = []
64
+ for j in range(len(target_neighbors)):
65
+ masked_residuals.append(residuals[:, :, cpu_mask[j] == 1])
66
+ masked_residuals = np.array(masked_residuals)
67
+
68
+ del mask_out
69
+ cuda.defer_cleanup()
70
+
71
+ # Calculate demean
72
+ target_residuals = masked_residuals.reshape(-1, n_p, n_neighbor)
73
+ mean_residuals = np.mean(target_residuals, axis = 1, keepdims=1)
74
+ target_residuals = (target_residuals - mean_residuals)
75
+
76
+ # Calculate covariance
77
+ if shrinkage_method == ShrinkageMethod.shrinkage_diag:
78
+ covariances = _covariance_diag(target_residuals)
79
+ elif shrinkage_method == ShrinkageMethod.shrinkage_eye:
80
+ covariances = _covariance_eye(target_residuals)
81
+
82
+ # Calculate precision matrix
83
+ stack_precisions = cp.linalg.inv(cp.asarray(covariances)).get()
84
+
85
+ # sync
86
+ cuda.synchronize()
87
+
88
+ # concat
89
+ stack_precisions = stack_precisions.reshape(len_target, n_run, n_neighbor, n_neighbor)
90
+ stack_precisions = stack_precisions[:, :, r, c]
91
+
92
+ # add chunk
93
+ chunk_precisions.append(stack_precisions)
94
+
95
+ # Clean data
96
+ cuda.defer_cleanup()
97
+ mempool.free_all_blocks()
98
+
99
+ return chunk_precisions
100
+
101
+ def calc_sl_rdm_crossnobis(n_split_data,
102
+ centers,
103
+ neighbors,
104
+ precs,
105
+ measurements,
106
+ masking_indexes,
107
+ conds,
108
+ sessions,
109
+ n_thread_per_block = 1000):
110
+ """
111
+ Calculate searchlight crossnobis rdm
112
+
113
+ :param n_split_data(int): how many datas to process at once
114
+ :param centers(np.array): centers, shape: (#center)
115
+ :param neighbors(np.array): neighbors , shape: (#center, #neighbor)
116
+ :param precs(np.array): precisions , shape: (#channel, #run, #precision_mat_element)
117
+ :param measurements(np.array): measurment values , shape: (#cond, #channel)
118
+ :param masking_indexes: (np.array) , shape: (#channel) , index of masking brain
119
+ :param conds: conds(np.array - 1d)
120
+ :param sessions(np.array - 1d): session corressponding to conds
121
+ :param n_thread_per_block(int): , block per thread
122
+
123
+ """
124
+ # Data configuration
125
+ n_run = len(np.unique(sessions))
126
+ n_cond = len(np.unique(conds))
127
+ n_dissim = int((n_cond * n_cond - n_cond) / 2)
128
+ n_neighbor = neighbors.shape[-1]
129
+ uq_conds = np.unique(conds)
130
+ n_channel = measurements.shape[-1]
131
+ uq_sessions = np.unique(sessions)
132
+
133
+ assert n_channel == masking_indexes.shape[0], "n_channel should be same"
134
+
135
+ # Fold
136
+ fold_info = cuda.to_device(list(itertools.combinations(np.arange(len(uq_sessions)), 2)))
137
+ n_fold = len(fold_info)
138
+ total_calculation = n_split_data * n_fold
139
+
140
+ # GPU Configuration
141
+ n_block = int(np.ceil(n_split_data / n_thread_per_block))
142
+ n_thread_per_block_2d = int(np.ceil(np.sqrt(n_thread_per_block)))
143
+ block_2ds = (total_calculation // n_thread_per_block_2d, total_calculation // n_thread_per_block_2d)
144
+ thread_2ds = (n_thread_per_block_2d, n_thread_per_block_2d)
145
+
146
+ # Memory pool
147
+ mempool = cp.get_default_memory_pool()
148
+
149
+ # Calculation
150
+ rdm_outs = []
151
+ for i in trange(0, len(centers), n_split_data):
152
+ # select neighbors
153
+ target_centers = centers[i:i + n_split_data]
154
+ target_neighbors = neighbors[i:i + n_split_data, :]
155
+
156
+ n_target_centers = len(target_centers)
157
+
158
+ # output_1d
159
+ mask_out = cuda.to_device(np.zeros((n_target_centers, n_channel)))
160
+
161
+ # Make mask - neighbor
162
+ set_mask[n_block, n_thread_per_block](target_neighbors, masking_indexes, mask_out)
163
+ cuda.synchronize()
164
+
165
+ # Apply mask
166
+ cpu_mask = mask_out.copy_to_host()
167
+ masked_measurements = []
168
+ for j in range(n_target_centers):
169
+ masked_measurements.append(measurements[:, cpu_mask[j] == 1])
170
+ masked_measurements = np.array(masked_measurements)
171
+ masked_measurements = cp.asarray(masked_measurements)
172
+
173
+ del mask_out
174
+ cuda.defer_cleanup()
175
+
176
+ # precision
177
+ prec_mat_shape = int((n_neighbor * n_neighbor - n_neighbor) / 2) + n_neighbor
178
+ target_precs = precs[i:i+n_target_centers].reshape(-1, prec_mat_shape)
179
+ target_precs = np.array([convert_1d_to_symmertic(pre, size = n_neighbor) for pre in target_precs])
180
+ variances = cp.linalg.inv(cp.asarray(target_precs))
181
+ variances = variances.reshape(n_target_centers, n_run, n_neighbor, n_neighbor).get()
182
+ fold_preicions = cp.linalg.inv(cp.asarray(mean_fold_variance(variances, fold_info.copy_to_host())))
183
+ fold_preicions = cuda.to_device(fold_preicions.reshape(n_target_centers, len(fold_info), n_neighbor, n_neighbor).get())
184
+ mempool.free_all_blocks()
185
+
186
+ # Avg conds per session
187
+ avg_measurements = []
188
+ avg_conds = []
189
+ for session in uq_sessions:
190
+ filtering_session = sessions == session
191
+ sess_cond = conds[filtering_session]
192
+ sess_measurements = cp.compress(filtering_session, masked_measurements, axis = 1)
193
+
194
+ mean_measurments = []
195
+ for cond in uq_conds:
196
+ filtering_cond = sess_cond == cond
197
+ cond_measurments = cp.compress(filtering_cond, sess_measurements, axis = 1)
198
+ mean_cond_measurement = cp.mean(cond_measurments, axis = 1)
199
+ mean_measurments.append(cp.expand_dims(mean_cond_measurement, axis = 1))
200
+
201
+ avg_conds.append(cond)
202
+
203
+ avg_measurements.append(cp.expand_dims(cp.concatenate(mean_measurments, axis = 1), axis = 1))
204
+ avg_measurements = cp.concatenate(avg_measurements, axis = 1).get()
205
+
206
+ avg_conds = np.array(avg_conds)
207
+
208
+ mempool.free_all_blocks()
209
+
210
+ # make kernel
211
+ avg_measurements = cuda.to_device(avg_measurements)
212
+
213
+ matmul1_out = cuda.to_device(np.zeros((n_target_centers, n_fold, n_cond, n_neighbor)))
214
+ kernel_out = cuda.to_device(np.zeros((n_target_centers, n_fold, n_cond, n_cond)))
215
+ calc_kernel[block_2ds, thread_2ds](avg_measurements, fold_preicions, fold_info, matmul1_out, kernel_out)
216
+
217
+ cuda.synchronize()
218
+ del matmul1_out
219
+ cuda.defer_cleanup()
220
+
221
+ rdm_out = cuda.to_device(np.zeros((n_target_centers, n_fold, n_dissim)))
222
+ rdm_from_kernel[block_2ds, thread_2ds](kernel_out, n_neighbor, rdm_out)
223
+
224
+ cuda.synchronize()
225
+
226
+ mean_rdms = cp.mean(rdm_out.copy_to_host(), axis = 1)
227
+ rdm_outs.append(mean_rdms)
228
+
229
+ del kernel_out
230
+ del rdm_out
231
+ cuda.defer_cleanup()
232
+
233
+ return rdm_outs, uq_conds
@@ -0,0 +1,84 @@
1
+ Metadata-Version: 2.1
2
+ Name: boostrsa
3
+ Version: 0.0.1.dev4
4
+ Summary: This is toolbox for boosting calculation speed using GPU
5
+ Home-page: https://github.com/SeojinYoon/boostrsa.git
6
+ Author: seojin
7
+ Author-email: pures1@hanyang.ac.kr
8
+ Classifier: Programming Language :: Python :: 3
9
+ Classifier: License :: OSI Approved :: MIT License
10
+ Classifier: Operating System :: OS Independent
11
+ Requires-Python: >=3.8
12
+ Description-Content-Type: text/markdown
13
+ License-File: LICENSE.txt
14
+ Requires-Dist: numpy
15
+ Requires-Dist: pandas
16
+ Requires-Dist: tqdm
17
+
18
+
19
+ # Boostrsa
20
+
21
+ This library is based on rsatoolbox(https://github.com/rsagroup/rsatoolbox).
22
+
23
+ The purpose of library is made to boost calcuation speed for searchlight RSA(Representational Similarity Analysis). However, It is still in development, so this library only includes tools for boosting crossnobis distance calculation for constructing RDM(Representational Dissimilartiy Matrix) on the whole brain.
24
+
25
+ ## How it works?
26
+
27
+ Basically, this library uses a Nvidia's GPU instead of CPU for parallel processing. In the searchlight analysis, the data targeted for constructing the RDM in volvxes a voxel and its neighboring voxels. That is well-suited for parallel processing since the calculations for each target are independent of one another. This library utilizes GPU-compatible libraries such as Numba and Cupy to facilitate this process.
28
+
29
+ ## Dependencies
30
+
31
+ To use this library, you need to have a Nvidia's GPU and CUDA. Additionally, this library heavily relies on Cupy and Numba. It is essential to install the appropriate versions of these libraries.
32
+
33
+ ### cupy
34
+
35
+ Cupy is designed to work with specific versions of CUDA. See cupy's guide and install appropriate version in correspond to your system (https://github.com/cupy/cupy).
36
+
37
+ Please check your cuda version to install cupy.
38
+ - versions
39
+ - cupy-cuda10x (for cuda 10)
40
+ - cupy-cuda11x (for cuda 11)
41
+ - cupy-cuda12x (for cuda 12)
42
+
43
+
44
+ If you installed the cuda10 in your computer, then install cupy-cuda10x. install cupy-cuda10x. ex) pip install cupy-cuda10x
45
+
46
+ ### numba
47
+
48
+ The numba library is a powerful tool that enbales python functions to be compiled to machine code at runtime using the LLVM. One of its key features is the ability to generate native code for different architectures, including CPUs and GPUs, which greatly accelerates the execution of data-heavy and computationally intense python code.
49
+
50
+ Please see installation guideline of numba (https://numba.pydata.org/numba-doc/latest/user/installing.html).
51
+
52
+ Pip installation).
53
+
54
+ - pip install numba
55
+
56
+ ### rsatoolbox
57
+
58
+ The rsatoolbox is a Python library specifically designed for Representational Similarity Analysis (RSA).
59
+
60
+ Please see installation guideline of rsatoolbox (https://github.com/rsagroup/rsatoolbox)
61
+
62
+ - pip install rsatoolbox
63
+
64
+ # Installation
65
+
66
+ pip install boostrsa
67
+
68
+ # Checked version
69
+
70
+ These are the latest checked environment.
71
+
72
+ - OS
73
+ - Linux, ubuntu - 21.10
74
+ - numba
75
+ - 0.57.0 ~ 0.59.1 is fine to use
76
+ - cupy
77
+ - cupy-cuda11x
78
+ - cupy-cuda12x
79
+
80
+ # Future works
81
+
82
+ - Add calculation sources to get neighbors and centers (boost)
83
+ - Add RSA sources (boost)
84
+ - Support other calculation methods except crossnobis distance
@@ -0,0 +1,21 @@
1
+ LICENSE.txt
2
+ README.md
3
+ setup.py
4
+ src/boostrsa/__init__.py
5
+ src/boostrsa/boostrsa_types.py
6
+ src/boostrsa/searchlight.py
7
+ src/boostrsa.egg-info/PKG-INFO
8
+ src/boostrsa.egg-info/SOURCES.txt
9
+ src/boostrsa.egg-info/dependency_links.txt
10
+ src/boostrsa.egg-info/requires.txt
11
+ src/boostrsa.egg-info/top_level.txt
12
+ src/boostrsa/cores/__init__.py
13
+ src/boostrsa/cores/cpgpu/__init__.py
14
+ src/boostrsa/cores/cpgpu/stats.py
15
+ src/boostrsa/cores/cpu/__init__.py
16
+ src/boostrsa/cores/cpu/matrix.py
17
+ src/boostrsa/cores/gpu/__init__.py
18
+ src/boostrsa/cores/gpu/basic_operations.py
19
+ src/boostrsa/cores/gpu/mask.py
20
+ src/boostrsa/cores/gpu/matrix.py
21
+ tests/test_module1.py
@@ -0,0 +1 @@
1
+ boostrsa
@@ -0,0 +1,3 @@
1
+
2
+ def test_example_function():
3
+ assert True
@@ -1,27 +0,0 @@
1
- Metadata-Version: 2.1
2
- Name: boostrsa
3
- Version: 0.0.1.dev0
4
- Summary: This is toolbox for boosting calculation speed using GPU
5
- Author: seojin
6
- Author-email: pures1@hanyang.ac.kr
7
- Classifier: Programming Language :: Python :: 3
8
- Classifier: License :: OSI Approved :: MIT License
9
- Classifier: Operating System :: OS Independent
10
- Requires-Python: >=3.9
11
- Description-Content-Type: text/markdown
12
- License-File: LICENSE.txt
13
-
14
-
15
- # Boostrsa
16
-
17
- blahblah
18
-
19
- ## Setup
20
-
21
- ### Dependencies
22
-
23
- numba
24
- cupy
25
-
26
- ### PIP
27
-
@@ -1,14 +0,0 @@
1
-
2
- # Boostrsa
3
-
4
- blahblah
5
-
6
- ## Setup
7
-
8
- ### Dependencies
9
-
10
- numba
11
- cupy
12
-
13
- ### PIP
14
-
@@ -1,27 +0,0 @@
1
- Metadata-Version: 2.1
2
- Name: boostrsa
3
- Version: 0.0.1.dev0
4
- Summary: This is toolbox for boosting calculation speed using GPU
5
- Author: seojin
6
- Author-email: pures1@hanyang.ac.kr
7
- Classifier: Programming Language :: Python :: 3
8
- Classifier: License :: OSI Approved :: MIT License
9
- Classifier: Operating System :: OS Independent
10
- Requires-Python: >=3.9
11
- Description-Content-Type: text/markdown
12
- License-File: LICENSE.txt
13
-
14
-
15
- # Boostrsa
16
-
17
- blahblah
18
-
19
- ## Setup
20
-
21
- ### Dependencies
22
-
23
- numba
24
- cupy
25
-
26
- ### PIP
27
-
@@ -1,17 +0,0 @@
1
- LICENSE.txt
2
- README.md
3
- setup.py
4
- src/boostrsa.egg-info/PKG-INFO
5
- src/boostrsa.egg-info/SOURCES.txt
6
- src/boostrsa.egg-info/dependency_links.txt
7
- src/boostrsa.egg-info/requires.txt
8
- src/boostrsa.egg-info/top_level.txt
9
- src/cores/__init__.py
10
- src/cores/cpgpu/__init__.py
11
- src/cores/cpgpu/stats.py
12
- src/cores/cpu/__init__.py
13
- src/cores/cpu/matrix.py
14
- src/cores/gpu/__init__.py
15
- src/cores/gpu/basic_operations.py
16
- src/cores/gpu/mask.py
17
- src/cores/gpu/matrix.py
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