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Andrei-Claudiu Roibu
BrainMapper
Commits
cb9bbda3
Commit
cb9bbda3
authored
Jul 10, 2020
by
Andrei Roibu
Browse files
replaced mean subtraction with mean regression, fixed data file reader
parent
209ce07e
Changes
3
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run.py
View file @
cb9bbda3
...
...
@@ -41,7 +41,7 @@ import numpy as np
from
solver
import
Solver
from
BrainMapperAE
import
BrainMapperAE3D
from
utils.data_utils
import
get_datasets
,
data_
test_train_validation_split
,
update_shuffling_flag
,
create_folder
from
utils.data_utils
import
get_datasets
,
data_
preparation
,
update_shuffling_flag
,
create_folder
import
utils.data_evaluation_utils
as
evaluations
from
utils.data_logging_utils
import
LogWriter
...
...
@@ -360,29 +360,29 @@ if __name__ == '__main__':
# Here we shuffle the data!
if
data_parameters
[
'data_split_flag'
]
==
True
:
print
(
'Data is shuffling... This could take a few minutes!'
)
if
data_parameters
[
'data_split_flag'
]
==
True
:
if
data_parameters
[
'use_data_file'
]
==
True
:
data_
test_train_validation_split
(
data_parameters
[
'data_folder_name'
],
data_
preparation
(
data_parameters
[
'data_folder_name'
],
data_parameters
[
'test_percentage'
],
data_parameters
[
'subject_number'
],
data_directory
=
data_parameters
[
'data_directory'
],
train_inputs
=
data_parameters
[
'train_data_file'
],
train_targets
=
data_parameters
[
'train_output_targets'
],
mean_mask_path
=
data_parameters
[
'mean_mask_path'
],
rsfMRI_mean_mask_path
=
data_parameters
[
'rsfmri_mean_mask_path'
],
dMRI_mean_mask_path
=
data_parameters
[
'dmri_mean_mask_path'
],
data_file
=
data_parameters
[
'data_file'
],
K_fold
=
data_parameters
[
'k_fold'
]
)
else
:
data_
test_train_validation_split
(
data_parameters
[
'data_folder_name'
],
data_
preparation
(
data_parameters
[
'data_folder_name'
],
data_parameters
[
'test_percentage'
],
data_parameters
[
'subject_number'
],
data_directory
=
data_parameters
[
'data_directory'
],
train_inputs
=
data_parameters
[
'train_data_file'
],
train_targets
=
data_parameters
[
'train_output_targets'
],
mean_mask_path
=
data_parameters
[
'mean_mask_path'
],
rsfMRI_mean_mask_path
=
data_parameters
[
'rsfmri_mean_mask_path'
],
dMRI_mean_mask_path
=
data_parameters
[
'dmri_mean_mask_path'
],
K_fold
=
data_parameters
[
'k_fold'
]
)
update_shuffling_flag
(
'settings.ini'
)
...
...
@@ -394,7 +394,6 @@ if __name__ == '__main__':
network_parameters
,
misc_parameters
)
# NOTE: THE EVAL FUNCTIONS HAVE NOT YET BEEN DEBUGGED (16/04/20)
# NOTE: THE EVAL-MAPPING FUNCTION HAS BEEN DEBUGGED (28/04/20)
elif
arguments
.
mode
==
'evaluate-score'
:
evaluate_score
(
training_parameters
,
...
...
settings.ini
View file @
cb9bbda3
[DATA]
data_folder_name
=
"datasets"
use_data_file
=
Tru
e
use_data_file
=
Fals
e
data_directory
=
"/well/win-biobank/projects/imaging/data/data3/subjectsAll/"
data_file
=
"/well/win-biobank/projects/imaging/data/data3/subjectsAll/subj_22k.txt"
k_fold
=
None
...
...
@@ -11,12 +11,14 @@ train_list = "datasets/train.txt"
validation_list
=
"datasets/validation.txt"
test_list
=
"datasets/test.txt"
scaling_factors
=
"datasets/scaling_factors.pkl"
regression_weights
=
"datasets/regression_weights.pkl"
train_data_file
=
"dMRI/autoptx_preproc/tractsNormSummed.nii.gz"
train_output_targets
=
"fMRI/rfMRI_25.dr/dr_stage2.nii.gz"
validation_data_file
=
"dMRI/autoptx_preproc/tractsNormSummed.nii.gz"
validation_target_file
=
"fMRI/rfMRI_25.dr/dr_stage2.nii.gz"
brain_mask_path
=
"utils/MNI152_T1_2mm_brain_mask.nii.gz"
mean_mask_path
=
"utils/mean_dr_stage2.nii.gz"
rsfmri_mean_mask_path
=
"utils/mean_dr_stage2.nii.gz"
dmri_mean_mask_path
=
"utils/mean_tractsNormSummed_downsampled.nii.gz"
mean_reduction
=
True
[TRAINING]
...
...
utils/data_utils.py
View file @
cb9bbda3
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