import sys
import numpy as np
dir_name = os.path.dirname(os.path.realpath(sys.argv[0]))
import matplotlib.pyplot as plt
import seaborn.apionly as sns
from modl.utils.system import get_output_dir
idx = pd.IndexSlice
run_id = 23
run_dir = join(get_output_dir(), 'multi_decompose_images', str(run_id), 'run')
analysis_dir = join(get_output_dir(), 'multi_decompose_images', str(run_id), 'analysis')
if not os.path.exists(analysis_dir):
os.makedirs(analysis_dir)
data = []
for this_dir in os.listdir(run_dir):
this_dir = join(run_dir, this_dir)
try:
config = json.load(open(join(this_dir, 'config.json'), 'r'))
info = json.load(open(join(this_dir, 'info.json'), 'r'))
except FileNotFoundError:
print('Skipping %s' % this_dir)
continue
method = config['method']
step_size = config['step_size']
from joblib import dump
import sys
import numpy as np
dir_name = os.path.dirname(os.path.realpath(sys.argv[0]))
import matplotlib.pyplot as plt
import seaborn.apionly as sns
from modl.utils.system import get_output_dir
idx = pd.IndexSlice
run_id = 14
run_dir = join(get_output_dir(), 'multi_decompose_fmri', str(run_id), 'run')
analysis_dir = join(get_output_dir(), 'multi_decompose_fmri', str(run_id),
'analysis')
if not os.path.exists(analysis_dir):
os.makedirs(analysis_dir)
data = []
for this_dir in os.listdir(run_dir):
this_dir = join(run_dir, this_dir)
try:
config = json.load(open(join(this_dir, 'config.json'), 'r'))
info = json.load(open(join(this_dir, 'info.json'), 'r'))
except FileNotFoundError:
print('Skipping %s' % this_dir)
continue
method = config['method']
import numpy as np
from sacred import Experiment
from sacred.observers import FileStorageObserver
from sklearn.externals.joblib import Parallel
from sklearn.externals.joblib import delayed
from sklearn.utils import check_random_state
from modl.utils.system import get_output_dir
# Add examples to known modules
sys.path.append(
path.dirname(path.dirname(path.dirname(path.abspath(__file__)))))
from exps.exp_decompose_fmri import exp as single_exp
exp = Experiment('multi_decompose_fmri')
basedir = join(get_output_dir(), 'multi_decompose_fmri')
if not os.path.exists(basedir):
os.makedirs(basedir)
exp.observers.append(FileStorageObserver.create(basedir=basedir))
@exp.config
def config():
n_jobs = 2
n_seeds = 1
seed = 1
@single_exp.config
def config():
n_components = 70
# License: BSD
import os
from os.path import join
import matplotlib.pyplot as plt
from sacred import Experiment
from sacred.observers import FileStorageObserver
from modl.datasets.image import load_image
from modl.decomposition.image import ImageDictFact, DictionaryScorer
from modl.feature_extraction.image import LazyCleanPatchExtractor
from modl.plotting.image import plot_patches
from modl.utils.system import get_output_dir
exp = Experiment('decompose_images')
base_artifact_dir = join(get_output_dir(), 'decompose_images')
exp.observers.append(FileStorageObserver.create(basedir=base_artifact_dir))
@exp.config
def config():
batch_size = 400
learning_rate = 0.92
reduction = 10
alpha = 0.08
n_epochs = 12
n_components = 100
test_size = 4000
max_patches = 10000
patch_size = (32, 32)
n_threads = 2
from cogspaces.datasets.utils import fetch_mask
from hcp_builder.dataset import fetch_hcp, fetch_hcp_timeseries
from modl.input_data.fmri.rest import create_raw_rest_data
from modl.utils.system import get_output_dir
smoothing_fwhm = 4
n_jobs = 20
imgs_list = fetch_hcp_timeseries(None, data_type='rest',
n_subjects=None, subjects=None,
on_disk=True)
root = '/storage/store/data/HCP900'
mask_img = fetch_mask()['icbm_gm']
artifact_dir = join(get_output_dir(), 'unmasked', 'hcp_icbm_gm')
if not os.path.exists(artifact_dir):
os.makedirs(artifact_dir)
create_raw_rest_data(imgs_list,
root=root,
raw_dir=artifact_dir,
overwrite=False,
mock=False,
masker_params=dict(smoothing_fwhm=smoothing_fwhm,
detrend=True,
standardize=True,
mask_img=mask_img),
memory=None,
n_jobs=n_jobs)
import numpy as np
from sacred import Experiment
from sacred.observers import FileStorageObserver
from sklearn.externals.joblib import Parallel
from sklearn.externals.joblib import delayed
from sklearn.utils import check_random_state
from modl.utils.system import get_output_dir
# Add examples to known modules
sys.path.append(
path.dirname(path.dirname(path.dirname(path.abspath(__file__)))))
from exps.exp_decompose_images import exp as single_exp
exp = Experiment('multi_decompose_images')
basedir = join(get_output_dir(), 'multi_decompose_images')
if not os.path.exists(basedir):
os.makedirs(basedir)
exp.observers.append(FileStorageObserver.create(basedir=basedir))
@exp.config
def config():
n_jobs = 15
n_seeds = 1
seed = 1
@single_exp.config
def config():
batch_size = 200
from sklearn.externals.joblib import Memory
from modl.input_data.fmri.rest import create_raw_rest_data
from modl.utils.system import get_cache_dirs, get_output_dir
smoothing_fwhm = 6
n_jobs = 20
dataset = fetch_adhd()
memory = Memory(cachedir=get_cache_dirs()[0])
imgs_list = dataset.rest
root = dataset.root
mask_img = dataset.mask
artifact_dir = join(get_output_dir(), 'unmasked', 'adhd_6')
if not os.path.exists(artifact_dir):
os.makedirs(artifact_dir)
create_raw_rest_data(imgs_list,
root=root,
raw_dir=artifact_dir,
overwrite=False,
mock=False,
masker_params=dict(smoothing_fwhm=smoothing_fwhm,
detrend=True,
standardize=True,
mask_img=mask_img),
memory=memory,
n_jobs=n_jobs)
from modl.input_data.fmri.rest import create_raw_rest_data
from modl.utils.system import get_cache_dirs, get_output_dir
from hcp_builder.dataset import fetch_hcp
smoothing_fwhm = 4
n_jobs = 3
dataset = fetch_hcp()
memory = Memory(cachedir=get_cache_dirs()[0])
imgs_list = dataset.rest
root = dataset.root
mask_img = dataset.mask
artifact_dir = join(get_output_dir(), 'unmasked', 'hcp')
if not os.path.exists(artifact_dir):
os.makedirs(artifact_dir)
create_raw_rest_data(imgs_list,
root=root,
raw_dir=artifact_dir,
overwrite=False,
mock=False,
masker_params=dict(smoothing_fwhm=smoothing_fwhm,
detrend=True,
standardize=True,
mask_img=mask_img),
memory=memory,
n_jobs=n_jobs)
def compute_components(n_components, batch_size, learning_rate, method,
reduction, alpha, step_size, n_jobs, n_epochs, verbose,
source, _run):
basedir = join(_run.observers[0].basedir, str(_run._id))
artifact_dir = join(basedir, 'artifacts')
if not os.path.exists(artifact_dir):
os.makedirs(artifact_dir)
if source == 'hcp':
# Hack to recover data from TSP
train_size = None
smoothing_fwhm = 3
test_size = 2
data_dir = get_data_dirs()[0]
mask = fetch_hcp_mask()
masker = MultiRawMasker(mask_img=mask,
smoothing_fwhm=smoothing_fwhm,
detrend=True,
standardize=True)
mapping = json.load(
open(join(data_dir, 'HCP_unmasked/mapping.json'), 'r'))
data = sorted(list(mapping.values()))
data = list(map(lambda x: join(data_dir, x), data))
data = pd.DataFrame(data, columns=['filename'])
else:
smoothing_fwhm = 6
train_size = 4
test_size = 4
raw_res_dir = join(get_output_dir(), 'unmasked', source)
try:
masker, data = get_raw_rest_data(raw_res_dir)
except ValueError: # On local machine:
raw_res_dir = join(get_output_dir(), 'unmask', source)
masker, data = get_raw_rest_data(raw_res_dir)
train_imgs, test_imgs = train_test_split(data,
test_size=test_size,
random_state=0,
train_size=train_size)
train_imgs = train_imgs['filename'].values
test_imgs = test_imgs['filename'].values
cb = rfMRIDictionaryScorer(test_imgs, info=_run.info)
dict_fact = fMRIDictFact(
method=method,
mask=masker,
verbose=verbose,
n_epochs=n_epochs,
n_jobs=n_jobs,
random_state=1,
n_components=n_components,
smoothing_fwhm=smoothing_fwhm,
learning_rate=learning_rate,
batch_size=batch_size,
reduction=reduction,
step_size=step_size,
alpha=alpha,
callback=cb,
)
dict_fact.fit(train_imgs)
dict_fact.components_img_.to_filename(
join(artifact_dir, 'components.nii.gz'))
fig = plt.figure()
display_maps(fig, dict_fact.components_img_)
plt.savefig(join(artifact_dir, 'components.png'))
fig, ax = plt.subplots(1, 1)
ax.plot(cb.cpu_time, cb.score, marker='o')
_run.info['time'] = cb.cpu_time
_run.info['score'] = cb.score
_run.info['iter'] = cb.iter
plt.savefig(join(artifact_dir, 'score.png'))
monkey_patch_nifti_image()
from sklearn.model_selection import train_test_split
from modl.input_data.fmri.rest import get_raw_rest_data
from modl.decomposition.fmri import fMRIDictFact, rfMRIDictionaryScorer
from modl.plotting.fmri import display_maps
from modl.utils.system import get_output_dir
from sacred import Experiment
import pandas as pd
exp = Experiment('decomppose_fmri')
base_artifact_dir = join(get_output_dir(), 'decompose_fmri')
exp.observers.append(FileStorageObserver.create(basedir=base_artifact_dir))
@exp.config
def config():
n_components = 70
batch_size = 100
learning_rate = 0.92
method = 'dictionary only'
reduction = 1
alpha = 1e-4
n_epochs = 100
verbose = 30
n_jobs = 5
step_size = 1e-5