def test_odd_even_split_nested(self):
measurements = np.random.rand(16, 10)
des = {'session': 0, 'subj': 0}
chn_des = {'rois': np.array([chr(l) for l in range(65, 75)])}
conds = np.array([str(i) for i in range(1, 5)])
runs = np.array([i for i in range(1, 5)])
self.full_data = rsd.Dataset(measurements=measurements,
descriptors=des,
obs_descriptors={
'conds':
np.hstack(
(conds, conds, conds, conds)),
'runs':
np.repeat(runs, 4)
},
channel_descriptors=chn_des)
self.odd_data = rsd.Dataset(measurements=np.append(measurements[0:4],
measurements[8:12],
axis=0),
descriptors=des,
obs_descriptors={
'conds': np.hstack((conds, conds)),
'runs': np.repeat(runs[0::2], 4)
},
channel_descriptors=chn_des)
self.even_data = rsd.Dataset(measurements=np.append(
measurements[4:8], measurements[12:16], axis=0),
descriptors=des,
obs_descriptors={
'conds': np.hstack((conds, conds)),
'runs': np.repeat(runs[1::2], 4)
},
channel_descriptors=chn_des)
self.odd_split, self.even_split = self.full_data.nested_odd_even_split(
'conds', 'runs')
self.odd_split.sort_by('runs')
self.even_split.sort_by('runs')
np.testing.assert_array_equal(self.odd_data.measurements,
self.odd_split.measurements)
self.assertEqual(self.odd_data.descriptors, self.odd_split.descriptors)
np.testing.assert_array_equal(self.odd_data.obs_descriptors['conds'],
self.odd_split.obs_descriptors['conds'])
np.testing.assert_array_equal(
self.odd_data.channel_descriptors['rois'],
self.odd_split.channel_descriptors['rois'])
np.testing.assert_array_equal(self.even_data.measurements,
self.even_split.measurements)
self.assertEqual(self.even_data.descriptors,
self.even_split.descriptors)
np.testing.assert_array_equal(self.even_data.obs_descriptors['conds'],
self.even_split.obs_descriptors['conds'])
np.testing.assert_array_equal(
self.even_data.channel_descriptors['rois'],
self.even_split.channel_descriptors['rois'])
def test_oe_split(self):
measurements = np.random.rand(4, 10)
des = {'session': 0, 'subj': 0}
chn_des = {'rois': np.array([chr(l) for l in range(65, 75)])}
self.full_data = rsd.Dataset(
measurements=measurements,
descriptors=des,
obs_descriptors={'conds': np.array([str(i) for i in range(1, 5)])},
channel_descriptors=chn_des)
self.odd_data = rsd.Dataset(measurements=measurements[0::2],
descriptors=des,
obs_descriptors={
'conds':
np.array(
[str(i) for i in range(1, 5, 2)])
},
channel_descriptors=chn_des)
self.even_data = rsd.Dataset(measurements=measurements[1::2],
descriptors=des,
obs_descriptors={
'conds':
np.array(
[str(i) for i in range(2, 5, 2)])
},
channel_descriptors=chn_des)
self.odd_split, self.even_split = \
self.full_data.odd_even_split('conds')
np.testing.assert_array_equal(self.odd_data.measurements,
self.odd_split.measurements)
self.assertEqual(self.odd_data.descriptors, self.odd_split.descriptors)
np.testing.assert_array_equal(self.odd_data.obs_descriptors['conds'],
self.odd_split.obs_descriptors['conds'])
np.testing.assert_array_equal(
self.odd_data.channel_descriptors['rois'],
self.odd_split.channel_descriptors['rois'])
np.testing.assert_array_equal(self.even_data.measurements,
self.even_split.measurements)
self.assertEqual(self.even_data.descriptors,
self.even_split.descriptors)
np.testing.assert_array_equal(self.even_data.obs_descriptors['conds'],
self.even_split.obs_descriptors['conds'])
np.testing.assert_array_equal(
self.even_data.channel_descriptors['rois'],
self.even_split.channel_descriptors['rois'])
def setUp(self):
measurements = np.random.rand(4, 10)
des = {'session': 0, 'subj': 0}
obs_des = {'conds': np.array([str(i) for i in range(1, 5)])}
chn_des = {'rois': np.array([chr(l) for l in range(65, 75)])}
self.test_data = rsd.Dataset(measurements=measurements,
descriptors=des,
obs_descriptors=obs_des,
channel_descriptors=chn_des)
def setUp(self):
measurements = np.random.rand(10, 5)
des = {'session': 0, 'subj': 0}
obs_des = {'conds': np.array([0, 0, 1, 1, 2, 2, 2, 3, 4, 5])}
chn_des = {'rois': np.array(['V1', 'V1', 'IT', 'IT', 'V4'])}
self.test_data = rsd.Dataset(measurements=measurements,
descriptors=des,
obs_descriptors=obs_des,
channel_descriptors=chn_des)
def setUp(self):
self.residuals = np.random.rand(100, 25)
self.residuals = self.residuals - np.mean(
self.residuals, axis=0, keepdims=True)
res_list = []
for i in range(3):
residuals = np.random.rand(100, 25)
residuals = residuals - np.mean(residuals, axis=0, keepdims=True)
res_list.append(residuals)
self.res_list = res_list
self.dataset = rsd.Dataset(
self.residuals,
obs_descriptors={'obs': np.repeat(np.arange(10), 10)})
def test_dataset_split_channel(self):
measurements = np.zeros((10, 5))
des = {'session': 0, 'subj': 0}
obs_des = {'conds': np.array([0, 0, 1, 1, 2, 2, 2, 3, 4, 5])}
chn_des = {'rois': np.array(['V1', 'V1', 'IT', 'IT', 'V4'])}
data = rsd.Dataset(measurements=measurements,
descriptors=des,
obs_descriptors=obs_des,
channel_descriptors=chn_des)
splited_list = data.split_channel('rois')
self.assertEqual(len(splited_list), 3)
self.assertEqual(splited_list[0].n_obs, 10)
self.assertEqual(splited_list[2].n_obs, 10)
self.assertEqual(splited_list[0].n_channel, 2)
self.assertEqual(splited_list[2].n_channel, 1)
self.assertEqual(splited_list[1].channel_descriptors['rois'][0], 'IT')
def test_dataset_full_init(self):
measurements = np.zeros((10, 5))
des = {'session': 0, 'subj': 0}
obs_des = {
'conds': np.array(['cond_' + str(x) for x in np.arange(10)])
}
chn_des = {'rois': np.array(['roi_' + str(x) for x in np.arange(5)])}
data = rsd.Dataset(measurements=measurements,
descriptors=des,
obs_descriptors=obs_des,
channel_descriptors=chn_des)
self.assertEqual(data.n_obs, 10)
self.assertEqual(data.n_channel, 5)
self.assertEqual(data.descriptors, des)
self.assertEqual(data.obs_descriptors, obs_des)
self.assertEqual(data.channel_descriptors, chn_des)
def setUp(self):
self.full_str = "slight not what is near through aiming at what is far"
self.unique_str = "slight not what is near through aiming at far"
self.full_ints = np.array([99, 4, 66, 4, 33, 99])
self.unique_ints = np.array([99, 4, 66, 33])
measurements = np.zeros((4, 5))
des = {'session': 0, 'subj': 0}
obs_des = {
'conds': np.array(['cond_foo', 'cond_bar', 'cond_foo', 'cond_bar'])
}
chn_des = {'rois': np.array(['V1', 'V1', 'IT', 'IT', 'V4'])}
self.data = rsd.Dataset(measurements=measurements,
descriptors=des,
obs_descriptors=obs_des,
channel_descriptors=chn_des)
def test_dataset_subset_obs(self):
measurements = np.zeros((10, 5))
des = {'session': 0, 'subj': 0}
obs_des = {'conds': np.array([0, 0, 1, 1, 2, 2, 2, 3, 4, 5])}
chn_des = {'rois': np.array(['V1', 'V1', 'IT', 'IT', 'V4'])}
data = rsd.Dataset(measurements=measurements,
descriptors=des,
obs_descriptors=obs_des,
channel_descriptors=chn_des)
subset = data.subset_obs(by='conds', value=2)
self.assertEqual(subset.n_obs, 3)
self.assertEqual(subset.n_channel, 5)
self.assertEqual(subset.obs_descriptors['conds'][0], 2)
subset = data.subset_obs(by='conds', value=[2, 3])
self.assertEqual(subset.n_obs, 4)
self.assertEqual(subset.n_channel, 5)
self.assertEqual(subset.obs_descriptors['conds'][0], 2)
def test_dict_conversion(self):
measurements = np.zeros((10, 5))
des = {'session': 0, 'subj': 0}
obs_des = {'conds': np.array([0, 0, 1, 1, 2, 2, 2, 3, 4, 5])}
chn_des = {'rois': np.array(['V1', 'V1', 'IT', 'IT', 'V4'])}
data = rsd.Dataset(measurements=measurements,
descriptors=des,
obs_descriptors=obs_des,
channel_descriptors=chn_des)
data_dict = data.to_dict()
data_loaded = rsd.dataset_from_dict(data_dict)
assert type(data_loaded) == type(data)
assert data_loaded.n_channel == data.n_channel
assert np.all(data_loaded.obs_descriptors['conds'] == obs_des['conds'])
assert np.all(
data_loaded.channel_descriptors['rois'] == chn_des['rois'])
assert data_loaded.descriptors['subj'] == 0
def test_save_load(self):
import io
f = io.BytesIO() # Essentially a Mock file
measurements = np.zeros((10, 5))
des = {'session': 0, 'subj': 0}
obs_des = {'conds': np.array([0, 0, 1, 1, 2, 2, 2, 3, 4, 5])}
chn_des = {'rois': np.array(['V1', 'V1', 'IT', 'IT', 'V4'])}
data = rsd.Dataset(measurements=measurements,
descriptors=des,
obs_descriptors=obs_des,
channel_descriptors=chn_des)
data.save(f, file_type='hdf5')
data_loaded = rsd.load_dataset(f, file_type='hdf5')
assert data_loaded.n_channel == data.n_channel
assert np.all(data_loaded.obs_descriptors['conds'] == obs_des['conds'])
assert np.all(
data_loaded.channel_descriptors['rois'] == chn_des['rois'])
assert data_loaded.descriptors['subj'] == 0
def test_example_dissimilarities(self):
# relevant imports
import numpy as np
from scipy import io
import rsatoolbox
import rsatoolbox.data as rsd # abbreviation to deal with dataset
import rsatoolbox.rdm as rsr
# create a dataset object
measurements = {'simTruePatterns': np.random.randn(92, 100)}
measurements = measurements['simTruePatterns']
nCond = measurements.shape[0]
nVox = measurements.shape[1]
# now create a dataset object
des = {'session': 1, 'subj': 1}
obs_des = {
'conds': np.array(['cond_' + str(x) for x in np.arange(nCond)])
}
chn_des = {
'voxels': np.array(['voxel_' + str(x) for x in np.arange(nVox)])
}
data = rsd.Dataset(measurements=measurements,
descriptors=des,
obs_descriptors=obs_des,
channel_descriptors=chn_des)
# calculate an RDM
RDM_euc = rsr.calc_rdm(data)
RDM_corr = rsr.calc_rdm(data, method='correlation', descriptor='conds')
# create an RDM object
rdm_des = {'RDM': np.array(['RDM_1'])}
RDM_euc2 = rsr.RDMs(
RDM_euc.dissimilarities,
dissimilarity_measure=RDM_euc.dissimilarity_measure,
descriptors=RDM_euc.descriptors,
rdm_descriptors=rdm_des,
pattern_descriptors=obs_des)
print(RDM_euc.dissimilarities) # here a vector
dist_matrix = RDM_euc.get_matrices()
print(dist_matrix)
def test_dataset_simple_init(self):
measurements = np.zeros((10, 5))
data = rsd.Dataset(measurements)
self.assertEqual(data.n_obs, 10)
self.assertEqual(data.n_channel, 5)
def test_example_dataset(self):
import numpy as np
import matplotlib.pyplot as plt
import rsatoolbox
import rsatoolbox.data as rsd # abbreviation to deal with dataset
# import the measurements for the dataset
measurements = {'simTruePatterns': np.random.randn(92, 100)}
measurements = measurements['simTruePatterns']
nCond = measurements.shape[0]
nVox = measurements.shape[1]
# plot the imported data
plt.imshow(measurements, cmap='gray')
plt.xlabel('Voxels')
plt.ylabel('Conditions')
plt.title('Measurements')
# now create a dataset object
des = {'session': 1, 'subj': 1}
obs_des = {
'conds': np.array(['cond_' + str(x) for x in np.arange(nCond)])
}
chn_des = {
'voxels': np.array(['voxel_' + str(x) for x in np.arange(nVox)])
}
data = rsd.Dataset(measurements=measurements,
descriptors=des,
obs_descriptors=obs_des,
channel_descriptors=chn_des)
print(data)
# create an example dataset with random data, subset some conditions
nChannel = 50
nObs = 12
randomData = np.random.rand(nObs, nChannel)
des = {'session': 1, 'subj': 1}
obs_des = {'conds': np.array([0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5])}
chn_des = {
'voxels':
np.array(['voxel_' + str(x) for x in np.arange(nChannel)])
}
data = rsd.Dataset(measurements=randomData,
descriptors=des,
obs_descriptors=obs_des,
channel_descriptors=chn_des)
# select a subset of the dataset: select data only from conditions 0:4
sub_data = data.subset_obs(by='conds', value=[0, 1, 2, 3, 4])
print(sub_data)
# Split by channels
nChannel = 3
nChannelVox = 10 # three ROIs, each with 10 voxels
nObs = 4
randomData = np.random.rand(nObs, nChannel * nChannelVox)
des = {'session': 1, 'subj': 1}
obs_des = {'conds': np.array([0, 1, 2, 3])}
chn_des = ['ROI1', 'ROI2', 'ROI3'] * nChannelVox
chn_des = {'ROIs': np.array(chn_des)}
data = rsd.Dataset(measurements=randomData,
descriptors=des,
obs_descriptors=obs_des,
channel_descriptors=chn_des)
split_data = data.split_channel(by='ROIs')
print(split_data)
# create a datasets with random data
nVox = 50 # 50 voxels/electrodes/measurement channels
nCond = 10 # 10 conditions
nSubj = 5 # 5 different subjects
randomData = np.random.rand(nCond, nVox, nSubj)
# We can then create a list of dataset objects
# by appending each dataset for each subject.
obs_des = {
'conds': np.array(['cond_' + str(x) for x in np.arange(nCond)])
}
chn_des = {
'voxels': np.array(['voxel_' + str(x) for x in np.arange(nVox)])
}
data = [] # list of dataset objects
for i in np.arange(nSubj):
des = {'session': 1, 'subj': i + 1}
# append the dataset object to the data list
data.append(
rsd.Dataset(measurements=randomData[:, :, 0],
descriptors=des,
obs_descriptors=obs_des,
channel_descriptors=chn_des))