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Fix gen design #381

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Merged
lcnature merged 7 commits into from
Sep 14, 2018
Merged

Fix gen design #381

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2b8116a
add a check in utils.gen_design so that when there is no event, an al…
Sep 10, 2018
d944873
add test for the changes
Sep 10, 2018
71cc6df
add the example stimulus timing file of AFNI style
Sep 10, 2018
32dc6c3
remove the printing test line
Sep 10, 2018
b24cc4d
removed the conditional clause in generate_stimfunction of fmrisim.py…
Sep 11, 2018
4daa70a
fix whitespace
Sep 11, 2018
1c5d20b
changed two `floor` to `round` in utils.gen_design, because in princi…
Sep 11, 2018
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4 changes: 0 additions & 4 deletions brainiak/utils/fmrisim.py
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Original file line number Diff line number Diff line change
Expand Up @@ -523,10 +523,6 @@ def generate_stimfunction(onsets,
# Store the weights
stimfunction[onset_idx:offset_idx, 0] = [weights[onset_counter]]

# Shorten the data if it's too long

@CameronTEllis CameronTEllis Sep 14, 2018

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Good point, this is unnecessary as you say

if stimfunction.shape[0] > total_time * temporal_resolution:
stimfunction = stimfunction[0:int(total_time * temporal_resolution), 0]

return stimfunction


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37 changes: 20 additions & 17 deletions brainiak/utils/utils.py
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Expand Up @@ -427,10 +427,10 @@ def gen_design(stimtime_files, scan_duration, TR, style='FSL',
n_C = len(stimtime_files) # number of conditions
n_S = np.size(scan_duration) # number of scans
if n_S > 1:
design = [np.empty([int(np.floor(duration / TR)), n_C])
design = [np.empty([int(np.round(duration / TR)), n_C])
for duration in scan_duration]
else:
design = [np.empty([int(np.floor(scan_duration / TR)), n_C])]
design = [np.empty([int(np.round(scan_duration / TR)), n_C])]

@CameronTEllis CameronTEllis Sep 14, 2018

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Makes sense

scan_onoff = np.insert(np.cumsum(scan_duration), 0, 0)
if style == 'FSL':
design_info = _read_stimtime_FSL(stimtime_files, n_C, n_S, scan_onoff)
Expand All @@ -445,21 +445,24 @@ def gen_design(stimtime_files, scan_duration, TR, style='FSL',
# generate design matrix
for i_s in range(n_S):
for i_c in range(n_C):
stimfunction = generate_stimfunction(
onsets=design_info[i_s][i_c]['onset'],
event_durations=design_info[i_s][i_c]['duration'],
total_time=scan_duration[i_s],
weights=design_info[i_s][i_c]['weight'],
temporal_resolution=1.0/temp_res)
hrf = _double_gamma_hrf(response_delay=response_delay,
undershoot_delay=undershoot_delay,
response_dispersion=response_disp,
undershoot_dispersion=undershoot_disp,
undershoot_scale=undershoot_scale,
temporal_resolution=1.0/temp_res)
design[i_s][:, i_c] = convolve_hrf(
stimfunction, TR, hrf_type=hrf, scale_function=0,
temporal_resolution=1.0 / temp_res).transpose() * temp_res
if len(design_info[i_s][i_c]['onset']) > 0:
stimfunction = generate_stimfunction(
onsets=design_info[i_s][i_c]['onset'],
event_durations=design_info[i_s][i_c]['duration'],
total_time=scan_duration[i_s],
weights=design_info[i_s][i_c]['weight'],
temporal_resolution=1.0/temp_res)
hrf = _double_gamma_hrf(response_delay=response_delay,
undershoot_delay=undershoot_delay,
response_dispersion=response_disp,
undershoot_dispersion=undershoot_disp,
undershoot_scale=undershoot_scale,
temporal_resolution=1.0/temp_res)
design[i_s][:, i_c] = convolve_hrf(
stimfunction, TR, hrf_type=hrf, scale_function=False,
temporal_resolution=1.0 / temp_res).transpose() * temp_res
else:
design[i_s][:, i_c] = 0.0
# We multiply the resulting design matrix with
# the temporal resolution to normalize it.
# We do not use the internal normalization
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1 change: 1 addition & 0 deletions tests/utils/example_stimtime_2_AFNI.txt
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@@ -0,0 +1 @@
-10.0
8 changes: 7 additions & 1 deletion tests/utils/test_utils.py
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Expand Up @@ -101,7 +101,8 @@ def test_gen_design():
import os.path
files = {'FSL1': 'example_stimtime_1_FSL.txt',
'FSL2': 'example_stimtime_2_FSL.txt',
'AFNI1': 'example_stimtime_1_AFNI.txt'}
'AFNI1': 'example_stimtime_1_AFNI.txt',
'AFNI2': 'example_stimtime_2_AFNI.txt'}
for key in files.keys():
files[key] = os.path.join(os.path.dirname(__file__), files[key])
design1 = gen_design(stimtime_files=files['FSL1'], scan_duration=[48, 20],
Expand Down Expand Up @@ -130,6 +131,11 @@ def test_gen_design():
scan_duration=[48, 20], TR=2, style='AFNI')
assert np.all(np.isclose(design1, design6)), (
'design matrices generated from AFNI style and FSL style do not match')
design7 = gen_design(stimtime_files=[files['AFNI2']],
scan_duration=[48], TR=2, style='AFNI')
assert np.all(design7 == 0.0), (
'A negative stimulus onset of AFNI style should result in an all-zero'
+ ' design matrix')

@CameronTEllis CameronTEllis Sep 14, 2018

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Good extra test to have



def test_center_mass_exp():
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