def test_workflow_func_motion_correct_no_slice_time():
import os
import nibabel as nb
import pkg_resources as p
from qap.functional_preproc import run_func_motion_correct
from qap.workflow_utils import build_test_case
func_scan = p.resource_filename("qap", os.path.join(test_sub_dir, "rest_1", "functional_scan", "rest.nii.gz"))
ref_graph = p.resource_filename(
"qap", os.path.join("test_data", "workflow_reference", "func_motion_correct", "graph_func_motion_correct.dot")
)
ref_inputs = p.resource_filename(
"qap", os.path.join("test_data", "workflow_reference", "func_motion_correct", "wf_inputs.txt")
)
# build the workflow
wf, base_dir = run_func_motion_correct(func_scan, 0, "End", False, False)
# get the workflow inputs of the workflow being tested
wf_inputs_string = str(wf.inputs).replace("\n", "")
wf_inputs_string = wf_inputs_string.replace(base_dir, "BASE_DIRECTORY_HERE")
wf_inputs_string = wf_inputs_string.replace(func_scan, "IN_FILE_A_HERE", 1)
wf_inputs_string = wf_inputs_string.replace(func_scan, "IN_FILES_HERE")
flag, err = build_test_case(wf, ref_inputs, ref_graph, wf_inputs_string)
assert flag == 2, err
def test_run_func_motion_correct_slice_time():
import os
import nibabel as nb
import pkg_resources as p
from qap.functional_preproc import run_func_motion_correct
if "func_motion_correct" in os.listdir(os.getcwd()):
err = "\n[!] The output folder for this workflow already exists.\n"
raise Exception(err)
func_scan = p.resource_filename("qap", os.path.join(test_sub_dir, "rest_1", "functional_scan", "rest.nii.gz"))
""" NEED A SLICE TIME CORRECTED VERSION OF THIS!!!! NOT COMPLETE """
ref_out = p.resource_filename(
"qap", os.path.join(test_sub_dir, "rest_1", "func_motion_correct", "rest_calc_tshift_resample_volreg.nii.gz")
)
# run the workflow
output = run_func_motion_correct(func_scan, 0, "End", True)
# make the correlation
ref_out_data = nb.load(ref_out).get_data()
output_data = nb.load(output).get_data()
os.system("rm -R func_motion_correct")
# create a vector of True and False values
bool_vector = ref_out_data == output_data
assert bool_vector.all()
def test_workflow_func_motion_correct_slice_time():
import os
import pkg_resources as p
from qap.functional_preproc import run_func_motion_correct
from qap.workflow_utils import build_test_case
func_scan = p.resource_filename("qap", os.path.join(test_sub_dir, \
"rest_1", \
"functional_scan", \
"rest.nii.gz"))
ref_graph = p.resource_filename("qap", os.path.join("test_data", \
"workflow_reference", \
"func_motion_correct_slice_time", \
"graph_func_motion_correct" \
"_slice_time.dot"))
ref_inputs = p.resource_filename("qap", os.path.join("test_data", \
"workflow_reference", \
"func_motion_correct_slice_time", \
"wf_inputs.txt"))
# build the workflow
wf, base_dir = run_func_motion_correct(func_scan, 0, "End", True, False)
# get the workflow inputs of the workflow being tested
wf_inputs_string = str(wf.inputs).replace("\n", "")
wf_inputs_string = wf_inputs_string.replace(base_dir, \
"BASE_DIRECTORY_HERE")
wf_inputs_string = wf_inputs_string.replace(func_scan, "IN_FILE_A_HERE",\
1)
wf_inputs_string = wf_inputs_string.replace(func_scan, "IN_FILES_HERE")
flag, err = build_test_case(wf, ref_inputs, ref_graph, wf_inputs_string)
assert flag == 2, err
def test_run_func_motion_correct_slice_time():
import os
import nibabel as nb
import pkg_resources as p
from qap.functional_preproc import run_func_motion_correct
if "func_motion_correct" in os.listdir(os.getcwd()):
err = "\n[!] The output folder for this workflow already exists.\n"
raise Exception(err)
func_scan = p.resource_filename("qap", os.path.join(test_sub_dir, \
"rest_1", \
"functional_scan", \
"rest.nii.gz"))
''' NEED A SLICE TIME CORRECTED VERSION OF THIS!!!! NOT COMPLETE '''
ref_out = p.resource_filename("qap", os.path.join(test_sub_dir, \
"rest_1", \
"func_motion_correct", \
"rest_calc_tshift_resample_volreg.nii.gz"))
# run the workflow
output = run_func_motion_correct(func_scan, 0, "End", True)
# make the correlation
ref_out_data = nb.load(ref_out).get_data()
output_data = nb.load(output).get_data()
os.system("rm -R func_motion_correct")
# create a vector of True and False values
bool_vector = ref_out_data == output_data
assert bool_vector.all()
