def test_run_no_mask(self):
rundata = FabberRunData()
rundata["model"] = "poly"
rundata["degree"] = "2"
# rundata["save-mean"] = "" FIXME causes error due to compatibility options
rundata["data"] = os.path.join(self.datadir, "test_data_small")
run = self.fab.run(rundata)
def test_model_evaluate(self):
rundata = FabberRunData()
rundata["model"] = "poly"
rundata["degree"] = "2"
ret = self.fab.model_evaluate(rundata, {"c0": 1, "c1": 2, "c2": 3}, 5)
self.assertEquals(5, len(ret))
for t in range(5):
self.assertEquals(1 + 2 * (t + 1) + 3 * (t + 1) * (t + 1), ret[t])
def test_get_model_params(self):
rundata = FabberRunData()
rundata["model"] = "poly"
rundata["degree"] = "2"
params = self.fab.get_model_params(rundata)
self.assertTrue("c0" in params)
self.assertTrue("c1" in params)
self.assertTrue("c2" in params)
def test_run_no_mask(self):
data = np.fromfunction(self.quad_data, (3, 3, 3, 3))
rundata = FabberRunData()
rundata["model"] = "poly"
rundata["degree"] = "2"
rundata["save-mean"] = ""
run = self.fab.run_with_data(rundata, {"data": data})
self.assertAlmostEqual(run.data["mean_c0"][0, 0, 0], c0, delta=0.1)
self.assertAlmostEqual(run.data["mean_c1"][0, 0, 0], c1, delta=0.1)
self.assertAlmostEqual(run.data["mean_c2"][0, 0, 0], c2, delta=0.1)
def test_run_empty_mask(self):
data = np.fromfunction(self.quad_data, (3, 3, 3, 3))
mask = np.zeros((3, 3, 3))
rundata = FabberRunData()
rundata["model"] = "poly"
rundata["degree"] = "2"
rundata["save-mean"] = ""
run = self.fab.run_with_data(rundata, {"data": data}, mask)
self.assertEqual(run.data["mean_c0"].max(), 0)
self.assertEqual(run.data["mean_c1"].max(), 0)
self.assertEqual(run.data["mean_c2"].max(), 0)
def test_run_cb(self):
data = np.fromfunction(self.quad_data, (3, 3, 3, 3))
rundata = FabberRunData()
rundata["model"] = "poly"
rundata["degree"] = "2"
rundata["save-mean"] = ""
run = self.fab.run_with_data(rundata, {"data": data},
progress_cb=self.progress_cb)
self.assertEquals(0, self.progress[0][0])
last = self.progress[-1]
self.assertTrue(last[0] > 0)
self.assertEquals(last[0], last[1])
Example: Create a test dataset for the simple polynomial model
generate_test_image.py --model=poly --degree=2 --param-c0=10,20,30 --param-c1=0.5,1,2 --param-c2=5 --nt=10
"""
import os, sys
import traceback
import numpy as np
import nibabel as nib
sys.path.insert(0, os.environ["FSLDIR"] + "/lib/python")
from fabber import FabberRunData, generate_test_data
try:
rundata = FabberRunData()
params = {}
model_libs = []
outfile="test_image.nii"
nt = 10
for arg in sys.argv[1:]:
if arg.startswith("--loadmodels"):
model_libs.append(arg.split("=")[1])
if arg.startswith("--outfile"):
outfile=arg.split("=")[1]
elif arg.startswith("--nt"):
nt = int(arg.split("=")[1])
elif arg.startswith("--param-"):
key, value = arg[8:].split("=")
params[key] = [float(v) for v in value.split(",")]
elif arg.startswith("--"):