def test_build_graph():
"""Test the method to build a graph from the heatmap."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Load the GT data
path_gt = [os.path.join(currdir, 'data', 'gt_folders', 'prostate')]
label_gt = ['prostate']
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt, path_gt)
# Build a heatmap from the dce data
# Reduce the number of bins to enforce low memory consumption
nb_bins = [100] * dce_mod.n_serie_
heatmap, bins_heatmap = dce_mod.build_heatmap(gt_mod.extract_gt_data(
label_gt[0]), nb_bins=nb_bins)
# Build the graph by taking the inverse exponential of the heatmap
graph = StandardTimeNormalization._build_graph(heatmap, .5)
graph_dense = graph.toarray()
data = np.load(os.path.join(currdir, 'data', 'graph.npy'))
assert_array_equal(graph_dense, data)
def test_fit():
"""Test the routine to fit the parameters of the dce normalization."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'full_dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Load the GT data
path_gt = [os.path.join(currdir, 'data', 'full_gt', 'prostate')]
label_gt = ['prostate']
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt, path_gt)
# Create the object to make the normalization
stn = StandardTimeNormalization(dce_mod)
# Create a synthetic model to fit on
stn.model_ = np.array([30., 30., 32., 31., 31., 30., 35., 55., 70., 80.])
stn.is_model_fitted_ = True
# Fit the parameters on the model
stn.fit(dce_mod, gt_mod, label_gt[0])
assert_almost_equal(stn.fit_params_['scale-int'], 1.2296657327848537,
decimal=PRECISION_DECIMAL)
assert_equal(stn.fit_params_['shift-time'], 0.0)
data = np.array([191.29, 193.28, 195.28, 195.28, 195.28, 197.28, 213.25,
249.18, 283.12, 298.10])
assert_array_almost_equal(stn.fit_params_['shift-int'], data,
decimal=PRECISION_DECIMAL)
def test_partial_fit_model_dict_wrong_type():
"""Test either if an error is raised when a parameters is a wrong
type in the dictionary."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Load the GT data
path_gt = [os.path.join(currdir, 'data', 'gt_folders', 'prostate')]
label_gt = ['prostate']
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt, path_gt)
# Create the object to make the normalization
stn = StandardTimeNormalization(dce_mod)
params = {'std': 50., 'exp': 25., 'alpha': .9, 'max_iter': 5.}
assert_raises(ValueError, stn.partial_fit_model, dce_mod,
ground_truth=gt_mod, cat=label_gt[0], params=params)
params = {'std': 50., 'exp': 25, 'alpha': .9, 'max_iter': 5}
assert_raises(ValueError, stn.partial_fit_model, dce_mod,
ground_truth=gt_mod, cat=label_gt[0], params=params)
def test_shift_heatmap_wrong_shift():
"""Test if an error is raised when the shidt provided is not consistent."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Load the GT data
path_gt = [os.path.join(currdir, 'data', 'gt_folders', 'prostate')]
label_gt = ['prostate']
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt, path_gt)
# Build a heatmap from the dce data
# Reduce the number of bins to enforce low memory consumption
nb_bins = [100] * dce_mod.n_serie_
heatmap, bins_heatmap = dce_mod.build_heatmap(gt_mod.extract_gt_data(
label_gt[0]), nb_bins=nb_bins)
# Create a list of shift which do not have the same number of entries
# than the heatmap - There is 4 series, let's create only 2
shift_arr = np.array([10] * 2)
assert_raises(ValueError, StandardTimeNormalization._shift_heatmap,
heatmap, shift_arr)
def test_save_model_wrong_ext():
"""Test either if an error is raised if the filename as a wrong
extension while storing the model."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'full_dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Load the GT data
path_gt = [os.path.join(currdir, 'data', 'full_gt', 'prostate')]
label_gt = ['prostate']
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt, path_gt)
# Create the object to make the normalization
stn = StandardTimeNormalization(dce_mod)
stn.partial_fit_model(dce_mod, gt_mod, label_gt[0])
# Try to store the file not with an npy file
assert_raises(ValueError, stn.save_model, os.path.join(currdir, 'data',
'model.rnd'))
def test_ese_transform_gt_cat():
"""Test the transform routine with a given ground-truth."""
# Create the normalization object with the right modality
dce_ese = EnhancementSignalExtraction(DCEModality())
# Try to fit an object with another modality
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_data)
# Load the GT data
path_gt = [os.path.join(currdir, 'data', 'gt_folders', 'prostate')]
label_gt = ['prostate']
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt, path_gt)
# Fit and raise the error
data = dce_ese.transform(dce_mod, gt_mod, label_gt[0])
# Check the size of the data
assert_equal(data.shape, (12899, 4))
# Check the hash of the data
data.flags.writeable = False
assert_equal(hash(data.data), -3808597525488161265)
def test_partial_fit_model_2():
"""Test the routine to fit two models."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'full_dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Load the GT data
path_gt = [os.path.join(currdir, 'data', 'full_gt', 'prostate')]
label_gt = ['prostate']
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt, path_gt)
# Create the object to make the normalization
stn = StandardTimeNormalization(dce_mod)
stn.partial_fit_model(dce_mod, gt_mod, label_gt[0])
stn.partial_fit_model(dce_mod, gt_mod, label_gt[0])
# Check the model computed
model_gt = np.array([22.26479174, 22.51070962, 24.66027277, 23.43488237,
23.75601817, 22.56173871, 26.86244505, 45.06227804,
62.34273874, 71.35327656])
assert_array_almost_equal(stn.model_, model_gt, decimal=PRECISION_DECIMAL)
assert_true(stn.is_model_fitted_)
def test_tqe_compute_fit_aif():
"""Test the fit function."""
# Try to fit an object with another modality
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir,
'../../preprocessing/tests/data/full_dce')
# Create an object to handle the data
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_data)
# Create the object for Tofts quantification extraction
tqe = ToftsQuantificationExtraction(DCEModality(), 1.6, 3.5,
random_state=RND_SEED)
# Perform the fitting
tqe.fit(dce_mod, fit_aif=True)
# Check the value fitted
assert_almost_equal(tqe.TR_, 0.00324, decimal=DECIMAL_PRECISION)
assert_almost_equal(tqe.flip_angle_, 10., decimal=DECIMAL_PRECISION)
assert_equal(tqe.start_enh_, 3)
cp_r_gt = np.array([3.71038e-02, 2.35853e-02, 4.21997e-13, 1.22529e-02,
2.46203e-02, 1.35724e-01, 3.06310e-01, 3.25429e-01,
2.94957e-01, 2.58964e-01])
assert_array_almost_equal(tqe.cp_t_, cp_r_gt, decimal=DECIMAL_PRECISION)
def test_tqe_compute_fit_no_aif():
"""Test the fit function."""
# Try to fit an object with another modality
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir,
'../../preprocessing/tests/data/full_dce')
# Create an object to handle the data
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_data)
# Create the object for Tofts quantification extraction
tqe = ToftsQuantificationExtraction(DCEModality(), 1.6, 3.5,
random_state=RND_SEED)
# Perform the fitting
tqe.fit(dce_mod, fit_aif=False)
# Check the value fitted
assert_almost_equal(tqe.TR_, 0.00324, decimal=DECIMAL_PRECISION)
assert_almost_equal(tqe.flip_angle_, 10., decimal=DECIMAL_PRECISION)
assert_equal(tqe.start_enh_, 3)
cp_r_gt = np.array([0., 0., 0., 0.13859428, 6.23675492, 6.90344512,
1.80619315, 2.22619032, 3.69060743, 3.32021637])
assert_array_almost_equal(tqe.cp_t_, cp_r_gt, decimal=DECIMAL_PRECISION)
def test_tqe_conv_signal_conc():
"""Test the conversion from signal to concentration."""
# Try to fit an object with another modality
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir,
'../../preprocessing/tests/data/full_dce')
# Create an object to handle the data
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_data)
# Create the object for the Tofts extraction
tqe = ToftsQuantificationExtraction(DCEModality(), 1.6, 3.5)
tqe.fit(dce_mod, fit_aif=False)
# Try to perform a conversion
signal = np.array([379., 366., 343., 355., 367., 470., 613., 628., 604.,
575.])
conc = tqe.signal_to_conc(signal, 343.)
conc_gt = np.array([2.15201846e-02, 1.36794587e-02, 2.44758162e-13,
7.10669089e-03, 1.42797742e-02, 7.87199894e-02,
1.77659845e-01, 1.88748637e-01, 1.71075044e-01,
1.50198853e-01])
assert_almost_equal(conc, conc_gt)
# Apply the back conversion
signal_back = tqe.conc_to_signal(conc, 343.)
assert_almost_equal(signal_back, signal, decimal=DECIMAL_PRECISION)
def test_qte_transform_regular():
"""Test the transform function for regular model."""
# Try to fit an object with another modality
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir,
'../../preprocessing/tests/data/full_dce')
# Create an object to handle the data
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_data)
# Create the gt data
gt_mod = GTModality()
gt_cat = ['cap']
path_data = [os.path.join(
currdir,
'../../preprocessing/tests/data/full_gt/cap')]
gt_mod.read_data_from_path(gt_cat, path_data)
# Create the object for the Tofts extraction
tqe = ToftsQuantificationExtraction(DCEModality(), 1.6, 3.5,
random_state=RND_SEED)
tqe.fit(dce_mod)
data = tqe.transform(dce_mod, gt_mod, gt_cat[0], kind='regular')
data_gt = np.load(os.path.join(currdir, 'data/tofts_reg_data.npy'))
assert_array_almost_equal(data, data_gt, decimal=DECIMAL_PRECISION)
def test_shift_heatmap():
"""Test the routine which shift the heatmap."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Load the GT data
path_gt = [os.path.join(currdir, 'data', 'gt_folders', 'prostate')]
label_gt = ['prostate']
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt, path_gt)
# Build a heatmap from the dce data
# Reduce the number of bins to enforce low memory consumption
nb_bins = [100] * dce_mod.n_serie_
heatmap, bins_heatmap = dce_mod.build_heatmap(gt_mod.extract_gt_data(
label_gt[0]), nb_bins=nb_bins)
# Create a list of shift which do not have the same number of entries
# than the heatmap - There is 4 series, let's create only 2
shift_arr = np.array([10] * 4)
heatmap_shifted = StandardTimeNormalization._shift_heatmap(heatmap,
shift_arr)
data = np.load(os.path.join(currdir, 'data', 'heatmap_shifted.npy'))
assert_array_equal(heatmap_shifted, data)
def test_dce_get_pdf_roi():
"""Test the function to get a pdf from ROI."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce_folders')
# Create the list of path
path_data_list = [os.path.join(path_data, 's_2'),
os.path.join(path_data, 's_1')]
# Create an object to handle the data
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_data_list)
# Create ground truth array
pos = np.ones((368, 448), dtype=bool)
neg = np.zeros((368, 448), dtype=bool)
gt_index = np.rollaxis(np.array([neg, pos, pos, pos, neg]), 0, 3)
# Compute the histgram for the required data
pdf, bins = dce_mod.get_pdf_list(roi_data=(gt_index))
pdf_roi = np.load(os.path.join(currdir, 'data', 'pdf_roi.npy'))
bins_roi = np.load(os.path.join(currdir, 'data', 'bins_roi.npy'))
for pdf_s, bins_s, pdf_gt, bins_gt in zip(pdf, bins,
pdf_roi, bins_roi):
assert_array_equal(pdf_s, pdf_gt)
assert_array_equal(bins_s, bins_gt)
def test_ese_fit():
"""Test either if an error is raised since that the function
is not implemented."""
# Create the normalization object with the right modality
dce_ese = EnhancementSignalExtraction(DCEModality())
# Open the DCE data
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_data)
# Fit and raise the error
assert_raises(NotImplementedError, dce_ese.fit, dce_mod)
def test_get_pdf_nb_bins_wrong_type():
""" Test either if an error is raised when an unknown parameter type
is passed."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Pass a single integer which is an unknown type
assert_raises(ValueError, dce_mod.get_pdf_list, roi_data=None, nb_bins=10)
def test_tqe_bad_mod_transform():
"""Test either if an error is raised when a modality to tranform does not
correspond to the template modality given at the construction."""
# Create the normalization object with the right modality
dce_tqe = ToftsQuantificationExtraction(DCEModality(), T10, CA)
# Try to fit an object with another modality
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_data)
# Fit and raise the error
assert_raises(RuntimeError, dce_tqe.transform, dce_mod)
def test_tqe_compute_aif_bad_estimator():
"""Test either if an error is raised when a wrong estimator is
given to compute the AIF."""
# Try to fit an object with another modality
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_data)
# Define the eccentricity with to large number
estimator = 'rnd'
assert_raises(ValueError, ToftsQuantificationExtraction.compute_aif,
dce_mod, estimator=estimator)
def test_gn_fit_wrong_modality():
""" Test either if an error is raised in case that a wrong
modality is provided for fitting. """
# Create a DCEModality object
currdir = os.path.dirname(os.path.abspath(__file__))
path_data_dce = os.path.join(currdir, 'data', 'dce')
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_data=path_data_dce)
# Create the Gaussian normalization object
gaussian_norm = GaussianNormalization(T2WModality())
# Try to make the fitting with another based modality
assert_raises(ValueError, gaussian_norm.fit, dce_mod)
def test_ese_wrong_gt_mod():
"""Test either if an error is raised when a wrong modality is given
as ground-truth."""
# Create the normalization object with the right modality
dce_ese = EnhancementSignalExtraction(DCEModality())
# Try to fit an object with another modality
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_data)
# Fit and raise the error
assert_raises(ValueError, dce_ese.transform, dce_mod, dce_mod, 'prostate')
def test_get_pdf_nb_bins_str_unknown():
""" Test either if an error is raised when the string for `nb_bins`
is unknown."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Pass an unknown string for `nb_bins`
assert_raises(ValueError, dce_mod.get_pdf_list,
roi_data=None, nb_bins='rnd')
def test_update_histogram_wrong_instance():
"""Test either if an error is raised with an type for `nb_bins`
argument."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Get the pdf with the wrong number of series in nb_bins
# There is only two series
assert_raises(ValueError, dce_mod.update_histogram, nb_bins=10)
def test_partial_fit_model_wt_gt_and_cat():
"""Test either if a warning is raised when a gt is not provided
and a cat is."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'full_dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Create the object to make the normalization
stn = StandardTimeNormalization(dce_mod)
assert_warns(UserWarning, stn.partial_fit_model, dce_mod, cat='prostate')
def test_get_pdf_wrong_bins():
"""Test either if an error is raised with inconsistent number of bins."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Get the pdf with the wrong number of series in nb_bins
# There is only two series
nb_bins = [100, 100, 100]
assert_raises(ValueError, dce_mod.get_pdf_list, nb_bins=nb_bins)
def test_ese_transform_wt_gt_and_cat():
"""Test either if a warning is raised when a gt is not provided
and a cat is."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Create the object to make the normalization
dce_ese = EnhancementSignalExtraction(dce_mod)
assert_warns(UserWarning, dce_ese.transform, dce_mod, cat='prostate')
def test_normalize_denormalize_3():
"""Test the data normalization and denormalization with shift > 0."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'full_dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Load the GT data
path_gt = [os.path.join(currdir, 'data', 'full_gt', 'prostate')]
label_gt = ['prostate']
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt, path_gt)
# Create the object to make the normalization
stn = StandardTimeNormalization(dce_mod)
# Simulate that we fitted the data
stn.model_ = np.array([30., 30., 32., 31., 31., 30., 35., 55., 70., 80.])
stn.is_model_fitted_ = True
stn.fit_params_ = {'scale-int': 1.2296657327848537,
'shift-time': 3.0,
'shift-int': np.array([191.29, 193.28, 195.28, 195.28,
195.28, 197.28, 213.25, 249.18,
283.12, 298.10])}
stn.is_fitted_ = True
# Store the data somewhere
data_gt_cp = dce_mod.data_.copy()
# Normalize the data
dce_mod_norm = stn.normalize(dce_mod)
# Check if the data are properly normalized
dce_mod_norm.data_.flags.writeable = False
data = np.load(os.path.join(currdir, 'data', 'data_normalized_dce_3.npy'))
assert_equal(hash(dce_mod_norm.data_.data), data)
dce_mod_norm.data_.flags.writeable = True
dce_mod_2 = stn.denormalize(dce_mod_norm)
dce_mod_2.data_.flags.writeable = False
assert_equal(hash(dce_mod_2.data_.data), -3781160829709175881)
def test_tqe_compute_aif_max():
"""Test the AIF computation when the max esatimator is used."""
# Try to fit an object with another modality
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir,
'../../preprocessing/tests/data/full_dce')
# Create an object to handle the data
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_data)
# Compute the AIF
signal_aif = ToftsQuantificationExtraction.compute_aif(
dce_mod, estimator='max', random_state=RND_SEED)
aif_gt = np.array([503., 482., 493., 467., 504., 648., 816., 850., 827.,
787.])
assert_array_equal(signal_aif, aif_gt)
def test_tqe_compute_aif_mean():
"""Test the AIF computation when the mean esatimator is used."""
# Try to fit an object with another modality
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir,
'../../preprocessing/tests/data/full_dce')
# Create an object to handle the data
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_data)
# Compute the AIF
signal_aif = ToftsQuantificationExtraction.compute_aif(
dce_mod, estimator='mean', random_state=RND_SEED)
aif_gt = np.array([347.29533, 332.32211, 317.53709, 322.32994, 336.03532,
441.30315, 586.89144, 598.05404, 585.32235, 562.42261])
assert_array_almost_equal(signal_aif, aif_gt, decimal=DECIMAL_PRECISION)
def test_tqe_compute_aif_default():
"""Test the AIF computation when the default parameters are used."""
# Try to fit an object with another modality
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir,
'../../preprocessing/tests/data/full_dce')
# Create an object to handle the data
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_data)
# Compute the AIF
signal_aif = ToftsQuantificationExtraction.compute_aif(
dce_mod, random_state=RND_SEED)
aif_gt = np.array([379., 366., 343., 355., 367., 470., 613., 628., 604.,
575.])
assert_array_equal(signal_aif, aif_gt)
def find_normalization_params(pat_dce, pat_gt, label, pat_model):
# Create the normalization object and load the model
dce_norm = StandardTimeNormalization(DCEModality())
dce_norm.load_model(pat_model)
# Read the DCE
dce_mod = DCEModality()
dce_mod.read_data_from_path(pat_dce)
# Read the GT
gt_mod = GTModality()
gt_mod.read_data_from_path(label, pat_gt)
# Find the normalization parameters
dce_norm.fit(dce_mod, ground_truth=gt_mod, cat=label[0])
return dce_norm
def test_update_histogram_wrong_bins_type_2():
"""Test either if an error is raised with an inconsistent type of data
in a list."""
# Load the data with only a single serie
currdir = os.path.dirname(os.path.abspath(__file__))
path_data = os.path.join(currdir, 'data', 'dce')
# Create an object to handle the data
dce_mod = DCEModality()
# Read the data
dce_mod.read_data_from_path(path_data)
# Get the pdf with the wrong number of series in nb_bins
# There is only two series
nb_bins = [100, 'a']
assert_raises(ValueError, dce_mod.update_histogram, nb_bins=nb_bins)
def find_normalization_params(pat_dce, pat_gt, label, pat_model):
# Create the normalization object and load the model
dce_norm = StandardTimeNormalization(DCEModality())
dce_norm.load_model(pat_model)
# Read the DCE
dce_mod = DCEModality()
dce_mod.read_data_from_path(pat_dce)
# Read the GT
gt_mod = GTModality()
gt_mod.read_data_from_path(label, pat_gt)
# Find the normalization parameters
dce_norm.fit(dce_mod, ground_truth=gt_mod, cat=label[0])
return dce_norm
# Generate the different path to be later treated
path_patients_list_dce = []
path_patients_list_gt = []
# Create the generator
id_patient_list = (name for name in os.listdir(path_patients)
if os.path.isdir(os.path.join(path_patients, name)))
for id_patient in id_patient_list:
# Append for the DCE data
path_patients_list_dce.append(os.path.join(path_patients, id_patient,
path_dce))
# Append for the GT data - Note that we need a list of gt path
path_patients_list_gt.append([os.path.join(path_patients, id_patient,
path_gt)])
# Create the model iteratively
dce_norm = StandardTimeNormalization(DCEModality())
for pat_dce, pat_gt in zip(path_patients_list_dce, path_patients_list_gt):
# Read the DCE
dce_mod = DCEModality()
dce_mod.read_data_from_path(pat_dce)
# Read the GT
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt, pat_gt)
# Fit the model
dce_norm.partial_fit_model(dce_mod, ground_truth=gt_mod,
cat=label_gt[0])
# Define the path where to store the model
path_store_model = '/data/prostate/pre-processing/lemaitre-2016-nov/model'
if os.path.isdir(os.path.join(path_patients, name))]
for id_patient in id_patient_list:
# Append for the DCE data
path_patients_list_dce.append(os.path.join(path_patients, id_patient,
path_dce))
# Append for the GT data - Note that we need a list of gt path
path_patients_list_gt.append([os.path.join(path_patients, id_patient,
path_gt)])
for p_dce, p_gt, pat in zip(path_patients_list_dce, path_patients_list_gt,
id_patient_list):
print 'Processing #{}'.format(pat)
# Create the Tofts Extractor
brix_ext = BrixQuantificationExtraction(DCEModality())
# Read the DCE
print 'Read DCE images'
dce_mod = DCEModality()
dce_mod.read_data_from_path(p_dce)
# Read the GT
print 'Read GT images'
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt, p_gt)
# Load the approproate normalization object
filename_norm = (pat.lower().replace(' ', '_') +
'_norm.p')
dce_norm = StandardTimeNormalization.load_from_pickles(
n_jobs=-1)
label_region = km2.fit_predict(region_feat_vec)
for i, gt in enumerate(label_gt):
# get the gt
all_label_img[gt[0]][np.nonzero(
all_label_img[gt[0]] == gt[1] + 1)] = 1
for sl in range(len(all_label_img)):
plt.figure()
plt.imshow(all_label_img[sl])
plt.savefig('{}_image_{}.png'.format(idx_patient, sl))
plt.figure()
plt.imshow(mod.data_[10, 50:size_image[1]/2, :, sl])
plt.savefig('{}_original_{}.png'.format(idx_patient, sl))
return label_region, label_gt, region_feat_vec
# Loop where we read every patient
for idx_lopo_cv in range(len(id_patient_list)):
# Read the DCE data
dce_mod = DCEModality()
dce_mod.read_data_from_path(os.path.join(path_data,
id_patient_list[idx_lopo_cv],
path_dce))
# Segment the aorta
lr, lgt, rfv = segmentation_aorta(dce_mod, idx_lopo_cv)
]
for id_patient in id_patient_list:
# Append for the DCE data
path_patients_list_dce.append(
os.path.join(path_patients, id_patient, path_dce))
# Append for the GT data - Note that we need a list of gt path
path_patients_list_gt.append(
[os.path.join(path_patients, id_patient, path_gt)])
for p_dce, p_gt, pat in zip(path_patients_list_dce, path_patients_list_gt,
id_patient_list):
print 'Processing #{}'.format(pat)
# Create the Tofts Extractor
pun_ext = PUNQuantificationExtraction(DCEModality())
# Read the DCE
print 'Read DCE images'
dce_mod = DCEModality()
dce_mod.read_data_from_path(p_dce)
# Read the GT
print 'Read GT images'
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt, p_gt)
# Fit the parameters for Brix
print 'Extract Weibull'
pun_ext.fit(dce_mod, ground_truth=gt_mod, cat=label_gt[0])
for id_patient in id_patient_list:
# Append for the DCE data
path_patients_list_dce.append(os.path.join(path_patients, id_patient,
path_dce))
# Append for the GT data - Note that we need a list of gt path
path_patients_list_gt.append([os.path.join(path_patients, id_patient, gt)
for gt in path_gt])
# Load all the data once. Splitting into training and testing will be done at
# the cross-validation time
for idx_pat in range(len(id_patient_list)):
print 'Read patient {}'.format(id_patient_list[idx_pat])
# Load the testing data that correspond to the index of the LOPO
# Create the object for the DCE
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_patients_list_dce[idx_pat])
print 'Read the DCE data for the current patient ...'
# Create the corresponding ground-truth
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt,
path_patients_list_gt[idx_pat])
print 'Read the GT data for the current patient ...'
# Load the approproate normalization object
filename_norm = (id_patient_list[idx_pat].lower().replace(' ', '_') +
'_norm.p')
dce_norm = StandardTimeNormalization.load_from_pickles(
os.path.join(path_norm, filename_norm))
if os.path.isdir(os.path.join(path_patients, name))]
for id_patient in id_patient_list:
# Append for the DCE data
path_patients_list_dce.append(os.path.join(path_patients, id_patient,
path_dce))
# Append for the GT data - Note that we need a list of gt path
path_patients_list_gt.append([os.path.join(path_patients, id_patient,
path_gt)])
for p_dce, p_gt, pat in zip(path_patients_list_dce, path_patients_list_gt,
id_patient_list):
print 'Processing #{}'.format(pat)
# Create the Tofts Extractor
tofts_ext = ToftsQuantificationExtraction(DCEModality(), T10, CA)
# Read the DCE
print 'Read DCE images'
dce_mod = DCEModality()
dce_mod.read_data_from_path(p_dce)
# Read the GT
print 'Read GT images'
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt, p_gt)
# Fit the parameters for Tofts
print 'Extract Tofts parameters'
tofts_ext.fit(dce_mod, ground_truth=gt_mod, cat=label_gt[0], fit_aif=True)
# Append for the DCE data
path_patients_list_dce.append(
os.path.join(path_patients, id_patient, path_dce))
# Append for the GT data - Note that we need a list of gt path
path_patients_list_gt.append(
[os.path.join(path_patients, id_patient, path_gt)])
# Compute the different AIF
aif_patient = []
aif_time = []
for pat_dce, pat_gt in zip(path_patients_list_dce, path_patients_list_gt):
print 'Processing {}'.format(pat_dce)
# Read the DCE
dce_mod = DCEModality()
dce_mod.read_data_from_path(pat_dce)
# Store the time
aif_time.append(dce_mod.time_info_)
aif_patient.append(
ToftsQuantificationExtraction.compute_aif(dce_mod, estimator='median'))
# Get the median time to resample later
aif_time = np.array(aif_time)
aif_time_median = np.median(aif_time, axis=0)
# Resample each aif
for idx_aif in range(len(aif_patient)):
aif_patient[idx_aif] = np.interp(aif_time_median, aif_time[idx_aif],
aif_patient[idx_aif])
from protoclass.data_management import DCEModality
from protoclass.data_management import GTModality
from protoclass.preprocessing import StandardTimeNormalization
# Define the path for the DCE
path_dce = '/data/prostate/experiments/Patient 383/DCE'
# Define the list of path for the GT
path_gt = ['/data/prostate/experiments/Patient 383/GT_inv/prostate']
# Define the associated list of label for the GT
label_gt = ['prostate']
# Read the DCE
dce_mod = DCEModality()
dce_mod.read_data_from_path(path_dce)
# Read the GT
gt_mod = GTModality()
gt_mod.read_data_from_path(label_gt, path_gt)
# Create the object to normalize the DCE data
dce_norm = StandardTimeNormalization(dce_mod)
# Fit the data to get the normalization parameters
dce_norm.partial_fit_model(dce_mod, ground_truth=gt_mod,
cat='prostate')
print dce_norm.model_
# Define the path for the DCE
# Append for the DCE data
path_patients_list_dce.append(
os.path.join(path_patients, id_patient, path_dce))
# Append for the GT data - Note that we need a list of gt path
path_patients_list_gt.append(
[os.path.join(path_patients, id_patient, path_gt)])
# Compute the different AIF
aif_patient = []
aif_time = []
for pat_dce, pat_gt in zip(path_patients_list_dce, path_patients_list_gt):
print 'Processing {}'.format(pat_dce)
# Read the DCE
dce_mod = DCEModality()
dce_mod.read_data_from_path(pat_dce)
for idx in range(dce_mod.data_.shape[0]):
dce_mod.data_[idx, :] += shift[idx]
dce_mod.update_histogram()
# Store the time
aif_time.append(dce_mod.time_info_)
aif_patient.append(
ToftsQuantificationExtraction.compute_aif(dce_mod, estimator='median'))
# Get the median time to resample later
aif_time = np.array(aif_time)
aif_time_median = np.median(aif_time, axis=0)
