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swap actual and desired in test #105

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51ddcdd
swap actual and desired in test
oscarjalnefjord Jun 5, 2025
6555490
corrected some typos in previous commit
oscarjalnefjord Jun 5, 2025
049d05d
brain data added to unit test
oscarjalnefjord Jun 10, 2025
d598d39
unique test reports for each data set
oscarjalnefjord Jun 11, 2025
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@
__pycache__/
*.nii.gz
*.nii
*.bval
*.bvec
*.dcm
*.mat
*.raw
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23 changes: 15 additions & 8 deletions src/wrappers/OsipiBase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -268,7 +268,7 @@ def osipi_author():
"""Author identification"""
return ''

def osipi_simple_bias_and_RMSE_test(self, SNR, bvalues, f, Dstar, D, noise_realizations=100):
def osipi_simple_bias_and_RMSE_test(self, SNR, bvalues, f, Dstar, D, noise_realizations=100, print_results=True):
# Generate signal
bvalues = np.asarray(bvalues)
signals = f*np.exp(-bvalues*Dstar) + (1-f)*np.exp(-bvalues*D)
Expand All @@ -282,7 +282,10 @@ def osipi_simple_bias_and_RMSE_test(self, SNR, bvalues, f, Dstar, D, noise_reali
noised_signal = np.array([norm.rvs(signal, sigma) for signal in signals])

# Perform fit with the noised signal
f_estimates[i], Dstar_estimates[i], D_estimates[i] = self.ivim_fit(noised_signal, bvalues)
fit = self.osipi_fit(noised_signal, bvalues)
f_estimates[i] = fit['f']
Dstar_estimates[i] = fit['Dp']
D_estimates[i] = fit['D']

# Calculate bias
f_bias = np.mean(f_estimates) - f
Expand All @@ -293,9 +296,13 @@ def osipi_simple_bias_and_RMSE_test(self, SNR, bvalues, f, Dstar, D, noise_reali
f_RMSE = np.sqrt(np.var(f_estimates) + f_bias**2)
Dstar_RMSE = np.sqrt(np.var(Dstar_estimates) + Dstar_bias**2)
D_RMSE = np.sqrt(np.var(D_estimates) + D_bias**2)

print(f"f bias:\t{f_bias}\nf RMSE:\t{f_RMSE}")
print(f"Dstar bias:\t{Dstar_bias}\nDstar RMSE:\t{Dstar_RMSE}")
print(f"D bias:\t{D_bias}\nD RMSE:\t{D_RMSE}")



if print_results:
print()
print(f"\tBias\t\tRMSE")
print(f"f\t{f_bias:.3}\t\t{f_RMSE:.3}")
print(f"D*\t{Dstar_bias:.3}\t\t{Dstar_RMSE:.3}")
print(f"D\t{D_bias:.3}\t{D_RMSE:.3}")
print()
else:
return {'f':f_bias,'Dstar':Dstar_bias,'D':D_bias}, {'f':f_RMSE,'Dstar':Dstar_RMSE,'D':D_RMSE}
6 changes: 3 additions & 3 deletions tests/IVIMmodels/unit_tests/test_ivim_fit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,11 +85,11 @@ def to_list_if_needed(value):
"atol": tolerances["atol"]
}
record_property('test_data', test_result)
npt.assert_allclose(fit_result['f'],data['f'], rtol=tolerances["rtol"]["f"], atol=tolerances["atol"]["f"])
npt.assert_allclose(data['f'], fit_result['f'], rtol=tolerances["rtol"]["f"], atol=tolerances["atol"]["f"])
if data['f']<0.80: # we need some signal for D to be detected
npt.assert_allclose(fit_result['D'],data['D'], rtol=tolerances["rtol"]["D"], atol=tolerances["atol"]["D"])
npt.assert_allclose(data['D'], fit_result['D'], rtol=tolerances["rtol"]["D"], atol=tolerances["atol"]["D"])
if data['f']>0.03: #we need some f for D* to be interpretable
npt.assert_allclose(fit_result['Dp'],data['Dp'], rtol=tolerances["rtol"]["Dp"], atol=tolerances["atol"]["Dp"])
npt.assert_allclose(data['Dp'], fit_result['Dp'], rtol=tolerances["rtol"]["Dp"], atol=tolerances["atol"]["Dp"])
#assert fit_result['D'] < fit_result['Dp'], f"D {fit_result['D']} is larger than D* {fit_result['Dp']} for {name}"
if not skiptime:
assert elapsed_time < 0.5, f"Algorithm {name} took {elapsed_time} seconds, which is longer than 2 second to fit per voxel" #less than 0.5 seconds per voxel
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20 changes: 12 additions & 8 deletions utilities/data_simulation/Download_data.py
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This is fine for me; but all of the osipi code is expecting the download to be in the defined folder destination. For what purpose do you want to put it elsewhere?

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@oscarjalnefjord oscarjalnefjord Jun 10, 2025 •
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Indeed. I just wanted to add some flexibility in case you want to place the data somewhere else and use for other purposes.

Original file line number Diff line number Diff line change
Expand Up @@ -12,16 +12,20 @@ def unzip_file(zip_file_path, extracted_folder_path):
zip_ref.extract(file_info, extracted_folder_path)


def download_data(force=False):
def download_data(force=False,folder=None):
# Check if the folder exists, and create it if not
curdir=os.getcwd()
base_folder = os.path.abspath(os.path.dirname(__file__))
base_folder = os.path.split(os.path.split(base_folder)[0])[0]
if not os.path.exists(os.path.join(base_folder,'download')):
os.makedirs(os.path.join(base_folder,'download'))
print(f"Folder '{'download'}' created.")
# Change to the specified folder
os.chdir(os.path.join(base_folder,'download'))
if folder is None:
base_folder = os.path.abspath(os.path.dirname(__file__))
base_folder = os.path.split(os.path.split(base_folder)[0])[0]
if not os.path.exists(os.path.join(base_folder,'download')):
os.makedirs(os.path.join(base_folder,'download'))
print(f"Folder '{'download'}' created.")
download_folder = os.path.join(base_folder,'download')
else:
download_folder = folder
# Change to the specified folder
os.chdir(download_folder)
subprocess.check_call(["zenodo_get", 'https://zenodo.org/records/14605039'])
# Open the zip file
if force or not os.path.exists('Data'):
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