while working to execute npgamma from dicom, i am getting following error. I tried to debug it, but failed in my attempt. I am getting the following error "
module ‘pymedphys’ has no attribute ‘data_path’"
kindly help me this regard.
Hi @mohamed,
Welcome to the PyMedPhys Discourse group 
Before being able to help you I’d like you to first provide some more information. What PyMedPhys version are you using? What Python version? And you’ve described using npgamma, can provide the complete code example that you’ve tried?
Cheers,
Simon
my python version is 3.8.5
pymedphys-gamma pymedphys-gamma<0.12.0,>=0.11.0
i tried the following code anaconda spider, and got the error message
"AttributeError: module 'pymedphys' has no attribute 'data_path'"
import numpy as np
import matplotlib.pyplot as plt
!pip install pydicom pymedphys
import pydicom
import pymedphys as pp
reference_filepath = pp.data_path("original_dose_beam_4.dcm")
reference_filepath
evaluation_filepath = pp.data_path("logfile_dose_beam_4.dcm")
evaluation_filepath
reference = pydicom.read_file(str(reference_filepath), force=True)
evaluation = pydicom.read_file(str(evaluation_filepath), force=True)
axes_reference, dose_reference = pymedphys.dicom.zyx_and_dose_from_dataset(reference)
axes_evaluation, dose_evaluation = pymedphys.dicom.zyx_and_dose_from_dataset(evaluation)
(z_ref, y_ref, x_ref) = axes_reference
(z_eval, y_eval, x_eval) = axes_evaluation
np.shape(z_ref)
np.shape(y_ref)
np.shape(x_ref)
np.shape(dose_reference)
gamma_options = {
'dose_percent_threshold': 1,
'distance_mm_threshold': 1,
'lower_percent_dose_cutoff': 20,
'interp_fraction': 10, # Should be 10 or more for more accurate results
'max_gamma': 2,
'random_subset': None,
'local_gamma': True,
'ram_available': 2**29 # 1/2 GB
}
gamma = pymedphys.gamma(
axes_reference, dose_reference,
axes_evaluation, dose_evaluation,
**gamma_options)
valid_gamma = gamma[~np.isnan(gamma)]
num_bins = (
gamma_options['interp_fraction'] * gamma_options['max_gamma'])
bins = np.linspace(0, gamma_options['max_gamma'], num_bins + 1)
plt.hist(valid_gamma, bins, density=True)
plt.xlim([0, gamma_options['max_gamma']])
pass_ratio = np.sum(valid_gamma <= 1) / len(valid_gamma)
plt.title("Local Gamma (0.5%/0.5mm) | Percent Pass: {0:.2f} %".format(pass_ratio*100))
# plt.savefig('gamma_hist.png', dpi=300)
max_ref_dose = np.max(dose_reference)
lower_dose_cutoff = gamma_options['lower_percent_dose_cutoff'] / 100 * max_ref_dose
relevant_slice = (
np.max(dose_reference, axis=(1, 2)) >
lower_dose_cutoff)
slice_start = np.max([
np.where(relevant_slice)[0][0],
0])
slice_end = np.min([
np.where(relevant_slice)[0][-1],
len(z_ref)])
z_vals = z_ref[slice(slice_start, slice_end, 5)]
eval_slices = [
dose_evaluation[np.where(z_i == z_eval)[0][0], :, :]
for z_i in z_vals
]
ref_slices = [
dose_reference[np.where(z_i == z_ref)[0][0], :, :]
for z_i in z_vals
]
gamma_slices = [
gamma[np.where(z_i == z_ref)[0][0], :, :]
for z_i in z_vals
]
diffs = [
eval_slice - ref_slice
for eval_slice, ref_slice
in zip(eval_slices, ref_slices)
]
max_diff = np.max(np.abs(diffs))
for i, (eval_slice, ref_slice, diff, gamma_slice) in enumerate(zip(eval_slices, ref_slices, diffs, gamma_slices)):
fig, ax = plt.subplots(figsize=(13,10), nrows=2, ncols=2)
c00 = ax[0,0].contourf(
x_eval, y_eval, eval_slice, 100,
vmin=0, vmax=max_ref_dose)
ax[0,0].set_title("Evaluation")
fig.colorbar(c00, ax=ax[0,0], label='Dose (Gy)')
ax[0,0].invert_yaxis()
ax[0,0].set_xlabel('x (mm)')
ax[0,0].set_ylabel('z (mm)')
c01 = ax[0,1].contourf(
x_ref, y_ref, ref_slice, 100,
vmin=0, vmax=max_ref_dose)
ax[0,1].set_title("Reference")
fig.colorbar(c01, ax=ax[0,1], label='Dose (Gy)')
ax[0,1].invert_yaxis()
ax[0,1].set_xlabel('x (mm)')
ax[0,1].set_ylabel('z (mm)')
c10 = ax[1,0].contourf(
x_ref, y_ref, diff, 100,
vmin=-max_diff, vmax=max_diff, cmap=plt.get_cmap('seismic'))
ax[1,0].set_title("Dose difference")
fig.colorbar(c10, ax=ax[1,0], label='[Dose Eval] - [Dose Ref] (Gy)')
ax[1,0].invert_yaxis()
ax[1,0].set_xlabel('x (mm)')
ax[1,0].set_ylabel('z (mm)')
c11 = ax[1,1].contourf(
x_ref, y_ref, gamma_slice, 100,
vmin=0, vmax=2, cmap=plt.get_cmap('coolwarm'))
ax[1,1].set_title(
f"Local Gamma ({gamma_options['dose_percent_threshold']} % / {gamma_options['distance_mm_threshold']} mm)")
fig.colorbar(c11, ax=ax[1,1], label='Gamma Value')
ax[1,1].invert_yaxis()
ax[1,1].set_xlabel('x (mm)')
ax[1,1].set_ylabel('z (mm)')
plt.show()
print("\n")
Yup, the issue is you’re using a very old version of PyMedPhys. The current PyMedPhys release is up to version 0.35.0:
Would you be able to install PyMedPhys with a forced upgrade to version 0.35.0 by running:
pip install pymedphys[user]==0.35.0
Then let me know how the code you just posted goes.