pylinac.form.md

CatPhan analysis with Python, PyLinac, and ScriptedForms

This is a ScriptedForm. It allows you to easily make printable user interfaces that can be hosted on your intranet. ScriptedForms are powered by Python and all the goodies that come with that.

ScriptedForms are created with a plain text file. Any editing of that plain text file will automatically update the displayed form. The plain text file for this form is found at this link. Open that link up in another tab, edit some of the file contents, save the result by pressing Ctrl + S, and then see the form update.

The Python goodie we will be focusing on in this form is PyLinac.

Select a DICOM zip file

To begin, select one of the zip files within the data directory. By default there is only one zip file in there containing a Cone Beam CT of a CatPhan. You can of course reuse this form and drop other files within the data directory as you please.

selected_zip_file

display(Markdown('Loading...'))
with warnings.catch_warnings():
    warnings.simplefilter("ignore")
    cbct = CatPhan504.from_zip(selected_zip_file)

number_of_slices = len(cbct.dicom_stack)
smallest_value = np.min([np.min(dcm.array) for dcm in cbct.dicom_stack])
largest_value = np.max([np.max(dcm.array) for dcm in cbct.dicom_stack])

display(Markdown('Successfully loaded `{}`'.format(selected_zip_file)))

Peruse Slices

Once you have loaded up a DICOM data set you may peruse the slices using the following slider.

chosen_slice

current_image = cbct.dicom_stack[chosen_slice - 1]
plt.figure(figsize=(11,11))
plt.imshow(current_image, vmin=smallest_value, vmax=largest_value);

Run Analysis

Once you have loaded up a DICOM data set you may analyse the CatPhan using PyLinac.

with warnings.catch_warnings():
    warnings.simplefilter("ignore")
    cbct.analyze()
    print(cbct.results())

    sub_images = ['hu', 'un', 'sp', 'lc', 'mtf', 'lin', 'prof']
    for sub_image in sub_images:
        cbct.plot_analyzed_subimage(sub_image)

Conclusion

ScriptedForms can bring Python tools such as PyLinac into our every day job with little friction.

For documentation on ScriptedForms see https://scriptedforms.com.au. For documentation on PyLinac see https://pylinac.readthedocs.io.

To facilitate transfer of DICOM files from the Linac or CT to the ScriptedForms server I recommend using Orthanc.

from glob import glob
import warnings

import numpy as np
import matplotlib.pyplot as plt

from IPython.display import display, Markdown

import pydicom
from pylinac import CatPhan504

zip_search_string = 'data/*.zip'
selected_zip_file = None
number_of_slices = 0
chosen_slice = 1
cbct = None

zip_filepaths = glob(zip_search_string)
if len(zip_filepaths) == 1:
    selected_zip_file = zip_filepaths[0]