pylinac 0.6.0.1__zip → 1.5.0__zip

{pylinac-0.6.0.1 → pylinac-1.5.0}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 1.1
 Name: pylinac
-Version: 0.6.0.1
+Version: 1.5.0
 Summary: A toolkit for performing TG-142 QA-related tasks on a linear accelerator
 Home-page: https://github.com/jrkerns/pylinac
 Author: James Kerns
 Author-email: jkerns100@gmail.com
-License: UNKNOWN
+License: MIT
 Description: UNKNOWN
 Keywords: medical physics AAPM TG142 quality assurance starshot cbct vmat dynalog trajectory log
 Platform: UNKNOWN

pylinac-1.5.0/README.rst

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+Pylinac
+=======
+
+.. image:: https://badges.gitter.im/Join%20Chat.svg
+   :alt: Join the chat at https://gitter.im/jrkerns/pylinac
+   :target: https://gitter.im/jrkerns/pylinac?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
+
+.. image:: https://img.shields.io/pypi/v/pylinac.svg
+    :target: https://pypi.python.org/pypi/pylinac
+    :alt: Latest Version
+
+.. image:: https://anaconda.org/jrkerns/pylinac/badges/installer/conda.svg
+    :target: https://anaconda.org/jrkerns/pylinac
+
+.. image:: https://img.shields.io/pypi/l/pylinac.svg
+    :target: https://pypi.python.org/pypi/pylinac/
+    :alt: MIT
+
+.. image:: https://travis-ci.org/jrkerns/pylinac.svg?branch=master
+    :target: https://travis-ci.org/jrkerns/pylinac
+    :alt: Travis CI
+
+.. image:: https://coveralls.io/repos/jrkerns/pylinac/badge.svg?branch=master
+    :target: https://coveralls.io/r/jrkerns/pylinac
+    :alt: Code Coverage
+
+.. image:: https://www.quantifiedcode.com/api/v1/project/25e3cefc2cc84052bbd127c3386adf69/badge.svg
+    :target: https://www.quantifiedcode.com/app/project/25e3cefc2cc84052bbd127c3386adf69
+    :alt: Code issues
+
+.. image:: https://readthedocs.org/projects/pylinac/badge/?version=stable
+    :target: http://pylinac.readthedocs.org/en/stable/?badge=stable
+    :alt: Documentation Status
+
+
+Pylinac provides TG-142 quality assurance (QA) tools to Python programmers as well as non-programmers in the field of 
+therapy medical physics. The package comes in two flavors: source-level and `web app <https://assuranceqa.herokuapp.com>`_. The source-level
+allows programmers and those familiar with Python to create custom tests with pylinac while the web app is for
+those who don't want or don't know how to program.
+
+Pylinac contains high-level modules for automatically analyzing images and data generated by linear accelerators.
+Most scripts can be utilized with <10 lines of code.
+
+The library also contains lower-level `hackable modules & tools <http://pylinac.readthedocs.org/en/latest/pylinac_core_hacking.html>`_
+for creating your own radiation therapy algorithms.
+
+Below are the high-level tools currently available:
+
+* `Continuous Directory Watching <http://pylinac.readthedocs.org/en/stable/watcher.html>`_ -
+   True, one-time "set it and forget it" service that analyzes any file that enters the folder. Files with
+   keywords and certain file types are analyzed automatically.
+   Only two lines of code: 1) install, 2) run::
+
+     $ pip install pylinac
+     $ pylinac watch "dir/to/watch"
+
+   And that's it! No code to write; no fuss, no muss.
+   Analysis settings are customizable and includes optional email service upon analysis.
+
+* `Planar Phantom Analysis (Leeds TOR, PipsPro QC-3) <http://pylinac.readthedocs.org/en/stable/planar_imaging.html>`_ -
+   The planar imaging module analyzes 2D phantoms. Currently only the LeedsTOR kV phantom and PipsPro QC-3 MV phantom.
+
+   Features:
+
+   * **Automatic phantom localization** - Set up your phantom any way you like; automatic positioning,
+     angle, and inversion correction mean you can set up how you like, nor will setup variations give you headache.
+   * **High and low contrast determination** - Analyze both low and high contrast ROIs. Set thresholds
+     as you see fit.
+
+   Example script::
+
+        from pylinac import LeedsTOR, PipsProQC3
+
+        path = 'path/to/leeds.dcm`
+        leeds = LeedsTOR(path)
+        leeds.analyze()
+        leeds.plot_analyzed_image()
+
+        path = 'path/to/pipspro.dcm'
+        pp = PipsProQC3(path)
+        pp.analyze()
+        pp.plot_analyzed_image()
+
+* `Winston-Lutz Analysis <http://pylinac.readthedocs.org/en/stable/winston_lutz.html>`_ -
+    The Winston-Lutz module analyzes EPID images taken of a small radiation field and BB to determine the 2D
+    distance from BB to field CAX. Additionally, the isocenter size of the gantry, collimator, and couch can
+    all be determined *without the BB being at isocenter*. Analysis is based on
+    `Winkler et al <http://iopscience.iop.org/article/10.1088/0031-9155/48/9/303/meta;jsessionid=269700F201744D2EAB897C14D1F4E7B3.c2.iopscience.cld.iop.org>`_
+    and `Du et al <http://scitation.aip.org/content/aapm/journal/medphys/37/5/10.1118/1.3397452>`_.
+
+    Features:
+
+    * **Automatic field & BB positioning** - When an image or directory is loaded, the field CAX and the BB
+      are automatically found, along with the vector and scalar distance between them.
+    * **Isocenter size determination** - Using backprojections of the EPID images, the 3D gantry isocenter size
+      and position can be determined *independent of the BB position*. Additionally, the 2D planar isocenter size
+      of the collimator and couch can also be determined.
+    * **Image plotting** - WL images can be plotted separately or together, each of which shows the field CAX, BB and
+      scalar distance from BB to CAX.
+    * **Gantry sag** - The sag of the gantry is also quantified and can be plotted.
+
+    Example script::
+
+        from pylinac import WinstonLutz
+
+        path = 'path/to/image/directory`
+        wl = WinstonLutz(path)  # images are analyzed upon loading
+        wl.plot_summary()
+        print(wl.results())
+
+* `Starshot Analysis <http://pylinac.readthedocs.org/en/stable/starshot_docs.html>`_ -
+    The Starshot module analyses a starshot image made of radiation spokes, whether gantry, collimator, MLC or couch.
+    It is based on ideas from `Depuydt et al <http://iopscience.iop.org/0031-9155/57/10/2997>`_
+    and `Gonzalez et al <http://dx.doi.org/10.1118/1.1755491>`_.
+
+    Features:
+
+    * **Analyze scanned film images, single EPID images, or a set of EPID images** -
+      Any image that you can load in can be analyzed, including 1 or a set of EPID DICOM images and
+      films that have been digitally scanned.
+    * **Any image size** - Have machines with different EPIDs? Scanned your film at different resolutions? No problem.
+    * **Dose/OD can be inverted** - Whether your device/image views dose as an increase in value or a decrease, pylinac
+      will detect it and invert if necessary.
+    * **Automatic noise detection & correction** - Sometimes there's dirt on the scanned film; sometimes there's a dead pixel on the EPID.
+      Pylinac will detect these spurious noise signals and can avoid or account for them.
+    * **Accurate, FWHM star line detection** - Pylinac uses not simply the maximum value to find the center of a star line,
+      but analyzes the entire star profile to determine the center of the FWHM, ensuring small noise or maximum value bias is avoided.
+    * **Adaptive searching** - If you passed pylinac a set of parameters and a good result wasn't found, pylinac can recover and
+      do an adaptive search by adjusting parameters to find a "reasonable" wobble.
+
+    Example script::
+
+        from pylinac import Starshot
+
+        star = Starshot("mystarshot.tif")
+        star.analyze(radius=60, tolerance=0.75)
+        print(star.return_results())  # prints out wobble information
+        star.plot_analyzed_image()  # shows a matplotlib figure
+
+* `VMAT QA <http://pylinac.readthedocs.org/en/stable/vmat_docs.html>`_ -
+    The VMAT module consists of the class VMAT, which is capable of loading an EPID DICOM Open field image and MLC field image and analyzing the
+    images according to the Varian RapidArc QA tests and procedures, specifically the Dose-Rate & Gantry-Speed (DRGS) and MLC speed (MLCS) tests.
+
+    Features:
+
+    * **Do both tests** - Pylinac can handle either DRGS or DRMLC tests.
+    * **Adjust for offsets** - Older VMAT patterns were off-center. Easily account for the offset by passing it in.
+    * **Automatic identification using file names** - If your file names are clear, the image type and test type don't even
+      have to be specified; just load and analyze.
+
+    Example script::
+
+        from pylinac import VMAT
+
+        vmat = VMAT.from_zip("myvmatimages.zip")
+        vmat.analyze(test='mlcs', tolerance=1.5)
+        print(vmat.return_results())  # prints out ROI information
+        vmat.plot_analyzed_image()  # shows a matplotlib figure
+
+* `CT & CBCT QA <http://pylinac.readthedocs.org/en/stable/cbct_docs.html>`_ -
+    The CBCT module automatically analyzes DICOM images of a CatPhan 504 or 503 acquired when doing CBCT or regular CT quality assurance. It can load a folder or zip file that
+    the images are in and automatically correct for phantom setup in 6 degrees.
+    It can analyze the HU regions and image scaling (CTP404), the high-contrast line pairs (CTP528) to calculate the modulation transfer function (MTF), and the HU
+    uniformity (CTP486) on the corresponding slice.
+
+    Features:
+
+    * **Automatic phantom registration** - Your phantom can be tilted, rotated, or translated--pylinac will register the phantom.
+    * **Automatic testing of 4 major modules** - Major modules are automatically registered and analyzed.
+    * **Any scan protocol** - Scan your CatPhan with any protocol; or even scan it in a regular CT scanner.
+      Any field size or field extent is allowed.
+
+    Example script::
+
+        from pylinac import CBCT
+
+        cbct = CBCT("my/cbct_image_folder")
+        cbct.analyze(hu_tolerance=40)
+        print(cbct.return_results())
+        cbct.plot_analyzed_image()
+
+* `Log Analysis <http://pylinac.readthedocs.org/en/stable/log_analyzer.html>`_ -
+    The log analyzer module reads and parses Varian linear accelerator machine logs, both Dynalogs and Trajectory logs. The module also
+    calculates actual and expected fluences as well as performing gamma evaluations. Data is structured to be easily accessible and
+    easily plottable.
+
+    Unlike most other modules of pylinac, the log analyzer module has no end goal. Data is parsed from the logs, but what is done with that
+    info, and which info is analyzed is up to the user.
+
+    Features:
+
+    * **Analyze Dynalogs or Trajectory logs** - Either platform is supported. Tlog versions 2.1 and 3.0 supported.
+    * **Save Trajectory log data to CSV** - The Trajectory log binary data format does not allow for easy export of data. Pylinac lets you do
+      that so you can use Excel or other software that you use with Dynalogs.
+    * **Plot or analyze any axis** - Every data axis can be plotted: the actual, expected, and even the difference.
+    * **View actual or expected fluences & calculate gamma** - View fluences and gamma maps for any log.
+    * **Anonymization** - Anonymize your logs so you can share them with others.
+
+    Example script::
+
+        from pylinac import MachineLog
+
+        log = MachineLog("tlog.bin")
+        # after loading, explore any Axis of the Varian structure
+        log.axis_data.gantry.plot_actual()  # plot the gantry position throughout treatment
+        log.fluence.gamma.calc_map(doseTA=1, distTA=1, threshold=10, resolution=0.1)
+        log.fluence.gamma.plot_map()  # show the gamma map as a matplotlib figure
+
+* `Picket Fence MLC Analysis <http://pylinac.readthedocs.org/en/stable/picketfence.html>`_ -
+    The picket fence module is meant for analyzing EPID images where a "picket fence" MLC pattern has been made.
+    Physicists regularly check MLC positioning through this test. This test can be done using film and one can
+    "eyeball" it, but this is the 21st century and we have numerous ways of quantifying such data. This module
+    attains to be one of them. It will load in an EPID dicom image and determine the MLC peaks, error of each MLC
+    pair to the picket, and give a few visual indicators for passing/warning/failing.
+
+    Features:
+
+    * **Analyze either HD or regular MLCs** - Just pass a flag and tell pylinac whether it's HD or not.
+    * **Easy-to-read pass/warn/fail overlay** - Analysis gives you easy-to-read tools for determining the status of an MLC pair.
+    * **Any Source-to-Image distance** - Whatever your clinic uses as the SID for picket fence, pylinac can account for it.
+    * **Account for panel translation** - Have an off-CAX setup? No problem. Translate your EPID and pylinac knows.
+    * **Account for panel sag** - If your EPID sags at certain angles, just tell pylinac and the results will be shifted.
+
+    Example script::
+
+        from pylinac import PicketFence
+
+        pf = PicketFence("mypf.dcm")
+        pf.analyze(tolerance=0.5, action_tolerance=0.25)
+        print(pf.return_results())
+        pf.plot_analyzed_image()
+
+* `Flatness/Symmetry Analysis <http://pylinac.readthedocs.org/en/stable/flatsym.html>`_ -
+    Analysis of Flatness & Symmetry of film or EPID images. Multiple equation definitions, in/cross plane.
+
+Documentation
+-------------
+To get started, install the package, run the demos, view the API docs, and learn the module design, visit the
+`Full Documentation <http://pylinac.readthedocs.org/>`_ on Read The Docs.
+
+Discussion
+----------
+Have questions? Ask them here on the `pylinac forum <https://groups.google.com/forum/#!forum/pylinac>`_.
+
+Contributing
+------------
+
+Contributions to pylinac can be many. The most useful things a non-programmer can contribute are images to analyze and bug reports. If
+you have VMAT images, starshot images, machine log files, CBCT DICOM files, or anything else you want analyzed, email or share them via Dropbox, Google Drive, etc: jkerns at gmail.com
+
+
+

pylinac-1.5.0/pylinac/__init__.py

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+
+__version__ = '1.5.0'
+__version_info__ = (1, 5, 0)
+
+import sys
+if sys.version_info[0] < 3:
+    raise ValueError("Pylinac is only supported on Python 3.x. It seems you are using Python 2; please use a different interpreter.")
+
+from pylinac.cbct import CBCT
+from pylinac.flatsym import BeamImage
+from pylinac.planar_imaging import LeedsTOR, PipsProQC3
+from pylinac.log_analyzer import MachineLog, MachineLogs
+from pylinac.picketfence import PicketFence
+from pylinac.starshot import Starshot
+from pylinac.vmat import VMAT
+from pylinac.winston_lutz import WinstonLutz
+from pylinac.core import decorators, geometry, image, io, mask, profile, roi, utilities