New upstream updates

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,24 @@
+---
+name: Bug report
+about: Create a report to help us improve
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,17 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.gitlab-ci.yml

@@ -12,7 +12,7 @@ test:
     # install your own package into the environment
     - python setup.py install
     # attempt to fix DISPLAY variable errors of matplotlib's. See: https://github.com/mwaskom/seaborn/pull/97
-    - cp tests/matplotlibrc .
+    - cp tests_basic/matplotlibrc .
   script:
     - python setup.py test
 #    - coverage run --source=pylinac setup.py test
@@ -23,7 +23,7 @@ coverage:
     # install your own package into the environment
     - python setup.py install
     # attempt to fix DISPLAY variable errors of matplotlib's. See: https://github.com/mwaskom/seaborn/pull/97
-    - cp tests/matplotlibrc .
+    - cp tests_basic/matplotlibrc .
   script:
 #    - python setup.py test
     - coverage run --source=pylinac setup.py test

.travis.yml

@@ -1,8 +1,7 @@
 language: python
 python:
-  - "3.4"
-  - "3.5"
   - "3.6"
+
 env:
   - NUMPY=1.12
   - NUMPY=1.13
@@ -42,7 +41,7 @@ install:
   # install your own package into the environment
   - python setup.py install
   # attempt to fix DISPLAY variable errors of matplotlib's. See: https://github.com/mwaskom/seaborn/pull/97
-  - cp tests/matplotlibrc .
+  - cp tests_basic/matplotlibrc .
 
 # test script
 script:

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2014-2016 James Kerns
+Copyright (c) 2014-2018 James Kerns
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
 documentation files (the "Software"), to deal in the Software without restriction, including without limitation

README.rst

@@ -34,7 +34,7 @@ The web app is a proof-of-concept taking pylinac into the web!
 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 built in GUI is also straight-forward although programming experience may help identify errors.
 
-The library also contains lower-level `hackable modules & tools <http://pylinac.readthedocs.org/en/latest/pylinac_core_hacking.html>`_
+The library also contains lower-level `hackable modules & tools <http://pylinac.readthedocs.org/en/stable/pylinac_core_hacking.html>`_
 for creating your own radiation therapy algorithms.
 
 The major features of the entire package include:
@@ -54,21 +54,13 @@ To get started, install the package, run the demos, view the API docs, and learn
 Installation
 ------------
 
-Pylinac should be installed via ``conda`` if available. First, add the proper channel, then install the package:
-
-.. code-block:: bash
-
-    $ conda config --add channels jrkerns
-    $ conda install pylinac
-
-You may also install via ``pip``, although you must have C compilers to build the
-`dependencies <http://pylinac.readthedocs.io/en/latest/installation.html#dependencies>`_ :
+Iinstall via ``pip``, just check the `dependencies <http://pylinac.readthedocs.io/en/stable/installation.html#dependencies>`_ first:
 
 .. code-block:: bash
 
     $ pip install pylinac
 
-See the `Installation page <http://pylinac.readthedocs.io/en/latest/installation.html>`_ for further details.
+See the `Installation page <http://pylinac.readthedocs.io/en/stable/installation.html>`_ for further details.
 
 Tools/Quick Start Guide
 -----------------------
@@ -83,7 +75,7 @@ Below are the high-level tools currently available:
     import pylinac
     pylinac.gui()  # that simple
 
-* `Continuous & One-Time Directory Analysis <http://pylinac.readthedocs.org/en/latest/watcher.html>`_ -
+* `Continuous & One-Time Directory Analysis <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. You can also specify "source" folders to pull new files from (e.g.
    a Varian shared drive holding Trajectory logs or QA images).
@@ -104,43 +96,61 @@ Below are the high-level tools currently available:
         process("dir/to/watch")  # will run once and then return
 
    And that's it! No code to write; no fuss, no muss.
-   Analysis settings are `customizable <http://pylinac.readthedocs.org/en/latest/watcher.html#configuration>`_
+   Analysis settings are `customizable <http://pylinac.readthedocs.org/en/stable/watcher.html#configuration>`_
    and includes optional email service upon analysis.
 
-* `TG-51 Absolute Dose Calibration <http://pylinac.readthedocs.org/en/latest/tg51_docs.html>`_ -
+* `TG-51 & TRS-398 Absolute Dose Calibration <http://pylinac.readthedocs.org/en/stable/calibration_docs.html>`_ -
    Input the raw data and pylinac can calculate either individual values (kQ, PDDx, Pion, etc) or use the
    provided classes to input all measurement data and have it calculate all factors and dose values automatically.
 
    Example script:
 
    .. code-block:: python
 
-            from pylinac import tg51
-
-            tg51_6x = tg51.TG51Photon(temp=TEMP, press=PRESS, model=CHAMBER,
-                                      n_dw=ND_w, p_elec=P_ELEC,
-                                      measured_pdd=66.4, lead_foil=None,
-                                      clinical_pdd=66.5, energy=ENERGY,
-                                      volt_high=-300, volt_low=-150,
-                                      m_raw=(25.65, 25.66, 25.65),
-                                      m_opp=(25.64, 25.65, 25.65),
-                                      m_low=(25.64, 25.63, 25.63),
-                                      mu=MU, tissue_correction=1.0)
+            from pylinac import tg51, trs398
+
+            ENERGY = 6
+            TEMP = 22.1
+            PRESS = tg51.mmHg2kPa(755.0)
+            CHAMBER = '30013'  # PTW
+            P_ELEC = 1.000
+            ND_w = 5.443  # Gy/nC
+            MU = 200
+            CLINICAL_PDD = 66.5
+
+            tg51_6x = tg51.TG51Photon(
+                unit='TrueBeam1',
+                chamber=CHAMBER,
+                temp=TEMP, press=PRESS,
+                n_dw=ND_w, p_elec=P_ELEC,
+                measured_pdd10=66.4, lead_foil=None,
+                clinical_pdd10=66.5, energy=ENERGY,
+                voltage_reference=-300, voltage_reduced=-150,
+                m_reference=(25.65, 25.66, 25.65),
+                m_opposite=(25.64, 25.65, 25.65),
+                m_reduced=(25.64, 25.63, 25.63),
+                mu=MU, tissue_correction=1.0
+            )
 
             # Done!
             print(tg51_6x.dose_mu_dmax)
 
             # examine other parameters
-            tg51_6x.pddx
-            tg51_6x.kq
-            tg51_6x.p_ion
+            print(tg51_6x.pddx)
+            print(tg51_6x.kq)
+            print(tg51_6x.p_ion)
 
             # change readings if you adjust output
-            tg51_6x.m_raw = (25.44, 25.44, 25.43)
+            tg51_6x.m_reference_adjusted = (25.44, 25.44, 25.43)
             # print new dose value
-            print(tg51_6x.dose_mu_dmax)
+            print(tg51_6x.dose_mu_dmax_adjusted)
+
+            # generate a PDF for record-keeping
+            tg51_6x.publish_pdf('TB1 6MV TG-51.pdf', notes=['My notes', 'I used Pylinac to do this; so easy!'], open_file=False)
+
+            # TRS-398 is very similar and just as easy!
 
-* `Planar Phantom Analysis (Leeds TOR, StandardImaging QC-3, Las Vegas) <http://pylinac.readthedocs.org/en/latest/planar_imaging.html>`_ -
+* `Planar Phantom Analysis (Leeds TOR, StandardImaging QC-3, Las Vegas) <http://pylinac.readthedocs.org/en/stable/planar_imaging.html>`_ -
    The planar imaging module analyzes 2D phantoms. Currently the LeedsTOR kV phantom, Standard Imaging QC-3 MV phantom, and Las Vegas phantom are supported,
    and more phantoms are in the works!
 
@@ -172,7 +182,7 @@ Below are the high-level tools currently available:
         lv.plot_analyzed_image()
         lv.publish_pdf('lv.pdf', open_file=True)  # open the PDF after publishing
 
-* `Winston-Lutz Analysis <http://pylinac.readthedocs.org/en/latest/winston_lutz.html>`_ -
+* `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
@@ -204,7 +214,7 @@ Below are the high-level tools currently available:
         print(wl.results())
         wl.publish_pdf('my_wl.pdf')
 
-* `Starshot Analysis <http://pylinac.readthedocs.org/en/latest/starshot_docs.html>`_ -
+* `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>`_.
@@ -236,30 +246,28 @@ Below are the high-level tools currently available:
         star.plot_analyzed_image()  # shows a matplotlib figure
         star.publish_pdf()  # publish a PDF report
 
-* `VMAT QA <http://pylinac.readthedocs.org/en/latest/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
+* `VMAT QA <http://pylinac.readthedocs.org/en/stable/vmat_docs.html>`_ -
+    The VMAT module consists of two classes: ``DRGS`` and ``DRMLC``, which are 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.
+    * **Adjust for offsets** - Older VMAT patterns were off-center. Pylinac will find the field regardless.
 
     Example script:
 
     .. code-block:: python
 
-        from pylinac import VMAT
+        from pylinac import DRGS, DRMLC
 
-        vmat = VMAT(images=["DRGSopen.dcm", "DRGSdmlc.dcm"], delivery_types=["open", "dmlc"])
-        vmat.analyze(test='drgs', tolerance=1.5)
-        print(vmat.return_results())  # prints out ROI information
-        vmat.plot_analyzed_image()  # shows a matplotlib figure
-        vmat.publish_pdf('myvmat.pdf')  # generate a PDF report
+        drgs = DRGS(image_paths=["path/to/DRGSopen.dcm", "path/to/DRGSdmlc.dcm"])
+        drgs.analyze(tolerance=1.5)
+        print(drgs.return_results())  # prints out ROI information
+        drgs.plot_analyzed_image()  # shows a matplotlib figure
+        drgs.publish_pdf('mydrgs.pdf')  # generate a PDF report
 
-* `CT & CBCT QA <http://pylinac.readthedocs.org/en/latest/cbct_docs.html>`_ -
+* `CT & CBCT QA <http://pylinac.readthedocs.org/en/stable/cbct_docs.html>`_ -
     The CBCT module automatically analyzes DICOM images of a CatPhan 504, 503, or 600 acquired when doing CT or CBCT quality assurance. It can load a folder or zip file that
     the images are in and automatically correct for phantom setup in 6 axes.
     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
@@ -276,7 +284,7 @@ Below are the high-level tools currently available:
 
     .. code-block:: python
 
-        from pylinac import CatPhan504, CatPhan503, CatPhan600
+        from pylinac import CatPhan504, CatPhan503, CatPhan600, CatPhan604
 
         # for this example, we'll use the CatPhan504
         cbct = CatPhan504("my/cbct_image_folder")
@@ -285,7 +293,7 @@ Below are the high-level tools currently available:
         cbct.plot_analyzed_image()
         cbct.publish_pdf('mycbct.pdf')
 
-* `Log Analysis <http://pylinac.readthedocs.org/en/latest/log_analyzer.html>`_ -
+* `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.
@@ -318,7 +326,7 @@ Below are the high-level tools currently available:
         dlog = load_log("dynalog.dlg")
         ...
 
-* `Picket Fence MLC Analysis <http://pylinac.readthedocs.org/en/latest/picketfence.html>`_ -
+* `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
@@ -345,7 +353,7 @@ Below are the high-level tools currently available:
         pf.plot_analyzed_image()
         pf.publish_pdf()
 
-* `Flatness/Symmetry Analysis <http://pylinac.readthedocs.org/en/latest/flatsym.html>`_ -
+* `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.
 
 Discussion

checklist.txt

@@ -1,6 +1,7 @@
 Version Release Checklist
 
 - Run tests: tests/_test_all.py
+- See if anything needs amending in the GUI or in the watcher since those are hard to test.
 - Increment version number in:
     - setup.py,
     - pylinac/__init__.py