updated functions of matplotlib and little more

PKG-INFO

@@ -0,0 +1,57 @@
+Metadata-Version: 1.1
+Name: dicompyler
+Version: 0.4.2
+Summary: Extensible radiation therapy research platform and viewer for DICOM and DICOM RT.
+Home-page: http://code.google.com/p/dicompyler/
+Author: Aditya Panchal
+Author-email: [email protected]
+License: BSD License
+Description: 
+            dicompyler
+            ==========
+
+            dicompyler is an extensible open source radiation therapy research 
+            platform based on the DICOM standard. It also functions as a 
+            cross-platform DICOM RT viewer.
+
+            dicompyler runs on Windows, Mac and Linux systems and is available in 
+            source and binary versions. Since dicompyler is based on modular 
+            architecture, it is easy to extend it with 3rd party plugins.
+
+            Visit the dicompyler _`home page`:
+            http://code.google.com/p/dicompyler/ for how-to information and guides.
+
+            Getting Help
+            ============
+
+            To get help with dicompyler, visit the _`mailing list`: 
+            http://groups.google.com/group/dicompyler/ or follow us on _`twitter`: 
+            http://twitter.com/dicompyler
+
+            Requirements
+            ============
+
+            dicompyler requires the following packages to run from source:
+
+            - Python 2.5 or higher (not tested on Python 3)
+            - wxPython 2.8.8.1 to 2.8.10.1
+            - matplotlib 0.99 to 1.10
+            - numpy 1.2.1 or higher
+            - PIL 1.1.7 or any version of Pillow
+            - pydicom 0.9.5 or 0.9.6
+            - simplejson (only for Python 2.5, Python 2.6+ includes JSON support)
+Keywords: radiation therapy research python dicom dicom-rt
+Platform: UNKNOWN
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 2.5
+Classifier: Programming Language :: Python :: 2.6
+Classifier: Programming Language :: Python :: 2.7
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Visualization

README.txt

@@ -0,0 +1,92 @@
+dicompyler Readme
+=================
+
+dicompyler is an extensible radiation therapy research platform and viewer for
+DICOM and DICOM RT.
+
+dicompyler is released under a BSD license. See the included license.txt file,
+or available online at: http://code.google.com/p/dicompyler/
+
+Full documentation and source code for dicompyler is available online at:
+http://code.google.com/p/dicompyler/
+
+Release notes for this version can be found online at:
+http://code.google.com/p/dicompyler/wiki/ReleaseNotes
+
+Features
+========
+
+- Import CT/PET/MRI Images, DICOM RT structure set, RT dose and RT plan files
+- Extensible plugin system with included plugins:
+    - 2D image viewer with dose and structure overlay
+    - Dose volume histogram viewer with the ability to analyze DVH parameters
+    - DICOM data tree viewer
+    - Patient anonymizer
+
+Quick Start
+===========
+
+If you have downloaded dicompyler as an application for Windows or Mac, please
+follow the normal process for running any other application on your system.
+
+If you are running from a Python package, a script called "dicompyler" is now
+present on your path, which you can run from your command line or terminal.
+
+If you are running from a source checkout, there is a script in the main folder
+called "dicompyler_app.py" which can be executed via your Python interpreter.
+
+Getting Started
+===============
+
+dicompyler will read properly formatted DICOM and DICOM-RT files. To get
+started, run dicompyler and click "Open Patient" to bring up a dialog box that
+will show the DICOM files in the last selected directory. You may click
+"Browse..." to navigate to other folders that contain DICOM data.
+
+In the current version of dicompyler, you can import any DICOM CT, PET,
+or MRI image series, DICOM RT structure set, RT dose and RT plan files.
+dicompyler will automatically highlight the deepest item for the patient.
+All related items (up the tree) will be automatically imported as well.
+
+Alternatively, you can selectively import data. For example, If you only want
+to import CT images and an RT structure set just highlight the RT structure set.
+If you are importing an RT dose file and the corresponding plan does not
+contain a prescription dose, enter one in the box first. To import the data,
+click "Select" and dicompyler will process the information.
+
+Once the DICOM data has been loaded, the main window will show the patient and
+plan information. Additionally it will show a list of structures and isodoses
+that are associated with the plan.
+
+Example DICOM-RT data is provided in the downloads tab on the project homepage:
+http://code.google.com/p/dicompyler/downloads/list
+
+Included Plugins
+================
+
+You can use the 2D View tab to navigate CT, PET or MRI data with corresponding
+structures and isodoses. The DVH tab can be used to inspect and analyze DVH
+curves. The DICOM tree view tab can be used to delve into the raw DICOM data of
+the imported files. You can anonymize the loaded DICOM files via the anonymizer
+found in the File --> Export menu.
+
+Custom Plugins
+==============
+
+Since dicompyler is based on a plugin architecture, users can write their own
+plugins with ease. For more information see the Plugin Development Guide on the
+dicompyler wiki: http://code.google.com/p/dicompyler/wiki/PluginDevelopmentGuide
+
+3rd-party plugins can be found at http://code.google.com/p/dicompyler-plugins/
+
+Bugs and Feedback
+=================
+
+Please report any bugs or feedback on the dicompyler discussion group found at:
+http://groups.google.com/group/dicompyler/
+
+Credits
+=======
+
+A number of individuals have contributed to dicompyler and can be found in the
+included credits.txt.

dicompyler.egg-info/PKG-INFO

@@ -0,0 +1,57 @@
+Metadata-Version: 1.1
+Name: dicompyler
+Version: 0.4.2
+Summary: Extensible radiation therapy research platform and viewer for DICOM and DICOM RT.
+Home-page: http://code.google.com/p/dicompyler/
+Author: Aditya Panchal
+Author-email: [email protected]
+License: BSD License
+Description: 
+            dicompyler
+            ==========
+
+            dicompyler is an extensible open source radiation therapy research 
+            platform based on the DICOM standard. It also functions as a 
+            cross-platform DICOM RT viewer.
+
+            dicompyler runs on Windows, Mac and Linux systems and is available in 
+            source and binary versions. Since dicompyler is based on modular 
+            architecture, it is easy to extend it with 3rd party plugins.
+
+            Visit the dicompyler _`home page`:
+            http://code.google.com/p/dicompyler/ for how-to information and guides.
+
+            Getting Help
+            ============
+
+            To get help with dicompyler, visit the _`mailing list`: 
+            http://groups.google.com/group/dicompyler/ or follow us on _`twitter`: 
+            http://twitter.com/dicompyler
+
+            Requirements
+            ============
+
+            dicompyler requires the following packages to run from source:
+
+            - Python 2.5 or higher (not tested on Python 3)
+            - wxPython 2.8.8.1 to 2.8.10.1
+            - matplotlib 0.99 to 1.10
+            - numpy 1.2.1 or higher
+            - PIL 1.1.7 or any version of Pillow
+            - pydicom 0.9.5 or 0.9.6
+            - simplejson (only for Python 2.5, Python 2.6+ includes JSON support)
+Keywords: radiation therapy research python dicom dicom-rt
+Platform: UNKNOWN
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 2.5
+Classifier: Programming Language :: Python :: 2.6
+Classifier: Programming Language :: Python :: 2.7
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Visualization

dicompyler.egg-info/SOURCES.txt

@@ -0,0 +1,67 @@
+MANIFEST.in
+README.txt
+dicompyler_app.py
+distribute_setup.py
+setup.py
+dicompyler/__init__.py
+dicompyler/credits.txt
+dicompyler/dicomgui.py
+dicompyler/dicomparser.py
+dicompyler/dvhcalc.py
+dicompyler/dvhdata.py
+dicompyler/dvhdoses.py
+dicompyler/guidvh.py
+dicompyler/guiutil.py
+dicompyler/license.txt
+dicompyler/main.py
+dicompyler/plugin.py
+dicompyler/preferences.py
+dicompyler/util.py
+dicompyler/wxmpl.py
+dicompyler.egg-info/PKG-INFO
+dicompyler.egg-info/SOURCES.txt
+dicompyler.egg-info/dependency_links.txt
+dicompyler.egg-info/entry_points.txt
+dicompyler.egg-info/not-zip-safe
+dicompyler.egg-info/requires.txt
+dicompyler.egg-info/top_level.txt
+dicompyler/baseplugins/2dview.py
+dicompyler/baseplugins/2dview.xrc
+dicompyler/baseplugins/__init__.py
+dicompyler/baseplugins/anonymize.py
+dicompyler/baseplugins/anonymize.xrc
+dicompyler/baseplugins/dvh.py
+dicompyler/baseplugins/dvh.xrc
+dicompyler/baseplugins/quickopen.py
+dicompyler/baseplugins/treeview.py
+dicompyler/baseplugins/treeview.xrc
+dicompyler/resources/accept.png
+dicompyler/resources/book.png
+dicompyler/resources/bricks.png
+dicompyler/resources/chart_bar.png
+dicompyler/resources/chart_bar_error.png
+dicompyler/resources/chart_curve.png
+dicompyler/resources/chart_curve_error.png
+dicompyler/resources/cog.png
+dicompyler/resources/contrast_high.png
+dicompyler/resources/dicomgui.xrc
+dicompyler/resources/dicompyler.icns
+dicompyler/resources/dicompyler.ico
+dicompyler/resources/dicompyler_icon11_16.png
+dicompyler/resources/dicompyler_logo.png
+dicompyler/resources/error.png
+dicompyler/resources/folder_image.png
+dicompyler/resources/folder_user.png
+dicompyler/resources/group.png
+dicompyler/resources/guiutil.xrc
+dicompyler/resources/magnifier_zoom_in.png
+dicompyler/resources/magnifier_zoom_out.png
+dicompyler/resources/main.xrc
+dicompyler/resources/pencil.png
+dicompyler/resources/pencil_error.png
+dicompyler/resources/plugin.png
+dicompyler/resources/plugin.xrc
+dicompyler/resources/plugin_disabled.png
+dicompyler/resources/preferences.xrc
+dicompyler/resources/table_multiple.png
+dicompyler/resources/user.png

dicompyler.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+https://pydicom.googlecode.com/files/pydicom-0.9.6.zip

dicompyler.egg-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+dicompyler = dicompyler.main:start
+

dicompyler.egg-info/not-zip-safe

@@ -0,0 +1 @@
+

dicompyler.egg-info/requires.txt

@@ -0,0 +1,4 @@
+matplotlib>=0.99, <=1.1.0
+numpy>=1.2.1
+pil>=1.1.7
+pydicom>=0.9.5, <0.9.7

dicompyler.egg-info/top_level.txt

@@ -0,0 +1 @@
+dicompyler

dicompyler/dvhcalc.py

@@ -12,7 +12,7 @@
 logger = logging.getLogger('dicompyler.dvhcalc')
 import numpy as np
 import numpy.ma as ma
-import matplotlib.nxutils as nx
+from matplotlib.path import Path
 
 def get_dvh(structure, dose, limit=None, callback=None):
     """Get a calculated cumulative DVH along with the associated parameters."""
@@ -99,9 +99,9 @@ def calculate_dvh(structure, dose, limit=None, callback=None):
             # depending if the contour is within the largest contour or not
             else:
                 contour['inside'] = False
+                path = Path(np.array(contours[largestIndex]['data']))
                 for point in contour['data']:
-                    if nx.pnpoly(point[0], point[1],
-                                 np.array(contours[largestIndex]['data'])):
+                    if path.contains_point([(point[0], point[1])]):
                         contour['inside'] = True
                         # Assume if one point is inside, all will be inside
                         break
@@ -160,8 +160,8 @@ def calculate_contour_areas(plane):
 
 def get_contour_mask(doselut, dosegridpoints, contour):
     """Get the mask for the contour with respect to the dose plane."""
-
-    grid = nx.points_inside_poly(dosegridpoints, contour)
+    path = Path(np.array(contour))
+    grid = path.contains_points(dosegridpoints)
     grid = grid.reshape((len(doselut[1]), len(doselut[0])))
 
     return grid

dicompyler/guiutil.py

@@ -78,12 +78,12 @@ def convert_pil_to_wx(pil, alpha=True):
         Code taken from Dave Witten's imViewer-Simple.py in pydicom contrib."""
     if alpha:
         image = apply(wx.EmptyImage, pil.size)
-        image.SetData(pil.convert("RGB").tostring())
-        image.SetAlphaData(pil.convert("RGBA").tostring()[3::4])
+        image.SetData(pil.convert("RGB").tobytes())
+        image.SetAlphaData(pil.convert("RGBA").tobytes()[3::4])
     else:
         image = wx.EmptyImage(pil.size[0], pil.size[1])
         new_image = pil.convert('RGB')
-        data = new_image.tostring()
+        data = new_image.tobytes()
         image.SetData(data)
     return image
 
@@ -114,7 +114,7 @@ def __init__(self):
         pre = wx.PreDialog()
         # the Create step is done by XRC.
         self.PostCreate(pre)
-    
+
     def Init(self, res, title=None):
         """Method called after the dialog has been initialized."""
 

dicompyler/wxmpl.py

@@ -22,7 +22,7 @@
 import matplotlib
 matplotlib.use('WXAgg')
 import numpy as np
-from matplotlib.axes import _process_plot_var_args
+from matplotlib.axes._base import _process_plot_var_args
 from matplotlib.backends.backend_agg import RendererAgg
 from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg
 from matplotlib.figure import Figure
@@ -2024,4 +2024,3 @@ def getY(self):
         there is no data available.
         """
         return None
-