Update to use JPype 0.7 (had breaking API changes)

pyconrad/__init__.py

@@ -12,20 +12,14 @@ except:
     __version__ = 'unknown'
 
 
-from jpype import JDouble, JArray, JInt, JString, JShort, JProxy, JByte, JBoolean, JChar, JLong, JFloat, JClass, JIterator, java, JPackage, attachThreadToJVM, detachThreadFromJVM
-try:
-    from jpype import JavaException as JException
-except Exception as e:
-    from jpype import JException 
+from jpype import JDouble, JArray, JInt, JString, JShort, JProxy, JByte, JBoolean, JChar, JLong, JFloat, JClass, JIterator, java, JPackage, attachThreadToJVM, JException, detachThreadFromJVM
 import jpype
 import jpype.imports
-# TODO: deprecate PyGrid
-from ._pygrid import PyGrid
 from pyconrad._pyconrad import setup_pyconrad, start_gui, start_reconstruction_pipeline_gui, is_initialized, is_gui_started, terminate_pyconrad
-from ._autocomplete_files.autocomplete_conrad import AutoCompleteConrad
+from pyconrad._autocomplete_files.autocomplete_conrad import AutoCompleteConrad
 from pyconrad._classgetter import ClassGetter
-from .constants import java_float_dtype
-from ._autocomplete import generate_autocomplete_file
+from pyconrad.constants import java_float_dtype
+from pyconrad._autocomplete import generate_autocomplete_file
 from pyconrad._imageutils import imshow, to_conrad_grid
 import pyconrad.config
 import jpype.imports

pyconrad/_autocomplete.py

-import pyconrad
 import os
+import warnings
+
+from mock import MagicMock
+
+import pyconrad
+
 
-def generate_autocomplete_file(file, conrad_dir:str, classname:str, alsoMembers = True):
+def generate_autocomplete_file(file, conrad_dir: str, classname: str, alsoMembers=True):
 
     if not pyconrad.is_initialized():
         pyconrad.setup_pyconrad(min_ram='50M')
 
-    dir_list = [ conrad_dir ]
+    dir_list = [conrad_dir]
     with open(file, 'w') as writer:
         zero_indentation = conrad_dir.count('/') + 1
         writer.writelines('import pyconrad\r\n')
@@ -29,7 +34,7 @@ def generate_autocomplete_file(file, conrad_dir:str, classname:str, alsoMembers
                     if os.path.basename(f) != 'coneBeam':
                         writer.writelines('    ' * indentation + 'class ' + os.path.basename(f) + ':\r\n')
                 for item in os.listdir(f):
-                    dir_list.append(os.path.join(f,item))
+                    dir_list.append(os.path.join(f, item))
             if os.path.isfile(f):
                 filename, extension = os.path.splitext(os.path.basename(f))
                 if extension == '.java' and filename != 'package-info':
@@ -37,28 +42,23 @@ def generate_autocomplete_file(file, conrad_dir:str, classname:str, alsoMembers
 
                     if alsoMembers:
                         try:
-                            jclass = pyconrad.JClass(classname.replace('/','.'))
+                            jclass = pyconrad.JClass(classname.replace('/', '.'))
                             writer.writelines('    ' * indentation + 'class ' + filename + ':\r\n')
                             for member in jclass.__dict__:
                                 if member != 'class' and member[0] != '_' and member != "and" and member != "lambda":
-                                    writer.writelines('    ' * (indentation +1) + member + ' = None\r\n')
+                                    writer.writelines('    ' * (indentation + 1) + member + ' = None\r\n')
 
                         except:
-                            print("fail " + classname.replace('/','.'))
+                            print("fail " + classname.replace('/', '.'))
                             writer.writelines('    ' * indentation + filename + ' = None\r\n')
                     else:
                         writer.writelines('    ' * indentation + filename + ' = None\r\n')
 
 
-
-
 if __name__ == '__main__':
 
     generate_autocomplete_file('/home/stephan/foo.py', '/home/stephan/projects/CONRAD/src', 'AutoCompleteConrad', True)
-    print(open('/home/stephan/foo.py','r').read())
+    print(open('/home/stephan/foo.py', 'r').read())
 
-import warnings
 
-class AutoCompleteConrad(pyconrad.ClassGetter):
-    def __init__(self):
-        warnings.warn('This class should never be initialized! Use it as type hint: #type: pyconrad.AutoCompleteConrad')
+AutoCompleteConrad = MagicMock()

pyconrad/_classgetter.py

-import pyconrad
 from jpype import JPackage
+
+import pyconrad
+from pyconrad._autocomplete import AutoCompleteConrad
 from pyconrad._pyconrad import assert_pyconrad_initialization
 
 
@@ -23,57 +25,57 @@ class ClassGetter:
         self._imported_namespaces.append(namespaces)
 
     @property
-    def SimpleVector(self) -> pyconrad.AutoCompleteConrad.edu.stanford.rsl.conrad.numerics.SimpleVector:
+    def SimpleVector(self) -> AutoCompleteConrad.edu.stanford.rsl.conrad.numerics.SimpleVector:
         assert_pyconrad_initialization()
         return pyconrad.JClass('edu.stanford.rsl.conrad.numerics.SimpleVector')
 
     @property
-    def PointND(self) -> pyconrad.AutoCompleteConrad.edu.stanford.rsl.conrad.geometry.shapes.simple.PointND:
+    def PointND(self) -> AutoCompleteConrad.edu.stanford.rsl.conrad.geometry.shapes.simple.PointND:
         assert_pyconrad_initialization()
         return pyconrad.JClass('edu.stanford.rsl.conrad.geometry.shapes.simple.PointND')
 
     @property
-    def SimpleMatrix(self) -> pyconrad.AutoCompleteConrad.edu.stanford.rsl.conrad.numerics.SimpleMatrix:
+    def SimpleMatrix(self) -> AutoCompleteConrad.edu.stanford.rsl.conrad.numerics.SimpleMatrix:
         assert_pyconrad_initialization()
         return pyconrad.JClass('edu.stanford.rsl.conrad.numerics.SimpleMatrix')
 
     @property
-    def NumericGrid(self) -> pyconrad.AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.NumericGrid:
+    def NumericGrid(self) -> AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.NumericGrid:
         assert_pyconrad_initialization()
         return pyconrad.JClass('edu.stanford.rsl.conrad.data.numeric.NumericGrid')
 
     @property
-    def Grid1D(self) -> pyconrad.AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.Grid1D:
+    def Grid1D(self) -> AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.Grid1D:
         assert_pyconrad_initialization()
         return pyconrad.JClass('edu.stanford.rsl.conrad.data.numeric.Grid1D')
 
     @property
-    def Grid2D(self) -> pyconrad.AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.Grid2D:
+    def Grid2D(self) -> AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.Grid2D:
         assert_pyconrad_initialization()
         return pyconrad.JClass('edu.stanford.rsl.conrad.data.numeric.Grid2D')
 
     @property
-    def Grid3D(self) -> pyconrad.AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.Grid3D:
+    def Grid3D(self) -> AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.Grid3D:
         assert_pyconrad_initialization()
         return pyconrad.JClass('edu.stanford.rsl.conrad.data.numeric.Grid3D')
 
     @property
-    def Grid4D(self) -> pyconrad.AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.Grid4D:
+    def Grid4D(self) -> AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.Grid4D:
         assert_pyconrad_initialization()
         return pyconrad.JClass('edu.stanford.rsl.conrad.data.numeric.Grid4D')
 
     @property
-    def OpenCLGrid1D(self) -> pyconrad.AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.opencl.OpenCLGrid1D:
+    def OpenCLGrid1D(self) -> AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.opencl.OpenCLGrid1D:
         assert_pyconrad_initialization()
         return pyconrad.JClass('edu.stanford.rsl.conrad.data.numeric.opencl.OpenCLGrid1D')
 
     @property
-    def OpenCLGrid2D(self) -> pyconrad.AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.opencl.OpenCLGrid2D:
+    def OpenCLGrid2D(self) -> AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.opencl.OpenCLGrid2D:
         assert_pyconrad_initialization()
         return pyconrad.JClass('edu.stanford.rsl.conrad.data.numeric.opencl.OpenCLGrid2D')
 
     @property
-    def OpenCLGrid3D(self) -> pyconrad.AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.opencl.OpenCLGrid3D:
+    def OpenCLGrid3D(self) -> AutoCompleteConrad.edu.stanford.rsl.conrad.data.numeric.opencl.OpenCLGrid3D:
         assert_pyconrad_initialization()
         return pyconrad.JClass('edu.stanford.rsl.conrad.data.numeric.opencl.OpenCLGrid3D')
 

pyconrad/_extend_conrad_classes.py

@@ -9,20 +9,24 @@ import numpy as np
 from jpype import JArray, JClass, JDouble, JInt, JPackage, JProxy
 
 import pyconrad
+from pyconrad._java_pyconrad import JavaPyConrad
+
+from ._imageutils import ImageUtil
+from ._pygrid import PyGrid
+from .constants import java_float_dtype
+
 try:
     import pyconrad._vtk
 except Exception:
     import warnings
     warnings.warn("Could not import pyconrad._vtk")
-from pyconrad._java_pyconrad import JavaPyConrad
 
-from ._imageutils import ImageUtil
-from ._pygrid import PyGrid
-from .constants import java_float_dtype
+
+del JClass.__setattr__
 
 try:
     import pyopencl as cl
-except:
+except Exception:
     cl = None
 
 
@@ -180,6 +184,10 @@ def _extend_numeric_grid():
     def _numeric_grid_shape(self):
         return tuple(reversed(self.getSize()[:]))
 
+    @property
+    def _numeric_grid_size(self):
+        return tuple(self.getSize()[:])
+
     @property
     def _numeric_grid_ndim(self):
         return len(self.getSize()[:])
@@ -232,6 +240,7 @@ def _extend_numeric_grid():
     grid_class.__getitem__ = _numeric_grid_getitem
     grid_class.__setitem__ = _numeric_grid_setitem
     grid_class.shape = _numeric_grid_shape
+    grid_class.size = _numeric_grid_size
     grid_class.ndim = _numeric_grid_ndim
     grid_class.pygrid = _pygrid
     grid_class.__array__ = _numpy_grid

pyconrad/_pyconrad.py

@@ -10,18 +10,20 @@ import warnings
 from os.path import join
 from pathlib import Path
 
+import jpype
 from jpype import (JArray, JClass, JDouble, JPackage, JProxy,
                    attachThreadToJVM, detachThreadFromJVM, getDefaultJVMPath,
                    isJVMStarted, java, shutdownJVM, startJVM)
+
+
+from . import _download_conrad, _extend_conrad_classes
+from . import _windowlistener as wl
+
 try:
     from jpype import JavaException as JException
 except Exception as e:
     from jpype import JException
 
-import jpype
-
-from . import _download_conrad, _extend_conrad_classes
-from . import _windowlistener as wl
 
 module_path = os.path.dirname(__file__)
 
@@ -114,7 +116,7 @@ class PyConrad:
                     _download_conrad.download_conrad()
                 os.chdir(self.__conrad_path)
                 startJVM(getDefaultJVMPath(), conrad_source_and_libs,
-                         "-Xmx%s" % max_ram, "-Xmn%s" % min_ram)
+                         "-Xmx%s" % max_ram, "-Xmn%s" % min_ram, convertStrings=True)
                 os.chdir(curr_directory)
 
                 self._check_jre_version()

pyconrad/_windowlistener.py

@@ -2,11 +2,11 @@
 # Copyright (C) 2010-2017 - Andreas Maier
 # CONRAD is developed as an Open Source project under the GNU General Public License (GPL-3.0)
 
-import jpype.awt.event.WindowAdapter as wa
+
 import pyconrad
 
 
-class WindowListener(wa):
+class WindowListener:
     def __init__(self, *mth, **kw):
         object.__init__(self)
 

pyconrad/config.py

 import numpy as np
 
+from pyconrad._classgetter import ClassGetter
 import pyconrad
 
+from ._autocomplete_files.autocomplete_conrad import AutoCompleteConrad
+
 _ = pyconrad.ClassGetter(
     'edu.stanford.rsl.conrad.utils',
     'java.beans',
@@ -10,14 +13,14 @@ _ = pyconrad.ClassGetter(
 )
 
 
-def get_conf() -> pyconrad.AutoCompleteConrad.edu.stanford.rsl.conrad.utils.Configuration:
+def get_conf() -> AutoCompleteConrad.edu.stanford.rsl.conrad.utils.Configuration:
     from edu.stanford.rsl.conrad.utils import Configuration
     conf = Configuration.getGlobalConfiguration()
 
     return conf
 
 
-def get_geometry() -> pyconrad.AutoCompleteConrad.edu.stanford.rsl.conrad.geometry.trajectories.Trajectory:
+def get_geometry() -> AutoCompleteConrad.edu.stanford.rsl.conrad.geometry.trajectories.Trajectory:
     from edu.stanford.rsl.conrad.utils import Configuration
     geo = Configuration.getGlobalConfiguration().getGeometry()
     return geo

pyconrad_examples/first_steps/_3_numpy_and_conrad.py

 
 # Copyright (C) 2010-2017 - Andreas Maier
 # CONRAD is developed as an Open Source project under the GNU General Public License (GPL-3.0)
-from pyconrad import setup_pyconrad, PyGrid, java_float_dtype, JArray, JDouble, ClassGetter
+from pyconrad import setup_pyconrad, java_float_dtype, JArray, JDouble, ClassGetter
 import pyconrad
 import numpy as np
 
@@ -11,7 +11,6 @@ pyconrad.setup_pyconrad(min_ram='500M', max_ram='8G', dev_dirs=[])
 _ = ClassGetter()
 
 
-# Create PyGrid from numpy array (more efficient if using Java float type pyconrad.java_float_dtype)
 array = np.random.rand(4, 2, 3).astype(pyconrad.java_float_dtype)
 grid = _.NumericGrid.from_numpy(array)
 
@@ -75,31 +74,3 @@ np_grid3D = java_grid3D.as_numpy()
 np_grid3D2 = java_grid3D2.as_numpy()
 np_grid3D3 = java_grid3D3.as_numpy()
 
-# Create PyGrid from Grid2D
-pygrid1 = PyGrid.from_grid(phantom)
-# use Java method
-pygrid1.grid.show()
-# use Python method
-# from scipy.misc import imshow
-# imshow(pygrid1)
-
-# Create PyGrid from numpy array (must be of type pyconrad.java_float_dtype)
-array = np.random.rand(4, 2, 3).astype(java_float_dtype)
-pygrid2 = PyGrid.from_numpy(array)
-
-# Manipulate data in using CONRAD at Position (x,y,z) = (1,2,4)
-pygrid2.grid.setValue(5.0, [0, 1, 3])
-
-# Print this pixel using Python indexes [z,y,x]
-print("Before update: %f" % pygrid2[3, 1, 0])
-# Python data must be synchronized with CONRAD
-pygrid2.update_numpy()
-print("After update: %f" % pygrid2[3, 1, 0])
-
-# Manipulate pixel using python
-pygrid2[1, 1, 1] = 3.0
-# Update CONRAD data
-pygrid2.update_grid()
-
-# Print
-print(pygrid2)

setup.py

@@ -67,12 +67,12 @@ def setup_package():
           author_email='andreas.maier@fau.de',
           license='GPL 3.0',
           install_requires=[
-               'jpype1', 'numpy', 'pathlib', 'urllib3', 'pyevtk', 'setuptools', 'vtk', 'procbridge', 'cppimport'
+               'jpype1>=0.7', 'numpy', 'pathlib', 'urllib3', 'pyevtk', 'setuptools', 'vtk', 'procbridge', 'cppimport'
           ],
           extras_require={'opencl': ['pyopencl']},
           cmdclass={'install': install},
           url='https://git5.cs.fau.de/PyConrad/pyCONRAD/',
-          description='Python wrapper for CONRAD (https://www5.cs.fau.de/conrad/), a framework for cone beam radiography',
+          description='Python wrapper for CONRAD (https://www5.cs.fau.de/conrad/), a framework for cone beam radiography',  # noqa
           long_description=read('README.rst'),
           entry_points={
               'gui_scripts': [