def create_overlay(mask):
'''Create a bitmask overlay from a numpy boolean array
mask - boolean numpy array organized as i,j = y,x
'''
assert mask.ndim == 2
mask = mask.transpose()
strides = np.array([1, mask.shape[0]])
imgFactory = J.make_instance(
"net/imglib2/img/planar/PlanarImgFactory", "()V")
bit_type = J.make_instance("net/imglib2/type/logic/BitType", "()V")
img = J.call(
imgFactory, "create",
"([JLnet/imglib2/type/NativeType;)Lnet/imglib2/img/planar/PlanarImg;",
np.array(mask.shape), bit_type)
J.static_call("net/imglib2/util/ImgUtil",
"copy", "([ZI[ILnet/imglib2/img/Img;)V",
mask.flatten(), 0, strides, img)
roi = J.make_instance(
"net/imglib2/roi/BinaryMaskRegionOfInterest",
"(Lnet/imglib2/img/Img;)V", img)
overlay = J.make_instance(
"imagej/data/roi/BinaryMaskOverlay",
"(Lnet/imglib2/roi/BinaryMaskRegionOfInterest;)V", roi)
return overlay
def create_dataset(context, pixel_data, name=None, axes=None):
"""Create a dataset from a numpy array
pixel_data - numpy array where index 0 is the I or Y axis, index 1 is the
J or X axis and index 2, if it exists, is the channel axis.
name - optional name for the dataset
"""
dataset_service = get_dataset_service(context)
if axes is None:
if pixel_data.ndim == 2:
axes = [Axes().X, Axes().Y]
pixel_data = pixel_data.transpose((1, 0))
else:
axes = [Axes().X, Axes().Y, Axes().CHANNEL]
pixel_data = pixel_data.transpose((1, 0, 2))
#
# Create a dataset of the correct shape, with the correct axes.
# We make a 64-bit floating point image.
#
dataset = dataset_service.create1(np.array(pixel_data.shape), name, axes, 64, True, True)
imgplus = dataset.getImgPlus()
#
# Now use a copying utility to fill the imgplus with array data
#
strides = np.cumprod([1] + list(pixel_data.shape[:0:-1]))[::-1]
J.static_call(
"net/imglib2/util/ImgUtil", "copy", "([DI[ILnet/imglib2/img/Img;)V", pixel_data.flatten(), 0, strides, imgplus
)
return dataset
def create_dataset(context, pixel_data, name=None, axes=None):
'''Create a dataset from a numpy array
pixel_data - numpy array where index 0 is the I or Y axis, index 1 is the
J or X axis and index 2, if it exists, is the channel axis.
name - optional name for the dataset
'''
dataset_service = get_dataset_service(context)
if axes is None:
if pixel_data.ndim == 2:
axes = [Axes().X, Axes().Y]
pixel_data = pixel_data.transpose((1, 0))
else:
axes = [Axes().X, Axes().Y, Axes().CHANNEL]
pixel_data = pixel_data.transpose((1, 0, 2))
#
# Create a dataset of the correct shape, with the correct axes.
# We make a 64-bit floating point image.
#
dataset = dataset_service.create1(np.array(pixel_data.shape), name, axes,
64, True, True)
imgplus = dataset.getImgPlus()
#
# Now use a copying utility to fill the imgplus with array data
#
strides = np.cumprod([1] + list(pixel_data.shape[:0:-1]))[::-1]
J.static_call("net/imglib2/util/ImgUtil", "copy",
"([DI[ILnet/imglib2/img/Img;)V", pixel_data.flatten(), 0,
strides, imgplus)
return dataset
def run(self, module,
pre = None,
post = None,
separateThread = False,
**kwargs):
'''Run a module
module - the module to run
pre - list of PreprocessorPlugins to run before running module
post - list of PostprocessorPlugins to run after running module
*kwargs - names and values for input parameters
'''
input_map = J.get_dictionary_wrapper(
J.make_instance('java/util/HashMap', '()V'))
for k,v in kwargs.iteritems():
input_map.put(k, v)
if pre is not None:
pre = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
pre)
if post is not None:
post = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
post)
future = J.call(
self.o, "run",
"(Limagej/ext/module/Module;Ljava/util/List;Ljava/util/List;Ljava/util/Map;)Ljava/util/concurrent/Future;",
module, pre, post, input_map)
return J.call(
self.o, "waitFor",
"(Ljava/util/concurrent/Future;)Limagej/ext/module/Module;",
future)
def run(self, module_info,
pre = None,
post = None,
**kwargs):
'''Run a module
module_info - the module_info of the module to run
pre - list of PreprocessorPlugins to run before running module
post - list of PostprocessorPlugins to run after running module
*kwargs - names and values for input parameters
'''
input_map = J.make_map(kwargs)
if pre is not None:
pre = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
pre)
if post is not None:
post = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
post)
future = J.call(
self.o, "run",
"(Limagej/module/ModuleInfo;"
"Ljava/util/List;"
"Ljava/util/List;"
"Ljava/util/Map;)"
"Ljava/util/concurrent/Future;",
module_info, pre, post, input_map)
return J.call(
self.o, "waitFor",
"(Ljava/util/concurrent/Future;)Limagej/module/Module;",
future)
def fn(command=command, options=options):
if options is None:
J.static_call("ij/IJ", "run", "(Ljava/lang/String;)V", command)
else:
J.static_call("ij/IJ", "run",
"(Ljava/lang/String;Ljava/lang/String;)V",
command, options)
def create_dataset(pixel_data, name = None, axes = None):
'''Create a dataset from a numpy array
pixel_data - numpy array where index 0 is the I or Y axis, index 1 is the
J or X axis and index 2, if it exists, is the channel axis.
name - optional name for the dataset
'''
if axes is None:
if pixel_data.ndim == 2:
axes = [Axes().X, Axes().Y]
pixel_data = pixel_data.transpose((1,0))
else:
axes = [Axes().X, Axes().Y, Axes().CHANNEL]
pixel_data = pixel_data.transpose((1,0,2))
#
# Create a dataset of the correct shape, with the correct axes.
# We make a 64-bit floating point image.
#
dataset = J.static_call(
"imagej/data/Dataset",
"create",
"([JLjava/lang/String;[Lnet/imglib2/img/Axis;IZZ)Limagej/data/Dataset;",
np.array(pixel_data.shape), name, axes, 64, True, True)
dataset = wrap_dataset(dataset)
imgplus = dataset.getImgPlus()
#
# Now use a copying utility to fill the imgplus with array data
#
strides = np.cumprod([1] + list(pixel_data.shape[:-1]))
J.static_call("net/imglib2/util/ImgUtil", "copy",
"([DI[ILnet/imglib2/img/Img;)V",
pixel_data.flatten(), 0, strides, imgplus)
return dataset
def create_overlay(mask):
'''Create a bitmask overlay from a numpy boolean array
mask - boolean numpy array organized as i,j = y,x
'''
assert mask.ndim == 2
mask = mask.transpose()
strides = np.array([1, mask.shape[0]])
imgFactory = J.make_instance("net/imglib2/img/planar/PlanarImgFactory",
"()V")
bit_type = J.make_instance("net/imglib2/type/logic/BitType", "()V")
img = J.call(
imgFactory, "create",
"([JLnet/imglib2/type/NativeType;)Lnet/imglib2/img/planar/PlanarImg;",
np.array(mask.shape), bit_type)
J.static_call("net/imglib2/util/ImgUtil", "copy",
"([ZI[ILnet/imglib2/img/Img;)V", mask.flatten(), 0, strides,
img)
roi = J.make_instance("net/imglib2/roi/BinaryMaskRegionOfInterest",
"(Lnet/imglib2/img/Img;)V", img)
overlay = J.make_instance(
"imagej/data/roi/BinaryMaskOverlay",
"(Lnet/imglib2/roi/BinaryMaskRegionOfInterest;)V", roi)
return overlay
def fn(command=command, options=options):
if options is None:
J.static_call("ij/IJ", "run", "(Ljava/lang/String;)V", command)
else:
J.static_call("ij/IJ", "run",
"(Ljava/lang/String;Ljava/lang/String;)V", command,
options)
def get_commands():
'''Return a list of the available command strings'''
hashtable = J.static_call('ij/Menus', 'getCommands',
'()Ljava/util/Hashtable;')
if hashtable is None:
#
# This is a little bogus, but works - trick IJ into initializing
#
execute_command("pleaseignorethis")
hashtable = J.static_call('ij/Menus', 'getCommands',
'()Ljava/util/Hashtable;')
if hashtable is None:
return []
keys = J.call(hashtable, "keys", "()Ljava/util/Enumeration;")
keys = J.jenumeration_to_string_list(keys)
values = J.call(hashtable, "values", "()Ljava/util/Collection;")
values = [
J.to_string(x) for x in J.iterate_java(
J.call(values, 'iterator', "()Ljava/util/Iterator;"))
]
class CommandList(list):
def __init__(self):
super(CommandList, self).__init__(keys)
self.values = values
return CommandList()
def run(self, module_info, pre=None, post=None, **kwargs):
'''Run a module
module_info - the module_info of the module to run
pre - list of PreprocessorPlugins to run before running module
post - list of PostprocessorPlugins to run after running module
*kwargs - names and values for input parameters
'''
input_map = J.make_map(kwargs)
if pre is not None:
pre = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
pre)
if post is not None:
post = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
post)
future = J.call(
self.o, "run", "(Limagej/module/ModuleInfo;"
"Ljava/util/List;"
"Ljava/util/List;"
"Ljava/util/Map;)"
"Ljava/util/concurrent/Future;", module_info, pre, post,
input_map)
return J.call(
self.o, "waitFor",
"(Ljava/util/concurrent/Future;)Limagej/module/Module;",
future)
def copy_plane(index, src):
p = J.call(planar_img, "getPlane", "(I)Ljava/lang/Object;", index)
dest = J.call(p, "getCurrentStorageArray", "()Ljava/lang/Object;")
length = np.prod(src.shape)
src = J.get_nice_arg(src, "[D")
J.static_call("java/lang/System", "arraycopy",
"(Ljava/lang/Object;ILjava/lang/Object;II)V", src, 0,
dest, 0, length)
def update_never_remind():
"""Tell ImageJ never to remind us of updates
Not as harsh as it sounds - this is done with headless preferences
which go to /dev/null.
"""
never = J.get_static_field("java/lang/Long", "MAX_VALUE", "J")
J.static_call("imagej/updater/core/UpToDate", "setLatestNag", "(J)V", never)
def execute_command(command, options = None):
'''Execute the named command within ImageJ'''
if options is None:
J.static_call("ij/IJ", "run", "(Ljava/lang/String;)V", command)
else:
J.static_call("ij/IJ", "run",
"(Ljava/lang/String;Ljava/lang/String;)V",
command, options)
def execute_command(command, options=None):
'''Execute the named command within ImageJ'''
if options is None:
J.static_call("ij/IJ", "run", "(Ljava/lang/String;)V", command)
else:
J.static_call("ij/IJ", "run",
"(Ljava/lang/String;Ljava/lang/String;)V", command,
options)
def copy_plane(index, src):
p = J.call(planar_img, "getPlane", "(I)Ljava/lang/Object;", index)
dest = J.call(p, "getCurrentStorageArray", "()Ljava/lang/Object;")
length = np.prod(src.shape)
src = J.get_nice_arg(src, "[D")
J.static_call("java/lang/System", "arraycopy",
"(Ljava/lang/Object;ILjava/lang/Object;II)V",
src, 0, dest, 0, length)
def update_never_remind():
'''Tell ImageJ never to remind us of updates
Not as harsh as it sounds - this is done with headless preferences
which go to /dev/null.
'''
never = J.get_static_field("java/lang/Long", "MAX_VALUE", "J")
J.static_call("imagej/updater/core/UpToDate", "setLatestNag", "(J)V",
never)
def __exit__(self, type_class, value, traceback):
if self.rdr is not None:
self.rdr.close()
del self.rdr.o
del self.rdr
if self.stream is not None:
jutil.call(self.stream, 'close', '()V')
del self.stream
#
# Run the Java garbage collector here.
#
jutil.static_call("java/lang/System", "gc","()V")
def __exit__(self, type_class, value, traceback):
if self.rdr is not None:
self.rdr.close()
del self.rdr.o
del self.rdr
if self.stream is not None:
jutil.call(self.stream, 'close', '()V')
del self.stream
#
# Run the Java garbage collector here.
#
jutil.static_call("java/lang/System", "gc", "()V")
def execute_macro(macro_text):
'''Execute a macro in ImageJ
macro_text - the macro program to be run
'''
if sys.platform == "darwin":
J.set_static_field("ij/macro/Interpreter", "batchMode", "Z", True)
J.static_call("ij/IJ", "runMacro",
"(Ljava/lang/String;)Ljava/lang/String;", macro_text)
else:
show_imagej()
interp = J.make_instance("ij/macro/Interpreter", "()V")
J.call(interp, "run", "(Ljava/lang/String;)V", macro_text)
def get_pixel_data(img):
"""Get the pixel data from an image"""
interval = wrap_interval(img)
dims = interval.dimensions()
#
# Make a Java double array
#
a = np.zeros(np.prod(dims), np.float64)
ja = J.get_env().make_double_array(np.ascontiguousarray(a))
strides = np.cumprod([1] + dims[:0:-1]).astype(int)[::-1]
J.static_call("net/imglib2/util/ImgUtil", "copy", "(Lnet/imglib2/img/Img;[DI[I)V", img, ja, 0, strides)
a = J.get_env().get_double_array_elements(ja)
a.shape = dims
return a
def execute_macro(macro_text):
'''Execute a macro in ImageJ
macro_text - the macro program to be run
'''
if sys.platform == "darwin":
J.set_static_field("ij/macro/Interpreter", "batchMode", "Z", True)
J.static_call("ij/IJ", "runMacro",
"(Ljava/lang/String;)Ljava/lang/String;",
macro_text)
else:
show_imagej();
interp = J.make_instance("ij/macro/Interpreter","()V");
J.call(interp, "run","(Ljava/lang/String;)V", macro_text);
def get_context():
'''Get the ImageJ context
This is a singleton ImageJ context. We need a singleton for now because
of http://trac.imagej.net/ticket/1413
This is an imagej.ImageJ, which at one point was the context.
Call self.getContext() to get the org.scijava.Context which may be
what you want.
'''
global the_imagej_context
if the_imagej_context is None:
the_imagej_context = create_context(None)
#
# We have to turn off the updater and tell ImageJ to never call
# System.exit. We have to tell ImageJ that we read the readme file.
#
# To Do: programatically turn off the updater and take control of
# the quitting and exit process.
#
max_value = J.run_script(
"java.lang.Long.toString(java.lang.Long.MAX_VALUE);")
prefs = [("imagej.updater.core.UpToDate", "latestNag", max_value),
("imagej.core.options.OptionsMisc", "exitWhenQuitting",
"false")]
plugin_service = the_imagej_context.getService(
"org.scijava.plugin.PluginService")
ui_interface = J.class_for_name("imagej.ui.UserInterface")
script = """
var result = java.lang.System.getProperty('ij.ui');
if (! result) {
var infos = pluginService.getPluginsOfType(ui_interface);
if (infos.size() > 0) {
result = infos.get(0).getClassName();
}
}
result;"""
ui_class = J.run_script(
script,
dict(pluginService=plugin_service, ui_interface=ui_interface))
first_run = "firstRun-" + the_imagej_context.getVersion()
if ui_class:
prefs.append((ui_class, first_run, "false"))
for class_name, key, value in prefs:
c = J.class_for_name(class_name)
J.static_call(
"imagej/util/Prefs", "put",
"(Ljava/lang/Class;Ljava/lang/String;Ljava/lang/String;)V", c,
key, value)
return the_imagej_context
def get_pixel_data(img):
'''Get the pixel data from an image'''
interval = wrap_interval(img)
dims = interval.dimensions()
#
# Make a Java double array
#
a = np.zeros(np.prod(dims), np.float64)
ja = J.get_env().make_double_array(np.ascontiguousarray(a))
strides = np.cumprod([1] + dims[:0:-1]).astype(int)[::-1]
J.static_call("net/imglib2/util/ImgUtil", "copy",
"(Lnet/imglib2/img/Img;[DI[I)V", img, ja, 0, strides)
a = J.get_env().get_double_array_elements(ja)
a.shape = dims
return a
def close_all_windows():
"""Close all ImageJ windows
Hide the ImageJ windows so that they don't go through the Save dialog,
then call the Window Manager's closeAllWindows to get the rest.
"""
jimage_list = J.static_call("ij/WindowManager", "getIDList", "()[I")
if jimage_list is None:
return
image_list = J.get_env().get_int_array_elements(jimage_list)
for image_id in image_list:
ip = J.static_call("ij/WindowManager", "getImage", "(I)Lij/ImagePlus;", image_id)
ip = get_imageplus_wrapper(ip)
ip.hide()
J.static_call("ij/WindowManager", "closeAllWindows", "()Z")
def get_context():
'''Get the ImageJ context
This is a singleton ImageJ context. We need a singleton for now because
of http://trac.imagej.net/ticket/1413
This is an imagej.ImageJ, which at one point was the context.
Call self.getContext() to get the org.scijava.Context which may be
what you want.
'''
global the_imagej_context
if the_imagej_context is None:
the_imagej_context = create_context(None)
#
# We have to turn off the updater and tell ImageJ to never call
# System.exit. We have to tell ImageJ that we read the readme file.
#
# To Do: programatically turn off the updater and take control of
# the quitting and exit process.
#
max_value = J.run_script(
"java.lang.Long.toString(java.lang.Long.MAX_VALUE);")
prefs = [
("imagej.updater.core.UpToDate", "latestNag", max_value),
("imagej.core.options.OptionsMisc", "exitWhenQuitting", "false")]
plugin_service = the_imagej_context.getService(
"org.scijava.plugin.PluginService")
ui_interface = J.class_for_name("imagej.ui.UserInterface")
script = """
var result = java.lang.System.getProperty('ij.ui');
if (! result) {
var infos = pluginService.getPluginsOfType(ui_interface);
if (infos.size() > 0) {
result = infos.get(0).getClassName();
}
}
result;"""
ui_class = J.run_script(script, dict(pluginService=plugin_service,
ui_interface=ui_interface))
first_run = "firstRun-"+the_imagej_context.getVersion()
if ui_class:
prefs.append((ui_class, first_run, "false"))
for class_name, key, value in prefs:
c = J.class_for_name(class_name)
J.static_call(
"imagej/util/Prefs", "put",
"(Ljava/lang/Class;Ljava/lang/String;Ljava/lang/String;)V",
c, key, value)
return the_imagej_context
def close_all_windows():
'''Close all ImageJ windows
Hide the ImageJ windows so that they don't go through the Save dialog,
then call the Window Manager's closeAllWindows to get the rest.
'''
jimage_list = J.static_call('ij/WindowManager', 'getIDList', '()[I')
if jimage_list is None:
return
image_list = J.get_env().get_int_array_elements(jimage_list)
for image_id in image_list:
ip = J.static_call('ij/WindowManager', 'getImage',
'(I)Lij/ImagePlus;', image_id)
ip = get_imageplus_wrapper(ip)
ip.hide()
J.static_call('ij/WindowManager', 'closeAllWindows', '()Z')
def get_current_image():
"""Get the WindowManager's current image
returns a wrapped ImagePlus object
"""
imageplus_obj = J.static_call("ij/WindowManager", "getCurrentImage", "()Lij/ImagePlus;")
return get_imageplus_wrapper(imageplus_obj)
def getGrayColorSpace():
"""Get a Java object that represents an RGB color space
See java.awt.color.ColorSpace: this returns the linear RGB color space
"""
cs_gray = jutil.get_static_field("java/awt/color/ColorSpace", "CS_GRAY", "I")
return jutil.static_call("java/awt/color/ColorSpace", "getInstance", "(I)Ljava/awt/color/ColorSpace;", cs_gray)
def show_imagej():
'''Show the ImageJ user interface'''
ij_obj = J.static_call("ij/IJ", "getInstance", "()Lij/ImageJ;")
if ij_obj is None:
ij_obj = J.make_instance("ij/ImageJ", "()V")
J.call(ij_obj, "setVisible", "(Z)V", True)
J.call(ij_obj, "toFront", "()V")
def createOMEXMLMetadata():
'''Creates an OME-XML metadata object using reflection, to avoid direct
dependencies on the optional loci.formats.ome package.
'''
return jutil.static_call('loci/formats/MetadataTools',
'createOMEXMLMetadata',
'()Lloci/formats/meta/IMetadata;')
def show_imagej():
'''Show the ImageJ user interface'''
ij_obj = J.static_call("ij/IJ", "getInstance", "()Lij/ImageJ;")
if ij_obj is None:
ij_obj = J.make_instance("ij/ImageJ", "()V")
J.call(ij_obj, "setVisible", "(Z)V", True)
J.call(ij_obj, "toFront", "()V")
def close_all_windows():
'''Close all ImageJ windows
Hide the ImageJ windows so that they don't go through the Save dialog,
then call the Window Manager's closeAllWindows to get the rest.
'''
jimage_list = J.static_call('ij/WindowManager', 'getIDList', '()[I')
if jimage_list is None:
return
image_list = J.get_env().get_int_array_elements(jimage_list)
for image_id in image_list:
ip = J.static_call('ij/WindowManager', 'getImage', '(I)Lij/ImagePlus;',
image_id)
ip = get_imageplus_wrapper(ip)
ip.hide()
J.static_call('ij/WindowManager', 'closeAllWindows', '()Z')
def get_current_image():
'''Get the WindowManager's current image
returns a wrapped ImagePlus object
'''
imageplus_obj = J.static_call('ij/WindowManager', 'getCurrentImage',
'()Lij/ImagePlus;')
return get_imageplus_wrapper(imageplus_obj)
def get_current_image():
'''Get the WindowManager's current image
returns a wrapped ImagePlus object
'''
imageplus_obj = J.static_call('ij/WindowManager','getCurrentImage',
'()Lij/ImagePlus;')
return get_imageplus_wrapper(imageplus_obj)
def make_color_rgb_from_html(s):
'''Make an imagej.util.ColorRGB from an HTML color
HTML colors have the form, #rrggbb or are one of the names
from the CSS-3 colors.
'''
return J.static_call("fromHTMLColor",
"(Ljava/lang/String;)Limagej/util/ColorRGB;", s)
def make_color_rgb_from_html(s):
'''Make an imagej.util.ColorRGB from an HTML color
HTML colors have the form, #rrggbb or are one of the names
from the CSS-3 colors.
'''
return J.static_call("fromHTMLColor",
"(Ljava/lang/String;)Limagej/util/ColorRGB;", s)
def test_01_09_jdictionary_to_string_dictionary(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
d = J.get_dictionary_wrapper(properties)
pyd = J.jdictionary_to_string_dictionary(properties)
keys = J.jenumeration_to_string_list(d.keys())
for key in keys:
value = J.to_string(d.get(key))
self.assertEqual(pyd[key], value)
def test_01_08_jenumeration_to_string_list(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
d = J.get_dictionary_wrapper(properties)
keys = J.jenumeration_to_string_list(d.keys())
enum = J.get_enumeration_wrapper(d.keys())
for i in range(d.size()):
key = J.to_string(enum.nextElement())
self.assertEqual(key, keys[i])
def getGrayColorSpace():
'''Get a Java object that represents an RGB color space
See java.awt.color.ColorSpace: this returns the linear RGB color space
'''
cs_gray = jutil.get_static_field('java/awt/color/ColorSpace', 'CS_GRAY',
'I')
return jutil.static_call('java/awt/color/ColorSpace', 'getInstance',
'(I)Ljava/awt/color/ColorSpace;', cs_gray)
def test_01_09_jdictionary_to_string_dictionary(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
d = J.get_dictionary_wrapper(properties)
pyd = J.jdictionary_to_string_dictionary(properties)
keys = J.jenumeration_to_string_list(d.keys())
for key in keys:
value = J.to_string(d.get(key))
self.assertEqual(pyd[key], value)
def test_01_08_jenumeration_to_string_list(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
d = J.get_dictionary_wrapper(properties)
keys = J.jenumeration_to_string_list(d.keys())
enum = J.get_enumeration_wrapper(d.keys())
for i in range(d.size()):
key = J.to_string(enum.nextElement())
self.assertEqual(key, keys[i])
def get_bit_data(img):
'''Get the pixel data from a binary mask
returns a Numpy array of boolean type
'''
interval = wrap_interval(img)
dims = interval.dimensions()
#
# Make a Java boolean array
#
a = np.zeros(np.prod(dims), np.float64)
ja = J.get_env().make_boolean_array(np.ascontiguousarray(a))
strides = np.cumprod([1] + dims[:0:-1]).astype(int)[::-1]
J.static_call("net/imglib2/util/ImgUtil", "copy",
"(Lnet/imglib2/img/Img;[ZI[I)V",
img, ja, 0, strides)
a = J.get_env().get_boolean_array_elements(ja)
a.shape = dims
return a
def create_overlay(context, mask):
"""Create a bitmask overlay from a numpy boolean array
mask - boolean numpy array organized as i,j = y,x
"""
assert mask.ndim == 2
mask = mask.transpose()
strides = np.array([mask.shape[1], 1], int)
img = make_bit_img(mask.shape)
J.static_call("net/imglib2/util/ImgUtil", "copy", "([ZI[ILnet/imglib2/img/Img;)V", mask.flatten(), 0, strides, img)
roi = J.make_instance("net/imglib2/roi/BinaryMaskRegionOfInterest", "(Lnet/imglib2/img/Img;)V", img)
overlay = J.make_instance(
"imagej/data/overlay/BinaryMaskOverlay",
"(Lorg/scijava/Context;Lnet/imglib2/roi/BinaryMaskRegionOfInterest;)V",
context.getContext(),
roi,
)
return overlay
def getGrayColorSpace():
'''Get a Java object that represents an RGB color space
See java.awt.color.ColorSpace: this returns the linear RGB color space
'''
cs_gray = jutil.get_static_field('java/awt/color/ColorSpace',
'CS_GRAY', 'I')
return jutil.static_call('java/awt/color/ColorSpace', 'getInstance',
'(I)Ljava/awt/color/ColorSpace;',
cs_gray)
def create_overlay(context, mask):
'''Create a bitmask overlay from a numpy boolean array
mask - boolean numpy array organized as i,j = y,x
'''
assert mask.ndim == 2
mask = mask.transpose()
strides = np.array([mask.shape[1], 1], int)
img = make_bit_img(mask.shape)
J.static_call("net/imglib2/util/ImgUtil", "copy",
"([ZI[ILnet/imglib2/img/Img;)V", mask.flatten(), 0, strides,
img)
roi = J.make_instance("net/imglib2/roi/BinaryMaskRegionOfInterest",
"(Lnet/imglib2/img/Img;)V", img)
overlay = J.make_instance(
"imagej/data/overlay/BinaryMaskOverlay",
"(Lorg/scijava/Context;Lnet/imglib2/roi/BinaryMaskRegionOfInterest;)V",
context.getContext(), roi)
return overlay
def test_01_06_get_enumeration_wrapper(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
keys = J.call(properties, "keys", "()Ljava/util/Enumeration;")
enum = J.get_enumeration_wrapper(keys)
has_java_vm_name = False
while (enum.hasMoreElements()):
key = J.to_string(enum.nextElement())
if key == "java.vm.name":
has_java_vm_name = True
self.assertTrue(has_java_vm_name)
def test_01_06_get_enumeration_wrapper(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
keys = J.call(properties, "keys", "()Ljava/util/Enumeration;")
enum = J.get_enumeration_wrapper(keys)
has_java_vm_name = False
while(enum.hasMoreElements()):
key = J.to_string(enum.nextElement())
if key == "java.vm.name":
has_java_vm_name = True
self.assertTrue(has_java_vm_name)
def get_output_fields_and_parameters(plugin):
'''Get the output parameters from a plugin
plugin - a Runnable plugin with @parameter annotations
returns a dictionary of field name and wrapped parameter
'''
parameters = J.static_call(
PARAMETER_HANDLER_CLASS, 'getOutputParameters',
'(L%(RUNNABLE_CLASS)s;)L%(ITERABLE_CLASS)s;' % globals(), plugin)
return get_fields_and_parameters_from_iterator(parameters)
def get_output_fields_and_parameters(plugin):
'''Get the output parameters from a plugin
plugin - a Runnable plugin with @parameter annotations
returns a dictionary of field name and wrapped parameter
'''
parameters = J.static_call(PARAMETER_HANDLER_CLASS,
'getOutputParameters',
'(L%(RUNNABLE_CLASS)s;)L%(ITERABLE_CLASS)s;' %
globals(), plugin)
return get_fields_and_parameters_from_iterator(parameters)
def fn():
hashtable = J.static_call('ij/Menus', 'getCommands',
'()Ljava/util/Hashtable;')
if hashtable is None:
#
# This is a little bogus, but works - trick IJ into initializing
#
execute_command("pleaseignorethis")
hashtable = J.static_call('ij/Menus', 'getCommands',
'()Ljava/util/Hashtable;')
if hashtable is None:
return []
keys = J.call(hashtable, "keys", "()Ljava/util/Enumeration;")
keys = J.jenumeration_to_string_list(keys)
values = J.call(hashtable, "values", "()Ljava/util/Collection;")
values = [J.to_string(x) for x in J.iterate_java(
J.call(values, 'iterator', "()Ljava/util/Iterator;"))]
class CommandList(list):
def __init__(self):
super(CommandList, self).__init__(keys)
self.values = values
return CommandList()
def create_mask(display):
'''Create a binary mask from a sequence of overlays
display - an image display
returns a binary mask
'''
jmask = J.static_call(
"org/cellprofiler/ijutils/OverlayUtils", "extractMask",
"(Limagej/data/display/ImageDisplay;)Lnet/imglib2/img/Img;", display.o)
if jmask is None:
return None
return get_bit_data(jmask)
def create_mask(display):
'''Create a binary mask from a sequence of overlays
display - an image display
returns a binary mask
'''
jmask = J.static_call(
"org/cellprofiler/ijutils/OverlayUtils",
"extractMask",
"(Limagej/data/display/ImageDisplay;)Lnet/imglib2/img/Img;",
display.o)
if jmask is None:
return None
return get_bit_data(jmask)
def setPixelsDimensionOrder(self, dimension_order, imageIndex, binDataIndex):
'''Set the dimension order for a series'''
# Post loci_tools 4.2 - use ome.xml.model.DimensionOrder
try:
jdimension_order = jutil.static_call(
'ome/xml/model/enums/DimensionOrder', 'fromString',
'(Ljava/lang/String;)Lome/xml/model/enums/DimensionOrder;',
dimension_order)
jutil.call(self.o, 'setPixelsDimensionOrder',
'(Lome/xml/model/enums/DimensionOrder;I)V',
jdimension_order, imageIndex)
except jutil.JavaException:
jutil.call(self.o, 'setPixelsDimensionOrder',
'(Ljava/lang/String;II)V',
dimension_order, imageIndex, binDataIndex)
def run(self,
module,
pre=None,
post=None,
separateThread=False,
**kwargs):
'''Run a module
module - the module to run
pre - list of PreprocessorPlugins to run before running module
post - list of PostprocessorPlugins to run after running module
*kwargs - names and values for input parameters
'''
input_map = J.get_dictionary_wrapper(
J.make_instance('java/util/HashMap', '()V'))
for k, v in kwargs.iteritems():
input_map.put(k, v)
if pre is not None:
pre = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
pre)
if post is not None:
post = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
post)
future = J.call(
self.o, "run",
"(Limagej/ext/module/Module;Ljava/util/List;Ljava/util/List;Ljava/util/Map;)Ljava/util/concurrent/Future;",
module, pre, post, input_map)
return J.call(
self.o, "waitFor",
"(Ljava/util/concurrent/Future;)Limagej/ext/module/Module;",
future)
def setPixelsDimensionOrder(self, dimension_order, imageIndex,
binDataIndex):
'''Set the dimension order for a series'''
# Post loci_tools 4.2 - use ome.xml.model.DimensionOrder
try:
jdimension_order = jutil.static_call(
'ome/xml/model/enums/DimensionOrder', 'fromString',
'(Ljava/lang/String;)Lome/xml/model/enums/DimensionOrder;',
dimension_order)
jutil.call(self.o, 'setPixelsDimensionOrder',
'(Lome/xml/model/enums/DimensionOrder;I)V',
jdimension_order, imageIndex)
except jutil.JavaException:
jutil.call(self.o, 'setPixelsDimensionOrder',
'(Ljava/lang/String;II)V', dimension_order, imageIndex,
binDataIndex)
def test_01_07_get_dictionary_wrapper(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
d = J.get_dictionary_wrapper(properties)
self.assertTrue(d.size() > 10)
self.assertFalse(d.isEmpty())
keys = J.get_enumeration_wrapper(d.keys())
values = J.get_enumeration_wrapper(d.elements())
n_elems = d.size()
for i in range(n_elems):
self.assertTrue(keys.hasMoreElements())
key = J.to_string(keys.nextElement())
self.assertTrue(values.hasMoreElements())
value = J.to_string(values.nextElement())
self.assertEqual(J.to_string(d.get(key)), value)
self.assertFalse(keys.hasMoreElements())
self.assertFalse(values.hasMoreElements())
def tearDownClass(cls):
del cls.context
J.static_call('java/lang/System', 'gc', '()V')
def start_cellprofiler_jvm():
'''Start the Java VM with arguments appropriate for CellProfiler'''
global logger
if hasattr(sys, 'frozen'):
if sys.platform != 'darwin':
root_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
bioformats_path = os.path.join(root_path, 'bioformats')
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
imagej_path = os.path.join(root_path, 'imagej', 'jars')
def sort_fn(a, b):
aa, bb = [(0 if x.startswith("cellprofiler-java") else 1, x)
for x in a, b]
return cmp(aa, bb)
jar_files = [
jar_filename for jar_filename in os.listdir(imagej_path)
if jar_filename.lower().endswith(".jar")
]
jar_files = sorted(jar_files, cmp=sort_fn)
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
jar_files = get_cellprofiler_jars()
imagej_path = os.path.join(root_path, 'imagej', 'jars')
class_path = os.pathsep.join(
[os.path.join(imagej_path, jar_file) for jar_file in jar_files])
if os.environ.has_key("CLASSPATH"):
class_path += os.pathsep + os.environ["CLASSPATH"]
if (get_ij_plugin_directory() is not None
and os.path.isdir(get_ij_plugin_directory())):
plugin_directory = get_ij_plugin_directory()
#
# Add the plugin directory to pick up .class files in a directory
# hierarchy.
#
class_path += os.pathsep + plugin_directory
#
# Add any .jar files in the directory
#
class_path += os.pathsep + os.pathsep.join([
os.path.join(plugin_directory, jarfile)
for jarfile in os.listdir(plugin_directory)
if jarfile.lower().endswith(".jar")
])
if sys.platform.startswith("win") and not hasattr(sys, 'frozen'):
# Have to find tools.jar
from cellprofiler.utilities.setup import find_jdk
jdk_path = find_jdk()
if jdk_path is not None:
tools_jar = os.path.join(jdk_path, "lib", "tools.jar")
class_path += os.pathsep + tools_jar
else:
logger.warning("Failed to find tools.jar")
jvm_arg = [
x.groups()[0] for x in
[re.match('--jvm-heap-size=([0-9]+[gGkKmM])', y) for y in sys.argv]
if x is not None
]
if len(jvm_arg) > 0:
jvm_arg = jvm_arg[0]
else:
jvm_arg = "512m"
args = [
r"-Djava.class.path=" + class_path,
r"-Dloci.bioformats.loaded=true",
#r"-verbose:class",
#r"-verbose:jni",
r"-Xmx%s" % jvm_arg
]
#
# Get the log4j logger setup from a file in the bioformats directory
# if such a file exists.
#
log4j_properties = os.path.join(bioformats_path, "log4j.properties")
if os.path.exists(log4j_properties):
log4j_properties = "file:/" + log4j_properties.replace(
os.path.sep, "/")
args += [r"-Dlog4j.configuration=" + log4j_properties]
init_logger = False
else:
init_logger = True
if get_headless():
# We're running silently, so don't change the Java preferences
# The following definition uses a process-scope preferences factory
args += [
"-Djava.util.prefs.PreferencesFactory="
"org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory"
]
run_headless = (get_headless()
and not os.environ.has_key("CELLPROFILER_USE_XVFB"))
run_headless = False
logger.debug("JVM arguments: " + " ".join(args))
jutil.start_vm(args, run_headless)
logger.debug("Java virtual machine started.")
jutil.attach()
try:
jutil.static_call("loci/common/Location", "cacheDirectoryListings",
"(Z)V", True)
except:
logger.warning(
"Bioformats version does not support directory cacheing")
#
# Start the log4j logger to avoid error messages.
#
if init_logger:
try:
jutil.static_call("org/apache/log4j/BasicConfigurator",
"configure", "()V")
log4j_logger = jutil.static_call("org/apache/log4j/Logger",
"getRootLogger",
"()Lorg/apache/log4j/Logger;")
warn_level = jutil.get_static_field("org/apache/log4j/Level",
"WARN",
"Lorg/apache/log4j/Level;")
jutil.call(log4j_logger, "setLevel", "(Lorg/apache/log4j/Level;)V",
warn_level)
del logger
del warn_level
except:
logger.error("Failed to initialize log4j\n", exc_info=True)
if not get_headless():
jutil.activate_awt()
def run_imagej(*args):
J.static_call("imagej/Main", "main", "([Ljava/lang/String;)V",
*[unicode(arg) for arg in args])