def inject_image(self, pixels, name=''):
'''inject an image into ImageJ for processing'''
ij_processor = ijiproc.make_image_processor((pixels * 255.0).astype('float32'))
image_plus = ijip.make_imageplus_from_processor(name, ij_processor)
if sys.platform == "darwin":
ijwm.set_temp_current_image(image_plus)
else:
ijwm.set_current_image(image_plus)
def test_01_02_make_image_processor(self):
np.random.seed(102)
image = np.random.uniform(size=(30, 50)).astype(np.float32)
image_processor = IP.make_image_processor(image)
result = IP.get_image(image_processor)
self.assertEqual(image.shape[0], result.shape[0])
self.assertEqual(image.shape[1], result.shape[1])
self.assertTrue(np.all(result == image))
def run(self, workspace):
jb.attach()#initialize JVM
input_image_name = self.input_image_name.value
output_image_name = self.output_image_name.value
self.gsize = self.input_gaussian_filter.value
self.rsize = self.input_rolling_ball.value
self.lowseed = self.input_low_seed.value
self.highseed = self.input_high_seed.value
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
#prepare input image
input_image = image_set.get_image(input_image_name, must_be_grayscale = True)
input_pixels = input_image.pixel_data
ij_processor = ijiproc.make_image_processor((input_pixels*255.0).astype('float32'))
#JavaScript API
script = """
var img=Packages.ij.ImagePlus(name,ij_processor);
Packages.ij.IJ.run(img, "8-bit", "");
var macro="g_size="+gsize+" r_size="+rsize+" low_edge="+lowseed+" high_edge="+highseed+" noise=-1";
java.lang.System.out.println(macro);
Packages.ij.IJ.run(img, "Hysteresis Segment", macro);
var output_proc=img.getProcessor();
"""
#img.show();
#Packages.ij.WindowManager.setCurrentWindow(img.getWindow());
#"""
in_params={
"name":output_image_name,
"ij_processor": ij_processor,
"gsize":self.gsize,
"rsize":self.rsize,
"lowseed":self.lowseed,
"highseed":self.highseed}
out_params={"output_proc":None}
r = jb.run_script(script, bindings_in = in_params,bindings_out = out_params)
#prepare output image
output_pixels = ijiproc.get_image(out_params["output_proc"], False)
output_image = cpi.Image(output_pixels, parent_image = input_image)
#write output
image_set.add(output_image_name, output_image)
if workspace.frame is not None:
workspace.display_data.input_pixels = input_pixels
workspace.display_data.output_pixels = output_pixels
jb.detach()#close JVM
def inject_image(self, pixels, name=''):
'''inject an image into ImageJ for processing'''
ij_processor = ijiproc.make_image_processor(
(pixels * 255.0).astype('float32'))
script = """
new java.lang.Runnable() {
run: function() {
var imp = Packages.ij.ImagePlus(name, ij_processor);
imp.show();
Packages.ij.WindowManager.setCurrentWindow(imp.getWindow());
}};"""
r = J.run_script(script, bindings_in = {
"name":name,
"ij_processor": ij_processor})
J.execute_runnable_in_main_thread(r, True)
def run(self, workspace):
"""Run the imageJ command"""
image_set = workspace.image_set
d = self.get_dictionary(workspace.image_set_list)
if self.wants_to_set_current_image:
input_image_name = self.current_input_image_name.value
img = image_set.get_image(input_image_name, must_be_grayscale=True)
if self.show_window:
workspace.display_data.image_sent_to_ij = img.pixel_data
else:
img = None
display_service = ij2.get_display_service(get_context())
#
# Run a command or macro on the first image of the set
#
if d.get(D_FIRST_IMAGE_SET) == image_set.image_number:
self.do_imagej(workspace, D_FIRST_IMAGE_SET)
ij1_mode = self.command_or_macro == CM_MACRO
#
# Install the input image as the current image
#
if img is not None:
ijpixels = img.pixel_data * IMAGEJ_SCALE
if ij1_mode:
ij_processor = ijiproc.make_image_processor(ijpixels.astype("float32"))
image_plus = ijip.make_imageplus_from_processor(input_image_name, ij_processor)
ijwm.set_current_image(image_plus)
else:
dataset = ij2.create_dataset(get_context(), ijpixels, input_image_name)
display = display_service.createDisplay(input_image_name, dataset)
display_service.setActiveDisplay(display)
self.do_imagej(workspace)
#
# Get the output image
#
if self.wants_to_get_current_image:
output_image_name = self.current_output_image_name.value
if ij1_mode:
image_plus = ijwm.get_current_image()
ij_processor = image_plus.getProcessor()
pixels = ijiproc.get_image(ij_processor).astype("float32") / IMAGEJ_SCALE
image = cpi.Image(pixels)
workspace.image_set.add(output_image_name, image)
else:
for attempt in range(4):
display = display_service.getActiveImageDisplay()
if display.o is not None:
break
#
# Possible synchronization problem with ImageJ 1.0
# Possible error involving user changing window focus
#
import time
time.sleep(0.25)
else:
raise ValueError("Failed to retrieve active display")
pixels = self.save_display_as_image(workspace, display, output_image_name)
if self.show_window:
workspace.display_data.image_acquired_from_ij = pixels
#
# Execute the post-group macro or command
#
if d.get(D_LAST_IMAGE_SET) == image_set.image_number:
self.do_imagej(workspace, D_LAST_IMAGE_SET)
#
# Save the current ImageJ image after executing the post-group
# command or macro
#
if self.post_group_choice != CM_NOTHING and self.wants_post_group_image:
output_image_name = self.post_group_output_image.value
if ij1_mode:
image_plus = ijwm.get_current_image()
ij_processor = image_plus.getProcessor()
pixels = ijiproc.get_image(ij_processor).astype("float32") / IMAGEJ_SCALE
image = cpi.Image(pixels, mask=mask)
workspace.image_set.add(output_image_name, image)
else:
display = display_service.getActiveImageDisplay()
self.save_display_as_image(workspace, display, output_image_name)
def execute_advanced_command(self, workspace, command, d):
'''Execute an advanced command
command - name of the command
d - dictionary to be used to find settings
'''
wants_display = workspace.frame is not None
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
key = command.get_unicode_value()
if bioformats.USE_IJ2:
node = command.get_selected_leaf()
module_info = node[2]
module = IJ2.wrap_module(module_info.createModule())
context = self.get_context()
display_service = IJ2.get_display_service(context)
display_dictionary = {}
for setting, module_item in d[key]:
field_type = module_item.getType()
if isinstance(setting, cps.ImageNameProvider):
continue
if field_type == IJ2.FT_BOOL:
value = J.make_instance("java/lang/Boolean",
"(Z)V", setting.value)
elif field_type == IJ2.FT_INTEGER:
value = J.make_instance("java/lang/Integer",
"(I)V", setting.value)
elif field_type == IJ2.FT_FLOAT:
value = J.make_instance("java/lang/Double",
"(D)V", setting.value)
elif field_type == IJ2.FT_STRING:
value = setting.value
elif field_type == IJ2.FT_COLOR:
value = IJ2.make_color_rgb_from_html(setting.value)
elif field_type == IJ2.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name)
dataset = IJ2.create_dataset(image.pixel_data,
setting.value)
display = display_service.createDisplay(dataset)
if image.has_mask:
overlay = IJ2.create_overlay(image.mask)
display.displayOverlay(overlay)
value = display
display_dictionary[module_item.getName()] = display
if wants_display:
input_images.append((image_name, image.pixel_data))
module.setInput(module_item.getName(), value)
module_service = IJ2.get_module_service(context)
module_service.run(module)
for setting, module_item in d[key]:
if isinstance(setting, cps.ImageNameProvider):
name = module_item.getName()
output_name = setting.value
if display_dictionary.has_key(name):
display = display_dictionary[name]
else:
display = IJ2.wrap_display(module.getOutput(name))
ds = display_service.getActiveDataset(display)
pixel_data = ds.get_pixel_data()
image = cpi.Image(pixel_data)
workspace.image_set.add(output_name, image)
if wants_display:
output_images.append((output_name, pixel_data))
for display in display_dictionary.values():
panel = IJ2.wrap_display_panel(display.getDisplayPanel())
panel.close()
else:
from imagej.imageplus import make_imageplus_from_processor
from imagej.imageplus import get_imageplus_wrapper
from imagej.imageprocessor import make_image_processor
from imagej.imageprocessor import get_image
command = command.value
settings = d[command]
classname = self.get_cached_commands()[command]
plugin = M.get_plugin(classname)
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
for (field, parameter), setting in zip(fp_in, settings[:len(fp_in)]):
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name,
must_be_grayscale = True)
pixel_data = (image.pixel_data * 255.0).astype(np.float32)
if wants_display:
input_images.append((image_name, pixel_data / 255.0))
processor = make_image_processor(pixel_data)
image_plus = make_imageplus_from_processor(image_name, processor)
field.set(plugin, image_plus)
del image_plus
del processor
elif field_type == P.FT_INTEGER:
field.setInt(plugin, setting.value)
elif field_type == P.FT_FLOAT:
field.setFloat(plugin, setting.value)
elif field_type == P.FT_BOOL:
field.setBoolean(plugin, setting.value)
else:
field.set(plugin, setting.value)
#
# There are two ways to run this:
# * Batch - just call plugin.run()
# * Interactive - use PlugInFunctions.runInteractively
#
if self.pause_before_proceeding:
J.execute_runnable_in_main_thread(J.run_script(
"""new java.lang.Runnable() { run:function() {
importClass(Packages.imagej.plugin.PlugInFunctions);
PlugInFunctions.runInteractively(plugin);
}};""", dict(plugin=plugin)), True)
else:
J.execute_runnable_in_main_thread(plugin, True)
setting_idx = len(fp_in)
fp_out = P.get_output_fields_and_parameters(plugin)
for field, parameter in fp_out:
field_type = P.get_field_type(field)
if field_type == P.FT_IMAGE:
image_name = settings[setting_idx].value
setting_idx += 1
image_plus = get_imageplus_wrapper(field.get(plugin))
processor = image_plus.getProcessor()
pixel_data = get_image(processor).astype(np.float32) / 255.0
if wants_display:
output_images.append((image_name, pixel_data))
image = cpi.Image(pixel_data)
image_set.add(image_name, image)
def run(self, workspace):
'''Run the imageJ command'''
image_set = workspace.image_set
d = self.get_dictionary(workspace.image_set_list)
if self.wants_to_set_current_image:
input_image_name = self.current_input_image_name.value
img = image_set.get_image(input_image_name, must_be_grayscale=True)
if self.show_window:
workspace.display_data.image_sent_to_ij = img.pixel_data
else:
img = None
display_service = ij2.get_display_service(get_context())
#
# Run a command or macro on the first image of the set
#
if d.get(D_FIRST_IMAGE_SET) == image_set.image_number:
self.do_imagej(workspace, D_FIRST_IMAGE_SET)
ij1_mode = self.command_or_macro == CM_MACRO
#
# Install the input image as the current image
#
if img is not None:
ijpixels = img.pixel_data * IMAGEJ_SCALE
if ij1_mode:
ij_processor = ijiproc.make_image_processor(
ijpixels.astype('float32'))
image_plus = ijip.make_imageplus_from_processor(
input_image_name, ij_processor)
ijwm.set_current_image(image_plus)
else:
dataset = ij2.create_dataset(get_context(), ijpixels,
input_image_name)
display = display_service.createDisplay(
input_image_name, dataset)
display_service.setActiveDisplay(display)
self.do_imagej(workspace)
#
# Get the output image
#
if self.wants_to_get_current_image:
output_image_name = self.current_output_image_name.value
if ij1_mode:
image_plus = ijwm.get_current_image()
ij_processor = image_plus.getProcessor()
pixels = ijiproc.get_image(ij_processor).\
astype('float32') / IMAGEJ_SCALE
image = cpi.Image(pixels)
workspace.image_set.add(output_image_name, image)
else:
for attempt in range(4):
display = display_service.getActiveImageDisplay()
if display.o is not None:
break
#
# Possible synchronization problem with ImageJ 1.0
# Possible error involving user changing window focus
#
import time
time.sleep(.25)
else:
raise ValueError("Failed to retrieve active display")
pixels = self.save_display_as_image(workspace, display,
output_image_name)
if self.show_window:
workspace.display_data.image_acquired_from_ij = pixels
#
# Execute the post-group macro or command
#
if d.get(D_LAST_IMAGE_SET) == image_set.image_number:
self.do_imagej(workspace, D_LAST_IMAGE_SET)
#
# Save the current ImageJ image after executing the post-group
# command or macro
#
if (self.post_group_choice != CM_NOTHING
and self.wants_post_group_image):
output_image_name = self.post_group_output_image.value
if ij1_mode:
image_plus = ijwm.get_current_image()
ij_processor = image_plus.getProcessor()
pixels = ijiproc.get_image(ij_processor).\
astype('float32') / IMAGEJ_SCALE
image = cpi.Image(pixels, mask=mask)
workspace.image_set.add(output_image_name, image)
else:
display = display_service.getActiveImageDisplay()
self.save_display_as_image(workspace, display,
output_image_name)
def execute_advanced_command(self, workspace, command, d):
'''Execute an advanced command
command - name of the command
d - dictionary to be used to find settings
'''
from imagej.imageplus import make_imageplus_from_processor
from imagej.imageplus import get_imageplus_wrapper
from imagej.imageprocessor import make_image_processor
from imagej.imageprocessor import get_image
settings = d[command]
classname = self.get_cached_commands()[command]
plugin = M.get_plugin(classname)
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
wants_display = workspace.frame is not None
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
for (field, parameter), setting in zip(fp_in, settings[:len(fp_in)]):
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name,
must_be_grayscale = True)
pixel_data = (image.pixel_data * 255.0).astype(np.float32)
if wants_display:
input_images.append((image_name, pixel_data / 255.0))
processor = make_image_processor(pixel_data)
image_plus = make_imageplus_from_processor(image_name, processor)
field.set(plugin, image_plus)
del image_plus
del processor
elif field_type == P.FT_INTEGER:
field.setInt(plugin, setting.value)
elif field_type == P.FT_FLOAT:
field.setFloat(plugin, setting.value)
elif field_type == P.FT_BOOL:
field.setBoolean(plugin, setting.value)
else:
field.set(plugin, setting.value)
#
# There are two ways to run this:
# * Batch - just call plugin.run()
# * Interactive - use PlugInFunctions.runInteractively
#
if self.pause_before_proceeding:
J.static_call('imagej/plugin/PlugInFunctions', 'runInteractively',
'(Ljava/lang/Runnable)V', plugin)
else:
J.call(plugin, 'run', '()V')
setting_idx = len(fp_in)
fp_out = P.get_output_fields_and_parameters(plugin)
for field, parameter in fp_out:
field_type = P.get_field_type(field)
if field_type == P.FT_IMAGE:
image_name = settings[setting_idx].value
setting_idx += 1
image_plus = get_imageplus_wrapper(field.get(plugin))
processor = image_plus.getProcessor()
pixel_data = get_image(processor).astype(np.float32) / 255.0
if wants_display:
output_images.append((image_name, pixel_data))
image = cpi.Image(pixel_data)
image_set.add(image_name, image)
def execute_advanced_command(self, workspace, command, d):
'''Execute an advanced command
command - name of the command
d - dictionary to be used to find settings
'''
wants_display = workspace.frame is not None
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
key = command.get_unicode_value()
if bioformats.USE_IJ2:
node = command.get_selected_leaf()
module_info = node[2]
module = IJ2.wrap_module(module_info.createModule())
context = self.get_context()
display_service = IJ2.get_display_service(context)
display_dictionary = {}
for setting, module_item in d[key]:
field_type = module_item.getType()
if isinstance(setting, cps.ImageNameProvider):
continue
if field_type == IJ2.FT_BOOL:
value = J.make_instance("java/lang/Boolean", "(Z)V",
setting.value)
elif field_type == IJ2.FT_INTEGER:
value = J.make_instance("java/lang/Integer", "(I)V",
setting.value)
elif field_type == IJ2.FT_FLOAT:
value = J.make_instance("java/lang/Double", "(D)V",
setting.value)
elif field_type == IJ2.FT_STRING:
value = setting.value
elif field_type == IJ2.FT_COLOR:
value = IJ2.make_color_rgb_from_html(setting.value)
elif field_type == IJ2.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name)
dataset = IJ2.create_dataset(image.pixel_data,
setting.value)
display = display_service.createDisplay(dataset)
if image.has_mask:
overlay = IJ2.create_overlay(image.mask)
display.displayOverlay(overlay)
value = display
display_dictionary[module_item.getName()] = display
if wants_display:
input_images.append((image_name, image.pixel_data))
module.setInput(module_item.getName(), value)
module_service = IJ2.get_module_service(context)
module_service.run(module)
for setting, module_item in d[key]:
if isinstance(setting, cps.ImageNameProvider):
name = module_item.getName()
output_name = setting.value
if display_dictionary.has_key(name):
display = display_dictionary[name]
else:
display = IJ2.wrap_display(module.getOutput(name))
ds = display_service.getActiveDataset(display)
pixel_data = ds.get_pixel_data()
image = cpi.Image(pixel_data)
workspace.image_set.add(output_name, image)
if wants_display:
output_images.append((output_name, pixel_data))
for display in display_dictionary.values():
panel = IJ2.wrap_display_panel(display.getDisplayPanel())
panel.close()
else:
from imagej.imageplus import make_imageplus_from_processor
from imagej.imageplus import get_imageplus_wrapper
from imagej.imageprocessor import make_image_processor
from imagej.imageprocessor import get_image
command = command.value
settings = d[command]
classname = self.get_cached_commands()[command]
plugin = M.get_plugin(classname)
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
for (field, parameter), setting in zip(fp_in,
settings[:len(fp_in)]):
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(
image_name, must_be_grayscale=True)
pixel_data = (image.pixel_data * 255.0).astype(np.float32)
if wants_display:
input_images.append((image_name, pixel_data / 255.0))
processor = make_image_processor(pixel_data)
image_plus = make_imageplus_from_processor(
image_name, processor)
field.set(plugin, image_plus)
del image_plus
del processor
elif field_type == P.FT_INTEGER:
field.setInt(plugin, setting.value)
elif field_type == P.FT_FLOAT:
field.setFloat(plugin, setting.value)
elif field_type == P.FT_BOOL:
field.setBoolean(plugin, setting.value)
else:
field.set(plugin, setting.value)
#
# There are two ways to run this:
# * Batch - just call plugin.run()
# * Interactive - use PlugInFunctions.runInteractively
#
if self.pause_before_proceeding:
J.static_call('imagej/plugin/PlugInFunctions',
'runInteractively', '(Ljava/lang/Runnable)V',
plugin)
else:
J.call(plugin, 'run', '()V')
setting_idx = len(fp_in)
fp_out = P.get_output_fields_and_parameters(plugin)
for field, parameter in fp_out:
field_type = P.get_field_type(field)
if field_type == P.FT_IMAGE:
image_name = settings[setting_idx].value
setting_idx += 1
image_plus = get_imageplus_wrapper(field.get(plugin))
processor = image_plus.getProcessor()
pixel_data = get_image(processor).astype(
np.float32) / 255.0
if wants_display:
output_images.append((image_name, pixel_data))
image = cpi.Image(pixel_data)
image_set.add(image_name, image)