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 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 image from the top of the batch mode image stack returns None or a wrapped imagePlus ''' image_plus = J.static_call("ij/macro/Interpreter", "getLastBatchModeImage", "()Lij/ImagePlus;") if image_plus is not None: return get_imageplus_wrapper(image_plus)
def get_current_image(): '''Get the image from the top of the batch mode image stack returns None or a wrapped imagePlus ''' image_plus = J.static_call("ij/macro/Interpreter", "getLastBatchModeImage", "()Lij/ImagePlus;") if image_plus is not None: return get_imageplus_wrapper(image_plus)
def get_temp_current_image(): '''Get the temporary ImagePlus object for the current thread''' script = """ new java.util.concurrent.Callable() { call: function() { return Packages.ij.WindowManager.getTempCurrentImage(); } }; """ gtci = J.make_future_task(J.run_script(script)) imageplus_obj = J.execute_future_in_main_thread(gtci) return get_imageplus_wrapper(imageplus_obj)
def get_temp_current_image(): '''Get the temporary ImagePlus object for the current thread''' script = """ new java.util.concurrent.Callable() { call: function() { return Packages.ij.WindowManager.getTempCurrentImage(); } }; """ gtci = J.make_future_task(J.run_script(script)) imageplus_obj = J.execute_future_in_main_thread(gtci) return get_imageplus_wrapper(imageplus_obj)
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 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 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 ''' # # Run this on the UI thread so its thread context is the same # as the macro invocation # script = """ new java.util.concurrent.Callable() { call: function() { return Packages.ij.WindowManager.getCurrentImage(); } }; """ gci = J.make_future_task(J.run_script(script)) imageplus_obj = J.execute_future_in_main_thread(gci) return get_imageplus_wrapper(imageplus_obj)
def get_current_image(): '''Get the WindowManager's current image returns a wrapped ImagePlus object ''' # # Run this on the UI thread so its thread context is the same # as the macro invocation # script = """ new java.util.concurrent.Callable() { call: function() { return Packages.ij.WindowManager.getCurrentImage(); } }; """ gci = J.make_future_task(J.run_script(script)) imageplus_obj = J.execute_future_in_main_thread(gci) return get_imageplus_wrapper(imageplus_obj)
def get_image_by_name(title): '''Get the ImagePlus object whose title (in the window) matches "title"''' return get_imageplus_wrapper( J.static_call('ij/WindowManager', 'getImage', '(Ljava/lang/String;)Lij/ImagePlus;', title))
def get_temp_current_image(): '''Get the temporary ImagePlus object for the current thread''' return get_imageplus_wrapper( J.static_call('ij/WindowManager', 'getTempCurrentImage', '()Lij/ImagePlus;'))
def get_image_by_id(imagej_id): """Get an ImagePlus object by its ID""" return get_imageplus_wrapper(J.static_call("ij/WindowManager", "getImage", "(I)Lij/ImagePlus;", imagej_id))
def get_image_by_id(imagej_id): '''Get an ImagePlus object by its ID''' return get_imageplus_wrapper( J.static_call('ij/WindowManager', 'getImage', '(I)Lij/ImagePlus;', imagej_id))
def get_temp_current_image(): '''Get the temporary ImagePlus object for the current thread''' return get_imageplus_wrapper(J.static_call( 'ij/WindowManager', 'getTempCurrentImage','()Lij/ImagePlus;'))
def get_image_by_name(title): '''Get the ImagePlus object whose title (in the window) matches "title"''' return get_imageplus_wrapper(J.static_call( 'ij/WindowManager', 'getImage', '(Ljava/lang/String;)Lij/ImagePlus;', title))
def get_image_by_id(imagej_id): '''Get an ImagePlus object by its ID''' return get_imageplus_wrapper(J.static_call( 'ij/WindowManager', 'getImage', '(I)Lij/ImagePlus;', imagej_id))
def get_temp_current_image(): """Get the temporary ImagePlus object for the current thread""" return get_imageplus_wrapper(J.static_call("ij/WindowManager", "getTempCurrentImage", "()Lij/ImagePlus;"))
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.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 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)