def test_09_08_check_stride(self): # Rotate the image by 90 degrees to make sure the pixel copy # was properly strided # svc = ij2.get_display_service(self.context) i, j = np.mgrid[0:5, 0:70:10] image = i + j ds = ij2.create_dataset(self.context, image, "Foo") display = svc.createDisplay("Foo", ds) outputs = dict(display=None) self.run_command("imagej.core.commands.rotate.Rotate90DegreesLeft", dict(display=display), outputs) display_out = ij2.wrap_display(outputs["display"]) dataset = ij2.wrap_dataset(display_out.getActiveView().getData()) image_out = dataset.get_pixel_data() self.assertSequenceEqual(image_out.shape, list(reversed(image.shape))) np.testing.assert_array_equal(np.rot90(image), image_out)
def test_09_08_check_stride(self): # Rotate the image by 90 degrees to make sure the pixel copy # was properly strided # svc = ij2.get_display_service(self.context) i, j = np.mgrid[0:5, 0:70:10] image = i+j ds = ij2.create_dataset(self.context, image, "Foo") display = svc.createDisplay("Foo", ds) outputs = dict(display=None) self.run_command("imagej.core.commands.rotate.Rotate90DegreesLeft", dict(display=display), outputs) display_out = ij2.wrap_display(outputs["display"]) dataset = ij2.wrap_dataset(display_out.getActiveView().getData()) image_out = dataset.get_pixel_data() self.assertSequenceEqual(image_out.shape, list(reversed(image.shape))) np.testing.assert_array_equal(np.rot90(image), image_out)
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)