def get_segmentation_mask_image(self, image_api=None): if image_api is None: image_api = ImageApi segmentation_mask_image_file = self.get_segmentation_mask_image_file() pixel_size = self.get_surface_2p_pixel_size_um() segmentation_mask_image = mpimg.imread(segmentation_mask_image_file) return ImageApi.serialize(segmentation_mask_image, [pixel_size / 1000., pixel_size / 1000.], 'mm')
def get_max_projection(self, image_api=None): if image_api is None: image_api = ImageApi maxInt_a13_file = self.get_max_projection_file() pixel_size = self.get_surface_2p_pixel_size_um() max_projection = mpimg.imread(maxInt_a13_file) return ImageApi.serialize(max_projection, [pixel_size / 1000., pixel_size / 1000.], 'mm')
def get_image(nwbfile: NWBFile, name: str, module: str) -> Image: nwb_img = nwbfile.processing[module].get_data_interface('images')[name] data = nwb_img.data resolution = nwb_img.resolution # px/cm spacing = [resolution * 10, resolution * 10] img = ImageApi.serialize(data, spacing, 'mm') img = ImageApi.deserialize(img=img) return img
def get_average_projection(self, image_api=None): if image_api is None: image_api = ImageApi avgint_a1X_file = ( self.extractor.get_average_intensity_projection_image_file()) pixel_size = self.extractor.get_surface_2p_pixel_size_um() average_image = mpimg.imread(avgint_a1X_file) return ImageApi.serialize(average_image, [pixel_size / 1000., pixel_size / 1000.], 'mm')
def get_image(self, name, module, image_api=None) -> sitk.Image: if image_api is None: image_api = ImageApi nwb_img = self.nwbfile.modules[module].get_data_interface( 'images')[name] data = nwb_img.data resolution = nwb_img.resolution # px/cm spacing = [resolution * 10, resolution * 10] return ImageApi.serialize(data, spacing, 'mm')
def _from_filepath(filepath: str, pixel_size: float) -> Image: """ :param filepath path to image :param pixel_size pixel size in um """ img = mpimg.imread(filepath) img = ImageApi.serialize(img, [pixel_size / 1000., pixel_size / 1000.], 'mm') img = ImageApi.deserialize(img=img) return img
def get_max_projection(self): return ImageApi.serialize(roi_1 + roi_2, [0.5, 1.], 'mm')
def get_segmentation_mask_image(self): data = roi_1 #useless image data here spacing = (1, 1) unit = 'index' return ImageApi.serialize(data, spacing, unit)