def test_manual_image_creation_from_file(self): from jicbioimage.core.image import Image # Preamble: let us define the path to a TIFF file and create a numpy # array from it. # from libtiff import TIFF # tif = TIFF.open(path_to_tiff, 'r') # ar = tif.read_image() path_to_tiff = os.path.join(DATA_DIR, 'single-channel.ome.tif') use_plugin('freeimage') ar = imread(path_to_tiff) # It is possible to create an image from a file. image = Image.from_file(path_to_tiff) self.assertEqual(len(image.history), 0) self.assertEqual(image.history.creation, 'Created Image from {}'.format(path_to_tiff)) # With name... image = Image.from_file(path_to_tiff, name='Test1') self.assertEqual(image.history.creation, 'Created Image from {} as Test1'.format(path_to_tiff)) # Without history... image = Image.from_file(path_to_tiff, log_in_history=False) self.assertEqual(len(image.history), 0) # It is worth noting the image can support more multiple channels. # This is particularly important when reading in images in rgb format. fpath = os.path.join(DATA_DIR, 'tjelvar.png') image = Image.from_file(fpath) self.assertEqual(image.shape, (50, 50, 3))
def test_scaling_of_written_files(self): from jicbioimage.core.image import Image3D, Image directory = os.path.join(TMP_DIR, "im3d") z0 = np.zeros((50,50), dtype=np.uint8) z1 = np.ones((50, 50), dtype=np.uint8) stack = np.dstack([z0, z1]) im3d = Image3D.from_array(stack) im3d.to_directory(directory) im0 = Image.from_file(os.path.join(directory, "z0.png")) im1 = Image.from_file(os.path.join(directory, "z1.png")) self.assertTrue(np.array_equal(z0, im0)) self.assertTrue(np.array_equal(z1*255, im1)) z2 = np.ones((50, 50), dtype=np.uint8) * 255 stack = np.dstack([z0, z1, z2]) im3d = Image3D.from_array(stack) im3d.to_directory(directory) im0 = Image.from_file(os.path.join(directory, "z0.png")) im1 = Image.from_file(os.path.join(directory, "z1.png")) im2 = Image.from_file(os.path.join(directory, "z2.png")) self.assertTrue(np.array_equal(z0, im0)) self.assertTrue(np.array_equal(z1, im1)) self.assertTrue(np.array_equal(z2*255, im1))
def test_scaling_of_written_files(self): from jicbioimage.core.image import Image3D, Image directory = os.path.join(TMP_DIR, "im3d") z0 = np.zeros((50, 50), dtype=np.uint8) z1 = np.ones((50, 50), dtype=np.uint8) stack = np.dstack([z0, z1]) im3d = Image3D.from_array(stack) im3d.to_directory(directory) im0 = Image.from_file(os.path.join(directory, "z0.png")) im1 = Image.from_file(os.path.join(directory, "z1.png")) self.assertTrue(np.array_equal(z0, im0)) self.assertTrue(np.array_equal(z1 * 255, im1)) z2 = np.ones((50, 50), dtype=np.uint8) * 255 stack = np.dstack([z0, z1, z2]) im3d = Image3D.from_array(stack) im3d.to_directory(directory) im0 = Image.from_file(os.path.join(directory, "z0.png")) im1 = Image.from_file(os.path.join(directory, "z1.png")) im2 = Image.from_file(os.path.join(directory, "z2.png")) self.assertTrue(np.array_equal(z0, im0)) self.assertTrue(np.array_equal(z1, im1)) self.assertTrue(np.array_equal(z2 * 255, im1))
def sample_image_from_lines(image_file, lines_file, dilation, reduce_method): data_image = Image.from_file(image_file) line_image = Image.from_file(lines_file) segmented_lines = segment(line_image, dilation) with open("all_series.csv", "w") as fh: fh.write(csv_header()) for n, line_region in enumerate(yield_line_masks(segmented_lines)): line_intensity = data_image * line_region if reduce_method == "max": line_profile = np.amax(line_intensity, axis=1) elif reduce_method == "mean": sum_intensity = np.sum(line_intensity, axis=1) sum_rows = np.sum(line_region, axis=1) line_profile = sum_intensity / sum_rows else: err_msg = "Unknown reduce method: {}".format(reduce_method) raise(RuntimeError(err_msg)) series_filename = "series_{:02d}.csv".format(n) save_line_profile(series_filename, line_profile, n) fh.write(csv_body(line_profile, n))
def find_kilobots(image_filename, output_filename): """Find kilobots in a still image file.""" kilobot_image = Image.from_file(image_filename) red_only = kilobot_image[:,:,0] imsave('red.png', red_only) edges = find_edges(red_only) blurred = gaussian_filter(edges, sigma=2) # bot_template = blurred[135:185,485:535] # imsave('bot_template.png', bot_template) bot_template = load_bot_template('bot_template.png') match_result = skimage.feature.match_template(blurred, bot_template, pad_input=True) imsave('match_result.png', match_result) selected_area = match_result > 0.6 imsave('selected_area.png', selected_area) ccs = find_connected_components(selected_area) centroids = component_centroids(ccs) return centroids
def find_grains(input_file, output_dir=None): """Return tuple of segmentaitons (grains, difficult_regions).""" name = fpath2name(input_file) name = "grains-" + name + ".png" if output_dir: name = os.path.join(output_dir, name) image = Image.from_file(input_file) intensity = mean_intensity_projection(image) image = remove_scalebar(intensity, np.mean(intensity)) image = threshold_abs(image, 75) image = invert(image) image = fill_holes(image, min_size=500) image = erode_binary(image, selem=disk(4)) image = remove_small_objects(image, min_size=500) image = dilate_binary(image, selem=disk(4)) dist = distance(image) seeds = local_maxima(dist) seeds = dilate_binary(seeds) # Merge spurious double peaks. seeds = connected_components(seeds, background=0) segmentation = watershed_with_seeds(dist, seeds=seeds, mask=image) # Need a copy to avoid over-writing original. initial_segmentation = np.copy(segmentation) # Remove spurious blobs. segmentation = remove_large_segments(segmentation, max_size=3000) segmentation = remove_small_segments(segmentation, min_size=500) props = skimage.measure.regionprops(segmentation) segmentation = remove_non_round(segmentation, props, 0.6) difficult = initial_segmentation - segmentation return segmentation, difficult
def analyse_file(fpath, output_directory): """Analyse a single file.""" logging.info("Analysing file: {}".format(fpath)) image = Image.from_file(fpath) image_output_fpath = os.path.join(output_directory, 'original.png') with open(image_output_fpath, 'wb') as fh: fh.write(image.png()) segmentation = preprocess_and_segment(image) false_colour_fpath = os.path.join(output_directory, 'false_color.png') with open(false_colour_fpath, 'wb') as fh: fh.write(segmentation.png()) rgb_segmentation_fpath = os.path.join(output_directory, 'segmentation.png') write_segmented_image_as_rgb(segmentation, rgb_segmentation_fpath) cell_info = parameterise_cells(segmentation) csv_fpath = os.path.join(output_directory, 'results.csv') write_cell_info_to_csv(cell_info, csv_fpath) label_image = generate_label_image(segmentation) label_image_fpath = os.path.join(output_directory, 'labels.png') with open(label_image_fpath, 'wb') as fh: fh.write(label_image.png())
def find_single_seed(image_filename, output_filename): image = Image.from_file(image_filename) w, h = 500, 500 tube_section = image[1024-w:1024+w,1024-h:1024+h] threshold = threshold_otsu(tube_section) thresholded = tube_section > threshold x, y, r = find_inner_circle_parameters(thresholded, 400, 500) # FIXME - think routine is finding outer circle stripped = strip_outside_circle(thresholded, (x, y), 300) eroded = binary_erosion(stripped, structure=np.ones((10, 10))) float_coords = map(np.mean, np.where(eroded > 0)) ix, iy = map(int, float_coords) w, h = 100, 100 selected = tube_section[ix-w:ix+w,iy-h:iy+h] with open(output_filename, 'wb') as f: f.write(selected.view(Image).png())
def process_single_identifier(dataset, identifier, output_path): print("Processing {}".format(identifier)) image = Image.from_file(dataset.abspath_from_identifier(identifier)) seeds = generate_seed_image(image, dataset, identifier) segmentation = segment(image, seeds) segmentation = filter_sides(segmentation) segmentation = filter_touching_border(segmentation) output_filename = generate_output_filename( dataset, identifier, output_path, '-segmented' ) save_segmented_image_as_rgb(segmentation, output_filename) false_colour_filename = generate_output_filename( dataset, identifier, output_path, '-false_colour' ) with open(false_colour_filename, 'wb') as fh: fh.write(segmentation.png())
def generate_composite_image(base_image, trajectory_image): still_image = Image.from_file(base_image) trajectories = Image.from_file(trajectory_image)[:,:,0] annotation_points = np.where(trajectories != 0) color = 255, 0, 0 for x, y in zip(*annotation_points): still_image[x, y] = color still_image[x+1, y] = color still_image[x-1, y] = color still_image[x, y+1] = color still_image[x, y-1] = color imsave('annotated_image.png', still_image)
def separate_plots(dataset, identifier, resource_dataset, working_dir): fpath = dataset.item_content_abspath(identifier) segmentation = load_segmentation_from_rgb_image(fpath) original_id = dataset.get_overlay('from')[identifier] original_fpath = resource_dataset.item_content_abspath(original_id) original_image = Image.from_file(original_fpath) approx_plot_locs = find_approx_plot_locs(dataset, identifier) sid_to_label = generate_segmentation_identifier_to_label_map( approx_plot_locs, segmentation ) outputs = [] for identifier in segmentation.identifiers: image_section = generate_region_image( original_image, segmentation, identifier ) fname = 'region_{}.png'.format(sid_to_label[identifier]) output_fpath = os.path.join(working_dir, fname) imsave(output_fpath, image_section) outputs.append((fname, {'plot_number': sid_to_label[identifier]})) return outputs
def find_grains(input_file, output_dir=None): """Return tuple of segmentaitons (grains, difficult_regions).""" name = fpath2name(input_file) name = "grains-" + name + ".png" if output_dir: name = os.path.join(output_dir, name) image = Image.from_file(input_file) intensity = mean_intensity_projection(image) # Median filter seems more robust than Otsu. # image = threshold_otsu(intensity) image = threshold_median(intensity, scale=0.8) image = invert(image) image = erode_binary(image, selem=disk(2)) image = dilate_binary(image, selem=disk(2)) image = remove_small_objects(image, min_size=200) image = fill_holes(image, min_size=50) dist = distance(image) seeds = local_maxima(dist) seeds = dilate_binary(seeds) # Merge spurious double peaks. seeds = connected_components(seeds, background=0) segmentation = watershed_with_seeds(dist, seeds=seeds, mask=image) # Remove spurious blobs. segmentation = remove_large_segments(segmentation, max_size=3000) segmentation = remove_small_segments(segmentation, min_size=100) return segmentation
def test_creating_transformations_from_scratch(self): # What if the default names of images was just the order in which they # were created? # Or perhaps the order + the function name, e.g. # 1_gaussian.png # 2_sobel.png # 3_gaussian.png # The order could be tracked in a class variable in an AutoName # object. The AutoName object could also store the output directory # as a class variable. from jicbioimage.core.image import Image from jicbioimage.core.transform import transformation from jicbioimage.core.io import AutoName AutoName.directory = TMP_DIR @transformation def identity(image): return image image = Image.from_file(os.path.join(DATA_DIR, 'tjelvar.png')) image = identity(image) self.assertEqual(len(image.history), 1, image.history) self.assertEqual(str(image.history[-1]), '<History.Event(identity(image))>') created_fpath = os.path.join(TMP_DIR, '1_identity.png') self.assertTrue(os.path.isfile(created_fpath), 'No such file: {}'.format(created_fpath))
def annotate_single_identifier(dataset, identifier, output_path): file_path = dataset.abspath_from_identifier(identifier) image = Image.from_file(file_path) grayscale = np.mean(image, axis=2) annotated = AnnotatedImage.from_grayscale(grayscale) xdim, ydim, _ = annotated.shape def annotate_location(fractional_coords): xfrac, yfrac = fractional_coords ypos = int(ydim * xfrac) xpos = int(xdim * yfrac) for x in range(-2, 3): for y in range(-2, 3): annotated.draw_cross( (xpos+x, ypos+y), color=(255, 0, 0), radius=50 ) for loc in find_approx_plot_locs(dataset, identifier): annotate_location(loc) output_basename = os.path.basename(file_path) full_output_path = os.path.join(output_path, output_basename) with open(full_output_path, 'wb') as f: f.write(annotated.png())
def analyse_file(fpath, output_directory): """Analyse a single file.""" logging.info("Analysing file: {}".format(fpath)) AutoName.directory = output_directory image = Image.from_file(fpath) image = identity(image)
def labels_to_joined_image(labels): images = [] for plot_label in labels: image_fpath = dataset.item_content_abspath(label_to_id[plot_label]) image = Image.from_file(image_fpath) images.append(image) return join_horizontally(images)
def load_and_downscale(input_filename): """Load the image, covert to grayscale and downscale as needed.""" image = Image.from_file(input_filename) blue_channel = image[:,:,2] downscaled = downscale_local_mean(blue_channel, (2, 2)) return downscaled
def identifiers_to_joined_image(identifiers): images = [] for identifier in identifiers: image_fpath = dataset.item_content_abspath(identifier) image = Image.from_file(image_fpath) images.append(image) return join_horizontally(images)
def annotate(input_file, output_dir): """Write an annotated image to disk.""" logger.info("---") logger.info('Input image: "{}"'.format(os.path.abspath(input_file))) image = Image.from_file(input_file) intensity = mean_intensity_projection(image) norm_intensity = normalise(intensity) norm_rgb = np.dstack([norm_intensity, norm_intensity, norm_intensity]) name = fpath2name(input_file) png_name = name + ".png" csv_name = name + ".csv" png_path = os.path.join(output_dir, png_name) csv_path = os.path.join(output_dir, csv_name) tubes = find_tubes(input_file, output_dir) grains, difficult = find_grains(input_file, output_dir) tubes = remove_tubes_not_touching_grains(tubes, grains) tubes = remove_tubes_that_are_grains(tubes, grains) ann = AnnotatedImage.from_grayscale(intensity) num_grains = 0 for n, i in enumerate(grains.identifiers): n = n + 1 region = grains.region_by_identifier(i) ann.mask_region(region.inner.inner.inner.border.dilate(), color=(0, 255, 0)) num_grains = n num_tubes = 0 for n, i in enumerate(tubes.identifiers): n = n + 1 region = tubes.region_by_identifier(i) highlight = norm_rgb * pretty_color(i) ann[region] = highlight[region] ann.mask_region(region.dilate(3).border.dilate(3), color=pretty_color(i)) num_tubes = n ann.text_at("Num grains: {:3d}".format(num_grains), (10, 10), antialias=True, color=(0, 255, 0), size=48) logger.info("Num grains: {:3d}".format(num_grains)) ann.text_at("Num tubes : {:3d}".format(num_tubes), (60, 10), antialias=True, color=(255, 0, 255), size=48) logger.info("Num tubes : {:3d}".format(num_tubes)) logger.info('Output image: "{}"'.format(os.path.abspath(png_path))) with open(png_path, "wb") as fh: fh.write(ann.png()) logger.info('Output csv: "{}"'.format(os.path.abspath(csv_path))) with open(csv_path, "w") as fh: fh.write("{},{},{}\n".format(png_name, num_grains, num_tubes)) return png_name, num_grains, num_tubes
def annotate(input_file, output_dir): """Write an annotated image to disk.""" logger.info("---") logger.info('Input image: "{}"'.format(os.path.abspath(input_file))) image = Image.from_file(input_file) intensity = mean_intensity_projection(image) name = fpath2name(input_file) png_name = name + ".png" csv_name = name + ".csv" png_path = os.path.join(output_dir, png_name) csv_path = os.path.join(output_dir, csv_name) grains = find_grains(input_file, output_dir) ann = AnnotatedImage.from_grayscale(intensity) # Determine the median grain size based on the segmented regions. areas = [] for i in grains.identifiers: region = grains.region_by_identifier(i) areas.append(region.area) median_grain_size = np.median(areas) num_grains = 0 for i in grains.identifiers: region = grains.region_by_identifier(i) color = pretty_color(i) num_grains_in_area = region.area / median_grain_size num_grains_in_area = int(round(num_grains_in_area)) if num_grains_in_area == 0: continue outer_line = region.dilate().border outline = region.border.dilate() * np.logical_not(outer_line) ann.mask_region(outline, color=color) ann.text_at(str(num_grains_in_area), region.centroid, color=(255, 255, 255)) num_grains = num_grains + num_grains_in_area ann.text_at("Num grains: {:3d}".format(num_grains), (10, 10), antialias=True, color=(0, 255, 0), size=48) logger.info("Num grains: {:3d}".format(num_grains)) logger.info('Output image: "{}"'.format(os.path.abspath(png_path))) with open(png_path, "wb") as fh: fh.write(ann.png()) logger.info('Output csv: "{}"'.format(os.path.abspath(csv_path))) with open(csv_path, "w") as fh: fh.write("{},{}\n".format(png_name, num_grains)) return png_name, num_grains
def generate_column(numbers): images = [] for i in numbers: i = selected[i] image_fpath = dataset.item_content_abspath(i) images.append( downscale_local_mean(Image.from_file(image_fpath), (5, 5, 1)) ) column = join_horizontally(images) return column
def yield_stack_from_path(input_stack_path): """Yield individual images from stack path.""" all_files = os.listdir(input_stack_path) image_files = filter(is_image_filename, all_files) sorted_image_files = sorted_nicely(image_files) full_image_paths = [os.path.join(input_stack_path, fn) for fn in sorted_image_files] images = (Image.from_file(f) for f in full_image_paths) return images
def generate_plot_image_list(dataset, dates_to_identifiers): images = [] sorted_dates = sorted(dates_to_identifiers) for date in sorted_dates: identifier = dates_to_identifiers[date] image_abspath = dataset.item_content_abspath(identifier) image = Image.from_file(image_abspath) image = generate_image_with_colour_summary(image) images.append(image) return images
def load_segmentation_from_rgb_image(filename): rgb_image = Image.from_file(filename) ydim, xdim, _ = rgb_image.shape segmentation = np.zeros((ydim, xdim), dtype=np.uint32) segmentation += rgb_image[:, :, 2] segmentation += rgb_image[:, :, 1].astype(np.uint32) * 256 segmentation += rgb_image[:, :, 0].astype(np.uint32) * 256 * 256 return segmentation.view(SegmentedImage)
def generate_plots_image(dataset, dates_to_identifiers): images = [] sorted_dates = sorted(dates_to_identifiers) for date in sorted_dates: identifier = dates_to_identifiers[date] image_abspath = dataset.item_content_abspath(identifier) image = Image.from_file(image_abspath) images.append(image) output_image = join_horizontally(images) return output_image
def test_plot_colour_summary(dataset, working_dir): identifiers = dataset.identifiers identifier = identifiers[2004] plot_image = Image.from_file(dataset.item_content_abspath(identifier)) output_image = generate_image_with_colour_summary(plot_image) output_fpath = os.path.join(working_dir, 'colour.png') with open(output_fpath, 'wb') as fh: fh.write(output_image.view(Image).png()) return [('colour.png', {})]
def analyse_file_org(fpath, output_directory): """Analyse a single file.""" logging.info("Analysing file: {}".format(fpath)) image = Image.from_file(fpath) image = identity(image) image = select_red(image) image = invert(image) image = threshold_otsu(image) seeds = remove_small_objects(image, min_size=1000) seeds = fill_small_holes(seeds, min_size=1000) seeds = erode_binary(seeds, selem=disk(30)) seeds = connected_components(seeds, background=0) watershed_with_seeds(-image, seeds=seeds, mask=image)
def main(): # Parse the command line arguments. parser = argparse.ArgumentParser(description=__doc__) parser.add_argument("input_file", help="Input file") parser.add_argument("mask_file", help="Mask file") parser.add_argument("parameters_file", help="Parameters file") parser.add_argument("output_dir", help="Output directory") parser.add_argument("--debug", default=False, action="store_true", help="Write out intermediate images") args = parser.parse_args() # Check that the input file exists. if not os.path.isfile(args.input_file): parser.error("{} not a file".format(args.input_file)) if not os.path.isfile(args.parameters_file): parser.error("{} not a file".format(args.parameters_file)) # Read in the parameters. params = Parameters.from_file(args.parameters_file) # Create the output directory if it does not exist. if not os.path.isdir(args.output_dir): os.mkdir(args.output_dir) AutoName.directory = args.output_dir # Only write out intermediate images in debug mode. if not args.debug: AutoWrite.on = False # Setup a logger for the script. log_fname = "audit.log" log_fpath = os.path.join(args.output_dir, log_fname) logging_level = logging.INFO if args.debug: logging_level = logging.DEBUG logging.basicConfig(filename=log_fpath, level=logging_level) # Log some basic information about the script that is running. logging.info("Script name: {}".format(__file__)) logging.info("Script version: {}".format(__version__)) logging.info("Parameters: {}".format(params)) # Run the analysis. mask_im = Image.from_file(args.mask_file) mask = Region.select_from_array(mask_im, 0) identity(mask) analyse_file(args.input_file, mask, args.output_dir, **params)
def test_parse_manifest_raises_backwards_compatible_with_abs_paths(self): # Create manifest.json file without fpath. manifest_fp = os.path.join(TMP_DIR, 'manifest.json') shutil.copy(os.path.join(DATA_DIR, "tjelvar.png"), TMP_DIR) abs_im_fpath = os.path.join(TMP_DIR, 'tjelvar.png') entry = dict(filename=abs_im_fpath, series=0, channel=0, zslice=0, timepoint=0) with open(manifest_fp, 'w') as fh: json.dump([entry], fh) from jicbioimage.core.image import ImageCollection, Image image_collection = ImageCollection() image_collection.parse_manifest(manifest_fp) im = image_collection[0].image expected_im = Image.from_file(abs_im_fpath) import numpy as np self.assertTrue(np.array_equal(im, expected_im))
def find_template_leader(filename): """Find template kilobot for matching. Currently hard-c""" kilobot_image = Image.from_file(filename) red_only = kilobot_image[:,:,0] edges = find_edges(red_only) blurred = gaussian_filter(edges, sigma=5) x1 = 255 x2 = 325 y1 = 650 y2 = 710 bot_template = blurred[x1:x2,y1:y2] return bot_template
def find_template(filename): """Find template kilobot for matching. Currently hard-c""" kilobot_image = Image.from_file(filename) red_only = kilobot_image[:,:,0] edges = find_edges(red_only) blurred = gaussian_filter(edges, sigma=2) x1 = 135 x2 = 185 y1 = 485 y2 = 535 bot_template = blurred[135:185,485:535] return bot_template
def read_image_and_output_json(input_segmentation_filename, input_metadata_filename, input_has_filename): common_metadata = extract_common_metadata(input_metadata_filename) has_data = extract_has_data(input_has_filename) common_metadata.update(has_data) segmented_image = Image.from_file(input_segmentation_filename) identifier_image = convert_rgb_array_to_uint32(segmented_image) all_identifiers = np.unique(identifier_image) cell_dict = cell_dict_from_identifier_image(identifier_image) for cell in cell_dict.values(): cell.update(common_metadata) all_cells = {"cells": cell_dict} print json.dumps(all_cells, indent=2)
def highlight_plot(input_file, ouput_file, plot_id): """Highlight a particular plot in a field image""" image = Image.from_file(input_file) # Debug speed up. # image = image[0:500, 0:500] # Quicker run time for debugging purposes. name, ext = os.path.splitext(input_file) plots = segment(image) ann = get_grayscale_ann(image) ann = color_in_plots(ann, image, plots) ann = outline_plots(ann, image, plots) ann = red_outline(ann, plots, plot_id) with open(ouput_file, "wb") as fh: fh.write(ann.png())
def test_storing_array_argument_as_string(self): import numpy as np from jicbioimage.core.image import Image from jicbioimage.core.transform import transformation from jicbioimage.core.io import AutoName AutoName.directory = TMP_DIR @transformation def red_channel(image): return image[:, :, 0] @transformation def green_channel(image): return image[:, :, 1] @transformation def channel_diff(im1, im2): return np.abs(im1 - im2) org_im = Image.from_file(os.path.join(DATA_DIR, 'tjelvar.png')) green = green_channel(org_im) red = red_channel(org_im) # Test with args. diff = channel_diff(red, green) last_event = diff.history[-1] self.assertEqual(last_event.args[0], repr(green)) pos = hex(id(green)) expected = """<History.Event(red_channel(image))> <History.Event(channel_diff(image, '<Image object at {}, dtype=uint8>'))>""".format( pos) actual = "\n".join([str(e) for e in diff.history]) self.assertEqual(actual, expected) # Test with kwargs. diff = channel_diff(red, im2=green) last_event = diff.history[-1] self.assertEqual(last_event.kwargs["im2"], repr(green)) expected = """<History.Event(red_channel(image))> <History.Event(channel_diff(image, im2='<Image object at {}, dtype=uint8>'))>""".format( pos) actual = "\n".join([str(e) for e in diff.history]) self.assertEqual(actual, expected)
def test_storing_array_argument_as_string(self): import numpy as np from jicbioimage.core.image import Image from jicbioimage.core.transform import transformation from jicbioimage.core.io import AutoName AutoName.directory = TMP_DIR @transformation def red_channel(image): return image[:, :, 0] @transformation def green_channel(image): return image[:, :, 1] @transformation def channel_diff(im1, im2): return np.abs(im1 - im2) org_im = Image.from_file(os.path.join(DATA_DIR, 'tjelvar.png')) green = green_channel(org_im) red = red_channel(org_im) # Test with args. diff = channel_diff(red, green) last_event = diff.history[-1] self.assertEqual(last_event.args[0], repr(green)) pos = hex(id(green)) expected = """<History.Event(red_channel(image))> <History.Event(channel_diff(image, '<Image object at {}, dtype=uint8>'))>""".format(pos) actual = "\n".join([str(e) for e in diff.history]) self.assertEqual(actual, expected) # Test with kwargs. diff = channel_diff(red, im2=green) last_event = diff.history[-1] self.assertEqual(last_event.kwargs["im2"], repr(green)) expected = """<History.Event(red_channel(image))> <History.Event(channel_diff(image, im2='<Image object at {}, dtype=uint8>'))>""".format(pos) actual = "\n".join([str(e) for e in diff.history]) self.assertEqual(actual, expected)
def test_repr_with_int_arg(self): from jicbioimage.core.image import Image from jicbioimage.core.transform import transformation from jicbioimage.core.io import AutoName AutoName.directory = TMP_DIR image = Image.from_file(os.path.join(DATA_DIR, 'tjelvar.png')) image = image[:, :, 0] @transformation def threshold_abs(image, cutoff): """Return thresholded image.""" return image > cutoff image = threshold_abs(image, 50) event = image.history[0] self.assertEqual(repr(event), "<History.Event(threshold_abs(image, 50))>")
def analyse_file(fpath, output_directory, test_data_only=False): """Analyse a single file.""" logging.info("Analysing file: {}".format(fpath)) AutoName.directory = output_directory image = Image.from_file(fpath) negative = get_negative_single_channel(image) seeds = find_seeds(negative) mask = find_mask(negative) eaten_leaf_segmentation = watershed_with_seeds(negative, seeds=seeds, mask=mask) whole_leaf_segmentation = post_process_segmentation( eaten_leaf_segmentation.copy()) ann = annotate(image, whole_leaf_segmentation, eaten_leaf_segmentation) ann_fpath = os.path.join(output_directory, "annotated.png") with open(ann_fpath, "wb") as fh: fh.write(ann.png())
def analyse_file(fpath, output_directory): """Analyse a single file.""" logging.info("Analysing file: {}".format(fpath)) image = Image.from_file(fpath) image = identity(image)
def test_16bit_tiff_file(self): from jicbioimage.core.image import Image im = Image.from_file(os.path.join(DATA_DIR, 'white-16bit.tiff')) self.assertEqual(im.dtype, np.uint16) self.assertEqual(np.max(im), np.iinfo(np.uint16).max)
def test_png_type(self): from jicbioimage.core.image import Image fpath = os.path.join(DATA_DIR, 'tjelvar.png') image = Image.from_file(fpath) self.assertEqual(type(image.png()), bytes)