def run(overlay, src):
subdirs = get_masks_to_process(src, STRAIGHTENED_MASKS_DIR)
for dir in subdirs:
masks = dir["files"]
avg_filename = generate_avg_filename(masks)
masks = [cv2.imread(m, cv2.IMREAD_GRAYSCALE) for m in masks]
avg_mask = create_average_mask(masks)
dest_dir = os.path.join(dir["path"], "..", AVERAGE_MASK_DIR)
try:
shutil.rmtree(dest_dir)
except Exception as e:
pass
os.makedirs(dest_dir, exist_ok=True)
cv2.imwrite(os.path.join(dest_dir, avg_filename), avg_mask)
if overlay:
avg_image = create_average_overlay(masks)
dest_dir = os.path.join(dir["path"], "..", AVERAGE_OVERLAY_DIR)
try:
shutil.rmtree(dest_dir)
except Exception as e:
pass
os.makedirs(dest_dir, exist_ok=True)
cv2.imwrite(os.path.join(dest_dir, avg_filename), avg_image)
def run(dest, destdir, destsub, visualize, keep, src):
if not src:
click.secho("No source specified. Use --src", fg="red")
return
subdirs = get_masks_to_process(src, STRAIGHTENED_MASKS_DIR)
regr = load("tip-mask-model.joblib")
# detip masks
with Pool(processes=cpu_count()) as pool:
pool.starmap(tip_mask,
[(dir["path"], regr, visualize) for dir in subdirs])
if dest:
if not os.path.exists(dest):
pathlib.Path(dest).mkdir(parents=True)
subdirs = get_masks_to_process(src, DETIPPED_MASKS_DIR)
# moving detipped masks
with Pool(processes=cpu_count()) as pool:
pool.starmap(copy_results, [(dir["path"], dest, destdir, destsub)
for dir in subdirs])
def run(dest, dry, src):
instances_dict = {}
subdirs = get_masks_to_process(src, BINARY_MASKS_DIR)
for dir in subdirs:
for file in dir["files"]:
try:
instance = assemble_instance(file)
instance_key = f"{instance['UID']}___{instance['Nut']}"
if instance_key not in instances_dict.keys():
instances_dict[instance_key] = {f"{instance['type']}": instance}
else:
instances_dict[instance_key][instance["type"]] = instance
if dry:
print(instance)
except Exception as e:
print(e)
if not dry:
spit_out_csv(instances_dict, dest)
def run(dest, destdir, destsub, keep, smoothen, src):
if not src:
click.secho("No source specified. Use --src", fg="red")
return
subdirs = get_masks_to_process(src, BINARY_MASKS_DIR)
# straighten masks
with Pool(processes=cpu_count()) as pool:
pool.starmap(straighten_binary_masks,
[(dir["path"], ) for dir in subdirs])
if dest and not os.path.exists(dest):
pathlib.Path(dest).mkdir(parents=True)
# moving masks
with Pool(processes=cpu_count()) as pool:
pool.starmap(copy_results, [(dir["path"], dest) for dir in subdirs])
def run(collection, csv, dry, src, type, verbose):
"""
Curvature: mm (describing the number of mm the carrot has been pulled down to center)
Biomass: mm^2
Max_width: mm
Length: mm
L/W ratio: mm / mm
Shoulder top / bottom: mm^2
Tip angle top / bottom: absolute value of angle up/down from center line
above tipangle top: mm2
above tipangle bottom: mm2
"""
mask_type = type
if mask_type is None and not csv:
click.echo("No mask type specified...")
click.echo("run 'python phenotype.py --help to see options'")
return
if src is None and csv is None:
click.echo("No source specified...")
click.echo("run 'python phenotype.py --help to see options'")
return
if src is not None and csv is not None:
click.echo(
"Both source and csv file specified. I can only do one thing at a time"
)
click.echo("run 'python phenotype.py --help to see options'")
return
if csv is not None and not csv.endswith(".csv"):
click.echo("That doesn't look like a csv file.")
return
tic = timeit.default_timer()
if dry:
collection = None
else:
collection = get_collection(collection)
inserted = 0
updated = 0
if src is not None:
type_map = {
"binary": BINARY_MASKS_DIR,
"straight": STRAIGHTENED_MASKS_DIR,
"detipped": DETIPPED_MASKS_DIR,
}
subdirs = get_masks_to_process(src, type_map[mask_type])
for dir in subdirs:
for file in dir["files"]:
try:
instance = assemble_instance(file)
except Exception as e:
print(e)
instance = None
click.secho(file, fg="red")
if instance is not None:
if dry:
print(instance)
else:
try:
action = insert_or_update_instance(
collection, instance, verbose)
except Exception as e:
click.secho(f"failed to insert {file}", fg="red")
if action == "inserted":
inserted += 1
elif action == "updated":
updated += 1
if csv is not None:
instances = assemble_instance_from_csv(csv)
for instance in instances:
if dry:
print(instance)
else:
action = insert_or_update_instance(collection, instance)
if action == "inserted":
inserted += 1
elif action == "updated":
updated += 1
toc = timeit.default_timer()
duration = toc - tic
msg = "Inserted %s and updated %s in %.2f seconds." % (inserted, updated,
duration)
click.secho(msg, fg="green")