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convert_firebase_to_labels.py
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import logging
logger = logging.getLogger()
logger.setLevel(logging.INFO)
import os
import json
from pathlib import Path
import numpy as np
import pandas as pd
import imageio
from Scantensus.datasets.unity import UnityO
from Scantensus.utils.json import get_cols_from_firebase_project_config, get_labels_from_firebase_project_data
HOST = "matt-laptop"
###############
if HOST == "server":
DATA_DIR = Path("/") / "mnt" / "Storage" / "scantensus-data"
OUTPUT_DIR = Path("/") / "mnt" / "Storage" / "matt-output"
elif HOST == "matt-laptop":
DATA_DIR = Path("/") / "Volumes" / "Matt-Data" / "Projects-Clone" / "scantensus-data"
OUTPUT_DIR = Path("/") / "Volumes" / "Matt-Data" / "matt-output"
else:
raise Exception
################
CSV_KEYS_IN_PATH = DATA_DIR / "resources" / "keys.csv"
MAPPING_DB_PATH = DATA_DIR / "resources" / "mapping.csv"
FIREBASE_IN_PATH = DATA_DIR / "firebase" / "scantensus-export.json"
PNG_CACHE_DIR = DATA_DIR / "png-cache"
####################
SOURCE = "d"
if SOURCE == "a":
GROUP = 'Unity'
PROJECTS = [
'luxy-chambers',
'unity-a2c-1',
'unity-a4c-1',
'unity-plax-1',
'imp-echo-ao-plax',
'unity-plax-1-b',
'imp-echo-stowell-a4c-lv-systole',
'imp-echo-stowell-a3c',
'imp-echo-shunshin-a5c-lv-segment',
'imp-echo-shunshin-plax-measure',
'imp-echo-shunshin-a4c-lv',
'imp-echo-stowell-plax-measure-train-b',
'imp-echo-shunshin-plax-measure-fix-1',
'imp-echo-shunshin-a4c-zoom-3point',
'imp-echo-shunshin-a4c-3point-difficult',
]
elif SOURCE == "b":
GROUP = 'james'
PROJECTS = [
'unity-a2c-1',
'unity-a4c-1',
'imp-echo-stowell-a4c-lv-systole',
'imp-echo-stowell-a3c',
'imp-echo-shunshin-a5c-lv-segment',
'imp-echo-shunshin-a4c-lv',
'imp-echo-shunshin-a4c-zoom-3point',
'imp-echo-shunshin-a4c-3point-difficult',
]
elif SOURCE == 'c':
GROUP = 'plax'
PROJECTS = [
'imp-echo-shunshin-plax-measure',
'imp-echo-stowell-plax-measure-train-b',
]
elif SOURCE == 'd':
GROUP = 'validation100-a4c-flick'
PROJECTS = [
"imp-echo-shunshin-validation100-a4c-flick"
]
else:
raise Exception
############
LABELS_OUT_DIR = DATA_DIR / "labels" / GROUP
os.makedirs(name=LABELS_OUT_DIR, exist_ok=True)
JSON_KEYS_OUT_PATH = LABELS_OUT_DIR / "keys.json"
JSON_ALL_LABELS_OUT_PATH = LABELS_OUT_DIR / "labels-all.json"
JSON_TRAIN_LABELS_OUT_PATH = LABELS_OUT_DIR / "labels-train.json"
JSON_VAL_LABELS_OUT_PATH = LABELS_OUT_DIR / "labels-val.json"
TXT_ALL_KEYS_OUT_PATH = LABELS_OUT_DIR / "labels-all.txt"
TXT_TRAIN_KEYS_OUT_PATH = LABELS_OUT_DIR / "labels-train.txt"
TXT_VAL_KEYS_OUT_PATH = LABELS_OUT_DIR / "labels-val.txt"
CSV_ALL_LABELS_OUT_PATH = LABELS_OUT_DIR / "labels-all.csv"
CSV_ALL_USER_LABELS_OUT_PATH = LABELS_OUT_DIR / "user-labels-all.csv"
#############
if __name__ == "__main__":
logging.info("Starting")
keys_db_pd = pd.read_csv(CSV_KEYS_IN_PATH, index_col='name')
keys_db_pd = keys_db_pd.loc[keys_db_pd['active'] == 'yes']
keys_db = keys_db_pd.to_dict("index")
with open(JSON_KEYS_OUT_PATH, 'w') as outfile:
json.dump(keys_db, outfile, indent=4)
mapping_db = pd.read_csv(MAPPING_DB_PATH)
with open(FIREBASE_IN_PATH, "r") as f:
firebase_data = json.load(f)
project_dbs = []
#PROJECTS = list(pd.unique(mapping_db['project']))
print(f'Projects to be included: {PROJECTS}')
for project in PROJECTS:
mapping_data = {}
for _, row in mapping_db[mapping_db['project'] == project].iterrows():
mapping_data[row['name_old']] = row['name_new']
project_config_data = firebase_data['fiducial'][project]['config']
col_data = get_cols_from_firebase_project_config(config_data=project_config_data)
print(col_data)
project_data = firebase_data['fiducial'][project]['labels']
db = get_labels_from_firebase_project_data(project_data=project_data,
project=project,
mapping_data=mapping_data)
project_dbs.extend(db)
db_all = pd.DataFrame(project_dbs)
db_all.to_csv(CSV_ALL_USER_LABELS_OUT_PATH)
db_final = db_all.sort_values(by=['file', 'label', 'time']).groupby(['file', 'label']).last().reset_index()
files = list(set(db_final['file']))
json_out = {}
for i, file in enumerate(files):
print(i)
file_out = {}
file_out['labels'] = {}
file_db = db_final[db_final['file'] == file]
file_projects = list(set(file_db['project']))
for label_name, label_data in keys_db.items():
file_label_out = {}
main_vis = [keys_db[label_name][x] == 'yes' for x in file_projects]
main_vis = any(main_vis)
file_label_row = file_db[file_db['label'] == label_name]
if len(file_label_row) == 0:
if main_vis:
true_vis = 'blurred'
else:
true_vis = 'off'
file_label_out['type'] = true_vis
file_label_out["y"] = ""
file_label_out["x"] = ""
file_out['labels'][label_name] = file_label_out
continue
else:
label_vis = file_label_row['vis'].item()
if not main_vis:
true_vis = 'off'
else:
true_vis = label_vis
if true_vis == 'off':
file_label_out['type'] = 'off'
file_label_out["y"] = ""
file_label_out["x"] = ""
file_out['labels'][label_name] = file_label_out
continue
if true_vis == 'blurred':
file_label_out['type'] = 'blurred'
file_label_out["y"] = ""
file_label_out["x"] = ""
file_out['labels'][label_name] = file_label_out
continue
file_label_out['type'] = label_data['type']
file_label_out["y"] = file_label_row['value_y'].item()
file_label_out["x"] = file_label_row['value_x'].item()
#file_label_out['time'] = file_label_row['time'].item()
#file_label_out['project'] = file_label_row['project'].item()
file_out['labels'][label_name] = file_label_out
json_out[file] = file_out
for file, node in json_out.items():
try:
# RV Apex
if node['labels']['curve-rv-endo']['type'] == 'curve':
x = node['labels']['curve-rv-endo']['x']
y = node['labels']['curve-rv-endo']['y']
x = [float(value) for value in x.split()]
y = [float(value) for value in y.split()]
min_y = min(y)
min_y_x = x[y.index(min_y)]
node['labels']['rv-apex-endo'] = {}
node['labels']['rv-apex-endo']['type'] = 'point'
node['labels']['rv-apex-endo']['x'] = str(min_y_x)
node['labels']['rv-apex-endo']['y'] = str(min_y)
else:
node['labels']['rv-apex-endo'] = {}
node['labels']['rv-apex-endo']['type'] = node['labels']['curve-rv-endo']['type']
node['labels']['rv-apex-endo']['x'] = ""
node['labels']['rv-apex-endo']['y'] = ""
# LV antsep-endo apex
if node['labels']['curve-lv-antsep-endo']['type'] == 'curve':
x = node['labels']['curve-lv-antsep-endo']['x']
y = node['labels']['curve-lv-antsep-endo']['y']
x = [float(value) for value in x.split()]
y = [float(value) for value in y.split()]
find_x = min(x)
find_x_y = y[x.index(find_x)]
node['labels']['lv-antsep-endo-apex'] = {}
node['labels']['lv-antsep-endo-apex']['type'] = 'point'
node['labels']['lv-antsep-endo-apex']['x'] = str(find_x)
node['labels']['lv-antsep-endo-apex']['y'] = str(find_x_y)
else:
node['labels']['lv-antsep-endo-apex'] = {}
node['labels']['lv-antsep-endo-apex']['type'] = node['labels']['curve-lv-antsep-endo']['type']
node['labels']['lv-antsep-endo-apex']['x'] = ""
node['labels']['lv-antsep-endo-apex']['y'] = ""
# LV antsep-endo base
if node['labels']['curve-lv-antsep-endo']['type'] == 'curve':
x = node['labels']['curve-lv-antsep-endo']['x']
y = node['labels']['curve-lv-antsep-endo']['y']
x = [float(value) for value in x.split()]
y = [float(value) for value in y.split()]
find_x = max(x)
find_x_y = y[x.index(find_x)]
node['labels']['lv-antsep-endo-base'] = {}
node['labels']['lv-antsep-endo-base']['type'] = 'point'
node['labels']['lv-antsep-endo-base']['x'] = str(find_x)
node['labels']['lv-antsep-endo-base']['y'] = str(find_x_y)
else:
node['labels']['lv-antsep-endo-base'] = {}
node['labels']['lv-antsep-endo-base']['type'] = node['labels']['curve-lv-antsep-endo']['type']
node['labels']['lv-antsep-endo-base']['x'] = ""
node['labels']['lv-antsep-endo-base']['y'] = ""
# LV antsep-rv apex
if node['labels']['curve-lv-antsep-rv']['type'] == 'curve':
x = node['labels']['curve-lv-antsep-rv']['x']
y = node['labels']['curve-lv-antsep-rv']['y']
x = [float(value) for value in x.split()]
y = [float(value) for value in y.split()]
find_x = min(x)
find_x_y = y[x.index(find_x)]
node['labels']['lv-antsep-rv-apex'] = {}
node['labels']['lv-antsep-rv-apex']['type'] = 'point'
node['labels']['lv-antsep-rv-apex']['x'] = str(find_x)
node['labels']['lv-antsep-rv-apex']['y'] = str(find_x_y)
else:
node['labels']['lv-antsep-rv-apex'] = {}
node['labels']['lv-antsep-rv-apex']['type'] = node['labels']['curve-lv-antsep-rv']['type']
node['labels']['lv-antsep-rv-apex']['y'] = ""
node['labels']['lv-antsep-rv-apex']['x'] = ""
# LV antsep-rv base
if node['labels']['curve-lv-antsep-rv']['type'] == 'curve':
x = node['labels']['curve-lv-antsep-rv']['x']
y = node['labels']['curve-lv-antsep-rv']['y']
x = [float(value) for value in x.split()]
y = [float(value) for value in y.split()]
find_x = max(x)
find_x_y = y[x.index(find_x)]
node['labels']['lv-antsep-rv-base'] = {}
node['labels']['lv-antsep-rv-base']['type'] = 'point'
node['labels']['lv-antsep-rv-base']['x'] = str(find_x)
node['labels']['lv-antsep-rv-base']['y'] = str(find_x_y)
else:
node['labels']['lv-antsep-rv-base'] = {}
node['labels']['lv-antsep-rv-base']['type'] = node['labels']['curve-lv-antsep-rv']['type']
node['labels']['lv-antsep-rv-base']['y'] = ""
node['labels']['lv-antsep-rv-base']['x'] = ""
# LV post-endo apex
if node['labels']['curve-lv-post-endo']['type'] == 'curve':
x = node['labels']['curve-lv-post-endo']['x']
y = node['labels']['curve-lv-post-endo']['y']
x = [float(value) for value in x.split()]
y = [float(value) for value in y.split()]
find_x = min(x)
find_x_y = y[x.index(find_x)]
node['labels']['lv-post-endo-apex'] = {}
node['labels']['lv-post-endo-apex']['type'] = 'point'
node['labels']['lv-post-endo-apex']['x'] = str(find_x)
node['labels']['lv-post-endo-apex']['y'] = str(find_x_y)
else:
node['labels']['lv-post-endo-apex'] = {}
node['labels']['lv-post-endo-apex']['type'] = node['labels']['curve-lv-post-endo']['type']
node['labels']['lv-post-endo-apex']['y'] = ""
node['labels']['lv-post-endo-apex']['x'] = ""
# LV post-endo base
if node['labels']['curve-lv-post-endo']['type'] == 'curve':
x = node['labels']['curve-lv-post-endo']['x']
y = node['labels']['curve-lv-post-endo']['y']
x = [float(value) for value in x.split()]
y = [float(value) for value in y.split()]
find_x = max(x)
find_x_y = y[x.index(find_x)]
node['labels']['lv-post-endo-base'] = {}
node['labels']['lv-post-endo-base']['type'] = 'point'
node['labels']['lv-post-endo-base']['x'] = str(find_x)
node['labels']['lv-post-endo-base']['y'] = str(find_x_y)
else:
node['labels']['lv-post-endo-base'] = {}
node['labels']['lv-post-endo-base']['type'] = node['labels']['curve-lv-post-endo']['type']
node['labels']['lv-post-endo-base']['y'] = ""
node['labels']['lv-post-endo-base']['x'] = ""
# LV post-epi apex
if node['labels']['curve-lv-post-epi']['type'] == 'curve':
x = node['labels']['curve-lv-post-epi']['x']
y = node['labels']['curve-lv-post-epi']['y']
x = [float(value) for value in x.split()]
y = [float(value) for value in y.split()]
find_x = min(x)
find_x_y = y[x.index(find_x)]
node['labels']['lv-post-epi-apex'] = {}
node['labels']['lv-post-epi-apex']['type'] = 'point'
node['labels']['lv-post-epi-apex']['x'] = str(find_x)
node['labels']['lv-post-epi-apex']['y'] = str(find_x_y)
else:
node['labels']['lv-post-epi-apex'] = {}
node['labels']['lv-post-epi-apex']['type'] = node['labels']['curve-lv-post-epi']['type']
node['labels']['lv-post-epi-apex']['y'] = ""
node['labels']['lv-post-epi-apex']['x'] = ""
# LV post-epi base
if node['labels']['curve-lv-post-epi']['type'] == 'curve':
x = node['labels']['curve-lv-post-epi']['x']
y = node['labels']['curve-lv-post-epi']['y']
x = [float(value) for value in x.split()]
y = [float(value) for value in y.split()]
find_x = max(x)
find_x_y = y[x.index(find_x)]
node['labels']['lv-post-epi-base'] = {}
node['labels']['lv-post-epi-base']['type'] = 'point'
node['labels']['lv-post-epi-base']['x'] = str(find_x)
node['labels']['lv-post-epi-base']['y'] = str(find_x_y)
else:
node['labels']['lv-post-epi-base'] = {}
node['labels']['lv-post-epi-base']['type'] = node['labels']['curve-lv-post-epi']['type']
node['labels']['lv-post-epi-base']['y'] = ""
node['labels']['lv-post-epi-base']['x'] = ""
top = node['labels']['lv-ivs-top']
bottom = node['labels']['lv-pw-bottom']
if top['type'] == bottom['type'] == "point":
x_top = float(top['x'])
y_top = float(top['y'])
x_bot = float(bottom['x'])
y_bot = float(bottom['y'])
x_mid = (x_top + x_bot) / 2
y_mid = (y_top + y_bot) / 2
x = [x_top, x_mid, x_bot]
y = [y_top, y_mid, y_bot]
node['labels']['curve-lv-ed-connect'] = {}
node['labels']['curve-lv-ed-connect']['type'] = 'curve'
node['labels']['curve-lv-ed-connect']['x'] = " ".join([str(round(value, 1)) for value in x])
node['labels']['curve-lv-ed-connect']['y'] = " ".join([str(round(value, 1)) for value in y])
unity_o = UnityO(unity_code=file, png_cache_dir=Path(PNG_CACHE_DIR))
img = imageio.imread(unity_o.get_frame_path())
x_dir = np.sign(x_bot - x_top)
y_dir = np.sign(y_bot - y_top)
x_step = (x_bot - x_top) / np.abs(y_bot - y_top)
y_step = (y_bot - y_top) / np.abs(x_bot - x_top)
if x_step > y_step:
test_y = (np.arange(0, 7) * y_step) + y_bot
test_x = (np.arange(0, 7) * x_dir) + x_bot
else:
test_y = (np.arange(0, 7) * y_dir) + y_bot
test_x = (np.arange(0, 7) * x_step) + x_bot
print(test_y, test_x)
values = img[np.round(test_y).astype(np.int), np.round(test_x).astype(np.int)]
values = values.astype(np.float)
if values.ndim == 2:
values = np.sum(values, axis=-1)
if np.argmax(values) == 0:
shift = 0
else:
shift = np.argmax(np.diff(values)) + 1
print(shift)
new_y_bot = test_y[shift]
new_x_bot = test_x[shift]
bottom['y'] = str(round(new_y_bot, 1))
bottom['x'] = str(round(new_x_bot, 1))
elif top == bottom == 'off':
node['labels']['curve-lv-ed-connect'] = {}
node['labels']['curve-lv-ed-connect']['type'] = 'off'
node['labels']['curve-lv-ed-connect']['y'] = ""
node['labels']['curve-lv-ed-connect']['x'] = ""
else:
node['labels']['curve-lv-ed-connect'] = {}
node['labels']['curve-lv-ed-connect']['type'] = 'blurred'
node['labels']['curve-lv-ed-connect']['y'] = ""
node['labels']['curve-lv-ed-connect']['x'] = ""
ant = node['labels']['mv-ant-hinge']
post = node['labels']['mv-post-hinge']
apex = node['labels']['lv-apex-endo']
curve_name = "curve-mv-hinge-connect"
if ant['type'] == post['type'] == 'point':
start_x = float(ant['x'])
start_y = float(ant['y'])
end_x = float(post['x'])
end_y = float(post['y'])
mid_x = (start_x + end_x) / 2
mid_y = (start_y + end_y) / 2
x = [start_x, mid_x, end_x]
y = [start_y, mid_y, end_y]
node['labels'][curve_name] = {}
node['labels'][curve_name]['type'] = 'curve'
node['labels'][curve_name]['x'] = " ".join([str(round(value, 1)) for value in x])
node['labels'][curve_name]['y'] = " ".join([str(round(value, 1)) for value in y])
elif ant['type'] == post['type'] == 'off':
node['labels'][curve_name] = {}
node['labels'][curve_name]['type'] = 'off'
node['labels'][curve_name]['y'] = ""
node['labels'][curve_name]['x'] = ""
else:
node['labels'][curve_name] = {}
node['labels'][curve_name]['type'] = 'blurred'
node['labels'][curve_name]['y'] = ""
node['labels'][curve_name]['x'] = ""
curve_name = "curve-mv-ant-apex-connect"
if ant['type'] == apex['type'] == 'point':
start_x = float(ant['x'])
start_y = float(ant['y'])
end_x = float(apex['x'])
end_y = float(apex['y'])
mid_x = (start_x + end_x) / 2
mid_y = (start_y + end_y) / 2
x = [start_x, mid_x, end_x]
y = [start_y, mid_y, end_y]
node['labels'][curve_name] = {}
node['labels'][curve_name]['type'] = 'curve'
node['labels'][curve_name]['x'] = " ".join([str(round(value, 1)) for value in x])
node['labels'][curve_name]['y'] = " ".join([str(round(value, 1)) for value in y])
elif ant['type'] == apex['type'] == 'off':
node['labels'][curve_name] = {}
node['labels'][curve_name]['type'] = 'off'
node['labels'][curve_name]['y'] = ""
node['labels'][curve_name]['x'] = ""
else:
node['labels'][curve_name] = {}
node['labels'][curve_name]['type'] = 'blurred'
node['labels'][curve_name]['y'] = ""
node['labels'][curve_name]['x'] = ""
curve_name = "curve-mv-post-apex-connect"
if post['type'] == apex['type'] == 'point':
start_x = float(post['x'])
start_y = float(post['y'])
end_x = float(apex['x'])
end_y = float(apex['y'])
mid_x = (start_x + end_x) / 2
mid_y = (start_y + end_y) / 2
x = [start_x, mid_x, end_x]
y = [start_y, mid_y, end_y]
node['labels'][curve_name] = {}
node['labels'][curve_name]['type'] = 'curve'
node['labels'][curve_name]['y'] = " ".join([str(round(value, 1)) for value in y])
node['labels'][curve_name]['x'] = " ".join([str(round(value, 1)) for value in x])
elif post['type'] == apex['type'] == 'off':
node['labels'][curve_name] = {}
node['labels'][curve_name]['type'] = 'off'
node['labels'][curve_name]['y'] = ""
node['labels'][curve_name]['x'] = ""
else:
node['labels'][curve_name] = {}
node['labels'][curve_name]['type'] = 'blurred'
node['labels'][curve_name]['y'] = ""
node['labels'][curve_name]['x'] = ""
except Exception as e:
print(e)
pass
json_train_out = {}
json_val_out = {}
if False:
new_json_out = {}
for file, node in json_out.items():
#if node['labels']["mv-ant-hinge"]['type'] == node['labels']["mv-post-hinge"]['type'] == node['labels']["lv-apex-endo"]['type'] == 'point' or node['labels']['curve-lv-endo']['type'] == 'curve':
if node['labels']["lv-ivs-top"]['type'] == node['labels']["lv-ivs-bottom"]['type'] == node['labels']["lv-pw-top"]['type'] == node['labels']["lv-pw-bottom"]['type'] == 'point':
new_json_out[file] = node
json_out = new_json_out
for image_fn, image_data in json_out.items():
num_split = int(image_fn.split("-")[1], 16) % 10
if num_split < 8:
json_train_out[image_fn] = image_data
else:
json_val_out[image_fn] = image_data
with open(JSON_ALL_LABELS_OUT_PATH, 'w') as outfile:
json.dump(json_out, outfile, indent=4)
with open(JSON_TRAIN_LABELS_OUT_PATH, 'w') as outfile:
json.dump(json_train_out, outfile, indent=4)
with open(JSON_VAL_LABELS_OUT_PATH, 'w') as outfile:
json.dump(json_val_out, outfile, indent=4)
all_keys = json_out.keys()
all_keys = map(lambda x: x + '\n', all_keys)
train_keys = json_train_out.keys()
train_keys = map(lambda x: x + '\n', train_keys)
val_keys = json_val_out.keys()
val_keys = map(lambda x: x + '\n', val_keys)
with open(TXT_ALL_KEYS_OUT_PATH, 'w') as outfile:
outfile.writelines(all_keys)
with open(TXT_TRAIN_KEYS_OUT_PATH, 'w') as outfile:
outfile.writelines(train_keys)
with open(TXT_VAL_KEYS_OUT_PATH, 'w') as outfile:
outfile.writelines(val_keys)
out_csv = []
points = ["lv-ivs-top", "lv-ivs-bottom", "lv-pw-top", "lv-pw-bottom"]
for file, node in json_out.items():
for point in points:
if node['labels'][point]['type'] == 'point':
out = {}
out['file'] = file
out['user'] = 'expert-last'
out['time'] = '2100-01-02T01:01:01.001Z'
out['label'] = point
out['type'] = node['labels'][point]['type']
out['y'] = node['labels'][point]['y']
out['x'] = node['labels'][point]['x']
out_csv.append(out)
out_csv = pd.DataFrame(out_csv)
out_csv.to_csv(CSV_ALL_LABELS_OUT_PATH)
print("finished")