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utils.py
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import yaml
import json
import os
import socket
import requests
import urllib.request
import shutil
import utilsDataman
import pickle
import glob
import mimetypes
import subprocess
import zipfile
import time
import numpy as np
import pandas as pd
from scipy import signal
from utilsAuth import getToken
from utilsAPI import getAPIURL
API_URL = getAPIURL()
API_TOKEN = getToken()
#%% Rest of utils
def getDataDirectory(isDocker=False):
computername = socket.gethostname()
# Paths to OpenPose folder for local testing.
if computername == 'SUHLRICHHPLDESK':
dataDir = 'C:/Users/scott.uhlrich/MyDrive/mobilecap/'
elif computername == "LAPTOP-7EDI4Q8Q":
dataDir = 'C:\MyDriveSym/mobilecap/'
elif computername == 'DESKTOP-0UPR1OH':
dataDir = 'C:/Users/antoi/Documents/MyRepositories/mobilecap_data/'
elif computername == 'HPL1':
dataDir = 'C:/Users/opencap/Documents/MyRepositories/mobilecap_data/'
elif computername == 'DESKTOP-GUEOBL2':
dataDir = 'C:/Users/opencap/Documents/MyRepositories/mobilecap_data/'
elif computername == 'DESKTOP-L9OQ0MS':
dataDir = 'C:/Users/antoi/Documents/MyRepositories/mobilecap_data/'
elif computername == 'clarkadmin-MS-7996':
dataDir = '/home/clarkadmin/Documents/MyRepositories/mobilecap_data/'
elif computername == 'DESKTOP-NJMGEBG':
dataDir = 'C:/Users/opencap/Documents/MyRepositories/mobilecap_data/'
elif isDocker:
dataDir = os.getcwd()
else:
dataDir = os.getcwd()
return dataDir
def getOpenPoseDirectory(isDocker=False):
computername = os.environ.get('COMPUTERNAME', None)
# Paths to OpenPose folder for local testing.
if computername == "DESKTOP-0UPR1OH":
openPoseDirectory = "C:/Software/openpose-1.7.0-binaries-win64-gpu-python3.7-flir-3d_recommended/openpose"
elif computername == "HPL1":
openPoseDirectory = "C:/Users/opencap/Documents/MySoftware/openpose-1.7.0-binaries-win64-gpu-python3.7-flir-3d_recommended/openpose"
elif computername == "DESKTOP-GUEOBL2":
openPoseDirectory = "C:/Software/openpose-1.7.0-binaries-win64-gpu-python3.7-flir-3d_recommended/openpose"
elif computername == "DESKTOP-L9OQ0MS":
openPoseDirectory = "C:/Software/openpose-1.7.0-binaries-win64-gpu-python3.7-flir-3d_recommended/openpose"
elif isDocker:
openPoseDirectory = "docker"
elif computername == 'SUHLRICHHPLDESK':
openPoseDirectory = "C:/openpose/"
elif computername == "LAPTOP-7EDI4Q8Q":
openPoseDirectory = "C:/openpose/"
elif computername == "DESKTOP-NJMGEBG":
openPoseDirectory = "C:/openpose/"
else:
openPoseDirectory = "C:/openpose/"
return openPoseDirectory
def getMMposeDirectory(isDocker=False):
computername = socket.gethostname()
# Paths to OpenPose folder for local testing.
if computername == "clarkadmin-MS-7996":
mmposeDirectory = "/home/clarkadmin/Documents/MyRepositories/MoVi_analysis/model_ckpts"
else:
mmposeDirectory = ''
return mmposeDirectory
def loadCameraParameters(filename):
open_file = open(filename, "rb")
cameraParams = pickle.load(open_file)
open_file.close()
return cameraParams
def importMetadata(filePath):
myYamlFile = open(filePath)
parsedYamlFile = yaml.load(myYamlFile, Loader=yaml.FullLoader)
return parsedYamlFile
def download_file(url, file_name):
with urllib.request.urlopen(url) as response, open(file_name, 'wb') as out_file:
shutil.copyfileobj(response, out_file)
def getTrialJson(trial_id):
trialJson = requests.get(API_URL + "trials/{}/".format(trial_id),
headers = {"Authorization": "Token {}".format(API_TOKEN)}).json()
return trialJson
def getSessionJson(session_id):
sessionJson = requests.get(API_URL + "sessions/{}/".format(session_id),
headers = {"Authorization": "Token {}".format(API_TOKEN)}).json()
# sort trials by time recorded
def getCreatedAt(trial):
return trial['created_at']
sessionJson['trials'].sort(key=getCreatedAt)
return sessionJson
def getSubjectJson(subject_id):
subjectJson = requests.get(API_URL + "subjects/{}/".format(subject_id),
headers = {"Authorization": "Token {}".format(API_TOKEN)}).json()
return subjectJson
def getTrialName(trial_id):
trial = getTrialJson(trial_id)
trial_name = trial['name']
trial_name = trial_name.replace(' ', '')
return trial_name
def writeMediaToAPI(API_URL,media_path,trial_id,tag=None,deleteOldMedia=False):
if deleteOldMedia:
deleteResult(trial_id, tag=tag)
for filename in os.listdir(media_path):
thisMimeType = mimetypes.guess_type(filename)
if thisMimeType[0] is not None and not os.path.isdir(filename):
print(filename)
fileType = thisMimeType[0][0:thisMimeType[0].find('/')]
if fileType == 'image' or fileType == 'video' or fileType == 'application':
fullpath = "{}/{}".format(media_path, filename)
if fileType == 'image' and tag == "calibration-img":
cam = filename[filename.find('Cam'):filename.find('.')]
if "altSoln" in filename:
altSoln = '_altSoln'
else:
altSoln = ''
device_id = cam + altSoln
else:
device_id = None
postFileToTrial(fullpath,trial_id,tag,device_id)
return
def getTrialNameIdMapping(session_id):
trials = getSessionJson(session_id)['trials']
# dict of session name->id and date
trialDict = {}
for t in trials:
trialDict[t['name']] = {'id':t['id'],'date':t['created_at']}
return trialDict
def postCalibrationOptions(session_path,session_id,overwrite=False):
calibration_id = getCalibrationTrialID(session_id)
trial = getTrialJson(calibration_id)
if trial['meta'] is None or overwrite == True:
calibOptionsJsonPath = os.path.join(session_path,'Videos','calibOptionSelections.json')
f = open(calibOptionsJsonPath)
calibOptionsJson = json.load(f)
f.close()
data = {
"meta":json.dumps({'calibration':calibOptionsJson})
}
trial_url = "{}{}{}/".format(API_URL, "trials/", calibration_id)
r= requests.patch(trial_url, data=data,
headers = {"Authorization": "Token {}".format(API_TOKEN)})
if r.status_code == 200:
print('Wrote calibration selections to metadata.')
def downloadVideosFromServer(session_id,trial_id, isDocker=True,
isCalibration=False, isStaticPose=False,
trial_name=None, session_name=None,
session_path=None, benchmark=False):
if session_name is None:
session_name = session_id
data_dir = getDataDirectory(isDocker)
if session_path is None:
session_path = os.path.join(data_dir,'Data', session_name)
if not os.path.exists(session_path):
os.makedirs(session_path, exist_ok=True)
trial = getTrialJson(trial_id)
if trial_name is None:
trial_name = trial['name']
trial_name = trial_name.replace(' ', '')
print("\nProcessing {}".format(trial_name))
# The videos are not always organized in the same order. Here, we save
# the order during the first trial processed in the session such that we
# can use the same order for the other trials.
if not benchmark:
if not os.path.exists(os.path.join(session_path, "Videos", 'mappingCamDevice.pickle')):
mappingCamDevice = {}
for k, video in enumerate(trial["videos"]):
os.makedirs(os.path.join(session_path, "Videos", "Cam{}".format(k), "InputMedia", trial_name), exist_ok=True)
video_path = os.path.join(session_path, "Videos", "Cam{}".format(k), "InputMedia", trial_name, trial_id + ".mov")
download_file(video["video"], video_path)
mappingCamDevice[video["device_id"].replace('-', '').upper()] = k
with open(os.path.join(session_path, "Videos", 'mappingCamDevice.pickle'), 'wb') as handle:
pickle.dump(mappingCamDevice, handle)
else:
with open(os.path.join(session_path, "Videos", 'mappingCamDevice.pickle'), 'rb') as handle:
mappingCamDevice = pickle.load(handle)
for video in trial["videos"]:
k = mappingCamDevice[video["device_id"].replace('-', '').upper()]
videoDir = os.path.join(session_path, "Videos", "Cam{}".format(k), "InputMedia", trial_name)
os.makedirs(videoDir, exist_ok=True)
video_path = os.path.join(videoDir, trial_id + ".mov")
if not os.path.exists(video_path):
if video['video'] :
download_file(video["video"], video_path)
# Import and save metadata
sessionYamlPath = os.path.join(session_path, "sessionMetadata.yaml")
if not os.path.exists(sessionYamlPath) or isStaticPose or isCalibration:
if isCalibration: # subject parameters won't be entered yet
session_desc = getMetadataFromServer(session_id,justCheckerParams = isCalibration)
else: # subject parameters will be entered when capturing static pose
session_desc = getMetadataFromServer(session_id)
# Load iPhone models.
phoneModel= []
for i,video in enumerate(trial["videos"]):
phoneModel.append(video['parameters']['model'])
session_desc['iphoneModel'] = {'Cam' + str(i) : phoneModel[i] for i in range(len(phoneModel))}
# Save metadata.
with open(sessionYamlPath, 'w') as file:
yaml.dump(session_desc, file)
return trial_name
def deleteCalibrationFiles(session_path):
calImagePath = os.path.join(session_path,'CalibrationImages')
if os.path.exists(calImagePath):
shutil.rmtree(calImagePath)
# Delete camera directories
camDirs = glob.glob(os.path.join(session_path,'Videos','Cam*'))
# Find extrinsic Filename
extrinsicFileFound = False
if len(camDirs)>1 and os.path.exists(os.path.join(camDirs[0], 'InputMedia')):
inputDir = os.path.join(camDirs[0], 'InputMedia')
dirContents = os.listdir(inputDir)
trialNames = [tName for tName in dirContents if os.path.isdir(os.path.join(inputDir,tName))]
for tName in trialNames:
if os.path.exists(os.path.join(inputDir,tName,'extrinsicImage0.png')):
extrinsicTrialName = tName
extrinsicFileFound = True
for camDir in camDirs:
extPath = os.path.join(camDir,'cameraIntrinsicsExtrinsics.pickle')
if os.path.exists(extPath):
os.remove(extPath)
#Find extrinsic Filename
if extrinsicFileFound:
extFolder = os.path.join(camDir,'InputMedia',extrinsicTrialName)
if os.path.isdir(extFolder):
shutil.rmtree(extFolder)
def deleteStaticFiles(session_path,staticTrialName='neutral'):
vidDir = os.path.join(session_path,'Videos')
camDirs = glob.glob(os.path.join(vidDir,'Cam*'))
markerDirs = glob.glob(os.path.join(session_path,'MarkerData'))
openSimDir = os.path.join(session_path,'OpenSimData')
# This is a hack, but os.walk doesn't work on attached server drives
for camDir in camDirs:
mediaDirs = glob.glob(os.path.join(camDir,'*'))
for medDir in mediaDirs:
try:
shutil.rmtree(os.path.join(camDir,medDir,staticTrialName))
_,camName = os.path.split()
print('deleting ' + camName + '/' + medDir + '/' + staticTrialName)
except:
pass
for mkrDir in markerDirs:
mkrFiles = glob.glob(os.path.join(mkrDir,'*'))
for mkrFile in mkrFiles:
if staticTrialName in mkrFile:
os.remove(mkrFile)
_,fName = os.split(mkrFile)
print('deleting '+ fName)
if os.path.exists(openSimDir):
shutil.rmtree(openSimDir) # Static will be the first opensim data saved, so this is safe
print('deleting openSimDir')
# # this works locally, but not on server drives. Saving in case we change storage
# for root, dirList, fileList in os.walk(session_path + './'):
# for thisFile in fileList:
# print(thisFile)
# if (bool(regex.match(staticTrialName + '.trc', thisFile)) or
# bool(regex.match(staticTrialName + '.mot', thisFile)) or
# bool(regex.match(staticTrialName + '.sto', thisFile))):
# filePath = os.path.join(root,thisFile)
# os.remove(filePath)
# print('removing ' + thisFile)
# for thisDir in dirList:
# print(thisDir)
# if thisDir == staticTrialName:
# dirPath = os.path.join(root,thisDir)
# shutil.rmtree(dirPath)
# print('removing ' + thisDir)
def switchCalibrationForCamera(cam,trial_id,session_path):
trialName = getTrialName(trial_id)
camPath = os.path.join(session_path,'Videos',cam)
trialPath = os.path.join(camPath,'InputMedia',trialName)
# change Picture
src = os.path.join(trialPath,'extrinsicCalib_soln1.jpg')
dest = os.path.join(session_path,'CalibrationImages','extrinsicCalib' + cam + '.jpg')
if os.path.exists(dest):
os.remove(dest)
shutil.copyfile(src,dest)
# change calibration parameters
src = os.path.join(trialPath,'cameraIntrinsicsExtrinsics_soln1.pickle')
dest = os.path.join(camPath,'cameraIntrinsicsExtrinsics.pickle')
if os.path.exists(dest):
os.remove(dest)
shutil.copyfile(src,dest)
def getMetadataFromServer(session_id,justCheckerParams=False):
defaultMetadataPath = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'defaultSessionMetadata.yaml')
session_desc = importMetadata(defaultMetadataPath)
# Get session-specific metadata from api.
session = getSessionJson(session_id)
if session['meta'] is not None:
if not justCheckerParams:
# Backward compatibility
if 'subject' in session['meta']:
session_desc["subjectID"] = session['meta']['subject']['id']
session_desc["mass_kg"] = float(session['meta']['subject']['mass'])
session_desc["height_m"] = float(session['meta']['subject']['height'])
# Before implementing the subject feature, the posemodel was stored
# in session['meta']['subject']. After implementing the subject
# feature, the posemodel is stored in session['meta']['settings']
# and there is no session['meta']['subject'].
try:
session_desc["posemodel"] = session['meta']['subject']['posemodel']
except:
session_desc["posemodel"] = 'openpose'
# This might happen if openSimModel/augmentermodel/filterfrequency/scalingsetup was changed post data collection.
if 'settings' in session['meta']:
try:
session_desc["openSimModel"] = session['meta']['settings']['openSimModel']
except:
session_desc["openSimModel"] = 'LaiUhlrich2022'
try:
session_desc["augmentermodel"] = session['meta']['settings']['augmentermodel']
except:
session_desc["augmentermodel"] = 'v0.2'
try:
session_desc["filterfrequency"] = session['meta']['settings']['filterfrequency']
if session_desc["filterfrequency"] != 'default':
session_desc["filterfrequency"] = float(session_desc["filterfrequency"])
except:
session_desc["filterfrequency"] = 'default'
try:
session_desc["scalingsetup"] = session['meta']['settings']['scalingsetup']
except:
session_desc["scalingsetup"] = 'upright_standing_pose'
else:
subject_info = getSubjectJson(session['subject'])
session_desc["subjectID"] = subject_info['name']
session_desc["mass_kg"] = subject_info['weight']
session_desc["height_m"] = subject_info['height']
try:
session_desc["posemodel"] = session['meta']['settings']['posemodel']
except:
session_desc["posemodel"] = 'openpose'
try:
session_desc["openSimModel"] = session['meta']['settings']['openSimModel']
except:
session_desc["openSimModel"] = 'LaiUhlrich2022'
try:
session_desc["augmentermodel"] = session['meta']['settings']['augmentermodel']
except:
session_desc["augmentermodel"] = 'v0.2'
try:
session_desc["filterfrequency"] = session['meta']['settings']['filterfrequency']
if session_desc["filterfrequency"] != 'default':
session_desc["filterfrequency"] = float(session_desc["filterfrequency"])
except:
session_desc["filterfrequency"] = 'default'
try:
session_desc["scalingsetup"] = session['meta']['settings']['scalingsetup']
except:
session_desc["scalingsetup"] = 'upright_standing_pose'
if 'sessionWithCalibration' in session['meta'] and 'checkerboard' not in session['meta']:
newSessionId = session['meta']['sessionWithCalibration']['id']
session = getSessionJson(newSessionId)
session_desc['checkerBoard']["squareSideLength_mm"] = float(session['meta']['checkerboard']['square_size'])
session_desc['checkerBoard']["black2BlackCornersWidth_n"] = int(session['meta']['checkerboard']['cols'])
session_desc['checkerBoard']["black2BlackCornersHeight_n"] = int(session['meta']['checkerboard']['rows'])
session_desc['checkerBoard']["placement"] = session['meta']['checkerboard']['placement']
else:
print('Couldn''t find session metadata in API, using default metadata. May be issues.')
return session_desc
def deleteResult(trial_id, tag=None,resultNum=None):
# Delete specific result number, or all results with a specific tag, or all results if tag==None
if resultNum != None:
resultNums = [resultNum]
elif tag != None:
trial = getTrialJson(trial_id)
resultNums = [r['id'] for r in trial['results'] if r['tag']==tag]
elif tag == None:
trial = getTrialJson(trial_id)
resultNums = [r['id'] for r in trial['results']]
for rNum in resultNums:
requests.delete(API_URL + "results/{}/".format(rNum),
headers = {"Authorization": "Token {}".format(API_TOKEN)})
def deleteAllResults(session_id):
session = getSessionJson(session_id)
for trial in session['trials']:
deleteResult(trial['id'])
def writeCalibrationOptionsToAPI(session_path,session_id,calibration_id=None,trialName = None):
if calibration_id == None:
calibration_id = getCalibrationTrialID(session_id)
if trialName == None:
trial = getTrialJson(calibration_id)
trialName = trial['name']
deleteResult(calibration_id, tag='camera_mapping')
videoDir = os.path.join(session_path,'Videos')
camDirs = glob.glob(os.path.join(videoDir,'Cam*'))
mapPath = os.path.join(videoDir, 'mappingCamDevice.pickle')
postFileToTrial(mapPath,calibration_id,'camera_mapping','all')
tag = 'calibration_parameters_options'
deleteResult(calibration_id, tag=tag)
for camDir in camDirs:
_,camName = os.path.split(camDir)
calibDir = os.path.join(camDir,'InputMedia',trialName)
# Post both solutions
for i in range(2):
filePath = os.path.join(calibDir,'cameraIntrinsicsExtrinsics_soln{}.pickle'.format(i))
device_id = camName+'_soln{}'.format(i)
postFileToTrial(filePath,calibration_id,tag,device_id)
def getCalibrationTrialID(session_id):
session = getSessionJson(session_id)
calib_ids = [t['id'] for t in session['trials'] if t['name'] == 'calibration']
if len(calib_ids)>0:
calibID = calib_ids[-1]
elif session['meta']['sessionWithCalibration']:
calibID = getCalibrationTrialID(session['meta']['sessionWithCalibration']['id'])
else:
raise Exception('No calibration trial in session.')
return calibID
def getNeutralTrialID(session_id):
session = getSessionJson(session_id)
neutral_ids = [t['id'] for t in session['trials'] if t['name'] == 'neutral']
if len(neutral_ids)>0:
neutralID = neutral_ids[-1]
elif session['meta']['neutral_trial']:
neutralID = session['meta']['neutral_trial']['id']
else:
raise Exception('No neutral trial in session.')
return neutralID
def postCalibration(session_id,session_path,calibTrialID=None):
videoDir = os.path.join(session_path,'Videos')
videoFolders = glob.glob(os.path.join(videoDir,'Cam*'))
if calibTrialID == None:
calibTrialID = getCalibrationTrialID(session_id)
# remove 'calibration_parameters' in case they exist already.
tag = 'calibration_parameters'
deleteResult(calibTrialID, tag=tag)
for vf in videoFolders:
_, camName = os.path.split(vf)
fPath = os.path.join(vf,'cameraIntrinsicsExtrinsics.pickle')
deviceID = camName
postFileToTrial(fPath,calibTrialID,'calibration_parameters',deviceID)
return
def getCalibration(session_id,session_path,trial_type='dynamic',getCalibrationOptions=False):
# look for calibration pickles on Django. If they are not there, then see if
# we need to do any switch calibration, then post the good calibration to django.
calibration_id = getCalibrationTrialID(session_id)
# Check if calibration has been posted to session
trial = getTrialJson(calibration_id)
calibResultTags = [res['tag'] for res in trial['results']]
# download the mapping
videoFolder = os.path.join(session_path,'Videos')
os.makedirs(videoFolder, exist_ok=True)
mapURL = trial['results'][calibResultTags.index('camera_mapping')]['media']
mapLocalPath = os.path.join(videoFolder,'mappingCamDevice.pickle')
download_file(mapURL,mapLocalPath)
# download calibration parameters and switch if necessary.
calibrationOptions = downloadAndSwitchCalibrationFromDjango(session_id,session_path,
calibTrialID=calibration_id,
getCalibrationOptions=getCalibrationOptions)
# Post calibration if neutral trial. The posted parameters are no longer
# used, but it is handy to know which ones were selected from both options.
if trial_type == 'static':
postCalibration(session_id,session_path,calibTrialID=calibration_id)
if getCalibrationOptions:
return calibrationOptions
def downloadAndSwitchCalibrationFromDjango(session_id,session_path,calibTrialID = None,
getCalibrationOptions=False):
if calibTrialID == None:
calibTrialID = getCalibrationTrialID(session_id)
trial = getTrialJson(calibTrialID)
calibURLs = {t['device_id']:t['media'] for t in trial['results'] if t['tag'] == 'calibration_parameters_options'}
if 'meta' in trial.keys() and trial['meta'] is not None and 'calibration' in trial['meta'].keys() and trial['meta']['calibration']:
calibDict = trial['meta']['calibration']
else:
print('No metadata for camera switching. Using first solution.')
calibDict = {'Cam'+str(i):0 for i in range(len(trial['videos']))}
for cam,calibNum in calibDict.items():
camDir = os.path.join(session_path,'Videos',cam)
os.makedirs(camDir,exist_ok=True)
file_name = os.path.join(camDir,'cameraIntrinsicsExtrinsics.pickle')
if calibNum == 0:
download_file(calibURLs[cam+'_soln0'], file_name)
print('Downloading calibration for ' + cam)
elif calibNum == 1:
download_file(calibURLs[cam+'_soln1'], file_name)
print('Downloading alternate calibration camera for ' + cam)
# If static trial and we are automatically selecting a calibration
if getCalibrationOptions:
tempPath = os.path.join(session_path,'tempCalib.pickle')
calibrationOptions = {}
for cam in calibDict.keys():
calibrationOptions[cam] = []
download_file(calibURLs[cam+'_soln0'], tempPath)
calibrationOptions[cam].append(loadCameraParameters(tempPath))
os.remove(tempPath)
download_file(calibURLs[cam+'_soln1'], tempPath)
calibrationOptions[cam].append(loadCameraParameters(tempPath))
os.remove(tempPath)
return calibrationOptions
else:
return None
def changeSessionMetadata(session_ids,newMetaDict):
if 'filterfrequency' in newMetaDict and newMetaDict['filterfrequency'] != 'default':
if type(newMetaDict['filterfrequency']) is not str:
newMetaDict['filterfrequency'] = str(newMetaDict['filterfrequency'])
else:
raise Exception('Filter frequency should be a number or default.')
if 'datasharing' in newMetaDict:
if newMetaDict['datasharing'] not in ['Share processed data and identified videos',
'Share processed data and de-identified videos',
'Share processed data',
'Share no data']:
raise Exception('datasharing is {} but should be one of the following options: "Share processed data and identified videos", "Share processed data and de-identified videos", "Share processed data", "Share no data".'.format(newMetaDict['datasharing']))
for session_id in session_ids:
session_url = "{}{}{}/".format(API_URL, "sessions/", session_id)
# get metadata
session = getSessionJson(session_id)
existingMeta = session['meta']
# Check if framerate is in metadata. If not, set to 60
if 'framerate' not in existingMeta:
framerate = 60
else:
framerate = existingMeta['framerate']
if 'filterfrequency' in newMetaDict:
if newMetaDict['filterfrequency'] != 'default':
if float(newMetaDict['filterfrequency']) > framerate/2:
raise Exception('Filter frequency cannot exceed Nyquist frequency (here {}Hz).'.format(framerate/2))
elif float(newMetaDict['filterfrequency']) < 0:
raise Exception('Filter frequency cannot be negative.')
# change metadata
# Hack: wrong mapping between metadata and yaml
# mass in metadata is mass_kg in yaml
# height in metadata is height_m in yaml
mapping_metadata = {'mass': 'mass_kg',
'height': 'height_m'}
addedKey= {}
for key in existingMeta.keys():
if key in mapping_metadata:
key_t = mapping_metadata[key]
else:
key_t = key
if key_t in newMetaDict.keys():
existingMeta[key] = newMetaDict[key_t]
addedKey[key_t] = newMetaDict[key_t]
if type(existingMeta[key]) is dict:
for key2 in existingMeta[key].keys():
if key2 in mapping_metadata:
key_t = mapping_metadata[key2]
else:
key_t = key2
if key_t in newMetaDict.keys():
existingMeta[key][key2] = newMetaDict[key_t]
addedKey[key_t] = newMetaDict[key_t]
# add metadata if not existing (eg, specifying OpenSim model)
# only entries in settings_fields below are supported.
for newMeta in newMetaDict:
if not newMeta in addedKey:
print("Could not find {} in existing metadata, trying to add it.".format(newMeta))
settings_fields = ['framerate', 'posemodel', 'openSimModel', 'augmentermodel', 'filterfrequency', 'scalingsetup', 'camerastouse']
if newMeta in settings_fields:
if 'settings' not in existingMeta:
existingMeta['settings'] = {}
existingMeta['settings'][newMeta] = newMetaDict[newMeta]
addedKey[newMeta] = newMetaDict[newMeta]
print("Added {}={} to settings in metadata".format(newMeta, newMetaDict[newMeta]))
else:
print("Could not add {}={} to the metadata; not recognized".format(newMeta, newMetaDict[newMeta]))
data = {"meta":json.dumps(existingMeta)}
r= requests.patch(session_url, data=data,
headers = {"Authorization": "Token {}".format(API_TOKEN)})
if r.status_code !=200:
print('Changing metadata failed.')
# Also change this in the metadata yaml in neutral trial
trial_id = getNeutralTrialID(session_id)
trial = getTrialJson(trial_id)
resultTags = [res['tag'] for res in trial['results']]
metaPath = os.path.join(os.getcwd(),'sessionMetadata.yaml')
if 'session_metadata' in resultTags:
yamlURL = trial['results'][resultTags.index('session_metadata')]['media']
download_file(yamlURL,metaPath)
metaYaml = importMetadata(metaPath)
addedKey= {}
for key in metaYaml.keys():
if key in newMetaDict.keys():
metaYaml[key] = newMetaDict[key]
addedKey[key] = newMetaDict[key]
if type(metaYaml[key]) is dict:
for key2 in metaYaml[key].keys():
if key2 in newMetaDict.keys():
metaYaml[key][key2] = newMetaDict[key2]
addedKey[key2] = newMetaDict[key2]
for newMeta in newMetaDict:
if not newMeta in addedKey:
print("Could not find {} in existing yaml, adding it.".format(newMeta))
metaYaml[newMeta] = newMetaDict[newMeta]
with open(metaPath, 'w') as file:
yaml.dump(metaYaml, file)
deleteResult(trial_id, tag='session_metadata')
postFileToTrial(metaPath,trial_id,tag='session_metadata',device_id='all')
os.remove(metaPath)
def makeSessionPublic(session_id,publicStatus=True):
session_url = "{}{}{}/".format(API_URL, "sessions/", session_id)
data = {
"public":publicStatus
}
r= requests.patch(session_url, data=data,
headers = {"Authorization": "Token {}".format(API_TOKEN)})
if r.status_code == 200:
print('Successfully made ' + session_id + ' public.')
else:
print('server resp was ' + str(r.status_code))
return
def postMotionData(trial_id,session_path,trial_name=None,isNeutral=False,
poseDetector='OpenPose', resolutionPoseDetection='default',
bbox_thr=0.8):
if trial_name == None:
trial_name = getTrialJson(trial_id)['id']
if poseDetector.lower() == 'openpose':
pklDir = os.path.join("OutputPkl_" + resolutionPoseDetection, trial_name)
elif poseDetector.lower() == 'hrnet':
pklDir = os.path.join("OutputPkl_mmpose_" + str(bbox_thr), trial_name)
else:
raise Exception('Unknown pose detector: {}'.format(poseDetector))
markerDir = os.path.join(session_path,'MarkerData','PostAugmentation')
# post settings
deleteResult(trial_id, tag='main_settings')
mainSettingsPath = os.path.join(markerDir,'Settings_{}.yaml'.format(trial_id))
postFileToTrial(mainSettingsPath,trial_id,tag='main_settings',device_id='all')
# post pose pickles
# If we parallelize this, this will be redundant, and we will want to delete this posting of pickles
deleteResult(trial_id, tag='pose_pickle')
camDirs = glob.glob(os.path.join(session_path,'Videos','Cam*'))
for camDir in camDirs:
outputPklFolder = os.path.join(camDir,pklDir)
pickle_files = glob.glob(os.path.join(outputPklFolder,'*_pp.pkl'))
if pickle_files:
pklPath = pickle_files[0]
_,camName = os.path.split(camDir)
postFileToTrial(pklPath,trial_id,tag='pose_pickle',device_id=camName)
# post marker data
deleteResult(trial_id, tag='marker_data')
markerPath = os.path.join(markerDir,trial_id + '.trc')
postFileToTrial(markerPath,trial_id,tag='marker_data',device_id='all')
if isNeutral:
# post model
deleteResult(trial_id, tag='opensim_model')
modelFolder = os.path.join(session_path,'OpenSimData','Model')
modelPath = glob.glob(modelFolder + '/*_scaled.osim')[0]
postFileToTrial(modelPath,trial_id,tag='opensim_model',device_id='all')
# post metadata
deleteResult(trial_id, tag='session_metadata')
metadataPath = os.path.join(session_path,'sessionMetadata.yaml')
postFileToTrial(metadataPath,trial_id,tag='session_metadata',device_id='all')
else:
# post ik data
deleteResult(trial_id, tag='ik_results')
ikPath = os.path.join(session_path,'OpenSimData','Kinematics',trial_id + '.mot')
postFileToTrial(ikPath,trial_id,tag='ik_results',device_id='all')
return
def getMotionData(trial_id,session_path,simplePath=False):
trial = getTrialJson(trial_id)
trial_name = trial['name']
resultTags = [res['tag'] for res in trial['results']]
# get marker data
if 'ik_results' in resultTags:
markerFolder = os.path.join(session_path,'MarkerData','PostAugmentation',trial_name)
if simplePath:
markerFolder = os.path.join(session_path,'MarkerData')
markerPath = os.path.join(markerFolder,trial_name + '.trc')
os.makedirs(markerFolder, exist_ok=True)
markerURL = trial['results'][resultTags.index('marker_data')]['media']
download_file(markerURL,markerPath)
# get IK data
if 'ik_results' in resultTags:
ikFolder = os.path.join(session_path,'OpenSimData','Kinematics')
if simplePath:
ikFolder = os.path.join(session_path,'OpenSimData','Kinematics')
ikPath = os.path.join(ikFolder,trial_name + '.mot')
os.makedirs(ikFolder, exist_ok=True)
ikURL = trial['results'][resultTags.index('ik_results')]['media']
download_file(ikURL,ikPath)
# TODO will want to get pose pickles eventually, once those are processed elsewhere
return
def getModelAndMetadata(session_id,session_path,simplePath=False):
neutral_id = getNeutralTrialID(session_id)
trial = getTrialJson(neutral_id)
resultTags = [res['tag'] for res in trial['results']]
# get metadata
metadataPath = os.path.join(session_path,'sessionMetadata.yaml')
if not os.path.exists(metadataPath) :
metadataURL = trial['results'][resultTags.index('session_metadata')]['media']
download_file(metadataURL, metadataPath)
# get model if does not exist
modelURL = trial['results'][resultTags.index('opensim_model')]['media']
modelName = modelURL[modelURL.rfind('-')+1:modelURL.rfind('?')]
modelFolder = os.path.join(session_path,'OpenSimData','Model')
if simplePath:
modelFolder = os.path.join(session_path,'OpenSimData','Model')
modelPath = os.path.join(modelFolder,modelName)
if not os.path.exists(modelPath):
os.makedirs(modelFolder, exist_ok=True)
download_file(modelURL, modelPath)
return
def postFileToTrial(filePath,trial_id,tag,device_id):
# get S3 link
data = {'fileName':os.path.split(filePath)[1]}
r = requests.get(API_URL + "sessions/null/get_presigned_url/",data=data).json()
# upload to S3
files = {'file': open(filePath, 'rb')}
requests.post(r['url'], data=r['fields'],files=files)
files["file"].close()
# post link to and data to results
data = {
"trial": trial_id,
"tag": tag,
"device_id" : device_id,
"media_url" : r['fields']['key']
}
rResult = requests.post(API_URL + "results/", data=data,
headers = {"Authorization": "Token {}".format(API_TOKEN)})
if rResult.status_code != 201:
print('server response was + ' + str(r.status_code))
else:
print('Result posted to S3.')
return
def getSyncdVideos(trial_id,session_path):
trial = getTrialJson(trial_id)
trial_name = trial['name']
if trial['results']:
for result in trial['results']:
if result['tag'] == 'video-sync':
url = result['media']
cam,suff = os.path.splitext(url[url.rfind('_')+1:])
lastIdx = suff.find('?')
if lastIdx >0:
suff = suff[:lastIdx]
syncVideoPath = os.path.join(session_path,'Videos',cam,'InputMedia',trial_name,trial_name + '_sync' + suff)
download_file(url,syncVideoPath)
def getPosePickles(trial_id,session_path, poseDetector='OpenPose',
resolutionPoseDetection='default', bbox_thr=0.8):
trial = getTrialJson(trial_id)
trial_name = trial['name']
if poseDetector.lower() == 'openpose':
pklDir = os.path.join("OutputPkl_" + resolutionPoseDetection, trial_name)
elif poseDetector.lower() == 'hrnet':
pklDir = os.path.join("OutputPkl_mmpose_" + str(bbox_thr), trial_name)
else:
raise Exception('Unknown pose detector: {}'.format(poseDetector))
trialPrefix = trial_id + "_rotated_pp.pkl"
if trial['results']:
for result in trial['results']:
if result['tag'] == 'pose_pickle':
url = result['media']
cam = result['device_id']
posePickleDir = os.path.join(session_path,'Videos',cam,pklDir)
os.makedirs(posePickleDir,exist_ok=True)
posePicklePath = os.path.join(posePickleDir,trialPrefix)
download_file(url,posePicklePath)
def checkAndGetPosePickles(trial_id, session_path, poseDetector, resolutionPoseDetection, bbox_thr):
# Check if the pose pickles for that set of settings exist.
# Load main_settings yaml.
main_settings = getMainSettings(trial_id)
if 'poseDetector' in main_settings:
usedPoseDetector = main_settings['poseDetector']
if poseDetector.lower() == 'openpose':
if 'resolutionPoseDetection' in main_settings:
usedResolution = main_settings['resolutionPoseDetection']
if usedPoseDetector.lower() == poseDetector.lower() and usedResolution == resolutionPoseDetection:
print('The pose pickles for {} {} already exist in the database. We will download them to avoid re-running pose estimation'.format(poseDetector, resolutionPoseDetection))
getPosePickles(trial_id,session_path, poseDetector=poseDetector, resolutionPoseDetection=resolutionPoseDetection)
else:
print('The pose pickles in the database are for {} {}, but you are now using {} {}. We will re-run pose estimation'.format(usedPoseDetector, usedResolution, poseDetector, resolutionPoseDetection))
else:
print('It is unclear which settings were used for pose estimation. We will re-run pose estimation')
elif poseDetector.lower() == 'hrnet':
# Hack: hrnet is sometimes called mmpose
if usedPoseDetector.lower() == 'mmpose':
usedPoseDetector = 'hrnet'
if 'bbox_thr' in main_settings:
usedBbox_thr = main_settings['bbox_thr']
else:
# There was a bug in main, where bbox_thr was not saved in main_settings.yaml.
# Since there is in practice no option to change bbox_thr in the GUI, we can
# assume that the default value was used.
usedBbox_thr = 0.8
if usedPoseDetector.lower() == poseDetector.lower() and usedBbox_thr == bbox_thr:
print('The pose pickles for {} {} already exist in the database. We will download them to avoid re-running pose estimation'.format(poseDetector, bbox_thr))
getPosePickles(trial_id,session_path, poseDetector=poseDetector, bbox_thr=bbox_thr)
else:
print('The pose pickles in the database are for {} {}, but you are now using {} {}. We will re-run pose estimation'.format(usedPoseDetector, usedBbox_thr, poseDetector, bbox_thr))
else:
print('It is unclear which settings were used for pose estimation. We will re-run pose estimation')
else:
print('It is unclear which settings were used for pose estimation. We will re-run pose estimation')
def getMainSettings(trial_id):
trial = getTrialJson(trial_id)
if len(trial['results'])>1:
for result in trial['results']:
if result['tag'] == 'main_settings':
url = result['media']
# Load yaml file
try:
with urllib.request.urlopen(url) as response:
yaml_content = response.read()
data = yaml.safe_load(yaml_content)
return data
except Exception as e:
print("An error occurred:", e)
return {} # Return an empty dictionary in case of an error
else:
return {}
def downloadAndZipSession(session_id,deleteFolderWhenZipped=True,isDocker=True,
writeToDjango=False,justDownload=False,data_dir=None,
useSubjectNameFolder=False):
session = getSessionJson(session_id)
if data_dir is None:
data_dir = os.path.join(getDataDirectory(isDocker=isDocker),'Data')
if useSubjectNameFolder:
folderName = session['name']
else:
folderName = session_id
session_path = os.path.join(data_dir,folderName)
calib_id = getCalibrationTrialID(session_id)
neutral_id = getNeutralTrialID(session_id)
dynamic_ids = [t['id'] for t in session['trials'] if (t['name'] != 'calibration' and t['name'] !='neutral')]
# Calibration
downloadVideosFromServer(session_id,calib_id,isDocker=isDocker,
isCalibration=True,isStaticPose=False)