def AnalyzeMultiAnimalVideo(
video,
DLCscorer,
trainFraction,
cfg,
dlc_cfg,
sess,
inputs,
outputs,
pdindex,
save_as_csv,
destfolder=None,
c_engine=False,
robust_nframes=False,
):
""" Helper function for analyzing a video with multiple individuals """
print("Starting to analyze % ", video)
vname = Path(video).stem
videofolder = str(Path(video).parents[0])
if destfolder is None:
destfolder = videofolder
auxiliaryfunctions.attempttomakefolder(destfolder)
dataname = os.path.join(destfolder, vname + DLCscorer + ".h5")
if os.path.isfile(dataname.split(".h5")[0] + "_full.pickle"):
print("Video already analyzed!", dataname)
else:
print("Loading ", video)
vid = VideoWriter(video)
if robust_nframes:
nframes = vid.get_n_frames(robust=True)
duration = vid.calc_duration(robust=True)
fps = nframes / duration
else:
nframes = len(vid)
duration = vid.calc_duration(robust=False)
fps = vid.fps
nx, ny = vid.dimensions
print(
"Duration of video [s]: ",
round(duration, 2),
", recorded with ",
round(fps, 2),
"fps!",
)
print(
"Overall # of frames: ",
nframes,
" found with (before cropping) frame dimensions: ",
nx,
ny,
)
start = time.time()
print("Starting to extract posture")
if int(dlc_cfg["batch_size"]) > 1:
PredicteData, nframes = GetPoseandCostsF(
cfg,
dlc_cfg,
sess,
inputs,
outputs,
vid,
nframes,
int(dlc_cfg["batch_size"]),
c_engine=c_engine,
)
else:
PredicteData, nframes = GetPoseandCostsS(cfg,
dlc_cfg,
sess,
inputs,
outputs,
vid,
nframes,
c_engine=c_engine)
stop = time.time()
if cfg["cropping"] == True:
coords = [cfg["x1"], cfg["x2"], cfg["y1"], cfg["y2"]]
else:
coords = [0, nx, 0, ny]
dictionary = {
"start": start,
"stop": stop,
"run_duration": stop - start,
"Scorer": DLCscorer,
"DLC-model-config file": dlc_cfg,
"fps": fps,
"batch_size": dlc_cfg["batch_size"],
"frame_dimensions": (ny, nx),
"nframes": nframes,
"iteration (active-learning)": cfg["iteration"],
"training set fraction": trainFraction,
"cropping": cfg["cropping"],
"cropping_parameters": coords,
}
metadata = {"data": dictionary}
print("Saving results in %s..." % (destfolder))
auxfun_multianimal.SaveFullMultiAnimalData(PredicteData, metadata,
dataname)
def evaluate_multianimal_full(
config,
Shuffles=[1],
trainingsetindex=0,
plotting=None,
show_errors=True,
comparisonbodyparts="all",
gputouse=None,
modelprefix="",
c_engine=False,
):
"""
WIP multi animal project.
"""
import os
from deeplabcut.pose_estimation_tensorflow.nnet import predict
from deeplabcut.pose_estimation_tensorflow.nnet import (
predict_multianimal as predictma, )
from deeplabcut.utils import auxiliaryfunctions, auxfun_multianimal
import tensorflow as tf
if "TF_CUDNN_USE_AUTOTUNE" in os.environ:
del os.environ[
"TF_CUDNN_USE_AUTOTUNE"] # was potentially set during training
tf.reset_default_graph()
os.environ["TF_CPP_MIN_LOG_LEVEL"] = "2" #
if gputouse is not None: # gpu selectinon
os.environ["CUDA_VISIBLE_DEVICES"] = str(gputouse)
start_path = os.getcwd()
##################################################
# Load data...
##################################################
cfg = auxiliaryfunctions.read_config(config)
if trainingsetindex == "all":
TrainingFractions = cfg["TrainingFraction"]
else:
TrainingFractions = [cfg["TrainingFraction"][trainingsetindex]]
# Loading human annotatated data
trainingsetfolder = auxiliaryfunctions.GetTrainingSetFolder(cfg)
Data = pd.read_hdf(
os.path.join(
cfg["project_path"],
str(trainingsetfolder),
"CollectedData_" + cfg["scorer"] + ".h5",
),
"df_with_missing",
)
# Get list of body parts to evaluate network for
comparisonbodyparts = auxiliaryfunctions.IntersectionofBodyPartsandOnesGivenbyUser(
cfg, comparisonbodyparts)
colors = visualization.get_cmap(len(comparisonbodyparts),
name=cfg["colormap"])
# Make folder for evaluation
auxiliaryfunctions.attempttomakefolder(
str(cfg["project_path"] + "/evaluation-results/"))
for shuffle in Shuffles:
for trainFraction in TrainingFractions:
##################################################
# Load and setup CNN part detector
##################################################
datafn, metadatafn = auxiliaryfunctions.GetDataandMetaDataFilenames(
trainingsetfolder, trainFraction, shuffle, cfg)
modelfolder = os.path.join(
cfg["project_path"],
str(
auxiliaryfunctions.GetModelFolder(
trainFraction, shuffle, cfg, modelprefix=modelprefix)),
)
path_test_config = Path(modelfolder) / "test" / "pose_cfg.yaml"
# Load meta data
(
data,
trainIndices,
testIndices,
trainFraction,
) = auxiliaryfunctions.LoadMetadata(
os.path.join(cfg["project_path"], metadatafn))
try:
dlc_cfg = load_config(str(path_test_config))
except FileNotFoundError:
raise FileNotFoundError(
"It seems the model for shuffle %s and trainFraction %s does not exist."
% (shuffle, trainFraction))
# TODO: IMPLEMENT for different batch sizes?
dlc_cfg["batch_size"] = 1 # due to differently sized images!!!
# Create folder structure to store results.
evaluationfolder = os.path.join(
cfg["project_path"],
str(
auxiliaryfunctions.GetEvaluationFolder(
trainFraction, shuffle, cfg, modelprefix=modelprefix)),
)
auxiliaryfunctions.attempttomakefolder(evaluationfolder,
recursive=True)
# path_train_config = modelfolder / 'train' / 'pose_cfg.yaml'
# Check which snapshots are available and sort them by # iterations
Snapshots = np.array([
fn.split(".")[0]
for fn in os.listdir(os.path.join(str(modelfolder), "train"))
if "index" in fn
])
if len(Snapshots) == 0:
print(
"Snapshots not found! It seems the dataset for shuffle %s and trainFraction %s is not trained.\nPlease train it before evaluating.\nUse the function 'train_network' to do so."
% (shuffle, trainFraction))
else:
increasing_indices = np.argsort(
[int(m.split("-")[1]) for m in Snapshots])
Snapshots = Snapshots[increasing_indices]
if cfg["snapshotindex"] == -1:
snapindices = [-1]
elif cfg["snapshotindex"] == "all":
snapindices = range(len(Snapshots))
elif cfg["snapshotindex"] < len(Snapshots):
snapindices = [cfg["snapshotindex"]]
else:
print(
"Invalid choice, only -1 (last), any integer up to last, or all (as string)!"
)
(
individuals,
uniquebodyparts,
multianimalbodyparts,
) = auxfun_multianimal.extractindividualsandbodyparts(cfg)
final_result = []
##################################################
# Compute predictions over images
##################################################
for snapindex in snapindices:
dlc_cfg["init_weights"] = os.path.join(
str(modelfolder), "train", Snapshots[snapindex]
) # setting weights to corresponding snapshot.
trainingsiterations = (
dlc_cfg["init_weights"].split(os.sep)[-1]
).split(
"-"
)[-1] # read how many training siterations that corresponds to.
# name for deeplabcut net (based on its parameters)
DLCscorer, DLCscorerlegacy = auxiliaryfunctions.GetScorerName(
cfg,
shuffle,
trainFraction,
trainingsiterations,
modelprefix=modelprefix,
)
print(
"Running ",
DLCscorer,
" with # of trainingiterations:",
trainingsiterations,
)
(
notanalyzed,
resultsfilename,
DLCscorer,
) = auxiliaryfunctions.CheckifNotEvaluated(
str(evaluationfolder),
DLCscorer,
DLCscorerlegacy,
Snapshots[snapindex],
)
if os.path.isfile(
resultsfilename.split(".h5")[0] + "_full.pickle"):
print("Model already evaluated.", resultsfilename)
else:
if plotting:
foldername = os.path.join(
str(evaluationfolder),
"LabeledImages_" + DLCscorer + "_" +
Snapshots[snapindex],
)
auxiliaryfunctions.attempttomakefolder(foldername)
# print(dlc_cfg)
# Specifying state of model (snapshot / training state)
sess, inputs, outputs = predict.setup_pose_prediction(
dlc_cfg)
PredicteData = {}
print("Analyzing data...")
for imageindex, imagename in tqdm(enumerate(
Data.index)):
image_path = os.path.join(cfg["project_path"],
imagename)
image = io.imread(image_path)
frame = img_as_ubyte(skimage.color.gray2rgb(image))
GT = Data.iloc[imageindex]
# Storing GT data as dictionary, so it can be used for calculating connection costs
groundtruthcoordinates = []
groundtruthidentity = []
for bptindex, bpt in enumerate(
dlc_cfg["all_joints_names"]):
coords = np.zeros([len(individuals), 2
]) * np.nan
identity = []
for prfxindex, prefix in enumerate(
individuals):
if bpt in uniquebodyparts and prefix == "single":
coords[prfxindex, :] = np.array([
GT[cfg["scorer"]][prefix][bpt]
["x"],
GT[cfg["scorer"]][prefix][bpt]
["y"],
])
identity.append(prefix)
elif (bpt in multianimalbodyparts
and prefix != "single"):
coords[prfxindex, :] = np.array([
GT[cfg["scorer"]][prefix][bpt]
["x"],
GT[cfg["scorer"]][prefix][bpt]
["y"],
])
identity.append(prefix)
else:
identity.append("nix")
groundtruthcoordinates.append(
coords[np.isfinite(coords[:, 0]), :])
groundtruthidentity.append(
np.array(identity)[np.isfinite(coords[:,
0])])
PredicteData[imagename] = {}
PredicteData[imagename]["index"] = imageindex
pred = predictma.get_detectionswithcostsandGT(
frame,
groundtruthcoordinates,
dlc_cfg,
sess,
inputs,
outputs,
outall=False,
nms_radius=dlc_cfg.nmsradius,
det_min_score=dlc_cfg.minconfidence,
c_engine=c_engine,
)
PredicteData[imagename]["prediction"] = pred
PredicteData[imagename]["groundtruth"] = [
groundtruthidentity,
groundtruthcoordinates,
GT,
]
if plotting:
coords_pred = pred["coordinates"][0]
probs_pred = pred["confidence"]
fig = visualization.make_multianimal_labeled_image(
frame,
groundtruthcoordinates,
coords_pred,
probs_pred,
colors,
cfg["dotsize"],
cfg["alphavalue"],
cfg["pcutoff"],
)
visualization.save_labeled_frame(
fig,
image_path,
foldername,
imageindex in trainIndices,
)
sess.close() # closes the current tf session
PredicteData["metadata"] = {
"nms radius":
dlc_cfg.nmsradius,
"minimal confidence":
dlc_cfg.minconfidence,
"PAFgraph":
dlc_cfg.partaffinityfield_graph,
"all_joints":
[[i] for i in range(len(dlc_cfg.all_joints))],
"all_joints_names": [
dlc_cfg.all_joints_names[i]
for i in range(len(dlc_cfg.all_joints))
],
"stride":
dlc_cfg.get("stride", 8),
}
print(
"Done and results stored for snapshot: ",
Snapshots[snapindex],
)
dictionary = {
"Scorer": DLCscorer,
"DLC-model-config file": dlc_cfg,
"trainIndices": trainIndices,
"testIndices": testIndices,
"trainFraction": trainFraction,
}
metadata = {"data": dictionary}
auxfun_multianimal.SaveFullMultiAnimalData(
PredicteData, metadata, resultsfilename)
tf.reset_default_graph()
# returning to intial folder
os.chdir(str(start_path))
def evaluate_multianimal_full(
config,
Shuffles=[1],
trainingsetindex=0,
plotting=None,
show_errors=True,
comparisonbodyparts="all",
gputouse=None,
modelprefix="",
c_engine=False,
):
from deeplabcut.pose_estimation_tensorflow.nnet import predict
from deeplabcut.pose_estimation_tensorflow.nnet import (
predict_multianimal as predictma, )
from deeplabcut.utils import auxiliaryfunctions, auxfun_multianimal
import tensorflow as tf
if "TF_CUDNN_USE_AUTOTUNE" in os.environ:
del os.environ[
"TF_CUDNN_USE_AUTOTUNE"] # was potentially set during training
tf.reset_default_graph()
os.environ["TF_CPP_MIN_LOG_LEVEL"] = "2" #
if gputouse is not None: # gpu selectinon
os.environ["CUDA_VISIBLE_DEVICES"] = str(gputouse)
start_path = os.getcwd()
##################################################
# Load data...
##################################################
cfg = auxiliaryfunctions.read_config(config)
if trainingsetindex == "all":
TrainingFractions = cfg["TrainingFraction"]
else:
TrainingFractions = [cfg["TrainingFraction"][trainingsetindex]]
# Loading human annotatated data
trainingsetfolder = auxiliaryfunctions.GetTrainingSetFolder(cfg)
Data = pd.read_hdf(
os.path.join(
cfg["project_path"],
str(trainingsetfolder),
"CollectedData_" + cfg["scorer"] + ".h5",
),
"df_with_missing",
)
# Handle data previously annotated on a different platform
sep = "/" if "/" in Data.index[0] else "\\"
if sep != os.path.sep:
Data.index = Data.index.str.replace(sep, os.path.sep)
# Get list of body parts to evaluate network for
comparisonbodyparts = auxiliaryfunctions.IntersectionofBodyPartsandOnesGivenbyUser(
cfg, comparisonbodyparts)
all_bpts = np.asarray(
len(cfg["individuals"]) * cfg["multianimalbodyparts"] +
cfg["uniquebodyparts"])
colors = visualization.get_cmap(len(comparisonbodyparts),
name=cfg["colormap"])
# Make folder for evaluation
auxiliaryfunctions.attempttomakefolder(
str(cfg["project_path"] + "/evaluation-results/"))
for shuffle in Shuffles:
for trainFraction in TrainingFractions:
##################################################
# Load and setup CNN part detector
##################################################
datafn, metadatafn = auxiliaryfunctions.GetDataandMetaDataFilenames(
trainingsetfolder, trainFraction, shuffle, cfg)
modelfolder = os.path.join(
cfg["project_path"],
str(
auxiliaryfunctions.GetModelFolder(
trainFraction, shuffle, cfg, modelprefix=modelprefix)),
)
path_test_config = Path(modelfolder) / "test" / "pose_cfg.yaml"
# Load meta data
(
data,
trainIndices,
testIndices,
trainFraction,
) = auxiliaryfunctions.LoadMetadata(
os.path.join(cfg["project_path"], metadatafn))
try:
dlc_cfg = load_config(str(path_test_config))
except FileNotFoundError:
raise FileNotFoundError(
"It seems the model for shuffle %s and trainFraction %s does not exist."
% (shuffle, trainFraction))
# TODO: IMPLEMENT for different batch sizes?
dlc_cfg["batch_size"] = 1 # due to differently sized images!!!
joints = dlc_cfg["all_joints_names"]
# Create folder structure to store results.
evaluationfolder = os.path.join(
cfg["project_path"],
str(
auxiliaryfunctions.GetEvaluationFolder(
trainFraction, shuffle, cfg, modelprefix=modelprefix)),
)
auxiliaryfunctions.attempttomakefolder(evaluationfolder,
recursive=True)
# path_train_config = modelfolder / 'train' / 'pose_cfg.yaml'
# Check which snapshots are available and sort them by # iterations
Snapshots = np.array([
fn.split(".")[0]
for fn in os.listdir(os.path.join(str(modelfolder), "train"))
if "index" in fn
])
if len(Snapshots) == 0:
print(
"Snapshots not found! It seems the dataset for shuffle %s and trainFraction %s is not trained.\nPlease train it before evaluating.\nUse the function 'train_network' to do so."
% (shuffle, trainFraction))
else:
increasing_indices = np.argsort(
[int(m.split("-")[1]) for m in Snapshots])
Snapshots = Snapshots[increasing_indices]
if cfg["snapshotindex"] == -1:
snapindices = [-1]
elif cfg["snapshotindex"] == "all":
snapindices = range(len(Snapshots))
elif cfg["snapshotindex"] < len(Snapshots):
snapindices = [cfg["snapshotindex"]]
else:
print(
"Invalid choice, only -1 (last), any integer up to last, or all (as string)!"
)
final_result = []
##################################################
# Compute predictions over images
##################################################
for snapindex in snapindices:
dlc_cfg["init_weights"] = os.path.join(
str(modelfolder), "train", Snapshots[snapindex]
) # setting weights to corresponding snapshot.
trainingsiterations = (
dlc_cfg["init_weights"].split(os.sep)[-1]
).split(
"-"
)[-1] # read how many training siterations that corresponds to.
# name for deeplabcut net (based on its parameters)
DLCscorer, DLCscorerlegacy = auxiliaryfunctions.GetScorerName(
cfg,
shuffle,
trainFraction,
trainingsiterations,
modelprefix=modelprefix,
)
print(
"Running ",
DLCscorer,
" with # of trainingiterations:",
trainingsiterations,
)
(
notanalyzed,
resultsfilename,
DLCscorer,
) = auxiliaryfunctions.CheckifNotEvaluated(
str(evaluationfolder),
DLCscorer,
DLCscorerlegacy,
Snapshots[snapindex],
)
if os.path.isfile(
resultsfilename.split(".h5")[0] + "_full.pickle"):
print("Model already evaluated.", resultsfilename)
else:
if plotting:
foldername = os.path.join(
str(evaluationfolder),
"LabeledImages_" + DLCscorer + "_" +
Snapshots[snapindex],
)
auxiliaryfunctions.attempttomakefolder(foldername)
# print(dlc_cfg)
# Specifying state of model (snapshot / training state)
sess, inputs, outputs = predict.setup_pose_prediction(
dlc_cfg)
PredicteData = {}
dist = np.full((len(Data), len(all_bpts)), np.nan)
conf = np.full_like(dist, np.nan)
distnorm = np.full(len(Data), np.nan)
print("Analyzing data...")
for imageindex, imagename in tqdm(enumerate(
Data.index)):
image_path = os.path.join(cfg["project_path"],
imagename)
image = io.imread(image_path)
frame = img_as_ubyte(skimage.color.gray2rgb(image))
GT = Data.iloc[imageindex]
df = GT.unstack("coords").reindex(
joints, level='bodyparts')
# Evaluate PAF edge lengths to calibrate `distnorm`
temp = GT.unstack("bodyparts")[joints]
xy = temp.values.reshape(
(-1, 2, temp.shape[1])).swapaxes(1, 2)
edges = xy[:, dlc_cfg["partaffinityfield_graph"]]
lengths = np.sum(
(edges[:, :, 0] - edges[:, :, 1])**2, axis=2)
distnorm[imageindex] = np.nanmax(lengths)
# FIXME Is having an empty array vs nan really that necessary?!
groundtruthidentity = list(
df.index.get_level_values(
"individuals").to_numpy().reshape((-1, 1)))
groundtruthcoordinates = list(
df.values[:, np.newaxis])
for i, coords in enumerate(groundtruthcoordinates):
if np.isnan(coords).any():
groundtruthcoordinates[i] = np.empty(
(0, 2), dtype=float)
groundtruthidentity[i] = np.array(
[], dtype=str)
PredicteData[imagename] = {}
PredicteData[imagename]["index"] = imageindex
pred = predictma.get_detectionswithcostsandGT(
frame,
groundtruthcoordinates,
dlc_cfg,
sess,
inputs,
outputs,
outall=False,
nms_radius=dlc_cfg.nmsradius,
det_min_score=dlc_cfg.minconfidence,
c_engine=c_engine,
)
PredicteData[imagename]["prediction"] = pred
PredicteData[imagename]["groundtruth"] = [
groundtruthidentity,
groundtruthcoordinates,
GT,
]
coords_pred = pred["coordinates"][0]
probs_pred = pred["confidence"]
for bpt, xy_gt in df.groupby(level="bodyparts"):
inds_gt = np.flatnonzero(
np.all(~np.isnan(xy_gt), axis=1))
n_joint = joints.index(bpt)
xy = coords_pred[n_joint]
if inds_gt.size and xy.size:
# Pick the predictions closest to ground truth,
# rather than the ones the model has most confident in
d = cdist(xy_gt.iloc[inds_gt], xy)
rows, cols = linear_sum_assignment(d)
min_dists = d[rows, cols]
inds = np.flatnonzero(all_bpts == bpt)
sl = imageindex, inds[inds_gt[rows]]
dist[sl] = min_dists
conf[sl] = probs_pred[n_joint][
cols].squeeze()
if plotting:
fig = visualization.make_multianimal_labeled_image(
frame,
groundtruthcoordinates,
coords_pred,
probs_pred,
colors,
cfg["dotsize"],
cfg["alphavalue"],
cfg["pcutoff"],
)
visualization.save_labeled_frame(
fig,
image_path,
foldername,
imageindex in trainIndices,
)
sess.close() # closes the current tf session
# Compute all distance statistics
df_dist = pd.DataFrame(dist, columns=df.index)
df_conf = pd.DataFrame(conf, columns=df.index)
df_joint = pd.concat([df_dist, df_conf],
keys=["rmse", "conf"],
names=["metrics"],
axis=1)
df_joint = df_joint.reorder_levels(list(
np.roll(df_joint.columns.names, -1)),
axis=1)
df_joint.sort_index(axis=1,
level=["individuals", "bodyparts"],
ascending=[True, True],
inplace=True)
write_path = os.path.join(
evaluationfolder,
f"dist_{trainingsiterations}.csv")
df_joint.to_csv(write_path)
# Calculate overall prediction error
error = df_joint.xs("rmse", level="metrics", axis=1)
mask = df_joint.xs("conf", level="metrics",
axis=1) >= cfg["pcutoff"]
error_masked = error[mask]
error_train = np.nanmean(error.iloc[trainIndices])
error_train_cut = np.nanmean(
error_masked.iloc[trainIndices])
error_test = np.nanmean(error.iloc[testIndices])
error_test_cut = np.nanmean(
error_masked.iloc[testIndices])
results = [
trainingsiterations,
int(100 * trainFraction),
shuffle,
np.round(error_train, 2),
np.round(error_test, 2),
cfg["pcutoff"],
np.round(error_train_cut, 2),
np.round(error_test_cut, 2),
]
final_result.append(results)
# For OKS/PCK, compute the standard deviation error across all frames
sd = df_dist.groupby("bodyparts",
axis=1).mean().std(axis=0)
sd["distnorm"] = np.sqrt(np.nanmax(distnorm))
sd.to_csv(write_path.replace("dist.csv", "sd.csv"))
if show_errors:
string = "Results for {} training iterations: {}, shuffle {}:\n" \
"Train error: {} pixels. Test error: {} pixels.\n" \
"With pcutoff of {}:\n" \
"Train error: {} pixels. Test error: {} pixels."
print(string.format(*results))
print("##########################################")
print(
"Average Euclidean distance to GT per individual (in pixels)"
)
print(
error_masked.groupby(
'individuals',
axis=1).mean().mean().to_string())
print(
"Average Euclidean distance to GT per bodypart (in pixels)"
)
print(
error_masked.groupby(
'bodyparts',
axis=1).mean().mean().to_string())
PredicteData["metadata"] = {
"nms radius":
dlc_cfg.nmsradius,
"minimal confidence":
dlc_cfg.minconfidence,
"PAFgraph":
dlc_cfg.partaffinityfield_graph,
"all_joints":
[[i] for i in range(len(dlc_cfg.all_joints))],
"all_joints_names": [
dlc_cfg.all_joints_names[i]
for i in range(len(dlc_cfg.all_joints))
],
"stride":
dlc_cfg.get("stride", 8),
}
print(
"Done and results stored for snapshot: ",
Snapshots[snapindex],
)
dictionary = {
"Scorer": DLCscorer,
"DLC-model-config file": dlc_cfg,
"trainIndices": trainIndices,
"testIndices": testIndices,
"trainFraction": trainFraction,
}
metadata = {"data": dictionary}
auxfun_multianimal.SaveFullMultiAnimalData(
PredicteData, metadata, resultsfilename)
tf.reset_default_graph()
if len(final_result
) > 0: # Only append if results were calculated
make_results_file(final_result, evaluationfolder,
DLCscorer)
# returning to intial folder
os.chdir(str(start_path))
def evaluate_multianimal_full(
config,
Shuffles=[1],
trainingsetindex=0,
plotting=False,
show_errors=True,
comparisonbodyparts="all",
gputouse=None,
modelprefix="",
):
from deeplabcut.pose_estimation_tensorflow.core import (
predict,
predict_multianimal as predictma,
)
from deeplabcut.utils import (
auxiliaryfunctions,
auxfun_multianimal,
auxfun_videos,
conversioncode,
)
import tensorflow as tf
if "TF_CUDNN_USE_AUTOTUNE" in os.environ:
del os.environ["TF_CUDNN_USE_AUTOTUNE"] # was potentially set during training
tf.compat.v1.reset_default_graph()
os.environ["TF_CPP_MIN_LOG_LEVEL"] = "2" #
if gputouse is not None: # gpu selectinon
os.environ["CUDA_VISIBLE_DEVICES"] = str(gputouse)
start_path = os.getcwd()
if plotting is True:
plotting = "bodypart"
##################################################
# Load data...
##################################################
cfg = auxiliaryfunctions.read_config(config)
if trainingsetindex == "all":
TrainingFractions = cfg["TrainingFraction"]
else:
TrainingFractions = [cfg["TrainingFraction"][trainingsetindex]]
# Loading human annotatated data
trainingsetfolder = auxiliaryfunctions.GetTrainingSetFolder(cfg)
Data = pd.read_hdf(
os.path.join(
cfg["project_path"],
str(trainingsetfolder),
"CollectedData_" + cfg["scorer"] + ".h5",
)
)
conversioncode.guarantee_multiindex_rows(Data)
# Get list of body parts to evaluate network for
comparisonbodyparts = auxiliaryfunctions.IntersectionofBodyPartsandOnesGivenbyUser(
cfg, comparisonbodyparts
)
all_bpts = np.asarray(
len(cfg["individuals"]) * cfg["multianimalbodyparts"] + cfg["uniquebodyparts"]
)
colors = visualization.get_cmap(len(comparisonbodyparts), name=cfg["colormap"])
# Make folder for evaluation
auxiliaryfunctions.attempttomakefolder(
str(cfg["project_path"] + "/evaluation-results/")
)
for shuffle in Shuffles:
for trainFraction in TrainingFractions:
##################################################
# Load and setup CNN part detector
##################################################
datafn, metadatafn = auxiliaryfunctions.GetDataandMetaDataFilenames(
trainingsetfolder, trainFraction, shuffle, cfg
)
modelfolder = os.path.join(
cfg["project_path"],
str(
auxiliaryfunctions.GetModelFolder(
trainFraction, shuffle, cfg, modelprefix=modelprefix
)
),
)
path_test_config = Path(modelfolder) / "test" / "pose_cfg.yaml"
# Load meta data
(
data,
trainIndices,
testIndices,
trainFraction,
) = auxiliaryfunctions.LoadMetadata(
os.path.join(cfg["project_path"], metadatafn)
)
try:
dlc_cfg = load_config(str(path_test_config))
except FileNotFoundError:
raise FileNotFoundError(
"It seems the model for shuffle %s and trainFraction %s does not exist."
% (shuffle, trainFraction)
)
pipeline = iaa.Sequential(random_order=False)
pre_resize = dlc_cfg.get("pre_resize")
if pre_resize:
width, height = pre_resize
pipeline.add(iaa.Resize({"height": height, "width": width}))
# TODO: IMPLEMENT for different batch sizes?
dlc_cfg["batch_size"] = 1 # due to differently sized images!!!
stride = dlc_cfg["stride"]
# Ignore best edges possibly defined during a prior evaluation
_ = dlc_cfg.pop("paf_best", None)
joints = dlc_cfg["all_joints_names"]
# Create folder structure to store results.
evaluationfolder = os.path.join(
cfg["project_path"],
str(
auxiliaryfunctions.GetEvaluationFolder(
trainFraction, shuffle, cfg, modelprefix=modelprefix
)
),
)
auxiliaryfunctions.attempttomakefolder(evaluationfolder, recursive=True)
# path_train_config = modelfolder / 'train' / 'pose_cfg.yaml'
# Check which snapshots are available and sort them by # iterations
Snapshots = np.array(
[
fn.split(".")[0]
for fn in os.listdir(os.path.join(str(modelfolder), "train"))
if "index" in fn
]
)
if len(Snapshots) == 0:
print(
"Snapshots not found! It seems the dataset for shuffle %s and trainFraction %s is not trained.\nPlease train it before evaluating.\nUse the function 'train_network' to do so."
% (shuffle, trainFraction)
)
else:
increasing_indices = np.argsort(
[int(m.split("-")[1]) for m in Snapshots]
)
Snapshots = Snapshots[increasing_indices]
if cfg["snapshotindex"] == -1:
snapindices = [-1]
elif cfg["snapshotindex"] == "all":
snapindices = range(len(Snapshots))
elif cfg["snapshotindex"] < len(Snapshots):
snapindices = [cfg["snapshotindex"]]
else:
print(
"Invalid choice, only -1 (last), any integer up to last, or all (as string)!"
)
final_result = []
##################################################
# Compute predictions over images
##################################################
for snapindex in snapindices:
dlc_cfg["init_weights"] = os.path.join(
str(modelfolder), "train", Snapshots[snapindex]
) # setting weights to corresponding snapshot.
trainingsiterations = (
dlc_cfg["init_weights"].split(os.sep)[-1]
).split("-")[
-1
] # read how many training siterations that corresponds to.
# name for deeplabcut net (based on its parameters)
DLCscorer, DLCscorerlegacy = auxiliaryfunctions.GetScorerName(
cfg,
shuffle,
trainFraction,
trainingsiterations,
modelprefix=modelprefix,
)
print(
"Running ",
DLCscorer,
" with # of trainingiterations:",
trainingsiterations,
)
(
notanalyzed,
resultsfilename,
DLCscorer,
) = auxiliaryfunctions.CheckifNotEvaluated(
str(evaluationfolder),
DLCscorer,
DLCscorerlegacy,
Snapshots[snapindex],
)
data_path = resultsfilename.split(".h5")[0] + "_full.pickle"
if plotting:
foldername = os.path.join(
str(evaluationfolder),
"LabeledImages_" + DLCscorer + "_" + Snapshots[snapindex],
)
auxiliaryfunctions.attempttomakefolder(foldername)
if plotting == "bodypart":
fig, ax = visualization.create_minimal_figure()
if os.path.isfile(data_path):
print("Model already evaluated.", resultsfilename)
else:
(sess, inputs, outputs,) = predict.setup_pose_prediction(
dlc_cfg
)
PredicteData = {}
dist = np.full((len(Data), len(all_bpts)), np.nan)
conf = np.full_like(dist, np.nan)
print("Network Evaluation underway...")
for imageindex, imagename in tqdm(enumerate(Data.index)):
image_path = os.path.join(cfg["project_path"], *imagename)
frame = auxfun_videos.imread(image_path, mode="skimage")
GT = Data.iloc[imageindex]
if not GT.any():
continue
# Pass the image and the keypoints through the resizer;
# this has no effect if no augmenters were added to it.
keypoints = [GT.to_numpy().reshape((-1, 2)).astype(float)]
frame_, keypoints = pipeline(
images=[frame], keypoints=keypoints
)
frame = frame_[0]
GT[:] = keypoints[0].flatten()
df = GT.unstack("coords").reindex(joints, level="bodyparts")
# FIXME Is having an empty array vs nan really that necessary?!
groundtruthidentity = list(
df.index.get_level_values("individuals")
.to_numpy()
.reshape((-1, 1))
)
groundtruthcoordinates = list(df.values[:, np.newaxis])
for i, coords in enumerate(groundtruthcoordinates):
if np.isnan(coords).any():
groundtruthcoordinates[i] = np.empty(
(0, 2), dtype=float
)
groundtruthidentity[i] = np.array([], dtype=str)
# Form 2D array of shape (n_rows, 4) where the last dimension
# is (sample_index, peak_y, peak_x, bpt_index) to slice the PAFs.
temp = df.reset_index(level="bodyparts").dropna()
temp["bodyparts"].replace(
dict(zip(joints, range(len(joints)))), inplace=True,
)
temp["sample"] = 0
peaks_gt = temp.loc[
:, ["sample", "y", "x", "bodyparts"]
].to_numpy()
peaks_gt[:, 1:3] = (peaks_gt[:, 1:3] - stride // 2) / stride
pred = predictma.predict_batched_peaks_and_costs(
dlc_cfg,
np.expand_dims(frame, axis=0),
sess,
inputs,
outputs,
peaks_gt.astype(int),
)
if not pred:
continue
else:
pred = pred[0]
PredicteData[imagename] = {}
PredicteData[imagename]["index"] = imageindex
PredicteData[imagename]["prediction"] = pred
PredicteData[imagename]["groundtruth"] = [
groundtruthidentity,
groundtruthcoordinates,
GT,
]
coords_pred = pred["coordinates"][0]
probs_pred = pred["confidence"]
for bpt, xy_gt in df.groupby(level="bodyparts"):
inds_gt = np.flatnonzero(
np.all(~np.isnan(xy_gt), axis=1)
)
n_joint = joints.index(bpt)
xy = coords_pred[n_joint]
if inds_gt.size and xy.size:
# Pick the predictions closest to ground truth,
# rather than the ones the model has most confident in
xy_gt_values = xy_gt.iloc[inds_gt].values
neighbors = _find_closest_neighbors(
xy_gt_values, xy, k=3
)
found = neighbors != -1
min_dists = np.linalg.norm(
xy_gt_values[found] - xy[neighbors[found]],
axis=1,
)
inds = np.flatnonzero(all_bpts == bpt)
sl = imageindex, inds[inds_gt[found]]
dist[sl] = min_dists
conf[sl] = probs_pred[n_joint][
neighbors[found]
].squeeze()
if plotting == "bodypart":
temp_xy = GT.unstack("bodyparts")[joints].values
gt = temp_xy.reshape(
(-1, 2, temp_xy.shape[1])
).T.swapaxes(1, 2)
h, w, _ = np.shape(frame)
fig.set_size_inches(w / 100, h / 100)
ax.set_xlim(0, w)
ax.set_ylim(0, h)
ax.invert_yaxis()
ax = visualization.make_multianimal_labeled_image(
frame,
gt,
coords_pred,
probs_pred,
colors,
cfg["dotsize"],
cfg["alphavalue"],
cfg["pcutoff"],
ax=ax,
)
visualization.save_labeled_frame(
fig,
image_path,
foldername,
imageindex in trainIndices,
)
visualization.erase_artists(ax)
sess.close() # closes the current tf session
# Compute all distance statistics
df_dist = pd.DataFrame(dist, columns=df.index)
df_conf = pd.DataFrame(conf, columns=df.index)
df_joint = pd.concat(
[df_dist, df_conf],
keys=["rmse", "conf"],
names=["metrics"],
axis=1,
)
df_joint = df_joint.reorder_levels(
list(np.roll(df_joint.columns.names, -1)), axis=1
)
df_joint.sort_index(
axis=1,
level=["individuals", "bodyparts"],
ascending=[True, True],
inplace=True,
)
write_path = os.path.join(
evaluationfolder, f"dist_{trainingsiterations}.csv"
)
df_joint.to_csv(write_path)
# Calculate overall prediction error
error = df_joint.xs("rmse", level="metrics", axis=1)
mask = (
df_joint.xs("conf", level="metrics", axis=1)
>= cfg["pcutoff"]
)
error_masked = error[mask]
error_train = np.nanmean(error.iloc[trainIndices])
error_train_cut = np.nanmean(error_masked.iloc[trainIndices])
error_test = np.nanmean(error.iloc[testIndices])
error_test_cut = np.nanmean(error_masked.iloc[testIndices])
results = [
trainingsiterations,
int(100 * trainFraction),
shuffle,
np.round(error_train, 2),
np.round(error_test, 2),
cfg["pcutoff"],
np.round(error_train_cut, 2),
np.round(error_test_cut, 2),
]
final_result.append(results)
if show_errors:
string = (
"Results for {} training iterations, training fraction of {}, and shuffle {}:\n"
"Train error: {} pixels. Test error: {} pixels.\n"
"With pcutoff of {}:\n"
"Train error: {} pixels. Test error: {} pixels."
)
print(string.format(*results))
print("##########################################")
print(
"Average Euclidean distance to GT per individual (in pixels; test-only)"
)
print(
error_masked.iloc[testIndices]
.groupby("individuals", axis=1)
.mean()
.mean()
.to_string()
)
print(
"Average Euclidean distance to GT per bodypart (in pixels; test-only)"
)
print(
error_masked.iloc[testIndices]
.groupby("bodyparts", axis=1)
.mean()
.mean()
.to_string()
)
PredicteData["metadata"] = {
"nms radius": dlc_cfg["nmsradius"],
"minimal confidence": dlc_cfg["minconfidence"],
"sigma": dlc_cfg.get("sigma", 1),
"PAFgraph": dlc_cfg["partaffinityfield_graph"],
"PAFinds": np.arange(
len(dlc_cfg["partaffinityfield_graph"])
),
"all_joints": [
[i] for i in range(len(dlc_cfg["all_joints"]))
],
"all_joints_names": [
dlc_cfg["all_joints_names"][i]
for i in range(len(dlc_cfg["all_joints"]))
],
"stride": dlc_cfg.get("stride", 8),
}
print(
"Done and results stored for snapshot: ",
Snapshots[snapindex],
)
dictionary = {
"Scorer": DLCscorer,
"DLC-model-config file": dlc_cfg,
"trainIndices": trainIndices,
"testIndices": testIndices,
"trainFraction": trainFraction,
}
metadata = {"data": dictionary}
_ = auxfun_multianimal.SaveFullMultiAnimalData(
PredicteData, metadata, resultsfilename
)
tf.compat.v1.reset_default_graph()
n_multibpts = len(cfg["multianimalbodyparts"])
if n_multibpts == 1:
continue
# Skip data-driven skeleton selection unless
# the model was trained on the full graph.
max_n_edges = n_multibpts * (n_multibpts - 1) // 2
n_edges = len(dlc_cfg["partaffinityfield_graph"])
if n_edges == max_n_edges:
print("Selecting best skeleton...")
n_graphs = 10
paf_inds = None
else:
n_graphs = 1
paf_inds = [list(range(n_edges))]
(
results,
paf_scores,
best_assemblies,
) = crossvalutils.cross_validate_paf_graphs(
config,
str(path_test_config).replace("pose_", "inference_"),
data_path,
data_path.replace("_full.", "_meta."),
n_graphs=n_graphs,
paf_inds=paf_inds,
oks_sigma=dlc_cfg.get("oks_sigma", 0.1),
margin=dlc_cfg.get("bbox_margin", 0),
symmetric_kpts=dlc_cfg.get("symmetric_kpts"),
)
if plotting == "individual":
assemblies, assemblies_unique, image_paths = best_assemblies
fig, ax = visualization.create_minimal_figure()
n_animals = len(cfg["individuals"])
if cfg["uniquebodyparts"]:
n_animals += 1
colors = visualization.get_cmap(n_animals, name=cfg["colormap"])
for k, v in tqdm(assemblies.items()):
imname = image_paths[k]
image_path = os.path.join(cfg["project_path"], *imname)
frame = auxfun_videos.imread(image_path, mode="skimage")
h, w, _ = np.shape(frame)
fig.set_size_inches(w / 100, h / 100)
ax.set_xlim(0, w)
ax.set_ylim(0, h)
ax.invert_yaxis()
gt = [
s.to_numpy().reshape((-1, 2))
for _, s in Data.loc[imname].groupby("individuals")
]
coords_pred = []
coords_pred += [ass.xy for ass in v]
probs_pred = []
probs_pred += [ass.data[:, 2:3] for ass in v]
if assemblies_unique is not None:
unique = assemblies_unique.get(k, None)
if unique is not None:
coords_pred.append(unique[:, :2])
probs_pred.append(unique[:, 2:3])
while len(coords_pred) < len(gt):
coords_pred.append(np.full((1, 2), np.nan))
probs_pred.append(np.full((1, 2), np.nan))
ax = visualization.make_multianimal_labeled_image(
frame,
gt,
coords_pred,
probs_pred,
colors,
cfg["dotsize"],
cfg["alphavalue"],
cfg["pcutoff"],
ax=ax,
)
visualization.save_labeled_frame(
fig, image_path, foldername, k in trainIndices,
)
visualization.erase_artists(ax)
df = results[1].copy()
df.loc(axis=0)[("mAP_train", "mean")] = [
d[0]["mAP"] for d in results[2]
]
df.loc(axis=0)[("mAR_train", "mean")] = [
d[0]["mAR"] for d in results[2]
]
df.loc(axis=0)[("mAP_test", "mean")] = [
d[1]["mAP"] for d in results[2]
]
df.loc(axis=0)[("mAR_test", "mean")] = [
d[1]["mAR"] for d in results[2]
]
with open(data_path.replace("_full.", "_map."), "wb") as file:
pickle.dump((df, paf_scores), file)
if len(final_result) > 0: # Only append if results were calculated
make_results_file(final_result, evaluationfolder, DLCscorer)
os.chdir(str(start_path))
def AnalyzeMultiAnimalVideo(
video,
DLCscorer,
trainFraction,
cfg,
dlc_cfg,
sess,
inputs,
outputs,
pdindex,
save_as_csv,
destfolder=None,
c_engine=False,
robust_nframes=False,
):
""" Helper function for analyzing a video with multiple individuals """
print("Starting to analyze % ", video)
vname = Path(video).stem
videofolder = str(Path(video).parents[0])
if destfolder is None:
destfolder = videofolder
auxiliaryfunctions.attempttomakefolder(destfolder)
dataname = os.path.join(destfolder, vname + DLCscorer + ".h5")
if os.path.isfile(dataname.split(".h5")[0] + "_full.pickle"):
print("Video already analyzed!", dataname)
else:
print("Loading ", video)
cap = cv2.VideoCapture(video)
if not cap.isOpened():
raise IOError(
"Video could not be opened. Please check that the path is valid."
)
if robust_nframes:
nframes = auxfun_videos.get_nframes_robust(video)
duration = auxfun_videos.get_duration(video)
fps = nframes / duration
else:
nframes = int(cap.get(cv2.CAP_PROP_FRAME_COUNT))
fps = int(cap.get(cv2.CAP_PROP_FPS))
duration = nframes / fps
size = (int(cap.get(4)), int(cap.get(3)))
ny, nx = size
print(
"Duration of video [s]: ",
round(duration, 2),
", recorded with ",
round(fps, 2),
"fps!",
)
print(
"Overall # of frames: ",
nframes,
" found with (before cropping) frame dimensions: ",
nx,
ny,
)
start = time.time()
print("Starting to extract posture")
if int(dlc_cfg["batch_size"]) > 1:
PredicteData, nframes = GetPoseandCostsF(
cfg,
dlc_cfg,
sess,
inputs,
outputs,
cap,
nframes,
int(dlc_cfg["batch_size"]),
c_engine=c_engine,
)
else:
PredicteData, nframes = GetPoseandCostsS(
cfg, dlc_cfg, sess, inputs, outputs, cap, nframes, c_engine=c_engine
)
stop = time.time()
if cfg["cropping"] == True:
coords = [cfg["x1"], cfg["x2"], cfg["y1"], cfg["y2"]]
else:
coords = [0, nx, 0, ny]
dictionary = {
"start": start,
"stop": stop,
"run_duration": stop - start,
"Scorer": DLCscorer,
"DLC-model-config file": dlc_cfg,
"fps": fps,
"batch_size": dlc_cfg["batch_size"],
"frame_dimensions": (ny, nx),
"nframes": nframes,
"iteration (active-learning)": cfg["iteration"],
"training set fraction": trainFraction,
"cropping": cfg["cropping"],
"cropping_parameters": coords,
}
metadata = {"data": dictionary}
print("Saving results in %s..." % (destfolder))
auxfun_multianimal.SaveFullMultiAnimalData(PredicteData, metadata, dataname)
