ivtmetrics

The ivtmetrics library provides a Python implementation of metrics for benchmarking surgical action triplet detection and recognition.

Features at a glance

The following are available with ivtmetrics:

1. Recognition Evaluation: Provides AP metrics to measure the performance of a model on action triplet recognition.

2. Detection Evaluation: Supports Intersection over Union distances measure of the triplet localization with respect to the instruments.

3. Flexible Analysis: (1) Supports for switching between frame-wise to video-wise averaging of the AP. (2) Supports disentangle prediction and obtained filtered performance for the various components of the triplets as well as their association performances at various levels.

Installation

Install via PyPi

To install ivtmetrics use pip

pip install ivtmetrics

Install via Conda

conda install -c nwoye ivtmetrics

Python 3.5-3.9 and numpy and scikit-learn are required.

Metrics

The metrics have been aligned with what is reported by CholecT50 benchmark. ivtmetrics can be imported in the following way:

import ivtmetrics

The metrics implement both recognition and detection evaluation. The metrics internally implement a disentangle function to help filter the triplet components as well as triplet different levels of association.

Recognition Metrics

Recognition ivtmetrics can be used in the following ways:

metric = ivtmetrics.Recognition(num_class)

This takes an argument num_class which is default to 100

The following function are possible with the Recognition class:

Name	Description
update(`targets, predictions`)	takes in a (batch of) vector predictions and their corresponding groundtruth. vector size must match `num_class` in the class initialization.
video_end()	Call to make the end of one video sequence.
reset()	Reset current records. Useful during training and can be called at the begining of each epoch to avoid overlapping epoch performances.
reset_global()	Reset all records. Useful for switching between training/validation/testing or can be called at the begining of new experiment.
compu te_AP(`component, ignore_null`)	Obtain the average precision on the fly. This gives the AP only on examples cases after the last `reset()` call. Useful for epoch performance during training.
compute_vid eo_AP(`component, ignore_null`)	(RECOMMENDED) compute video-wise AP performance as used in CholecT50 benchmarks.
compute_glob al_AP(`component, ignore_null`)	compute frame-wise AP performance for all seen samples.
topK(`k, component`)	Obtain top K performance on action triplet recognition for all seen examples. args `k` can be any int between 1-99. k = [5,10,15,20] have been used in benchmark papers.
topClass(`k, component`)	Obtain top K recognized classes on action triplet recognition for all seen examples. args `k` can be any int between 1-99. k = 10 have been used in benchmark papers.

args:

args component can be any of the following (‘i’, ‘v’, ‘t’, ‘iv’, ‘it’,‘ivt’) to compute performance for (instrument, verb, target, instrument-verb, instrument-target, instrument-verb-target) respectively. default is ‘ivt’ for triplets.
args ignore_null (optional, default=False): to ignore null triplet classes in the evaluation. This option is enabled in CholecTriplet2021 challenge.
the output is a dict with keys(“AP”, “mAP”) for per-class and mean AP respectively.

Example usage

import ivtmetrics
recognize = ivtmetrics.Recognition(num_class=100)
network = MyModel(...) # your model here
# training
for epoch in number-of-epochs:
  recognize.reset()
  for images, labels in dataloader(...): # your data loader
    predictions = network(image)
    recognize.update(labels, predictions)
  results_i = recognize.compute_AP('i')
  print("instrument per class AP", results_i["AP"])
  print("instrument mean AP", results_i["mAP"])
  results_ivt = recognize.compute_AP('ivt')
  print("triplet mean AP", results_ivt["mAP"])

# evaluation
recognize.reset_global()
for video in videos:
  for images, labels in dataloader(video, ..): # your data loader
    predictions = network(image)
    recognize.update(labels, predictions)
  recognize.video_end()

results_i = recognize.compute_video_AP('i')
print("instrument per class AP", results_i["AP"])
print("instrument mean AP", results_i["mAP"])

results_it = recognize.compute_video_AP('it')
print("instrument-target mean AP", results_it["mAP"])

results_ivt = recognize.compute_video_AP('ivt')
print("triplet mean AP", results_ivt["mAP"])

Any nan value in results is for classes with no occurrence in the data sample.

Detection Metrics

Detection ivtmetrics can be used in the following ways:

metric = ivtmetrics.Detection(num_class, num_tool, threshold=0.5)

This takes an argument num_class which is default to 100 and num_tool which is default to 6

The following function are possible with the Detection class:

Name	Description
update( `targets, predictions, format`)	input: takes in a (batch of) list/dict predictions and their corresponding groundtruth. Each frame prediction/groundtruth can be either as a `list of list` or as a `list of dict`. (more details below).
video_end()	Call to make the end of one video sequence.
reset()	Reset current records. Useful during training and can be called at the begining of each epoch to avoid overlapping epoch performances.
reset_global()	Reset all records. Useful for switching between training/validation/testing or can be called at the begining of new experiment.
compute_AP(`component`)	Obtain the average precision on the fly. This gives the AP only on examples cases after the last `reset()` call. Useful for epoch performance during training.
compute_video_AP(`component`)	(RECOMMENDED) compute video-wise AP performance as used in CholecT50 benchmarks.
compute_global_AP(`component`)	compute frame-wise AP performance for all seen samples.

args:

list of list format: [[tripletID, toolID, toolProbs, x, y, w, h], [tripletID, toolID, toolProbs, x, y, w, h], …], where:
- tripletID = triplet unique identity
- toolID = instrument unique identity
- toolProbs = instrument detection confidence
- x = bounding box x1 coordiante
- y = bounding box y1 coordinate
- w = width of the box
- h = height of the box
- The [x,y,w,h] are scaled between 0..1
list of dict format: [{“triplet”:tripletID, “instrument”:[toolID, toolProbs, x, y, w, h]}, {“triplet”:tripletID, “instrument”:[toolID, toolProbs, x, y, w, h]}, …].
format args describes the input format with either of the values (“list”, “dict”)
component can be any of the following (‘i’, ‘v’, ‘t’, ‘iv’, ‘it’,‘ivt’) to compute performance for (instrument, verb, target, instrument-verb, instrument-target, instrument-verb-target) respectively, default is ‘ivt’ for triplets.

the output is a dict with keys(“AP”, “mAP”, “Rec”, “mRec”, “Pre”, “mPre”) for per-class AP, mean AP, per-class Recall, mean Recall, per-class Precision and mean Precision respectively.

Example usage

import ivtmetrics
detect = ivtmetrics.Detection(num_class=100)

network = MyModel(...) # your model here

# training

format = "list"
for epoch in number of epochs:
  for images, labels in dataloader(...): # your data loader
    predictions = network(image)
    labels, predictions = formatYourLabels(labels, predictions)
    detect.update(labels, predictions, format=format)

  results_i = detect.compute_AP('i')
  print("instrument per class AP", results_i["AP"])
  print("instrument mean AP", results_i["mAP"])

  results_ivt = detect.compute_AP('ivt')
  print("triplet mean AP", results_ivt["mAP"])
  detect.reset()


# evaluation

format = "dict"
for video in videos:
  for images, labels in dataloader(video, ..): # your data loader
    predictions = network(image)
    labels, predictions = formatYourLabels(labels, predictions)
    detect.update(labels, predictions, format=format)
  detect.video_end()

results_ivt = detect.compute_video_AP('ivt')
print("triplet mean AP", results_ivt["mAP"])
print("triplet mean recall", results_ivt["mRec"])
print("triplet mean precision", results_ivt["mPre"])

Any nan value in results is for classes with no occurrence in the data sample.

Disentangle

Although, the Detection() and Recognition() classes uses the Disentangle() internally, this function can still be used independently for component filtering in the following ways:

filter = ivtmetrics.Disentangle()

Afterwards, any of the component's predictions/labels can be filtered from the main triplet's predictions/labels as follows:

i_labels = filter.extract(inputs=ivt_labels, component="i")
v_preds  = filter.extract(inputs=ivt_preds, component="v")
t_preds  = filter.extract(inputs=ivt_preds, component="t")
iv_labels = filter.extract(inputs=ivt_labels, component="iv")
it_labels = filter.extract(inputs=ivt_labels, component="it")

In this example, labels = (batch of) vector of groundtruth labels; preds = (batch of) vector of predicted probability scores.

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Citation

If you use this metrics in your project or research, please consider citing the associated publication:

@article{nwoye2022data,
   title={Data Splits and Metrics for Benchmarking Methods on Surgical Action Triplet Datasets},
   author={Nwoye, Chinedu Innocent and Padoy, Nicolas},
   journal={arXiv preprint arXiv:2204.05235},
   year={2022}
}

References

Nwoye, C. I., Yu, T., Gonzalez, C., Seeliger, B., Mascagni, P., Mutter, D., … & Padoy, N. (2021). Rendezvous: Attention Mechanisms for the Recognition of Surgical Action Triplets in Endoscopic Videos. arXiv preprint arXiv:2109.03223.
Nwoye, C. I., Gonzalez, C., Yu, T., Mascagni, P., Mutter, D., Marescaux, J., & Padoy, N. (2020, October). Recognition of instrument-tissue interactions in endoscopic videos via action triplets. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 364-374). Springer, Cham.
http://camma.u-strasbg.fr/datasets
https://cholectriplet2021.grand-challenge.org
https://cholectriplet2022.grand-challenge.org

License

BSD 2-Clause License

Copyright (c) 2022, Research Group CAMMA
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this
   list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.```

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README.rst

README.rst

ivtmetrics

Features at a glance

Installation

Install via PyPi

Install via Conda

Metrics

Recognition Metrics

args:

Example usage

Detection Metrics

args:

Example usage

Disentangle

Docker

Citation

References

License

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README.rst

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README.rst

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ivtmetrics

Features at a glance

Installation

Install via PyPi

Install via Conda

Metrics

Recognition Metrics

args:

Example usage

Detection Metrics

args:

Example usage

Disentangle

Docker

Citation

References

License