./test.sh: line 26: python: command not found (build.sh has succeed)

/home/evaluator/.local/lib/python3.9/site-packages/evalutils/evalutils.py:589: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  self._case_results = self._case_results.append(
/home/evaluator/.local/lib/python3.9/site-packages/evalutils/evalutils.py:589: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  self._case_results = self._case_results.append(
/home/evaluator/.local/lib/python3.9/site-packages/evalutils/evalutils.py:589: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  self._case_results = self._case_results.append(
/home/evaluator/.local/lib/python3.9/site-packages/evalutils/evalutils.py:589: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  self._case_results = self._case_results.append(
Could not serialize freq: 1 as json, so converting 1 to int.
Could not serialize count: 100 as json, so converting 100 to int.
Could not serialize freq: 1 as json, so converting 1 to int.
Could not serialize count: 100 as json, so converting 100 to int.
./test.sh: line 26: python: command not found
write /dev/stdout: broken pipe
Error response from daemon: remove fullysupplayground-output-003e399a443aa7a64df0a6a62c19a538: volume is in use - [d8754619242a1d117c2833f5dc2b153b857afd3ddb68ac4639eddf0216595d4b]

import SimpleITK
import numpy as np
import scipy.ndimage
from evalutils import ClassificationEvaluation
from evalutils.io import SimpleITKLoader
from evalutils.validators import (
    NumberOfCasesValidator, UniquePathIndicesValidator, UniqueImagesValidator
)

def compute_dice_coefficient(mask_gt, mask_pred):

  volume_sum = mask_gt.sum() + mask_pred.sum()
  if volume_sum == 0:
    return np.NaN
  volume_intersect = (mask_gt & mask_pred).sum()
  return 2 * volume_intersect / volume_sum



class fullysupplayground(ClassificationEvaluation):
    def __init__(self):
        super().__init__(
            file_loader=SimpleITKLoader(),
            validators=(
                NumberOfCasesValidator(num_cases=100),
                UniquePathIndicesValidator(),
                UniqueImagesValidator(),
            ),
        )

    def score_case(self, *, idx, case):
        gt_path = case["path_ground_truth"]
        pred_path = case["path_prediction"]

        # Load the images for this case
        gt = self._file_loader.load_image(gt_path)
        pred = self._file_loader.load_image(pred_path)


        # Check that they're the right images
        if (self._file_loader.hash_image(gt) != case["hash_ground_truth"] or
            self._file_loader.hash_image(pred) != case["hash_prediction"]):
            raise RuntimeError("Images do not match")

        gt_data = SimpleITK.GetArrayFromImage(gt).transpose(2, 1, 0)
        gt_data = np.uint8(gt_data)
        pred_data = SimpleITK.GetArrayFromImage(pred).transpose(2, 1, 0)
        pred_data = np.uint8(pred_data)

        # Score the case
        DSCs = list()
        for i in range(1, 5):
            if np.sum(gt_data == i) == 0 and np.sum(pred_data == i) == 0:
                DSC_i = 1
            elif np.sum(gt_data == i) == 0 and np.sum(pred_data == i) > 0:
                DSC_i = 0
            else:
                DSC_i = compute_dice_coefficient(gt_data == i, pred_data == i)
            DSCs.append(DSC_i)


        return {
            'MeanDSC': np.mean(DSCs),
            'LiverDSC': DSCs[0],
            'KidneyDSC': DSCs[1],
            'SpleenDSC': DSCs[2],
            'PancreasDSC': DSCs[3],
            'pred_fname': pred_path.name,
            'gt_fname': gt_path.name,
        }

if __name__ == "__main__":
    fullysupplayground().evaluate()

#!/usr/bin/env bash

SCRIPTPATH="$( cd "$(dirname "$0")" ; pwd -P )"

./build.sh

VOLUME_SUFFIX=$(dd if=/dev/urandom bs=32 count=1 | md5sum | cut --delimiter=' ' --fields=1)

docker volume create fullysupplayground-output-$VOLUME_SUFFIX

# Do not change any of the parameters to docker run, these are fixed
docker run --rm \
        --memory="4g" \
        --memory-swap="4g" \
        --network="none" \
        --cap-drop="ALL" \
        --security-opt="no-new-privileges" \
        --shm-size="128m" \
        --pids-limit="256" \
        -v $SCRIPTPATH/test/:/input/ \
        -v fullysupplayground-output-$VOLUME_SUFFIX:/output/ \
        fullysupplayground

docker run --rm \
        -v fullysupplayground-output-$VOLUME_SUFFIX:/output/ \
        python:3.9-slim cat /output/metrics.json | python -m json.tool

docker volume rm fullysupplayground-output-$VOLUME_SUFFIX