pathology/transformation_pipeline/ingestion_lib/gen_test_util.py

# Copyright 2023 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# ==============================================================================
"""Helper functions for tests."""

import io
import os

import numpy as np
import openslide
import PIL.Image
import pydicom

from pathology.shared_libs.pydicom_version_util import pydicom_version_util
from pathology.transformation_pipeline.ingestion_lib import ingest_const


def test_file_path(*path: str) -> str:
  """Returns path to file in unit test."""
  return os.path.normpath(
      os.path.join(
          os.path.dirname(__file__),
          '..',
          '..',
          'transformation_pipeline',
          'testdata',
          *path,
      )
  )


def create_mock_wsi_dicom_dataset(barcode_value: str = '') -> pydicom.Dataset:
  """Returns pydicom Dataset with mock wsi DICOM metadata."""
  ds = pydicom.Dataset()
  if barcode_value:
    ds.BarcodeValue = barcode_value
  ds.StudyInstanceUID = '1.2.3'
  ds.SeriesInstanceUID = '1.2.3.4'
  ds.SOPInstanceUID = '1.2.3.4.5'
  ds.SOPClassUID = ingest_const.DicomSopClasses.WHOLE_SLIDE_IMAGE.uid
  ds.Modality = 'SM'
  ds.BitsAllocated = 8
  ds.BitsStored = 8
  ds.HighBit = 7
  ds.SamplesPerPixel = 1
  ds.NumberOfFrames = 1
  ds.Rows = 1
  ds.Columns = 1
  ds.TotalPixelMatrixColumns = 1
  ds.TotalPixelMatrixRows = 1
  ds.SpecimenLabelInImage = 'NO'
  ds.BurnedInAnnotation = 'NO'
  ds.ImageType = '\\'.join(
      [ingest_const.ORIGINAL, ingest_const.PRIMARY, ingest_const.VOLUME]
  )
  return ds


def decode_image_from_bytes(image_bytes: bytes) -> np.ndarray:
  """Returns image from bytes."""
  with PIL.Image.open(io.BytesIO(image_bytes)) as image:
    return np.asarray(image)


def decode_image_from_file(path: str) -> np.ndarray:
  """Returns image from bytes."""
  with PIL.Image.open(path) as image:
    return np.asarray(image)


def write_test_dicom(path: str, base_ds: pydicom.Dataset):
  file_meta = pydicom.dataset.FileMetaDataset()
  file_meta.TransferSyntaxUID = (
      ingest_const.DicomImageTransferSyntax.EXPLICIT_VR_LITTLE_ENDIAN
  )
  ds = pydicom.dataset.FileDataset(
      '', base_ds, file_meta=file_meta, preamble=b'\0' * 128
  )
  pydicom_version_util.set_little_endian_explicit_vr(ds)
  ds.save_as(path)


def is_openslide_file_valid(path: str) -> bool:
  """Returns True if ndpi_test.ndpi file is available."""
  if not os.path.exists(path):
    return False
  try:
    _ = openslide.OpenSlide(path)
    return True
  except (openslide.OpenSlideError, OSError) as _:
    return False