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Feb 3, 2021
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Rename tests #1297

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6 changes: 3 additions & 3 deletions .github/workflows/build.wheel.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@ run_test() {
CPYTHON_VERSION=$($entry -c 'import sys; print(str(sys.version_info[0])+str(sys.version_info[1]))')
(cd wheelhouse && $entry -m pip install tensorflow_io-*-cp${CPYTHON_VERSION}-*.whl)
$entry -m pip install -q pytest pytest-benchmark boto3 fastavro avro-python3 scikit-image pandas pyarrow==3.0.0 google-cloud-pubsub==2.1.0 google-cloud-bigtable==1.6.0 google-cloud-bigquery-storage==1.1.0 google-cloud-bigquery==2.3.1 google-cloud-storage==1.32.0
(cd tests && $entry -m pytest --benchmark-disable -v --import-mode=append $(find . -type f \( -iname "test_*.py" ! \( -iname "test_*_eager.py" \) \)))
(cd tests && $entry -m pytest --benchmark-disable -v --import-mode=append $(find . -type f \( -iname "test_*_eager.py" ! \( -iname "test_bigquery_eager.py" \) \)))
(cd tests && $entry -m pytest --benchmark-disable -v --import-mode=append $(find . -type f \( -iname "test_*_v1.py" \)))
(cd tests && $entry -m pytest --benchmark-disable -v --import-mode=append $(find . -type f \( -iname "test_*.py" ! \( -iname "test_*_v1.py" -o -iname "test_bigquery.py" \) \)))
# GRPC and test_bigquery_eager tests have to be executed separately because of https://github.com/grpc/grpc/issues/20034
(cd tests && $entry -m pytest --benchmark-disable -v --import-mode=append $(find . -type f \( -iname "test_bigquery_eager.py" \)))
(cd tests && $entry -m pytest --benchmark-disable -v --import-mode=append $(find . -type f \( -iname "test_bigquery.py" \)))
}

PYTHON_VERSION=python
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13 changes: 6 additions & 7 deletions .github/workflows/build.yml
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Expand Up @@ -434,14 +434,13 @@ jobs:
python --version
python -m pip install -U pytest-benchmark
rm -rf tensorflow_io
(cd tests && python -m pytest -s -v test_lmdb_eager.py)
(python -m pytest -s -v test_image_eager.py -k "webp or ppm or bmp or bounding or exif or hdr or openexr or tiff or avif")
(python -m pytest -s -v test_serialization_eager.py)
(python -m pytest -s -v test_io_dataset_eager.py -k "numpy or hdf5 or audio or to_file")
(python -m pytest -s -v test_http_eager.py)
(cd tests && python -m pytest -s -v test_lmdb.py)
(python -m pytest -s -v test_image.py -k "webp or ppm or bmp or bounding or exif or hdr or openexr or tiff or avif")
(python -m pytest -s -v test_serialization.py)
(python -m pytest -s -v test_io_dataset.py -k "numpy or hdf5 or audio or to_file")
(python -m pytest -s -v test_http.py)
python -m pip install google-cloud-bigquery-storage==0.7.0 google-cloud-bigquery==1.22.0 fastavro
(python -m pytest -s -v test_bigquery_eager.py)
(python -m pytest -s -v test_dicom_eager.py)
(python -m pytest -s -v test_bigquery.py)
(python -m pytest -s -v test_dicom.py)

release:
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12 changes: 6 additions & 6 deletions docs/development.md
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Expand Up @@ -88,7 +88,7 @@ bazel build -s --verbose_failures $BAZEL_OPTIMIZATION //tensorflow_io/...
# `bazel-bin/tensorflow_io/core/python/ops/` and it is possible
# to run tests with `pytest`, e.g.:
sudo python3 -m pip install pytest
TFIO_DATAPATH=bazel-bin python3 -m pytest -s -v tests/test_serialization_eager.py
TFIO_DATAPATH=bazel-bin python3 -m pytest -s -v tests/test_serialization.py
```

NOTE: When running pytest, `TFIO_DATAPATH=bazel-bin` has to be passed so that python can utilize the generated shared libraries after the build process.
Expand Down Expand Up @@ -147,7 +147,7 @@ bazel build -s --verbose_failures $BAZEL_OPTIMIZATION //tensorflow_io/...
# `bazel-bin/tensorflow_io/core/python/ops/` and it is possible
# to run tests with `pytest`, e.g.:
sudo python3 -m pip install pytest
TFIO_DATAPATH=bazel-bin python3 -m pytest -s -v tests/test_serialization_eager.py
TFIO_DATAPATH=bazel-bin python3 -m pytest -s -v tests/test_serialization.py
```

##### CentOS 8
Expand Down Expand Up @@ -207,7 +207,7 @@ scl enable rh-python36 devtoolset-9 \

TFIO_DATAPATH=bazel-bin \
scl enable rh-python36 devtoolset-9 \
'python3 -m pytest -s -v tests/test_serialization_eager.py'
'python3 -m pytest -s -v tests/test_serialization.py'
```

#### Python Wheels
Expand Down Expand Up @@ -295,7 +295,7 @@ use:
$ bash -x -e tests/test_kafka/kafka_test.sh

# Run the tests
$ TFIO_DATAPATH=bazel-bin pytest -s -vv tests/test_kafka_eager.py
$ TFIO_DATAPATH=bazel-bin pytest -s -vv tests/test_kafka.py
```

Testing `Datasets` associated with tools such as `Elasticsearch` or `MongoDB`
Expand All @@ -307,7 +307,7 @@ require docker to be available on the system. In such scenarios, use:
$ bash tests/test_elasticsearch/elasticsearch_test.sh start

# Run the tests
$ TFIO_DATAPATH=bazel-bin pytest -s -vv tests/test_elasticsearch_eager.py
$ TFIO_DATAPATH=bazel-bin pytest -s -vv tests/test_elasticsearch.py

# Stop and remove the container
$ bash tests/test_elasticsearch/elasticsearch_test.sh stop
Expand All @@ -319,7 +319,7 @@ For example, to run tests related to `parquet` dataset's, use:

```sh
# Just run the test
$ TFIO_DATAPATH=bazel-bin pytest -s -vv tests/test_parquet_eager.py
$ TFIO_DATAPATH=bazel-bin pytest -s -vv tests/test_parquet.py
```


Expand Down
0 tests/test_archive_eager.py → tests/test_archive.py
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0 tests/test_arrow_eager.py → tests/test_arrow.py
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0 tests/test_audio_eager.py → tests/test_audio.py
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0 tests/test_audio_ops_eager.py → tests/test_audio_ops.py
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0 tests/test_avro_eager.py → tests/test_avro.py
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0 tests/test_bigquery_eager.py → tests/test_bigquery.py
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0 tests/test_bigtable_eager.py → tests/test_bigtable.py
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0 tests/test_color_eager.py → tests/test_color.py
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0 tests/test_csv_eager.py → tests/test_csv.py
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135 changes: 107 additions & 28 deletions tests/test_dicom.py
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Expand Up @@ -16,6 +16,7 @@


import os
import numpy as np
import pytest

import tensorflow as tf
Expand All @@ -35,8 +36,7 @@


def test_dicom_input():
"""test_dicom_input
"""
"""test_dicom_input"""
_ = tfio.image.decode_dicom_data
_ = tfio.image.decode_dicom_image
_ = tfio.image.dicom_tags
Expand Down Expand Up @@ -66,32 +66,26 @@ def test_dicom_input():
("MR-MONO2-12-shoulder.dcm", (1, 1024, 1024, 1)),
("OT-MONO2-8-a7.dcm", (1, 512, 512, 1)),
("US-PAL-8-10x-echo.dcm", (10, 430, 600, 3)),
("TOSHIBA_J2K_OpenJPEGv2Regression.dcm", (1, 512, 512, 1)),
],
)
def test_decode_dicom_image(fname, exp_shape):
"""test_decode_dicom_image
"""
"""test_decode_dicom_image"""

dcm_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "test_dicom", fname
)

g1 = tf.compat.v1.Graph()
file_contents = tf.io.read_file(filename=dcm_path)

with g1.as_default():
file_contents = tf.io.read_file(filename=dcm_path)
dcm_image = tfio.image.decode_dicom_image(
contents=file_contents,
dtype=tf.float32,
on_error="strict",
scale="auto",
color_dim=True,
)

sess = tf.compat.v1.Session(graph=g1)
dcm_image_np = sess.run(dcm_image)

assert dcm_image_np.shape == exp_shape
dcm_image = tfio.image.decode_dicom_image(
contents=file_contents,
dtype=tf.float32,
on_error="strict",
scale="auto",
color_dim=True,
)
assert dcm_image.numpy().shape == exp_shape


@pytest.mark.parametrize(
Expand Down Expand Up @@ -121,23 +115,108 @@ def test_decode_dicom_image(fname, exp_shape):
],
)
def test_decode_dicom_data(fname, tag, exp_value):
"""test_decode_dicom_data
"""
"""test_decode_dicom_data"""

dcm_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "test_dicom", fname
)

g1 = tf.compat.v1.Graph()
file_contents = tf.io.read_file(filename=dcm_path)

dcm_data = tfio.image.decode_dicom_data(contents=file_contents, tags=tag)

assert dcm_data.numpy() == exp_value


def test_dicom_image_shape():
"""test_decode_dicom_image"""

dcm_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"test_dicom",
"US-PAL-8-10x-echo.dcm",
)

dataset = tf.data.Dataset.from_tensor_slices([dcm_path])
dataset = dataset.map(tf.io.read_file)
dataset = dataset.map(lambda e: tfio.image.decode_dicom_image(e, dtype=tf.uint16))
dataset = dataset.map(lambda e: tf.image.resize(e, (224, 224)))


def test_dicom_image_concurrency():
"""test_decode_dicom_image_currency"""

with g1.as_default():
file_contents = tf.io.read_file(filename=dcm_path)
dcm_data = tfio.image.decode_dicom_data(contents=file_contents, tags=tag)
@tf.function
def preprocess(dcm_content):
tags = tfio.image.decode_dicom_data(
dcm_content, tags=[tfio.image.dicom_tags.PatientsName]
)
tf.print(tags)
image = tfio.image.decode_dicom_image(dcm_content, dtype=tf.float32)
return image

dcm_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"test_dicom",
"TOSHIBA_J2K_OpenJPEGv2Regression.dcm",
)

dataset = (
tf.data.Dataset.from_tensor_slices([dcm_path])
.repeat()
.map(tf.io.read_file)
.map(preprocess, num_parallel_calls=8)
.take(200)
)
for i, item in enumerate(dataset):
print(tf.shape(item), i)
assert np.array_equal(tf.shape(item), [1, 512, 512, 1])

dcm_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"test_dicom",
"US-PAL-8-10x-echo.dcm",
)

dataset = (
tf.data.Dataset.from_tensor_slices([dcm_path])
.repeat()
.map(tf.io.read_file)
.map(preprocess, num_parallel_calls=8)
.take(200)
)
for i, item in enumerate(dataset):
print(tf.shape(item), i)
assert np.array_equal(tf.shape(item), [10, 430, 600, 3])


def test_dicom_sequence():
"""test_decode_dicom_sequence"""

dcm_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"test_dicom",
"2.25.304589190180579357564631626197663875025.dcm",
)
dcm_content = tf.io.read_file(filename=dcm_path)

tags = tfio.image.decode_dicom_data(
dcm_content, tags=["[0x0008,0x1115][0][0x0008,0x1140][0][0x0008,0x1155]"]
)
assert np.array_equal(tags, [b"2.25.211904290918469145111906856660599393535"])

dcm_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"test_dicom",
"US-PAL-8-10x-echo.dcm",
)
dcm_content = tf.io.read_file(filename=dcm_path)

sess = tf.compat.v1.Session(graph=g1)
dcm_data_np = sess.run(dcm_data)
tags = tfio.image.decode_dicom_data(dcm_content, tags=["[0x0020,0x000E]"])
assert np.array_equal(tags, [b"999.999.94827453"])

assert dcm_data_np == exp_value
tags = tfio.image.decode_dicom_data(dcm_content, tags=["0x0020,0x000e"])
assert np.array_equal(tags, [b"999.999.94827453"])


if __name__ == "__main__":
Expand Down
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