3708 update testing data contrib

CONTRIBUTING.md

@@ -43,6 +43,7 @@ This section highlights all the necessary preparation steps required before send
 To collaborate efficiently, please read through this section and follow them.
 
 * [Checking the coding style](#checking-the-coding-style)
+* [Licensing information](#licensing-information)
 * [Unit testing](#unit-testing)
 * [Building documentation](#building-the-documentation)
 * [Signing your work](#signing-your-work)
@@ -63,7 +64,9 @@ python -m pip install -U -r requirements-dev.txt
 ./runtests.sh --autofix
 ```
 
-License information: all source code files should start with this paragraph:
+#### Licensing information
+All source code files should start with this paragraph:
+
 ```
 # Copyright (c) MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -119,6 +122,12 @@ If it requires any other external packages, please make sure:
 - the new test `test_[module_name].py` is added to the `exclude_cases` in [`./tests/min_tests.py`](./tests/min_tests.py) so that
 the minimal CI runner will not execute it.
 
+##### Testing data
+Testing data such as images and binary files should not be placed in the source code repository.
+Please deploy them to a reliable file sharing location (the current preferred one is [https://github.com/Project-MONAI/MONAI-extra-test-data/releases](https://github.com/Project-MONAI/MONAI-extra-test-data/releases)).
+At test time, the URLs within `tests/testing_data/data_config.json` are accessible
+via the APIs provided in `tests.utils`: `tests.utils.testing_data_config` and `tests.utils.download_url_or_skip_test`.
+
 _If it's not tested, it's broken_
 
 All new functionality should be accompanied by an appropriate set of tests.

tests/test_resample_to_match.py

@@ -14,29 +14,24 @@
 import unittest
 
 from monai.transforms import Compose, EnsureChannelFirstd, LoadImaged, ResampleToMatch, SaveImaged
-from tests.utils import assert_allclose, download_url_or_skip_test
+from tests.utils import assert_allclose, download_url_or_skip_test, testing_data_config
 
 
 class TestResampleToMatch(unittest.TestCase):
+    def setUp(self):
+        self.fnames = []
+        for key in ("0000_t2_tse_tra_4", "0000_ep2d_diff_tra_7"):
+            fname = os.path.join(os.path.dirname(__file__), "testing_data", f"test_{key}.nii.gz")
+            url = testing_data_config("images", key, "url")
+            hash_type = testing_data_config("images", key, "hash_type")
+            hash_val = testing_data_config("images", key, "hash_val")
+            download_url_or_skip_test(url=url, filepath=fname, hash_type=hash_type, hash_val=hash_val)
+            self.fnames.append(fname)
+
     def test_correct(self):
         with tempfile.TemporaryDirectory() as temp_dir:
-            url_1 = (
-                "https://github.com/rcuocolo/PROSTATEx_masks/raw/master/Files/"
-                + "lesions/Images/T2/ProstateX-0000_t2_tse_tra_4.nii.gz"
-            )
-            url_2 = (
-                "https://github.com/rcuocolo/PROSTATEx_masks/raw/master/Files/"
-                + "lesions/Images/ADC/ProstateX-0000_ep2d_diff_tra_7.nii.gz"
-            )
-            fname_1 = os.path.join(temp_dir, "file1.nii.gz")
-            fname_2 = os.path.join(temp_dir, "file2.nii.gz")
-            md5_1 = "adb3f1c4db66a6481c3e4a2a3033c7d5"
-            md5_2 = "f12a11ad0ebb0b1876e9e010564745d2"
-            download_url_or_skip_test(url=url_1, filepath=fname_1, hash_val=md5_1)
-            download_url_or_skip_test(url=url_2, filepath=fname_2, hash_val=md5_2)
-
             loader = Compose([LoadImaged(("im1", "im2")), EnsureChannelFirstd(("im1", "im2"))])
-            data = loader({"im1": fname_1, "im2": fname_2})
+            data = loader({"im1": self.fnames[0], "im2": self.fnames[1]})
 
             im_mod, meta = ResampleToMatch()(data["im2"], data["im2_meta_dict"], data["im1_meta_dict"])
             # for visual inspection

tests/test_resample_to_matchd.py

@@ -14,7 +14,7 @@
 import unittest
 
 from monai.transforms import Compose, CopyItemsd, EnsureChannelFirstd, Lambda, LoadImaged, ResampleToMatchd, SaveImaged
-from tests.utils import assert_allclose, download_url_or_skip_test
+from tests.utils import assert_allclose, download_url_or_skip_test, testing_data_config
 
 
 def update_fname(d):
@@ -23,23 +23,18 @@ def update_fname(d):
 
 
 class TestResampleToMatchd(unittest.TestCase):
+    def setUp(self):
+        self.fnames = []
+        for key in ("0000_t2_tse_tra_4", "0000_ep2d_diff_tra_7"):
+            fname = os.path.join(os.path.dirname(__file__), "testing_data", f"test_{key}.nii.gz")
+            url = testing_data_config("images", key, "url")
+            hash_type = testing_data_config("images", key, "hash_type")
+            hash_val = testing_data_config("images", key, "hash_val")
+            download_url_or_skip_test(url=url, filepath=fname, hash_type=hash_type, hash_val=hash_val)
+            self.fnames.append(fname)
+
     def test_correct(self):
         with tempfile.TemporaryDirectory() as temp_dir:
-            url_1 = (
-                "https://github.com/rcuocolo/PROSTATEx_masks/raw/master/Files/"
-                + "lesions/Images/T2/ProstateX-0000_t2_tse_tra_4.nii.gz"
-            )
-            url_2 = (
-                "https://github.com/rcuocolo/PROSTATEx_masks/raw/master/Files/"
-                + "lesions/Images/ADC/ProstateX-0000_ep2d_diff_tra_7.nii.gz"
-            )
-            fname_1 = os.path.join(temp_dir, "file1.nii.gz")
-            fname_2 = os.path.join(temp_dir, "file2.nii.gz")
-            md5_1 = "adb3f1c4db66a6481c3e4a2a3033c7d5"
-            md5_2 = "f12a11ad0ebb0b1876e9e010564745d2"
-            download_url_or_skip_test(url=url_1, filepath=fname_1, hash_val=md5_1)
-            download_url_or_skip_test(url=url_2, filepath=fname_2, hash_val=md5_2)
-
             transforms = Compose(
                 [
                     LoadImaged(("im1", "im2")),
@@ -50,7 +45,7 @@ def test_correct(self):
                     SaveImaged("im3", output_dir=temp_dir, output_postfix="", separate_folder=False),
                 ]
             )
-            data = transforms({"im1": fname_1, "im2": fname_2})
+            data = transforms({"im1": self.fnames[0], "im2": self.fnames[1]})
             assert_allclose(data["im1"].shape, data["im3"].shape)
 
 

tests/testing_data/data_config.json

@@ -24,6 +24,16 @@
             "url": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/Prostate_T2W_AX_1.nii",
             "hash_type": "sha256",
             "hash_val": "a14231f539c0f365a5f83f2a046969a9b9870e56ffd126fd8e7242364d25938a"
+        },
+        "0000_t2_tse_tra_4": {
+            "url": "https://github.com/rcuocolo/PROSTATEx_masks/raw/master/Files/lesions/Images/T2/ProstateX-0000_t2_tse_tra_4.nii.gz",
+            "hash_type": "md5",
+            "hash_val": "adb3f1c4db66a6481c3e4a2a3033c7d5"
+        },
+        "0000_ep2d_diff_tra_7": {
+            "url": "https://github.com/rcuocolo/PROSTATEx_masks/raw/master/Files/lesions/Images/ADC/ProstateX-0000_ep2d_diff_tra_7.nii.gz",
+            "hash_type": "md5",
+            "hash_val": "f12a11ad0ebb0b1876e9e010564745d2"
         }
     },
     "models": {