Merge branch 'master' into mb/rm-torch-install-doc

.gitignore

@@ -21,6 +21,9 @@ log.txt
 # Pycharm stuff
 .idea
 
+# VSCode stuff
+.vscode
+
 # Pytest Cache, anywhere:
 .pytest_cache/
 
@@ -33,4 +36,4 @@ data_multi_testing/
 .DS_Store
 
 # venv
-venv/
+venv/

ivadomed/loader/segmentation_pair.py

@@ -311,11 +311,11 @@ def convert_file_to_nifti(self, filename, extension, is_gt=False):
         # For '.png', '.tif', '.tiff', '.jpg' and 'jpeg' extentions
         # Read image as 8 bit grayscale in numpy array (behavior TBD in ivadomed for RGB, RBGA or higher bit depth)
         if "tif" in extension:
-            img = np.expand_dims(imageio.imread(filename, format='tiff-pil'), axis=-1).astype(np.uint8)
+            img = np.expand_dims(imageio.v2.imread(filename, format='tiff-pil'), axis=-1).astype(np.uint8)
             if len(img.shape) > 3:
-                img = np.expand_dims(imageio.imread(filename, format='tiff-pil', as_gray=True), axis=-1).astype(np.uint8)
+                img = np.expand_dims(imageio.v2.imread(filename, format='tiff-pil', as_gray=True), axis=-1).astype(np.uint8)
         else:
-            img = np.expand_dims(imageio.imread(filename, as_gray=True), axis=-1).astype(np.uint8)
+            img = np.expand_dims(imageio.v2.imread(filename, as_gray=True), axis=-1).astype(np.uint8)
 
         # Binarize ground-truth values (0-255) to 0 and 1 in uint8 with threshold 0.5
         if is_gt:

ivadomed/scripts/download_data.py

@@ -51,7 +51,7 @@
         "url": ["https://github.com/ivadomed/model_find_disc_t2/archive/r20200928.zip"],
         "description": "Intervertebral disc detection model trained on T2-weighted images."},
     "data_functional_testing": {
-        "url": ["https://github.com/ivadomed/data_functional_testing/archive/r20210617.zip"],
+        "url": ["https://github.com/ivadomed/data_functional_testing/archive/r20211002.zip"],
         "description": "Data used for functional testing in Ivadomed."},
     "data_axondeepseg_sem": {
         "url": ["https://github.com/axondeepseg/data_axondeepseg_sem/archive/r20211130.zip"],

requirements.txt

@@ -7,12 +7,12 @@
 pyparsing<3,>=2.0.2
 csv-diff>=1.0
 loguru~=0.5
+imageio~=2.19
 joblib~=1.0
 matplotlib>=3.3.0
 nibabel~=3.2
 onnxruntime==1.7.0
 pandas~=1.1
-pillow>=7.0.0
 pybids>=0.14.0
 scikit-learn>=0.20.3
 scikit-image~=0.17

testing/README.md

@@ -10,21 +10,22 @@ Checkout `ivadomed/.github/workflows/run_tests.yml` to see how tests are run on
 
 ## Running Locally
 
-1. Download the required dataset(s) using the `ivadomed` command line tools:
+1. Install dependencies
 ```
 cd ivadomed  # root of the repo
-ivadomed_download_data -d data_testing -o data_testing  # for unit tests
-ivadomed_download_data -d data_functional_testing -o data_functional_testing  # for functional tests
+pip install -e .[dev]
 ```
+
 2. To run all tests:
 ```
-pytest
+pytest -v
 ```
+
 or, to run specific tests:
 ```
-pytest testing/functional_tests/
-pytest testing/unit_tests/
-pytest testing/functional_tests/test_example.py
+pytest -v testing/functional_tests/
+pytest -v testing/unit_tests/
+pytest -v testing/functional_tests/test_example.py
 ```
 
 ## Wiki