Merge pull request #2 from Australian-Imaging-Service/openneuro-download

tclose · web-flow · commit 5d2c6bb428e9 · 2022-10-26T10:41:28.000+11:00
Openneuro download
diff --git a/README.rst b/README.rst
@@ -30,12 +30,29 @@ or include in your package's ``test_requires``.
 Usage
 -----
 
+Create a pytest fixture consisting of a dummy image with field-map metadata in DICOM format
+
 .. code-block:: python
 
     # Import medimages4tests generator functions
-    from medimages4tests.dicom.mri.fmap.ge.discovery_mr888.dv26_0_r05_2008a import sample_image
+    from medimages4tests.dummy.dicom.mri.fmap.ge.discovery_mr888.dv26_0_r05_2008a import get_image
 
     # Return generated images in pytest fixtures (or alternative test framework)
     @pytest.fixture()
     def ge_dicom_fmap():
-        return sample_image()
+        return get_image()
+
+Create a dummy NIfTI image
+
+.. code-block:: python
+
+    import numpy
+    # Import `get_image` function
+    from medimages4tests.dummy.nifti import get_image
+
+    # Create dummy nifti image of 10x10x10 containing all ones
+    @pytest.fixture()
+    def ones_nifti():
+        return get_image(
+            data=numpy.ones((10, 10, 10))
+        )
diff --git a/conftest.py b/conftest.py
@@ -4,7 +4,7 @@
 from importlib import import_module
 import pytest
 
-base_dicom_dir = Path(__file__).parent / 'medimages4tests' / 'dicom'
+base_dicom_dir = Path(__file__).parent / 'medimages4tests' / 'dummy' / 'dicom'
 dicom_modules = ['__'.join(p.relative_to(base_dicom_dir).with_suffix('').parts)
                  for p in base_dicom_dir.glob('**/*.py')
                  if p.stem != 'base']
@@ -17,7 +17,7 @@ def work_dir():
 
 @pytest.fixture(params=dicom_modules)
 def dicom_module(request):
-    module_path = 'medimages4tests.dicom.' + '.'.join(request.param.split('__'))
+    module_path = 'medimages4tests.dummy.dicom.' + '.'.join(request.param.split('__'))
     return import_module(module_path)
 
 
diff --git a/medimages4tests/dummy/__init__.py b/medimages4tests/dummy/__init__.py
diff --git a/medimages4tests/dummy/dicom/base.py b/medimages4tests/dummy/dicom/base.py
@@ -2,9 +2,9 @@
 import shutil
 from copy import copy
 import pydicom.dataset
-from .. import base_cache_dir
+from ... import base_cache_dir
 
-cache_dir = base_cache_dir / "dicom"
+cache_dir = base_cache_dir / "dummy" / "dicom"
 dicom_pkg_dir = Path(__file__).parent
 
 
diff --git a/medimages4tests/dummy/dicom/mri/dwi/siemens/skyra/syngo_d13c.py b/medimages4tests/dummy/dicom/mri/dwi/siemens/skyra/syngo_d13c.py
@@ -1,8 +1,8 @@
 
-from medimages4tests.dicom.base import generate_dicom, default_dicom_dir
+from medimages4tests.dummy.dicom.base import generate_dicom, default_dicom_dir
 
 
-def sample_image(out_dir=default_dicom_dir(__file__)):
+def get_image(out_dir=default_dicom_dir(__file__)):
     return generate_dicom(out_dir, num_vols, constant_hdr,
                           collated_data, varying_hdr)
 
diff --git a/medimages4tests/dummy/dicom/mri/fmap/ge/discovery_mr888/dv26_0_r05_2008a.py b/medimages4tests/dummy/dicom/mri/fmap/ge/discovery_mr888/dv26_0_r05_2008a.py
@@ -1,7 +1,7 @@
-from medimages4tests.dicom.base import generate_dicom, default_dicom_dir
+from medimages4tests.dummy.dicom.base import generate_dicom, default_dicom_dir
 
 
-def sample_image(out_dir=default_dicom_dir(__file__)):
+def get_image(out_dir=default_dicom_dir(__file__)):
     return generate_dicom(out_dir, num_vols, constant_hdr,
                           collated_data, varying_hdr)
 
diff --git a/medimages4tests/dummy/dicom/mri/fmap/siemens/skyra/syngo_d13c.py b/medimages4tests/dummy/dicom/mri/fmap/siemens/skyra/syngo_d13c.py
@@ -1,8 +1,8 @@
 
-from medimages4tests.dicom.base import generate_dicom, default_dicom_dir
+from medimages4tests.dummy.dicom.base import generate_dicom, default_dicom_dir
 
 
-def sample_image(out_dir=default_dicom_dir(__file__)):
+def get_image(out_dir=default_dicom_dir(__file__)):
     return generate_dicom(out_dir, num_vols, constant_hdr,
                           collated_data, varying_hdr)
 
diff --git a/medimages4tests/dummy/dicom/mri/t1w/siemens/skyra/syngo_d13c.py b/medimages4tests/dummy/dicom/mri/t1w/siemens/skyra/syngo_d13c.py
@@ -1,7 +1,7 @@
-from medimages4tests.dicom.base import generate_dicom, default_dicom_dir
+from medimages4tests.dummy.dicom.base import generate_dicom, default_dicom_dir
 
 
-def sample_image(out_dir=default_dicom_dir(__file__)):
+def get_image(out_dir=default_dicom_dir(__file__)):
     return generate_dicom(out_dir, num_vols, constant_hdr,
                           collated_data, varying_hdr)
 
diff --git a/medimages4tests/dummy/nifti.py b/medimages4tests/dummy/nifti.py
@@ -1,18 +1,22 @@
+import tempfile
 from pathlib import Path
 import gzip
 import shutil
 import numpy as np
 import nibabel as nb
 
 
-def sample_image(
-    out_file: Path,
+def get_image(
+    out_file: Path = None,
     data: np.ndarray = None,
     vox_sizes=(1.0, 1.0, 1.0),
     qform=(1, 2, 3, 1),
     compressed=False,
 ) -> Path:
     """Create a random Nifti file to satisfy BIDS parsers"""
+    if out_file is None:
+        out_file = Path(tempfile.mkdtemp()) / "sample.nii"
+
     if data is None:
         data = np.random.randint(0, 1, size=[10, 10, 10])
 
diff --git a/medimages4tests/mri/__init__.py b/medimages4tests/mri/__init__.py
diff --git a/medimages4tests/mri/neuro/__init__.py b/medimages4tests/mri/neuro/__init__.py
diff --git a/medimages4tests/mri/neuro/base.py b/medimages4tests/mri/neuro/base.py
diff --git a/medimages4tests/mri/neuro/t1w.py b/medimages4tests/mri/neuro/t1w.py
@@ -0,0 +1,18 @@
+from medimages4tests import base_cache_dir
+from medimages4tests.utils import retrieve_from_openneuro, OpenneuroSpec
+
+
+cache_dir = base_cache_dir / "mri" / "neuro" / "t1w"
+
+
+SAMPLES = {
+    "ds004130-ON01016": OpenneuroSpec(
+        dataset="ds004130",
+        tag="1.0.0",
+        path="sub-ON01016/anat/sub-ON01016_acq-fspgr_run-01_T1w",
+    )
+}
+
+
+def get_image(sample="ds004130-ON01016"):
+    return retrieve_from_openneuro(SAMPLES[sample], cache_dir / sample)
diff --git a/medimages4tests/utils.py b/medimages4tests/utils.py
@@ -0,0 +1,34 @@
+from tempfile import mkdtemp
+import shutil
+from pathlib import Path
+import openneuro
+import attrs
+
+
+@attrs.define
+class OpenneuroSpec:
+
+    dataset: str
+    tag: str
+    path: Path
+
+
+def retrieve_from_openneuro(
+    sample, cache_path, suffixes=(".nii.gz", ".json"), force_download=False
+):
+    if not cache_path.parent.exists():
+        cache_path.parent.mkdir(parents=True)
+    out_path = cache_path.with_suffix(suffixes[0])
+    if not out_path.exists() or force_download:
+        tmpdir = Path(mkdtemp())
+        openneuro.download(
+            dataset=sample.dataset,
+            tag=sample.tag,
+            target_dir=tmpdir,
+            include=[sample.path],
+        )
+        for ext in suffixes:
+            shutil.copyfile(
+                (tmpdir / sample.path).with_suffix(ext), cache_path.with_suffix(ext)
+            )
+    return out_path
diff --git a/scripts/import_dicom.py b/scripts/import_dicom.py
@@ -77,10 +77,10 @@ def generate_python_code(dpath: Path, image_type: str):
         collated_data=json.dumps(collated_data))
 
 
-FILE_TEMPLATE = """from medimages4tests.dicom.base import generate_dicom, default_dicom_dir
+FILE_TEMPLATE = """from medimages4tests.dummy.dicom.base import generate_dicom, default_dicom_dir
 
 
-def sample_image(out_dir=default_dicom_dir(__file__)):
+def get_image(out_dir=default_dicom_dir(__file__)):
     return generate_dicom(out_dir, num_vols, constant_hdr,
                           collated_data, varying_hdr)
 
diff --git a/setup.cfg b/setup.cfg
@@ -16,4 +16,25 @@ VCS = git
 style = pep440
 versionfile_source = medimages4tests/_version.py
 versionfile_build = medimages4tests/_version.py
-tag_prefix =
+tag_prefix =
+
+
+[flake8]
+doctests = True
+exclude =
+    **/__init__.py
+    *build/
+    docs/sphinxext/
+    docs/tools/
+    docs/conf.py
+    arcana/_version.py
+    versioneer.py
+    docs/source/conf.py
+max-line-length = 88
+select = C,E,F,W,B,B950
+extend-ignore = E203,E501
+per-file-ignores =
+    setup.py:F401
+
+[codespell]
+ignore-words = .codespell-ignorewords
diff --git a/setup.py b/setup.py
@@ -15,7 +15,9 @@
     long_description=open('README.rst').read(),
     install_requires=[
         'pydicom>=1.0.2',
-        "nibabel>=4.0.1"],
+        "nibabel>=4.0.1",
+        "openneuro-py>=2022.2.0",
+        "attrs>=21.4.0"],
     extras_require={
         'test': [
             'pytest>=5.4.3',
diff --git a/tests/test_dicom.py b/tests/test_dicom.py
@@ -8,7 +8,7 @@ def test_dicom_creation(dicom_module):
     out_dir = Path(tempfile.mkdtemp())
 
     # Generate DICOM files
-    dicom_module.sample_image(out_dir)
+    dicom_module.get_image(out_dir)
 
     assert len(list(out_dir.glob('*.dcm'))) == dicom_module.num_vols
 
diff --git a/tests/test_nifti.py b/tests/test_nifti.py
@@ -2,12 +2,12 @@
 import shutil
 import nibabel as nb
 import numpy as np
-from medimages4tests.nifti import sample_image
+from medimages4tests.dummy.nifti import get_image
 
 
 def test_nifti(work_dir):
 
-    nifti_fpath = sample_image(work_dir / "sample.nii")
+    nifti_fpath = get_image(work_dir / "sample.nii")
 
     nifti = nb.load(nifti_fpath)
 
@@ -16,7 +16,7 @@ def test_nifti(work_dir):
 
 def test_nifti_compressed(work_dir):
 
-    gz_fpath = sample_image(work_dir / "sample.nii.gz", compressed=True)
+    gz_fpath = get_image(work_dir / "sample.nii.gz", compressed=True)
     uncompressed_fpath = work_dir / "nifti.nii"
 
     with gzip.open(gz_fpath, 'rb') as f_in:
diff --git a/tests/test_openneuro.py b/tests/test_openneuro.py
@@ -0,0 +1,11 @@
+import nibabel as nb
+from medimages4tests.mri.neuro.t1w import get_image
+
+
+def test_openneuro_retrieve():
+
+    nifti_fpath = get_image()
+
+    nifti = nb.load(nifti_fpath)
+
+    assert nifti.shape == (204, 256, 256)
