From 7c7ed532fd5442748598a2b5212d21aec3ebf83a Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 28 Mar 2024 12:51:33 -0400
Subject: [PATCH] add dummy content in niftis

---
 fids/fids.py       | 49 ++++++++++++++++++++++++++++++++++++++++++++--
 pyproject.toml     |  4 +++-
 tests/test_fids.py |  2 +-
 3 files changed, 51 insertions(+), 4 deletions(-)

diff --git a/fids/fids.py b/fids/fids.py
index f762406..6f62a8d 100644
--- a/fids/fids.py
+++ b/fids/fids.py
@@ -4,7 +4,10 @@
 import json
 from pathlib import Path
 
+import nibabel as nib
+import numpy as np
 from bids import BIDSLayout
+from nibabel import Nifti1Image
 
 
 DEFAUTL_NIFTI_EXT = ".nii.gz"
@@ -30,7 +33,8 @@ def bids_fitler_file() -> dict[str, dict[str, list[str]]]:
     return {
         "fmap": {},
         "func": {"suffix": ["bold", "events"]},
-        "anat": {"suffix": ["T1w"]},
+        "dwi": {"suffix": ["dwi"]},
+        "anat": {"suffix": ["T1w", "T2w"]},
     }
 
 
@@ -95,7 +99,13 @@ def create_empty_file(layout: BIDSLayout, entities: dict[str, str | int]) -> Non
     )
     filepath = Path(filepath)
     filepath.parent.mkdir(parents=True, exist_ok=True)
-    filepath.touch()
+    if entities["extension"] in [".nii", ".nii.gz"]:
+        image = _img_3d_rand_eye()
+        if entities["datatype"] in ["func", "dwi"]:
+            image = _img_4d_rand_eye()
+        nib.save(image, filepath)
+    else:
+        filepath.touch()
 
 
 def create_sidecar(
@@ -115,5 +125,40 @@ def create_sidecar(
         json.dump(metadata, f, indent=4)
 
 
+def _rng(seed=42):
+    return np.random.default_rng(seed)
+
+
+def _affine_eye():
+    """Return an identity matrix affine."""
+    return np.eye(4)
+
+
+def _shape_3d_default():
+    """Return default shape for a 3D image."""
+    return (10, 10, 10)
+
+
+def _length_default():
+    return 10
+
+
+def _shape_4d_default():
+    """Return default shape for a 4D image."""
+    return (10, 10, 10, _length_default())
+
+
+def _img_3d_rand_eye(affine=_affine_eye()):
+    """Return random 3D Nifti1Image in MNI space."""
+    data = _rng().random(_shape_3d_default())
+    return Nifti1Image(data, affine)
+
+
+def _img_4d_rand_eye(affine=_affine_eye()):
+    """Return random 3D Nifti1Image in MNI space."""
+    data = _rng().random(_shape_4d_default())
+    return Nifti1Image(data, affine)
+
+
 if __name__ == "__main__":
     create_fake_bids_dataset()
diff --git a/pyproject.toml b/pyproject.toml
index f77069e..84b753f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,7 +23,9 @@ classifiers = [
     "Programming Language :: Python :: 3.12"
 ]
 dependencies = [
-    "pybids"
+    "pybids",
+    "numpy",
+    "nibabel"
 ]
 description = "fake bids dataset generator"
 # Version from setuptools_scm
diff --git a/tests/test_fids.py b/tests/test_fids.py
index 3108cc2..9bb59cb 100644
--- a/tests/test_fids.py
+++ b/tests/test_fids.py
@@ -7,7 +7,7 @@
 
 @pytest.mark.parametrize("subjects", ["01", 1, ["1", "baz"], [1, 2], ["boo", 2]])
 @pytest.mark.parametrize("sessions", [None, "01", 1, ["foo", "2"], [1, 2], ["bar", 2]])
-@pytest.mark.parametrize("datatypes", ["anat", "func", ["anat", "func"]])
+@pytest.mark.parametrize("datatypes", ["anat", "func", "dwi", ["anat", "func"]])
 def test_fids_smoke(tmp_path, subjects, sessions, datatypes):
     """Smoke test."""
     create_fake_bids_dataset(