From d749bb29a9734f71a4cc49ffe5f63016ef116a2e Mon Sep 17 00:00:00 2001
From: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com>
Date: Wed, 31 Jul 2024 10:50:58 -0400
Subject: [PATCH] Add placeholders for IO setup (#35)

---
 src/abcdmicro/dwi.py      | 23 +++++++++++++++++++++++
 src/abcdmicro/event.py    | 23 +++++++++++++++++++++++
 src/abcdmicro/io.py       | 15 +++++++++++++++
 src/abcdmicro/resource.py | 29 +++++++++++++++++++++++++++++
 4 files changed, 90 insertions(+)
 create mode 100644 src/abcdmicro/dwi.py
 create mode 100644 src/abcdmicro/event.py
 create mode 100644 src/abcdmicro/io.py
 create mode 100644 src/abcdmicro/resource.py

diff --git a/src/abcdmicro/dwi.py b/src/abcdmicro/dwi.py
new file mode 100644
index 0000000..4d5cb62
--- /dev/null
+++ b/src/abcdmicro/dwi.py
@@ -0,0 +1,23 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+
+from abcdmicro.event import AbcdEvent
+from abcdmicro.resource import BvalResource, BvecResource, VolumeResource
+
+
+@dataclass
+class Dwi:
+    """An ABCD diffusion weighted image."""
+
+    event: AbcdEvent
+    """The ABCD event associated with this DWI."""
+
+    volume: VolumeResource
+    """The DWI image volume."""
+
+    bval: BvalResource
+    """The DWI b-values"""
+
+    bvec: BvecResource
+    """The DWI b-vectors"""
diff --git a/src/abcdmicro/event.py b/src/abcdmicro/event.py
new file mode 100644
index 0000000..b83c4d5
--- /dev/null
+++ b/src/abcdmicro/event.py
@@ -0,0 +1,23 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+
+
+@dataclass
+class AbcdEvent:
+    """An ABCD event -- a particular subject and time point."""
+
+    subject_id: str
+    """The subject GUID defined in the NIMH Data Archive, for example 'NDAR_INV00U4FTRU'"""
+
+    eventname: str
+    """The ABCD Study event name, for example 'baseline_year_1_arm_1'"""
+
+    image_download_path: Path
+    """Path to the ABCD image download root directory. This would be the directory that
+    contains `fmriresults01/abcd-mproc-release5/` with some compressed images in there"""
+
+    tabular_data_path: Path
+    """Path to the extracted ABCD tabular data directory. This would contain subdirectories
+    like `core/mental-health/` with csv tables inside them."""
diff --git a/src/abcdmicro/io.py b/src/abcdmicro/io.py
new file mode 100644
index 0000000..f095f67
--- /dev/null
+++ b/src/abcdmicro/io.py
@@ -0,0 +1,15 @@
+from __future__ import annotations
+
+from abcdmicro.resource import BvalResource, BvecResource, VolumeResource
+
+
+class NiftiVolumeResrouce(VolumeResource):
+    pass
+
+
+class FslBvalResource(BvalResource):
+    pass
+
+
+class FslBvecResource(BvecResource):
+    pass
diff --git a/src/abcdmicro/resource.py b/src/abcdmicro/resource.py
new file mode 100644
index 0000000..2168570
--- /dev/null
+++ b/src/abcdmicro/resource.py
@@ -0,0 +1,29 @@
+from __future__ import annotations
+
+
+class Resource:
+    pass
+
+
+class VolumeResource(Resource):
+    pass
+
+
+class InMemoryVolumeResource(VolumeResource):
+    pass
+
+
+class BvalResource(Resource):
+    pass
+
+
+class InMemoryBvalResource(BvalResource):
+    pass
+
+
+class BvecResource(Resource):
+    pass
+
+
+class InMemoryBvecResource(BvecResource):
+    pass