initial medical image support

meerkat/columns/deferred/file.py

@@ -17,6 +17,7 @@
 from PIL import Image
 
 import meerkat.tools.docs as docs
+from meerkat import env
 from meerkat.block.deferred_block import DeferredOp
 from meerkat.columns.abstract import Column
 from meerkat.columns.deferred.base import DeferredCell, DeferredColumn
@@ -30,6 +31,11 @@
 from meerkat.interactive.formatter.base import FormatterGroup
 from meerkat.interactive.formatter.image import DeferredImageFormatterGroup
 
+if env.is_package_installed("voxel"):
+    import voxel
+else:
+    voxel = None
+
 logger = logging.getLogger(__name__)
 
 
@@ -485,6 +491,11 @@ def load_text(path: Union[str, io.BytesIO]):
         return f.read()
 
 
+# TODO: Add @requires decorator when available.
+def load_medimg(path: Union[str, io.BytesIO]):
+    return voxel.read(path)
+
+
 FILE_TYPES = {
     "image": {
         "loader": load_image,
@@ -512,6 +523,12 @@ def load_text(path: Union[str, io.BytesIO]):
         "formatters": CodeFormatterGroup,
         "exts": [".py", ".js", ".css", ".json", ".java", ".cpp", ".c", ".h", ".hpp"],
     },
+    "medimg": {
+        "loader": load_medimg,
+        "formatters": DeferredImageFormatterGroup,
+        "exts": [".dcm", ".nii", ".nii.gz"],
+        "defer": False,
+    },
 }
 
 

meerkat/interactive/app/src/lib/component/core/ndimage/NdImage.svelte

@@ -0,0 +1,15 @@
+<script lang="ts">
+	import type { Endpoint } from "$lib/utils/types";
+
+
+    export let data: string;
+    export let classes: string = '';
+
+    export let on_scroll: Endpoint = null;
+    export let on_scroll_axis_change: Endpoint = null;
+</script>
+
+
+<div>
+    <img class={classes} src={data} alt="A Meerkat cell." />
+</div>

meerkat/interactive/app/src/lib/component/core/ndimage/__init__.py

@@ -0,0 +1,2 @@
+class NdImage:
+    pass

setup.py

@@ -102,7 +102,7 @@
     "vision": ["torchvision>=0.9.0", "opencv-python", "Pillow"],
     "audio": ["torchaudio"],
     "medimg": [
-        "dosma>=0.0.13",
+        "pyvoxel",
         "kaggle",
         "google-cloud-storage",
         "google-cloud-bigquery[bqstorage,pandas]",