Disable tiling for NIFTI (activeloopai#2083)

* disable tiling for nifti * update
puyuanOT · Jan 3, 2023 · a8e8ba9 · a8e8ba9
1 parent 4383341
commit a8e8ba9
Show file tree

Hide file tree

Showing 4 changed files with 10 additions and 4 deletions.
diff --git a/deeplake/core/compression.py b/deeplake/core/compression.py
@@ -1164,7 +1164,7 @@ def _read_3d_data_meta(file: Union[bytes, memoryview, str]):
 def _open_nifti(file: Union[bytes, memoryview, str], gz: bool = False):
     if not _NIBABEL_INSTALLED:
         raise ModuleNotFoundError(
-            "nibabel is not installed. Please run `pip install deeplake[nifti]`"
+            "nibabel is not installed. Please run `pip install deeplake[medical]`"
         )
 
     if isinstance(file, str):

diff --git a/deeplake/core/serialize.py b/deeplake/core/serialize.py
@@ -3,6 +3,7 @@
     VIDEO_COMPRESSION,
     AUDIO_COMPRESSION,
     MESH_COMPRESSION,
+    NIFTI_COMPRESSION,
     get_compression_type,
 )
 from deeplake.core.fast_forwarding import version_compare
@@ -519,7 +520,12 @@ def serialize_sample_object(
 
         if (
             compression_type
-            not in (VIDEO_COMPRESSION, AUDIO_COMPRESSION, MESH_COMPRESSION)
+            not in (
+                VIDEO_COMPRESSION,
+                AUDIO_COMPRESSION,
+                MESH_COMPRESSION,
+                NIFTI_COMPRESSION,
+            )
             and len(compressed_bytes) > min_chunk_size
             and break_into_tiles
         ):

diff --git a/docs/source/_static/csv/installation.csv b/docs/source/_static/csv/installation.csv
@@ -2,7 +2,7 @@ Install command, Description, Dependencies installed
 "``pip install ""deeplake[av]""``", Audio and video support via PyAV, av
 "``pip install ""deeplake[visualizer]""``", Visualize Deep Lake datasets within notebooks. This is required for :meth:`Dataset.visualize <deeplake.core.dataset.Dataset.visualize>` to work., "IPython, flask"
 "``pip install ""deeplake[gcp]""``", GCS support, "google-cloud-storage, google-auth, google-auth-oauthlib"
-"``pip install ""deeplake[dicom]""``", DICOM data support, pydicom
+"``pip install ""deeplake[medical]""``", DICOM and NIfTI data support, "pydicom, nibabel"
 "``pip install ""deeplake[gdrive]""``", Google Drive support, "google-api-python-client, oauth2client, google-auth, google-auth-oauthlib"
 "``pip install ""deeplake[point_cloud]""``", Support for LiDAR point cloud data, laspy
 "``pip install ""deeplake[enterprise]""``", Installs Deep Lake's enterprise features, libdeeplake,

diff --git a/setup.py b/setup.py
@@ -34,7 +34,7 @@
     "av": ["av"],
     "gcp": ["google-cloud-storage", "google-auth", "google-auth-oauthlib"],
     "dicom": ["pydicom", "nibabel"],
-    "nifti": ["pydicom", "nibabel"],
+    "medical": ["pydicom", "nibabel"],
     "visualizer": ["IPython", "flask"],
     "gdrive": [
         "google-api-python-client",