Merge pull request #11 from ArcanaFramework/develop

Updated DicomSet -> DicomSeries to match change in fileformats
ArcanaFramework · Nov 15, 2023 · 7846a07 · 7846a07
2 parents 2432f9e + 7f877ae
commit 7846a07
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Showing 4 changed files with 11 additions and 11 deletions.
diff --git a/arcana/xnat/cli/tests/test_cli_dataset_export.py b/arcana/xnat/cli/tests/test_cli_dataset_export.py
@@ -6,7 +6,7 @@
 import requests
 from docker.errors import ContainerError
 import pytest
-from fileformats.medimage import DicomSet
+from fileformats.medimage import DicomSeries
 import medimages4tests.dummy.dicom.mri.t1w.siemens.skyra.syngo_d13c
 import medimages4tests.dummy.dicom.mri.fmap.siemens.skyra.syngo_d13c
 from arcana.core.cli.dataset import export
@@ -56,7 +56,7 @@ def test_bids_export(
                 [
                     FileBP(
                         path="DICOM",
-                        datatype=DicomSet,
+                        datatype=DicomSeries,
                         filenames=["dicom/t1w/*"],
                     )
                 ],
@@ -77,7 +77,7 @@ def test_bids_export(
     )
     original.add_source(
         name="anat/T1w",
-        datatype=DicomSet,
+        datatype=DicomSeries,
         path="mprage",
     )
     original.save()

diff --git a/arcana/xnat/data/api.py b/arcana/xnat/data/api.py
@@ -12,7 +12,7 @@
 import attrs
 import xnat.session
 from fileformats.core import FileSet, Field
-from fileformats.medimage import DicomSet
+from fileformats.medimage import DicomSeries
 from fileformats.core.exceptions import FormatRecognitionError
 from arcana.core.utils.misc import (
     path2varname,
@@ -127,7 +127,7 @@ def populate_row(self, row: DataRow):
                     for xresource in xscan.resources.values():
                         uri = self._get_resource_uri(xresource)
                         if xresource.label in ("DICOM", "secondary"):
-                            datatype = DicomSet
+                            datatype = DicomSeries
                             item_metadata = self.get_dicom_header(uri)
                         else:
                             datatype = FileSet

diff --git a/arcana/xnat/data/tests/test_store.py b/arcana/xnat/data/tests/test_store.py
@@ -8,7 +8,7 @@
 from functools import reduce
 import itertools
 import pytest
-from pydra.utils.hash import hash_single, Cache
+from pydra.utils.hash import hash_object
 from fileformats.generic import File
 from fileformats.field import Text as TextField
 from arcana.common import Clinical
@@ -183,6 +183,6 @@ def test_provenance_roundtrip(datatype: type, value: str, simple_dataset: Datase
 
 def test_dataset_bytes_hash(static_dataset):
 
-    hsh = hash_single(static_dataset, Cache({}))
+    hsh = hash_object(static_dataset)
     # Check hashing is stable
-    assert hash_single(static_dataset, Cache({})) == hsh
+    assert hash_object(static_dataset) == hsh
diff --git a/conftest.py b/conftest.py
@@ -22,10 +22,10 @@
 from arcana.core.deploy.image.base import BaseImage
 from arcana.common import Clinical
 from arcana.core.data.set import Dataset
-from fileformats.medimage import NiftiGzX, NiftiGz, DicomSet, NiftiX
+from fileformats.medimage import NiftiGzX, NiftiGz, DicomSeries, NiftiX
 from fileformats.text import Plain as Text
 from fileformats.image import Png
-from fileformats.serialization import Json
+from fileformats.application import Json
 from fileformats.generic import Directory
 from arcana.xnat.data.api import Xnat
 from arcana.xnat.utils.testing import (
@@ -171,7 +171,7 @@ def arcana_home(work_dir):
                 resources=[
                     FileBP(
                         path="DICOM",
-                        datatype=DicomSet,
+                        datatype=DicomSeries,
                         filenames=[
                             "dicom/fmap/1.dcm",
                             "dicom/fmap/2.dcm",