511 - anonymisation for spectroscopy data

pixl_dcmd/pyproject.toml

@@ -10,7 +10,7 @@ dependencies = [
     "core==0.2.0rc0",
     "arrow==1.3.0",
     "dicom-anonymizer==1.0.12",
-    "dicom-validator==0.6.2",
+    "dicom-validator==0.6.3",
     "logger==1.4",
     "pydicom==2.4.4",
     "pydicom-data",

projects/configs/tag-operations/mr-spectroscopy.yaml

@@ -0,0 +1,190 @@
+#  Copyright (c) University College London Hospitals NHS Foundation Trust
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+- name: Device Serial Number
+  group: 0x0018
+  element: 0x1000
+  op: keep
+- name: Content Qualification
+  group: 0x0018
+  element: 0x9004
+  op: keep
+- name: Pulse Sequence Name
+  group: 0x0018
+  element: 0x9005
+  op: keep
+- name: Echo Pulse Sequence
+  group: 0x0018
+  element: 0x9008
+  op: keep
+- name: Multi-planar Excitation
+  group: 0x0018
+  element: 0x9012
+  op: keep
+- name: Steady State Pulse Sequence
+  group: 0x0018
+  element: 0x9017
+  op: keep
+- name: Echo Planar Pulse Sequence
+  group: 0x0018
+  element: 0x9018
+  op: keep
+- name: Spectrally Selected Suppression
+  group: 0x0018
+  element: 0x9025
+  op: keep
+- name: Geometry of k-Space Traversal
+  group: 0x0018
+  element: 0x9032
+  op: keep
+- name: Segmented k-Space Traversal
+  group: 0x0018
+  element: 0x9033
+  op: keep
+- name: Spectral Width
+  group: 0x0018
+  element: 0x9052
+  op: keep
+- name: Chemical Shift Reference
+  group: 0x0018
+  element: 0x9053
+  op: keep
+- name: Volume Localization Technique
+  group: 0x0018
+  element: 0x9054
+  op: keep
+- name: De-coupling
+  group: 0x0018
+  element: 0x9059
+  op: keep
+- name: k-space Filtering
+  group: 0x0018
+  element: 0x9064
+  op: keep
+- name: Time Domain Filtering
+  group: 0x0018
+  element: 0x9065
+  op: keep
+- name: Number of Zero Fills
+  group: 0x0018
+  element: 0x9066
+  op: keep
+- name: Baseline Correction
+  group: 0x0018
+  element: 0x9067
+  op: keep
+- name: Acquisition Duration
+  group: 0x0018
+  element: 0x9073
+  op: keep
+- name: Number of k-Space Trajectories
+  group: 0x0018
+  element: 0x9093
+  op: keep
+- name: Transmitter Frequency
+  group: 0x0018
+  element: 0x9098
+  op: keep
+- name: Resonant Nucleus
+  group: 0x0018
+  element: 0x9100
+  op: keep
+- name: Frequency Correction
+  group: 0x0018
+  element: 0x9101
+  op: keep
+- name: Slab Thickness
+  group: 0x0018
+  element: 0x9104
+  op: keep
+- name: Slab Orientation
+  group: 0x0018
+  element: 0x9105
+  op: keep
+- name: Mid Slab Position
+  group: 0x0018
+  element: 0x9106
+  op: keep
+- name: Multiple Spin Echo
+  group: 0x0018
+  element: 0x9011
+  op: keep
+- name: Volume Localization Sequence
+  group: 0x0018
+  element: 0x9126
+  op: keep
+- name: Applicable Safety Standard Agency
+  group: 0x0018
+  element: 0x9174
+  op: keep
+- name: First Order Phase Correction
+  group: 0x0018
+  element: 0x9198
+  op: keep
+- name: Water Referenced Phase Correction
+  group: 0x0018
+  element: 0x9199
+  op: keep
+- name: MR Spectroscopy Acquisition Type
+  group: 0x0018
+  element: 0x9200
+  op: keep
+- name: Dimension Organization UID
+  group: 0x0020
+  element: 0x9164
+  op: keep
+- name: Dimension Index Pointer
+  group: 0x0020
+  element: 0x9165
+  op: keep
+- name: Dimension Organization Sequence
+  group: 0x0020
+  element: 0x9221
+  op: keep
+- name: Dimension Index Sequence
+  group: 0x0020
+  element: 0x9222
+  op: keep
+- name: Number of Frames
+  group: 0x0028
+  element: 0x0008
+  op: keep
+- name: Data Point Rows
+  group: 0x0028
+  element: 0x9001
+  op: keep
+- name: Data Point Columns
+  group: 0x0028
+  element: 0x9002
+  op: keep
+- name: Signal Domain Columns
+  group: 0x0028
+  element: 0x9003
+  op: keep
+- name: Data Representation
+  group: 0x0028
+  element: 0x9108
+  op: keep
+- name: Acquisition Context Sequence
+  group: 0x0040
+  element: 0x0555
+  op: keep
+- name: Shared Functional Groups Sequence
+  group: 0x5200
+  element: 0x9229
+  op: keep
+- name: Spectroscopy Data
+  group: 0x5600
+  element: 0x0020
+  op: keep

projects/configs/tag-operations/mri.yaml

@@ -20,6 +20,18 @@
 ################################### 0008 Group ###################################
 #
 #
+- name: Acquisition DateTime
+  group: 0x0008
+  element: 0x002A
+  op: replace
+- name: Content Date
+  group: 0x0008
+  element: 0x0023
+  op: replace
+- name: Content Time
+  group: 0x0008
+  element: 0x0033
+  op: replace
 - name: "Volumetric Properties"
   group: 0x0008
   element: 0x9206

projects/configs/test-mr-spectroscopy.yaml

@@ -0,0 +1,35 @@
+#  Copyright (c) 2022 University College London Hospitals NHS Foundation Trust
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+project:
+    name: "test-mr-spectroscopy"
+    modalities: ["MR"]
+
+tag_operation_files:
+    base:
+        - "base.yaml"
+        - "mri.yaml"
+        - "mr-spectroscopy.yaml"
+    manufacturer_overrides:
+        - "mri.yaml"
+
+series_filters:
+    - "localizer"
+    - "localiser"
+    - "scout"
+    - "positioning"
+
+destination:
+    dicom: "none"
+    parquet: "none"