Add thrombosis AF project

README.md

@@ -130,7 +130,7 @@ To configure a new project, follow these steps:
     git switch -c <branch-name>
     ```
 
-1. Copy the `template_config.yaml` file to a new file in the `projects/config` directory and fill
+1. Copy the [template_config.yaml](./template_config.yaml) file to a new file in the `projects/config` directory and fill
    in the details.
 1. The filename of the project config should be `<project-slug>`.yaml
 

orthanc/orthanc-anon/plugin/pixl.py

@@ -386,7 +386,7 @@ def _anonymise_study_and_upload(
 
         with logger.contextualize(pseudo_study_uid=anonymised_study_uid):
             _upload_instances(anonymised_instances_bytes)
-            logger.info("Anonymised and uploaded study")
+            logger.success("Anonymised and uploaded study '{}', {}", project_name, study_info)
 
         return anonymised_study_uid
 
@@ -517,7 +517,7 @@ def _anonymise_study_instances(
                 "The anonymisation introduced the following validation errors:\n{}",
                 parse_validation_results(dicom_validation_errors),
             )
-        logger.success("Finished anonymising project: '{}', {}", project_name, study_info)
+        logger.info("Finished anonymising project '{}', {}", project_name, study_info)
     return anonymised_instances_bytes, anonymised_study_uid
 
 

pixl_dcmd/src/pixl_dcmd/dicom_helpers.py

@@ -183,7 +183,7 @@ def _redirect_stdout_to_debug(_logger: Logger) -> Generator[None, None, None]:
     thread_local.stdout.seek(0)
     output = thread_local.stdout.readlines()
     for line in output:
-        _logger.debug(line.strip())
+        _logger.trace(line.strip())
 
 
 @dataclass

pixl_dcmd/src/pixl_dcmd/main.py

@@ -189,7 +189,7 @@ def anonymise_dicom(
     """
 
     study_info = get_study_info(dataset)
-    logger.debug(
+    logger.trace(
         f"Processing instance for project {config.project.name}:  {study_info}"
     )
 
@@ -205,7 +205,7 @@ def anonymise_dicom(
         msg = f"Dropping DICOM Modality: {dataset.Modality}"
         raise PixlSkipInstanceError(msg)
 
-    logger.debug("Anonymising instance for: {}", study_info)
+    logger.trace("Anonymising instance for: {}", study_info)
 
     # Apply any pixel cleaning prior to tag anonymisation
     # Do before anonymisation as some tag operations may rely on pixel data (e.g. burned in pixel detection).
@@ -245,7 +245,6 @@ def _clean_dicom_image_pixels(
     :param config: Project config to use for pixel cleaning
     """
     study_info = get_study_info(dataset)
-    logger.debug(f"Cleaning pixels for project {config.project.name}:  {study_info}")
 
     image_operations = load_image_operations(config)
     deid_recipe_path = image_operations.deid_recipes
@@ -254,11 +253,11 @@ def _clean_dicom_image_pixels(
     )  # current implementation permits only one recipe file
 
     if not deid_recipe_path:
-        logger.debug(
+        logger.trace(
             "No deid recipe provided for pixel cleaning, skipping pixel cleaning."
         )
         return
-
+    logger.debug(f"Cleaning pixels for project {config.project.name}:  {study_info}")
     burned_pixels = has_burned_pixels(dataset, deid=deid_recipe)
     cleaned_pixels = clean_pixel_data(dicom_file=dataset, results=burned_pixels)
 
@@ -331,7 +330,7 @@ def _secure_hash(
 
     if tag in dataset:
         message = f"Securely hashing: (0x{grp:04x},0x{el:04x})"
-        logger.debug(f"\t{message}")
+        logger.trace(message)
         if dataset[grp, el].VR == "LO":
             pat_value = str(dataset[grp, el].value)
             hashed_value = _hash_values(pat_value, project_slug, hash_len=64)

projects/configs/README.md

@@ -0,0 +1,8 @@
+# Project configurations for PIXL extractions
+
+This directory contains:
+
+- Configuration files for specific projects, including automated test cases, these reference the the sub-directories for their anonymisation rules. These are copied from [template_config.yaml](/template_config.yaml). Expand the [Setup PIXL in GAE section](/README.md#setup-pixl-in-gae) of the main readme find the `Configure a new project` section for more information
+- [image-operations](./image-operations/): Methods for removing identifiable information from the pixel data of DICOM data
+- [tag-operations](./tag-operations/): Allowlist for each DICOM tag. All projects are expected to use [tag-operations/base.yaml](./tag-operations/base.yaml), adding in extra configurations for each modality. Any DICOM tag not defined will be removed in anonymisation. 
+- In some cases, [tag-operations/manufacturer-overrides/](./tag-operations/manufacturer-overrides/) will be defined private DICOM tags are required from a manufacturer.

projects/configs/tag-operations/base.yaml

@@ -138,7 +138,7 @@
 - name: "Scan Options"
   group: 0x0018
   element: 0x0022
-  op: "replace"
+  op: "keep"
 #CT, MR, X-Ray
 - name: Slice Thickness
   group: 0x0018

projects/configs/tag-operations/thrombosis-af.yaml

@@ -0,0 +1,25 @@
+#  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.
+
+# Default `base.yaml` configuration file with commented links to their respective image modalities
+# `base.yaml` configuration file is expected to be part of all projects configuration files
+
+#################################### 0008 Group ###################################
+#
+#
+
+- name: "Study Date"
+  group: 0x0008
+  element: 0x0020
+  op: "keep"

projects/configs/uclh-investigating-correlations-of-thrombosis-risk-in-af.yaml

@@ -0,0 +1,43 @@
+#  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.
+
+project:
+    name: "uclh-investigating-correlations-of-thrombosis-risk-in-af"
+    modalities: ["CT"] # DICOM dataset modalities to retain
+    azure_kv_alias: null # Optional field to allow for a common secret prefix to be used
+
+tag_operation_files: # DICOM tag anonymisation operations
+    base:
+        - "base.yaml" # Base schema
+        - "ct.yaml"
+        - "thrombosis-af.yaml"
+    manufacturer_overrides: [] # Manufactuer-dependendent overrides
+
+allowed_manufacturers:
+  - regex: ".*"
+    exclude_series_numbers: []
+
+# Filter out any series with a single instance (e.g. PACS reports, screenshots)
+min_instances_per_series: 6
+
+series_filters:
+    - "localizer"
+    - "localiser"
+    - "scout"
+    - "positioning"
+    - "mip"  # for PET studies these series have PID
+
+destination:
+    dicom: "ftps" # alternatives: "dicomweb", "xnat", "none"
+    parquet: "ftps" # alternatives: "none"