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Merge pull request #4016 from melissalinkert/dicom-provide-metadata
Add API and DICOM-specific implementations for providing supplemental metadata during conversion
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components/formats-bsd/src/loci/formats/dicom/DicomJSONProvider.java
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| /* | ||
| * #%L | ||
| * BSD implementations of Bio-Formats readers and writers | ||
| * %% | ||
| * Copyright (C) 2005 - 2023 Open Microscopy Environment: | ||
| * - Board of Regents of the University of Wisconsin-Madison | ||
| * - Glencoe Software, Inc. | ||
| * - University of Dundee | ||
| * %% | ||
| * Redistribution and use in source and binary forms, with or without | ||
| * modification, are permitted provided that the following conditions are met: | ||
| * | ||
| * 1. Redistributions of source code must retain the above copyright notice, | ||
| * this list of conditions and the following disclaimer. | ||
| * 2. Redistributions in binary form must reproduce the above copyright notice, | ||
| * this list of conditions and the following disclaimer in the documentation | ||
| * and/or other materials provided with the distribution. | ||
| * | ||
| * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | ||
| * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | ||
| * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | ||
| * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE | ||
| * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR | ||
| * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF | ||
| * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS | ||
| * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN | ||
| * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) | ||
| * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE | ||
| * POSSIBILITY OF SUCH DAMAGE. | ||
| * #L% | ||
| */ | ||
|
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| package loci.formats.dicom; | ||
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| import java.io.IOException; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| import loci.common.Constants; | ||
| import loci.common.DataTools; | ||
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| import org.json.JSONArray; | ||
| import org.json.JSONException; | ||
| import org.json.JSONObject; | ||
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| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
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| /** | ||
| * Provide DICOM tags from a file containing JSON. | ||
| * Formal JSON schema yet to be determined, but the idea is to accept a hierarchy | ||
| * of tags of the form: | ||
| * | ||
| * { | ||
| * "BodyPartExamined": { | ||
| * "Value": "BRAIN", | ||
| * "VR": "CS", | ||
| * "Tag": "(0018,0015)" | ||
| * } | ||
| * "ContributingEquipmentSequence": { | ||
| * "VR": "SQ", | ||
| * "Tag": "(0018,a001)", | ||
| * "Sequence": { | ||
| * "Manufacturer": { | ||
| * "Value": "PixelMed", | ||
| * "VR": "LO", | ||
| * "Tag": "(0008,0070)" | ||
| * }, | ||
| * "ContributionDateTime": { | ||
| * "Value": "20210710234601.105+0000", | ||
| * "VR": "DT", | ||
| * "Tag": "(0018,a002)" | ||
| * } | ||
| * } | ||
| * } | ||
| * } | ||
| * | ||
| * This is similar to JSON examples in https://github.com/QIICR/dcmqi/tree/master/doc/examples, | ||
| * but allows for the VR (type) and tag to be explicitly stated, in addition to | ||
| * the more human-readable description. | ||
| */ | ||
| public class DicomJSONProvider implements ITagProvider { | ||
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| private static final Logger LOGGER = | ||
| LoggerFactory.getLogger(DicomJSONProvider.class); | ||
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| private List<DicomTag> tags = new ArrayList<DicomTag>(); | ||
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| @Override | ||
| public void readTagSource(String location) throws IOException { | ||
| String rawJSON = DataTools.readFile(location); | ||
| try { | ||
| JSONObject root = new JSONObject(rawJSON); | ||
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| for (String tagKey : root.keySet()) { | ||
| JSONObject tag = root.getJSONObject(tagKey); | ||
| String value = tag.has("Value") ? tag.getString("Value") : null; | ||
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| Integer intTagCode = lookupTag(tagKey, tag); | ||
| DicomVR vrEnum = lookupVR(intTagCode, tag); | ||
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| DicomTag dicomTag = new DicomTag(intTagCode, vrEnum); | ||
| dicomTag.value = value; | ||
| LOGGER.debug("Adding tag: {}, VR: {}, value: {}", | ||
| DicomAttribute.formatTag(intTagCode), vrEnum, value); | ||
| dicomTag.validateValue(); | ||
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| if (vrEnum == DicomVR.SQ && tag.has("Sequence")) { | ||
| readSequence(tag, dicomTag); | ||
| } | ||
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| ResolutionStrategy rs = vrEnum == DicomVR.SQ ? ResolutionStrategy.APPEND : ResolutionStrategy.REPLACE; | ||
| if (tag.has("ResolutionStrategy")) { | ||
| String strategy = tag.getString("ResolutionStrategy"); | ||
| rs = Enum.valueOf(ResolutionStrategy.class, strategy); | ||
| } | ||
| dicomTag.strategy = rs; | ||
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| tags.add(dicomTag); | ||
| } | ||
| } | ||
| catch (JSONException e) { | ||
| throw new IOException("Could not parse JSON", e); | ||
| } | ||
| } | ||
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| @Override | ||
| public List<DicomTag> getTags() { | ||
| return tags; | ||
| } | ||
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| private void readSequence(JSONObject rootTag, DicomTag parent) { | ||
| JSONObject sequence = rootTag.getJSONObject("Sequence"); | ||
| for (String key : sequence.keySet()) { | ||
| JSONObject tag = sequence.getJSONObject(key); | ||
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| Integer intTagCode = lookupTag(key, tag); | ||
| DicomVR vrEnum = lookupVR(intTagCode, tag); | ||
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| DicomTag dicomTag = new DicomTag(intTagCode, vrEnum); | ||
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| if (tag.has("Value")) { | ||
| dicomTag.value = tag.get("Value"); | ||
| } | ||
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| LOGGER.debug("Adding tag: {}, VR: {}, value: {}", intTagCode, vrEnum, dicomTag.value); | ||
| dicomTag.validateValue(); | ||
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| dicomTag.parent = parent; | ||
| parent.children.add(dicomTag); | ||
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| if (vrEnum == DicomVR.SQ && tag.get("Sequence") != null) { | ||
| readSequence(tag, dicomTag); | ||
| } | ||
| } | ||
| parent.children.sort(null); | ||
| } | ||
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| /** | ||
| * Get the tag code corresponding to the given JSON object. | ||
| * If "Tag" is not a defined attribute, lookup the default | ||
| * for the object name in the dictionary. | ||
| */ | ||
| private Integer lookupTag(String tagKey, JSONObject tag) { | ||
| Integer intTagCode = null; | ||
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| if (tag.has("Tag")) { | ||
| String[] tagCode = tag.getString("Tag").replaceAll("[()]", "").split(","); | ||
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| int tagUpper = Integer.parseInt(tagCode[0], 16); | ||
| int tagLower = Integer.parseInt(tagCode[1], 16); | ||
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| intTagCode = tagUpper << 16 | tagLower; | ||
| } | ||
| else { | ||
| intTagCode = DicomAttribute.getTag(tagKey); | ||
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| if (intTagCode == null) { | ||
| throw new IllegalArgumentException( | ||
| "Tag not defined and could not be determined from description '" + | ||
| tagKey + "'"); | ||
| } | ||
| } | ||
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| return intTagCode; | ||
| } | ||
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| /** | ||
| * Get the VR associated with the given tag code and JSON object. | ||
| * If "VR" is not a defined attribute, lookup the default for the | ||
| * given tag code in the dictionary. | ||
| */ | ||
| private DicomVR lookupVR(Integer intTagCode, JSONObject tag) { | ||
| DicomVR vrEnum = DicomAttribute.getDefaultVR(intTagCode); | ||
| if (tag.has("VR")) { | ||
| DicomVR userEnum = DicomVR.valueOf(DicomVR.class, tag.getString("VR")); | ||
| if (!vrEnum.equals(userEnum)) { | ||
| LOGGER.warn("User-defined VR ({}) for {} does not match expected VR ({})", | ||
| userEnum, DicomAttribute.formatTag(intTagCode), vrEnum); | ||
| if (userEnum != null) { | ||
| vrEnum = userEnum; | ||
| } | ||
| } | ||
| } | ||
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| return vrEnum; | ||
| } | ||
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| } |
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