Description: Migrate away from deprecated json-simple 1.x classes See json-simple 2.0.0 changelog: > * Deprecated JSONParse and JSONValue in favor of Jsoner. > * Deprecated JSONStreamAware and JSONAware in favor of Jsonable. > * Deprecated JSONObject in favor of JsonObject. > * Deprecated JSONArray in favor of JsonArray. . This patch uses the new json-simple Json* classes. It is compatible with both 2.x and 3.x json-simple releases, with a few ajustments regarding backward incompatible changes in json-simple 3.x: - The package name, changed to com.github.cliftonlabs.json_simple - The exception DeserializationExcetpion renamed as JsonException These two changes are handled using place-holders @JSON_SIMPLE_PACKAGE@ and @JSON_EXCETPION@ which are substituted at build time by debian/rules. . With these tricks the package is compatible with json-simple 2.x and 3.x. . Sebastien Jodogne has added a few fixes to the original patch. Author: Gilles Filippini --- This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ Index: OrthancImageJ-1.2/com/orthancserver/DicomDecoder.java =================================================================== --- OrthancImageJ-1.2.orig/com/orthancserver/DicomDecoder.java +++ OrthancImageJ-1.2/com/orthancserver/DicomDecoder.java @@ -28,7 +28,8 @@ import ij.process.ShortProcessor; import ij.process.ColorProcessor; import ij.io.FileInfo; import ij.measure.Calibration; -import org.json.simple.*; +import @JSON_SIMPLE_PACKAGE@.JsonObject; +import @JSON_SIMPLE_PACKAGE@.JsonArray; import java.util.List; import java.util.ArrayList; import java.util.Collections; @@ -92,10 +93,10 @@ public class DicomDecoder }; private static void ExtractCalibration(ImagePlus image, - JSONObject tags) + JsonObject tags) { - JSONObject rescaleIntercept = (JSONObject) tags.get("0028,1052"); - JSONObject rescaleSlope = (JSONObject) tags.get("0028,1053"); + JsonObject rescaleIntercept = (JsonObject) tags.get("0028,1052"); + JsonObject rescaleSlope = (JsonObject) tags.get("0028,1053"); if (rescaleIntercept != null && rescaleSlope != null) { @@ -108,9 +109,9 @@ public class DicomDecoder } private static void ExtractPixelSpacing(ImagePlus image, - JSONObject tags) + JsonObject tags) { - JSONObject pixelSpacing = (JSONObject) tags.get("0028,0030"); + JsonObject pixelSpacing = (JsonObject) tags.get("0028,0030"); if (pixelSpacing != null) { String[] tokens = ((String) pixelSpacing.get("Value")).split("\\\\"); @@ -130,7 +131,7 @@ public class DicomDecoder } private static void ExtractDicomInfo(ImagePlus image, - JSONObject tags) + JsonObject tags) { String info = new String(); @@ -143,7 +144,7 @@ public class DicomDecoder Collections.sort(tagsIndex); for (String tag : tagsIndex) { - JSONObject value = (JSONObject) tags.get(tag); + JsonObject value = (JsonObject) tags.get(tag); if (((String) value.get("Type")).equals("String")) { @@ -232,7 +233,7 @@ public class DicomDecoder private String[] SortSlicesBy3D(OrthancConnection c, - JSONArray instances) throws IOException + JsonArray instances) throws IOException { ArrayList slices = new ArrayList(); float normal[] = null; @@ -243,7 +244,7 @@ public class DicomDecoder for (int i = 0; i < instances.size(); i++) { String uuid = (String) instances.get(i); - JSONObject instance = (JSONObject) c.ReadJson("/instances/" + uuid + "/tags?simplify"); + JsonObject instance = (JsonObject) c.ReadJson("/instances/" + uuid + "/tags?simplify"); if (!instance.containsKey("ImageOrientationPatient") || !instance.containsKey("ImagePositionPatient")) { @@ -298,16 +299,21 @@ public class DicomDecoder private String[] SortSlicesByNumber(OrthancConnection c, - JSONArray instances) throws IOException + JsonArray instances) throws IOException { ArrayList slices = new ArrayList(); for (int i = 0; i < instances.size(); i++) { String uuid = (String) instances.get(i); - JSONObject instance = (JSONObject) c.ReadJson("/instances/" + uuid); - Long index = (Long) instance.get("IndexInSeries"); - slices.add(new Slice((float) index, uuid)); + JsonObject instance = (JsonObject) c.ReadJson("/instances/" + uuid); + + // Addition by Sebastien Jodogne + if (instance.containsKey("IndexInSeries")) + { + String index = instance.get("IndexInSeries").toString(); // This is a java.math.BigDecimal + slices.add(new Slice(Float.parseFloat(index), uuid)); + } } return SortSlices(slices); @@ -316,7 +322,7 @@ public class DicomDecoder private String[] GetSlices(OrthancConnection c, - JSONArray instances) throws IOException + JsonArray instances) throws IOException { String[] result; @@ -345,30 +351,30 @@ public class DicomDecoder String uuid) throws IOException, InterruptedException, ExecutionException { ImageStack stack = null; - JSONObject tags = null; + JsonObject tags = null; String tagsUri, name; if (isInstance) { name = "Instance " + uuid; - tags = (JSONObject) c.ReadJson("/instances/" + uuid + "/tags"); + tags = (JsonObject) c.ReadJson("/instances/" + uuid + "/tags"); stack = AddSlice(stack, c, uuid); } else { name = "Series " + uuid; - JSONObject series = (JSONObject) c.ReadJson("/series/" + uuid); - JSONArray instances = (JSONArray) series.get("Instances"); + JsonObject series = (JsonObject) c.ReadJson("/series/" + uuid); + JsonArray instances = (JsonArray) series.get("Instances"); try { - tags = (JSONObject) c.ReadJson("/series/" + uuid + "/shared-tags"); + tags = (JsonObject) c.ReadJson("/series/" + uuid + "/shared-tags"); } catch (Exception e) { // Fallback for old versions of Orthanc, without "shared-tags" - tags = (JSONObject) c.ReadJson("/instances/" + (String) instances.get(0) + "/tags"); + tags = (JsonObject) c.ReadJson("/instances/" + (String) instances.get(0) + "/tags"); } final String[] slices = GetSlices(c, instances); Index: OrthancImageJ-1.2/com/orthancserver/OrthancConfigurationDialog.java =================================================================== --- OrthancImageJ-1.2.orig/com/orthancserver/OrthancConfigurationDialog.java +++ OrthancImageJ-1.2/com/orthancserver/OrthancConfigurationDialog.java @@ -44,7 +44,7 @@ import javax.swing.JTree; import javax.swing.SwingWorker; import javax.swing.border.EmptyBorder; -import org.json.simple.JSONObject; +import @JSON_SIMPLE_PACKAGE@.JsonObject; public class OrthancConfigurationDialog extends JDialog @@ -110,7 +110,7 @@ public class OrthancConfigurationDialog OrthancConnection orthanc = CreateConnection(); try { - JSONObject system = (JSONObject) orthanc.ReadJson("system"); + JsonObject system = (JsonObject) orthanc.ReadJson("system"); JOptionPane.showMessageDialog(null, "Successfully connected to this Orthanc server " + "(version: " + (String) system.get("Version") + ")!", "Success", JOptionPane.INFORMATION_MESSAGE); Index: OrthancImageJ-1.2/com/orthancserver/OrthancConnection.java =================================================================== --- OrthancImageJ-1.2.orig/com/orthancserver/OrthancConnection.java +++ OrthancImageJ-1.2/com/orthancserver/OrthancConnection.java @@ -31,8 +31,9 @@ import java.net.URL; import java.net.URLConnection; import java.util.Base64; import javax.imageio.ImageIO; -import org.json.simple.JSONObject; -import org.json.simple.JSONValue; +import @JSON_SIMPLE_PACKAGE@.JsonObject; +import @JSON_SIMPLE_PACKAGE@.Jsoner; +import @JSON_SIMPLE_PACKAGE@.@JSON_EXCEPTION@; public class OrthancConnection { @@ -194,7 +195,13 @@ public class OrthancConnection public Object ReadJson(String uri) throws IOException { String content = ReadString(uri); - Object json = JSONValue.parse(content); + Object json; + try { + json = Jsoner.deserialize(content); + } + catch (@JSON_EXCEPTION@ e) { + json = null; + } if (json == null) { @@ -222,9 +229,9 @@ public class OrthancConnection name_ = name; } - public JSONObject Serialize() + public JsonObject Serialize() { - JSONObject json = new JSONObject(); + JsonObject json = new JsonObject(); json.put("Name", name_); json.put("Url", baseUrl_); @@ -236,7 +243,7 @@ public class OrthancConnection return json; } - public static OrthancConnection Unserialize(JSONObject json) + public static OrthancConnection Unserialize(JsonObject json) { OrthancConnection c = new OrthancConnection(); c.SetInsecure(true); // Fix issue 9 (cannot connect to self-signed certificates) Index: OrthancImageJ-1.2/com/orthancserver/SelectImageDialog.java =================================================================== --- OrthancImageJ-1.2.orig/com/orthancserver/SelectImageDialog.java +++ OrthancImageJ-1.2/com/orthancserver/SelectImageDialog.java @@ -21,9 +21,9 @@ package com.orthancserver; -import org.json.simple.JSONValue; -import org.json.simple.JSONArray; -import org.json.simple.JSONObject; +import @JSON_SIMPLE_PACKAGE@.Jsoner; +import @JSON_SIMPLE_PACKAGE@.JsonArray; +import @JSON_SIMPLE_PACKAGE@.JsonObject; import java.io.IOException; import java.util.ArrayList; import java.util.Base64; @@ -109,8 +109,8 @@ public class SelectImageDialog extends J { try { - JSONObject series = (JSONObject) orthanc_.ReadJson("series/" + uuid_); - JSONArray instances = (JSONArray) series.get("Instances"); + JsonObject series = (JsonObject) orthanc_.ReadJson("series/" + uuid_); + JsonArray instances = (JsonArray) series.get("Instances"); if (instances.size() > 0) { preview.Load(orthanc_, "/instances/" + instances.get(0) + "/preview"); @@ -150,12 +150,12 @@ public class SelectImageDialog extends J { List children = new ArrayList(); - JSONArray patients = (JSONArray) orthanc_.ReadJson("patients"); + JsonArray patients = (JsonArray) orthanc_.ReadJson("patients"); for (int i = 0; i < patients.size(); i++) { String uuid = (String) patients.get(i); - JSONObject patient = (JSONObject) orthanc_.ReadJson("patients/" + uuid); - JSONObject main = (JSONObject) patient.get("MainDicomTags"); + JsonObject patient = (JsonObject) orthanc_.ReadJson("patients/" + uuid); + JsonObject main = (JsonObject) patient.get("MainDicomTags"); String s = new String(); s = AddComponent(s, (String) main.get("PatientID")); @@ -171,13 +171,13 @@ public class SelectImageDialog extends J { List children = new ArrayList(); - JSONObject patient = (JSONObject) orthanc_.ReadJson("patients/" + uuid_); - JSONArray studies = (JSONArray) patient.get("Studies"); + JsonObject patient = (JsonObject) orthanc_.ReadJson("patients/" + uuid_); + JsonArray studies = (JsonArray) patient.get("Studies"); for (int i = 0; i < studies.size(); i++) { String uuid = (String) studies.get(i); - JSONObject study = (JSONObject) orthanc_.ReadJson("studies/" + uuid); - JSONObject main = (JSONObject) study.get("MainDicomTags"); + JsonObject study = (JsonObject) orthanc_.ReadJson("studies/" + uuid); + JsonObject main = (JsonObject) study.get("MainDicomTags"); String s = new String(); s = AddComponent(s, (String) main.get("StudyDescription")); @@ -193,13 +193,13 @@ public class SelectImageDialog extends J { List children = new ArrayList(); - JSONObject study = (JSONObject) orthanc_.ReadJson("studies/" + uuid_); - JSONArray seriesSet = (JSONArray) study.get("Series"); + JsonObject study = (JsonObject) orthanc_.ReadJson("studies/" + uuid_); + JsonArray seriesSet = (JsonArray) study.get("Series"); for (int i = 0; i < seriesSet.size(); i++) { String uuid = (String) seriesSet.get(i); - JSONObject series = (JSONObject) orthanc_.ReadJson("series/" + uuid); - JSONObject main = (JSONObject) series.get("MainDicomTags"); + JsonObject series = (JsonObject) orthanc_.ReadJson("series/" + uuid); + JsonObject main = (JsonObject) series.get("MainDicomTags"); String s = new String(); s = AddComponent(s, (String) main.get("Modality")); @@ -215,24 +215,25 @@ public class SelectImageDialog extends J { List children = new ArrayList(); - JSONObject series = (JSONObject) orthanc_.ReadJson("series/" + uuid_); - JSONArray instances = (JSONArray) series.get("Instances"); + JsonObject series = (JsonObject) orthanc_.ReadJson("series/" + uuid_); + JsonArray instances = (JsonArray) series.get("Instances"); for (int i = 0; i < instances.size(); i++) { String uuid = (String) instances.get(i); - JSONObject instance = (JSONObject) orthanc_.ReadJson("instances/" + uuid); - Long index = (Long) instance.get("IndexInSeries"); - String s; - if (index == null) + JsonObject instance = (JsonObject) orthanc_.ReadJson("instances/" + uuid); + + // Addition by Sebastien Jodogne + if (instance.containsKey("IndexInSeries")) { - s = uuid; + children.add(new MyTreeNode(orthanc_, ResourceType.INSTANCE, uuid, + instance.getString("IndexInSeries"))); } else { - s = String.valueOf(index); - } - - children.add(new MyTreeNode(orthanc_, ResourceType.INSTANCE, uuid, s)); + // No ordering of instances is available for this series: + // Use the UUID as the index of the instance. + children.add(new MyTreeNode(orthanc_, ResourceType.INSTANCE, uuid, uuid)); + } } return children; @@ -556,12 +557,12 @@ public class SelectImageDialog extends J // https://stackoverflow.com/a/13109632/881731 String decoded = OrthancConnection.DecodeBase64(s); - JSONArray config = (JSONArray) JSONValue.parse(decoded); + JsonArray config = Jsoner.deserialize(decoded, (JsonArray) null); if (config != null) { for (int i = 0; i < config.size(); i++) { - AddOrthancServer(OrthancConnection.Unserialize((JSONObject) config.get(i))); + AddOrthancServer(OrthancConnection.Unserialize((JsonObject) config.get(i))); } } } @@ -569,7 +570,7 @@ public class SelectImageDialog extends J public String Serialize() { - JSONArray servers = new JSONArray(); + JsonArray servers = new JsonArray(); for (int i = 0; i < root_.getChildCount(); i++) { @@ -577,7 +578,7 @@ public class SelectImageDialog extends J servers.add(node.GetConnection().Serialize()); } - String config = servers.toJSONString(); + String config = servers.toJson(); // https://stackoverflow.com/a/13109632/881731 return new String(Base64.getEncoder().encode(config.getBytes()));