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Cannot invoke "org.dcm4che3.opencv.StreamSegment.getImageDescriptor()" because "seg" is null #1403

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SaluRamos opened this issue Feb 24, 2024 · 3 comments
Open

Cannot invoke "org.dcm4che3.opencv.StreamSegment.getImageDescriptor()" because "seg" is null #1403

SaluRamos opened this issue Feb 24, 2024 · 3 comments

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@SaluRamos
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SaluRamos commented Feb 24, 2024 •
edited

Describe the bug

03:36:01.918 [main] DEBUG org.dcm4che3.imageio.plugins.dcm.DicomImageReader -- Decompressor: org.dcm4che3.opencv.NativeImageReader
03:36:01.923 [main] DEBUG org.dcm4che3.imageio.plugins.dcm.DicomImageReader -- Start decompressing frame #1
03:36:01.952 [main] ERROR org.dcm4che3.opencv.StreamSegment -- Building FileStreamSegment from SegmentedInputImageStream
java.lang.reflect.InaccessibleObjectException: Unable to make field private java.io.RandomAccessFile javax.imageio.stream.FileCacheImageInputStream.cache accessible: module java.desktop does not "opens javax.imageio.stream" to module dcm4che.imageio.opencv
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
	at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
	at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
	at dcm4che.imageio.opencv@5.31.2/org.dcm4che3.opencv.StreamSegment.getFileStreamSegment(StreamSegment.java:129)
	at dcm4che.imageio.opencv@5.31.2/org.dcm4che3.opencv.StreamSegment.getStreamSegment(StreamSegment.java:98)
	at dcm4che.imageio.opencv@5.31.2/org.dcm4che3.opencv.NativeImageReader.getNativeImage(NativeImageReader.java:260)
	at dcm4che.imageio.opencv@5.31.2/org.dcm4che3.opencv.NativeImageReader.read(NativeImageReader.java:251)
	at dcm4che.imageio@5.31.2/org.dcm4che3.imageio.plugins.dcm.DicomImageReader.readRaster(DicomImageReader.java:375)
	at com.webkriativa.noahviewer@0.4/com.webkriativa.noahviewer.graphics.FrameSetVolume.loadHounsfieldValue(FrameSetVolume.java:98)
	at com.webkriativa.noahviewer@0.4/com.webkriativa.noahviewer.graphics.FrameSetVolume.<init>(FrameSetVolume.java:35)
	at com.webkriativa.noahviewer@0.4/com.webkriativa.noahviewer.MRETest.loadImage(MRETest.java:68)
	at com.webkriativa.noahviewer@0.4/com.webkriativa.noahviewer.MRETest.main(MRETest.java:25)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at javafx.graphics/com.sun.javafx.application.LauncherImpl.launchApplicationWithArgs(LauncherImpl.java:465)
	at javafx.graphics/com.sun.javafx.application.LauncherImpl.launchApplication(LauncherImpl.java:364)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at java.base/sun.launcher.LauncherHelper$FXHelper.main(LauncherHelper.java:1085)

fev. 24, 2024 3:36:01 AM org.opencv.osgi.OpenCVNativeLoader init
INFO: Successfully loaded OpenCV native library.
java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at javafx.graphics/com.sun.javafx.application.LauncherImpl.launchApplicationWithArgs(LauncherImpl.java:465)
	at javafx.graphics/com.sun.javafx.application.LauncherImpl.launchApplication(LauncherImpl.java:364)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at java.base/sun.launcher.LauncherHelper$FXHelper.main(LauncherHelper.java:1085)
Caused by: java.lang.NullPointerException: Cannot invoke "org.dcm4che3.opencv.StreamSegment.getImageDescriptor()" because "seg" is null
	at dcm4che.imageio.opencv@5.31.2/org.dcm4che3.opencv.NativeImageReader.getNativeImage(NativeImageReader.java:261)
	at dcm4che.imageio.opencv@5.31.2/org.dcm4che3.opencv.NativeImageReader.read(NativeImageReader.java:251)
	at dcm4che.imageio@5.31.2/org.dcm4che3.imageio.plugins.dcm.DicomImageReader.readRaster(DicomImageReader.java:375)

Java correto 17.0.9, with gradle and modules. i just downloaded last dcm4che release 5.31.2.

this is my build.gradle

plugins {
    id "java"
    id "application"
    id "org.javamodularity.moduleplugin" version "1.8.12"
}

group "com.myapp"
version "0.1"

repositories {
    mavenCentral()
}

sourceCompatibility = "17"
targetCompatibility = "17"

tasks.withType(JavaCompile).configureEach {
    options.encoding = "UTF-8"
}

application {
    mainModule = "com.webkriativa.noahviewer"
    mainClass = "com.webkriativa.noahviewer.Main"
}

dependencies {
    implementation files("libs/dcm4che-5.31.2/lib/angus-activation-2.0.1.jar")
    implementation files("libs/dcm4che-5.31.2/lib/clibwrapper_jiio-1.2-pre-dr-b04.jar")
    implementation files("libs/dcm4che-5.31.2/lib/commons-cli-1.6.0.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-audit-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-conf-api-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-conf-api-hl7-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-conf-ldap-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-conf-ldap-audit-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-conf-ldap-hl7-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-conf-ldap-imageio-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-core-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-dcmr-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-deident-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-dict-priv-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-emf-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-hl7-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-image-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-imageio-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-imageio-opencv-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-imageio-rle-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-json-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-mime-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-net-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-net-audit-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-net-hl7-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-qstar-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-soundex-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-agfa2dcm-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-agfa2sr-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-common-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-dcm2dcm-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-dcm2jpg-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-dcm2json-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-dcm2pdf-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-dcm2str-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-dcm2xml-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-dcmassoc-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-dcmbenchmark-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-dcmdir-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-dcmdump-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-dcmldap-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-dcmqrscp-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-dcmvalidate-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-deidentify-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-emf2sf-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-findscu-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-fixlo2un-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-getscu-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-hl72xml-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-hl7pdq-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-hl7pix-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-hl7rcv-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-hl7snd-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-ianscp-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-ianscu-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-ihe-modality-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-jpg2dcm-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-json2dcm-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-json2index-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-json2props-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-json2rst-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-maskpxdata-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-mkkos-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-movescu-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-mppsscp-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-mppsscu-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-pdf2dcm-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-planarconfig-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-qstar-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-stgcmtscu-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-storescp-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-storescu-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-stowrs-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-stowrsd-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-swappxdata-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-syslog-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-syslogd-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-tpl2xml-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-upsscu-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-wadors-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-wadows-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-xml2dcm-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-xml2hl7-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-tool-xroad-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-ws-rs-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-xdsi-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/dcm4che-xroad-5.31.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/gmbal-api-only-4.0.3.jar")
    implementation files("libs/dcm4che-5.31.2/lib/istack-commons-runtime-4.1.1.jar")
//    implementation files("libs/dcm4che-5.31.2/lib/jai_imageio-1.2-pre-dr-b04.jar")
    implementation files("libs/dcm4che-5.31.2/lib/jakarta.activation-api-2.1.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/jakarta.json-api-2.1.2.jar")
    implementation files("libs/dcm4che-5.31.2/lib/jakarta.xml.bind-api-4.0.0.jar")
    implementation files("libs/dcm4che-5.31.2/lib/jakarta.xml.soap-api-3.0.0.jar")
    implementation files("libs/dcm4che-5.31.2/lib/jakarta.xml.ws-api-4.0.0.jar")
    implementation files("libs/dcm4che-5.31.2/lib/jaxb-core-4.0.1.jar")
    implementation files("libs/dcm4che-5.31.2/lib/jaxb-runtime-4.0.1.jar")
    implementation files("libs/dcm4che-5.31.2/lib/logback-classic-1.4.14.jar")
    implementation files("libs/dcm4che-5.31.2/lib/logback-core-1.4.14.jar")
    implementation files("libs/dcm4che-5.31.2/lib/mimepull-1.10.0.jar")
    implementation files("libs/dcm4che-5.31.2/lib/parsson-1.1.3.jar")
    implementation files("libs/dcm4che-5.31.2/lib/policy-4.0.0.jar")
    implementation files("libs/dcm4che-5.31.2/lib/rt-4.0.0.jar")
    implementation files("libs/dcm4che-5.31.2/lib/saaj-impl-3.0.0.jar")
    implementation files("libs/dcm4che-5.31.2/lib/slf4j-api-2.0.9.jar")
    implementation files("libs/dcm4che-5.31.2/lib/stax-ex-2.1.0.jar")
    implementation files("libs/dcm4che-5.31.2/lib/streambuffer-2.1.0.jar")
    implementation files("libs/dcm4che-5.31.2/lib/weasis-core-img-4.8.1.jar")

    compileOnly("org.projectlombok:lombok:1.18.28")
    annotationProcessor("org.projectlombok:lombok:1.18.28")
    testCompileOnly("org.projectlombok:lombok:1.18.28")
    testAnnotationProcessor("org.projectlombok:lombok:1.18.28")
}

run {
    jvmArgs = ['-Djava.library.path="libs/dcm4che-5.31.2/lib/windows-x86-64"', '--add-opens', 'java.desktop/javax.imageio.stream=ALL-UNNAMED', '--add-opens', 'java.' +
            'base/java.io=ALL-UNNAMED']
}

my module-info.java

module com.webkriativa.noahviewer {
    requires static lombok;
    requires dcm4che.core;
    requires dcm4che.image;
    requires dcm4che.imageio;
    requires dcm4che.imageio.opencv;
    requires org.slf4j;
    requires java.desktop;
}

code is:

try (DicomInputStream dis = new DicomInputStream(new File("some_dicom_file.dcm"))) {
            ImageReader reader = ImageIO.getImageReadersByFormatName("DICOM").next();
            try (ImageInputStream iis = ImageIO.createImageInputStream(dis)) {
                reader.setInput(iis, false);
                ImageReadParam param = reader.getDefaultReadParam();
                // note that a file may have multiple frames.
                // set frame number depending on your use case
                int frame = 0;
                Raster raster = reader.readRaster(frame, param);
                System.out.println(raster);
            } catch (IOException e) {
                throw new RuntimeException(e);
            }
        }
@nroduit
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nroduit commented Feb 24, 2024

Integration with a Java module is different from that of the classpath. You need to specify accesses, see this post.

@SaluRamos
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SaluRamos commented Feb 24, 2024 •
edited

Thanks for responding @nroduit , I've never worked with modules before, so I have some lay questions. from what I understand, in my module-info.java I can only open and export packages that I created, when I try to open java.desktop for javax.imageio.stream it says package not found for both.

module com.webkriativa.noahviewer {
requires static lombok;
requires dcm4che.core;
requires dcm4che.image;
requires dcm4che.imageio;
requires dcm4che.imageio.opencv;
requires org.slf4j;
requires java.desktop;
opens java.desktop to javax.imageio.stream;
}

@SaluRamos
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SaluRamos commented Feb 24, 2024 •
edited

Integration with a Java module is different from that of the classpath. You need to specify accesses, see this post.

After studying more about modules I managed to understand my error and solved it as follows:

jvmArgs = ['--add-opens', 'java.desktop/javax.imageio.stream=dcm4che.imageio.opencv',
'--add-opens', 'java.base/java.io=dcm4che.imageio.opencv']

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@nroduit @SaluRamos