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Universal viewing of digital microscopy, whole slide imaging and digital pathology data.
pma-java is a Java wrapper library for PMA.start (http://www.free.pathomation.com), a universal viewer by Pathomation for whole slide imaging and microscopy.
YOU NEED TO HAVE PMA.START (OR PMA.CORE) RUNNING IN ORDER TO USE THIS LIBRARY. PMA-JAVA IS NOT A STAND-ALONE LIBRARY FOR WSI.
package com.pathomation;
public class Main {
public static void main(String[] args) throws Exception {
String folder = "C:/Slides/a/dog-2.jpg";
String file = "C:\\Slides\\a";
file = file.replace("\\", "/");
System.out.println(folder.replace(file, ""));
}
// public static void upload() throws InterruptedException {
// String localSourceSlideVsi = "C:\\Slides\\download_check\\down\\Alfred_Olympus_VS120_brightfield_all-in-one.vsi";
// String targetFolder = "_sys_aws_s3/AuploadCheck";
// long bytes = 4096;
// long totaalBytes = 0;
// List slideRelatedFiles = (Core.enumerateFilesForSlide(localSourceSlideVsi,
// Core.getPmaCoreLiteSessionID()));
// List> lists = new ArrayList<>();
// List sizes = new ArrayList<>();
// for (String s : slideRelatedFiles) {
// File fileTest = new File(s);
// System.out.println(s + " s");
// System.out.println(fileTest.length());
// sizes.add(fileTest.length());
// }
// for (Long size : sizes) {
// System.out.println("dooooooooooooooooooooooo");
// while (totaalBytes < size) {
// Thread.sleep(50);
// totaalBytes += bytes;
// System.out.println(totaalBytes + " " + size);
// }
// }
// System.out.println(lists.size() + " size");
//
// ProgressHttpEntityWrapper.ProgressCallback progressCallbackVsi = new ProgressHttpEntityWrapper.ProgressCallback() {
//
// @Override
// public void progress(long bytesRead, long transferred, long totalBytes, String filename) {
// float progress = ((float) transferred / totalBytes) * 100;
// System.out.println(filename + ": " + bytesRead + " " + transferred + " (" + progress + " %)");
// }
//
// };
// try {
// Core.upload(localSourceSlideVsi, targetFolder, Core.connect("https://devtest.pathomation.com/test/pma.core.3/", "vitalij", "PMI9GH9I"), progressCallbackVsi);
// } catch (Exception e) {
// throw new RuntimeException(e);
// }
// }
// public static void executeUploadThreads() {
//
// Thread getter = new Thread() {
// @Override
// public void run() {
// int totaal = 0;
// while (true) {
// long downloaded = 0;
// downloaded = Core.readBytes();
// totaal += downloaded;
// if (downloaded == -1) {
// System.out.println("stop");
// break;
// }
// System.out.println(downloaded + " downloaded ++++++++++++++++++++ ");
// System.out.println(totaal + " totaal ************");
// }
//
// }
// };
// Thread setter = new Thread() {
// @Override
// public void run() {
// String localSourceSlidePng = "C:\\Slides\\download_check\\down\\test.png";
// String localSourceSlideZif = "C:\\Slides\\download_check\\down\\2DollarBill.zif";
// String localSourceSlideSvs = "C:\\Slides\\download_check\\down\\CMU-11.svs";
// String localSourceSlideNdpi = "C:\\Slides\\download_check\\down\\indp.ndpi";
// String localSourceSlideJpg = "C:\\Slides\\download_check\\down\\dog.jpg";
// String localSourceSlideTiff = "C:\\Slides\\download_check\\down\\testTif.tiff";
// String localSourceSlideSzi = "C:\\Slides\\download_check\\down\\2DollarBill2.szi";
// String localSourceSlideVsi = "C:\\Slides\\download_check\\down\\Alfred_Olympus_VS120_brightfield_all-in-one.vsi";
// String localSourceSlideMrxs = "C:\\Slides\\download_check\\down\\CMU-1.mrxs";
// String ets = "Alfred_Olympus_VS120_brightfield_all-in-one\\stack1\\frame_t.ets";
//
// String targetFolder = "_sys_aws_s3/AuploadCheck";
// ProgressHttpEntityWrapper.ProgressCallback progressCallback = new ProgressHttpEntityWrapper.ProgressCallback() {
// @Override
// public void progress(long bytesRead, long transferred, long totalBytes, String filename) {
// float progress = ((float) transferred / totalBytes) * 100;
// System.out.println(filename + ": " + transferred + " (" + progress + " %)");
// System.out.println(bytesRead + " bytesRead-----");
//
// }
// };
// try {
// Core.upload(localSourceSlideVsi, targetFolder, Core.connect("https://devtest.pathomation.com/test/pma.core.3/", "vitalij", "PMI9GH9I"), progressCallback);
// } catch (Exception e) {
// throw new RuntimeException(e);
// }
// }
// };
// System.out.println("allo");
// getter.start();
// setter.start();
// try {
// getter.join();
// setter.join();
// } catch (InterruptedException e) {
// throw new RuntimeException(e);
// }
//
// }
public static boolean downloadThreads() {
String vsi = "_sys_aws_s3/brightfield/Olympus/Alfred_Olympus_VS120_brightfield_all-in-one.vsi";
String jpg = "_sys_aws_s3/(TO DELETE) test PMATransfer Mehdi/a/dog-2.jpg";
String mrxs ="_sys_aws_s3/(TO DELETE) test PMATransfer Mehdi/renaming MRXS file.mrxs";
String tif = "_sys_aws_s3/(TO DELETE) test PMATransfer Mehdi/test2.tif";
String vsiGent = "_sys_aws_s3/(TO DELETE) test PMATransfer Mehdi/UGent.vsi";
String ets = "UGent/stack1/frame_t.ets";
String dat = "renaming MRXS file/Data0010.dat";
String datLocal = "C:\\Slides\\a\\renaming MRXS file\\Data0010.dat";
String etsLocal = "C:\\Slides\\a\\UGent\\stack1\\frame_t.ets";
String local = "C:\\Slides\\a";
final long[] bytes = {-1};
Thread setter = new Thread() {
@Override
public void run() {
try {
System.out.println(Core.download(jpg,
"C:\\Slides\\b",
Core.connect("https://devtest.pathomation.com/test/pma.core.3/", "vitalij", "PMI9GH9I")));
} catch (Exception e) {
throw new RuntimeException(e);
}
}
};
Thread getter = new Thread() {
@Override
public void run() {
while (true) {
bytes[0] += Core.readBytes();
System.out.println(bytes[0] + " readBytes");
}
}
};
setter.start();
getter.start();
while (bytes[0] != - 1) {
System.out.println("do");
}
return true;
}
// public static void download() {
// ProgressHttpEntityWrapper.ProgressCallback progressCallback = new ProgressHttpEntityWrapper.ProgressCallback() {
// @Override
// public void progress(long bytesRead, long transferred, long totalBytes, String filename) {
// float progress = ((float) transferred / totalBytes) * 100;
// System.out.println(filename + ": " + transferred + " (" + progress + " %)");
// System.out.println(bytesRead + " bytesRead-----");
//
// }
// };
// String vsi = "_sys_aws_s3/brightfield/Olympus/Alfred_Olympus_VS120_brightfield_all-in-one.vsi";
// String jpg = "_sys_aws_s3/(TO DELETE) test PMATransfer Mehdi/a/dog-2.jpg";
// String mrxs ="_sys_aws_s3/(TO DELETE) test PMATransfer Mehdi/renaming MRXS file.mrxs";
// String tif = "_sys_aws_s3/(TO DELETE) test PMATransfer Mehdi/test2.tif";
// String vsiGent = "_sys_aws_s3/(TO DELETE) test PMATransfer Mehdi/UGent.vsi";
// String ets = "UGent/stack1/frame_t.ets";
// String dat = "renaming MRXS file/Data0010.dat";
// String datLocal = "C:\\Slides\\a\\renaming MRXS file\\Data0010.dat";
// String etsLocal = "C:\\Slides\\a\\UGent\\stack1\\frame_t.ets";
// String local = "C:\\Slides\\a";
// try {
// Core.download(jpg,local,
// Core.connect("https://devtest.pathomation.com/test/pma.core.3/", "vitalij", "PMI9GH9I"), progressCallback);
// } catch (Exception e) {
// throw new RuntimeException(e);
// }
// }
// public static void executeUploadThreads() {
// ProgressHttpEntityWrapper.ProgressCallback progressCallbackPng = new ProgressHttpEntityWrapper.ProgressCallback() {
// @Override
// public void progress(float progress, String filename) {
// System.out.println(filename + ": " + progress + " /////////");
// }
// };
// Thread getter = new Thread() {
// @Override
// public void run() {
// while (true) {
// int downloaded = Core.getBytes();
// if (downloaded == -1) {
// break;
// }
// System.out.println(downloaded + " downloaded ++++++++++++++++++++ ");
// }
// }
// };
// Thread setter = new Thread() {
// @Override
// public void run() {
// try {
// Core.upload("C:\\Slides\\a\\dog-2.jpg", "_sys_aws_s3/(TO DELETE) test PMATransfer Mehdi/a/",
// Core.connect("https://devtest.pathomation.com/test/pma.core.3/", "vitalij", "PMI9GH9I"), progressCallbackPng);
// } catch (Exception e) {
// throw new RuntimeException(e);
// }
// }
// };
//
// System.out.println("allo");
// setter.start();
// getter.start();
// }
}
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