Mercurial > hg > orthanc-tests
changeset 251:16a5e79accff
testing WSI DICOM-izer
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 02 Aug 2019 16:04:41 +0200 |
| parents | 4831008d1500 |
| children | 01db33301c3d |
| files | Database/Lena.jpg Database/LenaGrayscale.png Database/WSI/LenaColorJpegRGB.tiff Database/WSI/LenaColorJpegYCbCr.tiff Database/WSI/LenaGrayscaleJpeg.tiff Database/WSI/NOTES.txt Plugins/WSI/Run.py |
| diffstat | 7 files changed, 214 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Database/WSI/NOTES.txt Fri Aug 02 16:04:41 2019 +0200 @@ -0,0 +1,23 @@ +Create a small image pyramid +---------------------------- + +./OrthancWSIDicomizer --pyramid=1 --smooth=1 --tile-width=64 --tile-height=64 --compression=jpeg ~/Subversion/orthanc-tests/Database/Lena.png +./OrthancWSIDicomToTiff 93463fca-b7a90ce3-e77d1d29-bd1c94f9-5aa91536 LenaColorJpegYCbCr.tiff + + + +./OrthancWSIDicomizer --pyramid=1 --smooth=1 --tile-width=64 --tile-height=64 --compression=jpeg ~/Subversion/orthanc-tests/Database/LenaGrayscale.png +./OrthancWSIDicomToTiff 93463fca-b7a90ce3-e77d1d29-bd1c94f9-5aa91536 LenaGrayscaleJpeg.tiff + + + + +Manually change photometric interpretation +------------------------------------------ + +cp LenaColorJpegYCbCr.tiff LenaColorJpegRGB.tiff +tiffset -d 0 -s 262 2 LenaColorJpegRGB.tiff +tiffset -d 1 -s 262 2 LenaColorJpegRGB.tiff +tiffset -d 2 -s 262 2 LenaColorJpegRGB.tiff +tiffset -d 3 -s 262 2 LenaColorJpegRGB.tiff +tiffinfo LenaColorJpegRGB.tiff | grep -aE 'Directory|Photometric'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Plugins/WSI/Run.py Fri Aug 02 16:04:41 2019 +0200 @@ -0,0 +1,191 @@ +#!/usr/bin/python +# -*- coding: utf-8 -*- + + +# Orthanc - A Lightweight, RESTful DICOM Store +# Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics +# Department, University Hospital of Liege, Belgium +# Copyright (C) 2017-2019 Osimis S.A., Belgium +# +# This program is free software: you can redistribute it and/or +# modify it under the terms of the GNU General Public License as +# published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. + + +import argparse +import os +import pprint +import re +import subprocess +import sys +import tempfile +import unittest +from shutil import copyfile + +sys.path.append(os.path.join(os.path.dirname(__file__), '..', '..', 'Tests')) +from Toolbox import * + + +## +## Parse the command-line arguments +## + +parser = argparse.ArgumentParser(description = 'Run the integration tests for the WSI Dicomizer.') + +parser.add_argument('--server', + default = 'localhost', + help = 'Address of the Orthanc server to test') +parser.add_argument('--rest', + type = int, + default = 8042, + help = 'Port to the REST API') +parser.add_argument('--username', + default = 'alice', + help = 'Username to the REST API') +parser.add_argument('--password', + default = 'orthanctest', + help = 'Password to the REST API') +parser.add_argument('--dicomizer', + default = '/home/jodogne/Subversion/orthanc-wsi/Applications/i/OrthancWSIDicomizer', + help = 'Password to the REST API') +parser.add_argument('--to-tiff', + default = '/home/jodogne/Subversion/orthanc-wsi/Applications/i/OrthancWSIDicomToTiff', + help = 'Password to the REST API') +parser.add_argument('--force', help = 'Do not warn the user', + action = 'store_true') +parser.add_argument('options', metavar = 'N', nargs = '*', + help='Arguments to Python unittest') + +args = parser.parse_args() + +if not args.force: + print(""" +WARNING: This test will remove all the content of your +Orthanc instance running on %s! + +Are you sure ["yes" to go on]?""" % args.server) + + if sys.stdin.readline().strip() != 'yes': + print('Aborting...') + exit(0) + + + + +## +## The tests +## + +ORTHANC = DefineOrthanc(server = args.server, + username = args.username, + password = args.password, + restPort = args.rest) + +def CallDicomizer(p): + subprocess.check_output([ args.dicomizer, + '--username=%s' % args.username, + '--password=%s' % args.password ] + p, + stderr=subprocess.STDOUT) + + +class Orthanc(unittest.TestCase): + def setUp(self): + if (sys.version_info >= (3, 0)): + # Remove annoying warnings about unclosed socket in Python 3 + import warnings + warnings.simplefilter("ignore", ResourceWarning) + + DropOrthanc(ORTHANC) + + + def test_single(self): + CallDicomizer([ GetDatabasePath('Lena.jpg') ]) + + i = DoGet(ORTHANC, '/instances') + self.assertEqual(1, len(i)) + + tags = DoGet(ORTHANC, '/instances/%s/tags?simplify' % i[0]) + self.assertEqual(1, int(tags['NumberOfFrames'])) + self.assertEqual(512, int(tags['Columns'])) + self.assertEqual(512, int(tags['Rows'])) + self.assertEqual('YBR_FULL_422', tags['PhotometricInterpretation']) + + s = DoGet(ORTHANC, '/series') + self.assertEqual(1, len(s)) + + pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) + self.assertEqual(s[0], pyramid['ID']) + self.assertEqual(1, len(pyramid['Resolutions'])) + self.assertEqual(1, len(pyramid['Sizes'])) + self.assertEqual(1, len(pyramid['TilesCount'])) + self.assertEqual(1, pyramid['Resolutions'][0]) + self.assertEqual(512, pyramid['Sizes'][0][0]) + self.assertEqual(512, pyramid['Sizes'][0][1]) + self.assertEqual(512, pyramid['TileWidth']) + self.assertEqual(512, pyramid['TileHeight']) + self.assertEqual(512, pyramid['TotalWidth']) + self.assertEqual(512, pyramid['TotalHeight']) + self.assertEqual(1, pyramid['TilesCount'][0][0]) + self.assertEqual(1, pyramid['TilesCount'][0][1]) + + + def test_grayscale_pyramid(self): + CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), '--tile-width=64', '--tile-height=64' ]) + + i = DoGet(ORTHANC, '/instances') + self.assertEqual(4, len(i)) + + for j in range(4): + tags = DoGet(ORTHANC, '/instances/%s/tags?simplify' % i[j]) + self.assertEqual(64, int(tags['Columns'])) + self.assertEqual(64, int(tags['Rows'])) + self.assertEqual('MONOCHROME2', tags['PhotometricInterpretation']) + + s = DoGet(ORTHANC, '/series') + self.assertEqual(1, len(s)) + + pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) + self.assertEqual(s[0], pyramid['ID']) + self.assertEqual(4, len(pyramid['Resolutions'])) + self.assertEqual(4, len(pyramid['Sizes'])) + self.assertEqual(4, len(pyramid['TilesCount'])) + self.assertEqual(1, pyramid['Resolutions'][0]) + self.assertEqual(2, pyramid['Resolutions'][1]) + self.assertEqual(4, pyramid['Resolutions'][2]) + self.assertEqual(8, pyramid['Resolutions'][3]) + self.assertEqual(512, pyramid['Sizes'][0][0]) + self.assertEqual(512, pyramid['Sizes'][0][1]) + self.assertEqual(256, pyramid['Sizes'][1][0]) + self.assertEqual(256, pyramid['Sizes'][1][1]) + self.assertEqual(128, pyramid['Sizes'][2][0]) + self.assertEqual(128, pyramid['Sizes'][2][1]) + self.assertEqual(64, pyramid['Sizes'][3][0]) + self.assertEqual(64, pyramid['Sizes'][3][1]) + self.assertEqual(64, pyramid['TileWidth']) + self.assertEqual(64, pyramid['TileHeight']) + self.assertEqual(512, pyramid['TotalWidth']) + self.assertEqual(512, pyramid['TotalHeight']) + self.assertEqual(8, pyramid['TilesCount'][0][0]) + self.assertEqual(8, pyramid['TilesCount'][0][1]) + self.assertEqual(4, pyramid['TilesCount'][1][0]) + self.assertEqual(4, pyramid['TilesCount'][1][1]) + self.assertEqual(2, pyramid['TilesCount'][2][0]) + self.assertEqual(2, pyramid['TilesCount'][2][1]) + self.assertEqual(1, pyramid['TilesCount'][3][0]) + self.assertEqual(1, pyramid['TilesCount'][3][1]) + +try: + print('\nStarting the tests...') + unittest.main(argv = [ sys.argv[0] ] + args.options) + +finally: + print('\nDone')