Mercurial > hg > orthanc-tests
view Plugins/WSI/Run.py @ 408:4e0b9fddbc71
test "Replace" for UID in subsequences
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 10 Jun 2021 13:10:11 +0200 |
parents | 27cb0b60f2d3 |
children | e769bcf2b94f |
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#!/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) 2017-2021 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('--valgrind', help = 'Use valgrind while running the DICOM-izer', action = 'store_true') 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 CallCommand(command): prefix = [] if args.valgrind: prefix = [ 'valgrind' ] log = subprocess.check_output(prefix + command, stderr=subprocess.STDOUT) # If using valgrind, only print the lines from the log starting # with '==' (they contain the report from valgrind) if args.valgrind: print('\n'.join(filter(lambda x: x.startswith('=='), log.splitlines()))) def CallDicomizer(suffix): CallCommand([ args.dicomizer, '--username=%s' % args.username, '--password=%s' % args.password ] + suffix) def CallDicomToTiff(suffix): CallCommand([ args.to_tiff, '--username=%s' % args.username, '--password=%s' % args.password ] + suffix) def CallTiffInfoOnSeries(series): with tempfile.NamedTemporaryFile(delete = False) as temp: temp.close() CallDicomToTiff([ series, temp.name ]) try: tiff = subprocess.check_output([ 'tiffinfo', temp.name ]) except: print('\ntiffinfo is probably not installed => sudo apt-get install libtiff-tools\n') tiff = None os.unlink(temp.name) return tiff 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(1, len(pyramid['TilesSizes'])) self.assertEqual(2, len(pyramid['TilesSizes'][0])) self.assertEqual(512, pyramid['TilesSizes'][0][0]) self.assertEqual(512, pyramid['TilesSizes'][0][1]) self.assertEqual(512, pyramid['TotalWidth']) self.assertEqual(512, pyramid['TotalHeight']) self.assertEqual(1, pyramid['TilesCount'][0][0]) self.assertEqual(1, pyramid['TilesCount'][0][1]) tiff = CallTiffInfoOnSeries(s[0]) p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) self.assertEqual(1, len(p)) self.assertTrue('YCbCr' in p[0]) 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(4, len(pyramid['TilesSizes'])) 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]) for i in range(4): self.assertEqual(2, len(pyramid['TilesSizes'][i])) self.assertEqual(64, pyramid['TilesSizes'][i][0]) self.assertEqual(64, pyramid['TilesSizes'][i][1]) 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]) tiff = CallTiffInfoOnSeries(s[0]) p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) self.assertEqual(4, len(p)) for j in range(4): self.assertTrue('min-is-black' in p[j]) def test_import_tiff_grayscale(self): CallDicomizer([ GetDatabasePath('WSI/LenaGrayscaleJpeg.tiff') ]) s = DoGet(ORTHANC, '/series') self.assertEqual(1, len(s)) pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) self.assertEqual(4, len(pyramid['Resolutions'])) tiff = CallTiffInfoOnSeries(s[0]) p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) self.assertEqual(4, len(p)) for j in range(4): self.assertTrue('min-is-black' in p[j]) def test_import_tiff_ycbcr(self): CallDicomizer([ GetDatabasePath('WSI/LenaColorJpegYCbCr.tiff') ]) s = DoGet(ORTHANC, '/series') self.assertEqual(1, len(s)) pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) self.assertEqual(4, len(pyramid['Resolutions'])) tiff = CallTiffInfoOnSeries(s[0]) p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) self.assertEqual(4, len(p)) for j in range(4): self.assertTrue('YCbCr' in p[j]) def test_import_tiff_rgb(self): CallDicomizer([ GetDatabasePath('WSI/LenaColorJpegRGB.tiff') ]) s = DoGet(ORTHANC, '/series') self.assertEqual(1, len(s)) pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) self.assertEqual(4, len(pyramid['Resolutions'])) tiff = CallTiffInfoOnSeries(s[0]) p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) self.assertEqual(4, len(p)) for j in range(4): self.assertTrue('RGB' in p[j]) def test_concatenation(self): # https://bugs.orthanc-server.com/show_bug.cgi?id=145 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), '--levels=1', ]) i = DoGet(ORTHANC, '/instances') self.assertEqual(1, len(i)) tags = DoGet(ORTHANC, '/instances/%s/tags?short' % i[0]) self.assertTrue('0020,0242' in tags) # SOP Instance UID of Concatenation Source self.assertTrue('0020,9161' in tags) # Concatenation UID self.assertTrue('0020,9162' in tags) # In-concatenation Number self.assertTrue('0020,9228' in tags) # Concatenation Frame Offset Number self.assertEqual('1', tags['0020,9162']) self.assertEqual('0', tags['0020,9228']) DropOrthanc(ORTHANC) # "--max-size" disables the concatenation CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), '--levels=1', '--max-size=0' ]) i = DoGet(ORTHANC, '/instances') self.assertEqual(1, len(i)) tags = DoGet(ORTHANC, '/instances/%s/tags?short' % i[0]) self.assertFalse('0020,0242' in tags) self.assertFalse('0020,9161' in tags) self.assertFalse('0020,9162' in tags) self.assertFalse('0020,9228' in tags) DropOrthanc(ORTHANC) # This creates a series with 2 instances of roughly 1.5MB (= 2 frames x 512 x 512 x 3 (RGB24) + DICOM overhead) CallDicomizer([ GetDatabasePath('WSI/Lena2x2.png'), '--levels=1', '--max-size=1', '--compression=none' ]) i = DoGet(ORTHANC, '/instances') self.assertEqual(2, len(i)) t1 = DoGet(ORTHANC, '/instances/%s/tags?short' % i[0]) t2 = DoGet(ORTHANC, '/instances/%s/tags?short' % i[1]) self.assertTrue('0020,0242' in t1) self.assertTrue('0020,9161' in t1) self.assertTrue('0020,9162' in t1) self.assertTrue('0020,9228' in t1) self.assertEqual(t1['0020,0242'], t2['0020,0242']) self.assertEqual(t1['0020,9161'], t2['0020,9161']) if t1['0020,9162'] == '1': self.assertEqual('1', t1['0020,9162']) self.assertEqual('0', t1['0020,9228']) self.assertEqual('2', t2['0020,9162']) self.assertEqual('2', t2['0020,9228']) else: self.assertEqual('1', t2['0020,9162']) self.assertEqual('0', t2['0020,9228']) self.assertEqual('2', t1['0020,9162']) self.assertEqual('2', t1['0020,9228']) def test_pixel_spacing(self): # https://bugs.orthanc-server.com/show_bug.cgi?id=139 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), # Image is 512x512 '--levels=4', '--tile-width=64', '--tile-height=64', '--max-size=0', '--imaged-width=20', '--imaged-height=10' ]) instances = DoGet(ORTHANC, '/instances') self.assertEqual(4, len(instances)) spacings = {} for i in instances: t = DoGet(ORTHANC, '/instances/%s/tags?short' % i) spacings[t['0028,0008']] = t['5200,9229'][0]['0028,9110'][0]['0028,0030'] self.assertEqual(4, len(spacings)) for i in range(4): s = spacings[str(4 ** i)].split('\\') self.assertEqual(2, len(s)) self.assertEqual(20.0 / 512.0 * (2.0 ** (3 - i)), float(s[0])) self.assertEqual(10.0 / 512.0 * (2.0 ** (3 - i)), float(s[1])) try: print('\nStarting the tests...') unittest.main(argv = [ sys.argv[0] ] + args.options) finally: print('\nDone')