def test_dcmread_get_dcmdir_qt(self):
dirpath = dcmr.get_dcmdir_qt()
#self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
reader = dcmr.DicomReader(dirpath)
self.data3d = reader.get_3Ddata()
self.metadata = reader.get_metaData()
def test_dcmread_select_series(self):
#dirpath = dcmr.get_dcmdir_qt()
dirpath = '/home/mjirik/data/medical/data_orig/46328096/'
#dirpath = dcmr.get_dcmdir_qt()
#app = QMainWindow()
reader = dcmr.DicomReader(dirpath, series_number = 55555)#, #qt_app =app)
#app.exit()
self.data3d = reader.get_3Ddata()
self.metadata = reader.get_metaData()
def test_dcmread_isbweb_phalanx1(self):
# dirpath = dcmr.get_dcmdir_qt()
dirpath = '~/data/medical/orig/isbweb/phalanx1/'
# dirpath = dcmr.get_dcmdir_qt()
# app = QMainWindow()
reader = dcmr.DicomReader(dirpath) # , #qt_app =app)
# app.exit()
self.data3d = reader.get_3Ddata()
self.metadata = reader.get_metaData()
def test_dcmread_piglets(self):
# dirpath = dcmr.get_dcmdir_qt()
dirpath = '~/data/medical/orig/piglets/P02/PRIVATE_MI_LIVER_CORROSIVE_(ADULT)_20131022_075148_171000/VEN_ABDOMEN_5_0_B31S_0002/'
# dirpath = dcmr.get_dcmdir_qt()
# app = QMainWindow()
reader = dcmr.DicomReader(dirpath) # , #qt_app =app)
# app.exit()
self.data3d = reader.get_3Ddata()
self.metadata = reader.get_metaData()
def test_dcmread_series_number(self):
dcmdir = lisa.dataset.join_sdp('jatra_5mm')
#dcmdir = '/home/mjirik/data/medical/data_orig/jatra-kma/jatra_5mm/'
#self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
# spravne cislo serie je 7
reader = dcmr.DicomReader(dcmdir,series_number = 7)
data3d = reader.get_3Ddata()
metadata = reader.get_metaData()
self.assertEqual(data3d.shape[2],512)
self.assertEqual(metadata['voxelsize_mm'][0],5)
def test_dcmread_select_series_reasmusplus(self):
# dirpath = dcmr.get_dcmdir_qt()
dirpath = '~/data/medical/orig/erazmusplus/44204675/'
# dirpath = dcmr.get_dcmdir_qt()
# app = QMainWindow()
reader = dcmr.DicomReader(dirpath,
series_number=55555) # , #qt_app =app)
# app.exit()
self.data3d = reader.get_3Ddata()
self.metadata = reader.get_metaData()
def test_dcmread(self):
dcmdir = lisa.dataset.join_sdp('jatra_5mm')
#dcmdir = '/home/mjirik/data/medical/data_orig/jatra-kma/jatra_5mm/'
#self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
reader = dcmr.DicomReader(dcmdir)
data3d = reader.get_3Ddata()
metadata = reader.get_metaData()
#slice size is 512x512
self.assertEqual(data3d.shape[2],512)
# voxelsize depth = 5 mm
self.assertEqual(metadata['voxelsize_mm'][0],5)
def test_DicomReader_overlay(self):
# import matplotlib.pyplot as plt
dcmdir = os.path.join(sample_data_path, '../sample_data/volumetrie/')
# dcmdir = '/home/mjirik/data/medical/data_orig/jatra-kma/jatra_5mm/'
# self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
reader = dcmr.DicomReader(dcmdir)
overlay = reader.get_overlay()
# import pdb; pdb.set_trace()
# plt.imshow(overlay[1][:,:,0])
# plt.show()
self.assertEqual(overlay[1][0, 200, 200], 1)
self.assertEqual(overlay[1][0, 100, 100], 0)
def test_dcmread_not_defined_slice_width(self):
# app = QApplication(sys.argv)
# dirpath = dcmr.get_dcmdir_qt()
dirpath = 'e:/data/medical/orig/chk/83674597/'
dirpath = 'e:/data/medical/orig/chk/84490561/'
# dirpath = dcmr.get_dcmdir_qt()
# app = QMainWindow()
reader = dcmr.DicomReader(
dirpath,
# qt_app=app,
series_number=8,
) # , #qt_app =app)
# app.exit()
self.data3d = reader.get_3Ddata()
self.metadata = reader.get_metaData()
sz = self.data3d.shape
print(sz)
def test_DicomReader_overlay(self):
import os.path as op
# sample_data_path = "~/data/medical/orig/sample_data/"
# sample_data_path = op.expanduser(sample_data_path)
sample_data_path = io3d.datasets.join_path("sample_data/")
#import matplotlib.pyplot as plt
# dcmdir = lisa.dataset.join_sdp('volumetrie/')
dcmdir = os.path.join(sample_data_path, 'volumetrie/')
# dcmdir = '/home/mjirik/data/medical/data_orig/jatra-kma/jatra_5mm/'
#self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
reader = dcmr.DicomReader(dcmdir)
overlay = reader.get_overlay()
#import pdb; pdb.set_trace()
#plt.imshow(overlay[1][:,:,0])
#plt.show()
self.assertEqual(overlay[1][0, 200, 200], 1)
self.assertEqual(overlay[1][0, 100, 100], 0)
def test_dcmread(self):
dcmdir = os.path.join(sample_data_path, '../sample_data/jatra_5mm')
# dcmdir = '/home/mjirik/data/medical/data_orig/jatra-kma/jatra_5mm/'
# self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
reader = dcmr.DicomReader(dcmdir)
data3d = reader.get_3Ddata()
metadata = reader.get_metaData()
stats = reader.dcmdirstats()
info_str = reader.print_series_info(stats, minimal_series_number=0)
# slice size is 512x512
self.assertEqual(data3d.shape[2], 512)
# voxelsize depth = 5 mm
self.assertEqual(metadata['voxelsize_mm'][0], 5)
# test stats
self.assertEqual(stats[7]['Modality'], 'CT')
self.assertTrue(info_str,
'7 (93, CT, DE_Abdom_1F 5.0 B30f M_0.3, )\n')
def test_dcmread_micro_ct_biodur_sample(self):
# TODO prepare dataset for this test
# there was problem with DICOMDIR file
dcmdir = io3d.datasets.join_path("sample_data/biodur_sample/")
reader = dcmr.DicomReader(dcmdir, force_create_dicomdir=True)
data3d = reader.get_3Ddata()
metadata = reader.get_metaData()
stats = reader.dcmdirstats()
info_str = reader.print_series_info(stats, minimal_series_number=0)
# slice size is 512x512
self.assertEqual(data3d.shape[2], 512)
# voxelsize depth = 5 mm
self.assertEqual(metadata['voxelsize_mm'][0], 5)
# test stats
self.assertEqual(stats[7]['Modality'], 'CT')
self.assertTrue(info_str,
'7 (93, CT, DE_Abdom_1F 5.0 B30f M_0.3, )\n')
def test_compare_dcmread_and_dataread(self):
# dcmdir = os.path.join(path_to_script, '../vincentka_2013_06mm/')
dcmdir = op.join(sample_data_path, 'vincentka_sample/')
# dcmdir = '/home/mjirik/data/medical/data_orig/jatra-kma/jatra_5mm/'
# self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
reader = dcmr.DicomReader(dcmdir)
data3d = reader.get_3Ddata()
# metadata = reader.get_metaData()
# import sed3
# ed = sed3.sed3(data3d)
# ed.show()
import io3d
dr = io3d.datareader.DataReader()
datap = dr.Get3DData(dcmdir, dataplus_format=True)
ddata3d = datap['data3d']
# import sed3
# ed = sed3.sed3(ddata3d)
# ed.show()
self.assertEqual(0, np.sum(np.abs(ddata3d - data3d)))
def test_dcmread_some_strange_data(self):
# there was problem with DICOMDIR file
dcmdir = "e:\\data\\medical\\orig\\chk\\84490561\\"
# os.path.join(sample_data_path, '../sample_data/jatra_5mm')
# dcmdir = '/home/mjirik/data/medical/data_orig/jatra-kma/jatra_5mm/'
# self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
reader = dcmr.DicomReader(dcmdir,
force_create_dicomdir=False,
series_number=10)
data3d = reader.get_3Ddata()
metadata = reader.get_metaData()
stats = reader.dcmdirstats()
info_str = reader.print_series_info(stats, minimal_series_number=0)
# slice size is 512x512
self.assertEqual(data3d.shape[2], 512)
# voxelsize depth = 5 mm
self.assertEqual(metadata['voxelsize_mm'][0], 5)
# test stats
self.assertEqual(stats[7]['Modality'], 'CT')
def test_dcmread_micro_ct(self):
# there was problem with DICOMDIR file
dcmdir = "e:\\data\\medical\\orig\\jatra_mikro_data\\Nejlepsi_rozliseni_nevycistene\\"
# os.path.join(sample_data_path, '../sample_data/jatra_5mm')
# dcmdir = '/home/mjirik/data/medical/data_orig/jatra-kma/jatra_5mm/'
# self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
reader = dcmr.DicomReader(dcmdir, force_create_dicomdir=True)
data3d = reader.get_3Ddata()
metadata = reader.get_metaData()
stats = reader.dcmdirstats()
info_str = reader.print_series_info(stats, minimal_series_number=0)
# slice size is 512x512
self.assertEqual(data3d.shape[2], 512)
# voxelsize depth = 5 mm
self.assertEqual(metadata['voxelsize_mm'][0], 5)
# test stats
self.assertEqual(stats[7]['Modality'], 'CT')
self.assertTrue(info_str,
'7 (93, CT, DE_Abdom_1F 5.0 B30f M_0.3, )\n')
def test_dcmread_perfusion_data_with_strange_serieses(self):
# there was problem with DICOMDIR file
dcmdir = alternative_data_path + "perfusion\\32584640\\"
# os.path.join(sample_data_path, '../sample_data/jatra_5mm')
# dcmdir = '/home/mjirik/data/medical/data_orig/jatra-kma/jatra_5mm/'
# self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
reader = dcmr.DicomReader(dcmdir,
force_create_dicomdir=True,
series_number=17)
data3d = reader.get_3Ddata()
metadata = reader.get_metaData()
stats = reader.dcmdirstats()
info_str = reader.print_series_info(stats, minimal_series_number=0)
# import sed3
# ed = sed3.sed3(data3d)
# ed.show()
# slice size is 512x512
self.assertEqual(data3d.shape[2], 512)
# voxelsize depth = 5 mm
self.assertLess(data3d[0, 0, 0], -1000)
# in the middle of image should be density higher than 50
self.assertGreater(np.max(data3d[:, 100:-100, 100:-100]), 50)
