Commit 257b1b6c authored by Joe Lyons's avatar Joe Lyons 🚴
Browse files

Merge branch 'apt_update_change' into 'master'

add apt update before installing packages

See merge request ynic-public/yias!6
parents 4d48b4e8 aa46c44b
Pipeline #1350 failed with stage
in 9 seconds
before_script:
- apt -y install python3-numpy python3-dicom python3-nibabel python3-pytest python3-pytest-cov dcm2niix
- apt -qq update && apt -qq install -y python3-numpy python3-dicom python3-nibabel python3-pytest python3-pytest-cov dcm2niix git
stages:
- build_test
......@@ -12,4 +12,3 @@ build_test:
- git clone https://vcs.ynic.york.ac.uk/ynic-public/yias-testdata.git
- mkdir -p tmp/
- TMPDIR=$(pwd)/tmp YIAS_TESTDATA=$(pwd)/yias-testdata py.test-3 -v -s --cov yias --cov-report=term-missing yias
......@@ -104,7 +104,7 @@ class BaseNiftiTests(BaseCopyTest):
class TestCaseSiemensFMRIAxialMosaicNIFTI(BaseNiftiTests):
inputs_dirs = ['siemens/10']
exp_dim = [4, 64, 64, 19, 3, 0, 0, 0]
exp_dim = [4, 64, 64, 19, 3, 1, 1, 1]
exp_pixdim = [1.0, 3.0, 3.0, 3.0, 3.0, 0.0, 0.0, 0.0]
exp_diminfo = [0, 1, 2]
......@@ -134,7 +134,7 @@ class TestCaseSiemensFMRICoronalMosaicNIFTI(BaseNiftiTests):
class TestCaseSiemensFMRINormalAxialNIFTI(BaseNiftiTests):
inputs_dirs = ['siemens/14']
exp_dim = [4, 128, 128, 25, 3, 0, 0, 0]
exp_dim = [4, 128, 128, 25, 3, 1, 1, 1]
exp_pixdim = [1.0, 2.0, 2.0, 2.5, 3.0, 0.0, 0.0, 0.0]
exp_diminfo = [0, 1, 2]
......@@ -174,7 +174,7 @@ class TestCaseSiemensFMRIMultipleEchoGRENIFTIAxialEcho1(BaseNiftiTests):
('siemens/16/MR.X.1.2.276.0.7230010.3.1.4.2836010529.1187.1490799879.%d' % d, \
'file%d' % d) for d in files_to_use ]
exp_dim = [3, 128, 128, 25, 1, 0, 0, 0]
exp_dim = [3, 128, 128, 25, 1, 1, 1, 1]
exp_pixdim = [1.0, 2.0, 2.0, 2.5, 0.65, 0.0, 0.0, 0.0]
exp_diminfo = [0, 1, 2]
......@@ -200,7 +200,7 @@ class TestCaseSiemensFMRIMultipleEchoGRENIFTIAxialEcho2(BaseNiftiTests):
('siemens/16/MR.X.1.2.276.0.7230010.3.1.4.2836010529.1187.1490799879.%d' % d, \
'file%d' % d) for d in files_to_use ]
exp_dim = [3, 128, 128, 25, 1, 0, 0, 0]
exp_dim = [3, 128, 128, 25, 1, 1, 1, 1]
exp_pixdim = [1.0, 2.0, 2.0, 2.5, 0.65, 0.0, 0.0, 0.0]
exp_diminfo = [0, 1, 2]
......@@ -215,7 +215,7 @@ class TestCaseSiemensFMRIMultipleEchoGRENIFTIAxialEcho2(BaseNiftiTests):
class TestCaseSiemensMPRAGESagittalNIFTI(BaseNiftiTests):
inputs_dirs = ['siemens/18']
exp_dim = [3, 176, 256, 256, 1, 0, 0, 0]
exp_dim = [3, 176, 256, 256, 1, 1, 1, 1]
exp_pixdim = [1.0, 1.0, 1.0, 1.0, 2.3, 0.0, 0.0, 0.0]
exp_diminfo = [1, 0, 2]
......@@ -229,7 +229,7 @@ class TestCaseSiemensMPRAGESagittalNIFTI(BaseNiftiTests):
class TestCaseSiemensMPRAGEAxialNIFTI(BaseNiftiTests):
inputs_dirs = ['siemens/19']
exp_dim = [3, 256, 256, 176, 1, 0, 0, 0]
exp_dim = [3, 256, 256, 176, 1, 1, 1, 1]
exp_pixdim = [1.0, 1.0, 1.0, 1.0, 2.3, 0.0, 0.0, 0.0]
exp_diminfo = [0, 1, 2]
......@@ -243,8 +243,8 @@ class TestCaseSiemensMPRAGEAxialNIFTI(BaseNiftiTests):
class TestCaseSiemensT2SPACESaggitalNIFTI(BaseNiftiTests):
inputs_dirs = ['siemens/20']
exp_dim = [3, 176, 512, 512, 1, 0, 0, 0]
exp_pixdim = [1.0, 0.900002, 0.5, 0.5, 3.2, 0.0, 0.0, 0.0]
exp_dim = [3, 176, 512, 512, 1, 1, 1, 1]
exp_pixdim = [1.0, 0.9, 0.5, 0.5, 3.2, 0.0, 0.0, 0.0]
exp_diminfo = [1, 0, 2]
pixel_checks = {
......@@ -257,8 +257,8 @@ class TestCaseSiemensT2SPACESaggitalNIFTI(BaseNiftiTests):
class TestCaseSiemensT2SPACEAxialNIFTI(BaseNiftiTests):
inputs_dirs = ['siemens/21']
exp_dim = [3, 512, 512, 176, 1, 0, 0, 0]
exp_pixdim = [1.0, 0.5, 0.5, 0.900002, 3.2, 0.0, 0.0, 0.0]
exp_dim = [3, 512, 512, 176, 1, 1, 1, 1]
exp_pixdim = [1.0, 0.5, 0.5, 0.9, 3.2, 0.0, 0.0, 0.0]
exp_diminfo = [0, 1, 2]
pixel_checks = {
......@@ -271,7 +271,7 @@ class TestCaseSiemensT2SPACEAxialNIFTI(BaseNiftiTests):
class TestCaseSiemensPDAxialNIFTI(BaseNiftiTests):
inputs_dirs = ['siemens/22']
exp_dim = [3, 640, 640, 35, 1, 0, 0, 0]
exp_dim = [3, 640, 640, 35, 1, 1, 1, 1]
exp_pixdim = [1.0, 0.34375, 0.34375, 3.899995, 3., 0.0, 0.0, 0.0]
exp_diminfo = [0, 1, 2]
......@@ -285,7 +285,7 @@ class TestCaseSiemensPDAxialNIFTI(BaseNiftiTests):
class TestCaseSiemensT1FLAIRNIFTI(BaseNiftiTests):
inputs_dirs = ['siemens/23']
exp_dim = [3, 320, 320, 27, 1, 0, 0, 0]
exp_dim = [3, 320, 320, 27, 1, 1, 1, 1]
exp_pixdim = [1.0, 0.6875, 0.6875, 5.199996, 2., 0.0, 0.0, 0.0]
exp_diminfo = [0, 1, 2]
......@@ -301,7 +301,7 @@ class TestCaseSiemensT1FLAIRNIFTI(BaseNiftiTests):
class TestCaseSiemensDTI1NIFTI(BaseNiftiTests):
inputs_dirs = ['siemens/24']
exp_dim = [4, 128, 128, 19, 7, 0, 0, 0]
exp_dim = [4, 128, 128, 19, 7, 1, 1, 1]
exp_pixdim = [1.0, 2.0, 2.0, 3.0, 6.5, 0.0, 0.0, 0.0]
exp_diminfo = [0, 1, 2]
......@@ -322,7 +322,7 @@ class TestCaseSiemensDTI1NIFTI(BaseNiftiTests):
class TestCaseSiemensDTI2NIFTI(BaseNiftiTests):
inputs_dirs = ['siemens/30']
exp_dim = [4, 128, 128, 19, 7, 0, 0, 0]
exp_dim = [4, 128, 128, 19, 7, 1, 1, 1]
exp_pixdim = [1.0, 2.0, 2.0, 3.0, 6.5, 0.0, 0.0, 0.0]
exp_diminfo = [0, 1, 2]
......
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