def setUp(self):
self.test_path = os.path.abspath(os.path.dirname(__file__))
self.user = User.objects.create(username='******')
self.client = Client()
self.client.login(username=self.user)
self.Collection1 = Collection(name='Collection1', owner=self.user)
self.Collection1.save()
self.unorderedAtlas = Atlas(name='unorderedAtlas',
description='',
collection=self.Collection1)
# Save new atlas object, unordered
print "Adding unordered and ordered atlas..."
nii_path = os.path.join(
self.test_path,
'test_data/api/VentralFrontal_thr75_summaryimage_2mm.nii.gz')
xml_path = os.path.join(
self.test_path,
'test_data/api/unordered_VentralFrontal_thr75_summaryimage_2mm.xml'
)
self.unorderedAtlas = save_atlas_form(nii_path=nii_path,
xml_path=xml_path,
collection=self.Collection1,
name="unorderedAtlas")
# Ordered
nii_path = os.path.join(
self.test_path,
'test_data/api/VentralFrontal_thr75_summaryimage_2mm.nii.gz')
xml_path = os.path.join(
self.test_path,
'test_data/api/VentralFrontal_thr75_summaryimage_2mm.xml')
self.orderedAtlas = save_atlas_form(nii_path=nii_path,
xml_path=xml_path,
collection=self.Collection1,
name="orderedAtlas")
# Statistical Map 1 and 2
print "Adding statistical maps..."
nii_path = os.path.join(self.test_path,
'test_data/statmaps/motor_lips.nii.gz')
self.Image1 = save_statmap_form(image_path=nii_path,
collection=self.Collection1)
nii_path = os.path.join(self.test_path,
'test_data/statmaps/beta_0001.nii.gz')
self.Image2 = save_statmap_form(image_path=nii_path,
collection=self.Collection1)
# Zip file with nidm results
print "Adding nidm results..."
zip_file = os.path.join(self.test_path,
'test_data/nidm/spm_example.nidm.zip')
self.nidm = save_nidm_form(zip_file=zip_file,
collection=self.Collection1)
def setUp(self):
self.test_path = os.path.abspath(os.path.dirname(__file__))
self.user = User.objects.create(username='******')
self.client = Client()
self.client.login(username=self.user)
self.Collection1 = Collection(name='Collection1', owner=self.user)
self.Collection1.save()
self.unorderedAtlas = Atlas(
name='unorderedAtlas', description='', collection=self.Collection1)
# Save new atlas object, unordered
print "Adding unordered and ordered atlas..."
nii_path = os.path.join(
self.test_path, 'test_data/api/VentralFrontal_thr75_summaryimage_2mm.nii.gz')
xml_path = os.path.join(
self.test_path, 'test_data/api/unordered_VentralFrontal_thr75_summaryimage_2mm.xml')
self.unorderedAtlas = save_atlas_form(nii_path=nii_path,
xml_path=xml_path,
collection=self.Collection1,
name="unorderedAtlas")
# Ordered
nii_path = os.path.join(
self.test_path, 'test_data/api/VentralFrontal_thr75_summaryimage_2mm.nii.gz')
xml_path = os.path.join(
self.test_path, 'test_data/api/VentralFrontal_thr75_summaryimage_2mm.xml')
self.orderedAtlas = save_atlas_form(nii_path=nii_path,
xml_path=xml_path,
collection=self.Collection1,
name="orderedAtlas")
# Statistical Map 1 and 2
print "Adding statistical maps..."
nii_path = os.path.join(
self.test_path, 'test_data/statmaps/motor_lips.nii.gz')
self.Image1 = save_statmap_form(
image_path=nii_path, collection=self.Collection1)
nii_path = os.path.join(
self.test_path, 'test_data/statmaps/beta_0001.nii.gz')
self.Image2 = save_statmap_form(
image_path=nii_path, collection=self.Collection1)
# Zip file with nidm results
print "Adding nidm results..."
zip_file = os.path.join(
self.test_path, 'test_data/nidm/spm_example.nidm.zip')
self.nidm = save_nidm_form(
zip_file=zip_file, collection=self.Collection1)
def setUp(self):
super(TestAtlasChange, self).setUp()
nii_path = self.abs_data_path(
'api/VentralFrontal_thr75_summaryimage_2mm.nii.gz')
xml_path = self.abs_data_path(
'api/unordered_VentralFrontal_thr75_summaryimage_2mm.xml')
self.item = save_atlas_form(nii_path=nii_path,
xml_path=xml_path,
collection=self.coll,
name="unorderedAtlas")
self.item_url = '/api/atlases/%s/' % self.item.pk
def setUp(self):
super(TestAtlasChange, self).setUp()
nii_path = self.abs_file_path(
'test_data/api/VentralFrontal_thr75_summaryimage_2mm.nii.gz'
)
xml_path = self.abs_file_path(
'test_data/api/unordered_VentralFrontal_thr75_summaryimage_2mm.xml'
)
self.item = save_atlas_form(nii_path=nii_path,
xml_path=xml_path,
collection=self.coll,
name="unorderedAtlas")
self.item_url = '/api/atlases/%s/' % self.item.pk
def setUp(self):
print "\n#### TESTING THRESHOLDED IMAGES IN COMPARISON\n"
self.tmpdir = tempfile.mkdtemp()
self.app_path = os.path.abspath(os.path.dirname(__file__))
self.u1 = User.objects.create(username='******')
self.comparisonCollection1 = Collection(name='comparisonCollection1', owner=self.u1,
DOI='10.3389/fninf.2015.00008')
self.comparisonCollection1.save()
self.comparisonCollection2 = Collection(name='comparisonCollection2', owner=self.u1,
DOI='10.3389/fninf.2015.00009')
self.comparisonCollection2.save()
self.comparisonCollection3 = Collection(name='comparisonCollection3', owner=self.u1,
DOI='10.3389/fninf.2015.00010')
self.comparisonCollection3.save()
self.comparisonCollection4 = Collection(name='comparisonCollection4', owner=self.u1,
DOI='10.3389/fninf.2015.00011')
self.comparisonCollection4.save()
# Image 1 is an atlas
print "Adding atlas image..."
nii_path = os.path.join(self.app_path,"test_data/api/VentralFrontal_thr75_summaryimage_2mm.nii.gz")
xml_path = os.path.join(self.app_path,"test_data/api/VentralFrontal_thr75_summaryimage_2mm.xml")
image1 = save_atlas_form(nii_path=nii_path,xml_path=xml_path,collection = self.comparisonCollection1)
self.pk1 = image1.id
# Image 2 is a statistical map
print "Adding statistical map..."
image_path = os.path.join(self.app_path,'test_data/statmaps/beta_0001.nii.gz')
image2 = save_statmap_form(image_path=image_path,collection = self.comparisonCollection2)
self.pk2 = image2.id
# Image 3 is a thresholded statistical map
print "Adding thresholded statistical map..."
image_paths = [os.path.join(self.app_path,'test_data/statmaps/box_0b_vs_1b.img'),
os.path.join(self.app_path,'test_data/statmaps/box_0b_vs_1b.hdr')]
image3 = save_statmap_form(image_path=image_paths, collection = self.comparisonCollection3,ignore_file_warning=True)
self.pk3 = image3.id
# Create similarity object
Similarity.objects.update_or_create(similarity_metric="pearson product-moment correlation coefficient",
transformation="voxelwise",
metric_ontology_iri="http://webprotege.stanford.edu/RCS8W76v1MfdvskPLiOdPaA",
transformation_ontology_iri="http://webprotege.stanford.edu/R87C6eFjEftkceScn1GblDL")
self.pearson_metric = Similarity.objects.filter(similarity_metric="pearson product-moment correlation coefficient",
transformation="voxelwise",
metric_ontology_iri="http://webprotege.stanford.edu/RCS8W76v1MfdvskPLiOdPaA",
transformation_ontology_iri="http://webprotege.stanford.edu/R87C6eFjEftkceScn1GblDL")
def setUp(self):
self.user = User.objects.create_user('NeuroGuy')
self.user.save()
self.collection = Collection(owner=self.user, name="Test Collection")
self.collection.save()
self.unorderedAtlas = save_atlas_form(
nii_path=self.abs_data_path(
'api/VentralFrontal_thr75_summaryimage_2mm.nii.gz'
),
xml_path=self.abs_data_path(
'api/unordered_VentralFrontal_thr75_summaryimage_2mm.xml'
),
collection=self.collection,
name="unorderedAtlas"
)
self.image1 = save_statmap_form(
image_path=self.abs_data_path(
'statmaps/motor_lips.nii.gz'
),
collection=self.collection
)
self.image2 = save_statmap_form(
image_path=self.abs_data_path(
'statmaps/beta_0001.nii.gz'
),
collection=self.collection
)
self.nidm = save_nidm_form(
zip_file=self.abs_data_path(
'nidm/spm_example.nidm.zip'
),
collection=self.collection
)
def setUp(self):
print "\n#### TESTING THRESHOLDED IMAGES IN COMPARISON\n"
self.tmpdir = tempfile.mkdtemp()
self.app_path = os.path.abspath(os.path.dirname(__file__))
self.u1 = User.objects.create(username='******')
self.comparisonCollection = Collection(name='comparisonCollection',owner=self.u1)
self.comparisonCollection.save()
# Image 1 is an atlas
print "Adding atlas image..."
nii_path = os.path.join(self.app_path,"test_data/api/VentralFrontal_thr75_summaryimage_2mm.nii.gz")
xml_path = os.path.join(self.app_path,"test_data/api/VentralFrontal_thr75_summaryimage_2mm.xml")
image1 = save_atlas_form(nii_path=nii_path,xml_path=xml_path,collection = self.comparisonCollection)
self.pk1 = image1.id
# Image 2 is a statistical map
print "Adding statistical map..."
image_path = os.path.join(self.app_path,'test_data/statmaps/beta_0001.nii.gz')
image2 = save_statmap_form(image_path=image_path,collection = self.comparisonCollection)
self.pk2 = image2.id
# Image 3 is a thresholded statistical map
print "Adding thresholded statistical map..."
image_paths = [os.path.join(self.app_path,'test_data/statmaps/box_0b_vs_1b.img'),
os.path.join(self.app_path,'test_data/statmaps/box_0b_vs_1b.hdr')]
image3 = save_statmap_form(image_path=image_paths, collection = self.comparisonCollection,ignore_file_warning=True)
self.pk3 = image3.id
# Create similarity object
Similarity.objects.update_or_create(similarity_metric="pearson product-moment correlation coefficient",
transformation="voxelwise",
metric_ontology_iri="http://webprotege.stanford.edu/RCS8W76v1MfdvskPLiOdPaA",
transformation_ontology_iri="http://webprotege.stanford.edu/R87C6eFjEftkceScn1GblDL")
self.pearson_metric = Similarity.objects.filter(similarity_metric="pearson product-moment correlation coefficient",
transformation="voxelwise",
metric_ontology_iri="http://webprotege.stanford.edu/RCS8W76v1MfdvskPLiOdPaA",
transformation_ontology_iri="http://webprotege.stanford.edu/R87C6eFjEftkceScn1GblDL")
