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")