Exemple #1
0
    def save(self, *args, **kwargs):
        if self.DOI is not None and self.DOI.strip() == "":
            self.DOI = None
        if self.private_token is not None and self.private_token.strip() == "":
            self.private_token = None

        if self.DOI and not self.private and not self.doi_add_date:
            self.doi_add_date = datetime.now()

        # run calculations when collection turns public
        privacy_changed = False
        DOI_changed = False
        if self.pk is not None:
            old_object = Collection.objects.get(pk=self.pk)
            old_is_private = old_object.private
            old_has_DOI = old_object.DOI is not None
            privacy_changed = old_is_private != self.private
            DOI_changed = old_has_DOI != (self.DOI is not None)

        super(Collection, self).save(*args, **kwargs)

        if (privacy_changed
                and not self.private) or (DOI_changed
                                          and self.DOI is not None):
            for image in self.basecollectionitem_set.instance_of(Image).all():
                if image.pk:
                    generate_glassbrain_image.apply_async([image.pk])
                    run_voxelwise_pearson_similarity.apply_async([image.pk])
Exemple #2
0
    def save(self, *args, **kwargs):
        if self.DOI is not None and self.DOI.strip() == "":
            self.DOI = None
        if self.private_token is not None and self.private_token.strip() == "":
            self.private_token = None

        if self.DOI and not self.private and not self.doi_add_date:
            self.doi_add_date = datetime.now()

        # run calculations when collection turns public
        privacy_changed = False
        DOI_changed = False
        if self.pk is not None:
            old_object = Collection.objects.get(pk=self.pk)
            old_is_private = old_object.private
            old_has_DOI = old_object.DOI is not None
            privacy_changed = old_is_private != self.private
            DOI_changed = old_has_DOI != (self.DOI is not None)

        super(Collection, self).save(*args, **kwargs)

        if (privacy_changed and not self.private) or (DOI_changed and self.DOI is not None):
            for image in self.basecollectionitem_set.instance_of(Image).all():
                if image.pk:
                    generate_glassbrain_image.apply_async([image.pk])
                    run_voxelwise_pearson_similarity.apply_async([image.pk])
Exemple #3
0
    def save(self, *args, **kwargs):
        if self.DOI is not None and self.DOI.strip() == "":
            self.DOI = None
        if self.private_token is not None and self.private_token.strip() == "":
            self.private_token = None
            
        if self.DOI and not self.private and not self.doi_add_date:
            self.doi_add_date = datetime.now()

        # run calculations when collection turns public
        privacy_changed = False
        if self.pk is not None:
            old_object = Collection.objects.get(pk=self.pk)
            old_is_private = old_object.private
            privacy_changed = old_is_private != self.private

        super(Collection, self).save(*args, **kwargs)

        assign_perm('delete_collection', self.owner, self)
        assign_perm('change_collection', self.owner, self)
        for image in self.image_set.all():
            assign_perm('change_image', self.owner, image)
            assign_perm('delete_image', self.owner, image)
        for nidmresult in self.nidmresults_set.all():
            assign_perm('change_nidmresults', self.owner, nidmresult)
            assign_perm('delete_nidmresults', self.owner, nidmresult)
        

        if privacy_changed and self.private == False:
            for image in self.image_set.all():
                if image.pk:
                    generate_glassbrain_image.apply_async([image.pk])
                    run_voxelwise_pearson_similarity.apply_async([image.pk])
Exemple #4
0
    def save(self):
        if self.perc_bad_voxels == None and self.file:
            import neurovault.apps.statmaps.utils as nvutils
            self.file.open()
            gzfileobj = GzipFile(filename=self.file.name,
                                 mode='rb',
                                 fileobj=self.file.file)
            nii = nb.Nifti1Image.from_file_map(
                {'image': nb.FileHolder(self.file.name, gzfileobj)})
            self.is_thresholded, ratio_bad = nvutils.is_thresholded(nii)
            self.perc_bad_voxels = ratio_bad * 100.0

        if self.brain_coverage == None and self.file:
            import neurovault.apps.statmaps.utils as nvutils
            self.file.open()
            gzfileobj = GzipFile(filename=self.file.name,
                                 mode='rb',
                                 fileobj=self.file.file)
            nii = nb.Nifti1Image.from_file_map(
                {'image': nb.FileHolder(self.file.name, gzfileobj)})
            self.not_mni, self.brain_coverage, self.perc_voxels_outside = nvutils.not_in_mni(
                nii)

        if self.map_type == self.OTHER:
            import neurovault.apps.statmaps.utils as nvutils
            self.file.open()
            gzfileobj = GzipFile(filename=self.file.name,
                                 mode='rb',
                                 fileobj=self.file.file)
            nii = nb.Nifti1Image.from_file_map(
                {'image': nb.FileHolder(self.file.name, gzfileobj)})
            self.map_type = nvutils.infer_map_type(nii)

        # Calculation of image reduced_representation and comparisons
        file_changed = False
        if self.pk is not None:
            existing = Image.objects.get(pk=self.pk)
            if existing.file != self.file:
                file_changed = True
        do_update = True if file_changed else False
        new_image = True if self.pk is None else False

        # If we have an update, delete old pkl and comparisons first before saving
        if do_update and self.collection:
            if self.reduced_representation:  # not applicable for private collections
                self.reduced_representation.delete()

                # If more than one metric is added to NeuroVault, this must also filter based on metric
                comparisons = Comparison.objects.filter(
                    Q(image1=self) | Q(image2=self))
                if comparisons:
                    comparisons.delete()
        super(BaseStatisticMap, self).save()

        # Calculate comparisons
        if do_update or new_image:
            run_voxelwise_pearson_similarity.apply_async([self.pk])

        self.file.close()
Exemple #5
0
    def save(self):
        if self.perc_bad_voxels == None and self.file:
            import neurovault.apps.statmaps.utils as nvutils
            self.file.open()
            gzfileobj = GzipFile(filename=self.file.name, mode='rb', fileobj=self.file.file)
            nii = nb.Nifti1Image.from_file_map({'image': nb.FileHolder(self.file.name, gzfileobj)})
            self.is_thresholded, ratio_bad = nvutils.is_thresholded(nii)
            self.perc_bad_voxels = ratio_bad*100.0

        if self.brain_coverage == None and self.file:
            import neurovault.apps.statmaps.utils as nvutils
            self.file.open()
            gzfileobj = GzipFile(filename=self.file.name, mode='rb', fileobj=self.file.file)
            nii = nb.Nifti1Image.from_file_map({'image': nb.FileHolder(self.file.name, gzfileobj)})
            self.not_mni, self.brain_coverage, self.perc_voxels_outside = nvutils.not_in_mni(nii)

        if self.map_type == self.OTHER:
            import neurovault.apps.statmaps.utils as nvutils
            self.file.open()
            gzfileobj = GzipFile(filename=self.file.name, mode='rb', fileobj=self.file.file)
            nii = nb.Nifti1Image.from_file_map({'image': nb.FileHolder(self.file.name, gzfileobj)})
            self.map_type = nvutils.infer_map_type(nii)

        # Calculation of image reduced_representation and comparisons
        file_changed = False
        if self.pk is not None:
            existing = Image.objects.get(pk=self.pk)
            if existing.file != self.file:
                file_changed = True
        do_update = True if file_changed else False
        new_image = True if self.pk is None else False

        # If we have an update, delete old pkl and comparisons first before saving
        if do_update and self.collection:
            if self.reduced_representation: # not applicable for private collections
                self.reduced_representation.delete()

                # If more than one metric is added to NeuroVault, this must also filter based on metric
                comparisons = Comparison.objects.filter(Q(image1=self) | Q(image2=self))
                if comparisons:
                    comparisons.delete()
        super(BaseStatisticMap, self).save()

        # Calculate comparisons
        if do_update or new_image:
            run_voxelwise_pearson_similarity.apply_async([self.pk])

        self.file.close()
Exemple #6
0
 def save(self):
     if self.DOI is not None and self.DOI.strip() == "":
         self.DOI = None
     if self.private_token is not None and self.private_token.strip() == "":
         self.private_token = None
     
     # run calculations when collection turns public
     privacy_changed = False
     if self.pk is not None:
         old_object = Collection.objects.get(pk=self.pk)
         old_is_private = old_object.private    
         privacy_changed = old_is_private != self.private        
             
     super(Collection, self).save()
     
     if privacy_changed and self.private == False:
         for image in self.image_set.all():
             if image.pk:
                 generate_glassbrain_image.apply_async([image.pk])
                 run_voxelwise_pearson_similarity.apply_async([image.pk])
django.setup()

from neurovault.apps.statmaps.models import Similarity, Comparison, Image, Collection
from neurovault.apps.statmaps.tasks import run_voxelwise_pearson_similarity

# Images should have the "transform" field after applying migrations (I think)

# First create/update the image similarity metric
pearson_metric = 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")

# Delete all old comparisons
all_comparisons = Comparison.objects.all().delete()

# Delete all reduced representations
for img in Image.objects.all():
    img.reduced_representation.delete()

# Filter down to images that are not private, not thresholded
# Now, we need to generate a "comparison" object for all files in the database
# We will use a celery task (as this will be integrated into upload workflow)
for collection in Collection.objects.filter(DOI__isnull=False):
    for image in collection.basecollectionitem_set.instance_of(Image).all():
        print "Calculating pearson similarity for images %s" % image
        run_voxelwise_pearson_similarity.apply_async([image.pk])
import os

os.environ.setdefault("DJANGO_SETTINGS_MODULE", "neurovault.settings")
django.setup()

from neurovault.apps.statmaps.models import Similarity, Comparison, Image, Collection
from neurovault.apps.statmaps.tasks import run_voxelwise_pearson_similarity

# Images should have the "transform" field after applying migrations (I think)

# First create/update the image similarity metric
pearson_metric = 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")

# Delete all old comparisons
all_comparisons = Comparison.objects.all().delete()

# Delete all reduced representations
for img in Image.objects.all():
    img.reduced_representation.delete()

# Filter down to images that are not private, not thresholded
# Now, we need to generate a "comparison" object for all files in the database
# We will use a celery task (as this will be integrated into upload workflow)
for collection in Collection.objects.filter(DOI__isnull=False):
    for image in collection.basecollectionitem_set.instance_of(Image).all():
      print "Calculating pearson similarity for images %s" %image
      run_voxelwise_pearson_similarity.apply_async([image.pk])