def view_collection(request, cid): collection = get_collection(cid, request) edit_permission = True if owner_or_contrib(request, collection) else False delete_permission = True if collection.owner == request.user else False images = collection.image_set.all() for image in images: if hasattr(image, 'nidm_results'): image.zip_name = os.path.split( image.nidm_results.zip_file.path)[-1] context = { 'collection': collection, 'images': images, 'user': request.user, 'delete_permission': delete_permission, 'edit_permission': edit_permission, 'cid': cid } if owner_or_contrib(request, collection): form = UploadFileForm() c = RequestContext(request) c.update(context) return render_to_response('statmaps/collection_details.html.haml', {'form': form}, c) else: return render(request, 'statmaps/collection_details.html.haml', context)
def edit_images(request, collection_cid): collection = get_collection(collection_cid, request) if not owner_or_contrib(request, collection): return HttpResponseForbidden() if request.method == "POST": formset = CollectionFormSet(request.POST, request.FILES, instance=collection) for n, form in enumerate(formset): # hack: check fields to determine polymorphic type if form.instance.polymorphic_ctype is None: atlas_f = 'image_set-{0}-label_description_file'.format(n) has_atlas = [v for v in form.files if v == atlas_f] if has_atlas: use_model = Atlas use_form = AtlasForm else: use_model = StatisticMap use_form = StatisticMapForm form.instance = use_model(collection=collection) form.base_fields = use_form.base_fields form.fields = use_form.base_fields if formset.is_valid(): formset.save() return HttpResponseRedirect(collection.get_absolute_url()) else: formset = CollectionFormSet(instance=collection) blank_statmap = StatisticMapForm(instance=StatisticMap( collection=collection)) blank_atlas = AtlasForm(instance=Atlas(collection=collection)) upload_form = UploadFileForm() context = { "formset": formset, "blank_statmap": blank_statmap, "blank_atlas": blank_atlas, "upload_form": upload_form } return render(request, "statmaps/edit_images.html", context)
def upload_folder(request, collection_cid): collection = get_collection(collection_cid, request) allowed_extensions = ['.nii', '.img', '.nii.gz'] niftiFiles = [] if request.method == 'POST': print request.POST print request.FILES form = UploadFileForm(request.POST, request.FILES) if form.is_valid(): tmp_directory = tempfile.mkdtemp() print tmp_directory try: # Save archive (.zip or .tar.gz) to disk if "file" in request.FILES: archive_name = request.FILES['file'].name if fnmatch(archive_name, '*.nidm.zip'): populate_nidm_results(request, collection) return HttpResponseRedirect( collection.get_absolute_url()) _, archive_ext = os.path.splitext(archive_name) if archive_ext == '.zip': compressed = zipfile.ZipFile(request.FILES['file']) elif archive_ext == '.gz': django_file = request.FILES['file'] django_file.open() compressed = tarfile.TarFile(fileobj=gzip.GzipFile( fileobj=django_file.file, mode='r'), mode='r') else: raise Exception("Unsupported archive type %s." % archive_name) compressed.extractall(path=tmp_directory) elif "file_input[]" in request.FILES: for f, path in zip(request.FILES.getlist("file_input[]"), request.POST.getlist("paths[]")): if fnmatch(f.name, '*.nidm.zip'): request.FILES['file'] = f populate_nidm_results(request, collection) continue new_path, _ = os.path.split( os.path.join(tmp_directory, path)) mkdir_p(new_path) filename = os.path.join(new_path, f.name) tmp_file = open(filename, 'w') tmp_file.write(f.read()) tmp_file.close() else: raise Exception("Unable to find uploaded files.") atlases = {} for root, subdirs, filenames in os.walk(tmp_directory): if detect_feat_directory(root): populate_feat_directory(request, collection, root) del (subdirs) filenames = [] # .gfeat parent dir under cope*.feat should not be added as statmaps # this may be affected by future nidm-results_fsl parsing changes if root.endswith('.gfeat'): filenames = [] filenames = [f for f in filenames if not f[0] == '.'] for fname in sorted(filenames): name, ext = splitext_nii_gz(fname) nii_path = os.path.join(root, fname) if ext == '.xml': print "found xml" dom = minidom.parse(os.path.join(root, fname)) for atlas in dom.getElementsByTagName( "summaryimagefile"): print "found atlas" path, base = os.path.split( atlas.lastChild.nodeValue) nifti_name = os.path.join(path, base) atlases[str(os.path.join( root, nifti_name[1:]))] = os.path.join( root, fname) if ext in allowed_extensions: nii = nib.load(nii_path) if detect_afni4D(nii): niftiFiles.extend(split_afni4D_to_3D(nii)) else: niftiFiles.append((fname, nii_path)) for label, fpath in niftiFiles: # Read nifti file information nii = nib.load(fpath) if len(nii.get_shape()) > 3 and nii.get_shape()[3] > 1: print "skipping wrong size" continue hdr = nii.get_header() raw_hdr = hdr.structarr # SPM only !!! # Check if filename corresponds to a T-map Tregexp = re.compile('spmT.*') # Fregexp = re.compile('spmF.*') if Tregexp.search(fpath) is not None: map_type = StatisticMap.T else: # Check if filename corresponds to a F-map if Tregexp.search(fpath) is not None: map_type = StatisticMap.F else: map_type = StatisticMap.OTHER path, name, ext = split_filename(fpath) dname = name + ".nii.gz" spaced_name = name.replace('_', ' ').replace('-', ' ') if ext.lower() != ".nii.gz": new_file_tmp_dir = tempfile.mkdtemp() new_file_tmp = os.path.join(new_file_tmp_dir, name) + '.nii.gz' nib.save(nii, new_file_tmp) f = ContentFile(open(new_file_tmp).read(), name=dname) shutil.rmtree(new_file_tmp_dir) label += " (old ext: %s)" % ext else: f = ContentFile(open(fpath).read(), name=dname) collection = get_collection(collection_cid, request) if os.path.join(path, name) in atlases: new_image = Atlas(name=spaced_name, description=raw_hdr['descrip'], collection=collection) new_image.label_description_file = ContentFile( open(atlases[os.path.join(path, name)]).read(), name=name + ".xml") else: new_image = StatisticMap(name=spaced_name, description=raw_hdr['descrip'] or label, collection=collection) new_image.map_type = map_type new_image.file = f new_image.save() except: raise error = traceback.format_exc().splitlines()[-1] msg = "An error occurred with this upload: {}".format(error) messages.warning(request, msg) return HttpResponseRedirect(collection.get_absolute_url()) finally: shutil.rmtree(tmp_directory) return HttpResponseRedirect(collection.get_absolute_url()) else: form = UploadFileForm() return render_to_response("statmaps/upload_folder.html", {'form': form}, RequestContext(request))