from .jsonutil import JsonTable class ArrayData(object): def __init__(self, interface): self._intf = interface def _get_array(self, query_string, project_id=None, subject_id=None, subject_label=None, experiment_id=None, experiment_label=None, experiment_type='xnat:subjectAssessorData', columns=None, constraints=None ): if constraints is None: constraints = {} uri = '%s/experiments?xsiType=%s' % (self._intf._get_entry_point(), experiment_type) if project_id is not None: uri += '&project=%s' % project_id if subject_id is not None: uri += '&%s/subject_id=%s' % (experiment_type, subject_id) # Subject Label is only held in the xnat:subjectData so look for it # there. This should join against whatever the experiment type is. if subject_label is not None: uri += '&xnat:subjectData/label=%s' % (subject_label) if experiment_id is not None: uri += '&ID=%s' % experiment_id if experiment_label is not None: uri += '&label=%s' % experiment_label uri += query_string if constraints != {}: uri += ',' + ','.join(constraints.keys()) if columns is not None: uri += ',' + ','.join(columns) c = {} [c.setdefault(key.lower(), value) for key, value in constraints.items() ] return JsonTable(self._intf._get_json(uri)).where(**c) def experiments(self, project_id=None, subject_id=None, subject_label=None, experiment_id=None, experiment_label=None, experiment_type='xnat:subjectAssessorData', columns=None, constraints=None): """ Returns a list of all visible experiment IDs of the specified type, filtered by optional constraints. Parameters ---------- project_id: string Name pattern to filter by project ID. subject_id: string Name pattern to filter by subject ID. subject_label: string Name pattern to filter by subject ID. experiment_id: string Name pattern to filter by experiment ID. experiment_label: string Name pattern to filter by experiment ID. experiment_type: string xsi path type; e.g. 'xnat:mrSessionData' columns: list Values to return. constraints: dict Dictionary of xsi_type (key--) and parameter (--value) pairs by which to filter. """ query_string = '&columns=ID,project,%s/subject_id' % experiment_type return self._get_array(query_string, project_id, subject_id, subject_label, experiment_id, experiment_label, experiment_type, columns, constraints ) def mrsessions(self, project_id=None, subject_id=None, subject_label=None, experiment_id=None, experiment_label=None, columns=None, constraints=None): """ Returns a list of all MR sessions, filtered by optional constraints. Parameters ---------- project_id: string Name pattern to filter by project ID. subject_id: string Name pattern to filter by subject ID. subject_label: string Name pattern to filter by subject ID. experiment_id: string Name pattern to filter by experiment ID. experiment_label: string Name pattern to filter by experiment ID. columns: list Values to return. constraints: dict Dictionary of xsi_type (key--) and parameter (--value) pairs by which to filter. """ return self.experiments(project_id, subject_id, subject_label, experiment_id, experiment_label, 'xnat:mrSessionData', columns, constraints ) def scans(self, project_id=None, subject_id=None, subject_label=None, experiment_id=None, experiment_label=None, experiment_type='xnat:imageSessionData', scan_type='xnat:imageScanData', columns=None, constraints=None ): """ Returns a list of all visible scan IDs of the specified type, filtered by optional constraints. Parameters ---------- project_id: string Name pattern to filter by project ID. subject_id: string Name pattern to filter by subject ID. subject_label: string Name pattern to filter by subject ID. experiment_id: string Name pattern to filter by experiment ID. experiment_label: string Name pattern to filter by experiment ID. experiment_type: string xsi path type; e.g. 'xnat:mrSessionData' scan_type: string xsi path type; e.g. 'xnat:mrScanData', etc. columns: list Values to return. constraints: dict Dictionary of xsi_type (key--) and parameter (--value) pairs by which to filter. """ query_string = '&columns=ID,project,%s/subject_id,%s/ID' % ( experiment_type, scan_type) array = self._get_array(query_string, project_id, subject_id, subject_label, experiment_id, experiment_label, experiment_type, columns, constraints) id_key = ('%s/ID' % scan_type).lower() return JsonTable([i for i in array if i[id_key]]) def mrscans(self, project_id=None, subject_id=None, subject_label=None, experiment_id=None, experiment_label=None, columns=None, constraints=None): """ Returns a list of all MR scans, filtered by optional constraints. Parameters ---------- project_id: string Name pattern to filter by project ID. subject_id: string Name pattern to filter by subject ID. subject_label: string Name pattern to filter by subject ID. experiment_id: string Name pattern to filter by experiment ID. experiment_label: string Name pattern to filter by experiment ID. columns: list Values to return. constraints: dict Dictionary of xsi_type (key--) and parameter (--value) pairs by which to filter. """ return self.scans(project_id, subject_id, subject_label, experiment_id, experiment_label, 'xnat:mrSessionData', 'xnat:mrScanData', columns, constraints ) def search_experiments(self, project_id=None, subject_id=None, subject_label=None, experiment_type='xnat:subjectAssessorData', columns=None, constraints=None ): """ Returns a list of all visible experiment IDs of the specified type, filtered by optional constraints. This function is a shortcut using the search engine. Parameters ---------- project_id: string Name pattern to filter by project ID. subject_id: string Name pattern to filter by subject ID. subject_label: string Name pattern to filter by subject ID. experiment_type: string xsi path type must be a leaf session type. defaults to 'xnat:mrSessionData' columns: List[string] list of xsi paths for names of columns to return. constraints: list[(tupple)] List of tupples for comparison in the form (key, comparison, value) valid comparisons are: =, <, <=,>,>=, LIKE """ if columns is None: columns = [] where_clause = [] if project_id is not None: item = ('%s/project' % experiment_type, "=", project_id) where_clause.append(item) if subject_id is not None: where_clause.append(('xnat:subjectData/ID', "=", subject_id)) if subject_label is not None: where_clause.append(('xnat:subjectData/LABEL', "=", subject_label)) if constraints is not None: where_clause.extend(constraints) if where_clause != []: where_clause.append('AND') if where_clause != []: sel = self._intf.select(experiment_type, columns=columns) table = sel.where(where_clause) return table else: table = self._intf.select(experiment_type, columns=columns) return table.all()