Source code for deepfinder.convert

import xml.etree.ElementTree as ET
from xml.dom import minidom

[docs]def objl_read(filename): tree = ET.parse(filename) objl_xml = tree.getroot() objl = [] for p in range(len(objl_xml)): # Mandatory attributes: lbl = int(objl_xml[p].get('class_label')) x = float(objl_xml[p].get('x')) y = float(objl_xml[p].get('y')) z = float(objl_xml[p].get('z')) # Optional attributes: tidx = objl_xml[p].get('tomo_idx') objid = objl_xml[p].get('obj_id') psi = objl_xml[p].get('psi') phi = objl_xml[p].get('phi') the = objl_xml[p].get('the') csize = objl_xml[p].get('cluster_size') # if optional attributes exist, then cast to correct type: if tidx != None: tidx = int(tidx) if objid != None: objid = int(objid) if csize != None: csize = int(csize) if psi != None or phi != None or the != None: psi = float(psi) phi = float(phi) the = float(the) obj = { 'tomo_idx': tidx, 'obj_id': objid, 'label': lbl, 'x': x, 'y': y, 'z': z, 'psi': phi, 'phi': psi, 'the': the, 'cluster_size': csize } objl.append(obj) return objl
[docs]def objl_write(objl, filename): objl_xml = ET.Element('objlist') for idx in range(len(objl)): tidx = objl[idx]['tomo_idx'] objid = objl[idx]['obj_id'] lbl = objl[idx]['label'] x = objl[idx]['x'] y = objl[idx]['y'] z = objl[idx]['z'] psi = objl[idx]['psi'] phi = objl[idx]['phi'] the = objl[idx]['the'] csize = objl[idx]['cluster_size'] obj = ET.SubElement(objl_xml, 'object') if tidx!=None: obj.set('tomo_idx', str(tidx)) if objid!=None: obj.set('obj_id', str(objid)) obj.set('class_label' , str(lbl)) obj.set('x' , '%.3f' % x) obj.set('y' , '%.3f' % y) obj.set('z' , '%.3f' % z) if psi!=None: obj.set('psi', '%.3f' % psi) if phi!=None: obj.set('phi', '%.3f' % phi) if the!=None: obj.set('the', '%.3f' % the) if csize!=None: obj.set('cluster_size', str(csize)) tree = ET.ElementTree(objl_xml) tree.write(filename)
[docs]def objl_add(objl, label, coord, obj_id=None, tomo_idx=None, orient=(None, None, None), cluster_size=None): obj = { 'tomo_idx': tomo_idx, 'obj_id': obj_id, 'label': label, 'x': coord[2], 'y': coord[1], 'z': coord[0], 'psi': orient[0], 'phi': orient[1], 'the': orient[2], 'cluster_size': cluster_size } objl.append(obj) return objl
[docs]def objl_get_labels(objl): """ Returns a list with different (unique) labels contained in input objl """ class_list = [] for idx in range(len(objl)): class_list.append(objl[idx]['label']) # Set only stores a value once even if it is inserted more then once: lbl_set = set(class_list) # insert the list to the set lbl_list = (list(lbl_set)) # convert the set to the list return lbl_list
[docs]def objl_get_class(objl, label): """ Get all objects of specified class. Args: objl (list of dict) label (int) Returns: list of dict: contains only objects from class 'label' """ idx_class = [] for idx in range(len(objl)): if str(objl[idx]['label'])==str(label): idx_class.append(idx) objlOUT = [] for idx in range(len(idx_class)): objlOUT.append(objl[idx_class[idx]]) return objlOUT
[docs]def objl_get_tomo(objl, tomo_idx): """ Get all objects originating from tomo 'tomo_idx'. Args: objl (list of dict): contains objects from various tomograms tomo_idx (int): tomogram index Returns: list of dict: contains objects from tomogram 'tomo_idx' """ idx_tomo = [] for idx in range(len(objl)): if objl[idx]['tomo_idx'] == tomo_idx: idx_tomo.append(idx) objlOUT = [] for idx in range(len(idx_tomo)): objlOUT.append(objl[idx_tomo[idx]]) return objlOUT
[docs]class ParamsGenTarget(): def __init__(self): self.path_objl = str() self.path_initial_vol = str() self.tomo_size = (int(), int(), int()) # (dimZ,dimY,dimX) self.strategy = str() self.radius_list = [int()] self.path_mask_list = [str()] self.path_target = str()
[docs] def write(self, filename): root = ET.Element('paramsGenerateTarget') p = ET.SubElement(root, 'path_objl') p.set('path', str(self.path_objl)) p = ET.SubElement(root, 'path_initial_vol') p.set('path', str(self.path_initial_vol)) p = ET.SubElement(root, 'tomo_size') pp = ET.SubElement(p, 'X') pp.set('size', str(self.tomo_size[2])) pp = ET.SubElement(p, 'Y') pp.set('size', str(self.tomo_size[1])) pp = ET.SubElement(p, 'Z') pp.set('size', str(self.tomo_size[0])) p = ET.SubElement(root, 'strategy') p.set('strategy', str(self.strategy)) p = ET.SubElement(root, 'radius_list') for idx in range(len(self.radius_list)): pp = ET.SubElement(p, 'class' + str(idx + 1)) pp.set('radius', str(self.radius_list[idx])) p = ET.SubElement(root, 'path_mask_list') for idx in range(len(self.path_mask_list)): pp = ET.SubElement(p, 'class'+str(idx + 1)) pp.set('path', str(self.path_mask_list[idx])) p = ET.SubElement(root, 'path_target') p.set('path', str(self.path_target)) tree = ET.ElementTree(root) tree.write(filename)
[docs]class ParamsTrain(): def __init__(self): self.path_out = str() self.path_tomo = [str()] self.path_target = [str()] self.path_objl_train = str() self.path_objl_valid = str() self.Ncl = int() self.psize = int() self.bsize = int() self.nepochs = int() self.steps_per_e = int() self.steps_per_v = int() self.flag_direct_read = bool() self.flag_bootstrap = bool() self.rnd_shift = int()
[docs] def write(self, filename): root = ET.Element('paramsTrain') p = ET.SubElement(root, 'path_out') p.set('path', str(self.path_out)) p = ET.SubElement(root, 'path_tomo') for idx in range(len(self.path_tomo)): pp = ET.SubElement(p, 'tomo' + str(idx)) pp.set('path', str(self.path_tomo[idx])) p = ET.SubElement(root, 'path_target') for idx in range(len(self.path_target)): pp = ET.SubElement(p, 'target' + str(idx)) pp.set('path', str(self.path_target[idx])) p = ET.SubElement(root, 'path_objl_train') p.set('path', str(self.path_objl_train)) p = ET.SubElement(root, 'path_objl_valid') p.set('path', str(self.path_objl_valid)) p = ET.SubElement(root, 'number_of_classes') p.set('n', str(self.Ncl)) p = ET.SubElement(root, 'patch_size') p.set('n', str(self.psize)) p = ET.SubElement(root, 'batch_size') p.set('n', str(self.bsize)) p = ET.SubElement(root, 'number_of_epochs') p.set('n', str(self.nepochs)) p = ET.SubElement(root, 'steps_per_epoch') p.set('n', str(self.steps_per_e)) p = ET.SubElement(root, 'steps_per_validation') p.set('n', str(self.steps_per_v)) p = ET.SubElement(root, 'flag_direct_read') p.set('flag', str(self.flag_direct_read)) p = ET.SubElement(root, 'flag_bootstrap') p.set('flag', str(self.flag_bootstrap)) p = ET.SubElement(root, 'random_shift') p.set('shift', str(self.rnd_shift)) tree = ET.ElementTree(root) tree.write(filename)