# -*- coding: utf-8 -*- # ----------------------------------------------------------------------------- # Copyright (c) 2009- Spyder Kernels Contributors # # Licensed under the terms of the MIT License # (see spyder_kernels/__init__.py for details) # ----------------------------------------------------------------------------- """ Input/Output Utilities Note: 'load' functions has to return a dictionary from which a globals() namespace may be updated """ from __future__ import print_function # Standard library imports import sys import os import os.path as osp import tarfile import tempfile import shutil import types import warnings import json import inspect import dis import copy import glob # Local imports from spyder_kernels.py3compat import getcwd, pickle, PY2, to_text_string from spyder_kernels.utils.lazymodules import ( FakeObject, numpy as np, pandas as pd, PIL, scipy as sp) class MatlabStruct(dict): """ Matlab style struct, enhanced. Supports dictionary and attribute style access. Can be pickled, and supports code completion in a REPL. Examples ======== >>> from spyder.utils.iofuncs import MatlabStruct >>> a = MatlabStruct() >>> a.b = 'spam' # a["b"] == 'spam' >>> a.c["d"] = 'eggs' # a.c.d == 'eggs' >>> print(a) {'c': {'d': 'eggs'}, 'b': 'spam'} """ def __getattr__(self, attr): """Access the dictionary keys for unknown attributes.""" try: return self[attr] except KeyError: msg = "'MatlabStruct' object has no attribute %s" % attr raise AttributeError(msg) def __getitem__(self, attr): """ Get a dict value; create a MatlabStruct if requesting a submember. Do not create a key if the attribute starts with an underscore. """ if attr in self.keys() or attr.startswith('_'): return dict.__getitem__(self, attr) frame = inspect.currentframe() # step into the function that called us if frame.f_back.f_back and self._is_allowed(frame.f_back.f_back): dict.__setitem__(self, attr, MatlabStruct()) elif self._is_allowed(frame.f_back): dict.__setitem__(self, attr, MatlabStruct()) return dict.__getitem__(self, attr) def _is_allowed(self, frame): """Check for allowed op code in the calling frame""" allowed = [dis.opmap['STORE_ATTR'], dis.opmap['LOAD_CONST'], dis.opmap.get('STOP_CODE', 0)] bytecode = frame.f_code.co_code instruction = bytecode[frame.f_lasti + 3] instruction = ord(instruction) if PY2 else instruction return instruction in allowed __setattr__ = dict.__setitem__ __delattr__ = dict.__delitem__ @property def __dict__(self): """Allow for code completion in a REPL""" return self.copy() def get_matlab_value(val): """ Extract a value from a Matlab file From the oct2py project, see https://pythonhosted.org/oct2py/conversions.html """ # Extract each item of a list. if isinstance(val, list): return [get_matlab_value(v) for v in val] # Ignore leaf objects. if not isinstance(val, np.ndarray): return val # Convert user defined classes. if hasattr(val, 'classname'): out = dict() for name in val.dtype.names: out[name] = get_matlab_value(val[name].squeeze().tolist()) cls = type(val.classname, (object,), out) return cls() # Extract struct data. elif val.dtype.names: out = MatlabStruct() for name in val.dtype.names: out[name] = get_matlab_value(val[name].squeeze().tolist()) val = out # Extract cells. elif val.dtype.kind == 'O': val = val.squeeze().tolist() if not isinstance(val, list): val = [val] val = get_matlab_value(val) # Compress singleton values. elif val.size == 1: val = val.item() # Compress empty values. elif val.size == 0: if val.dtype.kind in 'US': val = '' else: val = [] return val def load_matlab(filename): if sp.io is FakeObject: return None, '' try: out = sp.io.loadmat(filename, struct_as_record=True) data = dict() for (key, value) in out.items(): data[key] = get_matlab_value(value) return data, None except Exception as error: return None, str(error) def save_matlab(data, filename): if sp.io is FakeObject: return try: sp.io.savemat(filename, data, oned_as='row') except Exception as error: return str(error) def load_array(filename): if np.load is FakeObject: return None, '' try: name = osp.splitext(osp.basename(filename))[0] data = np.load(filename) if isinstance(data, np.lib.npyio.NpzFile): return dict(data), None elif hasattr(data, 'keys'): return data, None else: return {name: data}, None except Exception as error: return None, str(error) def __save_array(data, basename, index): """Save numpy array""" fname = basename + '_%04d.npy' % index np.save(fname, data) return fname if sys.byteorder == 'little': _ENDIAN = '<' else: _ENDIAN = '>' DTYPES = { "1": ('|b1', None), "L": ('|u1', None), "I": ('%si4' % _ENDIAN, None), "F": ('%sf4' % _ENDIAN, None), "I;16": ('|u2', None), "I;16S": ('%si2' % _ENDIAN, None), "P": ('|u1', None), "RGB": ('|u1', 3), "RGBX": ('|u1', 4), "RGBA": ('|u1', 4), "CMYK": ('|u1', 4), "YCbCr": ('|u1', 4), } def __image_to_array(filename): img = PIL.Image.open(filename) try: dtype, extra = DTYPES[img.mode] except KeyError: raise RuntimeError("%s mode is not supported" % img.mode) shape = (img.size[1], img.size[0]) if extra is not None: shape += (extra,) return np.array(img.getdata(), dtype=np.dtype(dtype)).reshape(shape) def load_image(filename): if PIL.Image is FakeObject or np.array is FakeObject: return None, '' try: name = osp.splitext(osp.basename(filename))[0] return {name: __image_to_array(filename)}, None except Exception as error: return None, str(error) def load_pickle(filename): """Load a pickle file as a dictionary""" try: if pd.read_pickle is not FakeObject: return pd.read_pickle(filename), None else: with open(filename, 'rb') as fid: data = pickle.load(fid) return data, None except Exception as err: return None, str(err) def load_json(filename): """Load a json file as a dictionary""" try: if PY2: args = 'rb' else: args = 'r' with open(filename, args) as fid: data = json.load(fid) return data, None except Exception as err: return None, str(err) def save_dictionary(data, filename): """Save dictionary in a single file .spydata file""" filename = osp.abspath(filename) old_cwd = getcwd() os.chdir(osp.dirname(filename)) error_message = None skipped_keys = [] data_copy = {} try: # Copy dictionary before modifying it to fix #6689 for obj_name, obj_value in data.items(): # Skip modules, since they can't be pickled, users virtually never # would want them to be and so they don't show up in the skip list. # Skip callables, since they are only pickled by reference and thus # must already be present in the user's environment anyway. if not (callable(obj_value) or isinstance(obj_value, types.ModuleType)): # If an object cannot be deepcopied, then it cannot be pickled. # Ergo, we skip it and list it later. try: data_copy[obj_name] = copy.deepcopy(obj_value) except Exception: skipped_keys.append(obj_name) data = data_copy if not data: raise RuntimeError('No supported objects to save') saved_arrays = {} if np.ndarray is not FakeObject: # Saving numpy arrays with np.save arr_fname = osp.splitext(filename)[0] for name in list(data.keys()): try: if (isinstance(data[name], np.ndarray) and data[name].size > 0): # Save arrays at data root fname = __save_array(data[name], arr_fname, len(saved_arrays)) saved_arrays[(name, None)] = osp.basename(fname) data.pop(name) elif isinstance(data[name], (list, dict)): # Save arrays nested in lists or dictionaries if isinstance(data[name], list): iterator = enumerate(data[name]) else: iterator = iter(list(data[name].items())) to_remove = [] for index, value in iterator: if (isinstance(value, np.ndarray) and value.size > 0): fname = __save_array(value, arr_fname, len(saved_arrays)) saved_arrays[(name, index)] = ( osp.basename(fname)) to_remove.append(index) for index in sorted(to_remove, reverse=True): data[name].pop(index) except (RuntimeError, pickle.PicklingError, TypeError, AttributeError, IndexError): # If an array can't be saved with numpy for some reason, # leave the object intact and try to save it normally. pass if saved_arrays: data['__saved_arrays__'] = saved_arrays pickle_filename = osp.splitext(filename)[0] + '.pickle' # Attempt to pickle everything. # If pickling fails, iterate through to eliminate problem objs & retry. with open(pickle_filename, 'w+b') as fdesc: try: pickle.dump(data, fdesc, protocol=2) except (pickle.PicklingError, AttributeError, TypeError, ImportError, IndexError, RuntimeError): data_filtered = {} for obj_name, obj_value in data.items(): try: pickle.dumps(obj_value, protocol=2) except Exception: skipped_keys.append(obj_name) else: data_filtered[obj_name] = obj_value if not data_filtered: raise RuntimeError('No supported objects to save') pickle.dump(data_filtered, fdesc, protocol=2) # Use PAX (POSIX.1-2001) format instead of default GNU. # This improves interoperability and UTF-8/long variable name support. with tarfile.open(filename, "w", format=tarfile.PAX_FORMAT) as tar: for fname in ([pickle_filename] + [fn for fn in list(saved_arrays.values())]): tar.add(osp.basename(fname)) os.remove(fname) except (RuntimeError, pickle.PicklingError, TypeError) as error: error_message = to_text_string(error) else: if skipped_keys: skipped_keys.sort() error_message = ('Some objects could not be saved: ' + ', '.join(skipped_keys)) finally: os.chdir(old_cwd) return error_message def load_dictionary(filename): """Load dictionary from .spydata file""" filename = osp.abspath(filename) old_cwd = getcwd() tmp_folder = tempfile.mkdtemp() os.chdir(tmp_folder) data = None error_message = None try: with tarfile.open(filename, "r") as tar: tar.extractall() pickle_filename = glob.glob('*.pickle')[0] # 'New' format (Spyder >=2.2 for Python 2 and Python 3) with open(pickle_filename, 'rb') as fdesc: data = pickle.loads(fdesc.read()) saved_arrays = {} if np.load is not FakeObject: # Loading numpy arrays saved with np.save try: saved_arrays = data.pop('__saved_arrays__') for (name, index), fname in list(saved_arrays.items()): arr = np.load(osp.join(tmp_folder, fname)) if index is None: data[name] = arr elif isinstance(data[name], dict): data[name][index] = arr else: data[name].insert(index, arr) except KeyError: pass # Except AttributeError from e.g. trying to load function no longer present except (AttributeError, EOFError, ValueError) as error: error_message = to_text_string(error) # To ensure working dir gets changed back and temp dir wiped no matter what finally: os.chdir(old_cwd) try: shutil.rmtree(tmp_folder) except OSError as error: error_message = to_text_string(error) return data, error_message class IOFunctions(object): def __init__(self): self.load_extensions = None self.save_extensions = None self.load_filters = None self.save_filters = None self.load_funcs = None self.save_funcs = None def setup(self): iofuncs = self.get_internal_funcs()+self.get_3rd_party_funcs() load_extensions = {} save_extensions = {} load_funcs = {} save_funcs = {} load_filters = [] save_filters = [] load_ext = [] for ext, name, loadfunc, savefunc in iofuncs: filter_str = to_text_string(name + " (*%s)" % ext) if loadfunc is not None: load_filters.append(filter_str) load_extensions[filter_str] = ext load_funcs[ext] = loadfunc load_ext.append(ext) if savefunc is not None: save_extensions[filter_str] = ext save_filters.append(filter_str) save_funcs[ext] = savefunc load_filters.insert(0, to_text_string("Supported files"+" (*"+\ " *".join(load_ext)+")")) load_filters.append(to_text_string("All files (*.*)")) self.load_filters = "\n".join(load_filters) self.save_filters = "\n".join(save_filters) self.load_funcs = load_funcs self.save_funcs = save_funcs self.load_extensions = load_extensions self.save_extensions = save_extensions def get_internal_funcs(self): return [ ('.spydata', "Spyder data files", load_dictionary, save_dictionary), ('.npy', "NumPy arrays", load_array, None), ('.npz', "NumPy zip arrays", load_array, None), ('.mat', "Matlab files", load_matlab, save_matlab), ('.csv', "CSV text files", 'import_wizard', None), ('.txt', "Text files", 'import_wizard', None), ('.jpg', "JPEG images", load_image, None), ('.png', "PNG images", load_image, None), ('.gif', "GIF images", load_image, None), ('.tif', "TIFF images", load_image, None), ('.pkl', "Pickle files", load_pickle, None), ('.pickle', "Pickle files", load_pickle, None), ('.json', "JSON files", load_json, None), ] def get_3rd_party_funcs(self): other_funcs = [] try: from spyder.otherplugins import get_spyderplugins_mods for mod in get_spyderplugins_mods(io=True): try: other_funcs.append((mod.FORMAT_EXT, mod.FORMAT_NAME, mod.FORMAT_LOAD, mod.FORMAT_SAVE)) except AttributeError as error: print("%s: %s" % (mod, str(error)), file=sys.stderr) except ImportError: pass return other_funcs def save(self, data, filename): ext = osp.splitext(filename)[1].lower() if ext in self.save_funcs: return self.save_funcs[ext](data, filename) else: return "Unsupported file type '%s'" % ext def load(self, filename): ext = osp.splitext(filename)[1].lower() if ext in self.load_funcs: return self.load_funcs[ext](filename) else: return None, "Unsupported file type '%s'" % ext iofunctions = IOFunctions() iofunctions.setup() def save_auto(data, filename): """Save data into filename, depending on file extension""" pass if __name__ == "__main__": import datetime testdict = {'d': 1, 'a': np.random.rand(10, 10), 'b': [1, 2]} testdate = datetime.date(1945, 5, 8) example = {'str': 'kjkj kj k j j kj k jkj', 'unicode': u'éù', 'list': [1, 3, [4, 5, 6], 'kjkj', None], 'tuple': ([1, testdate, testdict], 'kjkj', None), 'dict': testdict, 'float': 1.2233, 'array': np.random.rand(4000, 400), 'empty_array': np.array([]), 'date': testdate, 'datetime': datetime.datetime(1945, 5, 8), } import time t0 = time.time() save_dictionary(example, "test.spydata") print(" Data saved in %.3f seconds" % (time.time()-t0)) # spyder: test-skip t0 = time.time() example2, ok = load_dictionary("test.spydata") os.remove("test.spydata") print("Data loaded in %.3f seconds" % (time.time()-t0)) # spyder: test-skip