File: property.py

package info (click to toggle)
python-nixio 1.5.4%2Bdfsg-3
  • links: PTS, VCS
  • area: main
  • in suites: sid, trixie
  • size: 2,888 kB
  • sloc: python: 12,527; cpp: 832; makefile: 25
file content (385 lines) | stat: -rw-r--r-- 12,192 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
# -*- coding: utf-8 -*-
# Copyright © 2014, German Neuroinformatics Node (G-Node)
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted under the terms of the BSD License. See
# LICENSE file in the root of the Project.

try:
    from collections.abc import Sequence, Iterable
except ImportError:
    from collections import Sequence, Iterable
from enum import Enum
from numbers import Number
import numpy as np

from .datatype import DataType
from .entity import Entity
from . import util

def ensure_str(s):
    if isinstance(s, bytes):
        return s.decode()
    else:
        return s


class OdmlType(Enum):
    """
    OdmlType provides all types currently supported by the odML
    data format. It provides additional information about the
    nature of the values of an odML Property.
    """
    Boolean = 'boolean'
    Int = 'int'
    Float = 'float'
    String = 'string'
    Text = 'text'
    URL = 'url'
    Person = 'person'
    Datetime = 'datetime'
    Date = 'date'
    Time = 'time'

    def __str__(self):
        return self.value

    def compatible(self, value):
        """
        compatible returns True or False depending on whether a
        passed value can be mapped to an OdmlType or not.

        :param value: Any single value
        :return: Boolean
        """
        if (self in (self.String, self.Text, self.URL, self.Person) and
                DataType.get_dtype(value) == DataType.String):
            return True
        elif (self == self.Boolean and
              DataType.get_dtype(value) == DataType.Bool):
            return True
        elif (self == self.Float and
              DataType.get_dtype(value) == DataType.Double):
            return True
        elif self == self.Int and DataType.get_dtype(value) == DataType.Int64:
            return True
        elif (self in (self.Time, self.Date, self.Datetime) and
              DataType.get_dtype(value) == DataType.String):
            # This might need some extra work, treating as String for now, but
            # keeping it separated from other String values.
            return True

        return False

    @classmethod
    def get_odml_type(cls, dtype):
        """
        get_odml_type returns the appropriate OdmlType
        for a handed in nix value DataType.

        :param dtype: nix DataType
        :return: OdmlType
        """
        if dtype in DataType.FloatTypes:
            return cls.Float
        elif dtype in DataType.IntTypes:
            return cls.Int
        elif dtype == DataType.String:
            return cls.String
        elif dtype == DataType.Bool:
            return cls.Boolean

        raise TypeError("No available OdmlType for type '%s'" % dtype)


class Property(Entity):
    """An odML Property"""
    def __init__(self, nixfile, nixparent, h5dataset):
        super(Property, self).__init__(nixfile, nixparent, h5dataset)
        self._h5dataset = self._h5group

    @classmethod
    def create_new(cls, nixfile, nixparent, h5parent, name,
                   dtype, shape=None, oid=None):
        if shape is None or shape[0] == 0:
            shape = (8, )
        util.check_entity_name(name)
        dtype = cls._make_h5_dtype(dtype)

        h5dataset = h5parent.create_dataset(name, shape=shape, dtype=dtype)
        h5dataset.set_attr("name", name)

        if not util.is_uuid(oid):
            oid = util.create_id()

        h5dataset.set_attr("entity_id", oid)

        newentity = cls(nixfile, nixparent, h5dataset)
        newentity.force_created_at()
        newentity.force_updated_at()

        return newentity

    @property
    def name(self):
        return self._h5dataset.get_attr("name")

    @property
    def definition(self):
        return self._h5dataset.get_attr("definition")

    @definition.setter
    def definition(self, d):
        util.check_attr_type(d, str)
        self._h5dataset.set_attr("definition", d)

    @property
    def unit(self):
        return self._h5dataset.get_attr("unit")

    @unit.setter
    def unit(self, new):
        if new:
            new = util.units.sanitizer(new)

        if new == "":
            new = None

        util.check_attr_type(new, str)
        self._h5dataset.set_attr("unit", new)

    @property
    def uncertainty(self):
        dataset = self._h5dataset
        filever = tuple(dataset._parent.file.attrs["version"])
        if filever < (1, 1, 1):
            val = self._h5dataset.dataset[:]
            uncertainty = val[0]["uncertainty"]
            return uncertainty
        return self._h5dataset.get_attr("uncertainty")

    @uncertainty.setter
    def uncertainty(self, uncertainty):
        util.check_attr_type(uncertainty, Number)
        uncertainty = float(uncertainty) if uncertainty is not None else None
        self._h5dataset.set_attr("uncertainty", uncertainty)

    @property
    def reference(self):
        dataset = self._h5dataset
        filever = tuple(dataset._parent.file.attrs["version"])
        if filever < (1, 1, 1):
            val = self._h5dataset.dataset[:]
            reference = val[0]["reference"]
            return reference
        return self._h5dataset.get_attr("reference")

    @reference.setter
    def reference(self, ref):
        util.check_attr_type(ref, str)
        self._h5dataset.set_attr("reference", ref)

    @property
    def dependency(self):
        return self._h5dataset.get_attr("dependency")

    @dependency.setter
    def dependency(self, dep):
        util.check_attr_type(dep, str)
        self._h5dataset.set_attr("dependency", dep)

    @property
    def dependency_value(self):
        return self._h5dataset.get_attr("dependency_value")

    @dependency_value.setter
    def dependency_value(self, depval):
        util.check_attr_type(depval, str)
        self._h5dataset.set_attr("dependency_value", depval)

    @property
    def value_origin(self):
        return self._h5dataset.get_attr("value_origin")

    @value_origin.setter
    def value_origin(self, origin):
        util.check_attr_type(origin, str)
        self._h5dataset.set_attr("value_origin", origin)

    @property
    def odml_type(self):
        otype = self._h5dataset.get_attr("odml_type")
        if not otype:
            return None

        return OdmlType(otype)

    @odml_type.setter
    def odml_type(self, new_type):
        """
        odml_type can only be set if the handed in new type is a valid
        OdmlType and if it is compatible with the value data type of
        the property.

        :param new_type: OdmlType
        """
        if not isinstance(new_type, OdmlType):
            raise TypeError("'{}' is not a valid odml_type.".format(new_type))

        if not new_type.compatible(self.values[0]):
            raise TypeError("Type '{}' is incompatible "
                            "with property values".format(new_type))

        self._h5dataset.set_attr("odml_type", str(new_type))

    def _read_old_values(self):
        val = self._h5dataset.dataset[:]
        if len(val) > 0 and isinstance(val[0]["value"], bytes):
            return tuple(ensure_str(v["value"]) for v in val)
        return tuple(v["value"] for v in val)

    @property
    def values(self):
        dataset = self._h5dataset
        filever = tuple(dataset._parent.file.attrs["version"])
        if filever < (1, 1, 1):
            values = self._read_old_values()
            return values
        if not sum(dataset.shape):
            return tuple()

        data = dataset.read_data()

        def data_to_value(dat):
            if isinstance(dat, bytes):
                dat = dat.decode()
            return dat

        values = tuple(map(data_to_value, data))

        return values

    @values.setter
    def values(self, vals):
        """
        Set the value of the property discarding any previous information.

        :param vals: a single value or list of values.
        """
        # Make sure boolean value 'False' gets through as well...
        if vals is None or (isinstance(vals, (Sequence, Iterable)) and not len(vals)):
            self.delete_values()
            return

        if not isinstance(vals, (Sequence, Iterable)) or isinstance(vals, str):
            vals = [vals]

        # Make sure all values are of the same data type
        vtype = self._check_new_value_types(vals)
        if vtype == DataType.String:
            vals = [str(v) for v in vals]
        self._h5dataset.shape = np.shape(vals)
        data = np.array(vals, dtype=vtype)
        self._h5dataset.write_data(data)

    def extend_values(self, data):
        """
        Extends values to existing data.
        Suitable when new data is nested or original data is long.
        """
        vtype = self._check_new_value_types(data)

        arr = np.array(data, dtype=vtype).flatten('C')
        dataset = self._h5dataset
        src_len = len(self.values)
        dlen = len(arr)
        dataset.shape = (src_len + dlen,)
        dataset.write_data(arr, slc=np.s_[src_len: src_len + dlen])

    def _check_new_value_types(self, data):
        if isinstance(data, (Sequence, Iterable)) and not isinstance(data, str):
            single_val = data[0]
        else:
            single_val = data
            data = [data]

        def check_prop_consistent(vtype):
            # Check if the new data has the same type as the existing property
            # data
            if vtype != self.data_type:
                raise TypeError("New data type '{}' is inconsistent with the "
                                "Property's data type '{}'".format(
                                    vtype, self.data_type))

        def check_new_data_consistent(vtype):
            # Check if each value in the new data has the same type
            for val in data:
                if DataType.get_dtype(val) != vtype:
                    raise TypeError("Array contains inconsistent values. "
                                    "Only values of type '{}' can be "
                                    "assigned".format(vtype))

        if hasattr(data, "dtype"):
            # numpy array: no need to scan values, arrays are consistent but
            # check for 1D
            vtype = data.dtype
            check_prop_consistent(vtype)
        else:
            # Will raise an error, if the data type of the first value is not
            # valid
            vtype = DataType.get_dtype(single_val)
            check_prop_consistent(vtype)
            check_new_data_consistent(vtype)

        return vtype

    @property
    def data_type(self):
        return self._h5dataset.dtype

    def delete_values(self):
        self._h5dataset.shape = (0,)

    @staticmethod
    def _make_h5_dtype(valued_type):
        str_ = util.vlen_str_dtype

        if valued_type == DataType.String:
            valued_type = str_

        return valued_type

    def __str__(self):
        return "{}: {{name = {}}}".format(
            type(self).__name__, self.name
        )

    def __repr__(self):
        return self.__str__()

    def pprint(self, indent=2, max_length=80, current_depth=-1):
        """
        Pretty print method. Method is called in Section.pprint()
        """
        property_spaces = ""
        prefix = ""
        if current_depth >= 0:
            property_spaces = " " * ((current_depth + 2) * indent)
            prefix = "|-"
        if self.unit is None:
            value_string = str(self.values)
        else:
            value_string = "{}{}".format(self.values, self.unit)
        p_len = len(property_spaces) + len(self.name) + len(value_string)
        if p_len >= max_length - 4:
            split_len = int((max_length - len(property_spaces) +
                             len(self.name) - len(prefix)) / 2)
            str1 = value_string[0: split_len]
            str2 = value_string[-split_len:]
            print(("{}{} {}: {} ... {}".format(property_spaces, prefix,
                                               self.name, str1, str2)))
        else:
            print(("{}{} {}: {}".format(property_spaces, prefix, self.name,
                                        value_string)))