# Serialisation

These notes are a discussion of the serialisation libraries available to
MicroPython plus a tutorial on the use of a library supporting Google Protocol
Buffers (here abbreviated to `protobuf`). The aim is not to replace official
documentation but to illustrate the relative merits and drawbacks of the
various approaches.

##### [Main readme](./README.md)

# 1. The problem

The need for serialisation arises whenever data must be stored on disk or
communicated over an interface such as a socket, a UART or such interfaces as
I2C or SPI. All these require the data to be presented as linear sequences of
bytes. The problem is how to convert an arbitrary Python object to such a
sequence, and how subsequently to restore the object.

I am aware of four ways of achieving this, each with their own advantages and
drawbacks. In two cases the encoded strings comprise ASCII characters, in the
other two they are binary (bytes can take all possible values).

 1. ujson (ASCII, official)
 2. pickle (ASCII, official)
 3. ustruct (binary, official)
 4. protobuf [binary, unofficial](https://github.com/dogtopus/minipb)

The first two are self-describing: the format includes a definition of its
structure. This means that the decoding process can re-create the object in the
absence of information on its structure, which may therefore change at runtime.
Further, `ujson` and `pickle` produce human-readable byte sequences which aid
debugging. The drawback is inefficiency: the byte sequences are relatively
long. They are variable length. This means that the receiving process must be
provided with a means to determine when a complete string has been received.

The `ustruct` and `protobuf` solutions are binary formats: the byte sequences
comprise binary data which is neither human readable nor self-describing.
Binary sequences require that the receiver has information on their structure
in order to decode them. In the case of `ustruct` sequences are of a fixed
length which can be determined from the structure. `protobuf` sequences are
variable length requiring handling discussed below.

The benefit of binary sequences is efficiency: sequence length is closer to the
information-theoretic minimum, compared to the ASCII options.

# 2. ujson and pickle

These are very similar. `ujson` is documented
[here](http://docs.micropython.org/en/latest/library/ujson.html). `pickle` has
identical methods so this doc may be used for both.

The advantage of `ujson` is that JSON strings can be accepted by CPython and by
other languages. The drawback is that only a subset of Python object types can
be converted to legal JSON strings; this is a limitation of the 
[JSON specification](http://www.ecma-international.org/publications/files/ECMA-ST/ECMA-404.pdf).

The advantage of `pickle` is that it will accept any Python object except for
instances of user defined classes. The extremely simple source may be found in
[the official library](https://github.com/micropython/micropython-lib/tree/master/pickle).
The strings produced are incompatible with CPython's `pickle`, but can be
decoded in CPython by using the MicroPython decoder. There is a
[bug](https://github.com/micropython/micropython/issues/2280) in the
MicroPython implementation when running under MicroPython. A workround consists
of never encoding short strings which change repeatedly.

## 2.1 Usage examples

These may be copy-pasted to the MicroPython REPL.  
Pickle:  
```python
import pickle
data = {1:'test', 2:1.414, 3: [11, 12, 13]}
s = pickle.dumps(data)
print('Human readable data:', s)
v = pickle.loads(s)
print('Decoded data (partial):', v[3])
```
JSON. Note that dictionary keys must be strings:  
```python
import ujson
data = {'1':'test', '2':1.414, '3': [11, 12, 13]}
s = ujson.dumps(data)
print('Human readable data:', s)
v = ujson.loads(s)
print('Decoded data (partial):', v['3'])
```

## 2.2 Strings are variable length

In real applications the data, and hence the string length, vary at runtime.
The receiving process needs to know when a complete string has been received or
read from a file. In practice `ujson` and `pickle` do not include newline
characters in encoded strings. If the data being encoded includes a newline, it
is escaped in the string:
```python
import ujson
data = {'1':b'test\nmore', '2':1.414, '3': [11, 12, 13]}
s = ujson.dumps(data)
print('Human readable data:', s)
v = ujson.loads(s)
print('Decoded data (partial):', v['1'])
```
If this is pasted at the REPL you will observe that the human readable data
does not have a line break (while the decoded data does). Output:
```
Human readable data: {"2": 1.414, "3": [11, 12, 13], "1": "test\nmore"}
Decoded data (partial): test
more
```
Consequently encoded strings may be separated with `'\n'` before saving and
reading may be done using `readline` methods as in this code fragment where
`u` is a UART instance:

```python
s = ujson.dumps(data)
# pickle produces a bytes object whereas ujson produces a string
# In the case of ujson it is probably wise to convert to bytes
u.write(s.encode())
# Pickle:
# u.write(s)
u.write(b'\n')

# receiver
s = u.readline()
v = ujson.loads(s)  # ujson can cope with bytes object
# ujson and pickle can cope with trailing newline.
```

# 3. ustruct

This is documented
[here](http://docs.micropython.org/en/latest/library/ustruct.html). The binary
format is efficient, but the format of a sequence cannot change at runtime and
must be "known" to the decoding process. Records are of fixed length. If data
is to be stored in a binary random access file, the fixed record size means
that the offset of a given record may readily be calculated.

Write a 100 record file. Each record comprises three 32-bit integers:  
```python
import ustruct
fmt = 'iii'  # Record format: 3 signed ints
rlen = ustruct.calcsize(fmt)  # Record length
buf = bytearray(rlen)
with open('myfile', 'wb') as f:
    for x in range(100):
        y = x * x
        z = x * 10
        ustruct.pack_into(fmt, buf, 0, x, y, z)
        f.write(buf)
```
Read record no. 10 from that file:  
```python
import ustruct
fmt = 'iii'
rlen = ustruct.calcsize(fmt)  # Record length
buf = bytearray(rlen)
rnum = 10  # Record no.
with open('myfile', 'rb') as f:
    f.seek(rnum * rlen)
    f.readinto(buf)
    result = ustruct.unpack_from(fmt, buf)
print(result)
```
Owing to the fixed record length, integers must be constrained to fit the
length declared in the format string.

Binary formats cannot use delimiters as any delimiter character may be present
in the data - however the fixed length of `ustruct` records means that this is
not a problem.

For performance oriented applications, `ustruct` is the only serialisation
approach which can be used in a non-allocating fashion, by using pre-allocated
buffers as in the above example.

## 3.1 Strings

In `ustruct` the `s` data type is normally prefixed by a length (defaulting to
1). This ensures that records are of fixed size, but is potentially inefficient
as shorter strings will still occupy the same amount of space. Longer strings
will silently be truncated. Short strings are packed with zeros.

```python
import ustruct
fmt = 'ii30s'
rlen = ustruct.calcsize(fmt)  # Record length
buf = bytearray(rlen)
ustruct.pack_into(fmt, buf, 0, 11, 22, 'the quick brown fox')
ustruct.unpack_from(fmt, buf)
ustruct.pack_into(fmt, buf, 0, 11, 22, 'rats')
ustruct.unpack_from(fmt, buf)  # Packed with zeros
ustruct.pack_into(fmt, buf, 0, 11, 22, 'the quick brown fox jumps over the lazy dog')
ustruct.unpack_from(fmt, buf)  # Truncation
```
Output:
```python
(11, 22, b'the quick brown fox\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00')
(11, 22, b'rats\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00')
(11, 22, b'the quick brown fox jumps over')
```

# 4. Protocol Buffers

This is a [Google standard](https://developers.google.com/protocol-buffers/)
described in [this Wikipedia article](https://en.wikipedia.org/wiki/Protocol_Buffers).
The aim is to provide a language independent, efficient, binary data interface.
Records are variable length, and strings and integers of arbitrary size may be
accommodated. The
[implementation compatible with MicroPython](https://github.com/dogtopus/minipb)
is a "micro" implementation: `.proto` files are not supported. However the data
format aims to be a subset of the Google standard and claims compatibility with
other platforms and languages.

The principal benefit to developers using only CPython/MicroPython is its
efficient support for fields whose length varies at runtime. To my knowledge it
is the sole solution for encoding such data in a compact binary format.

The following notes should be read in conjunction with the official docs. The
notes aim to reduce the learning curve which I found a little challenging.

In normal use the object transmitted by `minipb` will be a `dict` with entries
having various predefined data types. Entries may be objects of variable length
including strings, lists and other `dict` instances. The structure of the
`dict` is defined using a `schema`. Sender and receiver share the `schema` with
each script using it to instantiate the `Wire` class. The `Wire` instance is
then repeatedly invoked to encode or decode the data.

The `schema` is a `tuple` defining the structure of the data `dict`. Each
element declares a key and its data type in an inner `tuple`. Elements of this
inner `tuple` are strings, with element 0 defining the field's key. Subsequent
elements define the field's data type; in most cases the data type is defined
by a single string.

## 4.1 Installation

The library comprises a single file `minipb.py`. It has a dependency, the
`logging` module `logging.py` which may be found in
[micropython-lib](https://github.com/micropython/micropython-lib/tree/master/logging).
On RAM constrained platforms `minipb.py` may be cross-compiled or frozen as
bytecode for even lower RAM consumption.

## 4.2 Data types

These are listed in
[the docs](https://github.com/dogtopus/minipb/wiki/Schema-Representations).
Many of these are intended to maximise compatibility with the native data types
of other languages. Where data will only be accessed by CPython or MicroPython,
a subset may be used which maps onto Python data types:

 1. 'U' A UTF8 encoded string.
 2. 'a' A `bytes` object.
 3. 'b' A `bool`.
 4. 'f' A `float` A 32-bit float: the usual MicroPython default.
 5. 'z' An `int`: a signed arbitrary length integer. Efficiently encoded with
 an ingenious algorithm.
 6. 'd' A double precision 64-bit float. The default on Pyboard D SF6. Also on
 other platforms with special firmware builds.
 7. 'X' An empty field.

## 4.2.1 Required and Optional fields

If a field is prefixed with `*` it is a `required` field, otherwise it is
optional. The field must still exist in the data: the only difference is that
a `required` field cannot be set to `None`. Optional fields can be useful,
notably for boolean types which can then represent three states.

## 4.3 Application design

The following is a minimal example which can be pasted at the REPL:
```python
import minipb

schema = (('value', 'z'),)  # Dict will hold a single integer
w = minipb.Wire(schema)

data = {'value': 0}
data['value'] = 150
tx = w.encode(data)
rx = w.decode(tx)  # received data
print(rx)
```
This example glosses over the fact that in a real application the data will
change and the length of the transmitted string `tx` will vary. The receiving
process needs to know the length of each string. Note that a consequence of the
binary format is that delimiters cannot be used. The length of each record must
be established and made available to the receiver. In the case where data is
being saved to a binary file, the file will need an index. Where data is to
be transmitted over and interface each string should be prepended with a fixed
length "size" field. The following example illustrates this.

## 4.4 Transmitter/Receiver example

These examples can't be cut and pasted at the REPL as they assume `send(n)` and
`receive(n)` functions which access the interface.

Sender example:
```python
import minipb
schema = (('value', 'z'),
          ('float', 'f'),
          ('signed', 'z'),)
w = minipb.Wire(schema)
# Create a dict to hold the data
data = {'value': 0,
        'float': 0.0,
        'signed' : 0,}
while True:
    # Update values then encode and transmit them, e.g.
    # data['signed'] = get_signed_value()
    tx = w.encode(data)
    # Data lengths may change on each iteration
    # here we encode the length in a single byte
    dlen = len(tx).to_bytes(1, 'little')
    send(dlen)
    send(tx)
```
Receiver example:
```python
import minipb
# schema must match transmitter. Typically both would import this.
schema = (('value', 'z'),
          ('float', 'f'),
          ('signed', 'z'),)

w = minipb.Wire(schema)
while True:
    dlen = receive(1)  # Data length stored in 1 byte
    data = receive(dlen)  # Retrieve actual data
    rx = w.decode(data)
    # Do something with the received dict
```

## 4.5 Repeating fields

This feature enables variable length lists to be encoded. List elements must
all be of the same (declared) data type. In this example the `value` and `txt`
fields are variable length lists denoted by the `'+'` prefix. The `value` field
holds a list of `int` values and `txt` holds strings:  
```python
import minipb
schema = (('value', '+z'),
          ('float', 'f'),
          ('txt', '+U'),
          )
w = minipb.Wire(schema)

data = {'value': [150, 123, 456],
        'float': 1.23,
        'txt' : ['abc', 'def', 'ghi'],
        }
tx = w.encode(data)
rx = w.decode(tx)
print(rx)
data['txt'][1] = 'the quick brown fox'  # Strings have variable length
data['txt'].append('the end')  # List has variable length
data['value'].append(999)  # Variable length
tx = w.encode(data)
rx = w.decode(tx)
print(rx)
```
### 4.5.1 Packed repeating fields

The author of `minipb` [does not recommend](https://github.com/dogtopus/minipb/issues/6)
their use. Their purpose appears to be in the context of fixed-length fields
which are outside the scope of pure Python programming.

## 4.6 Message fields (nested dicts)

The concept of message fields is a Protocol Buffer notion. In MicroPython
terminology a message field contains a `dict` whose contents are defined by
another schema. This enables nested dictionaries whose entries may be any valid
`protobuf` data type.

This is illustrated below. The example extends this by making the field a
variable length list of `dict` objects (with the `'+['` specifier):
```python
import minipb
# Schema for the nested dictionary instances
nested_schema = (('str2', 'U'),
                 ('num2', 'z'),)
# Outer schema
schema = (('number', 'z'),
          ('string', 'U'),
          ('nested', '+[', nested_schema, ']'),
          ('num', 'z'),)
w = minipb.Wire(schema)

data = {
    'number': 123,
    'string': 'test',
    'nested': [{'str2': 'string','num2': 888,},
               {'str2': 'another_string', 'num2': 12345,}, ],
    'num' : 42
}
tx = w.encode(data)
rx = w.decode(tx)
print(rx)
print(rx['nested'][0]['str2'])  # Access inner dict instances
print(rx['nested'][1]['str2'])
# Appending to the nested list of dicts
data['nested'].append({'str2': 'rats', 'num2':999})
tx = w.encode(data)
rx = w.decode(tx)
print(rx)
print(rx['nested'][2]['str2'])  # Access inner dict instances
```

### 4.6.1 Recursion

This is surely overkill in most MicroPython applications, but for the sake of
completeness message fields can be recursive:
```python
import minipb
inner_schema = (('str2', 'U'),
                ('num2', 'z'),)

nested_schema = (('inner', '+[', inner_schema, ']'),)

schema = (('number', 'z'),
          ('string', 'U'),
          ('nested', '[', nested_schema, ']'),
          ('num', 'z'),)

w = minipb.Wire(schema)

data = {
       'number': 123,
       'string': 'test',
       'nested': {'inner':({'str2': 'string', 'num2': 888,},
                           {'str2': 'another_string','num2': 12345,}, ),},
        'num' : 42
        }
tx = w.encode(data)
rx = w.decode(tx)
print(rx)
print(rx['nested']['inner'][0]['str2'])
```