After creating a NumPy array, and saving it as a Django context variable, I receive the following error when loading the webpage:
array([ 0, 239, 479, 717, 952, 1192, 1432, 1667], dtype=int64) is not JSON serializable
What does this mean?
3
14 Answers
I regularly “jsonify” np.arrays. Try using the “.tolist()” method on the arrays first, like this:
import numpy as np
import codecs, json
a = np.arange(10).reshape(2,5) # a 2 by 5 array
b = a.tolist() # nested lists with same data, indices
file_path = "/path.json" ## your path variable
json.dump(b, codecs.open(file_path, 'w', encoding='utf-8'),
separators=(',', ':'),
sort_keys=True,
indent=4) ### this saves the array in .json format
In order to “unjsonify” the array use:
obj_text = codecs.open(file_path, 'r', encoding='utf-8').read()
b_new = json.loads(obj_text)
a_new = np.array(b_new)
8
Why can it only be stored as a list of lists?
I don’t know but i expect np.array types have metadata that doesn’t fit into json (e.g. they specify the data type of each entry like float)
I tried your method, but it seems that the program stucked at
tolist().– Harvett@frankliuao I found the reason is that
tolist()takes a huge amount of time when the data is large.– Harvett@NikhilPrabhu JSON is Javascript Object Notation, and can therefore only represent the basic constructs from the javascript language: objects (analogous to python dicts), arrays (analogous to python lists), numbers, booleans, strings, and nulls (analogous to python Nones). Numpy arrays are not any of those things, and so cannot be serialised into JSON. Some can be converted to a JSO-like form (list of lists), which is what this answer does.
Store as JSON a numpy.ndarray or any nested-list composition.
class NumpyEncoder(json.JSONEncoder):
def default(self, obj):
if isinstance(obj, np.ndarray):
return obj.tolist()
return json.JSONEncoder.default(self, obj)
a = np.array([[1, 2, 3], [4, 5, 6]])
print(a.shape)
json_dump = json.dumps({'a': a, 'aa': [2, (2, 3, 4), a], 'bb': [2]},
cls=NumpyEncoder)
print(json_dump)
Will output:
(2, 3)
{"a": [[1, 2, 3], [4, 5, 6]], "aa": [2, [2, 3, 4], [[1, 2, 3], [4, 5, 6]]], "bb": [2]}
To restore from JSON:
json_load = json.loads(json_dump)
a_restored = np.asarray(json_load["a"])
print(a_restored)
print(a_restored.shape)
Will output:
[[1 2 3]
[4 5 6]]
(2, 3)
6
This should be way higher up the board, it’s the generalisable and properly abstracted way of doing this. Thanks!
– thclarkIs there a simple way to get the ndarray back from the list ?
This answer is great and can easily be extended to serialize numpy float32 and np.float64 values as json too:
if isinstance(obj, np.float32) or isinstance(obj, np.float64): return float(obj)– BensgeThis solution avoid you to cast manually every numpy array to list.
I found the best solution if you have nested numpy arrays in a dictionary:
import json
import numpy as np
class NumpyEncoder(json.JSONEncoder):
""" Special json encoder for numpy types """
def default(self, obj):
if isinstance(obj, np.integer):
return int(obj)
elif isinstance(obj, np.floating):
return float(obj)
elif isinstance(obj, np.ndarray):
return obj.tolist()
return json.JSONEncoder.default(self, obj)
dumped = json.dumps(data, cls=NumpyEncoder)
with open(path, 'w') as f:
json.dump(dumped, f)
Thanks to this guy.
6
Thanks for the helpful answer! I wrote the attributes to a json file, but am now having trouble reading back the parameters for Logistic Regression. Is there a ‘decoder’ for this saved json file?
– TTZOf course, to read the
jsonback you can use this:with open(path, 'r') as f:data = json.load(f), which returns a dictionary with your data.That’s for reading the
jsonfile and then to deserialize it’s output you can use this:data = json.loads(data)I had to add this to handle bytes datatype.. assuming all bytes are utf-8 string. elif isinstance(obj, (bytes,)): return obj.decode(“utf-8”)
+1. Why do we need the line “return json.JSONEncoder.default(self, obj)” at the end of “def default(self, obj)”?
– Hans
You can use Pandas:
import pandas as pd
pd.Series(your_array).to_json(orient="values")
2
Use the json.dumps default kwarg:
default should be a function that gets called for objects that can’t otherwise be serialized. … or raise a TypeError
In the default function check if the object is from the module numpy, if so either use ndarray.tolist for a ndarray or use .item for any other numpy specific type.
import numpy as np
def default(obj):
if type(obj).__module__ == np.__name__:
if isinstance(obj, np.ndarray):
return obj.tolist()
else:
return obj.item()
raise TypeError('Unknown type:', type(obj))
dumped = json.dumps(data, default=default)
3
What’s the role of the line
type(obj).__module__ == np.__name__:there? Would it not suffice to check for the instance?@RamonMartinez, to know that the object is a numpy object, this way i can use
.itemfor almost any numpy object.defaultfunction is called for all unknown typesjson.dumpsattempts to serialize. not just numpy– mosheviI think this also assists stackoverflow.com/questions/69920913/… though it would be nice to have a clean nested version too
This is not supported by default, but you can make it work quite easily! There are several things you’ll want to encode if you want the exact same data back:
- The data itself, which you can get with
obj.tolist()as @travelingbones mentioned. Sometimes this may be good enough. - The data type. I feel this is important in quite some cases.
- The dimension (not necessarily 2D), which could be derived from the above if you assume the input is indeed always a ‘rectangular’ grid.
- The memory order (row- or column-major). This doesn’t often matter, but sometimes it does (e.g. performance), so why not save everything?
Furthermore, your numpy array could part of your data structure, e.g. you have a list with some matrices inside. For that you could use a custom encoder which basically does the above.
This should be enough to implement a solution. Or you could use json-tricks which does just this (and supports various other types) (disclaimer: I made it).
pip install json-tricks
Then
data = [
arange(0, 10, 1, dtype=int).reshape((2, 5)),
datetime(year=2017, month=1, day=19, hour=23, minute=00, second=00),
1 + 2j,
Decimal(42),
Fraction(1, 3),
MyTestCls(s="ub", dct={'7': 7}), # see later
set(range(7)),
]
# Encode with metadata to preserve types when decoding
print(dumps(data))
I had a similar problem with a nested dictionary with some numpy.ndarrays in it.
def jsonify(data):
json_data = dict()
for key, value in data.iteritems():
if isinstance(value, list): # for lists
value = [ jsonify(item) if isinstance(item, dict) else item for item in value ]
if isinstance(value, dict): # for nested lists
value = jsonify(value)
if isinstance(key, int): # if key is integer: > to string
key = str(key)
if type(value).__module__=='numpy': # if value is numpy.*: > to python list
value = value.tolist()
json_data[key] = value
return json_data
You could also use default argument for example:
def myconverter(o):
if isinstance(o, np.float32):
return float(o)
json.dump(data, default=myconverter)
use NumpyEncoder it will process json dump successfully.without throwing – NumPy array is not JSON serializable
import numpy as np
import json
from numpyencoder import NumpyEncoder
arr = array([ 0, 239, 479, 717, 952, 1192, 1432, 1667], dtype=int64)
json.dumps(arr,cls=NumpyEncoder)
0
Also, some very interesting information further on lists vs. arrays in Python ~> Python List vs. Array – when to use?
It could be noted that once I convert my arrays into a list before saving it in a JSON file, in my deployment right now anyways, once I read that JSON file for use later, I can continue to use it in a list form (as opposed to converting it back to an array).
AND actually looks nicer (in my opinion) on the screen as a list (comma seperated) vs. an array (not-comma seperated) this way.
Using @travelingbones’s .tolist() method above, I’ve been using as such (catching a few errors I’ve found too):
SAVE DICTIONARY
def writeDict(values, name):
writeName = DIR+name+'.json'
with open(writeName, "w") as outfile:
json.dump(values, outfile)
READ DICTIONARY
def readDict(name):
readName = DIR+name+'.json'
try:
with open(readName, "r") as infile:
dictValues = json.load(infile)
return(dictValues)
except IOError as e:
print(e)
return('None')
except ValueError as e:
print(e)
return('None')
Hope this helps!
Here is an implementation that work for me and removed all nans (assuming these are simple object (list or dict)):
from numpy import isnan
def remove_nans(my_obj, val=None):
if isinstance(my_obj, list):
for i, item in enumerate(my_obj):
if isinstance(item, list) or isinstance(item, dict):
my_obj[i] = remove_nans(my_obj[i], val=val)
else:
try:
if isnan(item):
my_obj[i] = val
except Exception:
pass
elif isinstance(my_obj, dict):
for key, item in my_obj.iteritems():
if isinstance(item, list) or isinstance(item, dict):
my_obj[key] = remove_nans(my_obj[key], val=val)
else:
try:
if isnan(item):
my_obj[key] = val
except Exception:
pass
return my_obj
This is a different answer, but this might help to help people who are trying to save data and then read it again.
There is hickle which is faster than pickle and easier.
I tried to save and read it in pickle dump but while reading there were lot of problems and wasted an hour and still didn’t find solution though I was working on my own data to create a chat bot.
vec_x and vec_y are numpy arrays:
data=[vec_x,vec_y]
hkl.dump( data, 'new_data_file.hkl' )
Then you just read it and perform the operations:
data2 = hkl.load( 'new_data_file.hkl' )
May do simple for loop with checking types:
with open("jsondontdoit.json", 'w') as fp:
for key in bests.keys():
if type(bests[key]) == np.ndarray:
bests[key] = bests[key].tolist()
continue
for idx in bests[key]:
if type(bests[key][idx]) == np.ndarray:
bests[key][idx] = bests[key][idx].tolist()
json.dump(bests, fp)
fp.close()
TypeError: array([[0.46872085, 0.67374235, 1.0218339 , 0.13210179, 0.5440686 , 0.9140083 , 0.58720225, 0.2199381 ]], dtype=float32) is not JSON serializable
The above-mentioned error was thrown when i tried to pass of list of data to model.predict() when i was expecting the response in json format.
> 1 json_file = open('model.json','r')
> 2 loaded_model_json = json_file.read()
> 3 json_file.close()
> 4 loaded_model = model_from_json(loaded_model_json)
> 5 #load weights into new model
> 6 loaded_model.load_weights("model.h5")
> 7 loaded_model.compile(optimizer="adam", loss="mean_squared_error")
> 8 X = [[874,12450,678,0.922500,0.113569]]
> 9 d = pd.DataFrame(X)
> 10 prediction = loaded_model.predict(d)
> 11 return jsonify(prediction)
But luckily found the hint to resolve the error that was throwing
The serializing of the objects is applicable only for the following conversion
Mapping should be in following way
object – dict
array – list
string – string
integer – integer
If you scroll up to see the line number 10
prediction = loaded_model.predict(d) where this line of code was generating the output
of type array datatype , when you try to convert array to json format its not possible
Finally i found the solution just by converting obtained output to the type list by
following lines of code
prediction = loaded_model.predict(d)
listtype = prediction.tolist()
return jsonify(listtype)
Bhoom! finally got the expected output,
It means that somewhere, something is trying to dump a numpy array using the
jsonmodule. Butnumpy.ndarrayis not a type thatjsonknows how to handle. You’ll either need to write your own serializer, or (more simply) just passlist(your_array)to whatever is writing the json.Note
list(your_array)will not always work as it returns numpy ints, not native ints. Useyour_array.to_list()instead.a note about @ashishsingal’s comment, it should be your_array.tolist(), not to_list().