running float 32 images give json TypeError

[MargotCh]

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Hi Nimbus-Team,

when trying to run nimbus on a float 32 tiff image I get the following json TypeError while running nimbus.prepare_normalization_dict():

{ "name": "TypeError", "message": "Object of type float32 is not JSON serializable", "stack": "--------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In[19], line 1 ----> 1 nimbus.prepare_normalization_dict( 2 quantile=0.999, 3 n_subset=50, 4 clip_values=(0, 2), 5 multiprocessing=True, 6 overwrite=True 7 )

File ~/anaconda3/envs/nimbus-env/lib/python3.9/site-packages/nimbus_inference/nimbus.py:225, in Nimbus.prepare_normalization_dict(self, quantile, clip_values, n_subset, multiprocessing, overwrite) 223 else: 224 n_jobs = os.cpu_count() if multiprocessing else 1 --> 225 self.normalization_dict = prepare_normalization_dict( 226 self.dataset, self.output_dir, quantile, n_subset, 227 n_jobs 228 )

File ~/anaconda3/envs/nimbus-env/lib/python3.9/site-packages/nimbus_inference/utils.py:563, in prepare_normalization_dict(dataset, output_dir, quantile, n_subset, n_jobs, output_name) 561 # save normalization dict 562 with open(os.path.join(output_dir, output_name), 'w') as f: --> 563 json.dump(normalization_dict, f) 564 return normalization_dict

File ~/anaconda3/envs/nimbus-env/lib/python3.9/json/init.py:179, in dump(obj, fp, skipkeys, ensure_ascii, check_circular, allow_nan, cls, indent, separators, default, sort_keys, kw) 173 iterable = cls(skipkeys=skipkeys, ensure_ascii=ensure_ascii, 174 check_circular=check_circular, allow_nan=allow_nan, indent=indent, 175 separators=separators, 176 default=default, sort_keys=sort_keys, kw).iterencode(obj) 177 # could accelerate with writelines in some versions of Python, at 178 # a debuggability cost --> 179 for chunk in iterable: 180 fp.write(chunk)

File ~/anaconda3/envs/nimbus-env/lib/python3.9/json/encoder.py:431, in _make_iterencode.._iterencode(o, _current_indent_level) 429 yield from _iterencode_list(o, _current_indent_level) 430 elif isinstance(o, dict): --> 431 yield from _iterencode_dict(o, _current_indent_level) 432 else: 433 if markers is not None:

File ~/anaconda3/envs/nimbus-env/lib/python3.9/json/encoder.py:405, in _make_iterencode.._iterencode_dict(dct, _current_indent_level) 403 else: 404 chunks = _iterencode(value, _current_indent_level) --> 405 yield from chunks 406 if newline_indent is not None: 407 _current_indent_level -= 1

File ~/anaconda3/envs/nimbus-env/lib/python3.9/json/encoder.py:438, in _make_iterencode.._iterencode(o, _current_indent_level) 436 raise ValueError(\"Circular reference detected\") 437 markers[markerid] = o --> 438 o = _default(o) 439 yield from _iterencode(o, _current_indent_level) 440 if markers is not None:

File ~/anaconda3/envs/nimbus-env/lib/python3.9/json/encoder.py:179, in JSONEncoder.default(self, o) 160 def default(self, o): 161 \"\"\"Implement this method in a subclass such that it returns 162 a serializable object for o, or calls the base implementation 163 (to raise a TypeError). (...) 177 178 \"\"\" --> 179 raise TypeError(f'Object of type {o.class.name} ' 180 f'is not JSON serializable')

TypeError: Object of type float32 is not JSON serializable" }

Nimbus runs smoothly on unsigned 16 bit images. However, when I convert a previously running 16bit image to float32 it reproduces the same error.

Thank you for your help!!

Version information

---

alpineer NA nimbus_inference 0.0.2 session_info 1.0.0

PIL 11.0.0 appnope 0.1.4 asciitree NA asttokens NA backcall 0.2.0 backports NA certifi 2024.08.30 charset_normalizer 2.1.1 colorama 0.4.6 comm 0.2.2 cv2 4.10.0 cycler 0.12.1 cython_runtime NA dateutil 2.9.0 debugpy 1.6.7 decorator 5.1.1 dill 0.3.8 entrypoints 0.4 executing 2.1.0 filelock 3.16.1 huggingface_hub 0.25.2 idna 3.10 imagecodecs 2024.9.22 imageio 2.35.1 importlib_resources NA ipykernel 6.29.5 ipywidgets 8.1.5 jaraco NA jedi 0.19.1 joblib 1.4.2 kiwisolver 1.4.7 lazy_loader 0.4 lxml 5.3.0 matplotlib 3.9.2 more_itertools 10.3.0 mpl_toolkits NA natsort 8.4.0 numcodecs 0.12.1 numpy 2.0.2 packaging 24.1 pandas 2.2.3 parso 0.8.4 pexpect 4.9.0 pickleshare 0.7.5 pkg_resources NA platformdirs 4.3.6 prompt_toolkit 3.0.48 psutil 5.9.0 ptyprocess 0.7.0 pure_eval 0.2.3 pyarrow 17.0.0 pydev_ipython NA pydevconsole NA pydevd 2.9.5 pydevd_file_utils NA pydevd_plugins NA pydevd_tracing NA pygments 2.18.0 pyometiff 1.0.1 pyparsing 3.2.0 pytz 2024.1 requests 2.32.3 scipy 1.13.1 six 1.16.0 skimage 0.24.0 stack_data 0.6.2 tifffile 2024.8.30 torch 2.4.1 torchgen NA tornado 6.1 tqdm 4.66.5 traitlets 5.14.3 typing_extensions NA unicodedata2 NA urllib3 2.2.3 vscode NA wcwidth 0.2.13 yaml 6.0.2 zarr 2.18.2 zmq 25.1.2 zoneinfo NA

IPython 8.12.0 jupyter_client 7.3.4 jupyter_core 5.7.2

Python 3.9.20 | packaged by conda-forge | (main, Sep 30 2024, 17:48:00) [Clang 17.0.6 ] macOS-14.6.1-arm64-arm-64bit

Session information updated at 2024-10-30 14:41

[JLrumberger]

Hi @MargotCh,

thanks for opening this issue and highlighting this error case. I'll provide a fix for it and add accompanying test cases in the coming days.