FileNotFoundError: "... /style_tomato_sample.xml"

[ctyeong]

I was following your "AgML-Synthetic.ipynb" example.

I have run the code below:

generator.generate(name = 'tomato_sample', num_images = 3),

and an error follows:

FileNotFoundError                         Traceback (most recent call last)
/tmp/ipykernel_2880/388478152.py in <module>
      1 # Generate the data.
----> 2 generator.generate(name = 'tomato_sample', num_images = 3)

~/anaconda3/envs/agml/lib/python3.7/site-packages/agml/synthetic/generator.py in generate(self, name, num_images, output_dir, convert_data)
    355         xml_options = self._convert_options_to_xml()
    356         xml_file_base = f"style_{name}.xml"
--> 357         xml_options.write(os.path.join(XML_PATH, xml_file_base))
    358         xml_options.write(os.path.join(metadata_dir, xml_file_base))
    359 

~/anaconda3/envs/agml/lib/python3.7/xml/etree/ElementTree.py in write(self, file_or_filename, encoding, xml_declaration, default_namespace, method, short_empty_elements)
    758                 encoding = "us-ascii"
    759         enc_lower = encoding.lower()
--> 760         with _get_writer(file_or_filename, enc_lower) as write:
    761             if method == "xml" and (xml_declaration or
    762                     (xml_declaration is None and

~/anaconda3/envs/agml/lib/python3.7/contextlib.py in __enter__(self)
    110         del self.args, self.kwds, self.func
    111         try:
--> 112             return next(self.gen)
    113         except StopIteration:
    114             raise RuntimeError("generator didn't yield") from None

~/anaconda3/envs/agml/lib/python3.7/xml/etree/ElementTree.py in _get_writer(file_or_filename, encoding)
    795         else:
    796             file = open(file_or_filename, "w", encoding=encoding,
--> 797                         errors="xmlcharrefreplace")
    798         with file:
    799             yield file.write

FileNotFoundError: [Errno 2] No such file or directory: '/home/username/anaconda3/envs/agml/lib/python3.7/site-packages/agml/_helios/Helios/projects/SyntheticImageAnnotation/xml/style_tomato_sample.xml'

[amogh7joshi]

Can you show me the output of the following command?

1. tree /home/username/anaconda3/envs/agml/lib/python3.7/site-packages/agml/_helios/Helios/projects/SyntheticImageAnnotation (assuming username is your home directory, otherwise replace with the corresponding path).

[amogh7joshi]

I can't reproduce your error on my end, so there may be a path issue, or Helios may not have been fully installed. Try deleting the Helios directly and re-installing/compiling it.

[ctyeong]

Can you show me the output of the following command?

1. tree /home/username/anaconda3/envs/agml/lib/python3.7/site-packages/agml/_helios/Helios/projects/SyntheticImageAnnotation (assuming username is your home directory, otherwise replace with the corresponding path).

I can only find .gitignore under /home/username/anaconda3/envs/agml/lib/python3.7/site-packages/agml/_helios/Helios/projects. No SyntheticImageAnnotation.

[amogh7joshi]

Try deleting the Helios directory directly and re-installing/compiling it.

[ctyeong]

Okay. I think .../agml/_helios/Helios seems to be same as shown here: https://github.com/PlantSimulationLab/Helios, where the projects folder only contains .gitignore.

Try deleting the Helios directory directly and re-installing/compiling it.

Could you give me a more clarification on what to compile from this directory?

[amogh7joshi]

Delete the Helios directory in agml/_helios, then run agml.synthetic.reinstall_helios().

[ctyeong]

That worked! Actually, agml.synthetic.reinstall_helios() shows an error when there is no agml/_helios. So, I removed and re-installed the whole agml using pip to run agml.synthetic.reinstall_helios() afterwards. Then, generator.generate(name = 'tomato_sample', num_images = 3) went without issue. Thanks!