Invalid Namespace URI

[jcs-01]

When I reach the step of saving the .xml file in the ReadMe (Model.save_predictions(folderpath + 'MyResults') , I get the following error message. Has anyone else experienced this or know how to fix it? Thank you!

`---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[9], line 1
----> 1 Model.save_predictions(folderpath + 'MyResults')

File ~\conda\envs\envdeepslice\Lib\site-packages\DeepSlice\main.py:198, in DSModel.save_predictions(self, filename)
194 self.predictions.to_csv(filename + ".csv", index=False)
195 QuickNII_functions.write_QUINT_JSON(
196 df=self.predictions, filename=filename, aligner=aligner, target=target
197 )
--> 198 QuickNII_functions.write_QuickNII_XML(
199 df=self.predictions, filename=filename, aligner=aligner
200 )

File ~\conda\envs\envdeepslice\Lib\site-packages\DeepSlice\read_and_write\QuickNII_functions.py:45, in write_QuickNII_XML(df, filename, aligner)
17 out_df = pd.DataFrame(
18 {
19 "anchoring": "ox="
(...)
41 }
42 )
43 print(f"saving to {filename}.xml")
---> 45 out_df.to_xml(
46 filename + ".xml",
47 index=False,
48 root_name="series",
49 row_name="slice",
50 attr_cols=list(out_df.columns),
51 namespaces={
52 "first": df_temp.nr.values[0],
53 "last": df_temp.nr.values[-1],
54 "name": filename,
55 "aligner": aligner,
56 "": "",
57 },
58 )

File ~\conda\envs\envdeepslice\Lib\site-packages\pandas\util_decorators.py:333, in deprecate_nonkeyword_arguments..decorate..wrapper(*args, **kwargs)
327 if len(args) > num_allow_args:
328 warnings.warn(
329 msg.format(arguments=_format_argument_list(allow_args)),
330 FutureWarning,
331 stacklevel=find_stack_level(),
332 )
--> 333 return func(*args, **kwargs)

File ~\conda\envs\envdeepslice\Lib\site-packages\pandas\core\frame.py:3643, in DataFrame.to_xml(self, path_or_buffer, index, root_name, row_name, na_rep, attr_cols, elem_cols, namespaces, prefix, encoding, xml_declaration, pretty_print, parser, stylesheet, compression, storage_options)
3622 raise ValueError("Values for parser can only be lxml or etree.")
3624 xml_formatter = TreeBuilder(
3625 self,
3626 path_or_buffer=path_or_buffer,
(...)
3640 storage_options=storage_options,
3641 )
-> 3643 return xml_formatter.write_output()

File ~\conda\envs\envdeepslice\Lib\site-packages\pandas\io\formats\xml.py:338, in _BaseXMLFormatter.write_output(self)
336 @Final
337 def write_output(self) -> str | None:
--> 338 xml_doc = self._build_tree()
340 if self.path_or_buffer is not None:
341 with get_handle(
342 self.path_or_buffer,
343 "wb",
(...)
346 is_text=False,
347 ) as handles:

File ~\conda\envs\envdeepslice\Lib\site-packages\pandas\io\formats\xml.py:464, in LxmlXMLFormatter._build_tree(self)
452 """
453 Build tree from data.
454
455 This method initializes the root and builds attributes and elements
456 with optional namespaces.
457 """
458 from lxml.etree import (
459 Element,
460 SubElement,
461 tostring,
462 )
--> 464 self.root = Element(f"{self.prefix_uri}{self.root_name}", nsmap=self.namespaces)
466 for d in self.frame_dicts.values():
467 elem_row = SubElement(self.root, f"{self.prefix_uri}{self.row_name}")

File src\lxml\etree.pyx:3092, in lxml.etree.Element()

File src\lxml\apihelpers.pxi:138, in lxml.etree._makeElement()

File src\lxml\apihelpers.pxi:125, in lxml.etree._makeElement()

File src\lxml\apihelpers.pxi:222, in lxml.etree._setNodeNamespaces()

File src\lxml\apihelpers.pxi:1752, in lxml.etree._uriValidOrRaise()

ValueError: Invalid namespace URI`

[jcs-01]

Looks like the error is lines 52-56 in QuickNII_functions.py

[PolarBean]

I can't replicate this issue but lxml has caused problems in the past. I will remove the ability to save as xml for now.

[PolarBean]

please update DeepSlice and let me know whether your problem persists

[jcs-01]

That does solve the namespace URI issue, but I really need the xml file output unfortunately

[PolarBean]

The json has all the same information. What do you need the XML for?

[rdaggs]

Hi, I've had this same problem and it occurred due to the naming convention of my folder path....it had spaces in it. After a while I thought to change spaces with underscores and the 'Invalid namespace URI' error went away. Let me know if this works for you