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