[Feature Request] Segmentation Loader - Read additional metadata from .xml file

[lucas-diedrich]

I recently came across an LMD xml file that contained additional metadata (here: CapID) for each cell as a named tag (minimal example here). Would it be possible to parse these optional metadata tags in pyLMD and add them to the shapes class as additional attributes? I assume that this requires to slightly adjust the Shapes class. Would be happy to open a pull request addressing this.

<?xml version='1.0' encoding='UTF-8'?>
<ImageData>
  <GlobalCoordinates>1</GlobalCoordinates>
  <X_CalibrationPoint_1>0</X_CalibrationPoint_1>
  <Y_CalibrationPoint_1>-0</Y_CalibrationPoint_1>
  <X_CalibrationPoint_2>1</X_CalibrationPoint_2>
  <Y_CalibrationPoint_2>1</Y_CalibrationPoint_2>
  <X_CalibrationPoint_3>0</X_CalibrationPoint_3>
  <Y_CalibrationPoint_3>-1</Y_CalibrationPoint_3>
  <ShapeCount>1</ShapeCount>
  <Shape_1>
    <PointCount>4</PointCount>
    <CapID>A1</CapID>
    <X_1>0</X_1>
    <Y_1>-0</Y_1>
    <X_2>0</X_2>
    <Y_2>-1</Y_2>
    <X_3>1</X_3>
    <Y_3>-0</Y_3>
    <X_4>0</X_4>
    <Y_4>-0</Y_4>
  </Shape_1>
</ImageData>

[sophiamaedler]

The XML files generated by pyLMD do already have the CapID attribute. It is how we can sort specific cells into specific wells.

E.g. Here an excerpt from an XML generated with pyLMD.

<?xml version='1.0' encoding='UTF-8'?>
<ImageData>
  <GlobalCoordinates>1</GlobalCoordinates>
  <X_CalibrationPoint_1>163544</X_CalibrationPoint_1>
  <Y_CalibrationPoint_1>-224933</Y_CalibrationPoint_1>
  <X_CalibrationPoint_2>395437</X_CalibrationPoint_2>
  <Y_CalibrationPoint_2>-9368125</Y_CalibrationPoint_2>
  <X_CalibrationPoint_3>16341075</X_CalibrationPoint_3>
  <Y_CalibrationPoint_3>-163610</Y_CalibrationPoint_3>
  <ShapeCount>1995</ShapeCount>
  <Shape_1>
    <PointCount>28</PointCount>
    <CapID>B2</CapID>
    <X_1>14718600</X_1>
    <Y_1>-7059350</Y_1>
    <X_2>14719346</X_2>
    <Y_2>-7059254</Y_2>
    <X_3>14720103</X_3>
  </Shape_1>
</ImageData>

So I am guessing your problem arises when you try and read an XML into pyLMD? This probably wasn't implemented in the XML reader as it was a newer feature of pyLMD and we didn't go back and update all other functions like we should have. Should be a quick fix though. If you could make a PR that would be awesome :)

[lucas-diedrich]

Thanks for the explanation!

Made PR #32 addressing this