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Problem with "Distance File" widget

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Problem with "Distance File" widget

Postby raghumk » Mon May 17, 2010 16:06

Hi, I am experiencing a problem with the "Distance File" widget while using Orange 2.0b on a Mac (OS X 10.4.11). I tried to connect the "iris.tab" file to the "Distance File" widget in order to calculate the distances between the examples, but get the following error. Any suggestions or pointers would be welcome. Thanks!

Code: Select all
There were problems importing the following widgets:
   OWANOVA: No module named scipy.stats
   OWApproxProfiles: No module named scipy.stats
   OWDataDistance: No module named qt
   OWDisplayMotifs: name 'QwtCurve' is not defined
   OWEpistasisAnalysis: No module named qt
   OWExampleSelector: No module named qttable
   OWGenomeMap: No module named qtcanvas
   OWHypTest: No module named qt
   OWBagofWords: dlopen(/Applications/Orange.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/orange/add-ons/Text/_orngTextWrapper.so, 2): Symbol not found: _strerror$UNIX2003
  Referenced from: /Applications/Orange.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/orange/add-ons/Text/_orngTextWrapper.so
  Expected in: /usr/lib/libSystem.B.dylib

   OWLetterNgram: dlopen(/Applications/Orange.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/orange/add-ons/Text/_orngTextWrapper.so, 2): Symbol not found: _strerror$UNIX2003
  Referenced from: /Applications/Orange.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/orange/add-ons/Text/_orngTextWrapper.so
  Expected in: /usr/lib/libSystem.B.dylib

   OWTextDistance: dlopen(/Applications/Orange.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/orange/add-ons/Text/_orngTextWrapper.so, 2): Symbol not found: _strerror$UNIX2003
  Referenced from: /Applications/Orange.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/orange/add-ons/Text/_orngTextWrapper.so
  Expected in: /usr/lib/libSystem.B.dylib

   OWTextFeatureSelection: dlopen(/Applications/Orange.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/orange/add-ons/Text/_orngTextWrapper.so, 2): Symbol not found: _strerror$UNIX2003
  Referenced from: /Applications/Orange.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/orange/add-ons/Text/_orngTextWrapper.so
  Expected in: /usr/lib/libSystem.B.dylib

   OWTextPreprocess: dlopen(/Applications/Orange.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/orange/add-ons/Text/_orngTextWrapper.so, 2): Symbol not found: _strerror$UNIX2003
  Referenced from: /Applications/Orange.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/orange/add-ons/Text/_orngTextWrapper.so
  Expected in: /usr/lib/libSystem.B.dylib

   OWWordNgram: dlopen(/Applications/Orange.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/orange/add-ons/Text/_orngTextWrapper.so, 2): Symbol not found: _strerror$UNIX2003
  Referenced from: /Applications/Orange.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/orange/add-ons/Text/_orngTextWrapper.so
  Expected in: /usr/lib/libSystem.B.dylib

The following widgets could not be imported and will not be available: OWTextDistance, OWTextPreprocess, OWLetterNgram, OWTextFeatureSelection, OWBagofWords, OWWordNgram.
The following prototype widgets could not be imported and will not be available: OWGenomeMap, OWEpistasisAnalysis, OWDataDistance, OWANOVA, OWDisplayMotifs, OWApproxProfiles, OWHypTest, OWExampleSelector.

Unhandled exception of type AttributeError occured at 14:40:13:
Traceback:
  File: OWWidget.py, line 133 in reportAndFinish
  Code: self.sendReport()
    File: OWDistanceFile.py, line 231 in sendReport
    Code: ("Matrix dimension", self.matrix.dim),
      AttributeError: 'NoneType' object has no attribute 'dim'

Unhandled exception of type TypeError occured at 10:16:25:
Traceback:
  File: OWBaseWidget.py, line 593 in processSignals
  Code: handler(value)
    File: OWDistanceFile.py, line 215 in getExamples
    Code: self.relabel()
      File: OWDistanceFile.py, line 201 in relabel
      Code: [[str(l)] for l in self.labels])
        TypeError: 'NoneType' object is not iterable

Unhandled exception of type TypeError occured at 10:16:52:
Traceback:
  File: OWBaseWidget.py, line 593 in processSignals
  Code: handler(value)
    File: OWDistanceFile.py, line 215 in getExamples
    Code: self.relabel()
      File: OWDistanceFile.py, line 201 in relabel
      Code: [[str(l)] for l in self.labels])
        TypeError: 'NoneType' object is not iterable
unable to set setting  graph.NameAttr  to value  0
unable to set setting  graph.SizeAttr  to value  0
unable to set setting  graph.ShowName  to value  True
unable to set setting  graph.NumStressLines  to value  10
unable to set setting  graph.stressByTransparency  to value  True
unable to set setting  graph.ShowStress  to value  False
unable to set setting  graph.useAntialiasingStressFunc  to value  None
unable to set setting  graph.ShapeAttr  to value  0
unable to set setting  graph.proportionGraphed  to value  20
unable to set setting  graph.differentWidths  to value  True
unable to set setting  graph.PointSize  to value  5
unable to set setting  graph.ColorAttr  to value  0

Unhandled exception of type TypeError occured at 10:35:47:
Traceback:
  File: OWBaseWidget.py, line 593 in processSignals
  Code: handler(value)
    File: OWDistanceFile.py, line 215 in getExamples
    Code: self.relabel()
      File: OWDistanceFile.py, line 201 in relabel
      Code: [[str(l)] for l in self.labels])
        TypeError: 'NoneType' object is not iterable

Unhandled exception of type TypeError occured at 10:38:30:
Traceback:
  File: OWBaseWidget.py, line 593 in processSignals
  Code: handler(value)
    File: OWDistanceFile.py, line 215 in getExamples
    Code: self.relabel()
      File: OWDistanceFile.py, line 201 in relabel
      Code: [[str(l)] for l in self.labels])
        TypeError: 'NoneType' object is not iterable

Unhandled exception of type TypeError occured at 10:53:06:
Traceback:
  File: OWBaseWidget.py, line 593 in processSignals
  Code: handler(value)
    File: OWDistanceFile.py, line 215 in getExamples
    Code: self.relabel()
      File: OWDistanceFile.py, line 201 in relabel
      Code: [[str(l)] for l in self.labels])
        TypeError: 'NoneType' object is not iterable

Unhandled exception of type TypeError occured at 10:55:48:
Traceback:
  File: OWBaseWidget.py, line 593 in processSignals
  Code: handler(value)
    File: OWDistanceFile.py, line 215 in getExamples
    Code: self.relabel()
      File: OWDistanceFile.py, line 201 in relabel
      Code: [[str(l)] for l in self.labels])
        TypeError: 'NoneType' object is not iterable

Unhandled exception of type TypeError occured at 10:59:02:
Traceback:
  File: OWBaseWidget.py, line 593 in processSignals
  Code: handler(value)
    File: OWDistanceFile.py, line 215 in getExamples
    Code: self.relabel()
      File: OWDistanceFile.py, line 201 in relabel
      Code: [[str(l)] for l in self.labels])
        TypeError: 'NoneType' object is not iterable

Unhandled exception of type TypeError occured at 11:02:20:
Traceback:
  File: OWBaseWidget.py, line 593 in processSignals
  Code: handler(value)
    File: OWDistanceFile.py, line 215 in getExamples
    Code: self.relabel()
      File: OWDistanceFile.py, line 201 in relabel
      Code: [[str(l)] for l in self.labels])
        TypeError: 'NoneType' object is not iterable

Unhandled exception of type TypeError occured at 11:02:40:
Traceback:
  File: OWBaseWidget.py, line 593 in processSignals
  Code: handler(value)
    File: OWDistanceFile.py, line 215 in getExamples
    Code: self.relabel()
      File: OWDistanceFile.py, line 201 in relabel
      Code: [[str(l)] for l in self.labels])
        TypeError: 'NoneType' object is not iterable

Postby Ales » Mon May 17, 2010 16:43

You need to use the Example Distance widget for that. The Distance File widget loads an already precomputed distance matrix from a file.

Postby raghumk » Mon May 17, 2010 19:07

Thanks, Ales. I am looking to generate a distance matrix to input into the MDS wiget. From the description of the Distance File widget it appeared that an input of an Example table would produce a Distance matrix. Could you suggest how I could go about producing a Distance Martix in Orange? Thanks.

Postby Ales » Mon May 17, 2010 19:35

Load your data with 'File' widget (in the Data tab), and connect its output with the 'Example distance' widget (in the Unsupervised tab). Then connect it to the MDS widget.

So your schema should look like this

File -> Example distance -> MDS

Postby raghumk » Mon May 17, 2010 19:57

Thanks, Ales.


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