# Coordinates extracted from markup control points are inaccurate

**URL:** <https://discourse.slicer.org/t/coordinates-extracted-from-markup-control-points-are-inaccurate/18144>\
**Category:** Development\
**Created:** [June 15, 2021, 3:33pm UTC](https://discourse.slicer.org/t/coordinates-extracted-from-markup-control-points-are-inaccurate/18144 "2021-06-15T15:33:54Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![mau\_igna\_06](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mau_igna_06/32/9056_2.png) [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Post date:** [June 15, 2021, 3:33pm UTC](https://discourse.slicer.org/t/coordinates-extracted-from-markup-control-points-are-inaccurate/18144/1 "2021-06-15T15:33:55Z")

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Here is the code to reproduce the bug:

```auto
import numpy as np

lineNode = slicer.mrmlScene.CreateNodeByClass("vtkMRMLMarkupsLineNode")
lineNode.SetName("screwLine")
slicer.mrmlScene.AddNode(lineNode)
#display node of the plane
displayNode = lineNode.GetDisplayNode()
displayNode.UseGlyphScaleOff()
displayNode.SetGlyphSize(8)
displayNode.SetOpacity(1)
displayNode.SetLineThickness(0)

lineNode.AddControlPoint(vtk.vtkVector3d(45.0,11.0,0.0))
lineNode.AddControlPoint(vtk.vtkVector3d(-26.0,-10.0,0.0))

def moveLineOnLineDirection():
  lineStartPoint = np.array([0,0,0])
  lineEndPoint = np.array([0,0,0])
  lineNode.GetNthControlPointPosition(0,lineStartPoint)
  lineNode.GetNthControlPointPosition(1,lineEndPoint)
  lineDirection = (lineEndPoint - lineStartPoint)/np.linalg.norm(lineEndPoint - lineStartPoint)
  stepmm = 5
  stepDirection = lineDirection
  lineTranslationTransform = vtk.vtkTransform()
  lineTranslationTransform.PostMultiply()
  lineTranslationTransform.Translate(stepmm*stepDirection)
  lineTranslationTransformNode = slicer.vtkMRMLLinearTransformNode()
  lineTranslationTransformNode.SetName("lineTranslationTransform")
  slicer.mrmlScene.AddNode(lineTranslationTransformNode)
  lineTranslationTransformNode = slicer.vtkMRMLLinearTransformNode()
  lineTranslationTransformNode.SetName("screwToScrewLineTransform")
  slicer.mrmlScene.AddNode(lineTranslationTransformNode)
  lineTranslationTransformNode.SetMatrixTransformToParent(
    lineTranslationTransform.GetMatrix())
  lineNode.SetAndObserveTransformNodeID(lineTranslationTransformNode.GetID())
  lineNode.HardenTransform()
  slicer.mrmlScene.RemoveNode(lineTranslationTransformNode)
  translatedLineStartPoint = np.array([0,0,0])
  translatedLineEndPoint = np.array([0,0,0])
  lineNode.GetNthControlPointPosition(0,translatedLineStartPoint)
  lineNode.GetNthControlPointPosition(1,translatedLineEndPoint)
  translatedLineDirection = (translatedLineEndPoint - translatedLineStartPoint)/np.linalg.norm(translatedLineEndPoint - translatedLineStartPoint)
  cosOfAngle = vtk.vtkMath.Dot(lineDirection,translatedLineDirection)
  import math
  angleDifference = math.degrees(math.acos(cosOfAngle))
  print(angleDifference)

moveLineOnLineDirection()

```

Open Slicer, open the python interactor, paste the code, see that the printed angle difference is near 1degree and it should be zero, (optional, move the line control points, execute moveLineOnLineDirection again and see the angle difference result: it’s not always zero)

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 15, 2021, 4:45pm UTC](https://discourse.slicer.org/t/coordinates-extracted-from-markup-control-points-are-inaccurate/18144/2 "2021-06-15T16:45:51Z")

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The problem is that you create an integer numpy array for storing the coordinates. This leads to loss of precision. For example:

```auto
>>> a=np.array([0,0,0])
>>> a[0]=1.2
>>> a
array([1, 0, 0])

```

Example for markups:

```python
>>> translatedLineStartPoint = np.array([0,0,0]) # this is an int32 array
>>> lineNode.GetNthControlPointPosition(0,translatedLineStartPoint)
>>> translatedLineStartPoint
array([40, 9, 0])

>>> translatedLineStartPoint = np.zeros(3)
>>> lineNode.GetNthControlPointPosition(0,translatedLineStartPoint)
>>> translatedLineStartPoint
array([40.20532872, 9.58185779, 0.])

```

**Always use `np.zeros(3)` to create a numpy array initialized to zero.** It is shorter and it correctly creates a float array.

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<div class="post-metadata">

**Author:** ![mau\_igna\_06](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mau_igna_06/32/9056_2.png) [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Post date:** [June 15, 2021, 5:23pm UTC](https://discourse.slicer.org/t/coordinates-extracted-from-markup-control-points-are-inaccurate/18144/3 "2021-06-15T17:23:35Z")

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Yes Andras. Thank you very much!