Transforming Images (Applying Rotation, Translation, Scale and Mirroring)

What follows is a very simply demonstration of using the Transform object to transform EMData (image) objects. A very thorough explanation of using the Transform is presented in Using the EMAN2 Transform class and you are encouraged to at least be aware of that page's existence.

Using EMData.transform

The first example here is a 3D example.

   1 [someone@localhost]# e2.py
   2 
   3 Welcome to EMAN2
   4 Prompt provided by IPython
   5 Enter '?' for ipython help
   6 
   7 
   8 In [3]:  e = test_image_3d() # 3D test image
   9 
  10 In [4]:  t = Transform({"type":"eman","az":45,"alt":90})
  11 
  12 In [5]:  t.set_trans(1,-2,5)
  13 
  14 In [6]:  t.set_scale(2.0)
  15 
  16 In [7]:  e.transform(t)
  17 
  18 In [8]:  display(e)

This second example is a 2D example.

   1 In [9]:  e = test_image() # This is a 2D test image
   2 
   3 In [10]:  t = Transform({"type":"2d","alpha":45}) # Note 2D terminology
   4 
   5 In [11]:  t.set_trans(3,-2) # Note 2D translation
   6 
   7 In [12]:  t.set_mirror(True)
   8 
   9 In [13]:  e.transform(t)
  10 
  11 In [14]:  display(e)

Using the Processor Framework

You can use the processor framework to process an EMData object in and out of place. This can be useful when you wish to operate on a copy of the original image, as opposed to altering it.

   1 In [15]:  t = Transform(....) # Construct a transform as above
   2 
   3 In [16]:  out_of_place = e.process("xform",{"transform":t}) # Out of place
   4 
   5 In [17]:  e.process_inplace("xform",{"transform":t}) # Inplace
   6 
   7 In [18]:  e.transform(t) # exactly the same as line above

EMAN2/Tutorials/RotateTranslate (last edited 2015-05-04 18:17:02 by StephenMurray)

-  ⇤ ← Revision 1 as of 2007-12-10 22:47:19 → 
  Size: 670
  Editor: DavidWoolford
  Comment:
+   ← Revision 17 as of 2015-05-04 18:17:02 → ⇥
  Size: 1701
  Editor: StephenMurray
  Comment: changed math.transform to xform
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-{{{
[someone@localhost]$ e2.py
+<<TableOfContents>>

= Transforming Images (Applying Rotation, Translation, Scale and Mirroring) =

What follows is a very simply demonstration of using the Transform object to transform EMData (image) objects. A very thorough explanation of using the Transform is presented in [[Eman2TransformInPython|Using the EMAN2 Transform class]] and you are encouraged to at least be aware of that page's existence.

== Using EMData.transform ==

The first example here is a '''3D''' example.

{{{#!python
[someone@localhost]# e2.py
-Line 8:
+Line 18:
-In [3]:  e = EMData()
-Line 10:
+Line 19:
-In [4]:  e.set_size(32,32,32)
+In [3]:  e = test_image_3d() # 3D test image
-Line 12:
+Line 21:
-In [5]:  e.process_inplace('testimage.axes')
+In [4]:  t = Transform({"type":"eman","az":45,"alt":90})
-Line 14:
+Line 23:
-In [6]:  t = Transform3D(90,30,90)
+In [5]:  t.set_trans(1,-2,5)
-Line 16:
+Line 25:
-In [7]:  t.set_posttrans(1,-2,5)
+In [6]:  t.set_scale(2.0)
-Line 18:
+Line 27:
-In [8]:  t.set_pretrans(2,10,-20)
+In [7]:  e.transform(t)
-Line 20:
+Line 29:
-In [9]:  e.rotate_translate(t)

In [9]:  display(e)
+In [8]:  display(e)
-Line 26:
+Line 33:
-Notes:
+This second example is a '''2D''' example.
-Line 28:
+Line 35:
-. The Transform3D is initialized on line 6 with the arguments 90 (azimuth), 30 (altitude), and 90 (phi). This is ZXZ' rotation. You can do rotations using SPIDER, MRC, IMAGIC and many other conventions with the Transform3D object, but this is not demonstrated here.
+{{{#!python

In [9]:  e = test_image() # This is a 2D test image

In [10]:  t = Transform({"type":"2d","alpha":45}) # Note 2D terminology

In [11]:  t.set_trans(3,-2) # Note 2D translation

In [12]:  t.set_mirror(True)

In [13]:  e.transform(t)

In [14]:  display(e)

}}}


== Using the Processor Framework ==

You can use the processor framework to process an EMData object in and out of place. This can be useful when you wish to operate on a copy of the original image, as opposed to altering it.

{{{#!python

In [15]:  t = Transform(....) # Construct a transform as above

In [16]:  out_of_place = e.process("xform",{"transform":t}) # Out of place

In [17]:  e.process_inplace("xform",{"transform":t}) # Inplace

In [18]:  e.transform(t) # exactly the same as line above

}}}