Differences between revisions 26 and 37 (spanning 11 versions)

e2eulerxplor: EMAN2's EulerXplor Tool

Contents

e2eulerxplor: EMAN2's EulerXplor Tool
1. Mouse Handling
Inspecting EMData lists with euler_display from e2.py
1. Specialized Mouse Handling
Inspecting Transform lists with euler_display from e2.py

The four interfaces in e2eulerxplor. See the table below for more details

Figure Label	Description
A	This is a graphical depiction of orientations on the asymmetric unit. Click on one of the dots to display the associated class average and projection as shown in C. The color of the dot in the asymmetric unit shows the relative number of particles in the class: Blue indicates a class with a lot of particles in it, red indicates a class with few particles in it. White is in between.
B	This is main inspector, this appears when you middle click on A. You can select different refinement iterations to investigate how the class averages and aligned particles are changing through time.
C	Projection (left) and class average corresponding to selected orientation (yellow) in A
D	Aligned particles that formed the class average shown in C (right). If you select the projection in C (left) these particles will be shown unaligned. Blue squares indicate that the particle did not make it into the final class average

Mouse Handling

Mouse Action	Result
left button release	Select a cylinder/dot in A, resulting in update of the image in B (below) or C above
Right button drag	x and y movement
Shift + right button drag	z movement
Mouse wheel in and out	Zoom in and out, respectively
Left button drag	Object rotation, quaternion based
Middle button	Show inspector (B)

Inspecting EMData lists with euler_display from e2.py

You can open a list of EMData's with the EulerXplor tool if and only if they all have the xform.projection header attribute. Here is an example:

   1 a = EMData()
   2 b = a.read_images("bdb:refine_00#projections_00")
   3 euler_display(b)

Note that all projection and class average images produced by e2workflow have the xform.projection header attribute, which are located in directories called"refine_??" - you're safe to try this out using those images.

Typical screenshot of the Eulerxplor tool, launched using euler_display from e2.py

Figure Label	Description
A	Symmetrized orientation distribution. Cylinder heights are proportional to the "ptcl_repr" header attribute. You can change the header attribute that is represented by the cylinder height in the inspector (bottom of C)
B	The image corresponding to the selected (yellow) cylinder.
C	The inspector. Note you can uniformly enlarge the displayed cylinders using the "Point Height" and "Point Width" sliders

Specialized Mouse Handling

When you open a list of EMData objects from Python Eulerxplor handles mouse events slightly differently. The only way to view an image associated with a point on the sphere is to hold shift and click on it.

Mouse Action	Result
Shift + left click	Select a cylinder in A, resulting in update of the image in B

Inspecting Transform lists with euler_display from e2.py

Similarly you can look at a list of Transforms with the EulerXplor tool, using this syntax:

   1 sym = Symmetries.get("c1")
   2 orients = sym.gen_orientations("eman",{"delta":3,"inc_mirror":True})
   3 euler_display(orients)

-  ⇤ ← Revision 26 as of 2009-07-02 03:51:31 → 
  Size: 3086
  Editor: DavidWoolford
  Comment:
+   ← Revision 37 as of 2009-07-24 02:42:48 → ⇥
  Size: 3849
  Editor: bcm-10-134
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-<<TableOfContents>>

= EMAN2's EulerXplor Tool =
+= e2eulerxplor: EMAN2's EulerXplor Tool =
||<35%><<TableOfContents>>||
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+Line 8:
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+Line 20:
-|| left click release || Select a cylinder in '''A''', resulting in update of the image in '''B'''  ||
|| left click drag || Scene rotation ||
+|| left button release || Select a cylinder/dot in '''A''', resulting in update of the image in '''B''' (below) or '''C''' above  ||
|| Right button drag || x and y movement ||
|| Shift + right button drag || z movement ||
|| Mouse wheel in and out || Zoom in and out, respectively ||
|| Left button drag || Object rotation, quaternion based ||
|| Middle button || Show inspector ('''B''') ||
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+Line 29:
-You can open a list of EMData's with the EulerXplor tool if they all have the "xform.projection" header attribute. Use this syntax:
+You can open a list of EMData's with the EulerXplor tool '''if and only if''' they all have the '''xform.projection''' header attribute. Here is an example:
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+Note that all projection and class average images produced by e2workflow have the xform.projection header attribute, which are located in directories called"refine_??" - you're safe to try this out using those images.
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+Line 41:
-|| Typical screenshot of the Eulerxplor tool, launched using '''euler_display'''||
+|| Typical screenshot of the Eulerxplor tool, launched using '''euler_display''' from e2.py||
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+Line 44:
-|| A || Symmetrized orientation distribution. Cylinder heights are proportional to the "ptcl_repr" header attribute. You can choose which header attribute scales the cylinder height in the inspector (bottom of '''C''' ||
+|| A || Symmetrized orientation distribution. Cylinder heights are proportional to the "ptcl_repr" header attribute. You can change the header attribute that is represented by the cylinder height in the inspector (bottom of '''C''') ||
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+Line 46:
-|| C || The inspector. Note you can change uniformly enlarge the displayed cylinders using the "Point Height" and "Point Width" sliders ||
+|| C || The inspector. Note you can uniformly enlarge the displayed cylinders using the "Point Height" and "Point Width" sliders ||
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+Line 48:
-== Mouse Handling ==
+== Specialized Mouse Handling ==

When you open a list of EMData objects from Python Eulerxplor handles mouse events slightly differently. The only way to view an image associated with a point on the sphere is to hold shift and click on it.
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+Line 53:
-|| Shift + click|| Select a cylinder in '''A''', resulting in update of the image in '''B'''  ||
+|| Shift + left click|| Select a cylinder in '''A''', resulting in update of the image in '''B'''  ||