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Daniel Castaño: /* Parametrization of an angular grid */

2016-05-02T07:56:52Z

Parametrization of an angular grid

Daniel Castaño: /* Parametrization of an angular grid */

2016-05-02T07:56:02Z

Parametrization of an angular grid

Daniel Castaño at 12:20, 1 May 2016

2016-05-01T12:20:17Z

Daniel Castaño: /* Parametrization of an angular grid */

2016-05-01T12:19:33Z

Parametrization of an angular grid

Daniel Castaño: Created page with "The basic idea in a cross-correlation method is that the template is rotated several times, and each rotated copy is compared with the particle. ==Parametrization of an angul..."

2016-05-01T12:18:22Z

Created page with "The basic idea in a cross-correlation method is that the template is rotated several times, and each rotated copy is compared with the particle. ==Parametrization of an angul..."

New page

The basic idea in a cross-correlation method is that the template is rotated several times, and each rotated copy is compared with the particle.

==Parametrization of an angular grid==
In ''Dynamo'', an angular grid (i.e., a set of Euler triplets to be scanned) is defined by five parameters:
<tt>cone_range</tt>,<tt>cone_sampling</tt>,<tt>inplane_range</tt>,<tt>inplane_sampling</tt>,<tt>old _angles</tt>
The first four are project parameters that can be chosen by the user and will be applied for the analysis of all particles. The last one, <tt>old_angles</tt> is obviously different for each particle, and in runtime is read from the table (provided by the user or generated by ''Dynamo'' during the iteration procedure).
The <tt>cone_</tt> parameters define a set of orientations that will be sampled around a previously determined old orientation. Here we speak of orientations of the vertical axis of the template, not full unconstrained rotations. Allowing this axis to move inside a cone involves only two Euler angles (tdrot and tilt). ‘cone_range’, is the extent of this cone in degrees (360 being the full possible range of axis orientations). <tt>cone_sampling</tt> is the step inside this cone, also in degrees. The orientations are generated so as to provide an uniform coverage.
The <tt>inplane_</tt> parameters complete the set of scanned Euler triplets. After each of the axis reorentations defined by the <tt>cone_</tt> parameters, the template will be rotated about the new orientation of its axis. This is frequently referred to as ''azymuthal rotation''. This involves only the <tt>narot</tt> angle. The project parameter <tt>inplane_range</tt> defines the angular interval to be scanned around the old value of narot, and ‘inplane_sampling’ defines the interval.
By convention, passing value 0 to <tt>inplane_range</tt> generates ‘inplane’ rotations: only axis orientations of the axis will be scanned.

==Multilevel refinement of an angular grid==
Two further project parameters control the refinement of the grid: when ''Dynamo'' finds the triplet <tt>[tdrot,tilt,narot]</tt> that maximizes the similarity between rotated template and particle, a new grid is generated around this angles.
The project parameter <tt>refine</tt> defines how many times this process will be repeated for each particle. <tt>refine_factor</tt> defines the range of the new set of angles. A value of 2, for instance, means that the range of the new grid should twice as large as the step of the old grid.

@@ Line 8: / Line 8: @@
 *<tt>inplane_sampling</tt> (<tt>is</tt>)
 *<tt>old _angles</tt>
-The first four are project parameters that can be chosen by the user and will be applied for the analysis of all particles. The last one, <tt>old_angles</tt> is obviously different for each particle, and in runtime is read from the table (provided by the user or [[refinement table|generated]] by ''Dynamo'' during the iteration procedure).
+The first four are project parameters that can be chosen by the user and will be applied for the analysis of all particles. The last one, <tt>old_angles</tt> is obviously different for each particle, and in runtime is read from the table (provided by the user or [[Refined table|generated]] by ''Dynamo'' during the iteration procedure).
 The <tt>cone_</tt> parameters define a set of orientations that will be sampled around a previously determined old orientation. Here we speak of orientations of the vertical axis of the template, not full unconstrained rotations. Allowing this axis to move inside a cone involves only two Euler angles (tdrot and tilt). ‘cone_range’, is the extent of this cone in degrees (360 being the full possible range of axis orientations). <tt>cone_sampling</tt> is the step inside this cone, also in degrees. The orientations are generated so as to provide an uniform coverage.
 The <tt>inplane_</tt> parameters complete the set of scanned Euler triplets. After each of the axis reorentations defined by the <tt>cone_</tt> parameters, the template will be rotated about the new orientation of its axis. This is frequently referred to as ''azymuthal rotation''.  This involves only the <tt>narot</tt> angle. The project parameter <tt>inplane_range</tt> defines the angular interval to be scanned around the old value of narot, and ‘inplane_sampling’ defines the interval.

@@ Line 3: / Line 3: @@
 ==Parametrization of an angular grid==
 In ''Dynamo'', an angular grid (i.e., a set of Euler triplets to be scanned) is defined by five parameters:
-*<tt>cone_range</tt>,
+*<tt>cone_range</tt> (<tt>cr</tt>)
-*<tt>cone_sampling</tt>
+*<tt>cone_sampling</tt> (<tt>cs</tt>)
-*<tt>inplane_range</tt>
+*<tt>inplane_range</tt> (<tt>ir</tt>)
-*<tt>inplane_sampling</tt>
+*<tt>inplane_sampling</tt> (<tt>is</tt>)
 *<tt>old _angles</tt>
 The first four are project parameters that can be chosen by the user and will be applied for the analysis of all particles. The last one, <tt>old_angles</tt> is obviously different for each particle, and in runtime is read from the table (provided by the user or [[refinement table|generated]] by ''Dynamo'' during the iteration procedure).

@@ Line 11: / Line 11: @@
 The <tt>cone_</tt> parameters define a set of orientations that will be sampled around a previously determined old orientation. Here we speak of orientations of the vertical axis of the template, not full unconstrained rotations. Allowing this axis to move inside a cone involves only two Euler angles (tdrot and tilt). ‘cone_range’, is the extent of this cone in degrees (360 being the full possible range of axis orientations). <tt>cone_sampling</tt> is the step inside this cone, also in degrees. The orientations are generated so as to provide an uniform coverage.
 The <tt>inplane_</tt> parameters complete the set of scanned Euler triplets. After each of the axis reorentations defined by the <tt>cone_</tt> parameters, the template will be rotated about the new orientation of its axis. This is frequently referred to as ''azymuthal rotation''.  This involves only the <tt>narot</tt> angle. The project parameter <tt>inplane_range</tt> defines the angular interval to be scanned around the old value of narot, and ‘inplane_sampling’ defines the interval.
-By convention, passing value 0  to <tt>inplane_range</tt>  generates ‘inplane’ rotations: only  axis orientations of the axis will be scanned.
+By convention, passing value 0  to <tt>inplane_range</tt>  generates no ‘inplane’ rotations: only  axis orientations of the axis will be scanned.
 ==Multilevel refinement of an angular grid==
 Two further project parameters control the refinement of the grid: when ''Dynamo'' finds the triplet <tt>[tdrot,tilt,narot]</tt> that maximizes the similarity between rotated template and particle, a new grid is generated around this angles.
 The project parameter <tt>refine</tt> defines how many times this process will be repeated for each particle. <tt>refine_factor</tt> defines the range of the new set of angles. A value of 2, for instance, means that the range of the new grid should twice as large as the step of the old grid.