"Euler angles are a mean of representing the spatial orientation of any system of coordinates of the space as a composition of three rotations from a reference system of coordinates."

- the first rotation is denoted by phi and is around the z axis
- the second rotation is called theta and is around the new y-axis.
- the third rotation is denoted by psi and is around the new z axis

The three rotations may be expressed as a single 3x3 matriz called Euler matrix

r11 = cos(psi)*cos(theta)*cos(phi)-sin(psi)*sin(phi) r12 = cos(psi)*cos(theta)*sin(phi)+sin(psi)*cos(phi) r13 = -cos(psi)*sin(theta) r21 = -sin(psi)*cos(theta)*cos(phi)-cos(psi)*sin(phi) r22 = -sin(psi)*cos(theta)*sin(phi)+cos(psi)*cos(phi) r23 = sin(psi)*sin(theta) r31 = sin(theta)*cos(phi) r32 = sin(theta)*sin(phi) r33 = cos(theta) where the first index refers to rows and the second to columns

Apositive rotation implies a clockwise rotation of the OBJECT or a anti-clockwise rotation of the system of coordinates

Euler angles in Xmipp complies with the 3DEM standard (see http://www.ebi.ac.uk/pdbe/docs/3dem/test_image/3DEM_compliance.html for details)

In general, Xmipp can manage any Filename you can think of. However, there are some ideas that could help you to organize your data, and which might tell you more about the file only by its name. We could divide files in several classes:

Data type | Suggested extension | Suggested filenames |
---|---|---|

Images | .xmp | g1ta000001.xmp |

Volumes | .vol or .xmp | art000001.vol, wbp000001.vol, sirt000001.vol |

Selection Files | .sel | g1t.sel |

Document Files | .doc | angles.doc |

The class FileName assumes a filename structure as in g1ta000001.xmp, ie, a filename root (g1ta), a number (000001) and an extension (xmp) ("

Notice also that Spider requires all data files (volumes, images, document files, ...) to have the same extension. You might prefer this other convention if you don't want to make copies of the files, or to have to rename the files before entering in Spider.

The basic multidimensional classes implemented in this library admit two kinds of access: physical and logical. The physical positions are those indexes of the pixel inside the C matrix. Just an example, suppose we have a 65x65 image, then the physical indexes range from 0 to 64, being I[0][0] (if this could be written) the first pixel stored. However, we might be interested in writing procedures in a more mathematical fashion trying to access negative indexes (or even fractional ones!! See ImageOver) This conception is very useful when you want to represent a discretized plane whose origin is at the center of the image, for instance. So, you can express in a simpler way your algorithms without having to make a by hand translation from the logical positions to the physical ones.

Suppose now that we are interested to have the logical origin at the center of the image 65x65, ie, at physical position [32][32]. This would mean that the physical position [0][0] is now at logical position (-32,-32), and the logical indexes range now from -32 to 32.

This logical index defintion is done by means of the starting indexes of matrices (see matrix2D) where you can define which logical position is occupying the first physical pixel, ie,

I().startingY()=-32; I().startingX()=-32;

From now on you can start to access to logical positions even with negative indexes. The usual way of establishing loops inside this logical images is by using the starting and finishing information of its axes

Image I(65,65); I().init_random(); float sum=0; for (int i=STARTINGY(I()); i<=FINISHINGY(I()); i++) for (int j=STARTINGX(I()); j<=FINISHINGX(I()); j++) { sum += I(i,j); // sum += IMGPIXEL(i,j); }

Although the previous example has been used using the class Image, the logical access rely on the classes matrix1D, matrix2D, and matrix3D, and all the concepts explained for images are extensible for vectors and volumes. The related functions are STARTINGX, STARTINGY, STARTINGZ, FINISHINGX, FINISHINGY, FINISHINGZ, IMGPIXEL, DIRECT_IMGPIXEL, VOLVOXEL, DIRECT_VOLVOXEL, VEC_ELEM, MAT_ELEM, VOL_ELEM, DIRECT_VEC_ELEM, DIRECT_MAT_ELEM, DIRECT_VOL_ELEM

Pay attention to the index order when pointing to a pixel, first you have to give the most outer coordinate (which is the less varying one in the actual implementation), and then increase the coordinate. For volumes the usual way of making a loop is

Volume V(65,65,65); V().init_random(); float sum=0; for (int k=STARTINGZ(V()); k<=FINISHINGZ(V()); k++) for (int i=STARTINGY(I()); i<=FINISHINGY(I()); i++) for (int j=STARTINGX(I()); j<=FINISHINGX(I()); j++) { sum +=V(k,i,j); }

Notice that if you don't modify the origin of the multidimensional array then the physical and logical accesses are the same.

This means that for images with an even dimension, the center will be "displaced" in that direction. Let's have a look on the following two diagrams of cell indexes.