I3 Processor

This module implements the processing function for the I3 software package.

The module will create an I3 project directory.

processors.i3_processor.center_coordinates(coords, size, binning=1)
Given an XYZ tuple of particle coordinates and the reconstruction they came from, shift the

coordinates so that the origin is at the center of the tomogram

Parameters

  • coords – the (x, y, z) coordinates for the particle

  • size – the reconstruction MRC half-dimensions in (nx/2, ny/2, nz/2) form

  • binning – the bin factor from the original stack to the final reconstruction

Returns: the new coordinates as a (x, y, z) tuple

processors.i3_processor.check_and_fix_names_starting_with_numbers(name)
Since I3 map names cannot start with a number, add a letter ‘a’ to any names starting with a

number

Parameters

name – The name to check for a beginning number

Returns: The new name (unchanged if the name properly started with a letter)

processors.i3_processor.convert_tlt_eman2(info_file, map_file, output)

Given an EMAN2 tomogram info JSON file, write out an I3 format .tlt file for that tomogram

Parameters

  • info_file – The EMAN2 JSON info file for the tomogram

  • map_file – The map file to place at the head of the .tlt file

  • output – The output file path to write the new I3 .tlt file to

Returns: None

processors.i3_processor.convert_tlt_imod(map_file, tilt_angle, file_in, file_out)

Convert an IMOD .tlt file to I3 tilt file format :param map_file: The map MRC file (not the full path) :param tilt_angle: The angle to put as the tilt azimuth :param file_in: The IMOD .tlt file :param file_out: The I3 tilt file

Returns: None

processors.i3_processor.eman2_processor_to_i3(root, name, i3_args)

Implements the I3 processing of simulated data that was reconstructed using the EMAN2 Processor.

Parameters

  • root – The ETSimulations project root directory

  • name – The particle name

  • i3_args – The I3 Processor arguments

Returns: None

processors.i3_processor.eman2_real_to_i3(i3_args)

Implements the I3 processing of a real data set reconstructed/particle-picked with EMAN2

Parameters

i3_args – The I3 Processor arguments

Returns: None

processors.i3_processor.extract_e2_particles(stack_file, name, destination)

Unpack a stack of EMAN2 particles into individual sub-volume maps

Parameters

  • stack_file – The EMAN2 particle stack file (either a .lst set or .hdf stack)

  • name – The basename to assign to extracted maps

  • destination – The destination folder to place the extracted particles in

Returns: None

processors.i3_processor.get_eman2_tilts(info_file)
Given an EMAN2 tomogram info JSON file, extract an array of the tilt angles as would be given in

an IMOD .tlt file

Parameters

info_file – The tomogram JSON info file path

Returns: A tuple of (average tilt axis computed across all tilts,

a numpy array of the tilt angles for that tomogram)

processors.i3_processor.get_mrc_size(rec)
Return the half the size of each dimension for an MRC file, so that we can move the origin to

the center instead of the corner of the file

Parameters

rec – the MRC file to get the size of

Returns: A tuple (x/2, y/2, z/2) of the half-lengths in each dimension

processors.i3_processor.get_slicer_info(mod_file)

Open an IMOD .mod file and retrieve the Slicer information

Parameters

mod_file – The .mod file path

Returns: A list of Slicer point objects with keys {“angles”, “coords”}

processors.i3_processor.get_trf_lines_imod(slicer_info, basename)
Given the particle coordinates and angles for a tomogram, format them into a list of lines to

write out to a .trf file

Parameters

  • slicer_info – A list of dictionary objects with keys {“coords”, “angles”} for the particles in a tomogram (returned from get_slicer_info())

  • basename – A basename for the tomogram, to be put as the data subset identifier for the .trf

Returns: A list of lines to write out to a .trf file

processors.i3_processor.imod_processor_to_i3(root, name, i3_args)

Implements the I3 processing of simulated data that was reconstructed using the IMOD Processor.

Parameters

  • root – The ETSimulations project root directory

  • name – The particle name

  • i3_args – The I3 Processor arguments

Returns: None

processors.i3_processor.imod_real_to_i3(name, i3_args)

Implements the I3 processing of a real data set reconstructed/particle-picked with IMOD

Parameters

  • name – The particle name

  • i3_args – The I3 Processor arguments

Returns: None

processors.i3_processor.parse_lst_file(filename)
Read EMAN2 .lst particle sets and extract a dictionary of particle numbers mapped to the

particle’s tomogram info file, extracted stack file, and local particle number within that tomogram

Parameters

filename – The .lst file path

Returns: A tuple of
(

Dictionary of { particle number: {“info”, “stack”, “local_no”} } objects, Dictionary of { stack: number of particles in stack }

)

processors.i3_processor.read_particle_params(json_file)
Given a particle_parms_*.json file from EMAN2 STA, extract the particle list and their

transformation matrices.

Parameters

json_file – The particle_parms_*.json file path

Returns: A tuple of (.lst file name, dictionary of {particle number, transformation matrix})

processors.i3_processor.rotate_positions_around_z(positions)
Given a list of coordinates, rotate them all by 90 degrees around the z-axis. This is used to

convert particle coordinates from the raw tiltseries to the final reconstruction’s coordinate system for simulated data.

Parameters

positions – A list of [x, y, z] coordinates

Returns: None

processors.i3_processor.shift_coordinates_bottom_left(coords, size, binning=1)
Given an XYZ tuple of particle coordinates and the reconstruction they came from, shift the

coordinates so that the origin is at the bottom-left of the tomogram

Parameters

  • coords – the (x, y, z) coordinates for the particle

  • size – the reconstruction MRC half-dimensions in (nx/2, ny/2, nz/2) form

  • binning – the bin factor from the original stack to the final reconstruction, to be used if you are using coordinates based on the original unbinned coordinate system

Returns: the new coordinates as a (x, y, z) tuple

processors.i3_processor.slicer_angles_to_i3_matrix(angles)

Given a set of angles from IMOD’s Slicer, convert those angles to a rotation matrix.

Parameters

angles – The (x, y, z) Slicer angles

Returns

The corresponding rotation matrix

processors.i3_processor.split_coords(coords)
Given XYZ coordinates, split into the integer positions and displacements from the integer

position, as required by the trf files

Parameters

coords – The X, Y, Z coordinates

Returns: tuple (icoor, diff_coord) of the integer and decimal parts, respectively

processors.i3_processor.write_trf_eman2_extracted(set_name, translations, rot_matrix, trf_file)

Helper function to write out the .trf file for one extracted particle

Parameters

  • set_name – The I3 set name to write (should be the basename of the extracted map file)

  • translations – The particle translations

  • rot_matrix – The rotation matrix for the particle

  • trf_file – The output file path

Returns: None