multiple data block example

In this example, we will use starfile to read and write files containing multiple data blocks.

particles.star

data_optics

loop_
_rlnOpticsGroup #1
_rlnOpticsGroupName #2
_rlnSphericalAberration #3
_rlnVoltage #4
_rlnImagePixelSize #5
_rlnImageSize #6
_rlnImageDimensionality #7
1   opticsGroup1    2.700000    300.000000  3.300000    160 3

data_particles

loop_
_rlnCoordinateX #1
_rlnCoordinateY #2
_rlnCoordinateZ #3
_rlnAngleRot #4
_rlnAngleTilt #5
_rlnAnglePsi #6
_rlnImageName #7
_rlnCtfImage #8
_rlnRandomSubset #9
_rlnPixelSize #10
_rlnMicrographName #11
_rlnOpticsGroup #12
_rlnGroupNumber #13
_rlnOriginXAngst #14
_rlnOriginYAngst #15
_rlnOriginZAngst #16
_rlnClassNumber #17
_rlnNormCorrection #18
_rlnLogLikeliContribution #19
_rlnMaxValueProbDistribution #20
_rlnNrOfSignificantSamples #21
880.274000  895.057900  1107.245000 131.246000  106.820800  45.228430   subtomo_05Feb21/TS.mrc/TS.mrc_22redo_combined_0000000_3.30A.mrc subtomo_05Feb21/TS.mrc/TS.mrc_22redo_combined_0000000_ctf_3.30A.mrc 2   3.300000    TS.mrc.tomostar 1   1   0.000000    0.000000    0.000000    6   1.000000    4150981.000000  1.000000    1
973.165500  958.641800  1115.101000 87.247110   109.236500  45.323810   subtomo_05Feb21/TS.mrc/TS.mrc_22redo_combined_0000001_3.30A.mrc subtomo_05Feb21/TS.mrc/TS.mrc_22redo_combined_0000001_ctf_3.30A.mrc 1   3.300000    TS.mrc.tomostar 1   1   0.000000    0.000000    0.000000    4   1.000000    4150837.000000  1.000000    1
955.949400  960.465100  629.459100  9.331370    99.309980   11.024810   subtomo_05Feb21/TS.mrc/TS.mrc_22redo_combined_0000002_3.30A.mrc subtomo_05Feb21/TS.mrc/TS.mrc_22redo_combined_0000002_ctf_3.30A.mrc 1   3.300000    TS.mrc.tomostar 1   1   0.000000    0.000000    0.000000    3   1.000000    4150650.000000  1.000000    1
1175.177000 1135.731000 882.605200  -147.261200 81.605380   77.325710   subtomo_05Feb21/TS.mrc/TS.mrc_22redo_combined_0000003_3.30A.mrc subtomo_05Feb21/TS.mrc/TS.mrc_22redo_combined_0000003_ctf_3.30A.mrc 2   3.300000    TS.mrc.tomostar 1   1   0.000000    0.000000    0.000000    1   1.000000    4151420.000000  1.000000    1
1190.658000 1122.102000 1073.642000 40.404590   98.061770   42.563060   subtomo_05Feb21/TS.mrc/TS.mrc_22redo_combined_0000004_3.30A.mrc subtomo_05Feb21/TS.mrc/TS.mrc_22redo_combined_0000004_ctf_3.30A.mrc 1   3.300000    TS.mrc.tomostar 1   1   0.000000    0.000000    0.000000    6   1.000000    4150168.000000  1.000000    1

Reading

Reading a file with multiple data blocks is similar to reading a file with a single data block. In this case, a dictionary of dataframes or dictionaries is returned. The keys of this dictionary are the names of data blocks.

import starfile

star = starfile.read('particles.star')
optics_df = star['optics']
particle_df = star['particles']

Tip

starfile.read can be forced to always return a dictionary of entries.

starfile.read('particles.star', always_dict=True)

Writing

Writing a file containing multiple data blocks is similar, simply pass a dictionary of entries.

import starfile

starfile.write(
    {'optics': optics_df, 'particles': particle_df}, 'new_file.star'
)