Outputs¶
Within the parameter file the output filename is specified by the output_name parameter. This output file
will always be a HDF5 file. The dataset names described below are prefixed by the value of the output_prefix
parameter (which is empty by default). As example, if the value of output_prefix would be alpha_, the dataset
data is saved as alpha_data in the output file. By using the prefix multiple outputs can be written to the same
HDF5 file.
The output file typically holds three datasets:
The dataset data contains the averaged reconstruction of the normalized and drift aligned object holograms. If the defocus value
for the individual holograms (as specified by the parameters defocus_first and defocus_step) is
not zero, the holograms are propagated to the zero defocus. The dataset empty contains the averaged
reconstruction of the empty holograms.
As HDF5 files do not support datasets of complex numbers, the datasets are stored as a compound data type of 8 bytes
length. The compound has two members, both 32 bit floats. The first member r at byte offset 0, contains the real
part of the complex numbers, the second member i at byte offset 4 the imaginary part. This convention is recognized
by HDF5 python library (http://www.h5py.org) and the HDF5 Digital Micrograph plugin (
https://github.com/niermann/gms_plugin_hdf5).
The dataset variance contains the estimate of the per-pixel variance of the object hologram series (drift aligned
and propagated to zero defocus), this is stored as 32 bit float.
The datasets data and variance are not present, when the object hologram reconstruction is disabled by omitting
the object_names parameter. The dataset empty is not present, when the empty hologram reconstruction
is disabled by omitting the empty_names parameter.
If the parameter output_series is set, additionally a group series is present in the output file,
which contains datasets 000, 001, 002, … . These contain the reconstructions of the individual holograms
in the object series. The dataset 000 refers to the first hologram (as specified by the parameter
object_names and object_first). The consecutive numbers refer to the consecutive holograms
in the series. These are also stored as complex valued datasets.
If the parameter output_aligned is set, additional a group aligned_rois is present in the output file,
which contains datasets 000, 001, 002, etc. These contain the region of interest (parameter
roi) as tracked across the object series in the raw-alignment step. The datatype of the dataset is
typically the datatype used in the image files.
Additional the datasets/groups have attributes, which contain further metadata. Not all the following attributes are present in all datasets. This list is incomplete.
| Name | Type | Description |
|---|---|---|
| holoaverage_version | String | Version number of holoaverage used for averaging. |
| holoaverage_param | String | Parameter string passed to holoaverage (JSON). |
| align_roi | List of 4 Ints | Region of object holograms used for raw alignment (see align_roi) |
| binning | List of 2 Ints | (X, Y) Detector binning of series |
| carrier(nm-1) | List of 2 Floats | Spatial frequency of the reconstructed side band in 1/nm |
| convergence | List of Floats | Total squared residual for each iteration of averaging procedure |
| defocus(nm) | List of N Floats | Defocus of the individual holograms (after alignment) in nm |
| detector | String | Name of detector (according to image files) |
| dim_offset | List of 2 Floats | (X, Y) offset (according to image files) |
| dim_scale | List of 2 Floats | (X, Y) sampling |
| dim_unit | List of 2 Strings | (X, Y) units for dim_scale and dim_offset |
| error | List of N Floats | Squared residual between individual reconstruction and average |
| factor | List of Nx2 Floats | (real, imaginary) global amplitudes for individual holograms |
| microscope | String | Name of microscope (according to image files) |
| raw_shift | List of Nx2 Ints | (X, Y) shift of individual holograms in pixels after raw-alignment |
| reconstructionCutOff2(nm2) | 2x2 Floats | Squared cut-off frequency matrix (in 1/nm^2; see cut_off2) |
| reconstructionMaskType | … | Mask type as used for cutoff (see filter_func) |
| roi | List of 4 Ints | Reconstructed region of object holograms (see roi) |
| shift(nm) | List of Nx2 Floats | (X, Y) shift of individual holograms in nm (after fine-alignment) |
| tilt(1/nm) | List of Nx2 Floats | (X, Y) tilt of individual holograms in 1/nm (after alignment) |
| voltage(kV) | Float | Acceleration voltage in kV |