.. _sec-outputs: Outputs ======= Within the parameter file the output filename is specified by the :ref:`param-output_name` parameter. This output file will always be a HDF5 file. The dataset names described below are prefixed by the value of the :ref:`param-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 :ref:`param-defocus_first` and :ref:`param-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 (``_) and the HDF5 Digital Micrograph plugin ( ``_). 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 :ref:`param-object_names` parameter. The dataset ``empty`` is not present, when the empty hologram reconstruction is disabled by omitting the :ref:`param-empty_names` parameter. If the parameter :ref:`param-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 :ref:`param-object_names` and :ref:`param-object_first`). The consecutive numbers refer to the consecutive holograms in the series. These are also stored as complex valued datasets. If the parameter :ref:`param-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 :ref:`param-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 :ref:`param-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 :ref:`param-cut_off2`) reconstructionMaskType ... Mask type as used for cutoff (see :ref:`param-filter_func`) roi List of 4 Ints Reconstructed region of object holograms (see :ref:`param-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 =========================== =================== ================================================================================