Welcome to diffractem’s documentation!

diffractem is a package for processing Serial Electron Diffraction data, following the protocols as outlined in Bücker et al., Front. Mol. Biosci., 2021. See this paper for a general introduction and documentation diffractem is mostly intended to be used from within Jupyter notebooks, such as those available from here.

Please see Installation for how to install diffractem and CrystFEL such that you can get started.

Of particular interest might be the documentation of PreProcOpts, which explains the various options you can define for preprocessing.

For the full API documentation, see here

Table of contents

• Overview
  • Installation
    • Create conda enivronment
    • Install diffractem
  • Submodules
    • diffractem.adxv module
      • Adxv
    • diffractem.compute module
      • map_reduction_func()
    • diffractem.dataset module
      • Dataset
    • diffractem.io module
      • dict_to_h5()
      • expand_files()
      • h5_to_dict()
      • make_master_h5()
    • diffractem.map_image module
    • diffractem.nexus module
      • copy_h5()
      • get_meta_fields()
      • get_table()
      • meta_to_nxs()
      • store_table()
    • diffractem.pre_proc_opts module
      • PreProcOpts
    • diffractem.proc2d module
      • analyze_and_correct()
      • apply_flatfield()
      • apply_saturation_correction()
      • apply_virtual_detector()
      • center_image()
      • center_of_mass()
      • center_of_mass2()
      • correct_dead_pixels()
      • correct_image()
      • cut_peaks()
      • func_lorentz()
      • get_pattern_info()
      • get_peaks()
      • loop_over_stack()
      • lorentz_fast()
      • lorentz_fit()
      • mean_clip()
      • radial_proj()
      • remove_background()
      • stack_nested()
      • strip_img()
    • diffractem.proc_peaks module
      • Cell
      • center_friedel()
      • get_acf()
      • get_pk_data()
    • diffractem.stream_parser module
      • StreamParser
      • augment_stream()
      • chop_stream()
      • make_substream()
      • parse_str_val()
    • diffractem.tools module
      • analyze_hkl()
      • call_indexamajig()
      • call_indexamajig_slurm()
      • call_partialator()
      • call_partialator_simple()
      • chop_stream()
      • dataframe_hash()
      • dict2file()
      • get_hkl_settings()
      • insert_init()
      • make_command()
      • make_geometry()
      • make_reference()
      • quantize_y_scan()
      • set_frames()
      • strip_file_path()
      • update_det_shift()
  • Module contents
• The Dataset object
  • Shot list
  • Data stacks
    • Chunking
    • Lazy evaluation and persisting
• Diffractem NeXus files
• EDview
• CrystFEL integration
  • Stream parsing
  • Peak finders
  • Calling indexamajig

Indices and tables

• Index

• Module Index

• Search Page