CCPEM-pipeliner
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README
Getting started
Writing new jobs
Node type names
CCPEM-Pipeliner API
Command Line Tools
Pipeline Tools
Tools for Running Jobs
Star File Utilities
General Utilities
Pipeliner Jobs
Nodes
Job Options
Processes
CCPEM-pipeliner
Index
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D
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Y
A
abort_job() (in module pipeliner.job_manager)
(pipeliner.api.manage_project.PipelinerProject method)
accelerating_voltage (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
acquire() (pipeliner.utils.DirectoryBasedLock method)
active_job_from_proc() (in module pipeliner.job_factory)
actual_pixel_size (pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
add_all_settings() (pipeliner.user_settings.Settings method)
add_bool_setting() (pipeliner.user_settings.Settings method)
add_compatibility_joboptions() (pipeliner.pipeliner_job.PipelinerJob method)
add_int_setting() (pipeliner.user_settings.Settings method)
add_job() (pipeliner.project_graph.ProjectGraph method)
add_md_to_summary_data() (in module pipeliner.metadata_tools)
add_new_input_edge() (pipeliner.project_graph.ProjectGraph method)
add_new_output_edge() (pipeliner.project_graph.ProjectGraph method)
add_node() (pipeliner.project_graph.ProjectGraph method)
add_optional_int_setting() (pipeliner.user_settings.Settings method)
add_optional_string_setting() (pipeliner.user_settings.Settings method)
add_output_node() (pipeliner.pipeliner_job.PipelinerJob method)
add_path_list_setting() (pipeliner.user_settings.Settings method)
add_pipeline_control() (pipeliner.pipeliner_job.PipelinerCommand method)
add_process() (pipeliner.project_graph.ProjectGraph method)
add_string_setting() (pipeliner.user_settings.Settings method)
add_to_cif() (pipeliner.deposition_tools.onedep_deposition.DepositionData method)
add_to_node_display_file() (in module pipeliner.nodes)
additional_joboption_validation() (pipeliner.pipeliner_job.PipelinerJob method)
algorithm (pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
alias (pipeliner.pipeliner_job.PipelinerJob attribute)
(pipeliner.process.Process attribute)
alias_checks() (pipeliner.project_graph.ProjectGraph method)
all_options_as_dict() (pipeliner.starfile_handler.JobStar method)
allowed_ext (pipeliner.nodes.GenNodeFormatConverter attribute)
apix (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute)
associated_data (pipeliner.results_display_objects.ResultsDisplayGraph attribute)
(pipeliner.results_display_objects.ResultsDisplayImage attribute)
(pipeliner.results_display_objects.ResultsDisplayMapModel attribute)
(pipeliner.results_display_objects.ResultsDisplayMontage attribute)
(pipeliner.results_display_objects.ResultsDisplayPlotlyHistogram attribute)
(pipeliner.results_display_objects.ResultsDisplayPlotlyObj attribute)
(pipeliner.results_display_objects.ResultsDisplayPlotlyScatter attribute)
(pipeliner.results_display_objects.ResultsDisplayTable attribute)
(pipeliner.results_display_objects.ResultsDisplayText attribute)
AtomCoordsGroupMetadataNode (class in pipeliner.nodes)
AtomCoordsNode (class in pipeliner.nodes)
authors (pipeliner.pipeliner_job.Ref attribute)
average_exposure_time (pipeliner.deposition_tools.onedep_deposition_objects.EmImageRecording attribute)
avg_electron_dose_per_image (pipeliner.deposition_tools.onedep_deposition_objects.EmImageRecording attribute)
B
bodycount (pipeliner.starfile_handler.BodyFile attribute)
BodyFile (class in pipeliner.starfile_handler)
BooleanJobOption (class in pipeliner.job_options)
BoolSettingDefinition (class in pipeliner.user_settings)
C
calibrated_magnification (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
category (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarCorrectedMics attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarMovieSet attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.EmSoftware attribute)
CATEGORY_LABEL (pipeliner.pipeliner_job.PipelinerJob attribute)
check_condition_is_met() (pipeliner.job_options.JobOptionCondition method)
check_dir() (pipeliner.job_options.DirPathJobOption method)
(pipeliner.job_options.JobOption method)
check_file() (pipeliner.job_options.ExternalFileJobOption method)
(pipeliner.job_options.InputNodeJobOption method)
(pipeliner.job_options.JobOption method)
(pipeliner.job_options.MultiExternalFileJobOption method)
(pipeliner.job_options.MultiInputNodeJobOption method)
(pipeliner.job_options.SearchStringJobOption method)
check_file_is_cif() (in module pipeliner.nodes)
check_file_is_json() (in module pipeliner.nodes)
check_file_is_mrc() (in module pipeliner.nodes)
check_file_is_text() (in module pipeliner.nodes)
check_file_is_tif() (in module pipeliner.nodes)
check_for_extra_keys() (pipeliner.user_settings.Settings method)
check_for_illegal_symbols() (in module pipeliner.utils)
check_funct (pipeliner.nodes.GenNodeFormatConverter attribute)
check_joboption_is_now_deactivated() (pipeliner.pipeliner_job.PipelinerJob method)
check_joboption_is_now_required() (pipeliner.pipeliner_job.PipelinerJob method)
check_multiseries_arguments() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method)
check_plottype_list() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method)
check_process_completion() (pipeliner.project_graph.ProjectGraph method)
check_process_status() (pipeliner.project_graph.ProjectGraph static method)
check_required_not_empty() (pipeliner.job_options.JobOption method)
check_singleplot_arguments() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method)
check_subplot_arguments() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method)
cif_type (pipeliner.deposition_tools.onedep_deposition.DepositionData attribute)
cifformat() (pipeliner.deposition_tools.onedep_deposition.DepositionData static method)
citation_id (pipeliner.deposition_tools.onedep_deposition_objects.Em2dProjectionSelection attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
clean_job_dirname() (in module pipeliner.utils)
clean_jobname() (in module pipeliner.utils)
clean_up_job() (pipeliner.project_graph.ProjectGraph method)
cleanup_all() (pipeliner.api.manage_project.PipelinerProject method)
cleanup_all_jobs() (pipeliner.project_graph.ProjectGraph method)
close() (pipeliner.project_graph.ProjectGraph method)
column_as_list() (pipeliner.starfile_handler.DataStarFile method)
com (pipeliner.pipeliner_job.PipelinerCommand attribute)
command (pipeliner.pipeliner_job.ExternalProgram attribute)
compare_job_parameters() (pipeliner.api.manage_project.PipelinerProject method)
compare_nested_lists() (in module pipeliner.utils)
compare_starfiles() (in module pipeliner.starfile_handler)
concentration (pipeliner.deposition_tools.onedep_deposition_objects.EmSpecimen attribute)
continue_job() (pipeliner.api.manage_project.PipelinerProject method)
convert_old_relion_pipeline() (in module pipeliner.starfile_handler)
convert_pipeline() (in module pipeliner.api.manage_project)
convert_relative_filename() (in module pipeliner.utils)
count_block() (pipeliner.starfile_handler.DataStarFile method)
count_file_lines() (in module pipeliner.utils)
create_archive() (pipeliner.api.manage_project.PipelinerProject method)
create_input_nodes() (pipeliner.pipeliner_job.PipelinerJob method)
create_output_nodes() (pipeliner.pipeliner_job.PipelinerJob method)
create_post_run_output_nodes() (pipeliner.pipeliner_job.PipelinerJob method)
create_reference_report() (pipeliner.api.manage_project.PipelinerProject method)
create_results_display() (pipeliner.pipeliner_job.PipelinerJob method)
create_results_display_object() (in module pipeliner.display_tools)
ctf_correction_method (pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
D
data (pipeliner.results_display_objects.ResultsDisplayPlotlyHistogram attribute)
(pipeliner.results_display_objects.ResultsDisplayPlotlyObj attribute)
(pipeliner.results_display_objects.ResultsDisplayPlotlyScatter attribute)
(pipeliner.starfile_handler.DataStarFile attribute)
data_format (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarCorrectedMics attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarMovieSet attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
data_items (pipeliner.deposition_tools.onedep_deposition.DepositionData attribute)
data_series_labels (pipeliner.results_display_objects.ResultsDisplayGraph attribute)
DataStarFile (class in pipeliner.starfile_handler)
date (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
date_time_tag() (in module pipeliner.utils)
dc_type (pipeliner.deposition_tools.onedep_deposition.DepositionData attribute)
ddc (in module pipeliner.deposition_tools.onedep_deposition_objects)
decompose_pipeline_filename() (in module pipeliner.utils)
default (pipeliner.user_settings.BoolSettingDefinition attribute)
(pipeliner.user_settings.IntSettingDefinition attribute)
(pipeliner.user_settings.OptionalIntSettingDefinition attribute)
(pipeliner.user_settings.OptionalStringSettingDefinition attribute)
(pipeliner.user_settings.PathListSettingDefinition attribute)
(pipeliner.user_settings.SettingDefinition attribute)
(pipeliner.user_settings.StringSettingDefinition attribute)
default_results_display() (pipeliner.nodes.AtomCoordsNode method)
(pipeliner.nodes.DensityMapNode method)
(pipeliner.nodes.Image2DGroupMetadataNode method)
(pipeliner.nodes.Image2DNode method)
(pipeliner.nodes.Image2DStackNode method)
(pipeliner.nodes.Image3DNode method)
(pipeliner.nodes.LogFileNode method)
(pipeliner.nodes.Mask2DNode method)
(pipeliner.nodes.Mask3DNode method)
(pipeliner.nodes.MicrographCoordsGroupNode method)
(pipeliner.nodes.MicrographGroupMetadataNode method)
(pipeliner.nodes.MicrographMovieGroupMetadataNode method)
(pipeliner.nodes.MicrographMovieNode method)
(pipeliner.nodes.MicrographNode method)
(pipeliner.nodes.MlModelNode method)
(pipeliner.nodes.Node method)
(pipeliner.nodes.ParticleGroupMetadataNode method)
delete_job() (pipeliner.api.manage_project.PipelinerProject method)
(pipeliner.project_graph.ProjectGraph method)
delete_summary_data_archive() (in module pipeliner.api.manage_project)
delete_summary_data_metadata_report() (in module pipeliner.api.manage_project)
delete_summary_data_reference_report() (in module pipeliner.api.manage_project)
delete_temp_node_file() (pipeliner.project_graph.ProjectGraph method)
delete_temp_node_files() (pipeliner.project_graph.ProjectGraph method)
DensityMapGroupMetadataNode (class in pipeliner.nodes)
DensityMapMetadataNode (class in pipeliner.nodes)
DensityMapNode (class in pipeliner.nodes)
DepositionData (class in pipeliner.deposition_tools.onedep_deposition)
details (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarCorrectedMics attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarMovieSet attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.Em2dProjectionSelection attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.EmCtfCorrection attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.EmImageProcessing attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.EmImageRecording attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.EmSampleSupport attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.EmSoftware attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.EmSpecimen attribute)
detector_distance (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
detector_mode (pipeliner.deposition_tools.onedep_deposition_objects.EmImageRecording attribute)
dimx (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute)
dimy (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute)
directory (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarCorrectedMics attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarMovieSet attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
DirectoryBasedLock (class in pipeliner.utils)
DirPathJobOption (class in pipeliner.job_options)
display_data (pipeliner.results_display_objects.ResultsDisplayText attribute)
display_name (pipeliner.pipeliner_job.JobInfo attribute)
dobj_type (pipeliner.results_display_objects.ResultsDisplayObject attribute)
documentation (pipeliner.pipeliner_job.JobInfo attribute)
doi (pipeliner.pipeliner_job.Ref attribute)
dtype (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute)
E
edit_comment() (pipeliner.api.manage_project.PipelinerProject method)
edit_jobstar() (in module pipeliner.api.api_utils)
electron_source (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
Em2dProjectionSelection (class in pipeliner.deposition_tools.onedep_deposition_objects)
Em3dReconstruction (class in pipeliner.deposition_tools.onedep_deposition_objects)
embedding_applied (pipeliner.deposition_tools.onedep_deposition_objects.EmSpecimen attribute)
EmCtfCorrection (class in pipeliner.deposition_tools.onedep_deposition_objects)
EmImageProcessing (class in pipeliner.deposition_tools.onedep_deposition_objects)
EmImageRecording (class in pipeliner.deposition_tools.onedep_deposition_objects)
EmImaging (class in pipeliner.deposition_tools.onedep_deposition_objects)
empiar_check() (in module pipeliner.deposition_tools.empiar_deposition_objects)
empiar_type_is_valid() (in module pipeliner.deposition_tools.empiar_deposition_objects)
EmpiarCorrectedMics (class in pipeliner.deposition_tools.empiar_deposition_objects)
EmpiarData (class in pipeliner.deposition_tools.empiar_deposition_objects)
EmpiarMovieSet (class in pipeliner.deposition_tools.empiar_deposition_objects)
EmpiarParticles (class in pipeliner.deposition_tools.empiar_deposition_objects)
EmpiarRefinedParticles (class in pipeliner.deposition_tools.empiar_deposition_objects)
empty_trash() (pipeliner.api.manage_project.PipelinerProject static method)
EmSampleSupport (class in pipeliner.deposition_tools.onedep_deposition_objects)
EmSoftware (class in pipeliner.deposition_tools.onedep_deposition_objects)
EmSpecimen (class in pipeliner.deposition_tools.onedep_deposition_objects)
energy_filter (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
energy_window (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
entry_id (pipeliner.deposition_tools.onedep_deposition_objects.Em2dProjectionSelection attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.EmSampleSupport attribute)
env_vars (pipeliner.user_settings.SettingDefinition attribute)
euler_angles_details (pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
EulerAnglesNode (class in pipeliner.nodes)
EvaluationMetricNode (class in pipeliner.nodes)
exe_path (pipeliner.pipeliner_job.ExternalProgram attribute)
experiment_id (pipeliner.deposition_tools.onedep_deposition_objects.EmSpecimen attribute)
ext (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute)
ExternalFileJobOption (class in pipeliner.job_options)
ExternalProgram (class in pipeliner.pipeliner_job)
F
field_name (pipeliner.deposition_tools.onedep_deposition.DepositionData attribute)
file (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute)
file_in_project() (in module pipeliner.utils)
file_name (pipeliner.starfile_handler.StarFile attribute)
file_path (pipeliner.results_display_objects.ResultsDisplayJson attribute)
(pipeliner.results_display_objects.ResultsDisplayPdfFile attribute)
(pipeliner.results_display_objects.ResultsDisplayTextFile attribute)
files_exts() (in module pipeliner.job_options)
film_material (pipeliner.deposition_tools.onedep_deposition_objects.EmSampleSupport attribute)
film_or_detector_model (pipeliner.deposition_tools.onedep_deposition_objects.EmImageRecording attribute)
final_depobjs (pipeliner.deposition_tools.onedep_deposition.OneDepDeposition attribute)
find_common_string() (in module pipeliner.utils)
find_immediate_child_processes() (pipeliner.project_graph.ProjectGraph method)
find_job_by_comment() (pipeliner.api.manage_project.PipelinerProject method)
find_job_by_rank() (pipeliner.api.manage_project.PipelinerProject method)
find_node() (pipeliner.project_graph.ProjectGraph method)
find_process() (pipeliner.project_graph.ProjectGraph method)
fitting_id (pipeliner.deposition_tools.onedep_deposition_objects.EmSoftware attribute)
fix_reserved_words() (in module pipeliner.starfile_handler)
flag (pipeliner.results_display_objects.ResultsDisplayObject attribute)
FloatJobOption (class in pipeliner.job_options)
force_unavailable (pipeliner.pipeliner_job.JobInfo attribute)
format (pipeliner.nodes.Node attribute)
format_converter (pipeliner.nodes.Node attribute)
format_for_metadata() (in module pipeliner.metadata_tools)
format_string_to_type_objs() (in module pipeliner.utils)
frames_per_image (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarCorrectedMics attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarMovieSet attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
fsc_type (pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
G
gather_metadata() (pipeliner.pipeliner_job.PipelinerJob method)
gather_onedep_jobs_and_depobjects() (in module pipeliner.deposition_tools.onedep_deposition)
gen_nodetype() (pipeliner.nodes.GenNodeFormatConverter method)
generalise_format() (pipeliner.nodes.Node method)
generate_multiseries_plots() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method)
generate_subplots() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method)
GenNodeFormatConverter (class in pipeliner.nodes)
get_additional_program_paths() (in module pipeliner.user_settings)
get_additional_reference_info() (pipeliner.pipeliner_job.PipelinerJob method)
get_archives_list_from_summary_file() (in module pipeliner.api.manage_project)
get_basename_mapping() (pipeliner.job_options.ExternalFileJobOption method)
(pipeliner.job_options.InputNodeJobOption method)
(pipeliner.job_options.JobOption method)
(pipeliner.job_options.MultiExternalFileJobOption method)
(pipeliner.job_options.MultiInputNodeJobOption method)
get_block() (pipeliner.starfile_handler.DataStarFile method)
get_bool() (pipeliner.user_settings.Settings method)
get_boolean() (pipeliner.job_options.BooleanJobOption method)
(pipeliner.job_options.JobOption method)
get_category_label() (pipeliner.pipeliner_job.PipelinerJob method)
get_ccpem_share_dir() (in module pipeliner.user_settings)
get_commands() (pipeliner.pipeliner_job.PipelinerJob method)
get_commands_and_nodes() (in module pipeliner.api.manage_project)
get_ctffind_executable() (in module pipeliner.user_settings)
get_current_output_nodes() (pipeliner.pipeliner_job.PipelinerJob method)
get_default_nrmpi() (in module pipeliner.user_settings)
get_default_nrthreads() (in module pipeliner.user_settings)
get_default_params_dict() (pipeliner.pipeliner_job.PipelinerJob method)
get_downstream_network() (pipeliner.project_graph.ProjectGraph method)
get_extra_options() (pipeliner.pipeliner_job.PipelinerJob method)
get_file_size_mb() (in module pipeliner.utils)
get_final_commands() (pipeliner.pipeliner_job.PipelinerJob method)
get_gctf_executable() (in module pipeliner.user_settings)
get_imgfile_info() (in module pipeliner.deposition_tools.empiar_deposition_objects)
get_input_nodes() (pipeliner.job_options.InputNodeJobOption method)
(pipeliner.job_options.JobOption method)
(pipeliner.job_options.MultiInputNodeJobOption method)
get_int() (pipeliner.user_settings.Settings method)
get_job() (pipeliner.api.manage_project.PipelinerProject method)
get_job_from_entrypoint() (in module pipeliner.job_factory)
get_job_info() (in module pipeliner.api.api_utils)
get_job_metadata() (in module pipeliner.metadata_tools)
get_job_number() (in module pipeliner.utils)
get_job_runner_command() (in module pipeliner.utils)
get_job_script() (in module pipeliner.utils)
get_job_types() (in module pipeliner.job_factory)
get_joboption_groups() (pipeliner.pipeliner_job.PipelinerJob method)
get_list() (pipeliner.job_options.JobOption method)
(pipeliner.job_options.MultiExternalFileJobOption method)
(pipeliner.job_options.MultiInputNodeJobOption method)
(pipeliner.job_options.MultiStringJobOption method)
(pipeliner.job_options.SearchStringJobOption method)
(pipeliner.user_settings.Settings method)
get_metadata_chain() (in module pipeliner.metadata_tools)
get_metadata_reports_from_summary_file() (in module pipeliner.api.manage_project)
get_minimum_dedicated() (in module pipeliner.user_settings)
get_modelcraft_executable() (in module pipeliner.user_settings)
get_motioncor2_executable() (in module pipeliner.user_settings)
get_mpi_command() (pipeliner.pipeliner_job.PipelinerJob method)
get_mpi_max() (in module pipeliner.user_settings)
get_mpirun_command() (in module pipeliner.user_settings)
get_next_resultsfile_name() (in module pipeliner.results_display_objects)
get_node_name() (pipeliner.project_graph.ProjectGraph static method)
get_node_results_display_file_name() (in module pipeliner.nodes)
get_nr_mpi() (pipeliner.pipeliner_job.PipelinerJob method)
get_nr_threads() (pipeliner.pipeliner_job.PipelinerJob method)
get_number() (pipeliner.job_options.FloatJobOption method)
(pipeliner.job_options.IntJobOption method)
(pipeliner.job_options.JobOption method)
get_optional_int() (pipeliner.user_settings.Settings method)
get_optional_string() (pipeliner.user_settings.Settings method)
get_ordered_classes_arrays() (in module pipeliner.display_tools)
get_path_to_source_files() (in module pipeliner.user_settings)
get_pipeline_edges() (pipeliner.project_graph.ProjectGraph method)
get_pipeliner_root() (in module pipeliner.utils)
get_project_procs_list() (pipeliner.project_graph.ProjectGraph method)
get_python_command() (in module pipeliner.utils)
get_qsub_command() (in module pipeliner.user_settings)
get_qsub_extra_count() (in module pipeliner.user_settings)
get_qsub_extras() (in module pipeliner.user_settings)
(pipeliner.user_settings.Settings method)
get_qsub_template() (in module pipeliner.user_settings)
get_queue_name() (in module pipeliner.user_settings)
get_queue_use() (in module pipeliner.user_settings)
get_ref_reports_from_summary_file() (in module pipeliner.api.manage_project)
get_regenerate_results_command() (in module pipeliner.utils)
get_resmap_executable() (in module pipeliner.user_settings)
get_result_display_object() (pipeliner.nodes.Node method)
get_runtab_options() (pipeliner.pipeliner_job.PipelinerJob method)
get_scratch_dir() (in module pipeliner.user_settings)
get_setting_value() (pipeliner.user_settings.Settings method)
get_string() (pipeliner.job_options.JobOption method)
(pipeliner.user_settings.Settings method)
get_thread_max() (in module pipeliner.user_settings)
get_topaz_executable() (in module pipeliner.user_settings)
get_upstream_network() (pipeliner.project_graph.ProjectGraph method)
get_value_from_string() (pipeliner.user_settings.BoolSettingDefinition static method)
(pipeliner.user_settings.IntSettingDefinition static method)
(pipeliner.user_settings.OptionalIntSettingDefinition static method)
(pipeliner.user_settings.OptionalStringSettingDefinition static method)
(pipeliner.user_settings.PathListSettingDefinition static method)
(pipeliner.user_settings.SettingDefinition static method)
(pipeliner.user_settings.StringSettingDefinition static method)
get_version() (pipeliner.pipeliner_job.ExternalProgram method)
get_warning_local_mpi() (in module pipeliner.user_settings)
get_whole_project_network() (pipeliner.project_graph.ProjectGraph method)
graph_from_starfile_cols() (in module pipeliner.display_tools)
grid_material (pipeliner.deposition_tools.onedep_deposition_objects.EmSampleSupport attribute)
grid_mesh_size (pipeliner.deposition_tools.onedep_deposition_objects.EmSampleSupport attribute)
grid_type (pipeliner.deposition_tools.onedep_deposition_objects.EmSampleSupport attribute)
H
handle_doppio_uploads() (pipeliner.pipeliner_job.PipelinerJob method)
header_format (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarCorrectedMics attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarMovieSet attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
header_tooltips (pipeliner.results_display_objects.ResultsDisplayTable attribute)
headers (pipeliner.results_display_objects.ResultsDisplayTable attribute)
headtype (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute)
histogram_from_starfile_col() (in module pipeliner.display_tools)
html_dir (pipeliner.results_display_objects.ResultsDisplayHtml attribute)
html_file (pipeliner.results_display_objects.ResultsDisplayHtml attribute)
html_str (pipeliner.results_display_objects.ResultsDisplayHtml attribute)
I
id (pipeliner.deposition_tools.onedep_deposition_objects.OneDepData attribute)
illumination_mode (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
Image2DGroupMetadataNode (class in pipeliner.nodes)
Image2DMetadataNode (class in pipeliner.nodes)
Image2DNode (class in pipeliner.nodes)
Image2DStackNode (class in pipeliner.nodes)
Image3DGroupMetadataNode (class in pipeliner.nodes)
Image3DMetadataNode (class in pipeliner.nodes)
Image3DNode (class in pipeliner.nodes)
image_desc (pipeliner.results_display_objects.ResultsDisplayImage attribute)
image_height (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarCorrectedMics attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarMovieSet attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
image_path (pipeliner.results_display_objects.ResultsDisplayImage attribute)
image_processing_id (pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.EmCtfCorrection attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.EmSoftware attribute)
image_recording_id (pipeliner.deposition_tools.onedep_deposition_objects.EmImageProcessing attribute)
image_width (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarCorrectedMics attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarMovieSet attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
imaging_id (pipeliner.deposition_tools.onedep_deposition_objects.EmImageRecording attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.EmSoftware attribute)
imaging_mode (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
img (pipeliner.results_display_objects.ResultsDisplayMontage attribute)
increment_file_basenames() (in module pipeliner.utils)
input_for_processes_list (pipeliner.nodes.Node attribute)
input_nodes (pipeliner.pipeliner_job.PipelinerJob attribute)
(pipeliner.process.Process attribute)
InputNodeJobOption (class in pipeliner.job_options)
int_ids (pipeliner.deposition_tools.onedep_deposition.OneDepDeposition attribute)
interconvert_box_star_coords() (in module pipeliner.starfile_handler)
IntJobOption (class in pipeliner.job_options)
IntSettingDefinition (class in pipeliner.user_settings)
is_available (pipeliner.pipeliner_job.JobInfo property)
is_continue (pipeliner.pipeliner_job.PipelinerJob attribute)
(pipeliner.starfile_handler.JobStar attribute)
is_submit_to_queue() (pipeliner.pipeliner_job.PipelinerJob method)
is_tomo (pipeliner.pipeliner_job.PipelinerJob attribute)
(pipeliner.starfile_handler.JobStar attribute)
is_uuid4() (in module pipeliner.utils)
issue (pipeliner.pipeliner_job.Ref attribute)
J
job_author (pipeliner.pipeliner_job.JobInfo attribute)
job_can_run() (in module pipeliner.job_factory)
job_counter (pipeliner.project_graph.ProjectGraph attribute)
job_default_parameters_dict() (in module pipeliner.api.api_utils)
job_from_dict() (in module pipeliner.job_factory)
JobInfo (class in pipeliner.pipeliner_job)
jobinfo (pipeliner.pipeliner_job.PipelinerJob attribute)
JobOption (class in pipeliner.job_options)
joboption_type (pipeliner.job_options.BooleanJobOption attribute)
(pipeliner.job_options.DirPathJobOption attribute)
(pipeliner.job_options.ExternalFileJobOption attribute)
(pipeliner.job_options.FloatJobOption attribute)
(pipeliner.job_options.InputNodeJobOption attribute)
(pipeliner.job_options.IntJobOption attribute)
(pipeliner.job_options.JobOption attribute)
(pipeliner.job_options.MultiExternalFileJobOption attribute)
(pipeliner.job_options.MultiInputNodeJobOption attribute)
(pipeliner.job_options.MultipleChoiceJobOption attribute)
(pipeliner.job_options.MultiStringJobOption attribute)
(pipeliner.job_options.SearchStringJobOption attribute)
(pipeliner.job_options.StringJobOption attribute)
JobOptionCondition (class in pipeliner.job_options)
joboptions (pipeliner.pipeliner_job.PipelinerJob attribute)
(pipeliner.starfile_handler.JobStar attribute)
JobOptionValidationResult (class in pipeliner.job_options)
JobStar (class in pipeliner.starfile_handler)
jobtype (pipeliner.starfile_handler.JobStar attribute)
journal (pipeliner.pipeliner_job.Ref attribute)
K
kwds (pipeliner.nodes.Node attribute)
L
labels (pipeliner.results_display_objects.ResultsDisplayMontage attribute)
launch_detached_process() (in module pipeliner.utils)
LigandDescriptionNode (class in pipeliner.nodes)
load_results_display_file() (pipeliner.nodes.Node method)
load_results_display_files() (pipeliner.pipeliner_job.PipelinerJob method)
LogFileNode (class in pipeliner.nodes)
long_desc (pipeliner.pipeliner_job.JobInfo attribute)
look_for_project() (in module pipeliner.api.manage_project)
loop_as_list() (pipeliner.starfile_handler.StarFile method)
M
magnification_calibration (pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
make_additional_args() (pipeliner.pipeliner_job.PipelinerJob method)
make_deposition_data_object() (in module pipeliner.deposition_tools.onedep_deposition)
make_int_ids() (pipeliner.deposition_tools.onedep_deposition.OneDepDeposition method)
make_job_parameters_schema() (in module pipeliner.metadata_tools)
make_job_results_schema() (in module pipeliner.metadata_tools)
make_map_model_thumb_and_display() (in module pipeliner.display_tools)
make_maps_slice_montage_and_3d_display() (in module pipeliner.display_tools)
make_mrcs_central_slices_montage() (in module pipeliner.display_tools)
make_particle_coords_thumb() (in module pipeliner.display_tools)
make_pretty_header() (in module pipeliner.utils)
make_queue_options() (pipeliner.pipeliner_job.PipelinerJob method)
make_substitutions() (pipeliner.starfile_handler.JobStar method)
maps (pipeliner.results_display_objects.ResultsDisplayMapModel attribute)
maps_colours (pipeliner.results_display_objects.ResultsDisplayMapModel attribute)
maps_data (pipeliner.results_display_objects.ResultsDisplayMapModel attribute)
maps_opacity (pipeliner.results_display_objects.ResultsDisplayMapModel attribute)
Mask2DNode (class in pipeliner.nodes)
Mask3DNode (class in pipeliner.nodes)
merge_depdata_items() (in module pipeliner.deposition_tools.onedep_deposition)
merge_depobjs() (pipeliner.deposition_tools.onedep_deposition.OneDepDeposition method)
merge_strategy (pipeliner.deposition_tools.onedep_deposition.DepositionData attribute)
merged_depobjs (pipeliner.deposition_tools.onedep_deposition.OneDepDeposition attribute)
message (pipeliner.job_options.JobOptionValidationResult attribute)
method (pipeliner.deposition_tools.onedep_deposition_objects.Em2dProjectionSelection attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
Micrograph (class in pipeliner.deposition_tools.empiar_deposition_objects)
MicrographCoordsGroupNode (class in pipeliner.nodes)
MicrographCoordsNode (class in pipeliner.nodes)
MicrographGroupMetadataNode (class in pipeliner.nodes)
MicrographMetadataNode (class in pipeliner.nodes)
MicrographMovieGroupMetadataNode (class in pipeliner.nodes)
MicrographMovieMetadataNode (class in pipeliner.nodes)
MicrographMovieNode (class in pipeliner.nodes)
MicrographNode (class in pipeliner.nodes)
micrographs_file_pattern (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarCorrectedMics attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarMovieSet attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
microscope_model (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
MicroscopeDataNode (class in pipeliner.nodes)
mini_montage_from_many_files() (in module pipeliner.display_tools)
mini_montage_from_stack() (in module pipeliner.display_tools)
mini_montage_from_starfile() (in module pipeliner.display_tools)
MlModelNode (class in pipeliner.nodes)
mode (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
models (pipeliner.results_display_objects.ResultsDisplayMapModel attribute)
models_colours (pipeliner.results_display_objects.ResultsDisplayMapModel attribute)
models_data (pipeliner.results_display_objects.ResultsDisplayMapModel attribute)
modes (pipeliner.results_display_objects.ResultsDisplayGraph attribute)
modify() (pipeliner.starfile_handler.JobStar method)
module
pipeliner.api.api_utils
pipeliner.api.manage_project
pipeliner.data_structure
pipeliner.deposition_tools.empiar_deposition_objects
pipeliner.deposition_tools.onedep_deposition
pipeliner.deposition_tools.onedep_deposition_objects
pipeliner.display_tools
pipeliner.job_factory
pipeliner.job_manager
pipeliner.job_options
pipeliner.metadata_tools
pipeliner.nodes
pipeliner.pipeliner_job
pipeliner.process
pipeliner.project_graph
pipeliner.results_display_objects
pipeliner.scripts.job_runner
pipeliner.star_writer
pipeliner.starfile_handler
pipeliner.user_settings
pipeliner.utils
MultiExternalFileJobOption (class in pipeliner.job_options)
MultiInputNodeJobOption (class in pipeliner.job_options)
MultipleChoiceJobOption (class in pipeliner.job_options)
MultiStringJobOption (class in pipeliner.job_options)
N
n_frames (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute)
name (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarCorrectedMics attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarMovieSet attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.EmSoftware attribute)
(pipeliner.nodes.Node attribute)
(pipeliner.pipeliner_job.ExternalProgram attribute)
(pipeliner.process.Process attribute)
(pipeliner.project_graph.ProjectGraph property)
(pipeliner.user_settings.SettingDefinition attribute)
new_job_of_type() (in module pipeliner.job_factory)
Node (class in pipeliner.nodes)
node_list (pipeliner.project_graph.ProjectGraph attribute)
nominal_cs (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
nominal_defocus_max (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
nominal_defocus_min (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
nominal_magnification (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
nominal_pixel_size (pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
not_compatible_with_default_output() (pipeliner.nodes.Node method)
num_class_averages (pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
num_diffraction_images (pipeliner.deposition_tools.onedep_deposition_objects.EmImageRecording attribute)
num_grids_imaged (pipeliner.deposition_tools.onedep_deposition_objects.EmImageRecording attribute)
num_images_or_tilt_series (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarCorrectedMics attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarMovieSet attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
num_particles (pipeliner.deposition_tools.onedep_deposition_objects.Em2dProjectionSelection attribute)
(pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
num_real_images (pipeliner.deposition_tools.onedep_deposition_objects.EmImageRecording attribute)
O
OneDepData (class in pipeliner.deposition_tools.onedep_deposition_objects)
OneDepDeposition (class in pipeliner.deposition_tools.onedep_deposition)
OptimiserDataNode (class in pipeliner.nodes)
OptionalIntSettingDefinition (class in pipeliner.user_settings)
OptionalStringSettingDefinition (class in pipeliner.user_settings)
other_metadata (pipeliner.pipeliner_job.Ref attribute)
OUT_DIR (pipeliner.pipeliner_job.PipelinerJob attribute)
outdir (pipeliner.process.Process attribute)
output_dir (pipeliner.pipeliner_job.PipelinerJob attribute)
output_from_process (pipeliner.nodes.Node attribute)
output_nodes (pipeliner.pipeliner_job.PipelinerJob attribute)
(pipeliner.process.Process attribute)
P
p_type (pipeliner.process.Process attribute)
pages (pipeliner.pipeliner_job.Ref attribute)
pairs_as_dict() (pipeliner.starfile_handler.StarFile method)
ParamsDataNode (class in pipeliner.nodes)
parse_additional_args() (pipeliner.pipeliner_job.PipelinerJob method)
parse_proclist() (pipeliner.api.manage_project.PipelinerProject method)
parse_procname() (pipeliner.api.manage_project.PipelinerProject method)
ParticleGroupMetadataNode (class in pipeliner.nodes)
PathListSettingDefinition (class in pipeliner.user_settings)
picked_particles_file_pattern (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
pipeline_dir (pipeliner.project_graph.ProjectGraph property)
pipeline_name (pipeliner.api.manage_project.PipelinerProject attribute)
pipeliner.api.api_utils
module
pipeliner.api.manage_project
module
pipeliner.data_structure
module
pipeliner.deposition_tools.empiar_deposition_objects
module
pipeliner.deposition_tools.onedep_deposition
module
pipeliner.deposition_tools.onedep_deposition_objects
module
pipeliner.display_tools
module
pipeliner.job_factory
module
pipeliner.job_manager
module
pipeliner.job_options
module
pipeliner.metadata_tools
module
pipeliner.nodes
module
pipeliner.pipeliner_job
module
pipeliner.process
module
pipeliner.project_graph
module
pipeliner.results_display_objects
module
pipeliner.scripts.job_runner
module
pipeliner.star_writer
module
pipeliner.starfile_handler
module
pipeliner.user_settings
module
pipeliner.utils
module
PipelinerCommand (class in pipeliner.pipeliner_job)
PipelinerJob (class in pipeliner.pipeliner_job)
PipelinerProject (class in pipeliner.api.manage_project)
pixel_height (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarCorrectedMics attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarMovieSet attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
pixel_width (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarCorrectedMics attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarMovieSet attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
plot_type (pipeliner.results_display_objects.ResultsDisplayPlotlyObj attribute)
plotlyfig (pipeliner.results_display_objects.ResultsDisplayPlotlyHistogram attribute)
(pipeliner.results_display_objects.ResultsDisplayPlotlyObj attribute)
(pipeliner.results_display_objects.ResultsDisplayPlotlyScatter attribute)
prepare_clean_up_lists() (pipeliner.pipeliner_job.PipelinerJob method)
prepare_deposition() (pipeliner.api.manage_project.PipelinerProject static method)
(pipeliner.deposition_tools.onedep_deposition.OneDepDeposition method)
prepare_deposition_data() (pipeliner.pipeliner_job.PipelinerJob method)
prepare_empiar_mics() (in module pipeliner.deposition_tools.empiar_deposition_objects)
prepare_empiar_mics_parts_data() (in module pipeliner.deposition_tools.empiar_deposition_objects)
prepare_empiar_parts() (in module pipeliner.deposition_tools.empiar_deposition_objects)
prepare_empiar_raw_mics() (in module pipeliner.deposition_tools.empiar_deposition_objects)
prepare_metadata_report() (pipeliner.api.manage_project.PipelinerProject method)
prepare_to_run() (pipeliner.pipeliner_job.PipelinerJob method)
print_nice_columns() (in module pipeliner.utils)
Process (class in pipeliner.process)
process_list (pipeliner.project_graph.ProjectGraph attribute)
PROCESS_NAME (pipeliner.pipeliner_job.PipelinerJob attribute)
ProcessDataNode (class in pipeliner.nodes)
programs (pipeliner.pipeliner_job.JobInfo attribute)
ProjectGraph (class in pipeliner.project_graph)
R
raised_by (pipeliner.job_options.JobOptionValidationResult attribute)
raw_depobjs (pipeliner.deposition_tools.onedep_deposition.OneDepDeposition attribute)
raw_options (pipeliner.pipeliner_job.PipelinerJob attribute)
read() (pipeliner.pipeliner_job.PipelinerJob method)
read_job() (in module pipeliner.job_factory)
read_only (pipeliner.project_graph.ProjectGraph property)
recording_temperature_maximum (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
recording_temperature_minimum (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
Ref (class in pipeliner.pipeliner_job)
references (pipeliner.pipeliner_job.JobInfo attribute)
refinement_type (pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
release() (pipeliner.utils.DirectoryBasedLock method)
relion_control (pipeliner.pipeliner_job.PipelinerCommand attribute)
remake_node_directory() (pipeliner.project_graph.ProjectGraph method)
remove_from_node_display_file() (in module pipeliner.nodes)
remove_md_from_summary_data() (in module pipeliner.metadata_tools)
remove_nonexistent_nodes() (pipeliner.process.Process method)
resolution (pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
resolution_method (pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
RestraintsNode (class in pipeliner.nodes)
ResultsDisplayGraph (class in pipeliner.results_display_objects)
ResultsDisplayHistogram (class in pipeliner.results_display_objects)
ResultsDisplayHtml (class in pipeliner.results_display_objects)
ResultsDisplayImage (class in pipeliner.results_display_objects)
ResultsDisplayJson (class in pipeliner.results_display_objects)
ResultsDisplayMapModel (class in pipeliner.results_display_objects)
ResultsDisplayMontage (class in pipeliner.results_display_objects)
ResultsDisplayObject (class in pipeliner.results_display_objects)
ResultsDisplayPdfFile (class in pipeliner.results_display_objects)
ResultsDisplayPending (class in pipeliner.results_display_objects)
ResultsDisplayPlotlyHistogram (class in pipeliner.results_display_objects)
ResultsDisplayPlotlyObj (class in pipeliner.results_display_objects)
ResultsDisplayPlotlyScatter (class in pipeliner.results_display_objects)
ResultsDisplayRvapi (class in pipeliner.results_display_objects)
ResultsDisplayTable (class in pipeliner.results_display_objects)
ResultsDisplayText (class in pipeliner.results_display_objects)
ResultsDisplayTextFile (class in pipeliner.results_display_objects)
reverse (pipeliner.deposition_tools.onedep_deposition.DepositionData attribute)
RigidBodiesNode (class in pipeliner.nodes)
run_cleanup() (pipeliner.api.manage_project.PipelinerProject method)
run_job() (in module pipeliner.job_manager)
(pipeliner.api.manage_project.PipelinerProject method)
run_schedule() (in module pipeliner.job_manager)
(pipeliner.api.manage_project.PipelinerProject method)
run_scheduled_job() (in module pipeliner.job_manager)
(pipeliner.api.manage_project.PipelinerProject method)
run_subprocess() (in module pipeliner.utils)
rvapi_dir (pipeliner.results_display_objects.ResultsDisplayRvapi attribute)
S
sample_support_id (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
save_job_submission_script() (pipeliner.pipeliner_job.PipelinerJob method)
save_results_display_files() (pipeliner.pipeliner_job.PipelinerJob method)
schedule_continue_job() (pipeliner.api.manage_project.PipelinerProject method)
schedule_job() (in module pipeliner.job_manager)
(pipeliner.api.manage_project.PipelinerProject method)
SearchStringJobOption (class in pipeliner.job_options)
SequenceAlignmentNode (class in pipeliner.nodes)
SequenceGroupNode (class in pipeliner.nodes)
SequenceNode (class in pipeliner.nodes)
set_alias() (pipeliner.api.manage_project.PipelinerProject method)
set_job_alias() (pipeliner.project_graph.ProjectGraph method)
set_joboption_order() (pipeliner.pipeliner_job.PipelinerJob method)
set_multiplot_data() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method)
set_option() (pipeliner.pipeliner_job.PipelinerJob method)
set_singleplot_data() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method)
set_string() (pipeliner.job_options.JobOption method)
SettingDefinition (class in pipeliner.user_settings)
Settings (class in pipeliner.user_settings)
shadowing_applied (pipeliner.deposition_tools.onedep_deposition_objects.EmSpecimen attribute)
short_desc (pipeliner.pipeliner_job.JobInfo attribute)
smart_strip_quotes() (in module pipeliner.utils)
software (pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
software_name (pipeliner.deposition_tools.onedep_deposition_objects.Em2dProjectionSelection attribute)
specimen_holder_model (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
specimen_holder_type (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
spherical_abberation (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute)
staining_applied (pipeliner.deposition_tools.onedep_deposition_objects.EmSpecimen attribute)
star_file (pipeliner.project_graph.ProjectGraph property)
StarFile (class in pipeliner.starfile_handler)
start_collapsed (pipeliner.results_display_objects.ResultsDisplayGraph attribute)
(pipeliner.results_display_objects.ResultsDisplayHtml attribute)
(pipeliner.results_display_objects.ResultsDisplayImage attribute)
(pipeliner.results_display_objects.ResultsDisplayJson attribute)
(pipeliner.results_display_objects.ResultsDisplayMontage attribute)
(pipeliner.results_display_objects.ResultsDisplayObject attribute)
(pipeliner.results_display_objects.ResultsDisplayPdfFile attribute)
(pipeliner.results_display_objects.ResultsDisplayPlotlyHistogram attribute)
(pipeliner.results_display_objects.ResultsDisplayPlotlyObj attribute)
(pipeliner.results_display_objects.ResultsDisplayPlotlyScatter attribute)
(pipeliner.results_display_objects.ResultsDisplayRvapi attribute)
(pipeliner.results_display_objects.ResultsDisplayTable attribute)
(pipeliner.results_display_objects.ResultsDisplayText attribute)
(pipeliner.results_display_objects.ResultsDisplayTextFile attribute)
status (pipeliner.process.Process attribute)
stop_schedule() (pipeliner.api.manage_project.PipelinerProject method)
str_is_hex_colour() (in module pipeliner.utils)
StringJobOption (class in pipeliner.job_options)
StringSettingDefinition (class in pipeliner.user_settings)
StructureFactorsNode (class in pipeliner.nodes)
subprocess_popen() (in module pipeliner.utils)
symmetry_type (pipeliner.deposition_tools.onedep_deposition_objects.Em3dReconstruction attribute)
T
table_data (pipeliner.results_display_objects.ResultsDisplayTable attribute)
temperature (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
tilt_angle_max (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
tilt_angle_min (pipeliner.deposition_tools.onedep_deposition_objects.EmImaging attribute)
TiltSeriesGroupMetadataNode (class in pipeliner.nodes)
TiltSeriesMetadataNode (class in pipeliner.nodes)
TiltSeriesMovieGroupMetadataNode (class in pipeliner.nodes)
TiltSeriesMovieMetadataNode (class in pipeliner.nodes)
TiltSeriesMovieNode (class in pipeliner.nodes)
TiltSeriesNode (class in pipeliner.nodes)
title (pipeliner.pipeliner_job.Ref attribute)
(pipeliner.results_display_objects.ResultsDisplayGraph attribute)
(pipeliner.results_display_objects.ResultsDisplayImage attribute)
(pipeliner.results_display_objects.ResultsDisplayMapModel attribute)
(pipeliner.results_display_objects.ResultsDisplayMontage attribute)
(pipeliner.results_display_objects.ResultsDisplayObject attribute)
(pipeliner.results_display_objects.ResultsDisplayPlotlyHistogram attribute)
(pipeliner.results_display_objects.ResultsDisplayPlotlyObj attribute)
(pipeliner.results_display_objects.ResultsDisplayPlotlyScatter attribute)
(pipeliner.results_display_objects.ResultsDisplayTable attribute)
(pipeliner.results_display_objects.ResultsDisplayText attribute)
TomogramGroupMetadataNode (class in pipeliner.nodes)
TomogramMetadataNode (class in pipeliner.nodes)
TomogramNode (class in pipeliner.nodes)
TomoManifoldDataNode (class in pipeliner.nodes)
TomoOptimisationSetNode (class in pipeliner.nodes)
TomoTrajectoryDataNode (class in pipeliner.nodes)
toplevel_description (pipeliner.nodes.Node attribute)
toplevel_type (pipeliner.nodes.Node attribute)
touch() (in module pipeliner.utils)
touch_temp_node_file() (pipeliner.project_graph.ProjectGraph method)
touch_temp_node_files() (pipeliner.project_graph.ProjectGraph method)
truncate_number() (in module pipeliner.utils)
type (pipeliner.deposition_tools.onedep_deposition_objects.EmCtfCorrection attribute)
(pipeliner.job_options.JobOptionValidationResult attribute)
(pipeliner.nodes.Node attribute)
U
undelete_job() (pipeliner.api.manage_project.PipelinerProject method)
(pipeliner.project_graph.ProjectGraph method)
update_job_references() (pipeliner.deposition_tools.onedep_deposition.DepositionData method)
update_job_status() (pipeliner.api.manage_project.PipelinerProject method)
update_jobinfo_file() (pipeliner.process.Process method)
update_jobrefs() (pipeliner.deposition_tools.onedep_deposition.OneDepDeposition method)
update_lock_message() (pipeliner.project_graph.ProjectGraph method)
update_status() (pipeliner.project_graph.ProjectGraph method)
update_uids_to_int_ids() (pipeliner.deposition_tools.onedep_deposition.OneDepDeposition method)
V
validate() (pipeliner.job_options.BooleanJobOption method)
(pipeliner.job_options.DirPathJobOption method)
(pipeliner.job_options.ExternalFileJobOption method)
(pipeliner.job_options.FloatJobOption method)
(pipeliner.job_options.InputNodeJobOption method)
(pipeliner.job_options.IntJobOption method)
(pipeliner.job_options.JobOption method)
(pipeliner.job_options.MultiExternalFileJobOption method)
(pipeliner.job_options.MultiInputNodeJobOption method)
(pipeliner.job_options.MultipleChoiceJobOption method)
(pipeliner.job_options.MultiStringJobOption method)
(pipeliner.job_options.SearchStringJobOption method)
(pipeliner.job_options.StringJobOption method)
validate_dynamically_required_joboptions() (pipeliner.pipeliner_job.PipelinerJob method)
validate_input_files() (pipeliner.pipeliner_job.PipelinerJob method)
validate_joboptions() (pipeliner.pipeliner_job.PipelinerJob method)
validate_pipeline_file() (pipeliner.project_graph.ProjectGraph method)
validate_starfile() (in module pipeliner.api.api_utils)
vers_com (pipeliner.pipeliner_job.ExternalProgram attribute)
vers_lines (pipeliner.pipeliner_job.ExternalProgram attribute)
version (pipeliner.deposition_tools.onedep_deposition_objects.EmSoftware attribute)
(pipeliner.pipeliner_job.JobInfo attribute)
vitrification_applied (pipeliner.deposition_tools.onedep_deposition_objects.EmSpecimen attribute)
voltage (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute)
volume (pipeliner.pipeliner_job.Ref attribute)
voxel_type (pipeliner.deposition_tools.empiar_deposition_objects.EmpiarCorrectedMics attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarData attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarMovieSet attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarParticles attribute)
(pipeliner.deposition_tools.empiar_deposition_objects.EmpiarRefinedParticles attribute)
W
wait_for_job_to_finish() (in module pipeliner.job_manager)
working_dir (pipeliner.pipeliner_job.PipelinerJob attribute)
wrap_text() (in module pipeliner.utils)
write() (in module pipeliner.star_writer)
(pipeliner.starfile_handler.JobStar method)
write_default_jobstar() (in module pipeliner.api.api_utils)
write_default_result_file() (pipeliner.nodes.Node method)
write_default_runjob() (in module pipeliner.api.api_utils)
write_deposition_cif_file() (pipeliner.deposition_tools.onedep_deposition.OneDepDeposition method)
write_displayobj_file() (pipeliner.results_display_objects.ResultsDisplayObject method)
write_jobstar() (in module pipeliner.star_writer)
(pipeliner.pipeliner_job.PipelinerJob method)
write_json() (pipeliner.deposition_tools.onedep_deposition.DepositionData method)
write_runjob() (pipeliner.pipeliner_job.PipelinerJob method)
write_to_stream() (in module pipeliner.star_writer)
X
xaxis_label (pipeliner.results_display_objects.ResultsDisplayGraph attribute)
xrange (pipeliner.results_display_objects.ResultsDisplayGraph attribute)
xvalues (pipeliner.results_display_objects.ResultsDisplayGraph attribute)
(pipeliner.results_display_objects.ResultsDisplayMontage attribute)
Y
yaxis_label (pipeliner.results_display_objects.ResultsDisplayGraph attribute)
year (pipeliner.pipeliner_job.Ref attribute)
yrange (pipeliner.results_display_objects.ResultsDisplayGraph attribute)
yvalues (pipeliner.results_display_objects.ResultsDisplayGraph attribute)
(pipeliner.results_display_objects.ResultsDisplayMontage attribute)
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