amorphys
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Table of contents:
Why amorphys?
Motivations
Core concerns
Core concepts
How is it going to work?
Editor UI
Designer UI
Experiment runner
Overview of metadata organization
Sections
A recommended way of annotation
“section” class
Formatting options
Single-file format
Multi-file format
Making a project description
Organization of “project” section
“dataset” subsection
“people” subsection
“affiliations” subsection
“fundings” subsection
“data_published_by” subsection
Core objects (obsolete)
Entity
Entity class
Types of entities
Spatial entity
Temporal entity
Signals
Programs and Routines
Relationship
How Relationship works
Pre-defined relationship keys
Spatial relationships
Temporal relationships
Relationships between signals
Defining your own relationship key(s)
Context
Context class
Classes for measurements
Date
Time
Subject-related
Age
Sex
Death
Space
Quantity
Notes on unit usages
Description of protocol control
Overview
Unitary stimulus control
StimulusState
ApparatusState
Sequence-type stimulus description
Sequencer
StimulusBlock
StimulusGeneration
Context-dependent stimulus sequence
StateMachine
MachineState
MachineStateTransition
Behavioral model for a subject
Variables and expressions
Use of variables
Use of conditions
Expressions and formatters
Use of templates
Supplementary documents
Predefined subclasses for Spatial
Subject entity
Component entity
Predefined subclasses for Temporal
Procedure
Action and Block
Phase
Specific types of actions
Predefined subclasses for Signal
Sampled and its subclasses
Event and its subclasses
State
Definition of your own entity class
Metadata structure (obsolete)
Subject description
“subjects” section
Setups
“setups” section
Setup class
Acquisition
“acquisition” section
Procedures
“procedures” section
Task/Sweep control
“tasks” section
Experimental variables
An example
Scopes
Structure of scopes
Basic properties
Subsection for description of lower scope(s)
Class reference
Specification of metadata sections
section
project
“Referrable” objects
referrable
individual
institution class
person
contributor
license
citation
Miscellaneous
dataset
credit
funding
amorphys
Docs
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Core objects (obsolete)
»
Supplementary documents
»
Definition of your own entity class
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Definition of your own entity class
¶
TODO
It must be possible and recommended! Needs some way…