amorphys
stable
Table of contents:
Why amorphys?
Overview
Background
What is amorphys?
Structure
How is it going to work?
Editor UI
Designer UI
Experiment runner
Core objects
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
URI-based reference
Referrable class
Individual class
Person class
License class
Citation class
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
Overview
Sections
A recommended way of annotation
“section” class
Formatting options
Single-file format
Multi-file format
Project organization
“organization” section
Dataset class
Contributor class
Institution class
Funding class
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)
amorphys
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Index
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Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
Y
A
Acquisition (built-in class)
acquisition (built-in class)
Action (built-in class)
affiliation (Contributor attribute)
affiliations (organization attribute)
age (Animal attribute)
(Participant attribute)
(Subject attribute)
(Tissue attribute)
amplitude (StimulusState attribute)
Animal (built-in class)
Apparatus (built-in class)
ApparatusState (built-in class)
authors (License attribute)
B
Block (built-in class)
C
channel (StimulusGeneration attribute)
ChronicPreparation (built-in class)
Citation (built-in class)
Component (built-in class)
components (Setup attribute)
condition (built-in class)
contact (Person attribute)
Context (built-in class)
Contributor (built-in class)
control
conversion (acquisition attribute)
D
data (DataFile attribute)
DataFile (built-in class)
Dataset (built-in class)
dataset (organization attribute)
date (Acquisition attribute)
(Action attribute)
(Block attribute)
Date (built-in class)
date (ChronicPreparation attribute)
(Phase attribute)
(Procedure attribute)
death (Animal attribute)
default (condition attribute)
description
(Acquisition attribute)
(Action attribute)
(Animal attribute)
(Apparatus attribute)
(Block attribute)
(ChronicPreparation attribute)
(Component attribute)
(Context attribute)
(Dataset attribute)
(Device attribute)
(Entity attribute)
(Event attribute)
(MachineState attribute)
(Material attribute)
(Part attribute)
(Participant attribute)
(Phase attribute)
(Procedure attribute)
(Program attribute)
(Sampled attribute)
(Scan attribute)
(Sequencer attribute)
(Setup attribute)
(Signal attribute)
(Space attribute)
(Spatial attribute)
(State attribute)
(StateMachine attribute)
(StimulusBlock attribute)
(Subject attribute)
(Substance attribute)
(Temporal attribute)
(Tissue attribute)
(condition attribute)
(formatter attribute)
(variable attribute)
Device (built-in class)
duration (StimulusBlock attribute)
E
Entity (built-in class)
Event (built-in class)
extension (DataFile attribute)
F
firstnames (Person attribute)
format (DataFile attribute)
(Date attribute)
(Time attribute)
formatter (built-in class)
frequency (StimulusState attribute)
Funding (built-in class)
G
generates (Device attribute)
(Routine attribute)
I
implants (Subject attribute)
Individual (built-in class)
initial (StateMachine attribute)
Institution (built-in class)
K
keywords (Dataset attribute)
L
lastname (Person attribute)
layout (Setup attribute)
license (Animal attribute)
License (built-in class)
license (Dataset attribute)
(Participant attribute)
(Subject attribute)
(Tissue attribute)
LineScan (built-in class)
M
MachineState (built-in class)
MachineStateTransition (built-in class)
manipulations (ChronicPreparation attribute)
Material (built-in class)
MEA (built-in class)
mode (StimulusState attribute)
model (Apparatus attribute)
(Device attribute)
monitors (Device attribute)
N
name (Citation attribute)
(Dataset attribute)
(Individual attribute)
(Institution attribute)
(License attribute)
(Person attribute)
(Referrable attribute)
O
offset (StimulusState attribute)
order (Block attribute)
(Phase attribute)
(procedures attribute)
organization (built-in class)
origin (Tissue attribute)
output (StimulusBlock attribute)
P
Part (built-in class)
Participant (built-in class)
parts (Animal attribute)
(Apparatus attribute)
(Component attribute)
(Device attribute)
(Material attribute)
(Part attribute)
(Participant attribute)
(Spatial attribute)
(Subject attribute)
(Substance attribute)
(Tissue attribute)
people (organization attribute)
Person (built-in class)
Phase (built-in class)
phases (procedures attribute)
precision (Quantity attribute)
Procedure (built-in class)
procedures (Block attribute)
(Phase attribute)
(built-in class)
Program (built-in class)
programs (acquisition attribute)
properties (State attribute)
protocol (Routine attribute)
pulse (StimulusState attribute)
Q
quality (Event attribute)
(Sampled attribute)
(Scan attribute)
(Signal attribute)
(State attribute)
Quantity (built-in class)
R
range (Sampled attribute)
(Scan attribute)
(Signal attribute)
reads (Routine attribute)
reference (Acquisition attribute)
(Action attribute)
(Animal attribute)
(Apparatus attribute)
(Block attribute)
(ChronicPreparation attribute)
(Component attribute)
(Context attribute)
(Device attribute)
(Entity attribute)
(Event attribute)
(Material attribute)
(Part attribute)
(Participant attribute)
(Phase attribute)
(Procedure attribute)
(Program attribute)
(Sampled attribute)
(Scan attribute)
(Setup attribute)
(Signal attribute)
(Spatial attribute)
(State attribute)
(Subject attribute)
(Substance attribute)
(Temporal attribute)
(Tissue attribute)
references (Dataset attribute)
Referrable (built-in class)
role (Event attribute)
(Sampled attribute)
(Scan attribute)
(Signal attribute)
(State attribute)
roles (Contributor attribute)
Routine (built-in class)
routines (Program attribute)
runs (Device attribute)
S
Sampled (built-in class)
scale (Space attribute)
Scan (built-in class)
section (built-in class)
sequence (Sequencer attribute)
sequencer (Acquisition attribute)
Sequencer (built-in class)
setup (Acquisition attribute)
(Action attribute)
(Block attribute)
Setup (built-in class)
setup (ChronicPreparation attribute)
(Phase attribute)
(Procedure attribute)
setups (built-in class)
sex (Animal attribute)
sexuality (Participant attribute)
shape (Space attribute)
Signal (built-in class)
signals (acquisition attribute)
size (Scan attribute)
source (MachineStateTransition attribute)
Space (built-in class)
Spatial (built-in class)
State (built-in class)
state (StimulusGeneration attribute)
StateMachine (built-in class)
states (StateMachine attribute)
StimulusBlock (built-in class)
StimulusGeneration (built-in class)
StimulusState (built-in class)
stores (Routine attribute)
subject
Subject (built-in class)
subjects (built-in class)
Substance (built-in class)
supplier (Apparatus attribute)
(Component attribute)
(Device attribute)
(Material attribute)
(Part attribute)
(Program attribute)
(Substance attribute)
switch (condition attribute)
T
target (MachineStateTransition attribute)
tasks (built-in class)
Temporal (built-in class)
Time (built-in class)
timeout (MachineState attribute)
Tissue (built-in class)
transitions (MachineState attribute)
type (Acquisition attribute)
(Action attribute)
(Animal attribute)
(Apparatus attribute)
(Block attribute)
(ChronicPreparation attribute)
(Component attribute)
(Context attribute)
(Device attribute)
(Entity attribute)
(Event attribute)
(Material attribute)
(Part attribute)
(Participant attribute)
(Phase attribute)
(Procedure attribute)
(Program attribute)
(Quantity attribute)
(Sampled attribute)
(Scan attribute)
(Sequencer attribute)
(Setup attribute)
(Signal attribute)
(Spatial attribute)
(State attribute)
(StateMachine attribute)
(Subject attribute)
(Substance attribute)
(Temporal attribute)
(Tissue attribute)
U
unit (Quantity attribute)
(Space attribute)
uri (Citation attribute)
(Individual attribute)
(Institution attribute)
(License attribute)
(Person attribute)
(Referrable attribute)
V
value (Date attribute)
(Quantity attribute)
(Time attribute)
values (Event attribute)
(State attribute)
variable (built-in class)
Video (built-in class)
Volume (built-in class)
W
where (formatter attribute)
Y
year (License attribute)