Page History
H5M Convention
Version 0.1
Revision 15 Author: Gerco de Jager, MARIN MSG
Rev | When | Who | What & Why |
15 | 2018-03-13 | GdJ | SignalSet's 'programmeNo' renamed to 'programNo' to be consistent with the application pool. |
14 | 2018-02-27 | GdJ | Added kind of information per attribute: |
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| GdJ | Conformed signal set's 'projectNo' to MARIN integer representation. |
13 | 2018-01-31 | GdJ | Signal: added 'order' to indicate whether the signal represents a first or second order effect. Only if applicable. |
12 | 2018-01-30 | GdJ | Signal: unit is singular, not plural. |
11 | 2018-01-12 | GdJ | Meeting with DJN and JB: |
10 | 2018-01-09 | GdJ | Processed feedback of MP, HT, RH, NC: |
9 | 2017-12-19 | GdJ | Removed "rawUnits" and upgraded "units" to UTF-8.(Rationale: Leave interpretation of units to client code) |
|
| GdJ | Added signal attribute "baseNames" for informational purposes. Reason: ObjectReference does not render very descriptive. |
8 | 2017-12-14 | GdJ | changed "original*" prefix in "raw*" as it expresses the cause better. |
7 | 2017-12-08 | GdJ | removed 'format' prefix on file header. |
6 | 2017-11-28 | GdJ | changed 'reference' to 'referenceSystem' for clarity. |
5 | 2017-11-16 | GdJ | Support non-unit-definition-strings as Can-be-missing attribute "rawUnits". (a.r.o. units meeting EvdB et al dd 2017-11-16) |
4 | 2017-10-23 | GdJ | Unicode support in attributes and names. |
3 | 2017-10-12 | GdJ | Video chat with Gerd Heber (HDF Group) dd 2017-10-06. |
2 | 2017-10-02 | GdJ | Discarding Timezone information in datetime strings. |
1 | 2017-09-21 | GdJ | Results of meeting dd 21-09-2017. |
0 | 2017-09-20 | GdJ | First draft for H5M.NET, "MMS2 writes H5M". |
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Note before reading any further: This file format is still in development. Not all features and intended usages are supported yet by this standard. New features will be added gradually and lead to new versions of this standard.
Contents
1 Introduction
1.1 Intended usage
1.2 Supported features
2 Glossary
3 H5M Structure
3.1 Root : Group "/"
3.2 Signal Set : Group
3.3 Signal : Dataset
4 H5M Data Descriptions
4.1 Naming conventions
4.2 Attributes
4.3 Data types
4.3.1 Default value
4.3.2 Strings: favour unicode (UTF-8) over ascii
4.3.3 iso_fmt
4.3.4 unit_str
4.3.5 prop_str
4.3.6 obj_ref
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H5M is an acronym for HDF5 MARIN Datasets File.
The data which it contains can have any available source at MARIN: Basin measurements, simulator runs, CFD calculations, full scale measurements and post-processing cq analysis of this data.
This convention specifies how the content of a HDF5 file is organised for MARIN. For more information about HDF5 itself and for generic HDF5 viewers please visit https://support.hdfgroup.org/.
The glossary of terms is described in the next chapter.The data structure and their properties are specified in chapter 3.Details of the data types used and the followed naming convention are specified in chapter 4.
Anchor | ||||
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MARIN Internal use:
- Exchange and access results of the measurements in the basins to data analysts for further processing. This contains the raw data from MMS2 and supersedes the MMS format.
- Exchange the results of simulations and calculations.
- Exchange the results of analysis and other post-processing of raw data between data analysts and between departments.
MARIN External use:
- Exchange processed results of measurements or calculations or simulations or experiments or analysis with clients. (Portal, e-mail, ftp, …)
Anchor | ||||
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The specified format supports the following features:
- Identification of the software and system configuration used to write the data set.
- Identification of the process step(s) that generated the data set. (i.e. experiment number, project number, etc)
- Identification of the experiment variables (a.k.a. signals) and – if applicable - the sensors used.
- Grouping of signals with shared origin or properties. This is called a signal set.
- Link a signal set to another signal set to create a dependency of one to another.
- Time branching; The available Signal Sets can form a graph from which a Signals can be composed by following a specific path.
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ExperimentIn the context of this convention, any action that results in one or more signals that need to be stored. E.g. MMS2 Measurement, ReFresco Calculation, XMF Simulation, SHARK data analysis.
H5MMARIN convention of structuring the content of a HDF5 container for Experiment Datasets.
Master Signal Independent value range. E.g. the timestamp values for a time series signal that correspond with each sample value.
Signal Measured, calculated or simulated variable; range of values.
Signal SetSet of signals grouped by one or more common properties. E.g. origin, experiment run, sample rate, sample count, timestamp.
Slave SignalDependent value range. E.g. the sample values at each corresponding timestamp for a time series signal or the RAO value at certain values on several frequency axis.
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The H5M content is structured as depicted in the diagram below.
Each tree node item will be explained in the next paragraphs in this chapter.The location of the item is defined by it's address in the HDF5 file, called path. Also all available attributes are specified per item.
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The root group contains:
- attributes that identify the used H5M format.
- zero or more HDF Groups for each set of signals.
- attributes that identify the provenance of the file.
Attributes:
Name | Role | Data type | Exists? | Description | Convention / example |
name | i | utf8 | A | Name of the convention; constant | “H5M” |
description | i | utf8 | A | Description of the format; constant.: | “HDF5 MARIN Datasets File” |
version | a | utf8 | A | H5M Format version number | “0.1” |
documentation | i | utf8 | A | Where to find this convention | |
hdf5Version | i | utf8 | A | Version of HDF5 | “1.8.19” |
libraryName | i | utf8 | A | Name of the library that performed the actual writing. In case of appending signal sets only the last editor is tracked. | “pymarin”, “Marin.Experiments.IO.H5M” |
libraryVersion | i | utf8 | A | Version of this library | e.g. “7.0.1” |
applicationName | i | utf8 | NS | Name of the application that wrote this file | “SHARK”, “SHARK: some vistrail.vt” |
applicationVersion | i | utf8 | NS | Version of this application used. | “0.0.20” |
systemName | i | utf8 | O | Name of the system running the application. This not necessarely the system that performed the experiment (e.g. measurement). | “LP3138”, “MMS2” |
systemVersion | i | utf8 | O | Version or configuration of this systtem | (tbd) |
dateTimeOfCreation | i | iso_fmt | A | Date and time of the moment the file was created. | ISO 8601 “2017-09-27 T21:13:00.012345” |
userName | i | utf8 | NS | Name of user / author | “user123” |
notes | i | utf8 | NS | Any additional notes at file level. | (free text) |
writeErrors | i | utf8[] | O | Specifies any errors that occurred while writing the file.. |
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The signal set group contains a set of signals that are logically a single group. Such signals share common properties like number of samples andsample rate. Which properties are common has to be determined by the consumer of the data; either a human or an application.
Name: HDF Group name of the set of signals.
Path: "/<Signal set name>"
Attributes:
Name | Role | Data type | Exists? | Description | Convention / example |
type | a | utf8 | NS | type of signals in the set. Value NS maps to “General”. | “General”, “Frequency”, “Time” |
rawName | i | utf8 | O | original signal set name if this had to be renamed to be used as valid hdf5 name. |
|
description | i | utf8 | NS | additional description of the set | (tbd) |
parent | s | obj_ref | O | Link to parent signal set. | (tbd) |
parentName | s | utf8 | O | For information only: the name of the parent signal set. |
|
dataScale | a | float64 | A | Scale of the signal values in the set with respect to full scale | 1.0 ( full scale) 23.456 (model scale) 0.023456 (larger than life) |
waterDensityFactor | a | float64 | NS | water density factor to be used for scaling data values to full scale. | 1.432 |
stepSize | i | float64 | A | if one and only one master signal for all signals and it is equidistant a value; otherwise, NaN In case of a time master this is the inverse of the sample rate. |
|
dateTimeRecordingStart | a | iso_fmt | A | date and time of first sample of the time signal of measurement or simulation. | (tbd) |
dateTimeRecordingEnd | a | iso_fmt | O | date and time of last sample of the time signal of the measurement or simulation. | (tbd) |
projectNo | a | int32 | A | projectnumber | “80220” |
projectSubNo | i | int32 | NS | subnumber | “368” |
programNo | a | int32 | A | test programme number | 1 |
source | a | utf8 | A | name of the source application or facility | “SMB”, “ReFresco” |
categoryNo | a | int32 | A | Number of the test category used. | 2 |
testNo | a | int32 | A | Number of the test setup used. | 3 |
experimentNo | a | int32 | A | Number of the experiment settings used. | 4 |
measurementNo | a | int32 | A | Number of the actual measurement c.q. experiment execution | 2 |
modelScale | a | float64 | A | Scale of the model in this project. (Unrelated to the signal values in the set.) | 23.456 |
...
H5M is an acronym for HDF5 MARIN Datasets File.
The data which it contains can have any available source at MARIN: Basin measurements, simulator runs, CFD calculations, full scale measurements and post-processing cq analysis of this data.
This convention specifies how the content of a HDF5 file is organised for MARIN. For more information about HDF5 itself and for generic HDF5 viewers please visit https://support.hdfgroup.org/.
The glossary of terms is described in the next chapter.The data structure and their properties are specified in chapter 3.Details of the data types used and the followed naming convention are specified in chapter 4.
...
MARIN Internal use:
- Exchange and access results of the measurements in the basins to data analysts for further processing. This contains the raw data from MMS2 and supersedes the MMS format.
- Exchange the results of simulations and calculations.
- Exchange the results of analysis and other post-processing of raw data between data analysts and between departments.
MARIN External use:
- Exchange processed results of measurements or calculations or simulations or experiments or analysis with clients. (Portal, e-mail, ftp, …)
...
The specified format supports the following features:
- Identification of the software and system configuration used to write the data set.
- Identification of the process step(s) that generated the data set. (i.e. experiment number, project number, etc)
- Identification of the experiment variables (a.k.a. signals) and – if applicable - the sensors used.
- Grouping of signals with shared origin or properties. This is called a signal set.
- Link a signal set to another signal set to create a dependency of one to another.
- Time branching; The available Signal Sets can form a graph from which a Signals can be composed by following a specific path.
...
ExperimentIn the context of this convention, any action that results in one or more signals that need to be stored. E.g. MMS2 Measurement, ReFresco Calculation, XMF Simulation, SHARK data analysis.
H5MMARIN convention of structuring the content of a HDF5 container for Experiment Datasets.
Master Signal Independent value range. E.g. the timestamp values for a time series signal that correspond with each sample value.
Signal Measured, calculated or simulated variable; range of values.
Signal SetSet of signals grouped by one or more common properties. E.g. origin, experiment run, sample rate, sample count, timestamp.
Slave SignalDependent value range. E.g. the sample values at each corresponding timestamp for a time series signal or the RAO value at certain values on several frequency axis.
...
The H5M content is structured as depicted in the diagram below.
Each tree node item will be explained in the next paragraphs in this chapter.The location of the item is defined by it's address in the HDF5 file, called path. Also all available attributes are specified per item.
...
The root group contains:
- attributes that identify the used H5M format.
- zero or more HDF Groups for each set of signals.
- attributes that identify the provenance of the file.
...
Name | Role | Data type | Exists?A / O / NS | Description | Convention / example | |
name | i | utf8 | A | Name of the convention; constant | "H5M" | |
description | i | utf8 | A | Description of the format; constant.: | "HDF5 MARIN Datasets File" | |
version | a | utf8 | A | H5M Format version number | "0.1" | |
documentation | i | utf8 | A | Where to find this convention | "mods.marin.nl/dispay/H5M/convention_0_1" | |
hdf5Version | i | utf8 | A | Version of HDF5 | "1.8.19" | |
libraryName | i | utf8 | A | Name of the library that performed the actual writing. | "pymarin", "Marin.Experiments.IO.H5M" | |
libraryVersion | i | utf8 | A | Version of this library | e.g. "7.0.1" | |
applicationName | i | utf8 | NS | Name of the application that wrote this file | "SHARK", | |
applicationVersion | i | utf8 | NS | Version of this application used. | "0.0.20" | |
systemName | i | utf8 | O | Name of the system running the application. This not necessarely the system that performed the experiment (e.g. measurement). | "LP3138", "MMS2" | |
systemVersion | i | utf8 | O | Version or configuration of this systtem | (tbd) | |
dateTimeOfCreation | i | iso_fmt | A | Date and time of the moment the file was created. | ISO 8601 | |
userName | i | utf8 | NS | Name of user / author | "user123" | |
notes | i | utf8 | NS | Any additional notes at file levelinformation about this signal set. | (free text) | |
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="8ab884a4-44ea-4d15-b867-dc002a995754"><ac:plain-text-body><![CDATA[ | writeErrors | i | utf8[] | O | Specifies any errors that occurred while writing the file.signal set (group). | ]]></ac:plain-text-body></ac:structured-macro> |
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Dataset
The signal set group contains a set of signals that are logically a single group. Such signals share common properties like number of samples andsample rate. Which properties are common has to be determined by the consumer of the data; either a human or an applicationis a dataset containing the samples of the measurement or simulation or calculation or postprocessing step. A signal maps to an experiment variable.
Name: HDF Group name of the set of signalsDataset name; must be unique in the set. It is the HDF-safe name of the signal. For reference the original potentially HDF-unsafe name is provided with the data in the 'signalSource' attribute.
Path: "/<set name>/<Signal set <signal name>"
Attributes Additional properties of the signal are added as attributes. Below are the common attributes. In sub sections domain or source specific attributes can be found.
Attibutes:
Name | Role | Data type | Exists? | Description | Convention / example | type | a | ||
utf8 | NS | type of signals in the set. | "General", "Frequency", "Time" | rawName | i | utf8 | O | original signal set name if this had to be renamed reformatted to be used as valid hdf5 name. |
|
descriptionunit | iautf8 | unit_str | NS | additional description of the set | (tbd) | ||||
parent | s | obj_ref | O | Link to parent signal set. | (tbd) | ||||
parentName | s | utf8 | O | For information only: the name of the parent signal set. |
| ||||
dataScale | a | float64 | A | Scale of the signal values in the set with respect to full scale | 1.0 ( full scale) | ||||
waterDensityFactor | a | float64 | NS | water density factor to be used for scaling data values to full scale.Preferred 'not specified'over a default value. | 1.432 | ||||
stepSize | i | float64 | A | if one and only one master signal for all signals and it is equidistant a value; otherwise, NaN |
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dateTimeRecordingStart | a | iso_fmt | A | date and time of first sample of the time signal of measurement or simulation.Required for time series only.. | (tbd) | ||||
dateTimeRecordingEnd | a | iso_fmt | O | date and time of last sample of the time signal of the measurement or simulation. (May disappear in future versions.) | (tbd) | ||||
projectNo | a | int32 | A | projectnumber | "80220" | ||||
projectSubNo | i | int32 | NS | subnumber | "368" | ||||
programNo | a | int32 | A | test programme number | 1 | ||||
source | a | utf8 | A | name of the source application or facilityWithin one project each 'programmeNo' is a fixed combination with the 'source'. | "SMB", "ReFresco" | ||||
categoryNo | a | int32 | A | Number of the test category used. | 2 | ||||
testNo | a | int32 | A | Number of the test setup used. | 3 | ||||
experimentNo | a | int32 | A | Number of the experiment settings used. | 4 | ||||
measurementNo | a | int32 | A | Number of the actual measurement c.q. experiment execution | 2 | ||||
modelScale | a | float64 | A | Scale of the model in this project. (Unrelated to the signal values in the set.) | 23.456 | ||||
notes | i | utf8 | NS | Any additional information about this signal set. | (free text) | ||||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="d0e23a65-0655-42b8-9858-d2b115df80f5"><ac:plain-text-body><![CDATA[ | writeErrors | i | utf8[] | O | Specifies any errors that occurred while writing the signal set (group). |
| ]]></ac:plain-text-body></ac:structured-macro> |
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A | name of the unit of the signal. This defines the quantity of the experiment variable. | “m/s”, “-“, “rad” | |||
signalType | a | prop_str | NS | defines the experiment variable or simulation property or the kind of quantity. | “velocity”, etc “angular velocity” |
description | i | utf8 | A | description of the signal. More detail than name. E.g. the kind of quantity or experiment variable; whether it is an absolute value or a delta. | (tbd) |
timeOffset | a | float64 | NS | the time offset in seconds between real start time and the moment the timestamp is created. |
|
order | a | int32 | O | In case of frequency data specifies whether it is a first or second order effect or otherwise. | 1: first order. 2: second order. -1: Not applicable. |
position | a | float64[3] | NS | location of the variable in the specified Coordinate System. | [0.0, 0.0, 0.0] |
direction | a | float64[3] | NS | direction of the signal c.q. experiment variable in the specified CS. In case of a rotation it is the direction of the axis of rotation. | Roll in ACK: [1.0,0.0,0.0] Sway in ACK: [0.0, 1.0, 0.0] |
referenceSystem | a | utf8 | NS | specifies in which Coordinate Sytem position and direction are given. | “ACK”, (todo: complete list) |
signalSource | I | utf8 | O | holds information about the sensor. Depends on system used. Also contains the original signal name from the measurement system. | (tbd) |
channelNo | i | int32 | O | if no sensor information is provided holds the channel number in case of measured data. | 123 |
bases | s | obj_ref[] | O | List of object references to all datasets that are a master signal to this signal. | [objRef(“time”)] |
baseNames | s | utf8[] | O | Names of the base signals (informational only. Not intended for rebuilding the datamodel) |
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notes | i | utf8 | A | Any additional information about this signal. | (free text) |
The signal is a dataset containing the samples of the measurement or simulation or calculation or postprocessing step. A signal maps to an experiment variable.
Name: HDF Dataset name; must be unique in the set. It is the HDF-safe name of the signal. For reference the original potentially HDF-unsafe name is provided with the data in the 'signalSource' attribute.
Path: "/<set name>/<signal name>"
Additional properties of the signal are added as attributes. Below are the common attributes. In sub sections domain or source specific attributes can be found.
Attibutes:
Name | Role | Data type | Exists?A / O / NS | Description | Convention / example | ||
rawName | i | utf8 | O | original signal name if this had to be reformatted to be used as hdf5 name. |
| ||
unit | a | unit_str | A | name of the unit of the signal. This defines the quantity of the experiment variable. | "m/s", "-", "rad" | ||
signalType | a | prop_str | NS | defines the experiment variable or simulation property or the kind of quantity. | "velocity", etc | ||
description | i | utf8 | A | description of the signal. More detail than name. E.g. the kind of quantity or experiment variable; whether it is an absolute value or a delta. | (tbd) | ||
timeOffset | a | float64 | NS | the time offset in seconds between real start time and the moment the timestamp is created. |
| ||
order | a | int32 | O | In case of frequency data specifies whether it is a first or second order effect or otherwise. | 1: first order. | ||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="648e0998-c54e-4ae0-9053-49efa0c4786c"><ac:plain-text-body><![CDATA[ | position | a | float64[3] | NS | location of the variable in the specified Coordinate System. | [0.0, 0.0, 0.0] | ]]></ac:plain-text-body></ac:structured-macro> |
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="ae0a7916-d1c0-4e29-97b5-a78fbbd4c2a3"><ac:plain-text-body><![CDATA[ | direction | a | float64[3] | NS | direction of the signal c.q. experiment variable in the specified CS. In case of a rotation it is the direction of the axis of rotation. | Roll in ACK: | ]]></ac:plain-text-body></ac:structured-macro> |
referenceSystem | a | utf8 | NS | specifies in which Coordinate Sytem position and direction are given. | "ACK", (todo: complete list) | ||
signalSource | I | utf8 | O | holds information about the sensor. | (tbd) | ||
channelNo | i | int32 | O | if no sensor information is provided holds the channel number in case of measured data. | 123 | ||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="ceb434b5-4b1e-4eda-aa46-f4212bcc231f"><ac:plain-text-body><![CDATA[ | bases | s | obj_ref[] | O | List of object references to all datasets that are a master signal to this signal. | [objRef("time")] | ]]></ac:plain-text-body></ac:structured-macro> |
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="81be4bb2-7b30-4c6b-9c6f-a73dc4a9e67d"><ac:plain-text-body><![CDATA[ | baseNames | s | utf8[] | O | Names of the base signals (informational only. Not intended for rebuilding the datamodel) |
| ]]></ac:plain-text-body></ac:structured-macro> |
notes | i | utf8 | A | Any additional information about this signal. | (free text) | ||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="92f5282e-f8ae-44a7-9569-87a5283e0044"><ac:plain-text-body><![CDATA[ | |||||||
writeErrors | i | utf8[] | O | Specifies any errors that occurred while writing the signal (dataset). Mostly value errors. | ]]></ac:plain-text-body></ac:structured-macro> |
Note: There is no explicit sample rate property. Sample rate is a specific attribute of equidistant time based signals. If sample rate needs to be visible it can be specified in the attribute 'description' of the signal set group.
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