Examples¶
This is a collection of examples showing how fmu-dataio can be used in different contexts, and for different data types. The examples typically shows a Python script, together with a corresponding metadata file that would be produced when running the script.
If working inside RMS we often retrieve RMS data from the project itself. In the examples the syntax for that is commented out, but it is still shown so you can comment it out in your code.
The global variables used here¶
This is a snippet of the global_variables.yml file which holds the static metadata described in the
previous section. In real cases this file will be much longer.
# Autogenerated from global configuration.
# DO NOT EDIT THIS FILE MANUALLY!
# Machine st-linrgsxx.st.statoil.no by user nn, at 2021-06-23 07:35:54.428896, using fmu.config ver. 1.0.6.dev7+g6aee329
masterdata:
smda:
country:
- identifier: Norway
uuid: ad214d85-8a1d-19da-e053-c918a4889309
discovery:
- short_identifier: DROGON
uuid: ad214d85-8a1d-19da-e053-c918a4889309
field:
- identifier: DROGON
uuid: 00000000-0000-0000-0000-000000000000
coordinate_system:
identifier: ST_WGS84_UTM37N_P32637
uuid: ad214d85-dac7-19da-e053-c918a4889309
stratigraphic_column:
identifier: DROGON_2020
uuid: ad214d85-8a1d-19da-e053-c918a4889310
access:
asset:
name: Drogon
classification: internal
model:
name: ff
revision: 21.1.0.dev
stratigraphy:
MSL:
stratigraphic: false
name: MSL
Seabase:
stratigraphic: false
name: Seabase
TopVolantis:
stratigraphic: true
name: VOLANTIS GP. Top
alias:
- TopVOLANTIS
- TOP_VOLANTIS
stratigraphic_alias:
- TopValysar
- Valysar Fm. Top
TopTherys:
stratigraphic: true
name: Therys Fm. Top
TopVolon:
stratigraphic: true
name: Volon Fm. Top
BaseVolon:
stratigraphic: true
name: Volon Fm. Base
BaseVolantis:
stratigraphic: true
name: VOLANTIS GP. Base
Mantle:
stratigraphic: false
name: Mantle
Above:
stratigraphic: false
name: Above
Valysar:
stratigraphic: true
name: Valysar Fm.
Therys:
stratigraphic: true
name: Therys Fm.
Volon:
stratigraphic: true
name: Volon Fm.
Below:
stratigraphic: false
name: Below
global:
GLOBAL_VARS_EXAMPLE: 99
OTHER: skipped
rms:
horizons:
TOP_RES:
- TopVolantis
- TopTherys
- TopVolon
- BaseVolantis
zones:
ZONE_RES:
- Valysar
- Therys
- Volon
Exporting fault polygons¶
Python script¶
"""Export faultpolygons via dataio with metadata."""
import logging
from pathlib import Path
import xtgeo
from fmu import dataio
from fmu.config import utilities as utils
logger = logging.getLogger(__name__)
logger.setLevel(logging.WARNING)
CFG = utils.yaml_load("../../fmuconfig/output/global_variables.yml")
HORISONNAMES = CFG["rms"]["horizons"]["TOP_RES"]
# if inside RMS
RMS_POL_CATEGORY = "GL_faultlines_extract_postprocess"
# if running outside RMS using files that are stored e.g. on rms/output
FILEROOT = Path("../output/polygons")
def export_faultlines():
"""Return faultlines as both dataframe and original (xyz)"""
ed = dataio.ExportData(
config=CFG,
content="fault_lines",
unit="m",
vertical_domain="depth",
domain_reference="msl",
timedata=None,
is_prediction=True,
is_observation=False,
tagname="faultlines",
workflow="rms structural model",
)
for hname in HORISONNAMES:
# RMS version for reading polygons from a project:
# poly = xtgeo.polygons_from_roxar(project, hname, RMS_POL_CATEGORY)
# File version:
poly = xtgeo.polygons_from_file((FILEROOT / hname.lower()).with_suffix(".pol"))
poly.name = hname
# Export both csv (keeping xtgeo column names) and irap text format
# The difference bewtween "csv" and "csv|xtgeo" is that the latter will keep
# xtgeo column names as-is while "csv" will force column names to "X Y Z ID"
for fmt in ["csv|xtgeo", "irap_ascii"]:
ed.polygons_fformat = fmt
ed.export(poly)
if __name__ == "__main__":
export_faultlines()
Press + to see generated YAML file.
class: polygons
masterdata:
smda:
coordinate_system:
identifier: ST_WGS84_UTM37N_P32637
uuid: ad214d85-dac7-19da-e053-c918a4889309
country:
- identifier: Norway
uuid: ad214d85-8a1d-19da-e053-c918a4889309
discovery:
- short_identifier: DROGON
uuid: ad214d85-8a1d-19da-e053-c918a4889309
field:
- identifier: DROGON
uuid: 00000000-0000-0000-0000-000000000000
stratigraphic_column:
identifier: DROGON_2020
uuid: ad214d85-8a1d-19da-e053-c918a4889310
tracklog:
- datetime: '2025-03-17T07:20:22.055994Z'
event: created
user:
id: runner
sysinfo:
fmu-dataio:
version: 0.1.dev1+g074be76
operating_system:
hostname: fv-az1787-186
operating_system: Linux-6.8.0-1021-azure-x86_64-with-glibc2.39
release: 6.8.0-1021-azure
system: Linux
version: '#25-Ubuntu SMP Wed Jan 15 20:45:09 UTC 2025'
source: fmu
version: 0.9.0
$schema: https://main-fmu-schemas-prod.radix.equinor.com/schemas/0.9.0/fmu_results.json
fmu:
case:
name: xcase
user:
id: nn
uuid: 6fe60348-b386-4a68-9a0b-e8a4596af911
description:
- Generated by nn at 2021-06-08T13:17:06.485667
model:
name: ff
revision: 21.1.0.dev
context:
stage: realization
iteration:
id: 0
name: iter-0
uuid: 8483547b-2a22-2d07-5406-13493e216649
workflow:
reference: rms structural model
realization:
id: 0
name: realization-0
uuid: 709a05f8-a58f-ed00-9774-b536541b3d86
ert:
experiment:
id: 6a8e1e0f-9315-46bb-9648-8de87151f4c7
simulation_mode: test_run
access:
asset:
name: Drogon
classification: internal
ssdl:
access_level: internal
rep_include: false
data:
content: fault_lines
name: VOLANTIS GP. Top
alias:
- TopVOLANTIS
- TOP_VOLANTIS
- TopVolantis
tagname: faultlines
stratigraphic: true
bbox:
xmin: 459480.7
xmax: 465790.141
ymin: 5929993.362
ymax: 5937737.446
zmin: 1557.431
zmax: 1825.486
format: irap_ascii
is_observation: false
is_prediction: true
layout: unset
offset: 0.0
spec:
npolys: 6
undef_is_zero: false
unit: m
vertical_domain: depth
domain_reference: msl
file:
absolute_path: /home/runner/work/fmu-dataio/fmu-dataio/examples/s/d/nn/xcase/realization-0/iter-0/share/results/polygons/volantis_gp_top--faultlines.pol
relative_path: realization-0/iter-0/share/results/polygons/volantis_gp_top--faultlines.pol
checksum_md5: 7b85a0113a83a450eb945be37d75b537
display:
name: VOLANTIS GP. Top
_preprocessed: false
Exporting average maps from grid properties¶
Python script¶
"""Export maps that holds certain average gridmodel properties.
The files on disk are:
facies_fraction_channels_volon.gri
klogh_average_valysar.gri
phit_average_therys.gri
We wan to use the file names here to extract some data (like name of formation,
e.g. Therys).
"""
import logging
from pathlib import Path
import xtgeo
from fmu import dataio
from fmu.config import utilities as ut
logger = logging.getLogger(__name__)
logger.setLevel(logging.WARNING)
CFG = ut.yaml_load("../../fmuconfig/output/global_variables.yml")
# property attributes, the key is "pattern" and the value is generic name to be used:
TRANSLATE = {
"facies_fraction": "facies_fraction",
"phit": "porosity",
"klog": "permeability",
}
# name attributes, the key is "pattern" and the value is name to be used:
NAMETRANSLATE = {
"valysar": "Valysar",
"therys": "Therys",
"volon": "Volon",
}
INPUT_FOLDER = Path("../output/maps/grid_averages")
def main():
"""Exporting maps from clipboard"""
dataio.ExportData._inside_rms = True
files = INPUT_FOLDER.glob("*.gri")
for file in files:
surf = xtgeo.surface_from_file(file)
attribute = "unset"
for pattern, attr in TRANSLATE.items():
if pattern in str(file).lower():
attribute = attr
name = "unset"
for pattern, attr in NAMETRANSLATE.items():
if pattern in str(file).lower():
name = attr
ed = dataio.ExportData(
config=CFG,
name=name,
unit="fraction",
content="property",
content_metadata={"attribute": attribute, "is_discrete": False},
vertical_domain="depth",
domain_reference="msl",
timedata=None,
is_prediction=True,
is_observation=False,
tagname="average_" + attribute,
workflow="rms property model",
)
fname = ed.export(surf)
print(f"File name is {fname}")
if __name__ == "__main__":
main()
print("That's all")
Press + to see generated YAML file for metadata.
class: surface
masterdata:
smda:
coordinate_system:
identifier: ST_WGS84_UTM37N_P32637
uuid: ad214d85-dac7-19da-e053-c918a4889309
country:
- identifier: Norway
uuid: ad214d85-8a1d-19da-e053-c918a4889309
discovery:
- short_identifier: DROGON
uuid: ad214d85-8a1d-19da-e053-c918a4889309
field:
- identifier: DROGON
uuid: 00000000-0000-0000-0000-000000000000
stratigraphic_column:
identifier: DROGON_2020
uuid: ad214d85-8a1d-19da-e053-c918a4889310
tracklog:
- datetime: '2025-03-17T07:20:23.691788Z'
event: created
user:
id: runner
sysinfo:
fmu-dataio:
version: 0.1.dev1+g074be76
operating_system:
hostname: fv-az1787-186
operating_system: Linux-6.8.0-1021-azure-x86_64-with-glibc2.39
release: 6.8.0-1021-azure
system: Linux
version: '#25-Ubuntu SMP Wed Jan 15 20:45:09 UTC 2025'
source: fmu
version: 0.9.0
$schema: https://main-fmu-schemas-prod.radix.equinor.com/schemas/0.9.0/fmu_results.json
fmu:
case:
name: xcase
user:
id: nn
uuid: 6fe60348-b386-4a68-9a0b-e8a4596af911
description:
- Generated by nn at 2021-06-08T13:17:06.485667
model:
name: ff
revision: 21.1.0.dev
context:
stage: realization
iteration:
id: 0
name: iter-0
uuid: 8483547b-2a22-2d07-5406-13493e216649
workflow:
reference: rms property model
realization:
id: 0
name: realization-0
uuid: 709a05f8-a58f-ed00-9774-b536541b3d86
ert:
experiment:
id: 6a8e1e0f-9315-46bb-9648-8de87151f4c7
simulation_mode: test_run
access:
asset:
name: Drogon
classification: internal
ssdl:
access_level: internal
rep_include: false
data:
content: property
name: Therys Fm.
alias:
- Therys
tagname: average_porosity
stratigraphic: true
bbox:
xmin: 456012.5
xmax: 467540.52719139645
ymin: 5926500.0
ymax: 5939492.128806534
zmin: 0.0
zmax: 0.38215649127960205
format: irap_binary
is_observation: false
is_prediction: true
layout: regular
offset: 0.0
spec:
nrow: 440
ncol: 280
rotation: 30.0
undef: 1.0e+30
xinc: 25.0
yinc: 25.0
xori: 461500.0
yflip: 1
yori: 5926500.0
undef_is_zero: false
unit: fraction
vertical_domain: depth
domain_reference: msl
file:
absolute_path: /home/runner/work/fmu-dataio/fmu-dataio/examples/s/d/nn/xcase/realization-0/iter-0/share/results/maps/therys--average_porosity.gri
relative_path: realization-0/iter-0/share/results/maps/therys--average_porosity.gri
checksum_md5: 7b8d677044c2701d88f1a95e85aec142
display:
name: Therys Fm.
_preprocessed: false
Exporting 3D grids with properties¶
Python script¶
"""Export 3D griddata with properties."""
import logging
import pathlib
import xtgeo
from fmu import dataio
from fmu.config import utilities as ut
logging.basicConfig(level=logging.DEBUG)
logger = logging.getLogger(__name__)
CFG = ut.yaml_load("../../fmuconfig/output/global_variables.yml")
FOLDER = pathlib.Path("../output/grids")
GFILE = "gg"
GNAME = "geogrid"
PROPS_SEISMIC = ["phit", "sw"]
PROPS_OTHER = ["klogh", "facies"]
def export_geogrid_geometry():
filename = (FOLDER / GFILE).with_suffix(".roff")
grd = xtgeo.grid_from_file(filename)
ed = dataio.ExportData(
config=CFG,
name=GNAME,
content="depth",
unit="m",
vertical_domain="depth",
domain_reference="msl",
timedata=None,
is_prediction=True,
is_observation=False,
tagname="",
workflow="rms structural model",
)
out = ed.export(grd)
print(f"Stored grid as {out}")
return out
def export_geogrid_parameters(outgrid):
"""Export geogrid assosiated parameters based on user defined lists"""
props = PROPS_SEISMIC + PROPS_OTHER
print("Write grid properties...")
for propname in props:
filename = (FOLDER / (GFILE + "_" + propname)).with_suffix(".roff")
prop = xtgeo.gridproperty_from_file(filename)
ed = dataio.ExportData(
name=propname,
geometry=outgrid,
config=CFG,
content="property",
content_metadata={"is_discrete": False},
vertical_domain="depth",
domain_reference="msl",
timedata=None,
is_prediction=True,
is_observation=False,
workflow="rms property model",
)
out = ed.export(prop)
print(f"Stored {propname} as {out}")
if __name__ == "__main__":
outgrid = export_geogrid_geometry()
export_geogrid_parameters(outgrid)
print("Done.")
Press + to see generated YAML files for metadata.
class: cpgrid
masterdata:
smda:
coordinate_system:
identifier: ST_WGS84_UTM37N_P32637
uuid: ad214d85-dac7-19da-e053-c918a4889309
country:
- identifier: Norway
uuid: ad214d85-8a1d-19da-e053-c918a4889309
discovery:
- short_identifier: DROGON
uuid: ad214d85-8a1d-19da-e053-c918a4889309
field:
- identifier: DROGON
uuid: 00000000-0000-0000-0000-000000000000
stratigraphic_column:
identifier: DROGON_2020
uuid: ad214d85-8a1d-19da-e053-c918a4889310
tracklog:
- datetime: '2025-03-17T07:20:26.933730Z'
event: created
user:
id: runner
sysinfo:
fmu-dataio:
version: 0.1.dev1+g074be76
operating_system:
hostname: fv-az1787-186
operating_system: Linux-6.8.0-1021-azure-x86_64-with-glibc2.39
release: 6.8.0-1021-azure
system: Linux
version: '#25-Ubuntu SMP Wed Jan 15 20:45:09 UTC 2025'
source: fmu
version: 0.9.0
$schema: https://main-fmu-schemas-prod.radix.equinor.com/schemas/0.9.0/fmu_results.json
fmu:
case:
name: xcase
user:
id: nn
uuid: 6fe60348-b386-4a68-9a0b-e8a4596af911
description:
- Generated by nn at 2021-06-08T13:17:06.485667
model:
name: ff
revision: 21.1.0.dev
context:
stage: realization
iteration:
id: 0
name: iter-0
uuid: 8483547b-2a22-2d07-5406-13493e216649
workflow:
reference: rms structural model
realization:
id: 0
name: realization-0
uuid: 709a05f8-a58f-ed00-9774-b536541b3d86
ert:
experiment:
id: 6a8e1e0f-9315-46bb-9648-8de87151f4c7
simulation_mode: test_run
access:
asset:
name: Drogon
classification: internal
ssdl:
access_level: internal
rep_include: false
data:
content: depth
name: geogrid
alias: []
tagname: ''
stratigraphic: false
bbox:
xmin: 456063.6875
xmax: 467489.3438
ymin: 5926551.0
ymax: 5939441.0
zmin: 1554.2631
zmax: 2001.8425
format: roff
is_observation: false
is_prediction: true
layout: cornerpoint
offset: 0.0
spec:
nrow: 146
ncol: 92
nlay: 65
xshift: 0.0
yshift: 0.0
zshift: 0.0
xscale: 1.0
yscale: 1.0
zscale: 1.0
zonation:
- name: subgrid_0
min_layer_idx: 0
max_layer_idx: 18
- name: subgrid_1
min_layer_idx: 19
max_layer_idx: 47
- name: subgrid_2
min_layer_idx: 48
max_layer_idx: 61
undef_is_zero: false
unit: m
vertical_domain: depth
domain_reference: msl
file:
absolute_path: /home/runner/work/fmu-dataio/fmu-dataio/examples/s/d/nn/xcase/realization-0/iter-0/share/results/grids/geogrid.roff
relative_path: realization-0/iter-0/share/results/grids/geogrid.roff
checksum_md5: 7746feed7f22b61e2a666947cd5dc3e4
display:
name: geogrid
_preprocessed: false
class: cpgrid_property
masterdata:
smda:
coordinate_system:
identifier: ST_WGS84_UTM37N_P32637
uuid: ad214d85-dac7-19da-e053-c918a4889309
country:
- identifier: Norway
uuid: ad214d85-8a1d-19da-e053-c918a4889309
discovery:
- short_identifier: DROGON
uuid: ad214d85-8a1d-19da-e053-c918a4889309
field:
- identifier: DROGON
uuid: 00000000-0000-0000-0000-000000000000
stratigraphic_column:
identifier: DROGON_2020
uuid: ad214d85-8a1d-19da-e053-c918a4889310
tracklog:
- datetime: '2025-03-17T07:20:27.273876Z'
event: created
user:
id: runner
sysinfo:
fmu-dataio:
version: 0.1.dev1+g074be76
operating_system:
hostname: fv-az1787-186
operating_system: Linux-6.8.0-1021-azure-x86_64-with-glibc2.39
release: 6.8.0-1021-azure
system: Linux
version: '#25-Ubuntu SMP Wed Jan 15 20:45:09 UTC 2025'
source: fmu
version: 0.9.0
$schema: https://main-fmu-schemas-prod.radix.equinor.com/schemas/0.9.0/fmu_results.json
fmu:
case:
name: xcase
user:
id: nn
uuid: 6fe60348-b386-4a68-9a0b-e8a4596af911
description:
- Generated by nn at 2021-06-08T13:17:06.485667
model:
name: ff
revision: 21.1.0.dev
context:
stage: realization
iteration:
id: 0
name: iter-0
uuid: 8483547b-2a22-2d07-5406-13493e216649
workflow:
reference: rms property model
realization:
id: 0
name: realization-0
uuid: 709a05f8-a58f-ed00-9774-b536541b3d86
ert:
experiment:
id: 6a8e1e0f-9315-46bb-9648-8de87151f4c7
simulation_mode: test_run
access:
asset:
name: Drogon
classification: internal
ssdl:
access_level: internal
rep_include: false
data:
content: property
name: facies
alias: []
tagname: ''
stratigraphic: false
geometry:
name: geogrid
relative_path: realization-0/iter-0/share/results/grids/geogrid.roff
format: roff
is_observation: false
is_prediction: true
layout: cornerpoint
offset: 0.0
spec:
nrow: 146
ncol: 92
nlay: 65
undef_is_zero: false
unit: ''
vertical_domain: depth
domain_reference: msl
file:
absolute_path: /home/runner/work/fmu-dataio/fmu-dataio/examples/s/d/nn/xcase/realization-0/iter-0/share/results/grids/geogrid--facies.roff
relative_path: realization-0/iter-0/share/results/grids/geogrid--facies.roff
checksum_md5: 80cf3786d38cdca6ff63da647017c6da
display:
name: facies
_preprocessed: false
Exporting volume tables RMS or file¶
Below is an example of exporting volume tables from csv-files, while an example of easy export of RMS volumetrics can be found here example-export-volumes-rms.
Python script¶
"""Read volume table from RMS or file and export to CSV for SUMO.
In this example there is switch, IN_ROXAR which is set to True if using it inside
RMS (to demostrate how volume tables can be fetched via Roxar API).
For the file case, CSV files are read from disk. The dataio function is the same.
"""
import logging
import pathlib
import pandas as pd
import fmu.dataio
from fmu.config import utilities as ut
logger = logging.getLogger(__name__)
logger.setLevel(logging.WARNING)
CFG = ut.yaml_load("../../fmuconfig/output/global_variables.yml")
VFOLDER = "../output/volumes/"
VFILES = ["geogrid_vol.csv", "simgrid_vol.csv"]
TAGNAME = "volumes"
def volume_as_dataframe_files(vfile):
"""Read volume (CSV files) and return dataframe."""
# "geogrid_vol.csv" --> "geogrid" etc
gridname = vfile.replace("_vol.csv", "")
fname = pathlib.Path(VFOLDER) / vfile
dframe = pd.read_csv(fname)
return dframe, gridname
def export_dataio(df, gridname):
"""Get the dataframe and export to SUMO via dataio."""
exp = fmu.dataio.ExportData(
name=gridname,
config=CFG,
content="volumes",
unit="m",
is_prediction=True,
is_observation=False,
tagname=TAGNAME,
workflow="Volume calculation",
)
out = exp.export(df)
print(f"Exported volume table for {gridname} to {out}")
if __name__ == "__main__":
for vfile in VFILES:
df, gridname = volume_as_dataframe_files(vfile)
export_dataio(df, gridname)
class: table
masterdata:
smda:
coordinate_system:
identifier: ST_WGS84_UTM37N_P32637
uuid: ad214d85-dac7-19da-e053-c918a4889309
country:
- identifier: Norway
uuid: ad214d85-8a1d-19da-e053-c918a4889309
discovery:
- short_identifier: DROGON
uuid: ad214d85-8a1d-19da-e053-c918a4889309
field:
- identifier: DROGON
uuid: 00000000-0000-0000-0000-000000000000
stratigraphic_column:
identifier: DROGON_2020
uuid: ad214d85-8a1d-19da-e053-c918a4889310
tracklog:
- datetime: '2025-03-17T07:20:28.781386Z'
event: created
user:
id: runner
sysinfo:
fmu-dataio:
version: 0.1.dev1+g074be76
operating_system:
hostname: fv-az1787-186
operating_system: Linux-6.8.0-1021-azure-x86_64-with-glibc2.39
release: 6.8.0-1021-azure
system: Linux
version: '#25-Ubuntu SMP Wed Jan 15 20:45:09 UTC 2025'
source: fmu
version: 0.9.0
$schema: https://main-fmu-schemas-prod.radix.equinor.com/schemas/0.9.0/fmu_results.json
fmu:
case:
name: xcase
user:
id: nn
uuid: 6fe60348-b386-4a68-9a0b-e8a4596af911
description:
- Generated by nn at 2021-06-08T13:17:06.485667
model:
name: ff
revision: 21.1.0.dev
context:
stage: realization
iteration:
id: 0
name: iter-0
uuid: 8483547b-2a22-2d07-5406-13493e216649
workflow:
reference: Volume calculation
realization:
id: 0
name: realization-0
uuid: 709a05f8-a58f-ed00-9774-b536541b3d86
ert:
experiment:
id: 6a8e1e0f-9315-46bb-9648-8de87151f4c7
simulation_mode: test_run
access:
asset:
name: Drogon
classification: internal
ssdl:
access_level: internal
rep_include: false
data:
content: volumes
name: geogrid
alias: []
tagname: volumes
stratigraphic: false
format: csv
is_observation: false
is_prediction: true
layout: table
offset: 0.0
spec:
columns:
- 'Unnamed: 0'
- ZONE
- REGION
- BULK_OIL
- PORV_OIL
- HCPV_OIL
- STOIIP_OIL
- ASSOCIATEDGAS_OIL
- BULK_GAS
- PORV_GAS
- HCPV_GAS
- GIIP_GAS
- ASSOCIATEDOIL_GAS
- BULK_TOTAL
- PORV_TOTAL
num_columns: 15
num_rows: 21
size: 315
undef_is_zero: false
unit: m
vertical_domain: depth
domain_reference: msl
table_index:
- ZONE
- REGION
file:
absolute_path: /home/runner/work/fmu-dataio/fmu-dataio/examples/s/d/nn/xcase/realization-0/iter-0/share/results/tables/geogrid--volumes.csv
relative_path: realization-0/iter-0/share/results/tables/geogrid--volumes.csv
checksum_md5: f22adf8dca797f165c1c38fcc535e77c
display:
name: geogrid
_preprocessed: false
Exporting a faultroom plugin result surface¶
The FaultRoom plugin for RMS produces special json files that e.g. can be viewed with DynaGeo.
Python script¶
"""Export faultroom surfaces via dataio with metadata."""
import logging
from pathlib import Path
from fmu import dataio
from fmu.config import utilities as utils
logger = logging.getLogger(__name__)
logger.setLevel(logging.WARNING)
CFG = utils.yaml_load("../../fmuconfig/output/global_variables.yml")
# if running outside RMS using files that are stored e.g. on rms/output
FAULTROOM_FILE = Path("../output/faultroom/some_faultroom.json")
def export_faultroom_surface():
"""Export faultroom data, json files made by FaultRoom plugin in RMS"""
# read file and return a FaultRoomSurface instance
faultroom_object = dataio.readers.read_faultroom_file(FAULTROOM_FILE)
ed = dataio.ExportData(
config=CFG,
content="fault_properties",
unit="unset",
vertical_domain="depth",
domain_reference="msl",
is_prediction=True,
is_observation=False,
workflow="rms structural model",
tagname=faultroom_object.tagname,
)
ed.export(faultroom_object)
if __name__ == "__main__":
export_faultroom_surface()
{
"metadata": {
"source": "FaultRoom v.1.3.1",
"date_created": "2024-03-01",
"horizons": [
"TopVolantis"
],
"faults": {
"default": [
"F1",
"F2",
"F3",
"F4",
"F5",
"F6"
]
},
"juxtaposition": {
"fw": [
"Therys",
"Valysar",
"Volon"
],
"hw": [
"Therys",
"Valysar",
"Volon"
]
},
"properties": [
"Juxtaposition",
"displacement_avg",
"permeability_avg",
"transmissibility_avg"
]
},
"type": "FeatureCollection",
"crs": {
"type": "name",
"properties": {
"name": ""
}
},
"features": [
{
"type": "Feature",
"properties": {
"FaultID": "F1",
"HorizonID": "TopVolantis",
"SegmentID": 0,
"TriangleID": 0,
"Juxtaposition": 0.0,
"displacement_avg": 74.16522148649528,
"transmissibility_avg": 0.0,
"permeability_avg": 0.00015810546529826527
},
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Using fmu-dataio for post-processed data¶
The example below shows how fmu-dataio can be used in a post-processing context, here in a surface aggregation example.
When using ensemble-based methods for probabilistic modelling, the result is represented by the distribution of the realizations, not by the individual realizations themselves. In such a context, easy access to statistical representations of the ensemble is important. For surfaces, this typically includes point-wise mean, std, min/max, p10/p90 and others.
Aggregations in an FMU context are usually done by standalone Python scripts, but cloud services are also in the making (Sumo). The example below shows how fmu-dataio can be used to simplify an existing aggregation service, as well as make de-centralized methods more robust by centralizing the definitions and handling of metadata.
Note
It is common that surfaces exported from RMS or other sources have undefined areas. For some surfaces, typically various thickness surfaces (e.g. HCPV thickness from RMS volumetric jobs), undefined values shall be treated as zero (0.0) when included in statistical calculations. Therefore, when exporting surfaces of this type, set the undef_is_zero flag to True when exporting. This tells later consumers of the surface that they should handle UNDEF as zero.
Python script¶
"""Use fmu-dataio for aggregated surfaces created by an aggregation service."""
from __future__ import annotations
from pathlib import Path
import numpy as np
import xtgeo
import yaml
import fmu.dataio
import fmu.dataio._utils
def main():
"""Aggregate one surface across X realizations from the example case and store the
results. In this example, we emulate that fmu-dataio is called by another service.
Two contexts are demonstrated:
1) We are in a classical FMU setting, running this aggregation as a stand-alone
Python script (directly, or wrapped in an ERT workflow). In this context,
we want the resulting files to be stored to disk within the existing case. In
this context, fmu-dataio is responsible for storing the results.
2) We are in a cloud service. In this context, we don't want to store anything
on disk, as the results are to be pushed to other storage, i.e. Sumo. Hence,
we want fmu-dataio to provide us with the generated metadata only. In this
context, the service itself is responsible for storing the results.
Note that this example is showing the usage of fmu-dataio, it is not to be seen as
an example for the actual aggregation. The aggregation service shown here is
simplistic and its sole purpose is to facilitate the fmu-dataio example.
"""
# First we get the input data (the individual surfaces from each realization), which
# we assume are stored in classical FMU style on /scratch disk folder structure.
# IRL, these variables would typically be arguments to the aggregation script.
casepath = Path("../xcase/").resolve()
iter_name = "iter-0"
relative_path = (
"share/results/maps/topvolantis--ds_extract_geogrid.gri" # exists in all reals
)
realization_ids = _get_realization_ids(casepath)
# gather source surfaces and their associated metadata
source_surfaces, source_metadata = _get_source_surfaces_from_disk(
casepath=casepath,
iter_name=iter_name,
realization_ids=realization_ids,
relative_path=relative_path,
)
# These are the operations we want to do
operations = ["mean", "min", "max", "std"]
# This is the ID we assign to this set of aggregations
aggregation_id = str(fmu.dataio._utils.uuid_from_string("something_very_unique"))
# Initialize an AggregatedData object for this set of aggregations
exp = fmu.dataio.AggregatedData(
source_metadata=source_metadata,
aggregation_id=aggregation_id,
casepath=casepath,
)
for operation in operations:
print(f"Running aggregation: {operation}")
# Call the aggregation machine and create an aggregated surface
# Note that this is not part of fmu-dataio - it is merely a mock-up
# aggregation service for the sake of this example.
aggregated_surface = _aggregate(source_surfaces, operation)
# ==============================================================================
# Example 1: We want fmu-dataio to export the file + metadata to disk
saved_filename = exp.export(aggregated_surface, operation=operation)
print(f"Example 1: File saved to {saved_filename}")
# ==============================================================================
# Example 2: We only want the metadata (e.g. we are in a cloud service)
exp.generate_metadata(aggregated_surface, operation=operation)
print("Example 2: Metadata generated")
# At this point, we have the surface, the operation and the metadata
# These can be collected into e.g. a list or a dictionary for further usage,
# or we can upload to Sumo as part of the loop.
# ======================================================================================
# This concludes the main examples. Below are utility functions used by the example.
# ======================================================================================
def _aggregate(source_surfaces, operation):
"""Aggregate a set of surfaces, return the result.
This is a very simplistic and minimalistic aggregation method meant to power this
example only. Do not use in production setting.
"""
if operation == "mean":
return source_surfaces.apply(np.nanmean, axis=0)
if operation == "min":
return source_surfaces.apply(np.min, axis=0)
if operation == "max":
return source_surfaces.apply(np.max, axis=0)
if operation == "std":
return source_surfaces.apply(np.std, axis=0)
# In a real aggregation service, more options would of course be supported. However,
# in this example, we do not include anything beyond the basics.
raise NotImplementedError(
f"Aggregation method {operation} is not implemented in this example."
)
def _parse_yaml(fname):
"""Parse the yaml-file, return dict.
Args:
fname (Path): Absolute path to yaml file.
Returns:
dict
"""
with open(fname) as stream:
return yaml.safe_load(stream)
def _metadata_filename(fname):
"""From a regular filename, derive the corresponding metadata filename.
FMU standard: metadata filename = /path/.<stem.ext>.yml
"""
return Path(fname.parent, "." + fname.name + ".yml")
def _get_realization_ids(casepath):
"""Given a path to a case on the disk, get the individual realizations."""
# In reality we would traverse the disk to find out, use Sumo search, or preferably
# ask ERT for it. For the sake of the example we just hardcode it here.
return [0, 1, 9]
def _get_source_surfaces_from_disk(
casepath: Path,
iter_name: str,
realization_ids: list,
relative_path: Path,
):
"""Collect surfaces and metadata from disk.
This method collects the source surfaces from disk. Source surfaces are the
individual realization surfaces which shall be aggregated.
A similar method will exist for other sources than /scratch, e.g. Sumo.
Args:
casepath (Path): Absolute path to the case root.
iter_name (str): Name of the iteration (folder), e.g. "iter-0"
reals (list of ids): List of realization-ids, e.g. 0,1,2,3
relative_path (Path): Relative path below ERT RUNPATH to the surface
By combining the casepath and the relative path, parse the surfaces and metadata
and return surfaces as an xtgeo.Surfaces object and the metadata as a list of dicts.
"""
collected_data = []
for real in realization_ids:
surfacepath = casepath / f"realization-{real}" / iter_name / relative_path
surface = xtgeo.surface_from_file(surfacepath)
metadata = fmu.dataio.read_metadata(surfacepath)
# this example is minimalistic and super non-robust. In reality, there will
# be realizations missing which needs to be handled etc.
collected_data.append((surface, metadata))
source_surfaces = xtgeo.Surfaces([surface for surface, _ in collected_data])
source_metadata = [metadata for _, metadata in collected_data]
return source_surfaces, source_metadata
def _get_source_surfaces_from_sumo(
case_uuid: str,
iter_name: str,
realization_ids: list,
relative_path: Path,
):
"""Collect surfaces and metadata from Sumo.
Placeholder for a method getting surfaces and metadata from Sumo, complementing
the similar method for getting this from the disk. Only included since it is
referenced in the comments in main().
Not implemented.
"""
raise NotImplementedError
if __name__ == "__main__":
main()