Commit f144a460 authored by Paal Kvamme's avatar Paal Kvamme
Browse files

Initial commit of the OpenZGY SDK.

parent b2f14f85
build/deploy
build/testdata
build/temp
# Test files created in the source tree. Should be fixed.
**/tmp-*.zgy
**/test-venv
**/__pycache__
**/*.egg-info
python/build
python/test-venv
wrapper/build
wrapper/test-venv
native/sdglue/build
native/sdglue/test-venv
misc/**
.eggs
*~
__pycache__
htmlcov
/build
test-venv
*.egg-info
.eggs
.coverage
# These really shouldn't be in the source area.
/python/build
/wrapper/build
/native/sdglue/build
/native/windows/x64
/native/windows/.vs
*.VC.db
*.VC.opendb
# oldtools are binaries just for testing, comparing with old ZGY-Public.
# Not checked in because I want to avoid bloat in git.
/oldtools
# This is sort-of a submodule but not using git's submodule mechanism.
/seismic-service-bin
# Dependencies that this project has ought to have been
# checked in, but large binaries and git don't mix.
# Also, zfp is now built locally. So it ought to have
# been in a separate folder. Eventually I'd like to build
# the seismic store libraries locally as well.
/external/*.whl
/external/*.so
/external/*.sentinel
# Odds and ends too obscure to commit.
/misc
# Windows... Since I unpack the tar file on each build this ought to have
# been placed in some "build" folder.
/native/windows/zfp-0.5.5
/native/windows/packages
/native/windows/*.vcxproj.user
/native/windows/*.zgy
*.nupkg
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# Copyright 2017-2020, Schlumberger
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# Will export the following variables:
# HOSTDISTRO LINUXDISTRO (os name), BUILDROOT TESTRUNDIR (paths)
# PLATFORM CONFIG (consumed) MYPLATFORM MYCONFIG (produced)
include scripts/Make.defs
TAG = build-openzgy-$(LINUXDISTRO)
OPENZGY_TOKEN ?= $(firstword $(strip $(shell sdutil auth idtoken)))
export OPENZGY_TOKEN := $(OPENZGY_TOKEN)
NEWTOKEN := $(shell test ! -x private/refreshtoken.sh || private/refreshtoken.sh)
$(if $(NEWTOKEN),$(info Refreshed the SAuth token used for unit tests),$(info Makefile did not refresh SAuth token))
$(if $(NEWTOKEN),$(eval export override $(NEWTOKEN)))
undefine NEWTOKEN
MY_OVERRIDES =
MY_OVERRIDES += $(if $(SDAPI_INTERNAL),SD_ZIPFILE=$(BUILDROOT)/seismic-service-bin/$(PLATFORM)/sdapi_linux64_local.tar.gz)
.PHONY: python native wrapper build clean clobber docker-build docker-test docker noop
all: native sdglue wrapper python
noop:
@echo no-op
# TODO-Low clean up these dependencies.
#
# "python" depends on "sdglue" which in turn depends on "native"
# but the latter is only for unpacking Seismic-Store.
#
# "sdglue" is located below "native" but native/src and native/sdglue
# are separate packages; the only thing they have in common is that
# both use Seismic-Store. Maybe upack Seismic-Store twice?
#
# "wrapper" depends on "native" which it is wrapping; that one is
# obvious and should remain.
python: | $(TESTRUNDIR)
$(MAKE) $(MY_OVERRIDES) -C native/sdglue build
$(MAKE) $(MY_OVERRIDES) -C python all
native: | $(TESTRUNDIR)
$(MAKE) $(MY_OVERRIDES) -C native/src
sdglue: | $(TESTRUNDIR)
$(MAKE) $(MY_OVERRIDES) -C native/sdglue
wrapper: | $(TESTRUNDIR)
$(MAKE) $(MY_OVERRIDES) -C native/src build
$(MAKE) $(MY_OVERRIDES) -C wrapper
build: | $(TESTRUNDIR)
$(MAKE) $(MY_OVERRIDES) -C native/src build
$(MAKE) $(MY_OVERRIDES) -C native/sdglue build
$(MAKE) $(MY_OVERRIDES) -C wrapper build venv
$(MAKE) $(MY_OVERRIDES) -C python data build venv
doxygen: | $(TESTRUNDIR)
$(MAKE) -C native/src doxygen doxyint
$(MAKE) -C python doxygen doxyint
# Note, this recipe will be duplicated in the Azure build script
# instead of Azure running "make", which would give an additional
# dependency for the Azure agent. Also, the rule below assumes
# the developer has seismic-service-bin in the work area, or a symlink.
# The azure task will instead fetch it every time.
# The Azure task cannot use docker run -v ... because the agent itself
# might be running as a docker container.
# TODO-Low, cannot run more than one build of the exact same env
# because the docker names would collide.
docker-build:
$(if $(wildcard scripts/Dockerfile-$(LINUXDISTRO)),,$(error LINUXDISTRO=$(LINUXDISTRO) is not supported))
docker tag $(TAG) $(TAG):old || true
mkdir -p seismic-service-bin
docker build --pull -t $(TAG) -f scripts/Dockerfile-$(LINUXDISTRO) .
rmdir --ignore-fail-on-non-empty seismic-service-bin
docker rmi -f $(TAG):old $(TAG):test || true
$(RM) cid.txt
docker run --cidfile cid.txt -e OPENZGY_TOKEN=$$(echo $$(sdutil auth idtoken)) -e LINUXDISTRO=$(LINUXDISTRO) $(TAG) make SDAPI_INTERNAL=$(SDAPI_INTERNAL) $(if $(findstring xdoc, x$(strip $(LINUXDISTRO))),doxygen,build)
docker cp $$(cat cid.txt):/home/build/oz/build/deploy - | gzip -9 > deploy.tgz
docker commit $$(cat cid.txt) $(TAG):test
docker rm $$(cat cid.txt)
$(RM) cid.txt
docker-test:
@echo -e '\n*** Test native started at' $$(date)
docker run --rm -e OPENZGY_TOKEN -e LINUXDISTRO -e OPENZGY_SDURL -e OPENZGY_SDAPIKEY $(TAG):test make SDAPI_INTERNAL=$(SDAPI_INTERNAL) native
@echo -e '\n*** Test sdglue started at' $$(date)
docker run --rm -e OPENZGY_TOKEN -e LINUXDISTRO -e OPENZGY_SDURL -e OPENZGY_SDAPIKEY $(TAG):test make SDAPI_INTERNAL=$(SDAPI_INTERNAL) sdglue
@echo -e '\n*** Test wrapper started at' $$(date)
docker run --rm -e OPENZGY_TOKEN -e LINUXDISTRO -e OPENZGY_SDURL -e OPENZGY_SDAPIKEY $(TAG):test make SDAPI_INTERNAL=$(SDAPI_INTERNAL) wrapper
@echo -e '\n*** Test python started at' $$(date)
docker run --rm -e OPENZGY_TOKEN -e LINUXDISTRO -e OPENZGY_SDURL -e OPENZGY_SDAPIKEY $(TAG):test make SDAPI_INTERNAL=$(SDAPI_INTERNAL) python
@echo -e '*** Tests done at' $$(date) '\n'
docker: docker-build docker-test
@true
.PHONY: flexnet
flexnet:
zip -r OpenZGY.zip README.md python wrapper native scripts Makefile
clean:
$(MAKE) -C python $@
$(MAKE) -C wrapper $@
$(MAKE) -C native/sdglue $@
$(MAKE) -C native/src $@
clobber:
$(MAKE) -C python $@
$(MAKE) -C wrapper $@
$(MAKE) -C native/sdglue $@
$(MAKE) -C native/src $@
$(RM) -rf $(TESTRUNDIR)
$(RM) pure.tar native.tar wrap.tar deploy.tgz OpenZGY.zip
@echo Checking that ./build is empty after clobbering
test ! -d build || test `find build -type f -print | wc -l` -eq 0
$(TESTRUNDIR):
mkdir -p $(TESTRUNDIR)
.PHONY: todo-native todo-python todo eyesore
SELECT = $(addprefix --include=,\*.py \*.cpp \*.h \*.txt)
SELECT += --exclude-dir test-venv
COUNT1 = sed -e 's/^.*\(TODO[^ ,.:]*\).*/\1/' | sort | uniq -c
COUNT2 = sed -e 's/^.*\(TODO[^ ,.:]*\).*/(sum)/' | sort | uniq -c
todo-python:
@echo
@echo Python
@grep -r $(SELECT) TODO python/openzgy | $(COUNT1)
@grep -r $(SELECT) TODO python/openzgy | $(COUNT2)
todo-native:
@echo
@echo Native
@grep -r $(SELECT) TODO plans.txt native/src native/sdglue wrapper | $(COUNT1)
@grep -r $(SELECT) TODO plans.txt native/src native/sdglue wrapper | $(COUNT2)
NEED_EYESORE = *.* python/openzgy native/src native/sdglue wrapper
SELECT2 = $(SELECT) --include Makefile --include \*.defs
eyesore:
@echo
grep -rl $(SELECT2) 'http://www.apache.org/licenses/LICENSE-2.0' $(NEED_EYESORE) | sort -o eyesore_1
grep -rl $(SELECT2) 'WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND' $(NEED_EYESORE) | sort -o eyesore_2
grep -rl $(SELECT2) '.' $(NEED_EYESORE) | sort -o eyesore_3
comm -12 eyesore_1 eyesore_2 > eyesore_4
comm -23 eyesore_3 eyesore_4 > eyesore_missing
$(RM) eyesore_1 eyesore_2 eyesore_3 eyesore_4
@echo "The following files do not have a copyright notice:"
@echo
@cat eyesore_missing
todo: todo-python todo-native
@/bin/true
# Open ZGY
# OpenZGY library
Open ZGY is an open source library that deals with the ZGY file format developed by Schlumberger for storing 3D data for seismic interpretation.
[[_TOC_]]
# API documentation
The OpenZGY API can be seen under the doc folder.
## <span style="color:blue">What's in the box?</span>
# ZGY - SDK - R2 (Header + Binaries)
The ZGY SDK is available under the folder ZGY. This is the closed source ZGY-Public library that supports reading and writing of ZGY files on-premise. The API exposed won't necessarily match the OpenZGY API and new features will be only available via OpenZGY.
The ZGY file format was developed by Schlumberger for storing 3d data
for seismic interpretation.
The OpenZGY libraries allow reading and writing this format. There are
both C++ and Python versions. For Python you can choose between a thin
wrapper around the C++ implementation and a pure Python reference
implementation. In the reference implementation, zfp compression and
cloud access are separate binary packages but the core is only Python.
This is an alpha release and there are a number of known issues.
Especially regarding performance. The pure Python implementation can
only run single threaded. Ditto for local file access in OpenZGY/C++
on Windows. Accessing the Seismic Store from OpenZGY/C++ both Linux
and Windows suffers from high latency because it reads just one brick
at a time. That results in a block size that is way smaller than
recommended.
## <span style="color:blue">Documentation</span>
See the doc folder for human readable documentation.
The file format itself is explained in [doc/openzgy](./doc/openzgy.html).
Other files in that folder deal with more specific issues.
Documentation for the public API and for internal code is generated by
Doxygen in the Linux builds. You need to do a "make doxygen" at the top
level before the documentation becomes available in
\ No newline at end of file
build/deploy/{native,pure}/{apidoc,intdoc}.{tgz,pdf}
The .tgz files contain html pages. Unpack the tarball and open
html/index.html. If you have
[LaTeX](https://www.latex-project.org/)
installed when building there will also be a single-document pdf
versions of those two next to the .tgz files.
## <span style="color:blue">Building and testing the core parts</span>
### Building Linux core
The code should build pretty much out of the box as long as Seismic
Store access is not enabled. On Linux there is a top level Makefile.
"make" builds and tests everything, while "make build" only builds.
In both cases both C++ and Python versions are built / packaged.
### Building Windows core
Prerequisites are Visual Studio 2019 with Platform Toolset v142.
If building with cloud support you might also need NuGet,
or some other mechanism to consume the Seismic Store libraries.
On Windows there is a Visual Studio solution for building the C++ code
and you can run "cd python; python setup.py sdist bdist_wheel" to
package the pure Python version.
The Visual Studio solution includes a project for running the C++ tests.
#### Example Python manual tests
These are for windows.
You can run them on Linux also by adjusting the paths.
```sh
cd python
virtualenv vvv
vvv\Scripts\activate
pip install dist\OpenZGY-0.2.unknown-py3-none-any.whl
zgycopy --snr 30 original.zgy compressed.zgy
zgycopy compressed.zgy roundtrip.zgy
zgygui
```
#### Example C++ manual tests
```sh
set OPENZGY_TESTDATA=build\testdata
build\deploy\native\x64\Debug\OpenZGY.Test.exe
```
```sh
build\deploy\native\x64\Debug\OpenZGY.Tools.ZgyCopy.exe -i original.zgy -o compressed.zgy --sqnr 30 --float
build\deploy\native\x64\Debug\OpenZGY.Tools.ZgyCopy.exe -i compressed.zgy -o roundtrip.zgy
```
## <span style="color:blue">Building and testing with cloud access enabled</span>
### Building Linux cloud
If you want to use Seismic Store to access the cloud then there are
some additional steps needed. You will need to download and build the
Seismic Store SDK a.k.a. SDAPI. And then package the binaries so they
can be picked up by OpenZGY. The Linux build expects it to be
available as a tarball in the source tree. So if you want cloud
support this will need some manual tweaking.
See [Building the Seismic Store SDK on Linux](building-the-seismic-store-sdk-on-linux)
for more information.
In the C++ code the cloud support and the compression support will
automatically be included if the SDK is available in the source tree.
And they will be quietly support if the respective tar files are missing.
Alternatively you can explicitly add HAVE_SD=yes and HAVE_ZFP=yes to
make sure those get built and tested, with error messages if they are
not found. Or set to an empty string (not "no"!) if you don't want to
build them even if present.
In the Python code the cloud support gets compiled into a C++ Python
extension which needs to be installed (using pip) next to OpenZGY
itself.
### Building Windows cloud
By default, integration with Seismic Store is disabled for windows
build. To enable it you need to explicitly define HAVE_SD=yes and edit
the project OpenZGY.vcxproj to link with the Seismic Store SDK (a.k.a.
SDAPI) that can be downloaded from
[os-seismic-store-cpp-lib](https://dev.azure.com/slb-des-ext-collaboration/open-data-ecosystem/_git/os-seismic-store-cpp-lib).
On Windows the Visual Studio solution expects the SDAPI headers and
binaries to be available as a NuGet package. You will need to download
and build the Seismic Store SDK and push the binaries to NuGet.
To enable reading and writing seismic store files using the pure
Python implementation you will need to build a small binary Python
extension module that wraps the C++ SDAPI. This produces a wheel that
you can subsequently install. Currently this module only builds on
Linux.
The C++ Python extension that wraps the entire OpenZGY/C++
implementation also does not build yet. So for cloud access you are
currently limited to C++.
```sh
@rem ... Download https://dist.nuget.org/win-x86-commandline/latest/nuget.exe
@rem ... Download Visual Studio 2019 and Platform Toolset v142 from Microsoft
@rem ... Open a Developer Command prompt for VS 2019
git clone https://community.opengroup.org/osdu/platform/domain-data-mgmt-services/seismic/open-zgy.git
nuget.exe restore openzgy\native\windows\packages.config -PackagesDirectory openzgy\native\windows\packages
msbuild.exe openzgy\native\windows\OpenZGY.Test.vcxproj /p:Configuration=Debug /p:Platform="x64"
```
### Testing on the cloud
For running tests against the cloud you will also need to set
OPENZGY_SDAPIKEY, OPENZGY_SDURL, and OPENZGY_TOKEN to appropriate
values. Production code using OpenZGY will probably use a different
mechanism to configure cloud access. Also set OPENZGY_SDTESTDATA and
OPENZGY_SDTESTSINK to two locations in the cloud. The first one a
read-only folder of test data and the second one an empty folder for
tests to write to.
## <span style="color:blue">Feature matrix</span>
|Package |linux|windows|read|write|update|seisstore|zfp compress|old compress|
| :--- | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|OpenZGY/C++ |y|y|y|y|-|y|y|N/A|
|OpenZGY/C++ Python wrapper |y|-|y|y|-|y|y|N/A|
|OpenZGY/Python |y|y|y|y|N/A?|linux|y|N/A|
|ZGY-Public, ZGY-Cloud |y|y|y|y|y|y|N/A|y|
|Old Python wrapper |y|y|y|y|y|y|N/A|y|
## <span style="color:blue">Output folders</span>
On Linux, running "make build" or "make" at the top level produces the deliverables listed below. On Windows the output folder structure is similar.
| <span style="color:#FF6622; font-size: 14pt;">native</span> |
| ---------- |
| This is a C++ implementation of the OpenZGY library. |
build/deploy/native/include/openzgy/...
build/deploy/native/$arch/*.so* (linux), *.dll/*.lib (windows)
build/deploy/native/{apidoc,intdoc}.{tgz,pdf}
| <span style="color:#FF6622; font-size: 14pt;">wrapper</span> |
| ---------- |
| This is a Python wrapper around the native implementation. It is supposed to be functionally identical to the legacy python implementation. |
build/deploy/wrapper/$arch/OpenZgyBindings-*.whl
| <span style="color:#FF6622; font-size: 14pt;">python</span> |
| ---------- |
| This is a pure python implementation of the core OpenZGY library. Binary packages are needed for optional compression and seismic store access. |
build/deploy/pure/OpenZGY-*/OpenZGY-*.whl
build/deploy/pure/OpenZGY-*/OpenZGY-*.tar.gz
build/deploy/sdglue/$arch/SdGlue*.whl
build/deploy/pure/{apidoc,intdoc}.{tgz,pdf}
## <span style="color:blue">Building the Seismic Store SDK on Linux</span>
The Seismic Store SDK (a.k.a. SDAPI) source code can be downloaded from
[os-seismic-store-cpp-lib](https://dev.azure.com/slb-des-ext-collaboration/open-data-ecosystem/_git/os-seismic-store-cpp-lib).