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..

42 Commits

Author SHA1 Message Date
7044f7b085 Logger: handle situation when git sha1 is empty 2024-05-14 22:22:15 +02:00
165fe1a432 FPGA: build script is safe for situations when git is absent 2024-05-14 22:21:58 +02:00
ad2bc91582 Remove .gitmodules file 2024-05-14 21:53:43 +02:00
c1e9cc5d3c Update spdlog (working on better integration) 2024-05-14 21:51:17 +02:00
eb0e5daf8f catch2: download with CMake + update to recent Catch2 2024-05-14 21:31:34 +02:00
9f1b6a6e96 fast-feedback-indexer: download with CMake 2024-05-14 20:57:29 +02:00
81db3af275 slsDetectorPackage: download with CMake 2024-05-14 20:54:42 +02:00
8cd5787848 bitshuffle_hperf: put directly into the repository 2024-05-14 20:50:12 +02:00
ebd3628eab bitshuffle_hperf: put directly into the repository 2024-05-14 20:48:15 +02:00
e02f8692f9 zstd: built via cmake 2024-05-14 20:42:34 +02:00
f27126fa1f pistache: built via cmake 2024-05-14 20:36:50 +02:00
d2c5b9c038 tinycbor: internal to repository 2024-05-14 20:30:19 +02:00
ff191c8490 tinycbor: remove submodule 2024-05-14 20:28:43 +02:00
ced40a7170 PreviewImage: Add resolution ring (experimental) 2024-05-14 18:53:11 +02:00
37e825a018 FPGA: Spot finder masks module edges, improve testing in this regard 2024-05-14 18:01:40 +02:00
36257d7009 CI: Create release as part of CI - should be working now 2024-05-14 17:39:58 +02:00
786b28ed78 CI: Create release as part of CI (another try) 2024-05-14 17:21:22 +02:00
bd86809bdd CI: Create release as part of CI (another try) 2024-05-14 17:05:39 +02:00
af366acb08 CI: Create release as part of CI (another try) 2024-05-14 16:40:42 +02:00
4fe2904b47 CI: Create release as part of CI (try again) 2024-05-14 15:12:39 +02:00
c97749c16a CI: Create release as part of CI 2024-05-14 14:54:47 +02:00
bd43b09b4c Revert "CI: More serious test of package registry"
This reverts commit dcd6088afe.
2024-05-14 14:45:26 +02:00
dcd6088afe CI: More serious test of package registry 2024-05-14 14:39:26 +02:00
b4c26b036f CI: Try release pipeline with runner tag 2024-05-14 14:29:02 +02:00
b2a7dadef7 CI: Try release pipeline 2024-05-14 14:21:00 +02:00
5808d2c5bc VERSION: Add package version to git 2024-05-14 14:05:14 +02:00
c71728e16f Dockerfile: add comment for MAX IV 2024-05-14 13:49:42 +02:00
10b8398bd0 CI: test 2024-05-14 13:29:55 +02:00
9c1796a9e6 CMake: Remove ZeroMQ CMake module 2024-05-07 15:27:34 +02:00
3cbf675120 CI: Building HLS is NOT requirement to build firmware (it will fail anyway 2024-05-07 15:12:58 +02:00
1aa1da92ff CI: Fix FPGA .mcs name and FPGA build is optional if not required 2024-05-07 15:11:53 +02:00
07a1659e94 CI: Fix FPGA .mcs name 2024-05-07 15:09:53 +02:00
bc1285acc6 CI: FPGA HLS is built in parallel with 4 threads 2024-05-07 14:45:35 +02:00
c330a0ed81 CI: FPGA images are called jfjoch_fpga_{FLOW}.mcs 2024-05-07 14:43:30 +02:00
cdba3000d2 README.md: Linkt to broker/writer subdirectories 2024-05-07 14:34:24 +02:00
db47da3b6d README.md: Remove part on .mcs naming 2024-05-07 14:33:22 +02:00
d3420d7f0c CI: Fix driver artifact 2024-05-07 14:13:58 +02:00
975442f452 README.md: Remove CompressionBenchmark 2024-05-07 14:13:28 +02:00
4c87554233 nextgendcu/broker/README.md: Updates 2024-05-07 14:12:15 +02:00
b5da66baf6 CompressionBenchmark: Remove 2024-05-07 14:11:21 +02:00
69d34e22f7 CI: Update 2024-05-07 14:05:51 +02:00
89cf520e52 FPGAIntegrationTest: Truncate number of test images 2024-05-07 14:00:15 +02:00
93 changed files with 1005 additions and 3200 deletions

3
.gitignore vendored
View File

@@ -1,3 +0,0 @@
cmake-build-debug/
cmake-build-release/
build*/

View File

@@ -7,6 +7,7 @@ stages:
build:x86:gcc:
stage: build
variables:
GIT_SUBMODULE_STRATEGY: recursive
CC: gcc
CXX: g++
tags:
@@ -23,6 +24,7 @@ build:x86:gcc:
build:x86:gcc_writer:
stage: build
variables:
GIT_SUBMODULE_STRATEGY: recursive
CC: gcc
CXX: g++
tags:
@@ -34,11 +36,12 @@ build:x86:gcc_writer:
- cd build
- source /opt/rh/gcc-toolset-12/enable
- cmake -DCMAKE_BUILD_TYPE=Release -DJFJOCH_WRITER_ONLY=ON ..
- make -j48
- make -j48 jfjoch
build:x86:driver:
stage: build
variables:
GIT_SUBMODULE_STRATEGY: recursive
CC: gcc
CXX: g++
tags:
@@ -57,6 +60,8 @@ build:x86:driver:
build:x86:vitis_hls:
stage: build
variables:
GIT_SUBMODULE_STRATEGY: recursive
tags:
- x86
needs: []
@@ -79,43 +84,27 @@ build:x86:vitis_hls:
build:x86:frontend:
stage: build
variables:
GIT_SUBMODULE_STRATEGY: recursive
tags:
- x86
needs: []
script:
- mkdir build
- cd frontend_ui
- npm install
- npm run build
- cd build
- /usr/bin/cmake ..
- make frontend
- cd ../frontend_ui/build
- tar czf ../../jfjoch_frontend.tar.gz *
artifacts:
paths:
- jfjoch_frontend.tar.gz
expire_in: 1 week
build:x86:rpm:
stage: build
tags:
- x86
needs: []
script:
- mkdir build
- cd build
- source /opt/rh/gcc-toolset-12/enable
- cmake -DCMAKE_BUILD_TYPE=Release ..
- make frontend
- make -j48 package
- mv *.rpm ..
artifacts:
paths:
- "*.rpm"
expire_in: 1 week
test:x86:gcc:
stage: test
timeout: 90m
variables:
GIT_SUBMODULE_STRATEGY: recursive
CTEST_OUTPUT_ON_FAILURE: 1
CC: gcc
CXX: g++
@@ -129,9 +118,9 @@ test:x86:gcc:
- mkdir -p build
- cd build
- cmake -DCMAKE_BUILD_TYPE=Release ..
- make -j48 jfjoch_test HDF5DatasetWriteTest
- make -j48 CatchTest HDF5DatasetWriteTest
- cd tests
- ./jfjoch_test -r junit -o report.xml
- ./CatchTest -r junit -o report.xml
- cd ../tools
- ./HDF5DatasetWriteTest ../../tests/test_data/compression_benchmark.h5
artifacts:
@@ -143,6 +132,7 @@ test:x86:crystfel:
stage: test
timeout: 90m
variables:
GIT_SUBMODULE_STRATEGY: recursive
CTEST_OUTPUT_ON_FAILURE: 1
CC: gcc
CXX: g++
@@ -166,6 +156,7 @@ test:x86:xds_durin:
stage: test
timeout: 90m
variables:
GIT_SUBMODULE_STRATEGY: recursive
CTEST_OUTPUT_ON_FAILURE: 1
CC: gcc
CXX: g++
@@ -189,6 +180,7 @@ test:x86:xds_neggia:
stage: test
timeout: 90m
variables:
GIT_SUBMODULE_STRATEGY: recursive
CTEST_OUTPUT_ON_FAILURE: 1
CC: gcc
CXX: g++
@@ -212,6 +204,7 @@ test:x86:xia2.ssx:
stage: test
timeout: 90m
variables:
GIT_SUBMODULE_STRATEGY: recursive
CTEST_OUTPUT_ON_FAILURE: 1
CC: gcc
CXX: g++
@@ -237,6 +230,7 @@ synthesis:vivado_pcie_100g:
stage: synthesis
dependencies: []
variables:
GIT_SUBMODULE_STRATEGY: recursive
CC: gcc
CXX: g++
rules:
@@ -249,6 +243,8 @@ synthesis:vivado_pcie_100g:
- fpga/scripts/*
- fpga/xdc/*
- fpga/pcie_driver/jfjoch_fpga.h
- when: manual
allow_failure: true
tags:
- vivado
artifacts:
@@ -270,6 +266,7 @@ synthesis:vivado_pcie_8x10g:
stage: synthesis
dependencies: []
variables:
GIT_SUBMODULE_STRATEGY: recursive
CC: gcc
CXX: g++
rules:
@@ -282,6 +279,8 @@ synthesis:vivado_pcie_8x10g:
- fpga/xdc/*
- fpga/pcie_driver/jfjoch_fpga.h
allow_failure: true
- when: manual
allow_failure: true
tags:
- vivado
artifacts:
@@ -301,9 +300,7 @@ synthesis:vivado_pcie_8x10g:
release:
stage: release
rules:
- if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
when: manual
when: manual
tags:
- x86
dependencies:
@@ -311,16 +308,9 @@ release:
- synthesis:vivado_pcie_100g
- build:x86:frontend
- build:x86:driver
- build:x86:rpm
script:
- export PACKAGE_VERSION=`head -n1 VERSION`
- export PACKAGE_REGISTRY_URL="${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/generic/jungfraujoch/${PACKAGE_VERSION}"
- 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch-driver-dkms-${PACKAGE_VERSION}-1.el8.noarch.rpm "${PACKAGE_REGISTRY_URL}/jfjoch-driver-dkms-${PACKAGE_VERSION}-1.el8.noarch.rpm"'
- 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch-driver-dkms-${PACKAGE_VERSION}-1.el8.noarch.rpm "${PACKAGE_REGISTRY_URL}/jfjoch-driver-dkms.el8.noarch.rpm"'
- 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch-writer-${PACKAGE_VERSION}-1.el8.x86_64.rpm "${PACKAGE_REGISTRY_URL}/jfjoch-writer-${PACKAGE_VERSION}-1.el8.x86_64.rpm"'
- 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch-writer-${PACKAGE_VERSION}-1.el8.x86_64.rpm "${PACKAGE_REGISTRY_URL}/jfjoch-writer.el8.x86_64.rpm"'
- 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch-${PACKAGE_VERSION}-1.el8.x86_64.rpm "${PACKAGE_REGISTRY_URL}/jfjoch-${PACKAGE_VERSION}-1.el8.x86_64.rpm"'
- 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch-${PACKAGE_VERSION}-1.el8.x86_64.rpm "${PACKAGE_REGISTRY_URL}/jfjoch.el8.x86_64.rpm"'
- 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch_driver.tar.gz "${PACKAGE_REGISTRY_URL}/jfjoch_driver.tar.gz"'
- 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch_frontend.tar.gz "${PACKAGE_REGISTRY_URL}/jfjoch_frontend.tar.gz"'
- 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch_fpga_pcie_100g.mcs "${PACKAGE_REGISTRY_URL}/jfjoch_fpga_pcie_100g.mcs"'
@@ -331,9 +321,3 @@ release:
--assets-link "{\"name\":\"jfjoch_frontend.tar.gz\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch_frontend.tar.gz\"}"
--assets-link "{\"name\":\"jfjoch_fpga_pcie_8x10g.mcs\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch_fpga_pcie_8x10g.mcs\"}"
--assets-link "{\"name\":\"jfjoch_fpga_pcie_100g.mcs\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch_fpga_pcie_100g.mcs\"}"
--assets-link "{\"name\":\"jfjoch-${PACKAGE_VERSION}-1.el8.x86_64.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch-${PACKAGE_VERSION}-1.el8.x86_64.rpm\"}"
--assets-link "{\"name\":\"jfjoch-writer-${PACKAGE_VERSION}-1.el8.x86_64.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch-writer-${PACKAGE_VERSION}-1.el8.x86_64.rpm\"}"
--assets-link "{\"name\":\"jfjoch-driver-dkms-${PACKAGE_VERSION}-1.el8.noarch.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch-driver-dkms-${PACKAGE_VERSION}-1.el8.noarch.rpm\"}"
--assets-link "{\"name\":\"jfjoch.el8.x86_64.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch.el8.x86_64.rpm\"}"
--assets-link "{\"name\":\"jfjoch-writer.el8.x86_64.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch-writer.el8.x86_64.rpm\"}"
--assets-link "{\"name\":\"jfjoch-driver-dkms.el8.noarch.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch-driver-dkms.el8.noarch.rpm\"}"

View File

@@ -1,9 +1,7 @@
CMAKE_MINIMUM_REQUIRED(VERSION 3.19)
FILE(STRINGS VERSION JFJOCH_VERSION)
PROJECT(jfjoch VERSION 1.0.0 LANGUAGES C CXX)
SET(CMAKE_POLICY_DEFAULT_CMP0077 NEW)
PROJECT(Jungfraujoch VERSION 1.0 LANGUAGES C CXX)
LIST(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
SET(CMAKE_CXX_STANDARD 20)
SET(CMAKE_CXX_STANDARD_REQUIRED True)
@@ -11,31 +9,8 @@ SET(CMAKE_CXX_STANDARD_REQUIRED True)
SET(CMAKE_CXX_FLAGS_RELEASE "-O3 -march=native -mtune=native -Wno-deprecated-enum-enum-conversion")
SET(CMAKE_C_FLAGS_RELEASE "-O3 -march=native -mtune=native")
SET(BUILD_SHARED_LIBS OFF)
SET(BUILD_TESTING OFF)
SET(ZSTD_LEGACY_SUPPORT OFF)
SET(ZSTD_MULTITHREAD_SUPPORT OFF)
SET(ZSTD_BUILD_PROGRAMS OFF)
SET(ZSTD_BUILD_SHARED OFF)
SET(SLS_USE_RECEIVER OFF)
SET(SLS_USE_RECEIVER_BINARIES OFF)
SET(SLS_BUILD_SHARED_LIBRARIES OFF)
SET(BUILD_FAST_INDEXER OFF)
SET(BUILD_FAST_INDEXER_STATIC ON)
SET(HDF5_ENABLE_SZIP_SUPPORT OFF)
SET(HDF5_ENABLE_SZIP_ENCODING OFF)
SET(HDF5_BUILD_EXAMPLES OFF)
SET(HDF5_BUILD_CPP_LIB OFF)
SET(HDF5_ENABLE_Z_LIB_SUPPORT OFF)
SET(HDF5_EXTERNALLY_CONFIGURED 1)
SET(jbig OFF)
SET(zstd OFF)
SET(lzma OFF)
INCLUDE(CheckLanguage)
CHECK_LANGUAGE(CUDA)
@@ -56,28 +31,23 @@ SET(JFJOCH_WRITER_ONLY OFF CACHE BOOL "Compile HDF5 writer only")
INCLUDE_DIRECTORIES(include)
INCLUDE(CheckIncludeFile)
#This is to supress error in TORCH
IF ((NOT EXISTS /usr/bin/python) AND (EXISTS /usr/bin/python3))
SET(PYTHON_EXECUTABLE /usr/bin/python3)
ENDIF()
FIND_PACKAGE(Torch HINTS /opt/libtorch/share/cmake/Torch/)
FIND_LIBRARY(NUMA_LIBRARY NAMES numa DOC "NUMA Library")
CHECK_INCLUDE_FILE(numaif.h HAS_NUMAIF)
CHECK_INCLUDE_FILE(numa.h HAS_NUMA_H)
include(FetchContent)
FetchContent_Declare(tiff
GIT_REPOSITORY https://github.com/fleon-psi/libtiff
GIT_TAG v4.6.0
EXCLUDE_FROM_ALL)
FetchContent_Declare(hdf5
GIT_REPOSITORY https://github.com/HDFGroup/hdf5/
GIT_TAG hdf5_1.14.4.2
GIT_SHALLOW 1
EXCLUDE_FROM_ALL)
FetchContent_Declare(
pistache_http
GIT_REPOSITORY https://github.com/fleon-psi/pistache
GIT_TAG 51553b92cc7bb25ac792462722ddd4fae33d14b1
EXCLUDE_FROM_ALL
)
FetchContent_Declare(
@@ -85,7 +55,6 @@ FetchContent_Declare(
GIT_REPOSITORY https://github.com/facebook/zstd
GIT_TAG 794ea1b0afca0f020f4e57b6732332231fb23c70
SOURCE_SUBDIR build/cmake
EXCLUDE_FROM_ALL
)
FetchContent_Declare(
@@ -98,10 +67,9 @@ FetchContent_Declare(
catch2
GIT_REPOSITORY https://github.com/catchorg/Catch2
GIT_TAG 4e8d92b
EXCLUDE_FROM_ALL
)
FetchContent_MakeAvailable(pistache_http zstd sls_detector_package catch2 hdf5 tiff)
FetchContent_MakeAvailable(pistache_http zstd sls_detector_package catch2)
ADD_SUBDIRECTORY(jungfrau)
ADD_SUBDIRECTORY(compression)
@@ -112,6 +80,7 @@ ADD_SUBDIRECTORY(frame_serialize)
ADD_SUBDIRECTORY(detector_control)
IF (JFJOCH_WRITER_ONLY)
MESSAGE(STATUS "Compiling HDF5 writer only")
SET(jfjoch_executables jfjoch_writer)
ELSE()
ADD_SUBDIRECTORY(broker)
ADD_SUBDIRECTORY(fpga)
@@ -121,51 +90,17 @@ ELSE()
ADD_SUBDIRECTORY(tests)
ADD_SUBDIRECTORY(tools)
ADD_SUBDIRECTORY(preview)
ADD_SUBDIRECTORY(resonet)
SET(jfjoch_executables jfjoch_broker jfjoch_writer CatchTest CompressionBenchmark HDF5DatasetWriteTest jfjoch_udp_simulator sls_detector_put sls_detector_get)
ENDIF()
IF (NOT JFJOCH_WRITER_ONLY)
ADD_CUSTOM_COMMAND(OUTPUT frontend_ui/build/index.html
COMMAND npm install
COMMAND npm run build
COMMAND npm run redocly
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/frontend_ui)
ADD_CUSTOM_TARGET(frontend DEPENDS frontend_ui/build/index.html)
ADD_CUSTOM_COMMAND(OUTPUT frontend_ui/build/index.html
COMMAND npm run build
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/frontend_ui)
ADD_CUSTOM_TARGET(frontend DEPENDS frontend_ui/build/index.html)
INSTALL(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/fpga/pcie_driver/
DESTINATION /usr/src/jfjoch-1.0.0
COMPONENT driver-dkms
FILES_MATCHING PATTERN "*.c" PATTERN "*.h" PATTERN "Makefile" PATTERN "dkms.conf")
FILE(MAKE_DIRECTORY ${CMAKE_SOURCE_DIR}/frontend_ui/build/)
INSTALL(DIRECTORY ${CMAKE_SOURCE_DIR}/frontend_ui/build/ DESTINATION share/jfjoch/frontend COMPONENT jfjoch )
ENDIF()
ADD_CUSTOM_TARGET(jfjoch DEPENDS ${jfjoch_executables})
IF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
SET(CMAKE_INSTALL_PREFIX /opt/jfjoch CACHE PATH "Default directory" FORCE)
ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
# Set Package Name
set(CPACK_PACKAGE_NAME "jfjoch")
SET(CPACK_COMPONENTS_ALL jfjoch writer driver-dkms)
SET(CPACK_GENERATOR RPM)
SET(CPACK_RPM_COMPONENT_INSTALL ON)
SET(CPACK_RPM_MAIN_COMPONENT jfjoch)
SET(CPACK_RPM_PACKAGE_RELEASE_DIST ON)
SET(CPACK_RPM_FILE_NAME "RPM-DEFAULT")
SET(CPACK_RPM_PACKAGE_VERSION ${JFJOCH_VERSION})
SET(CPACK_RPM_PACKAGE_RELEASE 1)
SET(CPACK_RPM_PACKAGE_SUMMARY "Jungfraujoch data acquisition system")
SET(CPACK_RPM_PACKAGE_DESCRIPTION "Jungfraujoch")
SET(CPACK_RPM_DRIVER-DKMS_PACKAGE_REQUIRES "dkms, gcc, bash, sed")
SET(CPACK_RPM_DRIVER-DKMS_PACKAGE_ARCHITECTURE "noarch")
SET(CPACK_RPM_DRIVER-DKMS_POST_INSTALL_SCRIPT_FILE ${CMAKE_CURRENT_SOURCE_DIR}/fpga/pcie_driver/postinstall.sh)
SET(CPACK_RPM_DRIVER-DKMS_PRE_UNINSTALL_SCRIPT_FILE ${CMAKE_CURRENT_SOURCE_DIR}/fpga/pcie_driver/preuninstall.sh)
# Set The Vendor Name
SET(CPACK_PACKAGE_VENDOR "Paul Scherrer Institut")
# Set The License Information
SET(CPACK_RPM_PACKAGE_LICENSE "Proprietary")
INCLUDE(CPack)

View File

@@ -4,7 +4,7 @@ FROM harbor.maxiv.lu.se/dockerhub/library/ubuntu:22.04
RUN set -ex; \
apt-get update; \
apt-get install -y pkg-config git cmake make g++;\
apt-get install -y pkg-config git cmake make g++ libhdf5-dev libczmq-dev;\
rm -rf /var/lib/apt/lists/*

View File

@@ -33,24 +33,25 @@ Other linux platforms should work, but no tests were done so far.
### Dependencies
Required:
* C++20 compiler and C++20 standard library; recommended GCC 11+ or clang 14+ (Intel OneAPI, AMD AOCC)
* CMake version 3.21 or newer + GNU make tool
* CMake version 3.21 or newer + GNU make tool
* HDF5 library version 1.10 or newer
* TIFF library (with C++ headers)
* JPEG library (turbo-jpeg is also OK)
Optional:
* CUDA compiler version 11 or newer - required for MX fast feedback indexer
* CUDA compiler version 11 or newer - required for MX indexing and ML resolution estimation
* NUMA library - to pin threads to nodes/CPUs
* Node.js - to make frontend
* libtorch - for resolution estimation using model from Stanford - see below
Automatically downloaded by CMake and statically linked:
Automatically downloaded by CMake:
* SLS Detector Package - see [github.com/slsdetectorgroup/slsDetectorPackage](https://github.com/slsdetectorgroup/slsDetectorPackage)
* Zstandard (Facebook) - see [github.com/facebook/zstd](https://github.com/facebook/zstd)
* Pistache webserver - see [github.com/pistacheio/pistache](https://github.com/pistacheio/pistache)
* Fast feedback indexer (Hans-Christian Stadler, PSI) - see [github.com/paulscherrerinstitute/fast-feedback-indexer](https://github.com/paulscherrerinstitute/fast-feedback-indexer)
* Catch2 testing library - see [github.com/catchorg/Catch2](https://github.com/catchorg/Catch2)
* HDF5 library - see [github.com/HDFGroup/hdf5](https://github.com/HDFGroup/hdf5)
* TIFF library - see [gitlab.com/libtiff/libtiff](https://gitlab.com/libtiff/libtiff)
Please follow the link provided above to check for LICENSE file. Building code with dependencies above requires access from the build system to github.com.
Please follow the link provided above to check for LICENSE file
Directly included in the repository:
* JSON parser/writer from N. Lohmann - see [github.com/nlohmann/json](https://github.com/nlohmann/json)
@@ -75,6 +76,7 @@ For license check LICENSE file in respective directory
Use the following commands:
```
git submodule update --init --recursive
mkdir build
cd build
cmake ..
@@ -86,6 +88,7 @@ In most use cases it is better to have a separate machine, with access to distri
Such machine needs only a HDF5 writer service with fewer dependencies. For compilation use the following commands:
```
git submodule update --init --recursive
mkdir build
cd build
cmake -DJFJOCH_WRITER_ONLY=ON ..
@@ -109,6 +112,7 @@ Frontend is written in TypeScript. For details see [frontend_ui/](frontend_ui) d
Jungfraujoch Cmake scripts have an option to start frontend build with the following command:
```
git submodule update --init --recursive
mkdir build
cd build
cmake ..
@@ -118,7 +122,7 @@ Contrary to standard CMake way, frontend will be built in "source" `frontend_ui/
## Tests
Automated test routine is then accessible as `tests/jfjoch_test`. There are also benchmark routines:
Automated test routine is then accessible as `tests/CatchTest`. There are also benchmark routines:
* `HDF5DatasetWriteTest` to measure HDF5 dataset writing speed (single threaded)
* `jfjoch_spot_finding_test` to apply spot finding and indexing routines in Jungfraujoch to an example dataset - this is equivalent to FPGA spot finding algorithm, but NOT performance equivalent as it is particularly not-efficient
@@ -126,3 +130,16 @@ Automated test routine is then accessible as `tests/jfjoch_test`. There are also
In addition, tests are executed to verify that datasets written by Jungfraujoch are readable with XDS Durin plugin, XDS Neggia plygin and CrystFEL.
Input files for these programs are placed in `xds_durin`, `xds_neggia` and `crystfel` folders. See `.gitlab-ci.yml` for details.
## Resolution estimation
Resolution estimation can be done with a recent deep learning model by D. Mendez et al.
(see [Acta Cryst D, 80, 26-43](https://doi.org/10.1107/S2059798323010586)), adapted to Jungfraujoch.
Model used in the original paper is located in the [resonet/](resonet) directory, after converting to TorchScript format.
To use the feature it is necessary to install [libtorch](https://pytorch.org/) library, preferably in `/opt/libtorch` location. The C++11 ABI version needs to be chosen.
For RHEL 8 systems, please download older version 2.1.0, as version 2.2.0 requires newer `glibc` library than available with the operating system.
Version 2.1.0 can be downloaded with the following command:
```
wget https://download.pytorch.org/libtorch/cu121/libtorch-cxx11-abi-shared-with-deps-2.1.0%2Bcu121.zip
```

View File

@@ -1 +1 @@
1.0.0_rc.6
1.0.0-test5

View File

@@ -15,6 +15,4 @@ TARGET_LINK_LIBRARIES(JFJochBroker JFJochReceiver JFJochDetector JFJochCommon JF
ADD_EXECUTABLE(jfjoch_broker jfjoch_broker.cpp)
TARGET_LINK_LIBRARIES(jfjoch_broker JFJochBroker)
INSTALL(TARGETS jfjoch_broker RUNTIME COMPONENT jfjoch)
INSTALL(FILES redoc-static.html DESTINATION jfjoch/frontend COMPONENT jfjoch )
INSTALL(TARGETS jfjoch_broker RUNTIME)

View File

@@ -67,7 +67,6 @@ inline org::openapitools::server::model::Measurement_statistics Convert(const Me
if (input.bkg_estimate)
ret.setBkgEstimate(input.bkg_estimate.value());
ret.setUnitCell(input.unit_cell);
return ret;
}
@@ -652,6 +651,10 @@ void JFJochBrokerHttp::preview_image_tiff_get(Pistache::Http::ResponseWriter &re
response.send(Pistache::Http::Code::Not_Found);
}
void JFJochBrokerHttp::plot_resolution_estimate_histogram_get(Pistache::Http::ResponseWriter &response) {
GenericPlot(PlotType::ResEstimation, 0, response);
}
void JFJochBrokerHttp::config_internal_generator_image_put(const Pistache::Rest::Request &request,
Pistache::Http::ResponseWriter &response) {
int64_t image_number = 0;

View File

@@ -75,6 +75,8 @@ class JFJochBrokerHttp : public org::openapitools::server::api::DefaultApi {
void plot_rad_int_per_file_get(Pistache::Http::ResponseWriter &response) override;
void plot_resolution_estimate_histogram_get(Pistache::Http::ResponseWriter &response) override;
void statistics_calibration_get(Pistache::Http::ResponseWriter &response) override;
void statistics_data_collection_get(Pistache::Http::ResponseWriter &response) override;

View File

@@ -319,6 +319,7 @@ void ParseFacilityConfiguration(const nlohmann::json &input, const std::string&
"omega_axis must be float array of 3");
}
experiment.NeuralNetModelPath(GET_STR(j, "neural_net_model", ""));
if (j.contains("pedestal_g0_frames"))
experiment.PedestalG0Frames(GET_I64(j, "pedestal_g0_frames"));
if (j.contains("pedestal_g1_frames"))

View File

@@ -402,8 +402,6 @@ void JFJochStateMachine::SetFullMeasurementOutput(const JFJochServicesOutput &ou
tmp.detector_height = experiment.GetYPixelsNum();
tmp.detector_pixel_depth = experiment.GetPixelDepth();
tmp.images_expected = experiment.GetImageNum();
tmp.unit_cell = experiment.GetUnitCellString();
tmp.compression_ratio = output.receiver_output.status.compressed_ratio;
tmp.collection_efficiency = output.receiver_output.efficiency;
@@ -428,8 +426,6 @@ void JFJochStateMachine::ClearAndSetMeasurementStatistics() {
tmp.detector_width = experiment.GetYPixelsNum();
tmp.detector_pixel_depth = experiment.GetPixelDepth();
tmp.images_expected = experiment.GetImageNum();
tmp.unit_cell = experiment.GetUnitCellString();
measurement_statistics = tmp;
}
@@ -449,7 +445,6 @@ std::optional<MeasurementStatistics> JFJochStateMachine::GetMeasurementStatistic
tmp.detector_height = experiment.GetYPixelsNum();
tmp.detector_pixel_depth = experiment.GetPixelDepth();
tmp.images_expected = experiment.GetImageNum();
tmp.unit_cell = experiment.GetUnitCellString();
tmp.compression_ratio = rcv_status->compressed_ratio;
tmp.images_collected = rcv_status->images_collected;

View File

@@ -56,8 +56,6 @@ struct MeasurementStatistics {
std::optional<float> bkg_estimate;
std::optional<std::pair<float, float>> beam_center_drift_pxl;
std::string unit_cell;
};
struct DetectorSettings {

View File

@@ -25,6 +25,7 @@ To run the test:
### Compile Jungfraujoch with frontend
```
git submodule update --init --recursive
mkdir build
cd build
cmake ..

View File

@@ -56,6 +56,7 @@ void DefaultApi::setupRoutes() {
Routes::Get(*router, base + "/plot/rad_int_per_file", Routes::bind(&DefaultApi::plot_rad_int_per_file_get_handler, this));
Routes::Get(*router, base + "/plot/receiver_delay", Routes::bind(&DefaultApi::plot_receiver_delay_get_handler, this));
Routes::Get(*router, base + "/plot/receiver_free_send_buffers", Routes::bind(&DefaultApi::plot_receiver_free_send_buffers_get_handler, this));
Routes::Get(*router, base + "/plot/resolution_estimate_histogram", Routes::bind(&DefaultApi::plot_resolution_estimate_histogram_get_handler, this));
Routes::Get(*router, base + "/plot/roi_max_count", Routes::bind(&DefaultApi::plot_roi_max_count_get_handler, this));
Routes::Get(*router, base + "/plot/roi_sum", Routes::bind(&DefaultApi::plot_roi_sum_get_handler, this));
Routes::Get(*router, base + "/plot/roi_valid_pixels", Routes::bind(&DefaultApi::plot_roi_valid_pixels_get_handler, this));
@@ -671,6 +672,26 @@ void DefaultApi::plot_receiver_free_send_buffers_get_handler(const Pistache::Res
response.send(Pistache::Http::Code::Internal_Server_Error, e.what());
}
}
void DefaultApi::plot_resolution_estimate_histogram_get_handler(const Pistache::Rest::Request &, Pistache::Http::ResponseWriter response) {
try {
try {
this->plot_resolution_estimate_histogram_get(response);
} catch (Pistache::Http::HttpError &e) {
response.send(static_cast<Pistache::Http::Code>(e.code()), e.what());
return;
} catch (std::exception &e) {
const std::pair<Pistache::Http::Code, std::string> errorInfo = this->handleOperationException(e);
response.send(errorInfo.first, errorInfo.second);
return;
}
} catch (std::exception &e) {
response.send(Pistache::Http::Code::Internal_Server_Error, e.what());
}
}
void DefaultApi::plot_roi_max_count_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response) {
try {

View File

@@ -80,6 +80,7 @@ private:
void plot_rad_int_per_file_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
void plot_receiver_delay_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
void plot_receiver_free_send_buffers_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
void plot_resolution_estimate_histogram_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
void plot_roi_max_count_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
void plot_roi_sum_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
void plot_roi_valid_pixels_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
@@ -292,6 +293,13 @@ private:
/// <param name="binning">Binning of frames for the plot (0 &#x3D; default binning) (optional, default to 0)</param>
virtual void plot_receiver_free_send_buffers_get(const std::optional<int32_t> &binning, Pistache::Http::ResponseWriter &response) = 0;
/// <summary>
/// Generate resolution estimate histogram
/// </summary>
/// <remarks>
/// Generate histogram of crystal resolutions from 1.0 to 5.0 A based on ML model
/// </remarks>
virtual void plot_resolution_estimate_histogram_get(Pistache::Http::ResponseWriter &response) = 0;
/// <summary>
/// Generate plot of ROI max count
/// </summary>
/// <remarks>

View File

@@ -51,8 +51,6 @@ Measurement_statistics::Measurement_statistics()
m_Detector_pixel_depthIsSet = false;
m_Bkg_estimate = 0.0f;
m_Bkg_estimateIsSet = false;
m_Unit_cell = "";
m_Unit_cellIsSet = false;
}
@@ -108,7 +106,7 @@ bool Measurement_statistics::validate(std::stringstream& msg, const std::string&
}
}
return success;
}
@@ -160,10 +158,7 @@ bool Measurement_statistics::operator==(const Measurement_statistics& rhs) const
((!detectorPixelDepthIsSet() && !rhs.detectorPixelDepthIsSet()) || (detectorPixelDepthIsSet() && rhs.detectorPixelDepthIsSet() && getDetectorPixelDepth() == rhs.getDetectorPixelDepth())) &&
((!bkgEstimateIsSet() && !rhs.bkgEstimateIsSet()) || (bkgEstimateIsSet() && rhs.bkgEstimateIsSet() && getBkgEstimate() == rhs.getBkgEstimate())) &&
((!unitCellIsSet() && !rhs.unitCellIsSet()) || (unitCellIsSet() && rhs.unitCellIsSet() && getUnitCell() == rhs.getUnitCell()))
((!bkgEstimateIsSet() && !rhs.bkgEstimateIsSet()) || (bkgEstimateIsSet() && rhs.bkgEstimateIsSet() && getBkgEstimate() == rhs.getBkgEstimate()))
;
}
@@ -206,8 +201,6 @@ void to_json(nlohmann::json& j, const Measurement_statistics& o)
j["detector_pixel_depth"] = o.m_Detector_pixel_depth;
if(o.bkgEstimateIsSet())
j["bkg_estimate"] = o.m_Bkg_estimate;
if(o.unitCellIsSet())
j["unit_cell"] = o.m_Unit_cell;
}
@@ -288,11 +281,6 @@ void from_json(const nlohmann::json& j, Measurement_statistics& o)
j.at("bkg_estimate").get_to(o.m_Bkg_estimate);
o.m_Bkg_estimateIsSet = true;
}
if(j.find("unit_cell") != j.end())
{
j.at("unit_cell").get_to(o.m_Unit_cell);
o.m_Unit_cellIsSet = true;
}
}
@@ -551,23 +539,6 @@ void Measurement_statistics::unsetBkg_estimate()
{
m_Bkg_estimateIsSet = false;
}
std::string Measurement_statistics::getUnitCell() const
{
return m_Unit_cell;
}
void Measurement_statistics::setUnitCell(std::string const& value)
{
m_Unit_cell = value;
m_Unit_cellIsSet = true;
}
bool Measurement_statistics::unitCellIsSet() const
{
return m_Unit_cellIsSet;
}
void Measurement_statistics::unsetUnit_cell()
{
m_Unit_cellIsSet = false;
}
} // namespace org::openapitools::server::model

View File

@@ -163,13 +163,6 @@ public:
void setBkgEstimate(float const value);
bool bkgEstimateIsSet() const;
void unsetBkg_estimate();
/// <summary>
///
/// </summary>
std::string getUnitCell() const;
void setUnitCell(std::string const& value);
bool unitCellIsSet() const;
void unsetUnit_cell();
friend void to_json(nlohmann::json& j, const Measurement_statistics& o);
friend void from_json(const nlohmann::json& j, Measurement_statistics& o);
@@ -204,8 +197,6 @@ protected:
bool m_Detector_pixel_depthIsSet;
float m_Bkg_estimate;
bool m_Bkg_estimateIsSet;
std::string m_Unit_cell;
bool m_Unit_cellIsSet;
};

View File

@@ -500,8 +500,6 @@ components:
bkg_estimate:
type: number
format: float
unit_cell:
type: string
broker_status:
type: object
required:
@@ -1447,6 +1445,17 @@ paths:
application/json:
schema:
$ref: '#/components/schemas/plots'
/plot/resolution_estimate_histogram:
get:
summary: Generate resolution estimate histogram
description: Generate histogram of crystal resolutions from 1.0 to 5.0 A based on ML model
responses:
"200":
description: Everything OK
content:
application/json:
schema:
$ref: '#/components/schemas/plots'
/plot/rad_int:
get:
summary: Generate radial integration profile

View File

@@ -2,7 +2,7 @@
// Using OpenAPI licensed with Apache License 2.0
#include <vector>
#include <csignal>
#include <signal.h>
#include <fstream>
#include <nlohmann/json.hpp>
@@ -12,7 +12,7 @@
#include "JFJochBrokerHttp.h"
#include "JFJochBrokerParser.h"
#include "../frame_serialize/ZMQStream2Pusher.h"
#include "../frame_serialize/ZMQStream2PusherGroup.h"
#include "../frame_serialize/DumpCBORToFilePusher.h"
static Pistache::Http::Endpoint *httpEndpoint;
@@ -73,6 +73,8 @@ int main (int argc, char **argv) {
std::unique_ptr<JFJochReceiverService> receiver;
std::unique_ptr<ImagePusher> image_pusher;
ZMQContext context;
DiffractionExperiment experiment;
experiment.MaskChipEdges(true).MaskModuleEdges(true);
@@ -86,15 +88,9 @@ int main (int argc, char **argv) {
int32_t zmq_send_watermark = ParseInt32(input, "zmq_send_watermark", 100);
int32_t zmq_send_buffer_size = ParseInt32(input, "zmq_send_buffer_size", -1);
auto tmp = std::make_unique<ZMQStream2Pusher>(ParseStringArray(input, "zmq_image_addr"),
image_pusher = std::make_unique<ZMQStream2PusherGroup>(ParseStringArray(input, "zmq_image_addr"),
zmq_send_watermark,
zmq_send_buffer_size);
std::string preview_addr = ParseString(input, "zmq_preview_addr", "");
if (!preview_addr.empty())
tmp->PreviewSocket(preview_addr);
image_pusher = std::move(tmp);
} else if (pusher_type == "dump_cbor") {
image_pusher = std::make_unique<DumpCBORToFilePusher>();
} else

File diff suppressed because one or more lines are too long

View File

@@ -23,19 +23,14 @@ MESSAGE(STATUS "Jungfraujoch version: ${PACKAGE_VERSION}")
CONFIGURE_FILE("${CMAKE_CURRENT_SOURCE_DIR}/GitInfo.cpp.in" "${CMAKE_CURRENT_BINARY_DIR}/GitInfo.cpp" @ONLY)
ADD_LIBRARY(JFJochLogger STATIC
ADD_LIBRARY( JFJochCommon STATIC
Logger.cpp Logger.h
${CMAKE_CURRENT_BINARY_DIR}/GitInfo.cpp GitInfo.h
)
ADD_LIBRARY(JFJochZMQ STATIC ZMQWrappers.cpp ZMQWrappers.h)
ADD_LIBRARY(JFJochCommon STATIC
Coord.cpp Coord.h
DiffractionExperiment.cpp DiffractionExperiment.h
RawToConvertedGeometry.h
JFJochException.h
Definitions.h
${CMAKE_CURRENT_BINARY_DIR}/GitInfo.cpp GitInfo.h
ThreadSafeFIFO.h
DiffractionSpot.cpp DiffractionSpot.h
StatusVector.h
@@ -50,6 +45,7 @@ ADD_LIBRARY(JFJochCommon STATIC
RawToConvertedGeometryCore.h
Plot.h
../fpga/pcie_driver/jfjoch_fpga.h
ZMQWrappers.cpp ZMQWrappers.h
DatasetSettings.cpp DatasetSettings.h
ROIMap.cpp ROIMap.h
ROIElement.cpp ROIElement.h
@@ -61,9 +57,7 @@ ADD_LIBRARY(JFJochCommon STATIC
PixelMask.cpp PixelMask.h
)
TARGET_LINK_LIBRARIES(JFJochCommon JFJochLogger Compression JFCalibration -lrt)
TARGET_LINK_LIBRARIES(JFJochZMQ "$<BUILD_INTERFACE:libzmq-static>")
TARGET_LINK_LIBRARIES(JFJochCommon Compression JFCalibration "$<BUILD_INTERFACE:libzmq-static>" -lrt)
IF (CMAKE_CUDA_COMPILER)
TARGET_SOURCES(JFJochCommon PRIVATE CUDAWrapper.cu )

View File

@@ -9,7 +9,6 @@
#include "JFJochException.h"
#include "RawToConvertedGeometry.h"
#include "../fpga/pcie_driver/jfjoch_fpga.h"
#include "../include/spdlog/fmt/fmt.h"
using namespace std::literals::chrono_literals;
@@ -598,20 +597,6 @@ std::optional<UnitCell> DiffractionExperiment::GetUnitCell() const {
return dataset.GetUnitCell();
}
std::string DiffractionExperiment::GetUnitCellString() const {
auto uc = dataset.GetUnitCell();
if (uc.has_value()) {
return fmt::format("{:.1f}, {:.1f}, {:.1f}, {:.1f}, {:.1f} {:.1f}",
uc.value().a,
uc.value().b,
uc.value().c,
uc.value().alpha,
uc.value().beta,
uc.value().gamma);
} else
return "-";
}
Coord DiffractionExperiment::LabCoord(float detector_x, float detector_y) const {
// Assumes planar detector, 90 deg towards beam
return {(detector_x - GetBeamX_pxl()) * GetPixelSize_mm() ,
@@ -752,8 +737,6 @@ void DiffractionExperiment::FillMessage(StartMessage &message) const {
for (const auto &[x, y]: roi_mask.GetROINameMap())
message.roi_names.emplace_back(x);
message.data_reduction_factor_serialmx = GetDataReductionFactorSerialMX();
}
float DiffractionExperiment::GetPixelSize_mm() const {
@@ -1081,6 +1064,15 @@ const DetectorSetup &DiffractionExperiment::GetDetectorSetup() const {
return detector;
}
DiffractionExperiment &DiffractionExperiment::NeuralNetModelPath(const std::string &input) {
neural_net_model_path = input;
return *this;
}
std::string DiffractionExperiment::GetNeuralNetModelPath() const {
return neural_net_model_path;
}
DiffractionExperiment &DiffractionExperiment::PulsedSource(bool input) {
pulsed_source = input;
return *this;

View File

@@ -89,6 +89,8 @@ class DiffractionExperiment {
uint64_t series_id;
std::string neural_net_model_path;
bool rad_int_solid_angle_corr;
bool rad_int_polarization_corr;
float rad_int_polarization_factor{};
@@ -142,6 +144,7 @@ public:
DiffractionExperiment& FixedGainG1(bool input);
DiffractionExperiment& IncrementSeriesID();
DiffractionExperiment& ConversionOnFPGA(bool input);
DiffractionExperiment& NeuralNetModelPath(const std::string& input);
DiffractionExperiment& PulsedSource(bool input);
DiffractionExperiment& ImagesPerTrigger(int64_t input);
@@ -279,6 +282,7 @@ public:
bool IsConversionOnFPGA() const;
const DetectorSetup& GetDetectorSetup() const;
std::string GetNeuralNetModelPath() const;
bool IsPulsedSource() const;
@@ -295,7 +299,6 @@ public:
std::string GetImageAppendix() const;
float GetPhotonEnergyMultiplier() const;
std::optional<UnitCell> GetUnitCell() const;
std::string GetUnitCellString() const;
int64_t GetSpaceGroupNumber() const;
bool GetSaveCalibration() const;
int64_t GetSummation() const;

View File

@@ -46,6 +46,15 @@ NUMAHWPolicy::NUMAHWPolicy(const std::string &policy) : name(policy) {
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Unknown NUMA policy");
}
NUMAHWPolicy::NUMAHWPolicy(const NUMAHWPolicy &other) : bindings(other.bindings), name(other.name), curr_thread(0) {}
NUMAHWPolicy &NUMAHWPolicy::operator=(const NUMAHWPolicy &other) {
bindings = other.bindings;
name = other.name;
curr_thread = 0;
return *this;
}
NUMABinding NUMAHWPolicy::GetBinding(uint32_t thread) {
if (bindings.empty())
return NUMABinding{.cpu_node = -1, .mem_node = -1, .gpu = -1};
@@ -53,6 +62,14 @@ NUMABinding NUMAHWPolicy::GetBinding(uint32_t thread) {
return bindings.at(thread % bindings.size());
}
NUMABinding NUMAHWPolicy::GetBinding() {
return GetBinding(curr_thread++);
}
void NUMAHWPolicy::Bind() {
Bind(GetBinding());
}
void NUMAHWPolicy::Bind(uint32_t thread) {
Bind(GetBinding(thread));
}

View File

@@ -17,14 +17,19 @@ struct NUMABinding {
class NUMAHWPolicy {
std::string name;
std::vector<NUMABinding> bindings;
std::atomic<uint32_t> curr_thread = 0;
public:
NUMAHWPolicy() = default;
explicit NUMAHWPolicy(const std::string& policy);
NUMAHWPolicy(const NUMAHWPolicy& other);
NUMAHWPolicy& operator=(const NUMAHWPolicy& other);
NUMABinding GetBinding(uint32_t thread);
NUMABinding GetBinding(); // round-robin
const std::string &GetName() const;
void Bind(uint32_t thread);
void Bind(); // round-robin
static void Bind(const NUMABinding &binding);
static void RunOnNode(int32_t cpu_node);
static void MemOnNode(int32_t mem_node);

View File

@@ -9,7 +9,7 @@
enum class PlotType {BkgEstimate, RadInt, RadIntPerTimePoint, SpotCount, IndexingRate, IndexingRatePerTimePoint,
ErrorPixels, ImageCollectionEfficiency, ReceiverDelay, ReceiverFreeSendBuf, StrongPixels,
ROISum, ROIMaxCount, ROIPixels};
ROISum, ROIMaxCount, ROIPixels, ResEstimation};
struct PlotRequest {
PlotType type;

View File

@@ -8,7 +8,8 @@ ZMQContext::ZMQContext() {
// Default is to have 2 I/O threads per ZMQ context
if (zmq_ctx_set(context, ZMQ_IO_THREADS, 2) != 0)
throw JFJochException(JFJochExceptionCategory::ZeroMQ, "Cannot set number of I/O threads");
throw JFJochException(JFJochExceptionCategory::ZeroMQ,
"Cannot set number of I/O threads");
}
ZMQContext &ZMQContext::NumThreads(int32_t threads) {
@@ -26,7 +27,7 @@ void *ZMQContext::GetContext() const {
return context;
}
ZMQSocket::ZMQSocket(ZMQSocketType in_socket_type) : socket_type(in_socket_type) {
ZMQSocket::ZMQSocket(ZMQContext &context, ZMQSocketType in_socket_type) : socket_type(in_socket_type) {
socket = zmq_socket(context.GetContext(), static_cast<int>(socket_type));
if (socket == nullptr)

View File

@@ -42,15 +42,14 @@ public:
class ZMQSocket {
std::mutex m;
ZMQContext context;
ZMQSocketType socket_type;
void *socket;
void SetSocketOption(int32_t option_name, int32_t value);
public:
ZMQSocket(ZMQSocket &socket) = delete;
const ZMQSocket& operator=(ZMQSocket &socket) = delete;
explicit ZMQSocket(ZMQSocketType socket_type);
~ZMQSocket();
ZMQSocket(ZMQContext &context, ZMQSocketType socket_type);
~ZMQSocket();
void Connect(const std::string& addr);
void Disconnect(const std::string& addr);
void Bind(const std::string& addr);

View File

@@ -1,2 +1,6 @@
INSTALL(TARGETS sls_detector_put sls_detector_get RUNTIME)
ADD_LIBRARY(JFJochDetector STATIC DetectorWrapper.cpp DetectorWrapper.h)
TARGET_LINK_LIBRARIES(JFJochDetector JFJochCommon slsDetectorStatic slsSupportStatic)
TARGET_LINK_LIBRARIES(JFJochDetector JFJochCommon slsSupportShared slsDetectorShared)

View File

@@ -4,7 +4,7 @@ TARGET_LINK_LIBRARIES(JFJochDevice JFJochCommon)
ADD_EXECUTABLE(jfjoch_pcie_status jfjoch_pcie_status.cpp)
TARGET_LINK_LIBRARIES(jfjoch_pcie_status JFJochDevice )
INSTALL(TARGETS jfjoch_pcie_status RUNTIME COMPONENT jfjoch)
INSTALL(TARGETS jfjoch_pcie_status RUNTIME)
ADD_EXECUTABLE(jfjoch_pcie_set_network jfjoch_pcie_set_network.cpp)
TARGET_LINK_LIBRARIES(jfjoch_pcie_set_network JFJochDevice )

View File

@@ -1,5 +1,5 @@
PACKAGE_NAME=jfjoch
PACKAGE_VERSION=1.0.0
PACKAGE_VERSION=0.1
DEST_MODULE_LOCATION=/extra
BUILT_MODULE_NAME=jfjoch
@@ -7,4 +7,4 @@ BUILT_MODULE_LOCATION=src/
MAKE="'make' -C src/ all"
CLEAN="'make' -C src/ clean"
AUTOINSTALL="yes"
AUTOINSTALL="yes"

View File

@@ -1,11 +1,12 @@
#!/bin/bash
# Copyright (2019-2023) Paul Scherrer Institute
VERSION=1.0.0
VERSION=0.1
mkdir -p /usr/src/jfjoch-${VERSION}/src
cp dkms.conf /usr/src/jfjoch-${VERSION}
cp *.c *.h Makefile /usr/src/jfjoch-${VERSION}/src
cp *.c *.h Makefile ../../common/Definitions.h /usr/src/jfjoch-0.1/src
sed -i "s,../../common/Definitions.h,Definitions.h," /usr/src/jfjoch-0.1/src/jfjoch_drv.h
dkms add -m jfjoch -v ${VERSION}
dkms install -m jfjoch -v ${VERSION}

View File

@@ -11,7 +11,7 @@
MODULE_AUTHOR("Filip Leonarski; Paul Scherrer Institute");
MODULE_DESCRIPTION("Jungfraujoch device module");
MODULE_LICENSE("GPL");
MODULE_VERSION("1.0.0");
MODULE_VERSION("0.1");
#define XDMA_GEN4_x8 (0x9048)
#define XDMA_GEN3_x16 (0x903F)

View File

@@ -1,14 +0,0 @@
#!/bin/bash
# Taken from https://schneide.blog/2015/08/10/packaging-kernel-modulesdrivers-using-dkms/
VERSION="1.0.0"
occurrences=`/usr/sbin/dkms status | grep jfjoch | grep ${VERSION} | wc -l`
if [ ! occurrences > 0 ]; then
/usr/sbin/dkms add -m jfjoch -v ${VERSION}
fi
/usr/sbin/dkms build -m jfjoch -v ${VERSION}
/usr/sbin/dkms install -m jfjoch -v ${VERSION}
exit 0

View File

@@ -1,8 +0,0 @@
#!/bin/bash
# Taken from https://schneide.blog/2015/08/10/packaging-kernel-modulesdrivers-using-dkms/
VERSION="1.0.0"
/usr/sbin/dkms remove -m jfjoch -v ${VERSION} --all
exit 0

View File

@@ -636,8 +636,6 @@ namespace {
message.roi_names = j["roi_names"];
if (j.contains("write_master_file"))
message.write_master_file = j["write_master_file"];
if (j.contains("data_reduction_factor_serialmx"))
message.data_reduction_factor_serialmx = j["data_reduction_factor_serialmx"];
} catch (const std::exception &e) {
throw JFJochException(JFJochExceptionCategory::CBORError,
"Cannot parse user_data as valid JSON " + std::string(e.what()));

View File

@@ -316,8 +316,6 @@ inline void CBOR_ENC_START_USER_DATA(CborEncoder& encoder, const char* key,
j["gain_file_names"] = message.gain_file_names;
if (message.write_master_file)
j["write_master_file"] = message.write_master_file.value();
if (message.data_reduction_factor_serialmx)
j["data_reduction_factor_serialmx"] = message.data_reduction_factor_serialmx.value();
auto str = j.dump();

View File

@@ -20,8 +20,10 @@ TARGET_LINK_LIBRARIES(CBORStream2FrameSerialize tinycbor)
ADD_LIBRARY(ImagePusher STATIC
ImagePusher.cpp ImagePusher.h
TestImagePusher.cpp TestImagePusher.h
ZMQStream2Pusher.cpp ZMQStream2Pusher.h
ZMQStream2PusherGroup.cpp ZMQStream2PusherGroup.h
ZMQStream2Pusher.cpp
ZMQStream2Pusher.h
DumpCBORToFilePusher.cpp
DumpCBORToFilePusher.h)
TARGET_LINK_LIBRARIES(ImagePusher JFJochZMQ CBORStream2FrameSerialize JFJochCommon Compression)
TARGET_LINK_LIBRARIES(ImagePusher CBORStream2FrameSerialize JFJochCommon Compression)

View File

@@ -75,6 +75,8 @@ struct DataMessage {
std::optional<uint64_t> receiver_free_send_buf;
std::optional<uint64_t> storage_cell;
std::optional<float> resolution_estimation;
std::optional<uint64_t> xfel_pulse_id;
std::optional<uint64_t> xfel_event_code;
@@ -168,8 +170,6 @@ struct StartMessage {
}
std::string user_data;
std::optional<float> data_reduction_factor_serialmx;
};
struct EndMessage {

View File

@@ -1,117 +1,66 @@
// Copyright (2019-2024) Paul Scherrer Institute
#include "ZMQStream2Pusher.h"
#include "CBORStream2Serializer.h"
ZMQStream2Pusher::ZMQStream2Pusher(const std::vector<std::string> &addr,
int32_t send_buffer_high_watermark, int32_t send_buffer_size)
: serialization_buffer(256*1024*1024),
serializer(serialization_buffer.data(), serialization_buffer.size()),
preview_counter(std::chrono::seconds(1)) {
if (addr.empty())
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "No writer ZMQ address provided");
ZMQStream2Pusher::ZMQStream2Pusher(ZMQContext &context, const std::string &addr, int32_t send_buffer_high_watermark,
int32_t send_buffer_size)
: socket(context, ZMQSocketType::Push) {
Bind(addr, send_buffer_high_watermark, send_buffer_size);
}
for (const auto &a : addr) {
auto s = std::make_unique<ZMQSocket>(ZMQSocketType::Push);
if (send_buffer_size > 0)
s->SendBufferSize(send_buffer_size);
if (send_buffer_high_watermark > 0)
s->SendWaterMark(send_buffer_high_watermark);
s->SendTimeout(std::chrono::seconds(5)); // 5 seconds should be more than enough to flush buffers and to still give fast response
s->Bind(a);
socket.emplace_back(std::move(s));
}
ZMQStream2Pusher::ZMQStream2Pusher(const std::string &addr, int32_t send_buffer_high_watermark,
int32_t send_buffer_size)
: context(std::make_unique<ZMQContext>()),
socket(*context, ZMQSocketType::Push) {
Bind(addr, send_buffer_high_watermark, send_buffer_size);
}
void ZMQStream2Pusher::Bind(const std::string &addr, int32_t send_buffer_high_watermark, int32_t send_buffer_size) {
if (send_buffer_size > 0)
socket.SendBufferSize(send_buffer_size);
if (send_buffer_high_watermark > 0)
socket.SendWaterMark(send_buffer_high_watermark);
socket.SendTimeout(std::chrono::seconds(5)); // 5 seconds should be more than enough to flush buffers and to still give fast response
socket.Bind(addr);
}
void ZMQStream2Pusher::StartDataCollection(StartMessage &message) {
size_t approx_size = 1024*1024;
for (const auto &x : message.pixel_mask)
approx_size += x.size;
std::vector<uint8_t> serialization_buffer(approx_size);
CBORStream2Serializer serializer(serialization_buffer.data(), serialization_buffer.size());
serializer.SerializeSequenceStart(message);
if (!socket.Send(serialization_buffer.data(), serializer.GetBufferSize(), true))
throw JFJochException(JFJochExceptionCategory::ZeroMQ, "Timeout on pushing start message on addr " + GetAddress());
}
bool ZMQStream2Pusher::SendImage(const uint8_t *image_data, size_t image_size, int64_t image_number) {
if (preview_socket) {
if (preview_counter.GeneratePreview())
preview_socket->Send(image_data, image_size, false);
}
if (!socket.empty()) {
auto socket_number = (image_number / images_per_file) % socket.size();
return socket[socket_number]->Send(image_data, image_size, false);
} else
return false;
return socket.Send(image_data, image_size, false);
}
void ZMQStream2Pusher::SendImage(const uint8_t *image_data, size_t image_size, int64_t image_number,
ZeroCopyReturnValue *z) {
if (preview_socket) {
if (preview_counter.GeneratePreview())
preview_socket->Send(image_data, image_size, false);
}
if (!socket.empty()) {
auto socket_number = (image_number / images_per_file) % socket.size();
socket[socket_number]->SendZeroCopy(image_data, image_size, z);
} else
z->release();
ZeroCopyReturnValue *z) {
socket.SendZeroCopy(image_data,image_size, z);
}
void ZMQStream2Pusher::StartDataCollection(StartMessage& message) {
if (message.images_per_file < 1)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Images per file cannot be zero or negative");
images_per_file = message.images_per_file;
bool ZMQStream2Pusher::EndDataCollection(const EndMessage &message) {
std::vector<uint8_t> serialization_buffer(80 * 1024 * 1024);
CBORStream2Serializer serializer(serialization_buffer.data(), serialization_buffer.size());
serializer.SerializeSequenceStart(message);
for (auto &s: socket) {
if (!s->Send(serialization_buffer.data(), serializer.GetBufferSize(), true))
throw JFJochException(JFJochExceptionCategory::ZeroMQ, "Timeout on pushing start message on addr "
+ s->GetEndpointName());
if (message.write_master_file) {
message.write_master_file = false;
serializer.SerializeSequenceStart(message);
}
}
if (preview_socket)
preview_socket->Send(serialization_buffer.data(), serializer.GetBufferSize(), true);
serializer.SerializeSequenceEnd(message);
return socket.Send(serialization_buffer.data(), serializer.GetBufferSize(), true); // Blocking
}
bool ZMQStream2Pusher::SendCalibration(const CompressedImage &message) {
if (socket.empty())
return false;
std::vector<uint8_t> serialization_buffer(80 * 1024 * 1024);
CBORStream2Serializer serializer(serialization_buffer.data(), serialization_buffer.size());
serializer.SerializeCalibration(message);
return socket[0]->Send(serialization_buffer.data(), serializer.GetBufferSize(), true);
return socket.Send(serialization_buffer.data(), serializer.GetBufferSize(), true); // Blocking
}
bool ZMQStream2Pusher::EndDataCollection(const EndMessage& message) {
serializer.SerializeSequenceEnd(message);
bool ret = true;
for (auto &s: socket) {
if (!s->Send(serialization_buffer.data(), serializer.GetBufferSize(), true))
ret = false;
}
if (preview_socket)
preview_socket->Send(serialization_buffer.data(), serializer.GetBufferSize(), true);
return ret;
}
std::vector<std::string> ZMQStream2Pusher::GetAddress() {
std::vector<std::string> ret;
for (auto &p: socket)
ret.push_back(p->GetEndpointName());
return ret;
}
ZMQStream2Pusher &ZMQStream2Pusher::PreviewSocket(const std::string &addr) {
preview_socket = std::make_unique<ZMQSocket>(ZMQSocketType::Pub);
preview_socket->Bind(addr);
return *this;
}
std::string ZMQStream2Pusher::GetPreviewAddress() {
if (preview_socket)
return preview_socket->GetEndpointName();
else
return "";
std::string ZMQStream2Pusher::GetAddress() {
return socket.GetEndpointName();
}

View File

@@ -3,40 +3,30 @@
#ifndef JUNGFRAUJOCH_ZMQSTREAM2PUSHER_H
#define JUNGFRAUJOCH_ZMQSTREAM2PUSHER_H
#include <mutex>
#include "ImagePusher.h"
#include "../common/ZMQWrappers.h"
#include "../preview/PreviewCounter.h"
class ZMQStream2Pusher : public ImagePusher {
std::vector<uint8_t> serialization_buffer;
CBORStream2Serializer serializer;
std::vector<std::unique_ptr<ZMQSocket>> socket;
std::unique_ptr<ZMQSocket> preview_socket;
PreviewCounter preview_counter;
int64_t images_per_file = 1;
std::unique_ptr<ZMQContext> context;
ZMQSocket socket;
public:
explicit ZMQStream2Pusher(const std::vector<std::string>& addr,
ZMQStream2Pusher(ZMQContext& context,
const std::string& addr,
int32_t send_buffer_high_watermark = -1,
int32_t send_buffer_size = -1);
explicit ZMQStream2Pusher(const std::string& addr,
int32_t send_buffer_high_watermark = -1,
int32_t send_buffer_size = -1);
ZMQStream2Pusher& PreviewSocket(const std::string& addr);
std::string GetPreviewAddress();
std::vector<std::string> GetAddress();
// Strictly serial, as order of these is important
void Bind(const std::string& addr, int32_t send_buffer_high_watermark, int32_t send_buffer_size);
void StartDataCollection(StartMessage& message) override;
bool EndDataCollection(const EndMessage& message) override;
bool SendImage(const uint8_t *image_data, size_t image_size, int64_t image_number) override;
void SendImage(const uint8_t *image_data, size_t image_size, int64_t image_number, ZeroCopyReturnValue *z) override;
bool EndDataCollection(const EndMessage &message) override;
bool SendCalibration(const CompressedImage& message) override;
// Thread-safe
void SendImage(const uint8_t *image_data, size_t image_size, int64_t image_number, ZeroCopyReturnValue *z) override;
bool SendImage(const uint8_t *image_data, size_t image_size, int64_t image_number) override;
std::string GetAddress();
};
#endif //JUNGFRAUJOCH_ZMQSTREAM2PUSHER_H

View File

@@ -0,0 +1,75 @@
// Copyright (2019-2024) Paul Scherrer Institute
#include "ZMQStream2PusherGroup.h"
#include "CBORStream2Serializer.h"
ZMQStream2PusherGroup::ZMQStream2PusherGroup(ZMQContext &zmq_context, const std::vector<std::string> &addr,
int32_t send_buffer_high_watermark, int32_t send_buffer_size) {
if (addr.empty())
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"No writer ZMQ address provided");
for (const auto &a : addr)
pusher.emplace_back(std::make_unique<ZMQStream2Pusher>
(zmq_context, a, send_buffer_high_watermark, send_buffer_size));
}
ZMQStream2PusherGroup::ZMQStream2PusherGroup(const std::vector<std::string> &addr,
int32_t send_buffer_high_watermark, int32_t send_buffer_size) {
if (addr.empty())
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"No writer ZMQ address provided");
for (const auto &a : addr)
pusher.emplace_back(std::make_unique<ZMQStream2Pusher>
(a, send_buffer_high_watermark, send_buffer_size));
}
bool ZMQStream2PusherGroup::SendImage(const uint8_t *image_data, size_t image_size, int64_t image_number) {
if (!pusher.empty()) {
auto socket_number = (image_number / images_per_file) % pusher.size();
return pusher[socket_number]->SendImage(image_data, image_size, image_number);
} else
return false;
}
void ZMQStream2PusherGroup::SendImage(const uint8_t *image_data, size_t image_size, int64_t image_number,
ZeroCopyReturnValue *z) {
if (!pusher.empty()) {
auto socket_number = (image_number / images_per_file) % pusher.size();
pusher[socket_number]->SendImage(image_data, image_size, image_number, z);
}
}
void ZMQStream2PusherGroup::StartDataCollection(StartMessage& message) {
if (message.images_per_file < 1)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Images per file cannot be zero or negative");
images_per_file = message.images_per_file;
for (auto &p: pusher) {
p->StartDataCollection(message);
message.write_master_file = false;
}
}
bool ZMQStream2PusherGroup::SendCalibration(const CompressedImage &message) {
if (pusher.empty())
return false;
return pusher[0]->SendCalibration(message);
}
bool ZMQStream2PusherGroup::EndDataCollection(const EndMessage& message) {
bool ret = true;
for (auto &p: pusher) {
if (!p->EndDataCollection(message))
ret = false;
}
return ret;
}
std::vector<std::string> ZMQStream2PusherGroup::GetAddress() {
std::vector<std::string> ret;
for (auto &p: pusher)
ret.push_back(p->GetAddress());
return ret;
}

View File

@@ -0,0 +1,29 @@
// Copyright (2019-2024) Paul Scherrer Institute
#ifndef JUNGFRAUJOCH_ZMQSTREAM2PUSHERGROUP_H
#define JUNGFRAUJOCH_ZMQSTREAM2PUSHERGROUP_H
#include "ImagePusher.h"
#include "ZMQStream2Pusher.h"
#include "../common/ZMQWrappers.h"
class ZMQStream2PusherGroup : public ImagePusher {
std::vector<std::unique_ptr<ZMQStream2Pusher>> pusher;
int64_t images_per_file = 1;
public:
ZMQStream2PusherGroup(ZMQContext &context, const std::vector<std::string>& addr,
int32_t send_buffer_high_watermark = -1, int32_t send_buffer_size = -1);
// High performance implementation, where each socket has dedicated ZMQ context
explicit ZMQStream2PusherGroup(const std::vector<std::string>& addr,
int32_t send_buffer_high_watermark = -1, int32_t send_buffer_size = -1);
void StartDataCollection(StartMessage& message) override;
void SendImage(const uint8_t *image_data, size_t image_size, int64_t image_number, ZeroCopyReturnValue *z) override;
bool SendImage(const uint8_t *image_data, size_t image_size, int64_t image_number) override;
bool EndDataCollection(const EndMessage& message) override;
bool SendCalibration(const CompressedImage& message) override;
std::vector<std::string> GetAddress();
};
#endif //JUNGFRAUJOCH_ZMQSTREAM2PUSHERGROUP_H

File diff suppressed because it is too large Load Diff

View File

@@ -10,7 +10,6 @@
"@mui/icons-material": "^5.10.6",
"@mui/material": "^5.10.6",
"@mui/x-data-grid": "^5.17.14",
"@redocly/cli": "^1.12.2",
"@types/jest": "^29.2.4",
"@types/node": "^18.11.13",
"@types/react": "^18.0.26",
@@ -26,7 +25,6 @@
"scripts": {
"start": "REACT_APP_VERSION=$(git rev-parse --short HEAD) PORT=8000 react-scripts start",
"build": "REACT_APP_VERSION=$(git rev-parse --short HEAD) react-scripts build",
"redocly": "redocly build-docs ../broker/jfjoch_api.yaml --output=build/openapi.html",
"test": "react-scripts test",
"eject": "react-scripts eject",
"openapi": "openapi --input ../broker/jfjoch_api.yaml --output ./src/openapi"

View File

@@ -145,8 +145,7 @@ class App extends Component<MyProps, MyState> {
href="mailto:filip.leonarski@psi.ch">Filip Leonarski</a> <br/>
For more information see <a href="https://doi.org/10.1107/S1600577522010268"><i>J. Synchrotron
Rad.</i> (2023). <b>30</b>, 227234</a> <br/>
Build: {process.env.REACT_APP_VERSION}&nbsp;&nbsp;&nbsp;
<a href="/frontend/openapi.html">API reference</a></center>
Build: {process.env.REACT_APP_VERSION}</center>
<br/>
</ThemeProvider>
}

View File

@@ -9,7 +9,7 @@ type MyProps = {};
class BkgEstimatePlot extends Component<MyProps> {
render() {
return <Paper style={{textAlign: 'center'}} sx={{height: 500, width: "100%"}}>
return <Paper style={{textAlign: 'center'}} sx={{height: 450, width: "100%"}}>
<Box sx={{width: "100%", height: 50}}>
<br/>
<center><strong>Background estimate</strong></center>

View File

@@ -16,7 +16,9 @@ export enum PlotType {
STRONG_PIXELS,
ROI_SUM,
ROI_MAX_COUNT,
RECEIVER_FREE_SEND_BUFS
RES_ESTIMATION,
RECEIVER_FREE_SEND_BUFS,
BEAM_CENTER_DRIFT
}
type MyProps = {
@@ -143,6 +145,13 @@ class DataProcessingPlot extends Component<MyProps, MyState> {
this.setState({connection_error: true});
});
break;
case PlotType.RES_ESTIMATION:
DefaultService.getPlotResolutionEstimateHistogram()
.then(data => this.setState({plots: data, connection_error: false}))
.catch(error => {
this.setState({connection_error: true});
});
break;
case PlotType.RAD_INT_PER_FILE:
DefaultService.getPlotRadIntPerFile()
.then(data => this.setState({plots: data, connection_error: false}))

View File

@@ -69,6 +69,9 @@ class DataProcessingPlots extends Component<MyProps, MyState> {
case "11":
this.setState({type: PlotType.ROI_SUM, xlabel: "Image number", ylabel: "Photon count"});
break;
case "12":
this.setState({type: PlotType.RES_ESTIMATION, xlabel: "Resolution [&#8491;]", ylabel: "Number of crystals"});
break;
case "13":
this.setState({type: PlotType.RECEIVER_FREE_SEND_BUFS, xlabel: "Image number", ylabel: "Number of buffers"});
break;
@@ -97,6 +100,7 @@ class DataProcessingPlots extends Component<MyProps, MyState> {
<MenuItem value={3}>Azimuthal integration profile</MenuItem>
<MenuItem value={11}>ROI area sum</MenuItem>
<MenuItem value={6}>ROI area max count</MenuItem>
<MenuItem value={12}>Crystal resolution histogram</MenuItem>
<MenuItem value={4}>Indexing rate (per time point)</MenuItem>
<MenuItem value={5}>Azimuthal integration profile (per time point)</MenuItem>
<MenuItem value={8}>Error and saturated pixels</MenuItem>

View File

@@ -48,7 +48,7 @@ class MeasurementStatistics extends Component<MyProps, MyState> {
}
render() {
return <Paper style={{textAlign: 'center'}} sx={{ height: 500, width: '100%' }}>
return <Paper style={{textAlign: 'center'}} sx={{ height: 450, width: '100%' }}>
<Grid container spacing={0}>
<Grid item xs={1}/>
<Grid item xs={10}>
@@ -98,10 +98,6 @@ class MeasurementStatistics extends Component<MyProps, MyState> {
<TableCell align="right">{(this.state.s.bkg_estimate !== undefined)
? this.state.s.bkg_estimate.toPrecision(7) : "-"}</TableCell>
</TableRow>
<TableRow>
<TableCell component="th" scope="row"> Unit cell: </TableCell>
<TableCell align="right">{this.state.s.unit_cell}</TableCell>
</TableRow>
</TableBody>
</Table>
</TableContainer>

View File

@@ -28,7 +28,7 @@ class PreviewImage extends Component<MyProps, MyState> {
show_indexed: false,
resolution_ring: 0.5
},
s_url: null,
s_url: "",
update: true,
connection_error: true
}
@@ -124,12 +124,9 @@ class PreviewImage extends Component<MyProps, MyState> {
clearInterval(this.interval);
}
render() {
return <Paper sx={{height: 1050, width: 850, m: 2}}
component={Stack}
direction="column">
<br/>
<Stack spacing={2} direction="row" sx={{mb: 1}} alignItems="center">
preview() {
return <div><br/>
<Stack spacing={2} direction="row" sx={{ mb: 1 }} alignItems="center">
&nbsp;&nbsp;<strong>Preview image</strong>
<Switch disabled={this.state.connection_error} checked={this.state.update}
onChange={this.updateToggle} name="Update"/>
@@ -143,13 +140,13 @@ class PreviewImage extends Component<MyProps, MyState> {
<Switch disabled={this.state.connection_error} checked={this.state.settings.show_indexed}
onChange={this.showIndexedToggle} name="Show ROI"/>
Show only indexed images&nbsp;&nbsp;&nbsp;
<Box sx={{width: 200}}>
<Box sx={{ width: 200 }}>
<Slider disabled={this.state.connection_error}
value={Number(this.state.settings.saturation)} min={1} max={80}
onChange={this.setSaturation} valueLabelDisplay="auto"/> <br/>Saturation value
</Box>
&nbsp;&nbsp;&nbsp;
<Box sx={{width: 200}}>
<Box sx={{ width: 200 }}>
<Slider disabled={this.state.connection_error}
value={(this.state.settings.resolution_ring === undefined) ? 0.5 : Number(this.state.settings.resolution_ring)}
min={0.5} max={5.0} step={0.1}
@@ -158,7 +155,8 @@ class PreviewImage extends Component<MyProps, MyState> {
</Stack>
<br/>
{(!this.state.connection_error && (this.state.s_url !== null)) ?
{
this.state.s_url !== null ?
<Stack
direction="row"
justifyContent="center"
@@ -166,13 +164,20 @@ class PreviewImage extends Component<MyProps, MyState> {
>
<TransformWrapper>
<TransformComponent>
<img src={this.state.s_url} alt="Live preview"
style={{maxWidth: "100%", maxHeight: 900}}/>
<img src={this.state.s_url} alt="Live preview" style={{maxWidth: "100%", maxHeight: 900}}/>
</TransformComponent>
</TransformWrapper>
</Stack> : <div>Preview not available</div>
</Stack>: <div/>
}
<br/>
</div>
}
render() {
return <Paper sx={{height: 1050, width: 850, m: 2}}
component={Stack}
direction="column">
{(!this.state.connection_error && (this.state.s_url !== null)) ? this.preview() : "Preview not available"}
</Paper>
}
}

View File

@@ -31,7 +31,6 @@ export type measurement_statistics = {
detector_height?: number;
detector_pixel_depth?: measurement_statistics.detector_pixel_depth;
bkg_estimate?: number;
unit_cell?: string;
};
export namespace measurement_statistics {

View File

@@ -724,6 +724,19 @@ export class DefaultService {
});
}
/**
* Generate resolution estimate histogram
* Generate histogram of crystal resolutions from 1.0 to 5.0 A based on ML model
* @returns plots Everything OK
* @throws ApiError
*/
public static getPlotResolutionEstimateHistogram(): CancelablePromise<plots> {
return __request(OpenAPI, {
method: 'GET',
url: '/plot/resolution_estimate_histogram',
});
}
/**
* Generate radial integration profile
* Generate average radial integration profile

View File

@@ -21,8 +21,8 @@ IF (CMAKE_CUDA_COMPILER)
FetchContent_Declare(
fast-indexer
GIT_REPOSITORY https://github.com/fleon-psi/fast-feedback-indexer/
GIT_TAG 66c3f44
GIT_REPOSITORY https://github.com/paulscherrerinstitute/fast-feedback-indexer/
GIT_TAG 2d6fa7511f240eeb4918dd7647edd0642e987317
)
FetchContent_MakeAvailable(fast-indexer)

View File

@@ -27,12 +27,8 @@ MXAnalyzer::MXAnalyzer(const DiffractionExperiment &in_experiment)
: experiment(in_experiment) {
auto uc = experiment.GetUnitCell();
if (uc) {
try {
indexer = std::make_unique<IndexerWrapper>();
indexer->Setup(uc.value());
} catch (const std::exception &e) {
throw JFJochException(JFJochExceptionCategory::GPUCUDAError, e.what());
}
do_indexing = true;
indexer.Setup(uc.value());
}
if (experiment.IsSpotFindingEnabled())
find_spots = true;
@@ -77,13 +73,13 @@ void MXAnalyzer::Process(DataMessage &message, const SpotFindingSettings& settin
for (const auto &spot: spots_out)
message.spots.push_back(spot);
if (indexer && settings.indexing) {
if (do_indexing && settings.indexing) {
std::vector<Coord> recip;
recip.reserve(spots_out.size());
for (const auto &i: spots_out)
recip.push_back(i.ReciprocalCoord(experiment));
auto indexer_result = indexer->Run(recip, settings.indexing_tolerance);
auto indexer_result = indexer.Run(recip, settings.indexing_tolerance);
if (!indexer_result.empty()) {
message.indexing_result = true;

View File

@@ -9,7 +9,8 @@
class MXAnalyzer {
const DiffractionExperiment &experiment;
std::unique_ptr<IndexerWrapper> indexer;
IndexerWrapper indexer;
bool do_indexing = false;
bool find_spots = false;
std::vector<DiffractionSpot> spots;
constexpr static const float spot_distance_threshold_pxl = 2.0f;

View File

@@ -1,3 +1,4 @@
FIND_PACKAGE(TIFF COMPONENTS CXX REQUIRED)
FIND_PACKAGE(JPEG REQUIRED)
ADD_LIBRARY(JFJochPreview STATIC
@@ -8,7 +9,13 @@ ADD_LIBRARY(JFJochPreview STATIC
TARGET_LINK_LIBRARIES(JFJochPreview PUBLIC JFJochCommon)
TARGET_LINK_LIBRARIES(JFJochPreview PUBLIC tiff tiffxx)
IF((EXISTS ${TIFF_INCLUDE_DIR}/tiffio.hxx) AND (EXISTS ${TIFF_INCLUDE_DIR}/tiffio.h))
TARGET_INCLUDE_DIRECTORIES(JFJochPreview PRIVATE ${TIFF_INCLUDE_DIR})
TARGET_LINK_LIBRARIES(JFJochPreview PUBLIC ${TIFF_LIBRARIES})
MESSAGE(STATUS "TIFF headers present and library included")
ELSE()
MESSAGE(FATAL_ERROR "TIFF headers tiffio.h and tiffio.hxx not present")
ENDIF()
IF (EXISTS ${JPEG_INCLUDE_DIR}/jpeglib.h)
TARGET_INCLUDE_DIRECTORIES(JFJochPreview PRIVATE ${JPEG_INCLUDE_DIR})

View File

@@ -33,7 +33,6 @@ constexpr const static rgb gray = {.r = 0xbe, .g = 0xbe, .b = 0xbe};
PreviewImage::PreviewImage(const DiffractionExperiment &in_experiment) :
experiment(in_experiment),
initialized(false),
xpixel(experiment.GetXPixelsNum()),
ypixel(experiment.GetYPixelsNum()),
beam_x(experiment.GetBeamX_pxl()),
@@ -48,7 +47,6 @@ void PreviewImage::UpdateImage(const void *in_uncompressed_image,
const std::vector<SpotToSave> &in_spots) {
if (counter.GeneratePreview()) {
std::unique_lock<std::mutex> ul(m);
initialized = true;
memcpy(uncompressed_image.data(), in_uncompressed_image, xpixel * ypixel * pixel_depth_bytes);
spots = in_spots;
}
@@ -111,10 +109,6 @@ std::string PreviewImage::GenerateJPEG(const PreviewJPEGSettings &settings) cons
{
// JPEG compression is outside the critical loop protected by m
std::unique_lock<std::mutex> ul(m);
if (!initialized)
return {};
if (!pixel_is_signed) {
if (pixel_depth_bytes == 2)
v = GenerateRGB<uint16_t>((uint16_t *) uncompressed_image.data(), xpixel * ypixel,
@@ -147,9 +141,6 @@ std::string PreviewImage::GenerateJPEG(const PreviewJPEGSettings &settings) cons
std::string PreviewImage::GenerateTIFF() const {
std::unique_lock<std::mutex> ul(m);
if (!initialized)
return {};
std::string s = WriteTIFFToString(const_cast<uint8_t *>(uncompressed_image.data()),
xpixel, ypixel, pixel_depth_bytes, pixel_is_signed);
return s;
@@ -176,8 +167,6 @@ std::vector<uint16_t> GenerateDioptasPreview(const void* input, size_t xpixel, s
std::string PreviewImage::GenerateTIFFDioptas() const {
std::unique_lock<std::mutex> ul(m);
if (!initialized)
return {};
std::vector<uint16_t> vec;
if (pixel_is_signed) {

View File

@@ -29,7 +29,6 @@ class PreviewImage {
mutable std::mutex m;
DiffractionExperiment experiment;
bool initialized;
const ROIMap roi_map;
std::vector<uint8_t> uncompressed_image;
std::vector<SpotToSave> spots;

View File

@@ -11,8 +11,8 @@ ADD_LIBRARY(JFJochReceiver STATIC
LossyFilter.cpp
LossyFilter.h)
TARGET_LINK_LIBRARIES(JFJochReceiver ImagePusher JFJochImageAnalysis JFJochAcquisitionDevice JFJochCommon JFJochHLSSimulation JFJochPreview)
TARGET_LINK_LIBRARIES(JFJochReceiver ImagePusher JFJochImageAnalysis JFJochAcquisitionDevice JFJochCommon JFJochHLSSimulation JFJochPreview JFJochResonet)
ADD_EXECUTABLE(jfjoch_action_test jfjoch_action_test.cpp)
TARGET_LINK_LIBRARIES(jfjoch_action_test JFJochReceiver)
INSTALL(TARGETS jfjoch_action_test RUNTIME COMPONENT jfjoch)
INSTALL(TARGETS jfjoch_action_test RUNTIME)

View File

@@ -7,6 +7,7 @@
#include "../image_analysis/MXAnalyzer.h"
#include "../common/DiffractionGeometry.h"
#include "ImageMetadata.h"
#include "../resonet/NeuralNetResPredictor.h"
#include "../common/time_utc.h"
#include "../common/PixelMask.h"
@@ -67,9 +68,8 @@ JFJochReceiver::JFJochReceiver(const DiffractionExperiment& in_experiment,
images_to_go.Put(i);
// Setup frames summation and forwarding
for (uint32_t i = 0; i < frame_transformation_nthreads; i++) {
auto handle = std::async(std::launch::async, &JFJochReceiver::FrameTransformationThread,
this, i);
for (int i = 0; i < frame_transformation_nthreads; i++) {
auto handle = std::async(std::launch::async, &JFJochReceiver::FrameTransformationThread, this);
frame_transformation_futures.emplace_back(std::move(handle));
}
@@ -256,22 +256,21 @@ void JFJochReceiver::RetrievePedestal() {
}
}
void JFJochReceiver::FrameTransformationThread(uint32_t threadid) {
std::unique_ptr<MXAnalyzer> analyzer;
void JFJochReceiver::FrameTransformationThread() {
try {
numa_policy.Bind(threadid);
analyzer = std::make_unique<MXAnalyzer>(experiment);
numa_policy.Bind();
} catch (const JFJochException &e) {
frame_transformation_ready.count_down();
logger.Error("Thread setup error {}", e.what());
logger.Error("HW bind error {}", e.what());
Cancel(e);
return;
}
NeuralNetResPredictor neural_net_predictor(experiment.GetNeuralNetModelPath());
FrameTransformation transformation(experiment);
MXAnalyzer analyzer(experiment);
frame_transformation_ready.count_down();
uint16_t az_int_min_bin = std::floor(az_int_mapping.QToBin(experiment.GetLowQForBkgEstimate_recipA()));
@@ -316,7 +315,7 @@ void JFJochReceiver::FrameTransformationThread(uint32_t threadid) {
adu_histogram_module[module_abs_number].Add(*output);
az_int_profile_image.Add(*output);
analyzer->ReadFromFPGA(output, local_spot_finding_settings, module_abs_number);
analyzer.ReadFromFPGA(output, local_spot_finding_settings, module_abs_number);
transformation.ProcessModule(output, d);
} else
@@ -335,11 +334,12 @@ void JFJochReceiver::FrameTransformationThread(uint32_t threadid) {
continue;
}
analyzer->Process(message, local_spot_finding_settings);
analyzer.Process(message, local_spot_finding_settings);
message.receiver_free_send_buf = send_buf_ctrl.GetAvailBufLocations();
message.az_int_profile = az_int_profile_image.GetResult();
message.bkg_estimate = az_int_profile_image.GetMeanValueOfBins(az_int_min_bin, az_int_max_bin);
message.resolution_estimation = neural_net_predictor.Inference(experiment, transformation.GetImage());
plots.Add(message, image_number % experiment.GetTimePointNumber(), az_int_profile_image);
@@ -372,12 +372,12 @@ void JFJochReceiver::FrameTransformationThread(uint32_t threadid) {
size_t image_size = transformation.CompressImage(writer_buffer + serializer.GetImageAppendOffset());
serializer.AppendImage(image_size);
compressed_size += image_size;
image_pusher.SendImage(writer_buffer, serializer.GetBufferSize(), message.number, loc);
image_pusher.SendImage(writer_buffer, serializer.GetBufferSize(), image_number, loc);
images_sent++; // Handle case when image not sent properly
UpdateMaxImage(message.number);
UpdateMaxImage(image_number);
logger.Debug("Frame transformation thread - done sending image {} / {}", image_number, message.number);
logger.Debug("Frame transformation thread - done sending image {}", image_number);
} catch (const JFJochException &e) {
logger.ErrorException(e);
Cancel(e);
@@ -555,10 +555,10 @@ JFJochReceiverStatus JFJochReceiver::GetStatus() const {
if ((experiment.GetImageNum() > 0) && (compressed_size > 0)) {
ret.compressed_ratio = static_cast<double> ((images_sent + images_skipped)
* experiment.GetPixelDepth()
* experiment.GetModulesNum()
* RAW_MODULE_SIZE)
/ static_cast<double> (compressed_size);
* experiment.GetPixelDepth()
* experiment.GetModulesNum()
* RAW_MODULE_SIZE)
/ static_cast<double> (compressed_size);
}
ret.progress = GetProgress();

View File

@@ -114,7 +114,7 @@ class JFJochReceiver {
LossyFilter serialmx_filter;
void AcquireThread(uint16_t data_stream);
void FrameTransformationThread(uint32_t threadid);
void FrameTransformationThread();
void Cancel(const JFJochException &e);
void FinalizeMeasurement();
void RetrievePedestal();

View File

@@ -6,7 +6,7 @@ JFJochReceiverPlots::JFJochReceiverPlots(const DiffractionExperiment &experiment
const AzimuthalIntegrationMapping &mapping)
: indexing_solution_per_time_point(experiment.GetTimePointNumber()),
default_binning(experiment.GetDefaultPlotBinning()),
az_int_profile(mapping) {
az_int_profile(mapping), resolution_estimation(50, 1.0, 5.0) {
az_int_profile.SetTitle("dataset");
for (int i = 0; i < experiment.GetTimePointNumber(); i++) {
az_int_profile_per_time_point.emplace_back(mapping);
@@ -36,6 +36,9 @@ void JFJochReceiverPlots::Add(const DataMessage &msg, uint64_t file_number, cons
indexing_solution.AddElement(msg.number, msg.indexing_result);
indexing_solution_per_time_point.Add(file_number, msg.indexing_result);
if (msg.resolution_estimation)
resolution_estimation.Add(msg.resolution_estimation.value());
az_int_profile += profile;
az_int_profile_per_time_point.at(file_number) += profile;
@@ -118,6 +121,8 @@ MultiLinePlot JFJochReceiverPlots::GetPlots(const PlotRequest &request) {
ret.emplace_back(tmp.at(0));
}
return ret;
case PlotType::ResEstimation:
return resolution_estimation.GetPlot();
case PlotType::RadIntPerTimePoint:
tmp = az_int_profile.GetPlot();
ret.emplace_back(tmp.at(0));

View File

@@ -31,6 +31,7 @@ class JFJochReceiverPlots {
std::map<std::string, std::unique_ptr<StatusVector<int64_t>>> roi_sum;
std::map<std::string, std::unique_ptr<StatusVector<int64_t>>> roi_max_count;
std::map<std::string, std::unique_ptr<StatusVector<uint64_t>>> roi_pixels;
FloatHistogram resolution_estimation;
AzimuthalIntegrationProfile az_int_profile;
std::vector<AzimuthalIntegrationProfile> az_int_profile_per_time_point;

View File

@@ -2,7 +2,7 @@
#include "JFJochReceiverTest.h"
#include "JFJochReceiverService.h"
#include "../frame_serialize/ZMQStream2Pusher.h"
#include "../frame_serialize/ZMQStream2PusherGroup.h"
#include "../frame_serialize/TestImagePusher.h"
#define STORAGE_CELL_FOR_TEST 11

View File

@@ -19,6 +19,7 @@ void print_usage(Logger &logger) {
logger.Info(" -i<num> number of images");
logger.Info(" -N<num> number of image processing threads");
logger.Info(" -P<txt> NUMA Policy (none|n2g2|n8g4|n8g4_hbm), none is default");
logger.Info(" -D<path> use resonet deep learning model for resolution estimation - path to TorchScript");
logger.Info(" -B<num> size of send buffer in MiB (default 2048)");
}
@@ -36,6 +37,7 @@ int main(int argc, char **argv) {
std::string numa_policy_name;
bool raw_data = false;
bool force_32bit = false;
std::string resonet_path;
DetectorType detector_type = DetectorType::JUNGFRAU;
bool hls_simulation = false;
size_t send_buffer_size_MiB = 2048;
@@ -46,7 +48,7 @@ int main(int argc, char **argv) {
}
int opt;
while ((opt = getopt(argc, argv, "s:i:m:N:P:vRIS:EHB:")) != -1) {
while ((opt = getopt(argc, argv, "s:i:m:N:P:vRIS:D:EHB:")) != -1) {
switch (opt) {
case 'i':
nimages = atol(optarg);
@@ -75,6 +77,9 @@ int main(int argc, char **argv) {
case 'I':
force_32bit = true;
break;
case 'D':
resonet_path = std::string(optarg);
break;
case 'E':
detector_type = DetectorType::EIGER;
break;
@@ -109,6 +114,8 @@ int main(int argc, char **argv) {
if (force_32bit)
x.FPGAOutputMode(FPGAPixelOutput::Int32);
if (!resonet_path.empty())
x.NeuralNetModelPath(resonet_path);
logger.Info("Data streams {} Total modules {} Total images {} Threads {}", nstreams, nmodules, nimages, nthreads);

10
resonet/CMakeLists.txt Normal file
View File

@@ -0,0 +1,10 @@
ADD_LIBRARY(JFJochResonet STATIC NeuralNetResPredictor.cpp NeuralNetResPredictor.h)
TARGET_LINK_LIBRARIES(JFJochResonet JFJochCommon)
IF (${TORCH_FOUND})
TARGET_COMPILE_DEFINITIONS(JFJochResonet PUBLIC -DJFJOCH_USE_TORCH)
TARGET_LINK_LIBRARIES(JFJochResonet ${TORCH_LIBRARIES})
TARGET_INCLUDE_DIRECTORIES(JFJochResonet PUBLIC ${TORCH_INCLUDE_DIRS})
ADD_EXECUTABLE(resonet_test resonet_test.cpp)
TARGET_LINK_LIBRARIES(resonet_test JFJochResonet JFJochWriter)
ENDIF()

28
resonet/LICENSE.resonet Normal file
View File

@@ -0,0 +1,28 @@
BSD 3-Clause License
Copyright (c) 2023, Macromolecular Crystallography at SSRL
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

View File

@@ -0,0 +1,101 @@
// Copyright (2019-2024) Paul Scherrer Institute
#include "NeuralNetResPredictor.h"
#include <cmath>
#include "../common/JFJochException.h"
NeuralNetResPredictor::NeuralNetResPredictor(const std::string& model_path)
: model_input(512*512),
enable(!model_path.empty())
#ifdef JFJOCH_USE_TORCH
, device(torch::kCUDA)
#endif
{
#ifdef JFJOCH_USE_TORCH
if (enable) {
module = torch::jit::load(model_path);
module.to(device);
}
#else
enable = false;
#endif
}
template<class T>
void NeuralNetResPredictor::PrepareInternal(const DiffractionExperiment& experiment, const T* image) {
size_t pool_factor = GetMaxPoolFactor(experiment);
size_t xpixel = experiment.GetXPixelsNum();
size_t ypixel = experiment.GetYPixelsNum();
size_t start_x = std::lround(experiment.GetBeamX_pxl());
size_t start_y = std::lround(experiment.GetBeamY_pxl());
for (size_t y = 0; y < 512; y++) {
size_t y0 = y * pool_factor + start_y;
size_t min_yp = std::min(y0 + pool_factor, ypixel);
for (size_t x = 0; x < 512; x++) {
float val = 0.0;
size_t x0 = x * pool_factor + start_x;
size_t min_xp = std::min(x0 + pool_factor, ypixel);
for (size_t yp = y0; yp < min_yp; yp++) {
for (size_t xp = x0; xp < min_xp; xp++) {
int16_t pxl = image[yp * xpixel + xp];
if (val < pxl)
val = pxl;
}
}
float max_pool = floorf(sqrtf(val));
model_input[512 * y + x] = max_pool;
}
}
}
void NeuralNetResPredictor::Prepare(const DiffractionExperiment& experiment, const int16_t *image) {
PrepareInternal(experiment, image);
}
void NeuralNetResPredictor::Prepare(const DiffractionExperiment& experiment, const int32_t *image) {
PrepareInternal(experiment, image);
}
size_t NeuralNetResPredictor::GetMaxPoolFactor(const DiffractionExperiment& experiment) const {
float max_direction = std::max(experiment.GetXPixelsNum(), experiment.GetYPixelsNum()) / 2.0;
size_t pool_factor = std::lround(max_direction / 512.0f);
if (pool_factor <= 0)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Detector size is too small");
if (pool_factor > 8)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Detector size is too large");
return pool_factor;
}
std::optional<float> NeuralNetResPredictor::Inference(const DiffractionExperiment& experiment, const void *image) {
if (!enable)
return {};
#ifdef JFJOCH_USE_TORCH
if (experiment.GetPixelDepth() == 2)
Prepare(experiment, (int16_t *) image);
else
Prepare(experiment, (int32_t *) image);
auto options = torch::TensorOptions().dtype(at::kFloat);
auto model_input_tensor = torch::from_blob(model_input.data(), {1,1,512,512}, options).to(device);
std::vector<torch::jit::IValue> pixels;
pixels.emplace_back(std::move(model_input_tensor));
auto output = module.forward(pixels).toTensor();
auto tensor_output = output[0].item<float>();
float two_theta = atanf(((2.0f * experiment.GetPixelSize_mm() / experiment.GetDetectorDistance_mm()) * tensor_output));
float stheta = sinf(two_theta * 0.5f);
float resolution = experiment.GetWavelength_A() / (2.0f * stheta);
return resolution;
#else
return {};
#endif
}
const std::vector<float> &NeuralNetResPredictor::GetModelInput() const {
return model_input;
}

View File

@@ -0,0 +1,36 @@
// Copyright (2019-2024) Paul Scherrer Institute
#ifndef JUNGFRAUJOCH_NEURALNETRESPREDICTOR_H
#define JUNGFRAUJOCH_NEURALNETRESPREDICTOR_H
#ifdef JFJOCH_USE_TORCH
#include <torch/script.h>
#endif
#include "../common/DiffractionExperiment.h"
// Based on model described in:
// Mendez, D., Holton, J. M., Lyubimov, A. Y., Hollatz, S., Mathews, I. I., Cichosz, A., Martirosyan, V.,
// Zeng, T., Stofer, R., Liu, R., Song, J., McPhillips, S., Soltis, M. & Cohen, A. E. (2024).
// Acta Cryst. D80, 26-43.
class NeuralNetResPredictor {
std::vector<float> model_input;
bool enable;
#ifdef JFJOCH_USE_TORCH
torch::Device device;
torch::jit::script::Module module;
#endif
template<class T>
void PrepareInternal(const DiffractionExperiment& experiment, const T* image);
public:
explicit NeuralNetResPredictor(const std::string& model_path);
void Prepare(const DiffractionExperiment& experiment, const int16_t* image);
void Prepare(const DiffractionExperiment& experiment, const int32_t* image);
std::optional<float> Inference(const DiffractionExperiment& experiment, const void* image);
size_t GetMaxPoolFactor(const DiffractionExperiment& experiment) const;
const std::vector<float> &GetModelInput() const;
};
#endif //JUNGFRAUJOCH_NEURALNETRESPREDICTOR_H

51
resonet/resonet_test.cpp Normal file
View File

@@ -0,0 +1,51 @@
// Copyright (2019-2024) Paul Scherrer Institute
#include <iostream>
#include "NeuralNetResPredictor.h"
#include "../writer/HDF5Objects.h"
int main(int argc, char **argv) {
if (argc != 2) {
std::cerr << "Usage ./resonet_test <.pt file with traced model>" << std::endl;
exit(EXIT_FAILURE);
}
RegisterHDF5Filter();
DiffractionExperiment experiment(DetectorGeometry(8, 2, 8, 36));
experiment.DetectorDistance_mm(75).PhotonEnergy_keV(12.4).BeamY_pxl(1136).BeamX_pxl(1090);
NeuralNetResPredictor predictor(argv[1]);
HDF5ReadOnlyFile data("../../tests/test_data/compression_benchmark.h5");
HDF5DataSet dataset(data, "/entry/data/data");
HDF5DataSpace file_space(dataset);
std::vector<int16_t> image_conv (file_space.GetDimensions()[1] * file_space.GetDimensions()[2]);
std::vector<hsize_t> start = {4,0,0};
std::vector<hsize_t> file_size = {1, file_space.GetDimensions()[1], file_space.GetDimensions()[2]};
dataset.ReadVector(image_conv, start, file_size);
std::cout << "Max pooling " << predictor.GetMaxPoolFactor(experiment) << std::endl;
float x = 0;
size_t niterations = 25;
std::optional<float> result;
auto start_time = std::chrono::system_clock::now();
for (int i = 0; i < niterations; i++) {
result = predictor.Inference(experiment, image_conv.data());
if (result)
x += result.value();
}
auto end_time = std::chrono::system_clock::now();
auto elapsed = std::chrono::duration_cast<std::chrono::microseconds>(end_time - start_time);
int64_t frequency_Hz = (niterations * 1e6) / (double) (elapsed.count());
std::cout << ((double) elapsed.count()) / (1e3 * niterations) << " ms" << std::endl;
std::cout << frequency_Hz << " Hz" << std::endl;
if (result)
std::cout << "Resolution " << result.value() << std::endl;
}

Binary file not shown.

View File

@@ -64,8 +64,7 @@ TEST_CASE("CBORSerialize_Start", "[CBOR]") {
.total_flux = 123,
.attenuator_transmission = 0.345,
.write_master_file = true,
.user_data = "Some random string 12345",
.data_reduction_factor_serialmx = 0.75
.user_data = "Some random string 12345"
};
REQUIRE_NOTHROW(serializer.SerializeSequenceStart(message));
@@ -142,7 +141,6 @@ TEST_CASE("CBORSerialize_Start", "[CBOR]") {
CHECK(output_message.countrate_correction_enabled == message.countrate_correction_enabled);
CHECK(output_message.flatfield_enabled == message.flatfield_enabled);
CHECK(output_message.write_master_file == message.write_master_file);
CHECK(output_message.data_reduction_factor_serialmx == message.data_reduction_factor_serialmx);
}
TEST_CASE("CBORSerialize_Start_PixelMask", "[CBOR]") {

View File

@@ -1,4 +1,4 @@
ADD_EXECUTABLE(jfjoch_test
ADD_EXECUTABLE(CatchTest
DiffractionExperimentTest.cpp
RawToConvertedGeometryTest.cpp
../common/RawToConvertedGeometry.h
@@ -30,6 +30,7 @@ ADD_EXECUTABLE(jfjoch_test
TIFFTest.cpp
JFJochReceiverProcessingTest.cpp
JPEGTest.cpp
NeuralNetResPredictorTest.cpp
HistogramTest.cpp
FPGAEigerReorderTest.cpp
ROIMapTest.cpp
@@ -39,5 +40,7 @@ ADD_EXECUTABLE(jfjoch_test
RegressionTest.cpp
)
target_link_libraries(jfjoch_test Catch2WithMain JFJochBroker JFJochReceiver JFJochWriter JFJochImageAnalysis JFJochCommon JFJochHLSSimulation JFJochPreview)
target_include_directories(jfjoch_test PRIVATE .)
target_link_libraries(CatchTest Catch2WithMain JFJochBroker JFJochReceiver JFJochWriter JFJochImageAnalysis JFJochCommon JFJochHLSSimulation JFJochPreview JFJochResonet)
target_include_directories(CatchTest PRIVATE .)
INSTALL(TARGETS CatchTest RUNTIME)

View File

@@ -221,6 +221,8 @@ TEST_CASE("HDF5Writer", "[HDF5][Full]") {
TEST_CASE("HDF5Writer_Socket", "[HDF5][Full]") {
{
ZMQContext c;
RegisterHDF5Filter();
DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
std::vector<SpotToSave> spots;
@@ -231,10 +233,10 @@ TEST_CASE("HDF5Writer_Socket", "[HDF5][Full]") {
x.FillMessage(start_message);
HDF5Writer file_set(start_message);
file_set.SetupSocket("ipc://#1");
file_set.SetupSocket(c, "ipc://#1");
std::vector<uint16_t> image(x.GetPixelsNum());
ZMQSocket s(ZMQSocketType::Sub);
ZMQSocket s(c, ZMQSocketType::Sub);
s.Connect("ipc://#1");
s.SubscribeAll();
s.ReceiveTimeout(std::chrono::seconds(5));

View File

@@ -52,10 +52,13 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
aq_devices.Add(std::move(test));
ZMQStream2Pusher pusher({"ipc://*"});
StreamWriter writer(logger, pusher.GetAddress()[0]);
ZMQContext context;
ZMQStream2Pusher pusher(context, "ipc://*");
StreamWriter writer(context, logger, pusher.GetAddress());
auto writer_future = std::async(std::launch::async, &StreamWriter::Run, &writer);
context.NumThreads(4);
JFJochReceiverService service(aq_devices, logger, pusher);
service.NumThreads(nthreads);
@@ -124,8 +127,11 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJoc
test->SetInternalGeneratorFrame((uint16_t *) image_raw_geom.data() + m * RAW_MODULE_SIZE, m);
aq_devices.Add(std::move(test));
ZMQStream2Pusher pusher({"ipc://*"});
StreamWriter writer(logger, pusher.GetAddress()[0]);
ZMQContext context;
context.NumThreads(4);
ZMQStream2Pusher pusher(context, "ipc://*");
StreamWriter writer(context, logger, pusher.GetAddress());
auto writer_future = std::async(std::launch::async, &StreamWriter::Run, &writer);
JFJochReceiverService service(aq_devices, logger, pusher);
@@ -182,6 +188,73 @@ TEST_CASE("GenerateResolutionMap") {
experiment.GetYPixelsNum(), 4);
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_resolution", "[JFJochReceiver]") {
Logger logger("JFJochIntegrationTest_ZMQ_lysozyme_resolution");
RegisterHDF5Filter();
const uint16_t nthreads = 4;
DiffractionExperiment experiment(DetectorGeometry(8,2,8,36));
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
.FilePrefix("lyso_test_resolution").ConversionOnFPGA(false)
.DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).PhotonEnergy_keV(12.4)
.SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90})
.NeuralNetModelPath("../../resonet/traced_resnet_model.pt");
// Load example image
HDF5ReadOnlyFile data("../../tests/test_data/compression_benchmark.h5");
HDF5DataSet dataset(data, "/entry/data/data");
HDF5DataSpace file_space(dataset);
REQUIRE(file_space.GetDimensions()[2] == experiment.GetXPixelsNum());
REQUIRE(file_space.GetDimensions()[1] == experiment.GetYPixelsNum());
std::vector<int16_t> image_conv (file_space.GetDimensions()[1] * file_space.GetDimensions()[2]);
std::vector<hsize_t> start = {4,0,0};
std::vector<hsize_t> file_size = {1, file_space.GetDimensions()[1], file_space.GetDimensions()[2]};
dataset.ReadVector(image_conv, start, file_size);
std::vector<int16_t> image_raw_geom(experiment.GetModulesNum() * RAW_MODULE_SIZE);
ConvertedToRawGeometry(experiment, image_raw_geom.data(), image_conv.data());
logger.Info("Loaded image");
// Setup acquisition device
AcquisitionDeviceGroup aq_devices;
std::unique_ptr<HLSSimulatedDevice> test = std::make_unique<HLSSimulatedDevice>(0, 64);
for (int m = 0; m < experiment.GetModulesNum(); m++)
test->SetInternalGeneratorFrame((uint16_t *) image_raw_geom.data() + m * RAW_MODULE_SIZE, m);
aq_devices.Add(std::move(test));
ZMQContext context;
ZMQStream2Pusher pusher(context, "ipc://*");
StreamWriter writer(context, logger, pusher.GetAddress());
auto writer_future = std::async(std::launch::async, &StreamWriter::Run, &writer);
context.NumThreads(4);
JFJochReceiverService service(aq_devices, logger, pusher);
service.NumThreads(nthreads);
SpotFindingSettings settings = DiffractionExperiment::DefaultDataProcessingSettings();
settings.signal_to_noise_threshold = 2.5;
settings.photon_count_threshold = 5;
settings.min_pix_per_spot = 1;
settings.max_pix_per_spot = 200;
service.SetSpotFindingSettings(settings);
service.Start(experiment, nullptr);
auto receiver_out = service.Stop();
CHECK(receiver_out.efficiency == 1.0);
CHECK(receiver_out.status.indexing_rate == 1.0);
CHECK(receiver_out.status.images_sent == experiment.GetImageNum());
CHECK(!receiver_out.status.cancelled);
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
Logger logger("JFJochIntegrationTest_ZMQ_ROI");
@@ -235,8 +308,11 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
aq_devices.Add(std::move(test));
ZMQStream2Pusher pusher({"ipc://*"});
StreamWriter writer(logger, pusher.GetAddress()[0]);
ZMQContext context;
context.NumThreads(4);
ZMQStream2Pusher pusher(context, "ipc://*");
StreamWriter writer(context, logger, pusher.GetAddress());
auto writer_future = std::async(std::launch::async, &StreamWriter::Run, &writer);
JFJochReceiverService service(aq_devices, logger, pusher);
@@ -260,7 +336,6 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
REQUIRE(plot.size() == 2);
CHECK(plot[0].title == "roi0");
REQUIRE(!plot[0].x.empty());
CHECK(plot[0].x[0] == 0);
CHECK(plot[0].y[0] == roi_value);
CHECK(plot[1].title == "roi1");

View File

@@ -58,6 +58,7 @@ TEST_CASE("PreviewImage_GenerateJPEG","[JPEG]") {
{.x = 1200, .y = 500, .indexed = true}
};
PreviewImage image(experiment);
image.UpdateImage(image_conv_2.data(), spots);
PreviewJPEGSettings preview_settings{
.saturation_value = 5,
@@ -65,11 +66,6 @@ TEST_CASE("PreviewImage_GenerateJPEG","[JPEG]") {
.show_spots = true
};
REQUIRE(image.GenerateJPEG(preview_settings).empty());
image.UpdateImage(image_conv_2.data(), spots);
std::string s;
REQUIRE_NOTHROW(s = image.GenerateJPEG(preview_settings));
std::ofstream f("lyso_diff.jpeg", std::ios::binary);

View File

@@ -0,0 +1,51 @@
// Copyright (2019-2024) Paul Scherrer Institute
#include <catch2/catch_all.hpp>
#include "../writer/HDF5Objects.h"
#include "../resonet/NeuralNetResPredictor.h"
TEST_CASE("NeuralNetResPredictor_Prepare", "[LinearAlgebra][Coord]") {
DiffractionExperiment experiment(DetectorGeometry(8, 2, 8, 36));
experiment.DetectorDistance_mm(75).PhotonEnergy_keV(12.4).BeamX_pxl(1000).BeamY_pxl(1000);
std::vector<int16_t> v(experiment.GetPixelsNum(),0);
v[1000 * experiment.GetXPixelsNum() + 1000] = 100;
v[1000 * experiment.GetXPixelsNum() + 1001] = 20;
v[1001 * experiment.GetXPixelsNum() + 1000] = 30;
v[1001 * experiment.GetXPixelsNum() + 1001] = INT16_MIN;
v[1050 * experiment.GetXPixelsNum() + 1050] = 52;
v[2000 * experiment.GetXPixelsNum() + 1500] = 160;
NeuralNetResPredictor predictor("../../resonet/traced_resnet_model.pt");
REQUIRE(predictor.GetMaxPoolFactor(experiment) == 2);
predictor.Prepare(experiment, v.data());
auto nn_input = predictor.GetModelInput();
REQUIRE(nn_input[0] == 10);
REQUIRE(nn_input[25 * 512 + 25] == 7);
REQUIRE(nn_input[500 * 512 + 250] == 12);
}
TEST_CASE("NeuralNetResPredictor_Inference", "[LinearAlgebra][Coord]") {
DiffractionExperiment experiment(DetectorGeometry(8, 2, 8, 36));
experiment.DetectorDistance_mm(75).PhotonEnergy_keV(12.4).BeamY_pxl(1136).BeamX_pxl(1090);
NeuralNetResPredictor predictor("../../resonet/traced_resnet_model.pt");
HDF5ReadOnlyFile data("../../tests/test_data/compression_benchmark.h5");
HDF5DataSet dataset(data, "/entry/data/data");
HDF5DataSpace file_space(dataset);
std::vector<int16_t> image_conv (file_space.GetDimensions()[1] * file_space.GetDimensions()[2]);
std::vector<hsize_t> start = {4,0,0};
std::vector<hsize_t> file_size = {1, file_space.GetDimensions()[1], file_space.GetDimensions()[2]};
dataset.ReadVector(image_conv, start, file_size);
auto res = predictor.Inference(experiment, image_conv.data());
REQUIRE(res);
REQUIRE(res.value() < 1.5);
REQUIRE(res.value() > 1.4);
}

View File

@@ -4,13 +4,15 @@
#include <filesystem>
#include "../writer/StreamWriter.h"
#include "../frame_serialize/ZMQStream2Pusher.h"
#include "../frame_serialize/ZMQStream2PusherGroup.h"
#include "../receiver/JFJochReceiverService.h"
TEST_CASE("StreamWriterTest_ZMQ","[JFJochWriter]") {
RegisterHDF5Filter();
Logger logger("test");
ZMQContext context;
std::string zmq_addr = "ipc://*";
DiffractionExperiment x(DetectorGeometry(2));
x.FilePrefix("subdir/JFJochWriterTest").NumTriggers(1).ImagesPerTrigger(5)
@@ -21,7 +23,7 @@ TEST_CASE("StreamWriterTest_ZMQ","[JFJochWriter]") {
for (int i = 0; i < x.GetDataStreamsNum(); i++)
aq_devices.AddHLSDevice(64);
ZMQStream2Pusher pusher ({"ipc://*"});
ZMQStream2PusherGroup pusher (context, {zmq_addr});
JFJochReceiverService fpga_receiver_service(aq_devices, logger, pusher);
JFJochReceiverOutput receiver_output;
@@ -30,7 +32,7 @@ TEST_CASE("StreamWriterTest_ZMQ","[JFJochWriter]") {
REQUIRE(x.GetImageNum() == 5);
auto pusher_addr = pusher.GetAddress();
REQUIRE(pusher_addr.size() == 1);
REQUIRE_NOTHROW(writer = std::make_unique<StreamWriter>(logger, pusher_addr[0]));
REQUIRE_NOTHROW(writer = std::make_unique<StreamWriter>(context, logger, pusher_addr[0]));
CHECK (writer->GetStatistics().state == StreamWriterState::Idle);
REQUIRE_NOTHROW(fpga_receiver_service.Start(x, nullptr));

View File

@@ -3,7 +3,7 @@
#include <random>
#include <catch2/catch_all.hpp>
#include "../writer/ZMQImagePuller.h"
#include "../frame_serialize/ZMQStream2Pusher.h"
#include "../frame_serialize/ZMQStream2PusherGroup.h"
void test_puller(ZMQImagePuller *puller,
const DiffractionExperiment& x,
@@ -53,6 +53,7 @@ void test_puller(ZMQImagePuller *puller,
TEST_CASE("ZMQImageCommTest_1Writer","[ZeroMQ]") {
const size_t nframes = 256;
ZMQContext context;
Logger logger("test");
DiffractionExperiment x(DetectorGeometry(1));
x.Mode(DetectorMode::Raw);
@@ -70,10 +71,12 @@ TEST_CASE("ZMQImageCommTest_1Writer","[ZeroMQ]") {
std::vector<uint16_t> image1(x.GetPixelsNum()*nframes);
for (auto &i: image1) i = dist(g1);
std::string zmq_addr = "ipc://*";
// Puller needs to be declared first, but both objects need to exist till communication finished
// TODO: ImageSender should not allow if there are still completions to be done
ZMQImagePuller puller;
ZMQStream2Pusher pusher({"ipc://*"});
ZMQImagePuller puller(context);
ZMQStream2PusherGroup pusher(context, {zmq_addr});
std::vector<size_t> diff_size(1), diff_content(1), diff_split(1), nimages(1);
@@ -116,87 +119,11 @@ TEST_CASE("ZMQImageCommTest_1Writer","[ZeroMQ]") {
REQUIRE(diff_content[0] == 0);
}
TEST_CASE("ZMQImageCommTest_1Writer_Preview","[ZeroMQ]") {
const size_t nframes = 1;
Logger logger("test");
DiffractionExperiment x(DetectorGeometry(1));
x.Mode(DetectorMode::Raw);
x.PedestalG0Frames(0).NumTriggers(1).UseInternalPacketGenerator(false).PhotonEnergy_keV(12.4)
.ImagesPerTrigger(nframes);
std::vector<DiffractionSpot> empty_spot_vector;
std::vector<float> empty_rad_int_profile;
REQUIRE(x.GetImageNum() == nframes);
std::mt19937 g1(1387);
std::uniform_int_distribution<uint16_t> dist;
std::vector<uint16_t> image1(x.GetPixelsNum()*nframes);
for (auto &i: image1) i = dist(g1);
// Puller needs to be declared first, but both objects need to exist till communication finished
ZMQImagePuller puller;
ZMQStream2Pusher pusher({"ipc://*"});
REQUIRE(pusher.GetPreviewAddress().empty());
pusher.PreviewSocket("ipc://*");
REQUIRE(!pusher.GetPreviewAddress().empty());
ZMQSocket preview_sub_socket(ZMQSocketType::Sub);
preview_sub_socket.Connect(pusher.GetPreviewAddress());
preview_sub_socket.Subscribe("");
std::vector<size_t> diff_size(1), diff_content(1), diff_split(1), nimages(1);
auto pusher_addr = pusher.GetAddress();
puller.Connect(pusher_addr[0]);
std::thread sender_thread = std::thread([&] {
std::vector<uint8_t> serialization_buffer(16*1024*1024);
CBORStream2Serializer serializer(serialization_buffer.data(), serialization_buffer.size());
StartMessage message {
.images_per_file = 16,
.write_master_file = true
};
EndMessage end_message{};
pusher.StartDataCollection(message);
for (int i = 0; i < nframes; i++) {
DataMessage data_message;
data_message.number = i;
PrepareCBORImage(data_message, x, image1.data() + i * x.GetPixelsNum(), x.GetPixelsNum() * sizeof(uint16_t));
serializer.SerializeImage(data_message);
pusher.SendImage(serialization_buffer.data(), serializer.GetBufferSize(), i);
}
pusher.EndDataCollection(end_message);
});
std::thread puller_thread(test_puller, &puller, std::cref(x), std::cref(image1), 1, 0,
std::ref(diff_split), std::ref(diff_size), std::ref(diff_content),
std::ref(nimages));
sender_thread.join();
puller_thread.join();
puller.Disconnect();
REQUIRE(nimages[0] == nframes);
REQUIRE(diff_size[0] == 0);
REQUIRE(diff_content[0] == 0);
ZMQMessage msg;
REQUIRE(preview_sub_socket.Receive(msg));
REQUIRE(preview_sub_socket.Receive(msg));
REQUIRE(preview_sub_socket.Receive(msg));
}
TEST_CASE("ZMQImageCommTest_2Writers","[ZeroMQ]") {
const size_t nframes = 256;
ZMQContext context;
Logger logger("test");
DiffractionExperiment x(DetectorGeometry(1));
x.Mode(DetectorMode::Raw);
@@ -221,7 +148,7 @@ TEST_CASE("ZMQImageCommTest_2Writers","[ZeroMQ]") {
for (int i = 0; i < npullers; i++)
zmq_addr.push_back("ipc://*");
ZMQStream2Pusher pusher(zmq_addr);
ZMQStream2PusherGroup pusher(context, zmq_addr);
// Puller needs to be declared first, but both objects need to exist till communication finished
// TODO: ImageSender should not allow if there are still completions to be done
@@ -229,7 +156,7 @@ TEST_CASE("ZMQImageCommTest_2Writers","[ZeroMQ]") {
auto pusher_addr = pusher.GetAddress();
REQUIRE(pusher_addr.size() == 2);
for (int i = 0; i < npullers; i++) {
puller.push_back(std::make_unique<ZMQImagePuller>());
puller.push_back(std::make_unique<ZMQImagePuller>(context));
puller[i]->Connect(pusher_addr[i]);
}
@@ -286,6 +213,7 @@ TEST_CASE("ZMQImageCommTest_2Writers","[ZeroMQ]") {
TEST_CASE("ZMQImageCommTest_4Writers","[ZeroMQ]") {
const size_t nframes = 255;
ZMQContext context;
Logger logger("test");
DiffractionExperiment x(DetectorGeometry(1));
x.Mode(DetectorMode::Raw);
@@ -310,14 +238,14 @@ TEST_CASE("ZMQImageCommTest_4Writers","[ZeroMQ]") {
for (int i = 0; i < npullers; i++)
zmq_addr.push_back("ipc://*");
ZMQStream2Pusher pusher(zmq_addr);
ZMQStream2PusherGroup pusher(context, zmq_addr);
auto pusher_addr = pusher.GetAddress();
REQUIRE(pusher_addr.size() == npullers);
// Puller needs to be declared first, but both objects need to exist till communication finished
// TODO: ImageSender should not allow if there are still completions to be done
std::vector<std::unique_ptr<ZMQImagePuller> > puller;
for (int i = 0; i < npullers; i++) {
puller.push_back(std::make_unique<ZMQImagePuller>());
puller.push_back(std::make_unique<ZMQImagePuller>(context));
puller[i]->Connect(pusher_addr[i]);
}
@@ -382,7 +310,8 @@ TEST_CASE("ZMQImagePuller_abort","[ZeroMQ]") {
x.PedestalG0Frames(0).NumTriggers(1).UseInternalPacketGenerator(false).PhotonEnergy_keV(12.4)
.ImagesPerTrigger(nframes);
ZMQImagePuller puller;
ZMQContext context;
ZMQImagePuller puller(context);
std::vector<size_t> diff_size(1), diff_content(1), diff_split(1), nimages(1);
std::vector<uint16_t> image1(x.GetPixelsNum());
@@ -396,7 +325,7 @@ TEST_CASE("ZMQImagePuller_abort","[ZeroMQ]") {
}
TEST_CASE("ZMQImageCommTest_NoWriter","[ZeroMQ]") {
ZMQStream2Pusher pusher({"ipc://*"});
ZMQStream2PusherGroup pusher({"ipc://*"});
StartMessage msg;
REQUIRE_THROWS(pusher.StartDataCollection(msg));

View File

@@ -6,7 +6,7 @@
#include "../common/Logger.h"
#include "../receiver/FrameTransformation.h"
#include "../common/RawToConvertedGeometry.h"
#include "../frame_serialize/ZMQStream2Pusher.h"
#include "../frame_serialize/ZMQStream2PusherGroup.h"
#define BASE_TCP_PORT 8000
@@ -54,7 +54,7 @@ int main(int argc, char **argv) {
for (int i = 0; i < nsockets; i++)
zmq_addr.emplace_back("tcp://0.0.0.0:" + std::to_string(BASE_TCP_PORT + i));
ZMQStream2Pusher pusher(zmq_addr);
ZMQStream2PusherGroup pusher(context, zmq_addr);
FrameTransformation transformation(x);

View File

@@ -1,6 +1,8 @@
FIND_PACKAGE(HDF5 1.10 REQUIRED)
ADD_LIBRARY(JFJochHDF5Wrappers STATIC HDF5Objects.cpp HDF5Objects.h ../compression/bitshuffle/bshuf_h5filter.c)
TARGET_LINK_LIBRARIES(JFJochHDF5Wrappers Compression hdf5-static)
TARGET_LINK_LIBRARIES(JFJochHDF5Wrappers Compression ${HDF5_LIBRARIES})
TARGET_INCLUDE_DIRECTORIES(JFJochHDF5Wrappers PUBLIC ${HDF5_INCLUDE_DIRS})
ADD_LIBRARY(JFJochWriter STATIC
HDF5DataFile.h HDF5DataFile.cpp
@@ -19,9 +21,10 @@ ADD_LIBRARY(JFJochWriter STATIC
HDF5DataFilePluginAzInt.h
HDF5DataFilePluginJUNGFRAU.cpp
HDF5DataFilePluginJUNGFRAU.h
)
HDF5DataFilePluginResEstimation.cpp
HDF5DataFilePluginResEstimation.h)
TARGET_LINK_LIBRARIES(JFJochWriter JFJochZMQ JFJochLogger JFJochHDF5Wrappers CBORStream2FrameSerialize)
TARGET_LINK_LIBRARIES(JFJochWriter JFJochHDF5Wrappers JFJochCommon CBORStream2FrameSerialize)
ADD_EXECUTABLE(HDF5Sum HDF5Sum.cpp)
TARGET_LINK_LIBRARIES(HDF5Sum JFJochWriter)
@@ -34,4 +37,4 @@ TARGET_INCLUDE_DIRECTORIES(WriterAPI PUBLIC gen/model gen/api)
ADD_EXECUTABLE(jfjoch_writer jfjoch_writer.cpp JFJochWriterHttp.h JFJochWriterHttp.cpp)
TARGET_LINK_LIBRARIES(jfjoch_writer JFJochWriter WriterAPI)
INSTALL(TARGETS jfjoch_writer RUNTIME COMPONENT writer)
INSTALL(TARGETS jfjoch_writer RUNTIME)

View File

@@ -1,8 +1,6 @@
// Copyright (2019-2023) Paul Scherrer Institute
#include <sys/stat.h>
#include <filesystem>
#include "HDF5DataFile.h"
#include "../compression/JFJochCompressor.h"
@@ -10,6 +8,7 @@
#include "HDF5DataFilePluginMX.h"
#include "HDF5DataFilePluginXFEL.h"
#include "HDF5DataFilePluginJUNGFRAU.h"
#include "HDF5DataFilePluginResEstimation.h"
#include "../include/spdlog/fmt/fmt.h"
HDF5DataFile::HDF5DataFile(const std::string &in_filename,
@@ -28,6 +27,7 @@ HDF5DataFile::HDF5DataFile(const std::string &in_filename,
plugins.emplace_back(std::make_unique<HDF5DataFilePluginJUNGFRAU>());
plugins.emplace_back(std::make_unique<HDF5DataFilePluginAzInt>(in_rad_int_bin_to_q));
plugins.emplace_back(std::make_unique<HDF5DataFilePluginXFEL>());
plugins.emplace_back(std::make_unique<HDF5DataFilePluginResEstimation>());
plugins.emplace_back(std::make_unique<HDF5DataFilePluginMX>(in_max_spots));
}
@@ -52,9 +52,7 @@ std::optional<HDF5DataFileStatistics> HDF5DataFile::Close() {
data_set.reset();
}
data_file.reset();
if (!std::filesystem::exists(filename.c_str()))
std::rename(tmp_filename.c_str(), filename.c_str());
std::rename(tmp_filename.c_str(), filename.c_str());
closed = true;

View File

@@ -0,0 +1,20 @@
// Copyright (2019-2024) Paul Scherrer Institute
#include "HDF5DataFilePluginResEstimation.h"
void HDF5DataFilePluginResEstimation::OpenFile(HDF5File &data_file, const DataMessage &msg) {}
void HDF5DataFilePluginResEstimation::Write(const DataMessage &msg, uint64_t image_number) {
if (!msg.resolution_estimation)
return;
if (image_number >= res_estimation.size())
res_estimation.resize(image_number + 1);
res_estimation[image_number] = msg.resolution_estimation.value();
}
void HDF5DataFilePluginResEstimation::WriteFinal(HDF5File &data_file) {
if (!res_estimation.empty())
data_file.SaveVector("/entry/res_estimation", res_estimation);
}

View File

@@ -0,0 +1,17 @@
// Copyright (2019-2024) Paul Scherrer Institute
#ifndef JUNGFRAUJOCH_HDF5DATAFILEPLUGINRESESTIMATION_H
#define JUNGFRAUJOCH_HDF5DATAFILEPLUGINRESESTIMATION_H
#include "HDF5DataFilePlugin.h"
class HDF5DataFilePluginResEstimation : public HDF5DataFilePlugin {
std::vector<float> res_estimation;
public:
void OpenFile(HDF5File &data_file, const DataMessage &msg) override;
void Write(const DataMessage &msg, uint64_t image_number) override;
void WriteFinal(HDF5File &data_file) override;
};
#endif //JUNGFRAUJOCH_HDF5DATAFILEPLUGINRESESTIMATION_H

View File

@@ -36,8 +36,7 @@ NXmx::NXmx(const StartMessage &start)
}
NXmx::~NXmx() {
if (!std::filesystem::exists(filename.c_str()))
std::rename(tmp_filename.c_str(), filename.c_str());
std::rename(tmp_filename.c_str(), filename.c_str());
}
std::string HDF5Metadata::DataFileName(const std::string &prefix, int64_t file_number) {
@@ -116,9 +115,6 @@ void NXmx::Detector(const StartMessage &start) {
"ns");
}
if (start.data_reduction_factor_serialmx)
det_specific.SaveScalar("data_reduction_factor_serialmx", start.data_reduction_factor_serialmx.value());
if (!start.gain_file_names.empty())
det_specific.SaveVector("gain_file_names", start.gain_file_names);

View File

@@ -74,8 +74,8 @@ void HDF5Writer::AddStats(const std::optional<HDF5DataFileStatistics>& s) {
}
}
void HDF5Writer::SetupSocket(const std::string &addr) {
socket = std::make_unique<ZMQSocket>(ZMQSocketType::Pub);
void HDF5Writer::SetupSocket(ZMQContext &c, const std::string &addr) {
socket = std::make_unique<ZMQSocket>(c, ZMQSocketType::Pub);
socket->Bind(addr);
}

View File

@@ -25,7 +25,7 @@ public:
explicit HDF5Writer(const StartMessage &request);
void Write(const DataMessage& msg);
std::vector<HDF5DataFileStatistics> Finalize();
void SetupSocket(const std::string &addr);
void SetupSocket(ZMQContext &c, const std::string &addr);
std::optional<std::string> GetZMQAddr();
};

View File

@@ -6,11 +6,13 @@
#include "HDF5NXmx.h"
#include "MakeDirectory.h"
StreamWriter::StreamWriter(Logger &in_logger,
StreamWriter::StreamWriter(ZMQContext &in_context,
Logger &in_logger,
const std::string &zmq_addr,
const std::string &repub_address,
const std::string &in_file_done_address)
: image_puller(repub_address),
: zmq_context(in_context),
image_puller(in_context, repub_address),
logger(in_logger),
file_done_address(in_file_done_address) {
image_puller.Connect(zmq_addr);
@@ -44,7 +46,7 @@ void StreamWriter::CollectImages(std::vector<HDF5DataFileStatistics> &v) {
HDF5Writer writer(*image_puller_output.cbor->start_message);
if (!file_done_address.empty())
writer.SetupSocket(file_done_address);
writer.SetupSocket(zmq_context, file_done_address);
std::unique_ptr<NXmx> master_file;
if (!image_puller_output.cbor->start_message->write_master_file || image_puller_output.cbor->start_message->write_master_file.value())

View File

@@ -24,6 +24,7 @@ struct StreamWriterOutput {
};
class StreamWriter {
ZMQContext &zmq_context;
std::string file_done_address;
StreamWriterState state = StreamWriterState::Idle;
@@ -41,7 +42,8 @@ class StreamWriter {
void CollectImages(std::vector<HDF5DataFileStatistics> &v);
bool WaitForImage();
public:
StreamWriter(Logger &logger,
StreamWriter(ZMQContext& context,
Logger &logger,
const std::string& zmq_addr,
const std::string& repub_address = "",
const std::string& file_done_address = "");

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@@ -2,13 +2,13 @@
#include "ZMQImagePuller.h"
ZMQImagePuller::ZMQImagePuller(const std::string &repub_address) :
socket (ZMQSocketType::Pull) {
ZMQImagePuller::ZMQImagePuller(ZMQContext &context, const std::string &repub_address) :
socket (context, ZMQSocketType::Pull) {
socket.ReceiveWaterMark(ReceiverWaterMark);
socket.ReceiveTimeout(ReceiveTimeout);
if (!repub_address.empty()) {
repub_socket = std::make_unique<ZMQSocket>(ZMQSocketType::Push);
repub_socket = std::make_unique<ZMQSocket>(context, ZMQSocketType::Push);
repub_socket->SendWaterMark(100);
repub_socket->SendTimeout(std::chrono::milliseconds(100));
repub_socket->Bind(repub_address);

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@@ -42,7 +42,7 @@ class ZMQImagePuller {
void RepubThread();
Logger logger{"ZMQImagePuller"};
public:
explicit ZMQImagePuller(const std::string &repub_address = "");
explicit ZMQImagePuller(ZMQContext &context, const std::string &repub_address = "");
~ZMQImagePuller();
void Connect(const std::string &in_address);
void Disconnect();

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@@ -117,7 +117,7 @@ int main(int argc, char **argv) {
ZMQContext context;
Pistache::Address addr(Pistache::Ipv4::any(), Pistache::Port(http_port));
writer = new StreamWriter(logger, argv[first_argc], repub_zmq_addr, file_done_zmq_addr);
writer = new StreamWriter(context, logger, argv[first_argc], repub_zmq_addr, file_done_zmq_addr);
httpEndpoint = new Pistache::Http::Endpoint(addr);
auto router = std::make_shared<Pistache::Rest::Router>();