mirror of
https://github.com/slsdetectorgroup/aare.git
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reading raw moench files (PR#3) (#32)
* reading moench and raw files * read mythen3 files * read multiport mythen3 * delete .vscode and .env.dev --------- Co-authored-by: Bechir <bechir.brahem420@gmail.com>
This commit is contained in:
Bechir Braham
GitHub
parent
937acd1138
commit
bf216f55c6
2
.gitignore
vendored
2
.gitignore
vendored
@ -1,3 +1,5 @@
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.vscode
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.env.dev
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.cproject
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.project
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bin/
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23
.vscode/c_cpp_properties.json
vendored
23
.vscode/c_cpp_properties.json
vendored
@ -1,23 +0,0 @@
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{
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"configurations": [
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{
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"name": "Linux",
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"includePath": [
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"${workspaceFolder}/file_io/**",
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"${workspaceFolder}/core/**",
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"${workspaceFolder}/tests/**",
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"${workspaceFolder}/tests/**",
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"/usr/include"
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],
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"defines": [],
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"compilerPath": "/usr/bin/g++",
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"cStandard": "c17",
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"cppStandard": "c++17",
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"intelliSenseMode": "linux-gcc-x64",
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"configurationProvider": "ms-vscode.cmake-tools",
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"compilerArgs": [],
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"compileCommands": "/home/l_bechir/github/aare/build/compile_commands.json"
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}
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],
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"version": 4
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}
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55
.vscode/launch.json
vendored
55
.vscode/launch.json
vendored
@ -1,55 +0,0 @@
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{
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"configurations": [
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{
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"name": "(gdb) Launch",
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"type": "cppdbg",
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"request": "launch",
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"program": "${workspaceFolder}/build/examples/json_example",
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"args": [],
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"stopAtEntry": true,
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"cwd": "${fileDirname}",
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"environment": [{"name": "PROJECT_ROOT_DIR", "value": "/home/l_bechir/github/aare"}],
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"externalConsole": false,
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"MIMode": "gdb",
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"setupCommands": [
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{
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"description": "Enable pretty-printing for gdb",
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"text": "-enable-pretty-printing",
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"ignoreFailures": true
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},
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{
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"description": "Set Disassembly Flavor to Intel",
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"text": "-gdb-set disassembly-flavor intel",
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"ignoreFailures": true
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}
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]
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},
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{
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"name": "C/C++: g++ build and debug active file",
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"type": "cppdbg",
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"request": "launch",
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"program": "${fileDirname}/${fileBasenameNoExtension}",
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"args": [],
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"stopAtEntry": false,
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"cwd": "${fileDirname}",
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"environment": [],
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"externalConsole": false,
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"MIMode": "gdb",
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"setupCommands": [
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{
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"description": "Enable pretty-printing for gdb",
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"text": "-enable-pretty-printing",
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"ignoreFailures": true
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},
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{
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"description": "Set Disassembly Flavor to Intel",
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"text": "-gdb-set disassembly-flavor intel",
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"ignoreFailures": true
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}
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],
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"preLaunchTask": "C/C++: g++ build active file",
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"miDebuggerPath": "/usr/bin/gdb"
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}
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],
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"version": "2.0.0"
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}
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103
.vscode/settings.json
vendored
103
.vscode/settings.json
vendored
@ -1,103 +0,0 @@
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{
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"cmake.configureOnOpen": true,
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"files.associations": {
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"stdexcept": "cpp",
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"cstddef": "cpp",
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"cctype": "cpp",
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"clocale": "cpp",
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"cmath": "cpp",
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"cstdarg": "cpp",
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"cstdio": "cpp",
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"cstdlib": "cpp",
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"ctime": "cpp",
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"cwchar": "cpp",
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"cwctype": "cpp",
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"array": "cpp",
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"atomic": "cpp",
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"bit": "cpp",
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"*.tcc": "cpp",
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"codecvt": "cpp",
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"compare": "cpp",
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"concepts": "cpp",
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"cstdint": "cpp",
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"deque": "cpp",
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"string": "cpp",
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"unordered_map": "cpp",
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"vector": "cpp",
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"exception": "cpp",
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"algorithm": "cpp",
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"functional": "cpp",
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"iterator": "cpp",
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"memory": "cpp",
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"memory_resource": "cpp",
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"numeric": "cpp",
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"optional": "cpp",
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"random": "cpp",
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"ratio": "cpp",
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"string_view": "cpp",
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"system_error": "cpp",
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"tuple": "cpp",
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"type_traits": "cpp",
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"utility": "cpp",
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"initializer_list": "cpp",
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"iomanip": "cpp",
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"iosfwd": "cpp",
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"iostream": "cpp",
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"istream": "cpp",
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"limits": "cpp",
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"new": "cpp",
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"numbers": "cpp",
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"ostream": "cpp",
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"sstream": "cpp",
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"streambuf": "cpp",
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"cinttypes": "cpp",
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"typeinfo": "cpp",
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"filesystem": "cpp",
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"csignal": "cpp",
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"cstring": "cpp",
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"any": "cpp",
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"condition_variable": "cpp",
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"forward_list": "cpp",
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"list": "cpp",
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"map": "cpp",
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"set": "cpp",
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"unordered_set": "cpp",
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"fstream": "cpp",
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"mutex": "cpp",
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"ranges": "cpp",
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"semaphore": "cpp",
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"span": "cpp",
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"stop_token": "cpp",
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"thread": "cpp",
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"valarray": "cpp",
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"variant": "cpp",
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"bitset": "cpp",
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"charconv": "cpp",
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"chrono": "cpp",
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"format": "cpp",
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"__bit_reference": "cpp",
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"__config": "cpp",
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"__hash_table": "cpp",
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"__locale": "cpp",
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"__node_handle": "cpp",
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"__split_buffer": "cpp",
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"__threading_support": "cpp",
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"__verbose_abort": "cpp",
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"execution": "cpp",
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"ios": "cpp",
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"locale": "cpp",
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"__tree": "cpp",
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"queue": "cpp",
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"stack": "cpp",
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"shared_mutex": "cpp",
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"cfenv": "cpp",
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"complex": "cpp",
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"regex": "cpp",
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"source_location": "cpp",
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"future": "cpp",
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"typeindex": "cpp",
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"*.in": "c",
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"stdfloat": "cpp"
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},
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"C_Cpp.errorSquiggles": "enabled"
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}
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25
.vscode/tasks.json
vendored
25
.vscode/tasks.json
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@ -1,25 +0,0 @@
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{
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"tasks": [
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{
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"type": "cppbuild",
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"label": "C/C++: g++ build active file",
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"command": "/usr/bin/g++",
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"args": [
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"-fdiagnostics-color=always",
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"-g",
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"${file}",
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"-o",
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"${fileDirname}/${fileBasenameNoExtension}"
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],
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"options": {
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"cwd": "${fileDirname}"
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},
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"problemMatcher": [
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"$gcc"
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],
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"group": "build",
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"detail": "Task generated by Debugger."
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}
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],
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"version": "2.0.0"
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}
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@ -11,7 +11,7 @@ add_library(core STATIC ${SourceFiles})
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target_include_directories(core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include)
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target_link_libraries(core PUBLIC fmt::fmt PRIVATE aare_compiler_flags)
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target_link_libraries(core PUBLIC fmt::fmt PRIVATE aare_compiler_flags utils)
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if (AARE_PYTHON_BINDINGS)
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set_property(TARGET core PROPERTY POSITION_INDEPENDENT_CODE ON)
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@ -29,5 +29,5 @@ if(AARE_TESTS)
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)
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target_sources(tests PRIVATE ${TestSources} )
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target_link_libraries(tests PRIVATE core)
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target_link_libraries(tests PRIVATE core )
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endif()
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@ -34,7 +34,7 @@ struct xy {
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// using image_shape = std::array<ssize_t, 2>;
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using dynamic_shape = std::vector<ssize_t>;
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enum class DetectorType { Jungfrau, Eiger, Mythen3, Moench };
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enum class DetectorType { Jungfrau, Eiger, Mythen3, Moench,ChipTestBoard };
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enum class TimingMode {Auto, Trigger};
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@ -1,4 +1,5 @@
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#include "aare/Frame.hpp"
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#include "aare/utils/logger.hpp"
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#include <iostream>
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#include <cassert>
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Frame::Frame(std::byte* bytes, ssize_t rows, ssize_t cols, ssize_t bitdepth):
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@ -10,13 +10,14 @@ template <> std::string toString(DetectorType type) {
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return "Mythen3";
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case DetectorType::Moench:
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return "Moench";
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case DetectorType::ChipTestBoard:
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return "ChipTestBoard";
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default:
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return "Unknown";
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}
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}
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template <> DetectorType StringTo(std::string name) {
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template <> DetectorType StringTo(std::string name) {
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if (name == "Jungfrau")
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return DetectorType::Jungfrau;
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else if (name == "Eiger")
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@ -25,18 +26,20 @@ template <> std::string toString(DetectorType type) {
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return DetectorType::Mythen3;
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else if (name == "Moench")
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return DetectorType::Moench;
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else if (name == "ChipTestBoard")
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return DetectorType::ChipTestBoard;
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else {
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auto msg = fmt::format("Could not decode dector from: \"{}\"", name);
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throw std::runtime_error(msg);
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}
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}
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template <> TimingMode StringTo(std::string mode){
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template <> TimingMode StringTo(std::string mode) {
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if (mode == "auto")
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return TimingMode::Auto;
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else if(mode == "trigger")
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else if (mode == "trigger")
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return TimingMode::Trigger;
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else{
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else {
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auto msg = fmt::format("Could not decode timing mode from: \"{}\"", mode);
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throw std::runtime_error(msg);
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}
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80
data/jungfrau/read_multiport.py
Normal file
80
data/jungfrau/read_multiport.py
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import numpy as np
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import matplotlib.pyplot as plt
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plt.ion()
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header_dt = np.dtype(
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[
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("Frame Number", "u8"),
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("SubFrame Number/ExpLength", "u4"),
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("Packet Number", "u4"),
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("Bunch ID", "u8"),
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("Timestamp", "u8"),
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("Module Id", "u2"),
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("Row", "u2"),
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("Column", "u2"),
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("Reserved", "u2"),
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("Debug", "u4"),
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("Round Robin Number", "u2"),
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("Detector Type", "u1"),
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("Header Version", "u1"),
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("Packets caught mask", "8u8")
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]
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)
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# Read three frames from a jungfrau file with a single interface
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frames = 1
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parts = 2
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frame_cols = 1024
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frame_rows = 512
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part_cols = 1024
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part_rows = 256
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parts_data = np.zeros((frames,parts,part_rows,part_cols), dtype = np.uint16)
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data = np.zeros((frames,frame_rows,frame_cols), dtype = np.uint16)
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header = np.zeros((frames,parts), dtype = header_dt)
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for frame in range(frames):
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for part in range(parts):
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file_name = f'jungfrau_double_d{part}_f{frame}_{0}.raw'
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print("Reading file:", file_name)
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with open(file_name) as f:
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header[frame,part] = np.fromfile(f, dtype=header_dt, count = 1)
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parts_data[frame,part] = np.fromfile(f, dtype=np.uint16,count = part_rows*part_cols).reshape(part_rows,part_cols)
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data[frame] = np.concatenate((parts_data[frame,0],parts_data[frame,1]),axis=0)
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# for frame in range(frames):
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# print("Frame:", frame)
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# print("Data:\n", data[frame])
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# print(data[0,0,0])
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# print(data[0,0,1])
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# print(data[0,0,50])
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print(data[0,0,0])
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print(data[0,0,1])
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print(data[0,255,1023])
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print(data[0,511,1023])
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# print()
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# print(parts_data[0,0,0,0])
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# print(parts_data[0,0,0,1])
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# print(parts_data[0,0,1,0])
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# print(data.shape)
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#fig, ax = plt.subplots()
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#im = ax.imshow(data[0])
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#im.set_clim(2000,4000)
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BIN
data/moench/moench04_noise_200V_sto_both_100us_no_light_thresh_900_d0_f0_0.raw
Executable file
BIN
data/moench/moench04_noise_200V_sto_both_100us_no_light_thresh_900_d0_f0_0.raw
Executable file
Binary file not shown.
@ -0,0 +1,40 @@
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Version : 6.4
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TimeStamp : Wed Aug 31 09:08:49 2022
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Detector Type : ChipTestBoard
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Timing Mode : auto
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Geometry : [1, 1]
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Image Size : 360000 bytes
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Pixels : [96, 1]
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Max Frames Per File : 20000
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Frame Discard Policy : nodiscard
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Frame Padding : 1
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Scan Parameters : [disabled]
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Total Frames : 100
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Exptime : 100us
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Period : 4ms
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Ten Giga : 1
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ADC Mask : 0xffffffff
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Analog Flag : 1
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Analog Samples : 5000
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Digital Flag : 1
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Digital Samples : 5000
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Dbit Offset : 0
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Dbit Bitset : 0
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Frames in File : 100
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#Frame Header
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Frame Number : 8 bytes
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SubFrame Number/ExpLength : 4 bytes
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Packet Number : 4 bytes
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Bunch ID : 8 bytes
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Timestamp : 8 bytes
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Module Id : 2 bytes
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Row : 2 bytes
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Column : 2 bytes
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Reserved : 2 bytes
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Debug : 4 bytes
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Round Robin Number : 2 bytes
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Detector Type : 1 byte
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Header Version : 1 byte
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Packets Caught Mask : 64 bytes
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BIN
data/mythen/scan242_d0_f0_3.raw
Executable file
BIN
data/mythen/scan242_d0_f0_3.raw
Executable file
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BIN
data/mythen/scan242_d1_f0_3.raw
Executable file
BIN
data/mythen/scan242_d1_f0_3.raw
Executable file
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BIN
data/mythen/scan242_d2_f0_3.raw
Executable file
BIN
data/mythen/scan242_d2_f0_3.raw
Executable file
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BIN
data/mythen/scan242_d3_f0_3.raw
Executable file
BIN
data/mythen/scan242_d3_f0_3.raw
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40
data/mythen/scan242_master_3.raw
Executable file
40
data/mythen/scan242_master_3.raw
Executable file
@ -0,0 +1,40 @@
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Version : 6.2
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TimeStamp : Mon Sep 14 16:21:09 2020
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Detector Type : Mythen3
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Timing Mode : auto
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Geometry : [4, 1]
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Image Size : 5120 bytes
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Pixels : [1280, 1]
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Max Frames Per File : 10000
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Frame Discard Policy : nodiscard
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Frame Padding : 1
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Scan Parameters : [disabled]
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Total Frames : 1
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Dynamic Range : 32
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Ten Giga : 1
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Period : 0ns
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Counter Mask : 0x1
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Exptime1 : 0.2s
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Exptime2 : 0.2s
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Exptime3 : 0.2s
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GateDelay1 : 0.1s
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GateDelay2 : 0.1s
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GateDelay3 : 0.1s
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Gates : 1
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#Frame Header
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Frame Number : 8 bytes
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SubFrame Number/ExpLength : 4 bytes
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Packet Number : 4 bytes
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Bunch ID : 8 bytes
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Timestamp : 8 bytes
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Module Id : 2 bytes
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Row : 2 bytes
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Column : 2 bytes
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Reserved : 2 bytes
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Debug : 4 bytes
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Round Robin Number : 2 bytes
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Detector Type : 1 byte
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Header Version : 1 byte
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Packets Caught Mask : 64 bytes
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@ -1,4 +1,5 @@
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set(EXAMPLE_LIST "json_example;logger_example;numpy_example;multiport_example")
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set(EXAMPLE_LIST "json_example;logger_example;numpy_example;multiport_example;raw_example;mythen_example")
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foreach(example ${EXAMPLE_LIST})
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add_executable(${example} ${example}.cpp)
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||||
target_link_libraries(${example} PUBLIC aare PRIVATE aare_compiler_flags)
|
||||
|
||||
@ -17,8 +17,7 @@ void test(File *f, int frame_number) {
|
||||
int main() {
|
||||
ContextManager ctx_manager;
|
||||
auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR_VAR));
|
||||
std::filesystem::path fpath(PROJECT_ROOT_DIR / "data" / "jungfrau_single_master_0.json");
|
||||
// std::filesystem::path fpath(PROJECT_ROOT_DIR / "data" / "test_numpy_file.npy");
|
||||
std::filesystem::path fpath(PROJECT_ROOT_DIR / "data" /"jungfrau"/ "jungfrau_single_master_0.json");
|
||||
std::cout << fpath << std::endl;
|
||||
|
||||
|
||||
@ -26,6 +25,4 @@ int main() {
|
||||
test(file, 0);
|
||||
test(file, 2);
|
||||
test(file, 9);
|
||||
|
||||
aare::logger::debug(LOCATION,"Hello", "World");
|
||||
}
|
||||
@ -1,7 +1,7 @@
|
||||
// Your First C++ Program
|
||||
#include "aare/ContextManager.hpp"
|
||||
#include <iostream>
|
||||
#include "aare/utils/logger.hpp"
|
||||
#include <iostream>
|
||||
|
||||
#define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
|
||||
|
||||
@ -9,26 +9,18 @@ void test(File *f, int frame_number) {
|
||||
std::cout << "frame number: " << frame_number << std::endl;
|
||||
Frame frame = f->get_frame(frame_number);
|
||||
std::cout << *((uint16_t *)frame.get(0, 0)) << std::endl;
|
||||
std::cout << *((uint16_t *)frame.get(0,1)) << std::endl;
|
||||
std::cout << *((uint16_t *)frame.get(0, 1)) << std::endl;
|
||||
std::cout << *((uint16_t *)frame.get(255, 1023)) << std::endl;
|
||||
std::cout << *((uint16_t *)frame.get(511, 1023)) << std::endl;
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
int main() {
|
||||
ContextManager ctx_manager;
|
||||
auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR_VAR));
|
||||
std::filesystem::path fpath(PROJECT_ROOT_DIR / "data" / "jungfrau_double_master_0.json");
|
||||
std::filesystem::path fpath(PROJECT_ROOT_DIR / "data" / "jungfrau" / "jungfrau_double_master_0.json");
|
||||
std::cout << fpath << std::endl;
|
||||
|
||||
|
||||
File *file = ctx_manager.get_file(fpath);
|
||||
test(file, 0);
|
||||
test(file, 9);
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
48
examples/mythen_example.cpp
Normal file
48
examples/mythen_example.cpp
Normal file
@ -0,0 +1,48 @@
|
||||
// Your First C++ Program
|
||||
#include "aare/ContextManager.hpp"
|
||||
#include "aare/utils/logger.hpp"
|
||||
#include <iostream>
|
||||
|
||||
#define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
|
||||
|
||||
void test1(File *f, int frame_number) {
|
||||
std::cout << "frame number: " << frame_number << std::endl;
|
||||
Frame frame = f->get_frame(frame_number);
|
||||
std::cout << *((uint32_t *)frame.get(0, 0)) << std::endl;
|
||||
std::cout << *((uint32_t *)frame.get(0, 1)) << std::endl;
|
||||
std::cout << *((uint32_t *)frame.get(0, 3839)) << std::endl;
|
||||
|
||||
for (int i = 0; i < 3840; i++) {
|
||||
uint16_t x = *((uint32_t *)frame.get(0, i));
|
||||
if (x != i) {
|
||||
aare::logger::error("error at i", i, "x", x);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
void test2(File *f, int frame_number) {
|
||||
std::cout << "frame number: " << frame_number << std::endl;
|
||||
Frame frame = f->get_frame(frame_number);
|
||||
std::cout << *((uint32_t *)frame.get(0, 0)) << std::endl;
|
||||
std::cout << *((uint32_t *)frame.get(0, 1)) << std::endl;
|
||||
std::cout << *((uint32_t *)frame.get(0, 1280*4 -1)) << std::endl;
|
||||
}
|
||||
|
||||
int main() {
|
||||
ContextManager ctx_manager;
|
||||
auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR_VAR));
|
||||
if (PROJECT_ROOT_DIR.empty()) {
|
||||
throw std::runtime_error("environment variable PROJECT_ROOT_DIR is not set");
|
||||
}
|
||||
std::filesystem::path fpath(PROJECT_ROOT_DIR / "data" / "mythen" / "m3_master_0.json");
|
||||
File *file = ctx_manager.get_file(fpath);
|
||||
test1(file, 0);
|
||||
|
||||
fpath = (PROJECT_ROOT_DIR / "data" / "mythen" / "scan242_master_3.raw");
|
||||
file = ctx_manager.get_file(fpath);
|
||||
test2(file, 0);
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
@ -4,29 +4,24 @@
|
||||
|
||||
#define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
|
||||
|
||||
void test(File* f, int frame_number) {
|
||||
void test(File *f, int frame_number) {
|
||||
std::cout << "frame number: " << frame_number << std::endl;
|
||||
Frame frame = f->get_frame(frame_number);
|
||||
std::cout << *((uint16_t *)frame.get(0, 0)) << std::endl;
|
||||
std::cout << *((uint16_t *)frame.get(0, 1)) << std::endl;
|
||||
std::cout << *((uint16_t *)frame.get(1, 0)) << std::endl;
|
||||
std::cout << *((uint16_t *)frame.get(49, 49)) << std::endl;
|
||||
|
||||
}
|
||||
|
||||
int main() {
|
||||
ContextManager ctx_manager;
|
||||
|
||||
auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR_VAR));
|
||||
// std::filesystem::path fpath(PROJECT_ROOT_DIR / "data" / "jungfrau_single_master_0.json");
|
||||
std::filesystem::path fpath(PROJECT_ROOT_DIR / "data" / "test_numpy_file.npy");
|
||||
std::filesystem::path fpath(PROJECT_ROOT_DIR / "data" / "numpy" / "test_numpy_file.npy");
|
||||
std::cout << fpath << std::endl;
|
||||
|
||||
File* file = ctx_manager.get_file(fpath);
|
||||
File *file = ctx_manager.get_file(fpath);
|
||||
test(file, 0);
|
||||
test(file, 2);
|
||||
test(file, 24);
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
27
examples/raw_example.cpp
Normal file
27
examples/raw_example.cpp
Normal file
@ -0,0 +1,27 @@
|
||||
// Your First C++ Program
|
||||
#include "aare/ContextManager.hpp"
|
||||
#include <iostream>
|
||||
#include "aare/utils/logger.hpp"
|
||||
|
||||
#define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
|
||||
|
||||
void test(File *f, int frame_number) {
|
||||
std::cout << "frame number: " << frame_number << std::endl;
|
||||
Frame frame = f->get_frame(frame_number);
|
||||
std::cout << *((uint16_t *)frame.get(0, 0)) << std::endl;
|
||||
std::cout << *((uint16_t *)frame.get(0, 1)) << std::endl;
|
||||
std::cout << *((uint16_t *)frame.get(0, 95)) << std::endl;
|
||||
}
|
||||
|
||||
int main() {
|
||||
ContextManager ctx_manager;
|
||||
auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR_VAR));
|
||||
if (PROJECT_ROOT_DIR.empty()) {
|
||||
throw std::runtime_error("environment variable PROJECT_ROOT_DIR is not set");
|
||||
}
|
||||
std::filesystem::path fpath(PROJECT_ROOT_DIR / "data" /"moench"/ "moench04_noise_200V_sto_both_100us_no_light_thresh_900_master_0.raw");
|
||||
File *file = ctx_manager.get_file(fpath);
|
||||
test(file, 0);
|
||||
test(file, 2);
|
||||
test(file, 99);
|
||||
}
|
||||
@ -3,8 +3,8 @@ abstract class FileFactory{
|
||||
{static} +getFactory(path):FileFactory
|
||||
{abstract} +loadFile(path):File
|
||||
}
|
||||
class JsonFileFactory{
|
||||
+loadFile(path):JsonFile
|
||||
class RawFileFactory{
|
||||
+loadFile(path):RawFile
|
||||
}
|
||||
class RawFileFactory{
|
||||
+loadFile(path):RawFile
|
||||
@ -16,7 +16,7 @@ class NumpyFileFactory{
|
||||
abstract File{
|
||||
}
|
||||
|
||||
class JsonFile{
|
||||
class RawFile{
|
||||
}
|
||||
class RawFile{
|
||||
}
|
||||
@ -25,9 +25,9 @@ class NumpyFile{
|
||||
|
||||
FileFactory <|-- RawFileFactory
|
||||
FileFactory <|-- NumpyFileFactory
|
||||
FileFactory <|-- JsonFileFactory
|
||||
FileFactory <|-- RawFileFactory
|
||||
|
||||
File <|-- JsonFile
|
||||
File <|-- RawFile
|
||||
File <|-- RawFile
|
||||
File <|-- NumpyFile
|
||||
|
||||
|
||||
@ -8,8 +8,8 @@ set(SourceFiles
|
||||
${CMAKE_CURRENT_SOURCE_DIR}/src/File.cpp
|
||||
${CMAKE_CURRENT_SOURCE_DIR}/src/FileFactory.cpp
|
||||
${CMAKE_CURRENT_SOURCE_DIR}/src/helpers.cpp
|
||||
${CMAKE_CURRENT_SOURCE_DIR}/src/JsonFile.cpp
|
||||
${CMAKE_CURRENT_SOURCE_DIR}/src/JsonFileFactory.cpp
|
||||
${CMAKE_CURRENT_SOURCE_DIR}/src/RawFile.cpp
|
||||
${CMAKE_CURRENT_SOURCE_DIR}/src/RawFileFactory.cpp
|
||||
${CMAKE_CURRENT_SOURCE_DIR}/src/SubFile.cpp
|
||||
${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyFile.cpp
|
||||
${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyFileFactory.cpp
|
||||
|
||||
@ -1,18 +0,0 @@
|
||||
#include "aare/FileFactory.hpp"
|
||||
#include "aare/JsonFile.hpp"
|
||||
class JsonFileFactory: public FileFactory
|
||||
{
|
||||
private:
|
||||
/* data */
|
||||
public:
|
||||
JsonFileFactory(std::filesystem::path fpath);
|
||||
virtual JsonFile* load_file() override;
|
||||
void parse_metadata(File*) override;
|
||||
void parse_fname(File*) override;
|
||||
void open_subfiles(File*);
|
||||
sls_detector_header read_header(const std::filesystem::path &fname);
|
||||
void find_geometry(File*);
|
||||
|
||||
|
||||
|
||||
};
|
||||
@ -4,7 +4,7 @@
|
||||
#include "aare/File.hpp"
|
||||
|
||||
|
||||
class JsonFile : public File {
|
||||
class RawFile : public File {
|
||||
|
||||
using config = RawFileConfig;
|
||||
public:
|
||||
@ -38,5 +38,5 @@ class JsonFile : public File {
|
||||
return this->base_path / fmt::format("{}_d{}_f{}_{}.raw", this->base_name, file_id, mod_id, this->findex);
|
||||
}
|
||||
|
||||
~JsonFile();
|
||||
~RawFile();
|
||||
};
|
||||
@ -1,8 +1,16 @@
|
||||
#include "aare/File.hpp"
|
||||
#include <filesystem>
|
||||
class RawFileFactory{
|
||||
public:
|
||||
// RawFileFactory();
|
||||
// ~RawFileFactory();
|
||||
File loadFile(std::filesystem::path fpath);
|
||||
};
|
||||
#include "aare/FileFactory.hpp"
|
||||
#include "aare/RawFile.hpp"
|
||||
class RawFileFactory : public FileFactory {
|
||||
private:
|
||||
void parse_json_metadata(RawFile *file);
|
||||
void parse_raw_metadata(RawFile *file);
|
||||
|
||||
public:
|
||||
RawFileFactory(std::filesystem::path fpath);
|
||||
virtual RawFile *load_file() override;
|
||||
void parse_metadata(File *) override;
|
||||
void parse_fname(File *) override;
|
||||
void open_subfiles(File *);
|
||||
sls_detector_header read_header(const std::filesystem::path &fname);
|
||||
void find_geometry(File *);
|
||||
};
|
||||
|
||||
@ -19,6 +19,8 @@ class SubFile {
|
||||
std::map<std::pair<DetectorType, int>, pfunc> read_impl_map = {
|
||||
{{DetectorType::Moench, 16}, &SubFile::read_impl_reorder<uint16_t>},
|
||||
{{DetectorType::Jungfrau, 16}, &SubFile::read_impl_normal},
|
||||
{{DetectorType::ChipTestBoard,16}, &SubFile::read_impl_normal},
|
||||
{{DetectorType::Mythen3, 32}, &SubFile::read_impl_normal}
|
||||
};
|
||||
|
||||
|
||||
|
||||
@ -1,7 +1,8 @@
|
||||
#include "aare/FileFactory.hpp"
|
||||
#include "aare/File.hpp"
|
||||
#include "aare/JsonFileFactory.hpp"
|
||||
#include "aare/RawFileFactory.hpp"
|
||||
#include "aare/NumpyFileFactory.hpp"
|
||||
#include "aare/utils/logger.hpp"
|
||||
#include <iostream>
|
||||
|
||||
FileFactory *FileFactory::get_factory(std::filesystem::path fpath) {
|
||||
@ -10,16 +11,13 @@ FileFactory *FileFactory::get_factory(std::filesystem::path fpath) {
|
||||
throw std::runtime_error("File does not exist");
|
||||
}
|
||||
|
||||
if (fpath.extension() == ".raw") {
|
||||
std::cout << "Loading raw file" << std::endl;
|
||||
throw std::runtime_error("Raw file not implemented");
|
||||
} else if (fpath.extension() == ".json") {
|
||||
std::cout << "Loading json file" << std::endl;
|
||||
return new JsonFileFactory(fpath);
|
||||
}
|
||||
if (fpath.extension() == ".raw" || fpath.extension() == ".json"){
|
||||
aare::logger::info("Loading",fpath.extension(),"file");
|
||||
return new RawFileFactory(fpath);
|
||||
}
|
||||
// check if extension is numpy
|
||||
else if (fpath.extension() == ".npy") {
|
||||
std::cout << "Loading numpy file" << std::endl;
|
||||
aare::logger::info("Loading numpy file");
|
||||
return new NumpyFileFactory(fpath);
|
||||
}
|
||||
|
||||
|
||||
@ -1,119 +0,0 @@
|
||||
#include "aare/JsonFileFactory.hpp"
|
||||
#include "aare/JsonFile.hpp"
|
||||
#include "aare/SubFile.hpp"
|
||||
#include "aare/defs.hpp"
|
||||
#include "aare/helpers.hpp"
|
||||
#include "aare/utils/logger.hpp"
|
||||
|
||||
#include <fstream>
|
||||
#include <iostream>
|
||||
#include <nlohmann/json.hpp>
|
||||
|
||||
using json = nlohmann::json;
|
||||
|
||||
JsonFileFactory::JsonFileFactory(std::filesystem::path fpath) {
|
||||
if (not is_master_file(fpath))
|
||||
throw std::runtime_error("Json file is not a master file");
|
||||
this->m_fpath = fpath;
|
||||
}
|
||||
|
||||
void JsonFileFactory::parse_metadata(File *_file) {
|
||||
auto file = dynamic_cast<JsonFile *>(_file);
|
||||
std::ifstream ifs(file->master_fname());
|
||||
json j;
|
||||
ifs >> j;
|
||||
double v = j["Version"];
|
||||
std::cout << "Version: " << v << std::endl;
|
||||
file->version = fmt::format("{:.1f}", v);
|
||||
file->type = StringTo<DetectorType>(j["Detector Type"].get<std::string>());
|
||||
file->timing_mode = StringTo<TimingMode>(j["Timing Mode"].get<std::string>());
|
||||
file->total_frames = j["Frames in File"];
|
||||
file->subfile_rows = j["Pixels"]["y"];
|
||||
file->subfile_cols = j["Pixels"]["x"];
|
||||
file->max_frames_per_file = j["Max Frames Per File"];
|
||||
try {
|
||||
file->bitdepth = j.at("Dynamic Range");
|
||||
} catch (const json::out_of_range &e) {
|
||||
file->bitdepth = 16;
|
||||
}
|
||||
// only Eiger had quad
|
||||
if (file->type == DetectorType::Eiger) {
|
||||
file->quad = (j["Quad"] == 1);
|
||||
}
|
||||
|
||||
file->geometry = {j["Geometry"]["y"], j["Geometry"]["x"]};
|
||||
file->n_subfile_parts = file->geometry.row * file->geometry.col;
|
||||
}
|
||||
|
||||
void JsonFileFactory::open_subfiles(File *_file) {
|
||||
auto file = dynamic_cast<JsonFile *>(_file);
|
||||
for (size_t i = 0; i != file->n_subfiles; ++i) {
|
||||
auto v = std::vector<SubFile *>(file->n_subfile_parts);
|
||||
for (size_t j = 0; j != file->n_subfile_parts; ++j) {
|
||||
v[j]=new SubFile(file->data_fname(i, j), file->type, file->subfile_rows,
|
||||
file->subfile_cols, file->bitdepth);
|
||||
}
|
||||
file->subfiles.push_back(v);
|
||||
}
|
||||
}
|
||||
|
||||
JsonFile *JsonFileFactory::load_file() {
|
||||
JsonFile *file = new JsonFile();
|
||||
file->fname = this->m_fpath;
|
||||
this->parse_fname(file);
|
||||
this->parse_metadata(file);
|
||||
file->find_number_of_subfiles();
|
||||
|
||||
this->find_geometry(file);
|
||||
this->open_subfiles(file);
|
||||
|
||||
return file;
|
||||
}
|
||||
|
||||
sls_detector_header JsonFileFactory::read_header(const std::filesystem::path &fname) {
|
||||
sls_detector_header h{};
|
||||
FILE *fp = fopen(fname.c_str(), "r");
|
||||
if (!fp)
|
||||
throw std::runtime_error(fmt::format("Could not open: {} for reading", fname.c_str()));
|
||||
|
||||
size_t rc = fread(reinterpret_cast<char *>(&h), sizeof(h), 1, fp);
|
||||
fclose(fp);
|
||||
if (rc != 1)
|
||||
throw std::runtime_error("Could not read header from file");
|
||||
return h;
|
||||
}
|
||||
|
||||
void JsonFileFactory::find_geometry(File *_file) {
|
||||
auto file = dynamic_cast<JsonFile *>(_file);
|
||||
uint16_t r{};
|
||||
uint16_t c{};
|
||||
for (size_t i = 0; i < file->n_subfile_parts; i++) {
|
||||
for (size_t j = 0; j != file->n_subfiles; ++j) {
|
||||
auto h = this->read_header(file->data_fname(j, i));
|
||||
r = std::max(r, h.row);
|
||||
c = std::max(c, h.column);
|
||||
|
||||
file->positions.push_back({h.row, h.column});
|
||||
}
|
||||
}
|
||||
|
||||
r++;
|
||||
c++;
|
||||
|
||||
file->rows = r * file->subfile_rows;
|
||||
file->cols = c * file->subfile_cols;
|
||||
|
||||
file->rows += (r - 1) * file->cfg.module_gap_row;
|
||||
}
|
||||
|
||||
void JsonFileFactory::parse_fname(File *file) {
|
||||
|
||||
file->base_path = this->m_fpath.parent_path();
|
||||
file->base_name = this->m_fpath.stem();
|
||||
file->ext = this->m_fpath.extension();
|
||||
|
||||
auto pos = file->base_name.rfind("_");
|
||||
file->findex = std::stoi(file->base_name.substr(pos + 1));
|
||||
pos = file->base_name.find("_master_");
|
||||
file->base_name.erase(pos);
|
||||
}
|
||||
@ -1,7 +1,7 @@
|
||||
#include "aare/JsonFile.hpp"
|
||||
#include "aare/RawFile.hpp"
|
||||
#include "aare/utils/logger.hpp"
|
||||
|
||||
Frame JsonFile::get_frame(size_t frame_number) {
|
||||
Frame RawFile::get_frame(size_t frame_number) {
|
||||
if (frame_number > this->total_frames) {
|
||||
throw std::runtime_error("Frame number out of range");
|
||||
}
|
||||
@ -39,7 +39,7 @@ Frame JsonFile::get_frame(size_t frame_number) {
|
||||
return f;
|
||||
}
|
||||
|
||||
JsonFile::~JsonFile() {
|
||||
RawFile::~RawFile() {
|
||||
for (auto &vec : subfiles) {
|
||||
for (auto subfile : vec) {
|
||||
delete subfile;
|
||||
182
file_io/src/RawFileFactory.cpp
Normal file
182
file_io/src/RawFileFactory.cpp
Normal file
@ -0,0 +1,182 @@
|
||||
#include "aare/RawFileFactory.hpp"
|
||||
#include "aare/RawFile.hpp"
|
||||
#include "aare/SubFile.hpp"
|
||||
#include "aare/defs.hpp"
|
||||
#include "aare/helpers.hpp"
|
||||
#include "aare/utils/logger.hpp"
|
||||
|
||||
#include <fstream>
|
||||
#include <iostream>
|
||||
#include <nlohmann/json.hpp>
|
||||
|
||||
using json = nlohmann::json;
|
||||
|
||||
RawFileFactory::RawFileFactory(std::filesystem::path fpath) {
|
||||
if (not is_master_file(fpath))
|
||||
throw std::runtime_error("Json file is not a master file");
|
||||
this->m_fpath = fpath;
|
||||
}
|
||||
|
||||
void RawFileFactory::parse_metadata(File *_file) {
|
||||
auto file = dynamic_cast<RawFile *>(_file);
|
||||
if (file->ext == ".raw") {
|
||||
this->parse_raw_metadata(file);
|
||||
if (file->bitdepth == 0) {
|
||||
switch (file->type) {
|
||||
case DetectorType::Eiger:
|
||||
file->bitdepth = 32;
|
||||
break;
|
||||
|
||||
default:
|
||||
file->bitdepth = 16;
|
||||
}
|
||||
}
|
||||
} else if (file->ext == ".json") {
|
||||
this->parse_json_metadata(file);
|
||||
} else {
|
||||
throw std::runtime_error("Unsupported file type");
|
||||
}
|
||||
file->n_subfile_parts = file->geometry.row * file->geometry.col;
|
||||
}
|
||||
|
||||
void RawFileFactory::parse_raw_metadata(RawFile *file) {
|
||||
std::ifstream ifs(file->master_fname());
|
||||
for (std::string line; std::getline(ifs, line);) {
|
||||
if (line == "#Frame Header")
|
||||
break;
|
||||
auto pos = line.find(":");
|
||||
auto key_pos = pos;
|
||||
while (key_pos != std::string::npos && std::isspace(line[--key_pos]))
|
||||
;
|
||||
if (key_pos != std::string::npos) {
|
||||
auto key = line.substr(0, key_pos + 1);
|
||||
auto value = line.substr(pos + 2);
|
||||
// do the actual parsing
|
||||
if (key == "Version") {
|
||||
file->version = value;
|
||||
} else if (key == "TimeStamp") {
|
||||
|
||||
} else if (key == "Detector Type") {
|
||||
file->type = StringTo<DetectorType>(value);
|
||||
} else if (key == "Timing Mode") {
|
||||
file->timing_mode = StringTo<TimingMode>(value);
|
||||
} else if (key == "Pixels") {
|
||||
// Total number of pixels cannot be found yet looking at
|
||||
// submodule
|
||||
pos = value.find(',');
|
||||
file->subfile_cols = std::stoi(value.substr(1, pos));
|
||||
file->subfile_rows = std::stoi(value.substr(pos + 1));
|
||||
} else if (key == "Total Frames") {
|
||||
file->total_frames = std::stoi(value);
|
||||
} else if (key == "Dynamic Range") {
|
||||
file->bitdepth = std::stoi(value);
|
||||
} else if (key == "Quad") {
|
||||
file->quad = (value == "1");
|
||||
} else if (key == "Max Frames Per File") {
|
||||
file->max_frames_per_file = std::stoi(value);
|
||||
} else if (key == "Geometry") {
|
||||
pos = value.find(',');
|
||||
file->geometry = {std::stoi(value.substr(1, pos)), std::stoi(value.substr(pos + 1))};
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
void RawFileFactory::parse_json_metadata(RawFile *file) {
|
||||
std::ifstream ifs(file->master_fname());
|
||||
json j;
|
||||
ifs >> j;
|
||||
double v = j["Version"];
|
||||
std::cout << "Version: " << v << std::endl;
|
||||
file->version = fmt::format("{:.1f}", v);
|
||||
file->type = StringTo<DetectorType>(j["Detector Type"].get<std::string>());
|
||||
file->timing_mode = StringTo<TimingMode>(j["Timing Mode"].get<std::string>());
|
||||
file->total_frames = j["Frames in File"];
|
||||
file->subfile_rows = j["Pixels"]["y"];
|
||||
file->subfile_cols = j["Pixels"]["x"];
|
||||
file->max_frames_per_file = j["Max Frames Per File"];
|
||||
try {
|
||||
file->bitdepth = j.at("Dynamic Range");
|
||||
} catch (const json::out_of_range &e) {
|
||||
file->bitdepth = 16;
|
||||
}
|
||||
// only Eiger had quad
|
||||
if (file->type == DetectorType::Eiger) {
|
||||
file->quad = (j["Quad"] == 1);
|
||||
}
|
||||
|
||||
file->geometry = {j["Geometry"]["y"], j["Geometry"]["x"]};
|
||||
}
|
||||
|
||||
void RawFileFactory::open_subfiles(File *_file) {
|
||||
auto file = dynamic_cast<RawFile *>(_file);
|
||||
for (size_t i = 0; i != file->n_subfiles; ++i) {
|
||||
auto v = std::vector<SubFile *>(file->n_subfile_parts);
|
||||
for (size_t j = 0; j != file->n_subfile_parts; ++j) {
|
||||
v[j] =
|
||||
new SubFile(file->data_fname(i, j), file->type, file->subfile_rows, file->subfile_cols, file->bitdepth);
|
||||
}
|
||||
file->subfiles.push_back(v);
|
||||
}
|
||||
}
|
||||
|
||||
RawFile *RawFileFactory::load_file() {
|
||||
RawFile *file = new RawFile();
|
||||
file->fname = this->m_fpath;
|
||||
this->parse_fname(file);
|
||||
this->parse_metadata(file);
|
||||
file->find_number_of_subfiles();
|
||||
|
||||
this->find_geometry(file);
|
||||
this->open_subfiles(file);
|
||||
|
||||
return file;
|
||||
}
|
||||
|
||||
sls_detector_header RawFileFactory::read_header(const std::filesystem::path &fname) {
|
||||
sls_detector_header h{};
|
||||
FILE *fp = fopen(fname.c_str(), "r");
|
||||
if (!fp)
|
||||
throw std::runtime_error(fmt::format("Could not open: {} for reading", fname.c_str()));
|
||||
|
||||
size_t rc = fread(reinterpret_cast<char *>(&h), sizeof(h), 1, fp);
|
||||
fclose(fp);
|
||||
if (rc != 1)
|
||||
throw std::runtime_error("Could not read header from file");
|
||||
return h;
|
||||
}
|
||||
|
||||
void RawFileFactory::find_geometry(File *_file) {
|
||||
auto file = dynamic_cast<RawFile *>(_file);
|
||||
uint16_t r{};
|
||||
uint16_t c{};
|
||||
for (size_t i = 0; i < file->n_subfile_parts; i++) {
|
||||
for (size_t j = 0; j != file->n_subfiles; ++j) {
|
||||
auto h = this->read_header(file->data_fname(j, i));
|
||||
r = std::max(r, h.row);
|
||||
c = std::max(c, h.column);
|
||||
|
||||
file->positions.push_back({h.row, h.column});
|
||||
}
|
||||
}
|
||||
|
||||
r++;
|
||||
c++;
|
||||
|
||||
file->rows = r * file->subfile_rows;
|
||||
file->cols = c * file->subfile_cols;
|
||||
|
||||
file->rows += (r - 1) * file->cfg.module_gap_row;
|
||||
}
|
||||
|
||||
void RawFileFactory::parse_fname(File *file) {
|
||||
|
||||
file->base_path = this->m_fpath.parent_path();
|
||||
file->base_name = this->m_fpath.stem();
|
||||
file->ext = this->m_fpath.extension();
|
||||
|
||||
auto pos = file->base_name.rfind("_");
|
||||
file->findex = std::stoi(file->base_name.substr(pos + 1));
|
||||
pos = file->base_name.find("_master_");
|
||||
file->base_name.erase(pos);
|
||||
}
|
||||
@ -12,7 +12,7 @@ SubFile::SubFile(std::filesystem::path fname, DetectorType detector, ssize_t row
|
||||
this->m_bitdepth = bitdepth;
|
||||
this->n_frames = std::filesystem::file_size(fname) / (sizeof(sls_detector_header) + rows * cols * bitdepth / 8);
|
||||
if (read_impl_map.find({detector, bitdepth}) == read_impl_map.end()) {
|
||||
throw std::runtime_error("Unsupported detector/bitdepth combination");
|
||||
throw std::runtime_error(LOCATION+"Unsupported detector/bitdepth combination");
|
||||
}
|
||||
this->read_impl = read_impl_map.at({detector, bitdepth});
|
||||
|
||||
|
||||
@ -1,17 +1,16 @@
|
||||
#include <catch2/catch_test_macros.hpp>
|
||||
#include <fstream>
|
||||
#include <filesystem>
|
||||
#include <fstream>
|
||||
|
||||
#include "test_config.hpp"
|
||||
|
||||
|
||||
TEST_CASE("Test suite can find data assets"){
|
||||
auto fpath = test_data_path()/ "test_numpy_file.npy";
|
||||
TEST_CASE("Test suite can find data assets") {
|
||||
auto fpath = test_data_path() / "numpy" / "test_numpy_file.npy";
|
||||
REQUIRE(std::filesystem::exists(fpath));
|
||||
}
|
||||
|
||||
TEST_CASE("Test suite can open data assets"){
|
||||
auto fpath = test_data_path()/ "test_numpy_file.npy";
|
||||
TEST_CASE("Test suite can open data assets") {
|
||||
auto fpath = test_data_path() / "numpy" / "test_numpy_file.npy";
|
||||
auto f = std::ifstream(fpath, std::ios::binary);
|
||||
REQUIRE(f.is_open());
|
||||
}
|
||||
Loading…
x
Reference in New Issue
Block a user