Commit b0778ded authored by Sophie Wenzel-Teuber's avatar Sophie Wenzel-Teuber
Browse files

Change physical and logical layout of the code 

Change the file and folder layout, adding inline namespaces so the logical
namespaces match the physical locations of the files.
This also improves the organization and presentation of Doxygen documentation.

Change log:
* general:
    - Change names of classes and files to Snake case, starting with a capital
      letter
    - Tidy documentation and add @briefs everywhere
    - Adding namespaces inside #ifdef __cplusplus pragmas to C-files, such that
      the members will appear at the correct location in the documentation
* flow:
    - Move most of the classes in the flow namespace to a detail namespace
* piol:
    - Move communicator to utils namespace and rename CommunicatorInterface.hh
      to just Communicator.hh
    - Move Read and Write classes to namespace file and rename to Input_file and
      Output_file
    - Move Object read/Write-classes to detail namespace inside namespace file
    - Move ExSeis[PIOL] to configuration namespace
    - Rename Binary_file to IO_driver and move to own namespace
    - Create metadata namespace with Trace_metadata_key (formerly Meta) and a
      rules namespace containing everything concerning the rules for SEGY files
    - Create namespace segy for utilities and Trace header offsets (formerly Tr)
    - Create sort namespace inside operations namespace for the sort operations
* utils:
    - Move Distributed_vector classes to namespace of the same name
    - Remove mpi namespace and create mpi_utils for utilities and move
      MPI_Distributed_vector to distributed_vector namespace and MPI_types to
      types namespace
    - Create types namespace for various kinds of type definitions
parent 1e5d8c12

CMakeLists.txt

+37 −40
Original line number Diff line number Diff line
@@ -145,46 +145,43 @@ include(third_party/third_party.cmake) 
add_library(

    exseisdat



    src/PIOL_C_bindings.cc



    src/flow/Cache.cc

    src/flow/Flow_C_bindings.cc

    src/flow/RadonGatherState.cc

    src/flow/Set.cc



    src/piol/mpi/MPI_Binary_file.cc

    src/piol/segy/utils.cc



    src/CommunicatorMPI.cc

    src/ExSeis.cc

    src/ExSeisPIOL.cc

    src/ObjectInterface.cc

    src/ObjectSEGY.cc

    src/ReadInterface.cc

    src/ReadSEGY.cc

    src/ReadSEGYModel.cc

    src/Rule.cc

    src/Trace_metadata.cc

    src/WriteInterface.cc

    src/WriteSEGY.cc



    src/gather.cc

    src/minmax.cc

    src/sort.cc

    src/temporalfilter.cc



    src/utils/decomposition/block_decomposition.cc

    src/utils/encoding/character_encoding.cc

    src/utils/encoding/number_encoding.cc

    src/utils/logging/Log.cc

    src/utils/logging/Status.cc

    src/utils/mpi/MPI_error_to_string.cc

    src/utils/mpi/MPI_max_array_length.cc

    src/utils/signal_processing/AGC.cc

    src/utils/signal_processing/Gain_function.cc

    src/utils/signal_processing/Taper_function.cc

    src/utils/signal_processing/mute.cc

    src/utils/signal_processing/taper.cc

    src/exseisdat/flow/detail/Cache.cc

    src/exseisdat/flow/Flow_C_bindings.cc

    src/exseisdat/flow/detail/Radon_gather_state.cc

    src/exseisdat/flow/Set.cc



    src/exseisdat/piol/configuration/ExSeis.cc

    src/exseisdat/piol/configuration/ExSeisPIOL.cc

    src/exseisdat/piol/file/Input_file.cc

    src/exseisdat/piol/file/Input_file_segy.cc

    src/exseisdat/piol/file/detail/ObjectInterface.cc

    src/exseisdat/piol/file/detail/ObjectSEGY.cc

    src/exseisdat/piol/file/detail/ReadSEGYModel.cc

    src/exseisdat/piol/file/Output_file.cc

    src/exseisdat/piol/file/Output_file_segy.cc

    src/exseisdat/piol/io_driver/IO_driver_mpi.cc

    src/exseisdat/piol/metadata/rules/Rule.cc

    src/exseisdat/piol/metadata/Trace_metadata.cc

    src/exseisdat/piol/operations/gather.cc

    src/exseisdat/piol/operations/minmax.cc

    src/exseisdat/piol/operations/sort_operations/sort.cc

    src/exseisdat/piol/PIOL_C_bindings.cc

    src/exseisdat/piol/segy/utils.cc



    src/exseisdat/utils/communicator/Communicator_mpi.cc

    src/exseisdat/utils/decomposition/block_decomposition.cc

    src/exseisdat/utils/encoding/character_encoding.cc

    src/exseisdat/utils/encoding/number_encoding.cc

    src/exseisdat/utils/logging/Log.cc

    src/exseisdat/utils/logging/Status.cc

    src/exseisdat/utils/mpi_utils/MPI_error_to_string.cc

    src/exseisdat/utils/mpi_utils/MPI_max_array_length.cc

    src/exseisdat/utils/signal_processing/AGC.cc

    src/exseisdat/utils/signal_processing/Gain_function.cc

    src/exseisdat/utils/signal_processing/Taper_function.cc

    src/exseisdat/utils/signal_processing/mute.cc

    src/exseisdat/utils/signal_processing/taper.cc

    src/exseisdat/utils/signal_processing/temporalfilter.cc

)



target_compile_features(exseisdat PUBLIC cxx_std_14)

doc/CMakeLists.txt

+13 −5
Original line number Diff line number Diff line
@@ -8,7 +8,7 @@ configure_file( 
    @ONLY

)



set(INCLUDE_DOXYFILE "@INCLUDE = Doxyfile")

set(INCLUDE_DOXYFILE "@INCLUDE = ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile")

configure_file(

    ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile-man.in

    ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile-man
@@ -66,14 +66,22 @@ add_custom_command( 
    COMMENT "Building the documentation..."

)



add_custom_target(make_man_directory)

add_custom_command(

    OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/man/exseis-extract-metadata.1

    TARGET make_man_directory PRE_BUILD

    COMMAND ${CMAKE_COMMAND} -E make_directory man

    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}

)



add_custom_command(

    OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/man/man/exseis-extract-metadata.1

    COMMAND ${DOXYGEN_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile-man"

    MAIN_DEPENDENCY ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile-man.in

    DEPENDS

        make_man_directory

        ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile-man.in

        ${EXSEISDAT_DOCUMENTED_EXAMPLES}

    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}

    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/man

    COMMENT "Building the documentation..."

)
@@ -82,7 +90,7 @@ add_custom_target( 
    doc ALL

    DEPENDS

        ${CMAKE_CURRENT_BINARY_DIR}/html/index.html

        ${CMAKE_CURRENT_BINARY_DIR}/man/exseis-extract-metadata.1

        ${CMAKE_CURRENT_BINARY_DIR}/man/man/exseis-extract-metadata.1

)



# Set install target

doc/Doxyfile-man.in

+1 −0
Original line number Diff line number Diff line
@@ -6,6 +6,7 @@ 
PROJECT_NAME  = ExSeisDat



GENERATE_HTML = NO

GENERATE_XML = NO

GENERATE_MAN  = YES

INPUT         = @CMAKE_SOURCE_DIR@/util

doc/Doxyfile.in

+3 −2
Original line number Diff line number Diff line
@@ -36,7 +36,6 @@ WARN_AS_ERROR = YES 
INPUT                  =         \

    @CMAKE_SOURCE_DIR@/doc/namespaces.dox \

    @CMAKE_SOURCE_DIR@/include   \

    @CMAKE_SOURCE_DIR@/util      \

    @CMAKE_SOURCE_DIR@/README.md \

    @CMAKE_CURRENT_BINARY_DIR@/examples/documented \

    @CMAKE_SOURCE_DIR@/examples/README.md
@@ -82,7 +81,9 @@ ENABLE_PREPROCESSING = YES 
MACRO_EXPANSION        = YES

PREDEFINED             = __cplusplus

SEARCH_INCLUDES        = YES

INCLUDE_PATH           = 



GENERATE_XML           = YES

XML_NS_MEMB_FILE_SCOPE = YES



# Aliases for implicit members

ALIASES += special_member_functions="Special Member Functions"

doc/namespaces.dox

+105 −0
Original line number Diff line number Diff line
@@ -18,6 +18,63 @@ 
///          etc.

///



///

/// @namespace exseis::utils::communicator

///

/// @brief Interface and implementations of a communicator that is used for

///        message passing between the processes.

///



///

/// @namespace exseis::utils::decomposition

///

/// @brief Functions for splitting ranges across processes.

///



///

/// @namespace exseis::utils::distributed_vector

///

/// @brief Interface and implementations of a vector that is distributed

///        over several processes.

///



///

/// @namespace exseis::utils::encoding

///

/// @brief Functions for different kinds of encodings.

///



///

/// @namespace exseis::utils::logging

///

/// @brief Logging utilities.

///



///

/// @namespace exseis::utils::mpi_utils

///

/// @brief MPI utilities.

///



///

/// @namespace exseis::utils::signal_processing

///

/// @brief Functions for processing seismic signals.

///



///

/// @namespace exseis::utils::types

///

/// @brief Aliases for fundamental types and conversions used throughout the

///        ExSeisDat project.

///



///

/// @namespace exseis::utils::types::mpi

///

/// @brief Aliases for MPI datatypes

///



///

/// @namespace exseis::piol

///
@@ -33,6 +90,54 @@ 
///          files.

///



///

/// @namespace exseis::piol::configuration

///

/// @brief Classes for storing configurations of the program.

///



///

/// @namespace exseis::piol::file

///

/// @brief Basic read and write classes.

///



///

/// @namespace exseis::piol::io_driver

///

/// @brief Interface and implementations that perform I/O operations

///



///

/// @namespace exseis::piol::metadata

///

/// @brief Seismic metadata utilities

///



///

/// @namespace exseis::piol::metadata::rules

///

/// @brief Rules associated with trace parameters

///



///

/// @namespace exseis::piol::operations

///

/// @brief Basic operations performed on the file data

///



///

/// @namespace exseis::piol::operations::sort_operations

///

/// @brief Classes and functions for sorting the data

///



///

/// @namespace exseis::piol::segy

///

/// @brief SEGY specific parameters and functions

///



///

/// @namespace exseis::flow

///