Commit 63f82073 authored by Sophie Wenzel-Teuber's avatar Sophie Wenzel-Teuber
Browse files

Changing the physical layout of the code (include and src) and adding inline 

namespaces to reflect the physical layout logically.

Change log:
namespace and folder are interchangable in the following:
* 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 detailed 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 object 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:
    - Create 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/object/ObjectInterface.cc

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

    src/exseisdat/piol/file/object/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

+116 −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 +90,65 @@ 
///          files.

///



///

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

///

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

///



///

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

///

/// @brief Basic read and write classes.

///



///

<<<<<<< HEAD

=======

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

///

/// @brief classes to.......

///

/// @todo document!

///



///

>>>>>>> b6d20c75c4294edab32b0cff7259765af98af594

/// @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

///