ITableWorkspace.cpp

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// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
//   NScD Oak Ridge National Laboratory, European Spallation Source,
//   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidAPI/ITableWorkspace.h"
#include "MantidAPI/AnalysisDataService.h"
#include "MantidAPI/Column.h"
#include "MantidAPI/TableRow.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidAPI/WorkspaceProperty.h"
#include "MantidKernel/V3D.h"
#include "MantidKernel/WarningSuppressions.h"
#include "MantidPythonInterface/api/RegisterWorkspacePtrToPython.h"
#include "MantidPythonInterface/core/Converters/CloneToNDArray.h"
#include "MantidPythonInterface/core/Converters/NDArrayToVector.h"
#include "MantidPythonInterface/core/Converters/PySequenceToVector.h"
#include "MantidPythonInterface/core/GetPointer.h"
#include "MantidPythonInterface/core/NDArray.h"
#include "MantidPythonInterface/core/Policies/VectorToNumpy.h"
#include "MantidPythonInterface/core/VersionCompat.h"
 
#include <boost/preprocessor/list/for_each.hpp>
#include <boost/preprocessor/tuple/to_list.hpp>
#include <boost/python/class.hpp>
#include <boost/python/converter/builtin_converters.hpp>
#include <boost/python/dict.hpp>
#include <boost/python/list.hpp>
#include <boost/python/make_constructor.hpp>
#include <boost/python/overloads.hpp>
 
#include <cstring>
#include <vector>
 
// See
// http://docs.scipy.org/doc/numpy/reference/c-api.array.html#PY_ARRAY_UNIQUE_SYMBOL
#define PY_ARRAY_UNIQUE_SYMBOL API_ARRAY_API
#define NO_IMPORT_ARRAY
#include <numpy/arrayobject.h>
 
using namespace Mantid::API;
using Mantid::PythonInterface::NDArray;
using Mantid::PythonInterface::Registry::RegisterWorkspacePtrToPython;
namespace Policies = Mantid::PythonInterface::Policies;
namespace Converters = Mantid::PythonInterface::Converters;
using namespace boost::python;
 
GET_POINTER_SPECIALIZATION(ITableWorkspace)
 
namespace {
 
// Numpy PyArray_IsIntegerScalar is broken for Python 3 for numpy < 1.11
#define TO_LONG PyLong_AsLong
#define STR_CHECK PyUnicode_Check
#if NPY_API_VERSION < 0x0000000a //(1.11)
#define IS_ARRAY_INTEGER(obj) (PyLong_Check(obj) || PyArray_IsScalar((obj), Integer))
#else
#define IS_ARRAY_INTEGER PyArray_IsIntegerScalar
#endif
 
#define BUILTIN_TYPES BOOST_PP_TUPLE_TO_LIST(8, (double, std::string, int, size_t, uint32_t, int64_t, float, uint64_t))
#define USER_TYPES BOOST_PP_TUPLE_TO_LIST(1, (Mantid::Kernel::V3D))
#define ARRAY_TYPES BOOST_PP_TUPLE_TO_LIST(2, (std::vector<int>, std::vector<double>))
 
PyObject *getValue(const Mantid::API::Column_const_sptr &column, const std::type_info &typeID, const int row) {
  if (typeID.hash_code() == typeid(Mantid::API::Boolean).hash_code()) {
    bool res = column->cell<Mantid::API::Boolean>(row);
    return to_python_value<const bool &>()(res);
  }
 
#define GET_BUILTIN(R, _, T)                                                                                           \
  else if (typeID.hash_code() == typeid(T).hash_code()) {                                                              \
    result = to_python_value<const T &>()(column->cell<T>(row));                                                       \
  }
#define GET_USER(R, _, T)                                                                                              \
  else if (typeID.hash_code() == typeid(T).hash_code()) {                                                              \
    const converter::registration *entry = converter::registry::query(typeid(T));                                      \
    if (!entry)                                                                                                        \
      throw std::invalid_argument("Cannot find converter from C++ type.");                                             \
    result = entry->to_python((const void *)&column->cell<T>(row));                                                    \
  }
#define GET_ARRAY(R, _, T)                                                                                             \
  else if (typeID.hash_code() == typeid(T).hash_code()) {                                                              \
    result = Converters::Clone::apply<T::value_type>::create1D(column->cell<T>(row));                                  \
  }
 
  // -- Use the boost preprocessor to generate a list of else if clause to cut
  // out copy and pasted code.
  PyObject *result(nullptr);
  if (false) {
  } // So that it always falls through to the list checking
  BOOST_PP_LIST_FOR_EACH(GET_BUILTIN, _, BUILTIN_TYPES)
  BOOST_PP_LIST_FOR_EACH(GET_ARRAY, _, ARRAY_TYPES)
  BOOST_PP_LIST_FOR_EACH(GET_USER, _, USER_TYPES)
  else {
    throw std::invalid_argument("Cannot convert C++ type to Python: " + column->type());
  }
  return result;
}
 
void setValue(const Column_sptr &column, const int row, const object &value) {
  const auto &typeID = column->get_type_info();
 
  // Special case: Treat Mantid Boolean as normal bool
  if (typeID.hash_code() == typeid(Mantid::API::Boolean).hash_code()) {
    column->cell<Mantid::API::Boolean>(row) = extract<bool>(value)();
    return;
  }
 
  // Special case: Boost has issues with NumPy ints, so use Python API instead
  // to check this first
  if (typeID.hash_code() == typeid(int).hash_code() && IS_ARRAY_INTEGER(value.ptr())) {
    column->cell<int>(row) = static_cast<int>(TO_LONG(value.ptr()));
    return;
  }
 
// Macros for all other types
#define SET_CELL(R, _, T)                                                                                              \
  else if (typeID.hash_code() == typeid(T).hash_code()) {                                                              \
    column->cell<T>(row) = extract<T>(value)();                                                                        \
  }
#define SET_VECTOR_CELL(R, _, T)                                                                                       \
  else if (typeID.hash_code() == typeid(T).hash_code()) {                                                              \
    if (!NDArray::check(value)) {                                                                                      \
      column->cell<T>(row) = Converters::PySequenceToVector<T::value_type>(value)();                                   \
    } else {                                                                                                           \
      column->cell<T>(row) = Converters::NDArrayToVector<T::value_type>(value)();                                      \
    }                                                                                                                  \
  }
 
  // -- Use the boost preprocessor to generate a list of else if clause to cut
  // out copy and pasted code.
  if (false) {
  } // So that it always falls through to the list checking
  BOOST_PP_LIST_FOR_EACH(SET_CELL, _, BUILTIN_TYPES)
  BOOST_PP_LIST_FOR_EACH(SET_CELL, _, USER_TYPES)
  BOOST_PP_LIST_FOR_EACH(SET_VECTOR_CELL, _, ARRAY_TYPES)
  else {
    throw std::invalid_argument("Cannot convert Python type to C++: " + column->type());
  }
}
 
bool addColumnPlotType(ITableWorkspace &self, const std::string &type, const std::string &name, int plottype) {
  auto newColumn = self.addColumn(type, name);
 
  if (newColumn)
    newColumn->setPlotType(plottype);
 
  return newColumn != nullptr;
}
 
bool addColumnSimple(ITableWorkspace &self, const std::string &type, const std::string &name) {
  return self.addColumn(type, name) != nullptr;
}
 
bool addReadOnlyColumn(ITableWorkspace &self, const std::string &type, const std::string &name) {
  auto newColumn = self.addColumn(type, name);
  newColumn->setReadOnly(true);
  return true;
}
 
int getPlotType(ITableWorkspace &self, const object &column) {
  // Find the column
  Mantid::API::Column_const_sptr colptr;
  if (STR_CHECK(column.ptr())) {
    colptr = self.getColumn(extract<std::string>(column)());
  } else {
    colptr = self.getColumn(extract<int>(column)());
  }
 
  return colptr->getPlotType();
}
 
void setPlotType(ITableWorkspace &self, const object &column, int ptype, int linkedCol = -1) {
  // Find the column
  Mantid::API::Column_sptr colptr;
  if (STR_CHECK(column.ptr())) {
    colptr = self.getColumn(extract<std::string>(column)());
  } else {
    colptr = self.getColumn(extract<int>(column)());
  }
  colptr->setPlotType(ptype);
  if (linkedCol >= 0) {
    colptr->setLinkedYCol(linkedCol);
  }
  self.modified();
}
 
GNU_DIAG_OFF("unused-local-typedef")
// Ignore -Wconversion warnings coming from boost::python
// Seen with GCC 7.1.1 and Boost 1.63.0
GNU_DIAG_OFF("conversion")
BOOST_PYTHON_FUNCTION_OVERLOADS(setPlotType_overloads, setPlotType, 3, 4)
GNU_DIAG_ON("conversion")
GNU_DIAG_ON("unused-local-typedef")
 
int getLinkedYCol(ITableWorkspace &self, const object &column) {
  // Find the column
  Mantid::API::Column_const_sptr colptr;
  if (STR_CHECK(column.ptr())) {
    colptr = self.getColumn(extract<std::string>(column)());
  } else {
    colptr = self.getColumn(extract<int>(column)());
  }
 
  return colptr->getLinkedYCol();
}
 
void setLinkedYCol(ITableWorkspace &self, const object &errColumn, const int dataColomn) {
  // Find the column
  Mantid::API::Column_sptr colptr;
  if (STR_CHECK(errColumn.ptr())) {
    colptr = self.getColumn(extract<std::string>(errColumn)());
  } else {
    colptr = self.getColumn(extract<int>(errColumn)());
  }
 
  colptr->setLinkedYCol(dataColomn);
}
 
PyObject *column(const ITableWorkspace &self, const object &value) {
  // Find the column and row
  Mantid::API::Column_const_sptr column;
  if (STR_CHECK(value.ptr())) {
    column = self.getColumn(extract<std::string>(value)());
  } else {
    column = self.getColumn(extract<int>(value)());
  }
  const std::type_info &typeID = column->get_type_info();
  const auto numRows = static_cast<int>(column->size());
 
  PyObject *result = PyList_New(numRows);
  for (int i = 0; i < numRows; i++) {
    if (PyList_SetItem(result, i, getValue(column, typeID, i)))
      throw std::runtime_error("Error while building list");
  }
 
  return result;
}
 
PyObject *row(ITableWorkspace &self, int row) {
  if (row < 0)
    throw std::invalid_argument("Cannot specify negative row number");
  if (row >= static_cast<int>(self.rowCount()))
    throw std::invalid_argument("Cannot specify row larger than number of rows");
 
  auto numCols = static_cast<int>(self.columnCount());
 
  PyObject *result = PyDict_New();
 
  for (int columnIndex = 0; columnIndex < numCols; columnIndex++) {
    Mantid::API::Column_const_sptr col = self.getColumn(columnIndex);
    const std::type_info &typeID = col->get_type_info();
 
    if (PyDict_SetItemString(result, col->name().c_str(), getValue(col, typeID, row)))
      throw std::runtime_error("Error while building dict");
  }
 
  return result;
}
 
boost::python::list columnTypes(ITableWorkspace &self) {
  auto numCols = static_cast<int>(self.columnCount());
 
  boost::python::list types;
 
  for (int colIndex = 0; colIndex < numCols; colIndex++) {
    const auto col = self.getColumn(colIndex);
    const auto &type = col->type();
    types.append(type);
  }
 
  return types;
}
 
void addRowFromDict(ITableWorkspace &self, const dict &rowItems) {
  // rowItems must contain an entry for every column
  auto nitems = boost::python::len(rowItems);
  if (nitems != static_cast<decltype(nitems)>(self.columnCount())) {
    throw std::invalid_argument("Number of values given does not match the number of columns. "
                                "Expected: " +
                                std::to_string(self.columnCount()));
  }
 
  // Add a new row to populate with values
  const auto rowIndex = static_cast<int>(self.rowCount());
  self.appendRow();
 
  // Declared in this scope so we can access them in catch block
  Column_sptr col; // Column in table
  object value;    // Value from dictionary
 
  try {
    // Retrieve and set the value for each column
    auto columns = self.getColumnNames();
    for (auto &iter : columns) {
      col = self.getColumn(iter);
      value = rowItems[iter];
      setValue(col, rowIndex, value);
    }
  } catch (error_already_set &) {
    // One of the columns wasn't found in the dictionary
    if (PyErr_ExceptionMatches(PyExc_KeyError)) {
      std::ostringstream msg;
      msg << "Missing key-value entry for column ";
      msg << "<" << col->name() << ">";
      PyErr_SetString(PyExc_KeyError, msg.str().c_str());
    }
 
    // Wrong type of data for one of the columns
    if (PyErr_ExceptionMatches(PyExc_TypeError)) {
      std::ostringstream msg;
      msg << "Wrong datatype for column <" << col->name() << "> ";
      msg << "(expected <" << col->type() << ">)";
      PyErr_SetString(PyExc_TypeError, msg.str().c_str());
    }
 
    // Remove the new row since populating it has failed
    self.removeRow(rowIndex);
    throw;
  }
  self.modified();
}
 
void addRowFromSequence(ITableWorkspace &self, const object &rowItems) {
  // rowItems must contain an entry for every column
  auto nitems = boost::python::len(rowItems);
  if (nitems != static_cast<decltype(nitems)>(self.columnCount())) {
    throw std::invalid_argument("Number of values given does not match the number of columns. "
                                "Expected: " +
                                std::to_string(self.columnCount()));
  }
 
  // Add a new row to populate with values
  const auto rowIndex = static_cast<int>(self.rowCount());
  self.appendRow();
 
  // Loop over sequence and set each column value in same order
  for (decltype(nitems) i = 0; i < nitems; ++i) {
    auto col = self.getColumn(i);
    auto value = rowItems[i];
 
    try {
      setValue(col, rowIndex, value);
    } catch (error_already_set &) {
      // Wrong type of data for one of the columns
      if (PyErr_ExceptionMatches(PyExc_TypeError)) {
        std::ostringstream msg;
        msg << "Wrong datatype for column <" << col->name() << "> ";
        msg << "(expected <" << col->type() << ">)";
        PyErr_SetString(PyExc_TypeError, msg.str().c_str());
      }
 
      // Remove the new row since populating it has failed
      self.removeRow(rowIndex);
      throw;
    }
  }
  self.modified();
}
 
void getCellLoc(ITableWorkspace &self, const object &col_or_row, const int row_or_col, Column_sptr &column,
                int &rowIndex) {
  if (STR_CHECK(col_or_row.ptr())) {
    column = self.getColumn(extract<std::string>(col_or_row)());
    rowIndex = row_or_col;
  } else {
    rowIndex = extract<int>(col_or_row)();
    column = self.getColumn(row_or_col);
  }
}
 
PyObject *cell(ITableWorkspace &self, const object &value, int row_or_col) {
  // Find the column and row
  Mantid::API::Column_sptr col;
  int rowIndex;
  getCellLoc(self, value, row_or_col, col, rowIndex);
  const std::type_info &typeID = col->get_type_info();
  return getValue(col, typeID, rowIndex);
}
 
void setCell(ITableWorkspace &self, const object &col_or_row, const int row_or_col, const object &value,
             const bool &notify_replace) {
  Mantid::API::Column_sptr col;
  int rowIndex;
  getCellLoc(self, col_or_row, row_or_col, col, rowIndex);
  setValue(col, rowIndex, value);
 
  if (notify_replace) {
    self.modified();
  }
}
 
bool isColumnReadOnly(ITableWorkspace &self, const object &column) {
  // Find the column
  Mantid::API::Column_const_sptr colptr;
  if (STR_CHECK(column.ptr())) {
    colptr = self.getColumn(extract<std::string>(column)());
  } else {
    colptr = self.getColumn(extract<int>(column)());
  }
  return colptr->getReadOnly();
}
 
void setColumnReadOnly(ITableWorkspace &self, const object &column, const bool readOnly) {
  // Find the column
  Mantid::API::Column_sptr colptr;
  if (STR_CHECK(column.ptr())) {
    colptr = self.getColumn(extract<std::string>(column)());
  } else {
    colptr = self.getColumn(extract<int>(column)());
  }
  colptr->setReadOnly(readOnly);
  self.modified();
}
} // namespace
 
dict toDict(const ITableWorkspace &self) {
  dict result;
 
  for (const auto &name : self.getColumnNames()) {
    handle<> handle(column(self, object(name)));
    object values(handle);
    result[name] = values;
  }
 
  return result;
}
 
class ITableWorkspacePickleSuite : public boost::python::pickle_suite {
public:
  static dict getstate(const ITableWorkspace &ws) {
    dict data;
    data["data"] = toDict(ws);
    data["meta_data"] = writeMetaData(ws);
    return data;
  }
 
  static void setstate(ITableWorkspace &ws, const dict &state) {
    readMetaData(ws, state);
    readData(ws, state);
  }
 
private:
  static dict writeMetaData(const ITableWorkspace &ws) {
    list columnTypes;
    list columnNames;
 
    const auto &names = ws.getColumnNames();
    for (const auto &name : names) {
      const auto &column = ws.getColumn(name);
      columnNames.append(name);
      columnTypes.append(column->type());
    }
 
    dict metaData;
    metaData["column_names"] = columnNames;
    metaData["column_types"] = columnTypes;
    return metaData;
  }
 
  static void readMetaData(ITableWorkspace &ws, const dict &state) {
    const auto &metaData = state["meta_data"];
    const auto &columnNames = metaData["column_names"];
    const auto &columnTypes = metaData["column_types"];
 
    auto numColumns = len(columnNames);
    for (decltype(numColumns) colIndex = 0; colIndex < numColumns; ++colIndex) {
      const auto &key = columnNames[colIndex];
      const auto &value = columnTypes[colIndex];
      const auto &name = extract<std::string>(key);
      const auto &type = extract<std::string>(value);
      ws.addColumn(type, name);
    }
  }
 
  static void readData(ITableWorkspace &ws, const dict &state) {
    const auto &data = state["data"];
    const auto &names = ws.getColumnNames();
 
    if (names.empty()) {
      return;
    }
 
    auto numRows = len(data[names[0]]);
    for (int rowIndex = 0; rowIndex < numRows; ++rowIndex) {
      ws.appendRow();
      for (const auto &name : names) {
        setValue(ws.getColumn(name), static_cast<int>(rowIndex), data[name][rowIndex]);
      }
    }
  }
};
 
void export_ITableWorkspace() {
  using Mantid::PythonInterface::Policies::VectorToNumpy;
 
  std::string iTableWorkspace_docstring = "Most of the information from a table workspace is returned ";
  iTableWorkspace_docstring += "as native copies. All of the column accessors return lists while the ";
  iTableWorkspace_docstring += "rows return dicts. This object does support the idom 'for row in ";
  iTableWorkspace_docstring += "ITableWorkspace'.";
 
  class_<ITableWorkspace, bases<Workspace>, boost::noncopyable>("ITableWorkspace", iTableWorkspace_docstring.c_str(),
                                                                no_init)
      .def_pickle(ITableWorkspacePickleSuite())
      .def("addColumn", &addColumnSimple, (arg("self"), arg("type"), arg("name")),
           "Add a named column with the given type. Recognized types are: "
           "int,float,double,bool,str,V3D,long64")
 
      .def("addColumn", &addColumnPlotType, (arg("self"), arg("type"), arg("name"), arg("plottype")),
           "Add a named column with the given datatype "
           "(int,float,double,bool,str,V3D,long64) "
           "\nand plottype "
           "(0 = None, 1 = X, 2 = Y, 3 = Z, 4 = xErr, 5 = yErr, 6 = Label).")
 
      .def("addReadOnlyColumn", &addReadOnlyColumn, (arg("self"), arg("type"), arg("name")),
           "Add a read-only, named column with the given type. Recognized types are: "
           "int,float,double,bool,str,V3D,long64")
 
      .def("getPlotType", &getPlotType, (arg("self"), arg("column")),
           "Get the plot type of given column as an integer. "
           "Accepts column name or index. \nPossible return values: "
           "(0 = None, 1 = X, 2 = Y, 3 = Z, 4 = xErr, 5 = yErr, 6 = Label).")
 
      .def("setPlotType", setPlotType,
           setPlotType_overloads((arg("self"), arg("column"), arg("ptype"), arg("linkedCol") = -1),
                                 "Set the plot type of given column. "
                                 "Accepts column name or index. \nPossible type values: "
                                 "(0 = None, 1 = X, 2 = Y, 3 = Z, 4 = xErr, 5 = yErr, 6 = "
                                 "Label)."))
 
      .def("getLinkedYCol", &getLinkedYCol, (arg("self"), arg("column")),
           "Get the data column associated with a given error column. ")
 
      .def("setLinkedYCol", &setLinkedYCol, (arg("self"), arg("errColumn"), arg("dataColumn")),
           "Set the data column associated with a given error column. ")
 
      .def("removeColumn", &ITableWorkspace::removeColumn, (arg("self"), arg("name")), "Remove the named column.")
 
      .def("columnCount", &ITableWorkspace::columnCount, arg("self"), "Returns the number of columns in the workspace.")
 
      .def("rowCount", &ITableWorkspace::rowCount, arg("self"), "Returns the number of rows within the workspace.")
 
      .def("setRowCount", &ITableWorkspace::setRowCount, (arg("self"), arg("count")),
           "Resize the table to contain count rows.")
 
      .def("__len__", &ITableWorkspace::rowCount, arg("self"), "Returns the number of rows within the workspace.")
 
      .def("getColumnNames", &ITableWorkspace::getColumnNames, arg("self"),
           boost::python::return_value_policy<VectorToNumpy>(), "Return a list of the column names.")
 
      .def("keys", &ITableWorkspace::getColumnNames, arg("self"), boost::python::return_value_policy<VectorToNumpy>(),
           "Return a list of the column names.")
 
      .def("column", &column, (arg("self"), arg("column")), "Return all values of a specific column as a list.")
 
      .def("row", &row, (arg("self"), arg("row")), "Return all values of a specific row as a dict.")
 
      .def("columnTypes", &columnTypes, arg("self"), "Return the types of the columns as a list")
 
      // FromSequence must come first since it takes an object parameter
      // Otherwise, FromDict will never be called as object accepts anything
      .def("addRow", &addRowFromSequence, (arg("self"), arg("row_items_seq")),
           "Appends a row with the values from the given sequence. "
           "It it assumed that the items are in the correct order for the "
           "defined columns.")
 
      .def("addRow", &addRowFromDict, (arg("self"), arg("row_items_dict")),
           "Appends a row with the values from the dictionary.")
 
      .def("cell", &cell, (arg("self"), arg("value"), arg("row_or_column")),
           "Return the value in the given cell. If the value argument is a "
           "number then it is interpreted as a row otherwise it "
           "is interpreted as a column name.")
 
      .def("setCell", &setCell,
           (arg("self"), arg("row_or_column"), arg("column_or_row"), arg("value"), arg("notify_replace") = true),
           "Sets the value of a given cell. If the row_or_column argument is a "
           "number then it is interpreted as a row otherwise it "
           "is interpreted as a column name. If notify replace is false, then "
           "the replace workspace event is not triggered.")
 
      .def("toDict", &toDict, (arg("self")),
           "Gets the values of this workspace as a dictionary. The keys of the "
           "dictionary will be the names of the columns of the table. The "
           "values of the entries will be lists of values for each column.")
 
      .def("setColumnReadOnly", &setColumnReadOnly, (arg("self"), arg("column"), arg("read_only")),
           "Sets whether or not a given column of this workspace should be read-only. Columns can be "
           "selected by name or by index")
 
      .def("isColumnReadOnly", &isColumnReadOnly, (arg("self"), arg("column")),
           "Gets whether or not a given column of this workspace is be read-only. Columns can be "
           "selected by name or by index");
 
  //-------------------------------------------------------------------------------------------------
 
  RegisterWorkspacePtrToPython<ITableWorkspace>();
}